Analysis of conservation priorities of Iberoamerican cattle based on autosomal microsatellite markers

PubMed Central

2013-01-01

Background Determining the value of livestock breeds is essential to define conservation priorities, manage genetic diversity and allocate funds. Within- and between-breed genetic diversity need to be assessed to preserve the highest intra-specific variability. Information on genetic diversity and risk status is still lacking for many Creole cattle breeds from the Americas, despite their distinct evolutionary trajectories and adaptation to extreme environmental conditions. Methods A comprehensive genetic analysis of 67 Iberoamerican cattle breeds was carried out with 19 FAO-recommended microsatellites to assess conservation priorities. Contributions to global diversity were investigated using alternative methods, with different weights given to the within- and between-breed components of genetic diversity. Information on Iberoamerican plus 15 worldwide cattle breeds was used to investigate the contribution of geographical breed groups to global genetic diversity. Results Overall, Creole cattle breeds showed a high level of genetic diversity with the highest level found in breeds admixed with zebu cattle, which were clearly differentiated from all other breeds. Within-breed kinships revealed seven highly inbred Creole breeds for which measures are needed to avoid further genetic erosion. However, if contribution to heterozygosity was the only criterion considered, some of these breeds had the lowest priority for conservation decisions. The Weitzman approach prioritized highly differentiated breeds, such as Guabalá, Romosinuano, Cr. Patagonico, Siboney and Caracú, while kinship-based methods prioritized mainly zebu-related breeds. With the combined approaches, breed ranking depended on the weights given to the within- and between-breed components of diversity. Overall, the Creole groups of breeds were generally assigned a higher priority for conservation than the European groups of breeds. Conclusions Conservation priorities differed significantly according to the weight given to within- and between-breed genetic diversity. Thus, when establishing conservation programs, it is necessary to also take into account other features. Creole cattle and local isolated breeds retain a high level of genetic diversity. The development of sustainable breeding and crossbreeding programs for Creole breeds, and the added value resulting from their products should be taken into consideration to ensure their long-term survival. PMID:24079454

Tracking the Genetic Stability of a Honey Bee (Hymenoptera: Apidae) Breeding Program With Genetic Markers.

PubMed

Bourgeois, Lelania; Beaman, Lorraine

2017-08-01

A genetic stock identification (GSI) assay was developed in 2008 to distinguish Russian honey bees from other honey bee stocks that are commercially produced in the United States. Probability of assignment (POA) values have been collected and maintained since the stock release in 2008 to the Russian Honey Bee Breeders Association. These data were used to assess stability of the breeding program and the diversity levels of the contemporary breeding stock through comparison of POA values and genetic diversity parameters from the initial release to current values. POA values fluctuated throughout 2010-2016, but have recovered to statistically similar levels in 2016 (POA(2010) = 0.82, POA(2016) = 0.74; P = 0.33). Genetic diversity parameters (i.e., allelic richness and gene diversity) in 2016 also remained at similar levels when compared to those in 2010. Estimates of genetic structure revealed stability (FST(2009/2016) = 0.0058) with a small increase in the estimate of the inbreeding coefficient (FIS(2010) = 0.078, FIS(2016) = 0.149). The relationship among breeding lines, based on genetic distance measurement, was similar in 2008 and 2016 populations, but with increased homogeneity among lines (i.e., decreased genetic distance). This was expected based on the closed breeding system used for Russian honey bees. The successful application of the GSI assay in a commercial breeding program demonstrates the utility and stability of such technology to contribute to and monitor the genetic integrity of a breeding stock of an insect species. Published by Oxford University Press on behalf of Entomological Society of America 2017. This work is written by US Government employees and is in the public domain in the US.

A Ranking Approach to Genomic Selection.

PubMed

Blondel, Mathieu; Onogi, Akio; Iwata, Hiroyoshi; Ueda, Naonori

2015-01-01

Genomic selection (GS) is a recent selective breeding method which uses predictive models based on whole-genome molecular markers. Until now, existing studies formulated GS as the problem of modeling an individual's breeding value for a particular trait of interest, i.e., as a regression problem. To assess predictive accuracy of the model, the Pearson correlation between observed and predicted trait values was used. In this paper, we propose to formulate GS as the problem of ranking individuals according to their breeding value. Our proposed framework allows us to employ machine learning methods for ranking which had previously not been considered in the GS literature. To assess ranking accuracy of a model, we introduce a new measure originating from the information retrieval literature called normalized discounted cumulative gain (NDCG). NDCG rewards more strongly models which assign a high rank to individuals with high breeding value. Therefore, NDCG reflects a prerequisite objective in selective breeding: accurate selection of individuals with high breeding value. We conducted a comparison of 10 existing regression methods and 3 new ranking methods on 6 datasets, consisting of 4 plant species and 25 traits. Our experimental results suggest that tree-based ensemble methods including McRank, Random Forests and Gradient Boosting Regression Trees achieve excellent ranking accuracy. RKHS regression and RankSVM also achieve good accuracy when used with an RBF kernel. Traditional regression methods such as Bayesian lasso, wBSR and BayesC were found less suitable for ranking. Pearson correlation was found to correlate poorly with NDCG. Our study suggests two important messages. First, ranking methods are a promising research direction in GS. Second, NDCG can be a useful evaluation measure for GS.

Joint genomic evaluation of French dairy cattle breeds using multiple-trait models.

PubMed

Karoui, Sofiene; Carabaño, María Jesús; Díaz, Clara; Legarra, Andrés

2012-12-07

Using a multi-breed reference population might be a way of increasing the accuracy of genomic breeding values in small breeds. Models involving mixed-breed data do not take into account the fact that marker effects may differ among breeds. This study was aimed at investigating the impact on accuracy of increasing the number of genotyped candidates in the training set by using a multi-breed reference population, in contrast to single-breed genomic evaluations. Three traits (milk production, fat content and female fertility) were analyzed by genomic mixed linear models and Bayesian methodology. Three breeds of French dairy cattle were used: Holstein, Montbéliarde and Normande with 2976, 950 and 970 bulls in the training population, respectively and 964, 222 and 248 bulls in the validation population, respectively. All animals were genotyped with the Illumina Bovine SNP50 array. Accuracy of genomic breeding values was evaluated under three scenarios for the correlation of genomic breeding values between breeds (r(g)): uncorrelated (1), r(g) = 0; estimated r(g) (2); high, r(g) = 0.95 (3). Accuracy and bias of predictions obtained in the validation population with the multi-breed training set were assessed by the coefficient of determination (R(2)) and by the regression coefficient of daughter yield deviations of validation bulls on their predicted genomic breeding values, respectively. The genetic variation captured by the markers for each trait was similar to that estimated for routine pedigree-based genetic evaluation. Posterior means for rg ranged from -0.01 for fertility between Montbéliarde and Normande to 0.79 for milk yield between Montbéliarde and Holstein. Differences in R(2) between the three scenarios were notable only for fat content in the Montbéliarde breed: from 0.27 in scenario (1) to 0.33 in scenarios (2) and (3). Accuracies for fertility were lower than for other traits. Using a multi-breed reference population resulted in small or no increases in accuracy. Only the breed with a small data set and large genetic correlation with the breed with a large data set showed increased accuracy for the traits with moderate (milk) to high (fat content) heritability. No benefit was observed for fertility, a lowly heritable trait.

Joint genomic evaluation of French dairy cattle breeds using multiple-trait models

PubMed Central

2012-01-01

Background Using a multi-breed reference population might be a way of increasing the accuracy of genomic breeding values in small breeds. Models involving mixed-breed data do not take into account the fact that marker effects may differ among breeds. This study was aimed at investigating the impact on accuracy of increasing the number of genotyped candidates in the training set by using a multi-breed reference population, in contrast to single-breed genomic evaluations. Methods Three traits (milk production, fat content and female fertility) were analyzed by genomic mixed linear models and Bayesian methodology. Three breeds of French dairy cattle were used: Holstein, Montbéliarde and Normande with 2976, 950 and 970 bulls in the training population, respectively and 964, 222 and 248 bulls in the validation population, respectively. All animals were genotyped with the Illumina Bovine SNP50 array. Accuracy of genomic breeding values was evaluated under three scenarios for the correlation of genomic breeding values between breeds (rg): uncorrelated (1), rg = 0; estimated rg (2); high, rg = 0.95 (3). Accuracy and bias of predictions obtained in the validation population with the multi-breed training set were assessed by the coefficient of determination (R2) and by the regression coefficient of daughter yield deviations of validation bulls on their predicted genomic breeding values, respectively. Results The genetic variation captured by the markers for each trait was similar to that estimated for routine pedigree-based genetic evaluation. Posterior means for rg ranged from −0.01 for fertility between Montbéliarde and Normande to 0.79 for milk yield between Montbéliarde and Holstein. Differences in R2 between the three scenarios were notable only for fat content in the Montbéliarde breed: from 0.27 in scenario (1) to 0.33 in scenarios (2) and (3). Accuracies for fertility were lower than for other traits. Conclusions Using a multi-breed reference population resulted in small or no increases in accuracy. Only the breed with a small data set and large genetic correlation with the breed with a large data set showed increased accuracy for the traits with moderate (milk) to high (fat content) heritability. No benefit was observed for fertility, a lowly heritable trait. PMID:23216664

Genome wide linkage disequilibrium and genetic structure in Sicilian dairy sheep breeds.

PubMed

Mastrangelo, Salvatore; Di Gerlando, Rosalia; Tolone, Marco; Tortorici, Lina; Sardina, Maria Teresa; Portolano, Baldassare

2014-10-10

The recent availability of sheep genome-wide SNP panels allows providing background information concerning genome structure in domestic animals. The aim of this work was to investigate the patterns of linkage disequilibrium (LD), the genetic diversity and population structure in Valle del Belice, Comisana, and Pinzirita dairy sheep breeds using the Illumina Ovine SNP50K Genotyping array. Average r (2) between adjacent SNPs across all chromosomes was 0.155 ± 0.204 for Valle del Belice, 0.156 ± 0.208 for Comisana, and 0.128 ± 0.188 for Pinzirita breeds, and some variations in LD value across chromosomes were observed, in particular for Valle del Belice and Comisana breeds. Average values of r (2) estimated for all pairwise combinations of SNPs pooled over all autosomes were 0.058 ± 0.023 for Valle del Belice, 0.056 ± 0.021 for Comisana, and 0.037 ± 0.017 for Pinzirita breeds. The LD declined as a function of distance and average r (2) was lower than the values observed in other sheep breeds. Consistency of results among the several used approaches (Principal component analysis, Bayesian clustering, F ST, Neighbor networks) showed that while Valle del Belice and Pinzirita breeds formed a unique cluster, Comisana breed showed the presence of substructure. In Valle del Belice breed, the high level of genetic differentiation within breed, the heterogeneous cluster in Admixture analysis, but at the same time the highest inbreeding coefficient, suggested that the breed had a wide genetic base with inbred individuals belonging to the same flock. The Sicilian breeds were characterized by low genetic differentiation and high level of admixture. Pinzirita breed displayed the highest genetic diversity (He, Ne) whereas the lowest value was found in Valle del Belice breed. This study has reported for the first time estimates of LD and genetic diversity from a genome-wide perspective in Sicilian dairy sheep breeds. Our results indicate that breeds formed non-overlapping clusters and are clearly separated populations and that Comisana sheep breed does not constitute a homogenous population. The information generated from this study has important implications for the design and applications of association studies as well as for development of conservation and/or selection breeding programs.

Will genomic selection be a practical method for plant breeding?

PubMed

Nakaya, Akihiro; Isobe, Sachiko N

2012-11-01

Genomic selection or genome-wide selection (GS) has been highlighted as a new approach for marker-assisted selection (MAS) in recent years. GS is a form of MAS that selects favourable individuals based on genomic estimated breeding values. Previous studies have suggested the utility of GS, especially for capturing small-effect quantitative trait loci, but GS has not become a popular methodology in the field of plant breeding, possibly because there is insufficient information available on GS for practical use. In this review, GS is discussed from a practical breeding viewpoint. Statistical approaches employed in GS are briefly described, before the recent progress in GS studies is surveyed. GS practices in plant breeding are then reviewed before future prospects are discussed. Statistical concepts used in GS are discussed with genetic models and variance decomposition, heritability, breeding value and linear model. Recent progress in GS studies is reviewed with a focus on empirical studies. For the practice of GS in plant breeding, several specific points are discussed including linkage disequilibrium, feature of populations and genotyped markers and breeding scheme. Currently, GS is not perfect, but it is a potent, attractive and valuable approach for plant breeding. This method will be integrated into many practical breeding programmes in the near future with further advances and the maturing of its theory.

Efficient Breeding by Genomic Mating.

PubMed

Akdemir, Deniz; Sánchez, Julio I

2016-01-01

Selection in breeding programs can be done by using phenotypes (phenotypic selection), pedigree relationship (breeding value selection) or molecular markers (marker assisted selection or genomic selection). All these methods are based on truncation selection, focusing on the best performance of parents before mating. In this article we proposed an approach to breeding, named genomic mating, which focuses on mating instead of truncation selection. Genomic mating uses information in a similar fashion to genomic selection but includes information on complementation of parents to be mated. Following the efficiency frontier surface, genomic mating uses concepts of estimated breeding values, risk (usefulness) and coefficient of ancestry to optimize mating between parents. We used a genetic algorithm to find solutions to this optimization problem and the results from our simulations comparing genomic selection, phenotypic selection and the mating approach indicate that current approach for breeding complex traits is more favorable than phenotypic and genomic selection. Genomic mating is similar to genomic selection in terms of estimating marker effects, but in genomic mating the genetic information and the estimated marker effects are used to decide which genotypes should be crossed to obtain the next breeding population.

Captive breeding of pangolins: current status, problems and future prospects.

PubMed

Hua, Liushuai; Gong, Shiping; Wang, Fumin; Li, Weiye; Ge, Yan; Li, Xiaonan; Hou, Fanghui

2015-01-01

Pangolins are unique placental mammals with eight species existing in the world, which have adapted to a highly specialized diet of ants and termites, and are of significance in the control of forest termite disaster. Besides their ecological value, pangolins are extremely important economic animals with the value as medicine and food. At present, illegal hunting and habitat destruction have drastically decreased the wild population of pangolins, pushing them to the edge of extinction. Captive breeding is an important way to protect these species, but because of pangolin's specialized behaviors and high dependence on natural ecosystem, there still exist many technical barriers to successful captive breeding programs. In this paper, based on the literatures and our practical experience, we reviewed the status and existing problems in captive breeding of pangolins, including four aspects, the naturalistic habitat, dietary husbandry, reproduction and disease control. Some recommendations are presented for effective captive breeding and protection of pangolins.

solGS: a web-based tool for genomic selection

USDA-ARS?s Scientific Manuscript database

Genomic selection (GS) promises to improve accuracy in estimating breeding values and genetic gain for quantitative traits compared to traditional breeding methods. Its reliance on high-throughput genome-wide markers and statistical complexity, however, is a serious challenge in data management, ana...

A Comparison of Phenotypic Traits Related to Trypanotolerance in Five West African Cattle Breeds Highlights the Value of Shorthorn Taurine Breeds

PubMed Central

Berthier, David; Peylhard, Moana; Dayo, Guiguigbaza-Kossigan; Flori, Laurence; Sylla, Souleymane; Bolly, Seydou; Sakande, Hassane; Chantal, Isabelle; Thevenon, Sophie

2015-01-01

Background Animal African Trypanosomosis particularly affects cattle and dramatically impairs livestock development in sub-Saharan Africa. African Zebu (AFZ) or European taurine breeds usually die of the disease in the absence of treatment, whereas West African taurine breeds (AFT), considered trypanotolerant, are able to control the pathogenic effects of trypanosomosis. Up to now, only one AFT breed, the longhorn N’Dama (NDA), has been largely studied and is considered as the reference trypanotolerant breed. Shorthorn taurine trypanotolerance has never been properly assessed and compared to NDA and AFZ breeds. Methodology/Principal Findings This study compared the trypanotolerant/susceptible phenotype of five West African local breeds that differ in their demographic history. Thirty-six individuals belonging to the longhorn taurine NDA breed, two shorthorn taurine Lagune (LAG) and Baoulé (BAO) breeds, the Zebu Fulani (ZFU) and the Borgou (BOR), an admixed breed between AFT and AFZ, were infected by Trypanosoma congolense IL1180. All the cattle were genetically characterized using dense SNP markers, and parameters linked to parasitaemia, anaemia and leukocytes were analysed using synthetic variables and mixed models. We showed that LAG, followed by NDA and BAO, displayed the best control of anaemia. ZFU showed the greatest anaemia and the BOR breed had an intermediate value, as expected from its admixed origin. Large differences in leukocyte counts were also observed, with higher leukocytosis for AFT. Nevertheless, no differences in parasitaemia were found, except a tendency to take longer to display detectable parasites in ZFU. Conclusions We demonstrated that LAG and BAO are as trypanotolerant as NDA. This study highlights the value of shorthorn taurine breeds, which display strong local adaptation to trypanosomosis. Thanks to further analyses based on comparisons of the genome or transcriptome of the breeds, these results open up the way for better knowledge of host-pathogen interactions and, furthermore, for identifying key biological pathways. PMID:25954819

A comparison of phenotypic traits related to trypanotolerance in five west african cattle breeds highlights the value of shorthorn taurine breeds.

PubMed

Berthier, David; Peylhard, Moana; Dayo, Guiguigbaza-Kossigan; Flori, Laurence; Sylla, Souleymane; Bolly, Seydou; Sakande, Hassane; Chantal, Isabelle; Thevenon, Sophie

2015-01-01

Animal African Trypanosomosis particularly affects cattle and dramatically impairs livestock development in sub-Saharan Africa. African Zebu (AFZ) or European taurine breeds usually die of the disease in the absence of treatment, whereas West African taurine breeds (AFT), considered trypanotolerant, are able to control the pathogenic effects of trypanosomosis. Up to now, only one AFT breed, the longhorn N'Dama (NDA), has been largely studied and is considered as the reference trypanotolerant breed. Shorthorn taurine trypanotolerance has never been properly assessed and compared to NDA and AFZ breeds. This study compared the trypanotolerant/susceptible phenotype of five West African local breeds that differ in their demographic history. Thirty-six individuals belonging to the longhorn taurine NDA breed, two shorthorn taurine Lagune (LAG) and Baoulé (BAO) breeds, the Zebu Fulani (ZFU) and the Borgou (BOR), an admixed breed between AFT and AFZ, were infected by Trypanosoma congolense IL1180. All the cattle were genetically characterized using dense SNP markers, and parameters linked to parasitaemia, anaemia and leukocytes were analysed using synthetic variables and mixed models. We showed that LAG, followed by NDA and BAO, displayed the best control of anaemia. ZFU showed the greatest anaemia and the BOR breed had an intermediate value, as expected from its admixed origin. Large differences in leukocyte counts were also observed, with higher leukocytosis for AFT. Nevertheless, no differences in parasitaemia were found, except a tendency to take longer to display detectable parasites in ZFU. We demonstrated that LAG and BAO are as trypanotolerant as NDA. This study highlights the value of shorthorn taurine breeds, which display strong local adaptation to trypanosomosis. Thanks to further analyses based on comparisons of the genome or transcriptome of the breeds, these results open up the way for better knowledge of host-pathogen interactions and, furthermore, for identifying key biological pathways.

Assessing genomic selection prediction accuracy in a dynamic barley breeding

USDA-ARS?s Scientific Manuscript database

Genomic selection is a method to improve quantitative traits in crops and livestock by estimating breeding values of selection candidates using phenotype and genome-wide marker data sets. Prediction accuracy has been evaluated through simulation and cross-validation, however validation based on prog...

Rindsel: an R package for phenotypic and molecular selection indices used in plant breeding.

PubMed

Perez-Elizalde, Sergío; Cerón-Rojas, Jesús J; Crossa, José; Fleury, Delphine; Alvarado, Gregorio

2014-01-01

Selection indices are estimates of the net genetic merit of the individual candidates for selection and are calculated based on phenotyping and molecular marker information collected on plants under selection in a breeding program. They reflect the breeding value of the plants and help breeders to choose the best ones for next generation. Rindsel is an R package that calculates phenotypic and molecular selection indices.

Assessing the impact of natural service bulls and genotype by environment interactions on genetic gain and inbreeding in organic dairy cattle genomic breeding programs.

PubMed

Yin, T; Wensch-Dorendorf, M; Simianer, H; Swalve, H H; König, S

2014-06-01

The objective of the present study was to compare genetic gain and inbreeding coefficients of dairy cattle in organic breeding program designs by applying stochastic simulations. Evaluated breeding strategies were: (i) selecting bulls from conventional breeding programs, and taking into account genotype by environment (G×E) interactions, (ii) selecting genotyped bulls within the organic environment for artificial insemination (AI) programs and (iii) selecting genotyped natural service bulls within organic herds. The simulated conventional population comprised 148 800 cows from 2976 herds with an average herd size of 50 cows per herd, and 1200 cows were assigned to 60 organic herds. In a young bull program, selection criteria of young bulls in both production systems (conventional and organic) were either 'conventional' estimated breeding values (EBV) or genomic estimated breeding values (GEBV) for two traits with low (h 2=0.05) and moderate heritability (h 2=0.30). GEBV were calculated for different accuracies (r mg), and G×E interactions were considered by modifying originally simulated true breeding values in the range from r g=0.5 to 1.0. For both traits (h 2=0.05 and 0.30) and r mg⩾0.8, genomic selection of bulls directly in the organic population and using selected bulls via AI revealed higher genetic gain than selecting young bulls in the larger conventional population based on EBV; also without the existence of G×E interactions. Only for pronounced G×E interactions (r g=0.5), and for highly accurate GEBV for natural service bulls (r mg>0.9), results suggests the use of genotyped organic natural service bulls instead of implementing an AI program. Inbreeding coefficients of selected bulls and their offspring were generally lower when basing selection decisions for young bulls on GEBV compared with selection strategies based on pedigree indices.

Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size.

PubMed

Medugorac, Ivica; Medugorac, Ana; Russ, Ingolf; Veit-Kensch, Claudia E; Taberlet, Pierre; Luntz, Bernhard; Mix, Henry M; Förster, Martin

2009-08-01

In times of rapid global and unforeseeable environmental changes, there is an urgent need for a sustainable cattle breeding policy, based on a global view. Most of the indigenous breeds are specialized in a particular habitat or production system but are rapidly disappearing. Thus, they represent an important resource to meet present and future breeding objectives. Based on 105 microsatellites, we obtained thorough information on genetic diversity and population structure of 16 cattle breeds that cover a geographical area from the domestication centre near Anatolia, through the Balkan and alpine regions, to the North-West of Europe. Breeds under strict artificial selection and indigenous breeds under traditional breeding schemes were included. The overall results showed that the genetic diversity is widespread in Busa breeds in the Anatolian and Balkan areas, when compared with the alpine and north-western European breeds. Our results reflect long-term evolutionary and short-term breeding events very well. The regular pattern of allele frequency distribution in the entire cattle population studied clearly suggests conservation of rare alleles by conservation of preferably unselected traditional breeds with large effective population sizes. From a global and long-term conservation genetics point of view, the native and highly variable breeds closer to the domestication centre could serve as valuable sources of genes for future needs, not only for cattle but also for other farm animals.

Comparison of three models to estimate breeding values for percentage of loin intramuscular fat in Duroc swine.

PubMed

Newcom, D W; Baas, T J; Stalder, K J; Schwab, C R

2005-04-01

Three selection models were evaluated to compare selection candidate rankings based on EBV and to evaluate subsequent effects of model-derived EBV on the selection differential and expected genetic response in the population. Data were collected from carcass- and ultrasound-derived estimates of loin i.m. fat percent (IMF) in a population of Duroc swine under selection to increase IMF. The models compared were Model 1, a two-trait animal model used in the selection experiment that included ultrasound IMF from all pigs scanned and carcass IMF from pigs slaughtered to estimate breeding values for both carcass (C1) and ultrasound IMF (U1); Model 2, a single-trait animal model that included ultrasound IMF values on all pigs scanned to estimate breeding values for ultrasound IMF (U2); and Model 3, a multiple-trait animal model including carcass IMF from slaughtered pigs and the first three principal components from a total of 10 image parameters averaged across four longitudinal ultrasound images to estimate breeding values for carcass IMF (C3). Rank correlations between breeding value estimates for U1 and C1, U1 and U2, and C1 and C3 were 0.95, 0.97, and 0.92, respectively. Other rank correlations were 0.86 or less. In the selection experiment, approximately the top 10% of boars and 50% of gilts were selected. Selection differentials for pigs in Generation 3 were greatest when ranking pigs based on C1, followed by U1, U2, and C3. In addition, selection differential and estimated response were evaluated when simulating selection of the top 1, 5, and 10% of sires and 50% of dams. Results of this analysis indicated the greatest selection differential was for selection based on C1. The greatest loss in selection differential was found for selection based on C3 when selecting the top 10 and 1% of boars and 50% of gilts. The loss in estimated response when selecting varying percentages of boars and the top 50% of gilts was greatest when selection was based on C3 (16.0 to 25.8%) and least for selection based on U1 (1.3 to 10.9%). Estimated genetic change from selection based on carcass IMF was greater than selection based on ultrasound IMF. Results show that selection based on a combination of ultrasonically predicted IMF and sib carcass IMF produced the greatest selection differentials and should lead to the greatest genetic change.

Economic values for health and feed efficiency traits of dual-purpose cattle in marginal areas.

PubMed

Krupová, Z; Krupa, E; Michaličková, M; Wolfová, M; Kasarda, R

2016-01-01

Economic values of clinical mastitis, claw disease, and feed efficiency traits along with 16 additional production and functional traits were estimated for the dairy population of the Slovak Pinzgau breed using a bioeconomic approach. In the cow-calf population (suckler cow population) of the same breed, the economic values of feed efficiency traits along with 15 further production and functional traits were calculated. The marginal economic values of clinical mastitis and claw disease incidence in the dairy system were -€ 70.65 and -€ 26.73 per case per cow and year, respectively. The marginal economic values for residual feed intake were -€ 55.15 and -€ 54.64/kg of dry matter per day for cows and breeding heifers in the dairy system and -€ 20.45, -€ 11.30, and -€ 6.04/kg of dry matter per day for cows, breeding heifers, and fattened animals in the cow-calf system, respectively, all expressed per cow and year. The sums of the relative economic values for the 2 new health traits in the dairy system and for residual feed intake across all cattle categories in both systems were 1.4 and 8%, respectively. Within the dairy production system, the highest relative economic values were for milk yield (20%), daily gain of calves (20%), productive lifetime (10%), and cow conception rate (8%). In the cow-calf system, the most important traits were weight gain of calves from 120 to 210 d and from birth to 120 d (19 and 14%, respectively), productive lifetime (17%), and cow conception rate (13%). Based on the calculation of economic values for traits in the dual-purpose Pinzgau breed, milk production and growth traits remain highly important in the breeding goal, but their relative importance should be adapted to new production and economic conditions. The economic importance of functional traits (especially of cow productive lifetime and fertility) was sufficiently high to make the inclusion of these traits into the breeding goal necessary. An increased interest of consumers in animal welfare and quality of dairy farm products should probably lead to the incorporation of health traits (clinical mastitis incidence and somatic cells score) into the breeding goal. However, keeping carcass traits in the breeding goal of the Slovak Pinzgau breed does not seem to be relevant to the long-term market situation. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Will genomic selection be a practical method for plant breeding?

PubMed Central

Nakaya, Akihiro; Isobe, Sachiko N.

2012-01-01

Background Genomic selection or genome-wide selection (GS) has been highlighted as a new approach for marker-assisted selection (MAS) in recent years. GS is a form of MAS that selects favourable individuals based on genomic estimated breeding values. Previous studies have suggested the utility of GS, especially for capturing small-effect quantitative trait loci, but GS has not become a popular methodology in the field of plant breeding, possibly because there is insufficient information available on GS for practical use. Scope In this review, GS is discussed from a practical breeding viewpoint. Statistical approaches employed in GS are briefly described, before the recent progress in GS studies is surveyed. GS practices in plant breeding are then reviewed before future prospects are discussed. Conclusions Statistical concepts used in GS are discussed with genetic models and variance decomposition, heritability, breeding value and linear model. Recent progress in GS studies is reviewed with a focus on empirical studies. For the practice of GS in plant breeding, several specific points are discussed including linkage disequilibrium, feature of populations and genotyped markers and breeding scheme. Currently, GS is not perfect, but it is a potent, attractive and valuable approach for plant breeding. This method will be integrated into many practical breeding programmes in the near future with further advances and the maturing of its theory. PMID:22645117

Accuracy of predicting genomic breeding values for residual feed intake in Angus and Charolais beef cattle.

PubMed

Chen, L; Schenkel, F; Vinsky, M; Crews, D H; Li, C

2013-10-01

In beef cattle, phenotypic data that are difficult and/or costly to measure, such as feed efficiency, and DNA marker genotypes are usually available on a small number of animals of different breeds or populations. To achieve a maximal accuracy of genomic prediction using the phenotype and genotype data, strategies for forming a training population to predict genomic breeding values (GEBV) of the selection candidates need to be evaluated. In this study, we examined the accuracy of predicting GEBV for residual feed intake (RFI) based on 522 Angus and 395 Charolais steers genotyped on SNP with the Illumina Bovine SNP50 Beadchip for 3 training population forming strategies: within breed, across breed, and by pooling data from the 2 breeds (i.e., combined). Two other scenarios with the training and validation data split by birth year and by sire family within a breed were also investigated to assess the impact of genetic relationships on the accuracy of genomic prediction. Three statistical methods including the best linear unbiased prediction with the relationship matrix defined based on the pedigree (PBLUP), based on the SNP genotypes (GBLUP), and a Bayesian method (BayesB) were used to predict the GEBV. The results showed that the accuracy of the GEBV prediction was the highest when the prediction was within breed and when the validation population had greater genetic relationships with the training population, with a maximum of 0.58 for Angus and 0.64 for Charolais. The within-breed prediction accuracies dropped to 0.29 and 0.38, respectively, when the validation populations had a minimal pedigree link with the training population. When the training population of a different breed was used to predict the GEBV of the validation population, that is, across-breed genomic prediction, the accuracies were further reduced to 0.10 to 0.22, depending on the prediction method used. Pooling data from the 2 breeds to form the training population resulted in accuracies increased to 0.31 and 0.43, respectively, for the Angus and Charolais validation populations. The results suggested that the genetic relationship of selection candidates with the training population has a greater impact on the accuracy of GEBV using the Illumina Bovine SNP50 Beadchip. Pooling data from different breeds to form the training population will improve the accuracy of across breed genomic prediction for RFI in beef cattle.

Impact of fitting dominance and additive effects on accuracy of genomic prediction of breeding values in layers.

PubMed

Heidaritabar, M; Wolc, A; Arango, J; Zeng, J; Settar, P; Fulton, J E; O'Sullivan, N P; Bastiaansen, J W M; Fernando, R L; Garrick, D J; Dekkers, J C M

2016-10-01

Most genomic prediction studies fit only additive effects in models to estimate genomic breeding values (GEBV). However, if dominance genetic effects are an important source of variation for complex traits, accounting for them may improve the accuracy of GEBV. We investigated the effect of fitting dominance and additive effects on the accuracy of GEBV for eight egg production and quality traits in a purebred line of brown layers using pedigree or genomic information (42K single-nucleotide polymorphism (SNP) panel). Phenotypes were corrected for the effect of hatch date. Additive and dominance genetic variances were estimated using genomic-based [genomic best linear unbiased prediction (GBLUP)-REML and BayesC] and pedigree-based (PBLUP-REML) methods. Breeding values were predicted using a model that included both additive and dominance effects and a model that included only additive effects. The reference population consisted of approximately 1800 animals hatched between 2004 and 2009, while approximately 300 young animals hatched in 2010 were used for validation. Accuracy of prediction was computed as the correlation between phenotypes and estimated breeding values of the validation animals divided by the square root of the estimate of heritability in the whole population. The proportion of dominance variance to total phenotypic variance ranged from 0.03 to 0.22 with PBLUP-REML across traits, from 0 to 0.03 with GBLUP-REML and from 0.01 to 0.05 with BayesC. Accuracies of GEBV ranged from 0.28 to 0.60 across traits. Inclusion of dominance effects did not improve the accuracy of GEBV, and differences in their accuracies between genomic-based methods were small (0.01-0.05), with GBLUP-REML yielding higher prediction accuracies than BayesC for egg production, egg colour and yolk weight, while BayesC yielded higher accuracies than GBLUP-REML for the other traits. In conclusion, fitting dominance effects did not impact accuracy of genomic prediction of breeding values in this population. © 2016 Blackwell Verlag GmbH.

Variance component and breeding value estimation for genetic heterogeneity of residual variance in Swedish Holstein dairy cattle.

PubMed

Rönnegård, L; Felleki, M; Fikse, W F; Mulder, H A; Strandberg, E

2013-04-01

Trait uniformity, or micro-environmental sensitivity, may be studied through individual differences in residual variance. These differences appear to be heritable, and the need exists, therefore, to fit models to predict breeding values explaining differences in residual variance. The aim of this paper is to estimate breeding values for micro-environmental sensitivity (vEBV) in milk yield and somatic cell score, and their associated variance components, on a large dairy cattle data set having more than 1.6 million records. Estimation of variance components, ordinary breeding values, and vEBV was performed using standard variance component estimation software (ASReml), applying the methodology for double hierarchical generalized linear models. Estimation using ASReml took less than 7 d on a Linux server. The genetic standard deviations for residual variance were 0.21 and 0.22 for somatic cell score and milk yield, respectively, which indicate moderate genetic variance for residual variance and imply that a standard deviation change in vEBV for one of these traits would alter the residual variance by 20%. This study shows that estimation of variance components, estimated breeding values and vEBV, is feasible for large dairy cattle data sets using standard variance component estimation software. The possibility to select for uniformity in Holstein dairy cattle based on these estimates is discussed. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Genomic-based multiple-trait evaluation in Eucalyptus grandis using dominant DArT markers.

PubMed

Cappa, Eduardo P; El-Kassaby, Yousry A; Muñoz, Facundo; Garcia, Martín N; Villalba, Pamela V; Klápště, Jaroslav; Marcucci Poltri, Susana N

2018-06-01

We investigated the impact of combining the pedigree- and genomic-based relationship matrices in a multiple-trait individual-tree mixed model (a.k.a., multiple-trait combined approach) on the estimates of heritability and on the genomic correlations between growth and stem straightness in an open-pollinated Eucalyptus grandis population. Additionally, the added advantage of incorporating genomic information on the theoretical accuracies of parents and offspring breeding values was evaluated. Our results suggested that the use of the combined approach for estimating heritabilities and additive genetic correlations in multiple-trait evaluations is advantageous and including genomic information increases the expected accuracy of breeding values. Furthermore, the multiple-trait combined approach was proven to be superior to the single-trait combined approach in predicting breeding values, in particular for low-heritability traits. Finally, our results advocate the use of the combined approach in forest tree progeny testing trials, specifically when a multiple-trait individual-tree mixed model is considered. Copyright © 2018 Elsevier B.V. All rights reserved.

Fitness prospects: effects of age, sex and recruitment age on reproductive value in a long-lived seabird.

PubMed

Zhang, He; Rebke, Maren; Becker, Peter H; Bouwhuis, Sandra

2015-01-01

Reproductive value is an integrated measure of survival and reproduction fundamental to understanding life-history evolution and population dynamics, but little is known about intraspecific variation in reproductive value and factors explaining such variation, if any. By applying generalized additive mixed models to longitudinal individual-based data of the common tern Sterna hirundo, we estimated age-specific annual survival probability, breeding probability and reproductive performance, based on which we calculated age-specific reproductive values. We investigated effects of sex and recruitment age (RA) on each trait. We found age effects on all traits, with survival and breeding probability declining with age, while reproductive performance first improved with age before levelling off. We only found a very small, marginally significant, sex effect on survival probability, but evidence for decreasing age-specific breeding probability and reproductive performance with RA. As a result, males had slightly lower age-specific reproductive values than females, while birds of both sexes that recruited at the earliest ages of 2 and 3 years (i.e. 54% of the tern population) had somewhat higher fitness prospects than birds recruiting at later ages. While the RA effects on breeding probability and reproductive performance were statistically significant, these effects were not large enough to translate to significant effects on reproductive value. Age-specific reproductive values provided evidence for senescence, which came with fitness costs in a range of 17-21% for the sex-RA groups. Our study suggests that intraspecific variation in reproductive value may exist, but that, in the common tern, the differences are small. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information.

PubMed

Cortés, O; Martinez, A M; Cañon, J; Sevane, N; Gama, L T; Ginja, C; Landi, V; Zaragoza, P; Carolino, N; Vicente, A; Sponenberg, P; Delgado, J V

2016-07-01

Criollo pig breeds are descendants from pigs brought to the American continent starting with Columbus second trip in 1493. Pigs currently play a key role in social economy and community cultural identity in Latin America. The aim of this study was to establish conservation priorities among a comprehensive group of Criollo pig breeds based on a set of 24 microsatellite markers and using different criteria. Spain and Portugal pig breeds, wild boar populations of different European geographic origins and commercial pig breeds were included in the analysis as potential genetic influences in the development of Criollo pig breeds. Different methods, differing in the weight given to within- and between-breed genetic variability, were used in order to estimate the contribution of each breed to global genetic diversity. As expected, the partial contribution to total heterozygosity gave high priority to Criollo pig breeds, whereas Weitzman procedures prioritized Iberian Peninsula breeds. With the combined within- and between-breed approaches, different conservation priorities were achieved. The Core Set methodologies highly prioritized Criollo pig breeds (Cr. Boliviano, Cr. Pacifico, Cr. Cubano and Cr. Guadalupe). However, weighing the between- and within-breed components with FST and 1-FST, respectively, resulted in higher contributions of Iberian breeds. In spite of the different conservation priorities according to the methodology used, other factors in addition to genetic information also need to be considered in conservation programmes, such as the economic, cultural or historical value of the breeds involved.

Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information

PubMed Central

Cortés, O; Martinez, A M; Cañon, J; Sevane, N; Gama, L T; Ginja, C; Landi, V; Zaragoza, P; Carolino, N; Vicente, A; Sponenberg, P; Delgado, J V

2016-01-01

Criollo pig breeds are descendants from pigs brought to the American continent starting with Columbus second trip in 1493. Pigs currently play a key role in social economy and community cultural identity in Latin America. The aim of this study was to establish conservation priorities among a comprehensive group of Criollo pig breeds based on a set of 24 microsatellite markers and using different criteria. Spain and Portugal pig breeds, wild boar populations of different European geographic origins and commercial pig breeds were included in the analysis as potential genetic influences in the development of Criollo pig breeds. Different methods, differing in the weight given to within- and between-breed genetic variability, were used in order to estimate the contribution of each breed to global genetic diversity. As expected, the partial contribution to total heterozygosity gave high priority to Criollo pig breeds, whereas Weitzman procedures prioritized Iberian Peninsula breeds. With the combined within- and between-breed approaches, different conservation priorities were achieved. The Core Set methodologies highly prioritized Criollo pig breeds (Cr. Boliviano, Cr. Pacifico, Cr. Cubano and Cr. Guadalupe). However, weighing the between- and within-breed components with FST and 1-FST, respectively, resulted in higher contributions of Iberian breeds. In spite of the different conservation priorities according to the methodology used, other factors in addition to genetic information also need to be considered in conservation programmes, such as the economic, cultural or historical value of the breeds involved. PMID:27025169

Methods to determine the relative value of genetic traits in dairy cows to reduce greenhouse gas emissions along the chain.

PubMed

van Middelaar, C E; Berentsen, P B M; Dijkstra, J; van Arendonk, J A M; de Boer, I J M

2014-01-01

Current decisions on breeding in dairy farming are mainly based on economic values of heritable traits, as earning an income is a primary objective of farmers. Recent literature, however, shows that breeding also has potential to reduce greenhouse gas (GHG) emissions. The objective of this paper was to compare 2 methods to determine GHG values of genetic traits. Method 1 calculates GHG values using the current strategy (i.e., maximizing labor income), whereas method 2 is based on minimizing GHG per kilogram of milk and shows what can be achieved if the breeding results are fully directed at minimizing GHG emissions. A whole-farm optimization model was used to determine results before and after 1 genetic standard deviation improvement (i.e., unit change) of milk yield and longevity. The objective function of the model differed between method 1 and 2. Method 1 maximizes labor income; method 2 minimizes GHG emissions per kilogram of milk while maintaining labor income and total milk production at least at the level before the change in trait. Results show that the full potential of the traits to reduce GHG emissions given the boundaries that were set for income and milk production (453 and 441kg of CO2 equivalents/unit change per cow per year for milk yield and longevity, respectively) is about twice as high as the reduction based on maximizing labor income (247 and 210kg of CO2 equivalents/unit change per cow per year for milk yield and longevity, respectively). The GHG value of milk yield is higher than that of longevity, especially when the focus is on maximizing labor income. Based on a sensitivity analysis, it was shown that including emissions from land use change and using different methods for handling the interaction between milk and meat production can change results, generally in favor of milk yield. Results can be used by breeding organizations that want to include GHG values in their breeding goal. To verify GHG values, the effect of prices and emissions factors should be considered, as well as the potential effect of variation between farm types. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

The contribution of migrant breeds to the genetic gain of beef traits of German Vorderwald and Hinterwald cattle.

PubMed

Hartwig, S; Wellmann, R; Hamann, H; Bennewitz, J

2014-12-01

During the past decades, migrant contributions have accumulated in many local breeds. Cross-breeding was carried out to mitigate the risk of inbreeding depression and to improve the performance of local breeds. However, breeding activities for local breeds were not as intensive and target oriented as for popular high-yielding breeds. Therefore, even if performance improved, the gap between the performance of local and popular breeds increased for many traits. Furthermore, the genetic originality of local breeds declined due to the increasing contributions of migrant breeds. This study examined the importance of migrant breed influences for the realization of breeding progress of beef traits of German Vorderwald and Hinterwald cattle. The results show that there is a high amount of migrant contributions and their effects on performance are substantial for most traits. The effect of the French cattle breed Montbéliard (p-value 0.014) on daily gain of Vorderwald bulls at test station was positive. The effects of Vorderwald ancestors (p-value for daily gain 0.007 and p-value for net gain 0.004) were positive for both traits under consideration in the population of Hinterwald cattle. Additionally, the effect of remaining breeds (p-value 0.030) on net gain of Hinterwald cattle in the field was also positive. The estimated effect of Fleckvieh ancestors on net gain of Hinterwald cattle was even larger but not significant. Breeding values adjusted for the effects of the migrant breeds showed little genetic trend. © 2014 Blackwell Verlag GmbH.

Captive breeding of pangolins: current status, problems and future prospects

PubMed Central

Hua, Liushuai; Gong, Shiping; Wang, Fumin; Li, Weiye; Ge, Yan; Li, Xiaonan; Hou, Fanghui

2015-01-01

Abstract Pangolins are unique placental mammals with eight species existing in the world, which have adapted to a highly specialized diet of ants and termites, and are of significance in the control of forest termite disaster. Besides their ecological value, pangolins are extremely important economic animals with the value as medicine and food. At present, illegal hunting and habitat destruction have drastically decreased the wild population of pangolins, pushing them to the edge of extinction. Captive breeding is an important way to protect these species, but because of pangolin’s specialized behaviors and high dependence on natural ecosystem, there still exist many technical barriers to successful captive breeding programs. In this paper, based on the literatures and our practical experience, we reviewed the status and existing problems in captive breeding of pangolins, including four aspects, the naturalistic habitat, dietary husbandry, reproduction and disease control. Some recommendations are presented for effective captive breeding and protection of pangolins. PMID:26155072

A Genetic Analysis of Taoyuan Pig and Its Phylogenetic Relationship to Eurasian Pig Breeds

PubMed Central

Li, Kuan-Yi; Li, Kuang-Ti; Cheng, Chun-Chun; Chen, Chia-Hsuan; Hung, Chien-Yi; Ju, Yu-Ten

2015-01-01

Taoyuan pig is a native Taiwan breed. According to the historical record, the breed was first introduced to Taiwan from Guangdong province, Southern China, around 1877. The breed played an important role in Taiwan’s early swine industry. It was classified as an indigenous breed in 1986. After 1987, a conserved population of Taoyuan pig was collected and reared in isolation. In this study, mitochondrial DNA sequences and 18 microsatellite markers were used to investigate maternal lineage and genetic diversity within the Taoyuan pig population. Population differentiation among Taoyuan, Asian type, and European type pig breeds was also evaluated using differentiation indices. Only one D-loop haplotype of the Taoyuan pig was found. It clustered with Lower Changjiang River Basin and Central China Type pig breeds. Based on the polymorphism of microsatellite markers, a positive fixation index value (FIS) indicates that the conserved Taoyuan population suffers from inbreeding. In addition, high FST values (>0.2105) were obtained, revealing high differentiation among these breeds. Non-metric multi-dimensional scaling showed a clear geometric structure among 7 breeds. Together these results indicate that maternally Taoyuan pig originated in the Lower Changjiang River Basin and Central China; however, since being introduced to Taiwan differentiation has occurred. In addition, Taoyuan pig has lost genetic diversity in both its mitochondrial and nuclear genomes. PMID:25656199

Exploitation of data from breeding programs supports rapid implementation of genomic selection for key agronomic traits in perennial ryegrass.

PubMed

Pembleton, Luke W; Inch, Courtney; Baillie, Rebecca C; Drayton, Michelle C; Thakur, Preeti; Ogaji, Yvonne O; Spangenberg, German C; Forster, John W; Daetwyler, Hans D; Cogan, Noel O I

2018-06-02

Exploitation of data from a ryegrass breeding program has enabled rapid development and implementation of genomic selection for sward-based biomass yield with a twofold-to-threefold increase in genetic gain. Genomic selection, which uses genome-wide sequence polymorphism data and quantitative genetics techniques to predict plant performance, has large potential for the improvement in pasture plants. Major factors influencing the accuracy of genomic selection include the size of reference populations, trait heritability values and the genetic diversity of breeding populations. Global diversity of the important forage species perennial ryegrass is high and so would require a large reference population in order to achieve moderate accuracies of genomic selection. However, diversity of germplasm within a breeding program is likely to be lower. In addition, de novo construction and characterisation of reference populations are a logistically complex process. Consequently, historical phenotypic records for seasonal biomass yield and heading date over a 18-year period within a commercial perennial ryegrass breeding program have been accessed, and target populations have been characterised with a high-density transcriptome-based genotyping-by-sequencing assay. Ability to predict observed phenotypic performance in each successive year was assessed by using all synthetic populations from previous years as a reference population. Moderate and high accuracies were achieved for the two traits, respectively, consistent with broad-sense heritability values. The present study represents the first demonstration and validation of genomic selection for seasonal biomass yield within a diverse commercial breeding program across multiple years. These results, supported by previous simulation studies, demonstrate the ability to predict sward-based phenotypic performance early in the process of individual plant selection, so shortening the breeding cycle, increasing the rate of genetic gain and allowing rapid adoption in ryegrass improvement programs.

Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle

PubMed Central

Mészáros, Gábor; Boison, Solomon A.; Pérez O'Brien, Ana M.; Ferenčaković, Maja; Curik, Ino; Da Silva, Marcos V. Barbosa; Utsunomiya, Yuri T.; Garcia, Jose F.; Sölkner, Johann

2015-01-01

Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore, the routine collection of genomic information would be an invaluable resource for effective management of breeding programs in small, endangered populations. The objective of the paper was to demonstrate how genomic data could be used to analyse (1) linkage disequlibrium (LD), LD decay and the effective population size (NeLD); (2) Inbreeding level and effective population size (NeROH) based on runs of homozygosity (ROH); (3) Prediction of genomic breeding values (GEBV) using small within-breed and genomic information from other breeds. The Tyrol Grey population was used as an example, with the goal to highlight the potential of genomic analyses for small breeds. In addition to our own results we discuss additional use of genomics to assess relatedness, admixture proportions, and inheritance of harmful variants. The example data set consisted of 218 Tyrol Grey bull genotypes, which were all available AI bulls in the population. After standard quality control restrictions 34,581 SNPs remained for the analysis. A separate quality control was applied to determine ROH levels based on Illumina GenCall and Illumina GenTrain scores, resulting into 211 bulls and 33,604 SNPs. LD was computed as the squared correlation coefficient between SNPs within a 10 mega base pair (Mb) region. ROHs were derived based on regions covering at least 4, 8, and 16 Mb, suggesting that animals had common ancestors approximately 12, 6, and 3 generations ago, respectively. The corresponding mean inbreeding coefficients (FROH) were 4.0% for 4 Mb, 2.9% for 8 Mb and 1.6% for 16 Mb runs. With an average generation interval of 5.66 years, estimated NeROH was 125 (NeROH>16 Mb), 186 (NeROH>8 Mb) and 370 (NeROH>4 Mb) indicating strict avoidance of close inbreeding in the population. The LD was used as an alternative method to infer the population history and the Ne. The results show a continuous decrease in NeLD, to 780, 120, and 80 for 100, 10, and 5 generations ago, respectively. Genomic selection was developed for and is working well in large breeds. The same methodology was applied in Tyrol Grey cattle, using different reference populations. Contrary to the expectations, the accuracy of GEBVs with very small within breed reference populations were very high, between 0.13–0.91 and 0.12–0.63, when estimated breeding values and deregressed breeding values were used as pseudo-phenotypes, respectively. Subsequent analyses confirmed the high accuracies being a consequence of low reliabilities of pseudo-phenotypes in the validation set, thus being heavily influenced by parent averages. Multi-breed and across breed reference sets gave inconsistent and lower accuracies. Genomic information may have a crucial role in management of small breeds, even if its primary usage differs from that of large breeds. It allows to assess relatedness between individuals, trends in inbreeding and to take decisions accordingly. These decisions would be based on the real genome architecture, rather than conventional pedigree information, which can be missing or incomplete. We strongly suggest the routine genotyping of all individuals that belong to a small breed in order to facilitate the effective management of endangered livestock populations. PMID:26074948

Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle.

PubMed

Mészáros, Gábor; Boison, Solomon A; Pérez O'Brien, Ana M; Ferenčaković, Maja; Curik, Ino; Da Silva, Marcos V Barbosa; Utsunomiya, Yuri T; Garcia, Jose F; Sölkner, Johann

2015-01-01

Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore, the routine collection of genomic information would be an invaluable resource for effective management of breeding programs in small, endangered populations. The objective of the paper was to demonstrate how genomic data could be used to analyse (1) linkage disequlibrium (LD), LD decay and the effective population size (NeLD); (2) Inbreeding level and effective population size (NeROH) based on runs of homozygosity (ROH); (3) Prediction of genomic breeding values (GEBV) using small within-breed and genomic information from other breeds. The Tyrol Grey population was used as an example, with the goal to highlight the potential of genomic analyses for small breeds. In addition to our own results we discuss additional use of genomics to assess relatedness, admixture proportions, and inheritance of harmful variants. The example data set consisted of 218 Tyrol Grey bull genotypes, which were all available AI bulls in the population. After standard quality control restrictions 34,581 SNPs remained for the analysis. A separate quality control was applied to determine ROH levels based on Illumina GenCall and Illumina GenTrain scores, resulting into 211 bulls and 33,604 SNPs. LD was computed as the squared correlation coefficient between SNPs within a 10 mega base pair (Mb) region. ROHs were derived based on regions covering at least 4, 8, and 16 Mb, suggesting that animals had common ancestors approximately 12, 6, and 3 generations ago, respectively. The corresponding mean inbreeding coefficients (F ROH) were 4.0% for 4 Mb, 2.9% for 8 Mb and 1.6% for 16 Mb runs. With an average generation interval of 5.66 years, estimated NeROH was 125 (NeROH>16 Mb), 186 (NeROH>8 Mb) and 370 (NeROH>4 Mb) indicating strict avoidance of close inbreeding in the population. The LD was used as an alternative method to infer the population history and the Ne. The results show a continuous decrease in NeLD, to 780, 120, and 80 for 100, 10, and 5 generations ago, respectively. Genomic selection was developed for and is working well in large breeds. The same methodology was applied in Tyrol Grey cattle, using different reference populations. Contrary to the expectations, the accuracy of GEBVs with very small within breed reference populations were very high, between 0.13-0.91 and 0.12-0.63, when estimated breeding values and deregressed breeding values were used as pseudo-phenotypes, respectively. Subsequent analyses confirmed the high accuracies being a consequence of low reliabilities of pseudo-phenotypes in the validation set, thus being heavily influenced by parent averages. Multi-breed and across breed reference sets gave inconsistent and lower accuracies. Genomic information may have a crucial role in management of small breeds, even if its primary usage differs from that of large breeds. It allows to assess relatedness between individuals, trends in inbreeding and to take decisions accordingly. These decisions would be based on the real genome architecture, rather than conventional pedigree information, which can be missing or incomplete. We strongly suggest the routine genotyping of all individuals that belong to a small breed in order to facilitate the effective management of endangered livestock populations.

The differentiation of camel breeds based on meat measurements using discriminant analysis.

PubMed

Al-Atiyat, Raed Mahmoud; Suliman, Gamal; AlSuhaibani, Entissar; El-Waziry, Ahmad; Al-Owaimer, Abdullah; Basmaeil, Saeid

2016-06-01

The meat productivity of camel in the tropics is still under investigation for identification of better meat breed or type. Therefore, four one-humped Saudi Arabian (SA) camel breeds, Majaheem, Maghateer, Hamrah, and Safrah were experimented in order to differentiate them from each other based on meat measurements. The measurements were biometrical meat traits measured on six intact males from each breed. The results showed higher values of the Majaheem breed than that obtained for the other breeds except few cases such dressing percentage and rib-eye area. In differentiation analysis, the most discriminating meat variables were myofibrillar protein index, meat color components (L* and a*, b*), and cooking loss. Consequently, the Safrah and the Majaheem breeds presented the largest dissimilarity as evidenced by their multivariate means. The canonical discriminant analysis allowed an additional understanding of the differentiation between breeds. Furthermore, two large clusters, one formed by Hamrah and Maghateer in one group along with Safrah. These classifications may assign each breed into one cluster considering they are better as meat producers. The Majaheem was clustered alone in another cluster that might be a result of being better as milk producers. Nevertheless, the productivity type of the camel breeds of SA needs further morphology and genetic descriptions.

Heritability and phenotypic variation of canine hip dysplasia radiographic traits in a cohort of Australian German shepherd dogs.

PubMed

Wilson, Bethany J; Nicholas, Frank W; James, John W; Wade, Claire M; Tammen, Imke; Raadsma, Herman W; Castle, Kao; Thomson, Peter C

2012-01-01

Canine Hip Dysplasia (CHD) is a common, painful and debilitating orthopaedic disorder of dogs with a partly genetic, multifactorial aetiology. Worldwide, potential breeding dogs are evaluated for CHD using radiographically based screening schemes such as the nine ordinally-scored British Veterinary Association Hip Traits (BVAHTs). The effectiveness of selective breeding based on screening results requires that a significant proportion of the phenotypic variation is caused by the presence of favourable alleles segregating in the population. This proportion, heritability, was measured in a cohort of 13,124 Australian German Shepherd Dogs born between 1976 and 2005, displaying phenotypic variation for BVAHTs, using ordinal, linear and binary mixed models fitted by a Restricted Maximum Likelihood method. Heritability estimates for the nine BVAHTs ranged from 0.14-0.24 (ordinal models), 0.14-0.25 (linear models) and 0.12-0.40 (binary models). Heritability for the summed BVAHT phenotype was 0.30 ± 0.02. The presence of heritable variation demonstrates that selection based on BVAHTs has the potential to improve BVAHT scores in the population. Assuming a genetic correlation between BVAHT scores and CHD-related pain and dysfunction, the welfare of Australian German Shepherds can be improved by continuing to consider BVAHT scores in the selection of breeding dogs, but that as heritability values are only moderate in magnitude the accuracy, and effectiveness, of selection could be improved by the use of Estimated Breeding Values in preference to solely phenotype based selection of breeding animals.

Determination of non-market values to inform conservation strategies for the threatened Alistana-Sanabresa cattle breed.

PubMed

Martin-Collado, D; Diaz, C; Drucker, A G; Carabaño, M J; Zander, K K

2014-08-01

Livestock breed-related public good functions are often used to justify support for endangered breed conservation despite the fact that little is known about such non-market values. We show how stated preference techniques can be used to assess the non-market values that people place on livestock breeds. Through the application of a case study choice experiment survey in Zamora province, Spain, the total economic value (TEV) of the threatened Alistana-Sanabresa (AS) cattle breed was investigated. An analysis of the relative importance of the non-market components of its TEV and an assessment of the socio-economic variables that influence people's valuation of such components is used to inform conservation strategy design. Overall, the findings reveal that the AS breed had significant non-market values associated with it and that the value that respondents placed on each specific public good function also varied significantly. Functions related with indirect use cultural and existence values were much more highly valued than landscape maintenance values. These high cultural and existence values (totalling over 80% of TEV) suggest that an AS in situ conservation strategy will be required to secure such values. As part of such a strategy, incentive mechanisms will be needed to permit farmers to capture some of these public good values and thus be able to afford to maintain breed population numbers at socially desirable levels. One such mechanism could be related to the development of breed-related agritourism initiatives, with a view to enhancing private good values and providing an important addition to continued direct support. Where linked with cultural dimensions, niche product market development, including through improving AS breed-related product quality and brand recognition may also have a role to play as part of such an overall conservation and use strategy. We conclude that livestock breed conservation strategies with the highest potential to maximise societal welfare would be those that secure the breed-related functions that people value most, with appropriate in situ conservation interventions and strategies being identified accordingly.

Parameter-based stochastic simulation of selection and breeding for multiple traits

Treesearch

Jennifer Myszewski; Thomas Byram; Floyd Bridgwater

2006-01-01

To increase the adaptability and economic value of plantations, tree improvement professionals often manage multiple traits in their breeding programs. When these traits are unfavorably correlated, breeders must weigh the economic importance of each trait and select for a desirable aggregate phenotype. Stochastic simulation allows breeders to test the effects of...

Selection and use of microsatellite markers for individual identification and meat traceability of six swine breeds in the Chinese market.

PubMed

Zhao, Jie; Li, Tingting; Zhu, Chao; Jiang, Xiaoling; Zhao, Yan; Xu, Zhenzhen; Yang, Shuming; Chen, Ailiang

2018-06-01

Meat traceability based on molecular markers is exerting a great influence on food safety and will enhance its key role in the future. This study aimed to investigate and verify the polymorphism of 23 microsatellite markers and select the most suitable markers for individual identification and meat traceability of six swine breeds in the Chinese market. The mean polymorphism information content value of these 23 loci was 0.7851, and each locus exhibited high polymorphism in the pooled population. There were 10 loci showing good polymorphism in each breed, namely, Sw632, S0155, Sw2406, Sw830, Sw2525, Sw72, Sw2448, Sw911, Sw122 and CGA. When six highly polymorphic loci were combined, the match probability value for two random individual genotypes among the pig breeds (Beijing Black, Sanyuan and Taihu) was lower than 1.151 E-06. An increasing number of loci indicated a gradually decreasing match probability value and therefore enhanced traceability accuracy. The validation results of tracing 18 blood and corresponding meat samples based on five highly polymorphic loci (Sw2525, S0005, Sw0107, Sw911 and Sw857) were successful, with 100% conformation probability, which provided a foundation for establishing a traceability system for pork in the Chinese market.

Accuracy of genomic breeding values for meat tenderness in Polled Nellore cattle.

PubMed

Magnabosco, C U; Lopes, F B; Fragoso, R C; Eifert, E C; Valente, B D; Rosa, G J M; Sainz, R D

2016-07-01

Zebu () cattle, mostly of the Nellore breed, comprise more than 80% of the beef cattle in Brazil, given their tolerance of the tropical climate and high resistance to ectoparasites. Despite their advantages for production in tropical environments, zebu cattle tend to produce tougher meat than Bos taurus breeds. Traditional genetic selection to improve meat tenderness is constrained by the difficulty and cost of phenotypic evaluation for meat quality. Therefore, genomic selection may be the best strategy to improve meat quality traits. This study was performed to compare the accuracies of different Bayesian regression models in predicting molecular breeding values for meat tenderness in Polled Nellore cattle. The data set was composed of Warner-Bratzler shear force (WBSF) of longissimus muscle from 205, 141, and 81 animals slaughtered in 2005, 2010, and 2012, respectively, which were selected and mated so as to create extreme segregation for WBSF. The animals were genotyped with either the Illumina BovineHD (HD; 777,000 from 90 samples) chip or the GeneSeek Genomic Profiler (GGP Indicus HD; 77,000 from 337 samples). The quality controls of SNP were Hard-Weinberg Proportion -value ≥ 0.1%, minor allele frequency > 1%, and call rate > 90%. The FImpute program was used for imputation from the GGP Indicus HD chip to the HD chip. The effect of each SNP was estimated using ridge regression, least absolute shrinkage and selection operator (LASSO), Bayes A, Bayes B, and Bayes Cπ methods. Different numbers of SNP were used, with 1, 2, 3, 4, 5, 7, 10, 20, 40, 60, 80, or 100% of the markers preselected based on their significance test (-value from genomewide association studies [GWAS]) or randomly sampled. The prediction accuracy was assessed by the correlation between genomic breeding value and the observed WBSF phenotype, using a leave-one-out cross-validation methodology. The prediction accuracies using all markers were all very similar for all models, ranging from 0.22 (Bayes Cπ) to 0.25 (Bayes B). When preselecting SNP based on GWAS results, the highest correlation (0.27) between WBSF and the genomic breeding value was achieved using the Bayesian LASSO model with 15,030 (3%) markers. Although this study used relatively few animals, the design of the segregating population ensured wide genetic variability for meat tenderness, which was important to achieve acceptable accuracy of genomic prediction. Although all models showed similar levels of prediction accuracy, some small advantages were observed with the Bayes B approach when higher numbers of markers were preselected based on their -values resulting from a GWAS analysis.

[Estimation of Genetic Diversity of Romanov Sheep by the Coefficient of Genetic Originality Based on ISSR-Fingerprinting Data].

PubMed

Nesteruk, L V; Makarova, N N; Svishcheva, G R; Stolpovsky, Yu A

2015-07-01

Estimation of the state of the genetic diversity and the originality of the breed structure is required for the conservation and management of domestic breeds of agricultural animals. The Romanov breed of sheep from the leading breeding and gene pool farms in Yaroslavl oblast (Russia) is the object of our study. ISS R fingerprinting was used as a molecular method of the study of sheep gene pools. Forty-three DNA fragments were detected (25 and 18, respectively) by two primers ((AG)9C and (GA)9C). Of the discovered ISSR markers, 81% were polymorphic. The coefficient of genetic originality was for the first time used for the study of the specificity and originality of the Romanov-breed gene pool. Based on its values, the studied individuals were divided into five classes depending on the frequency of the ISSR fragment. The most original or the rarest, as well as typical genotypes, were singled out in the Romanov sheep gene pool. Use the obtained data on genetic originality was proposed as a means to increase the efficiency of selection and breeding during the breeding of autochthonous breeds of domesticated animal species.

Therapeutic Value or Harm of Neuregulin 1 in Demyelinating Disorders

DTIC Science & Technology

2012-10-01

the WSU animal facility: our animal room is infected by rotavirus on May 10, 2012. Therefore, we have to stop breeding the colony since the virus...the treatment to the virus will take 6 weeks, w have to wait to breed mice again until the room becomes to rotavirus negative. 3) Based on the mice

Prediction of genetic values of quantitative traits in plant breeding using pedigree and molecular markers.

PubMed

Crossa, José; Campos, Gustavo de Los; Pérez, Paulino; Gianola, Daniel; Burgueño, Juan; Araus, José Luis; Makumbi, Dan; Singh, Ravi P; Dreisigacker, Susanne; Yan, Jianbing; Arief, Vivi; Banziger, Marianne; Braun, Hans-Joachim

2010-10-01

The availability of dense molecular markers has made possible the use of genomic selection (GS) for plant breeding. However, the evaluation of models for GS in real plant populations is very limited. This article evaluates the performance of parametric and semiparametric models for GS using wheat (Triticum aestivum L.) and maize (Zea mays) data in which different traits were measured in several environmental conditions. The findings, based on extensive cross-validations, indicate that models including marker information had higher predictive ability than pedigree-based models. In the wheat data set, and relative to a pedigree model, gains in predictive ability due to inclusion of markers ranged from 7.7 to 35.7%. Correlation between observed and predictive values in the maize data set achieved values up to 0.79. Estimates of marker effects were different across environmental conditions, indicating that genotype × environment interaction is an important component of genetic variability. These results indicate that GS in plant breeding can be an effective strategy for selecting among lines whose phenotypes have yet to be observed.

Relationship between commercially available DNA analysis and phenotypic observations on beef quality and tenderness.

PubMed

Magolski, J D; Buchanan, D S; Maddock-Carlin, K R; Anderson, V L; Newman, D J; Berg, E P

2013-11-01

Warner-Bratzler shear force values from 560 mixed breed heifers and steers were used to determine estimates of genetic selection. Cattle were marketed from 2008 to 2011, and included five feedlot based research projects at the North Dakota State University-Carrington Research Extension Center. Samples were collected for IGENITY® analysis providing information that included selection indices and estimated breeding values for carcass traits. DNA-based test results were compared with actual carcass measurements. Marbling accounted for over 10% of the variation in WBSF while hot carcass weight was the second most influential carcass trait accounting for 4% (P<0.01). Regression coefficients of IGENITY® molecular breeding value on phenotype for WBSF, marbling, ribeye area, yield grade, and fat thickness were low (R(2)=0.14, 0.02, 0.03, 0.03, and 0.02, respectively). Therefore selecting cattle for a higher degree of marbling and feeding a diet that meets or exceeds recommended nutrients for growth are the most important factors influencing beef tenderness and acceptability. Copyright © 2013 Elsevier Ltd. All rights reserved.

D-loop haplotype diversity in Brazilian horse breeds

PubMed Central

Ianella, Patrícia; Albuquerque, Maria do Socorro Maués; Paiva, Samuel Rezende; do Egito, Andréa Alves; Almeida, Leonardo Daniel; Sereno, Fabiana T. P. S.; Carvalho, Luiz Felipe Ramos; Mariante, Arthur da Silva; McManus, Concepta Margaret

2017-01-01

Abstract The first horses were brought to Brazil by the colonizers after 1534. Over the centuries, these animals evolved and adapted to local environmental conditions usually unsuitable for exotic breeds, thereby originating locally adapted Brazilian breeds. The present work represents the first description of maternal genetic diversity in these horse breeds based on D-loop sequences. A D-Loop HSV-I fragment of 252 bp, from 141 horses belonging to ten Brazilian breeds / genetic groups (locally adapted and specialized breeds) were analysed. Thirty-five different haplotypes belonging to 18 haplogroups were identified with 33 polymorphic sites. Haplotype diversity (varying from 0.20 to 0.96) and nucleotide diversity (varying from 0.0039 to 0.0239) was lower for locally adapted than for specialized breeds, with the same pattern observed for FST values. Haplogroups identified in Brazilian breeds are in agreement with previous findings in South American samples. The low variability observed mainly in locally adapted breeds, indicates that, to ensure conservation of these breeds, careful reproductive management is needed. Additional genetic characterization studies are required to support accurate decision-making. PMID:28863209

Retrospective Analysis for Genetic Improvement of Hip Joints of Cohort Labrador Retrievers in the United States: 1970–2007

PubMed Central

Lust, George; Zhu, Lan; Zhang, Zhiwu; Todhunter, Rory J.

2010-01-01

Background Canine Hip Dysplasia (CHD) is a common inherited disease that affects dog wellbeing and causes a heavy financial and emotional burden to dog owners and breeders due to secondary hip osteoarthritis. The Orthopedic Foundation for Animals (OFA) initiated a program in the 1960's to radiograph hip and elbow joints and release the OFA scores to the public for breeding dogs against CHD. Over last four decades, more than one million radiographic scores have been released. Methodology/Principal Findings The pedigrees in the OFA database consisted of 258,851 Labrador retrievers, the major breed scored by the OFA (25% of total records). Of these, 154,352 dogs had an OFA hip score reported between 1970 and 2007. The rest of the dogs (104,499) were the ancestors of the 154,352 dogs to link the pedigree relationships. The OFA hip score is based on a 7-point scale with the best ranked as 1 (excellent) and the worst hip dysplasia as 7. A mixed linear model was used to estimate the effects of age, sex, and test year period and to predict the breeding value for each dog. Additive genetic and residual variances were estimated using the average information restricted maximum likelihood procedure. The analysis also provided an inbreeding coefficient for each dog. The hip scores averaged 1.93 (±SD = 0.59) and the heritability was 0.21. A steady genetic improvement has accrued over the four decades. The breeding values decreased (improved) linearly. By the end of 2005, the total genetic improvement was 0.1 units, which is equivalent to 17% of the total phenotypic standard deviation. Conclusion/Significance A steady genetic improvement has been achieved through the selection based on the raw phenotype released by the OFA. As the heritability of the hip score was on the low end (0.21) of reported ranges, we propose that selection based on breeding values will result in more rapid genetic improvement than breeding based on phenotypic selection alone. PMID:20195372

Incorporating molecular breeding values with variable call rates into genetic evaluations

USDA-ARS?s Scientific Manuscript database

A partial genotype for an animal can result from panels with low call rates used to calculate a molecular breeding value. A molecular breeding value can still be calculated using a partial genotype by replacing the missing marker covariates with their mean value. This approach is expected to chang...

Genomic evaluation of regional dairy cattle breeds in single-breed and multibreed contexts.

PubMed

Jónás, D; Ducrocq, V; Fritz, S; Baur, A; Sanchez, M-P; Croiseau, P

2017-02-01

An important prerequisite for high prediction accuracy in genomic prediction is the availability of a large training population, which allows accurate marker effect estimation. This requirement is not fulfilled in case of regional breeds with a limited number of breeding animals. We assessed the efficiency of the current French routine genomic evaluation procedure in four regional breeds (Abondance, Tarentaise, French Simmental and Vosgienne) as well as the potential benefits when the training populations consisting of males and females of these breeds are merged to form a multibreed training population. Genomic evaluation was 5-11% more accurate than a pedigree-based BLUP in three of the four breeds, while the numerically smallest breed showed a < 1% increase in accuracy. Multibreed genomic evaluation was beneficial for two breeds (Abondance and French Simmental) with maximum gains of 5 and 8% in correlation coefficients between yield deviations and genomic estimated breeding values, when compared to the single-breed genomic evaluation results. Inflation of genomic evaluation of young candidates was also reduced. Our results indicate that genomic selection can be effective in regional breeds as well. Here, we provide empirical evidence proving that genetic distance between breeds is only one of the factors affecting the efficiency of multibreed genomic evaluation. © 2016 Blackwell Verlag GmbH.

A genetic analysis of post-weaning feedlot performance and profitability in Bonsmara cattle.

PubMed

van der Westhuizen, R R; van der Westhuizen, J; Schoeman, S J

2009-02-25

The aim of this study was to identify factors influencing profitability in a feedlot environment and to estimate genetic parameters for and between a feedlot profit function and productive traits measured in growth tests. The heritability estimate of 0.36 for feedlot profitability shows that this trait is genetically inherited and that it can be selected for. The genetic correlations between feedlot profitability and production and efficiency varied from negligible to high. The genetic correlation estimate of -0.92 between feed conversion ratio and feedlot profitability is largely due to the part-whole relationship between these two traits. Consequently, a multiple regression equation was developed to estimate a feed intake value for all performance-tested Bonsmara bulls, which were group fed and whose feed intakes were unknown. These predicted feed intake values enabled the calculation of a post-weaning growth or feedlot profitability value for all tested bulls, even where individual feed intakes were unknown. Subsequently, a feedlot profitability value for each bull was calculated in a favorable economic environment, an average economic environment and in an unfavorable economic environment. The high Pearson and Spearman correlations between the estimate breeding values based on the average economic environment and the other two environments suggested that the average economic environment could be used to calculate estimate breeding values for feedlot profitability. It is therefore not necessary to change the carcass, weaned calf or feed price on a regular basis to allow for possible re-rankings based on estimate breeding values.

Efficient SNP Discovery by Combining Microarray and Lab-on-a-Chip Data for Animal Breeding and Selection

PubMed Central

Huang, Chao-Wei; Lin, Yu-Tsung; Ding, Shih-Torng; Lo, Ling-Ling; Wang, Pei-Hwa; Lin, En-Chung; Liu, Fang-Wei; Lu, Yen-Wen

2015-01-01

The genetic markers associated with economic traits have been widely explored for animal breeding. Among these markers, single-nucleotide polymorphism (SNPs) are gradually becoming a prevalent and effective evaluation tool. Since SNPs only focus on the genetic sequences of interest, it thereby reduces the evaluation time and cost. Compared to traditional approaches, SNP genotyping techniques incorporate informative genetic background, improve the breeding prediction accuracy and acquiesce breeding quality on the farm. This article therefore reviews the typical procedures of animal breeding using SNPs and the current status of related techniques. The associated SNP information and genotyping techniques, including microarray and Lab-on-a-Chip based platforms, along with their potential are highlighted. Examples in pig and poultry with different SNP loci linked to high economic trait values are given. The recommendations for utilizing SNP genotyping in nimal breeding are summarized. PMID:27600241

Application of a computer model to predict optimum slaughter end points for different biological types of feeder cattle.

PubMed

Williams, C B; Bennett, G L

1995-10-01

A bioeconomic model was developed to predict slaughter end points of different genotypes of feeder cattle, where profit/rotation and profit/day were maximized. Growth, feed intake, and carcass weight and composition were simulated for 17 biological types of steers. Distribution of carcass weight and proportion in four USDA quality and five USDA yield grades were obtained from predicted carcass weights and composition. Average carcass value for each genotype was calculated from these distributions under four carcass pricing systems that varied from value determined on quality grade alone to value determined on yield grade alone. Under profitable market conditions, rotation length was shorter and carcass weights lighter when the producer's goal was maximum profit/day, compared with maximum profit/rotation. A carcass value system based on yield grade alone resulted in greater profit/rotation and in lighter and leaner carcasses than a system based on quality grade alone. High correlations ( > .97) were obtained between breed profits obtained with different sets of input/output prices and carcass price discount weight ranges. This suggests that breed rankings on the basis of breed profits may not be sensitive to changes in input/output market prices. Steers that were on a grower-stocker system had leaner carcasses, heavier optimum carcass weight, greater profits, and less variation in optimum carcass weights between genotypes than steers that were started on a high-energy finishing diet at weaning. Overall results suggest that breed choices may change with different carcass grading and value systems and postweaning production systems. This model has potential to provide decision support in marketing fed cattle.

Genome-based prediction of test cross performance in two subsequent breeding cycles.

PubMed

Hofheinz, Nina; Borchardt, Dietrich; Weissleder, Knuth; Frisch, Matthias

2012-12-01

Genome-based prediction of genetic values is expected to overcome shortcomings that limit the application of QTL mapping and marker-assisted selection in plant breeding. Our goal was to study the genome-based prediction of test cross performance with genetic effects that were estimated using genotypes from the preceding breeding cycle. In particular, our objectives were to employ a ridge regression approach that approximates best linear unbiased prediction of genetic effects, compare cross validation with validation using genetic material of the subsequent breeding cycle, and investigate the prospects of genome-based prediction in sugar beet breeding. We focused on the traits sugar content and standard molasses loss (ML) and used a set of 310 sugar beet lines to estimate genetic effects at 384 SNP markers. In cross validation, correlations >0.8 between observed and predicted test cross performance were observed for both traits. However, in validation with 56 lines from the next breeding cycle, a correlation of 0.8 could only be observed for sugar content, for standard ML the correlation reduced to 0.4. We found that ridge regression based on preliminary estimates of the heritability provided a very good approximation of best linear unbiased prediction and was not accompanied with a loss in prediction accuracy. We conclude that prediction accuracy assessed with cross validation within one cycle of a breeding program can not be used as an indicator for the accuracy of predicting lines of the next cycle. Prediction of lines of the next cycle seems promising for traits with high heritabilities.

Accuracy of the unified approach in maternally influenced traits - illustrated by a simulation study in the honey bee (Apis mellifera)

PubMed Central

2013-01-01

Background The honey bee is an economically important species. With a rapid decline of the honey bee population, it is necessary to implement an improved genetic evaluation methodology. In this study, we investigated the applicability of the unified approach and its impact on the accuracy of estimation of breeding values for maternally influenced traits on a simulated dataset for the honey bee. Due to the limitation to the number of individuals that can be genotyped in a honey bee population, the unified approach can be an efficient strategy to increase the genetic gain and to provide a more accurate estimation of breeding values. We calculated the accuracy of estimated breeding values for two evaluation approaches, the unified approach and the traditional pedigree based approach. We analyzed the effects of different heritabilities as well as genetic correlation between direct and maternal effects on the accuracy of estimation of direct, maternal and overall breeding values (sum of maternal and direct breeding values). The genetic and reproductive biology of the honey bee was accounted for by taking into consideration characteristics such as colony structure, uncertain paternity, overlapping generations and polyandry. In addition, we used a modified numerator relationship matrix and a realistic genome for the honey bee. Results For all values of heritability and correlation, the accuracy of overall estimated breeding values increased significantly with the unified approach. The increase in accuracy was always higher for the case when there was no correlation as compared to the case where a negative correlation existed between maternal and direct effects. Conclusions Our study shows that the unified approach is a useful methodology for genetic evaluation in honey bees, and can contribute immensely to the improvement of traits of apicultural interest such as resistance to Varroa or production and behavioural traits. In particular, the study is of great interest for cases where negative correlation between maternal and direct effects and uncertain paternity exist, thus, is of relevance for other species as well. The study also provides an important framework for simulating genomic and pedigree datasets that will prove to be helpful for future studies. PMID:23647776

Accuracy of the unified approach in maternally influenced traits--illustrated by a simulation study in the honey bee (Apis mellifera).

PubMed

Gupta, Pooja; Reinsch, Norbert; Spötter, Andreas; Conrad, Tim; Bienefeld, Kaspar

2013-05-06

The honey bee is an economically important species. With a rapid decline of the honey bee population, it is necessary to implement an improved genetic evaluation methodology. In this study, we investigated the applicability of the unified approach and its impact on the accuracy of estimation of breeding values for maternally influenced traits on a simulated dataset for the honey bee. Due to the limitation to the number of individuals that can be genotyped in a honey bee population, the unified approach can be an efficient strategy to increase the genetic gain and to provide a more accurate estimation of breeding values. We calculated the accuracy of estimated breeding values for two evaluation approaches, the unified approach and the traditional pedigree based approach. We analyzed the effects of different heritabilities as well as genetic correlation between direct and maternal effects on the accuracy of estimation of direct, maternal and overall breeding values (sum of maternal and direct breeding values). The genetic and reproductive biology of the honey bee was accounted for by taking into consideration characteristics such as colony structure, uncertain paternity, overlapping generations and polyandry. In addition, we used a modified numerator relationship matrix and a realistic genome for the honey bee. For all values of heritability and correlation, the accuracy of overall estimated breeding values increased significantly with the unified approach. The increase in accuracy was always higher for the case when there was no correlation as compared to the case where a negative correlation existed between maternal and direct effects. Our study shows that the unified approach is a useful methodology for genetic evaluation in honey bees, and can contribute immensely to the improvement of traits of apicultural interest such as resistance to Varroa or production and behavioural traits. In particular, the study is of great interest for cases where negative correlation between maternal and direct effects and uncertain paternity exist, thus, is of relevance for other species as well. The study also provides an important framework for simulating genomic and pedigree datasets that will prove to be helpful for future studies.

Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels.

PubMed

Erbe, M; Hayes, B J; Matukumalli, L K; Goswami, S; Bowman, P J; Reich, C M; Mason, B A; Goddard, M E

2012-07-01

Achieving accurate genomic estimated breeding values for dairy cattle requires a very large reference population of genotyped and phenotyped individuals. Assembling such reference populations has been achieved for breeds such as Holstein, but is challenging for breeds with fewer individuals. An alternative is to use a multi-breed reference population, such that smaller breeds gain some advantage in accuracy of genomic estimated breeding values (GEBV) from information from larger breeds. However, this requires that marker-quantitative trait loci associations persist across breeds. Here, we assessed the gain in accuracy of GEBV in Jersey cattle as a result of using a combined Holstein and Jersey reference population, with either 39,745 or 624,213 single nucleotide polymorphism (SNP) markers. The surrogate used for accuracy was the correlation of GEBV with daughter trait deviations in a validation population. Two methods were used to predict breeding values, either a genomic BLUP (GBLUP_mod), or a new method, BayesR, which used a mixture of normal distributions as the prior for SNP effects, including one distribution that set SNP effects to zero. The GBLUP_mod method scaled both the genomic relationship matrix and the additive relationship matrix to a base at the time the breeds diverged, and regressed the genomic relationship matrix to account for sampling errors in estimating relationship coefficients due to a finite number of markers, before combining the 2 matrices. Although these modifications did result in less biased breeding values for Jerseys compared with an unmodified genomic relationship matrix, BayesR gave the highest accuracies of GEBV for the 3 traits investigated (milk yield, fat yield, and protein yield), with an average increase in accuracy compared with GBLUP_mod across the 3 traits of 0.05 for both Jerseys and Holsteins. The advantage was limited for either Jerseys or Holsteins in using 624,213 SNP rather than 39,745 SNP (0.01 for Holsteins and 0.03 for Jerseys, averaged across traits). Even this limited and nonsignificant advantage was only observed when BayesR was used. An alternative panel, which extracted the SNP in the transcribed part of the bovine genome from the 624,213 SNP panel (to give 58,532 SNP), performed better, with an increase in accuracy of 0.03 for Jerseys across traits. This panel captures much of the increased genomic content of the 624,213 SNP panel, with the advantage of a greatly reduced number of SNP effects to estimate. Taken together, using this panel, a combined breed reference and using BayesR rather than GBLUP_mod increased the accuracy of GEBV in Jerseys from 0.43 to 0.52, averaged across the 3 traits. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Invited review: Current state of genetic improvement in dairy sheep.

PubMed

Carta, A; Casu, Sara; Salaris, S

2009-12-01

Dairy sheep have been farmed traditionally in the Mediterranean basin in southern Europe, central Europe, eastern Europe, and in Near East countries. Currently, dairy sheep farming systems vary from extensive to intensive according to the economic relevance of the production chain and the specific environment and breed. Modern breeding programs were conceived in the 1960s. The most efficient selection scheme for local dairy sheep breeds is based on pyramidal management of the population with the breeders of nucleus flocks at the top, where pedigree and official milk recording, artificial insemination, controlled natural mating, and breeding value estimation are carried out to generate genetic progress. The genetic progress is then transferred to the commercial flocks through artificial insemination or natural-mating rams. Increasing milk yield is still the most profitable breeding objective for several breeds. Almost all milk is used for cheese production and, consequently, milk content traits are very important. Moreover, other traits are gaining interest for selection: machine milking ability and udder morphology, resistance to diseases (mastitis, internal parasites, scrapie), and traits related to the nutritional value of milk (fatty acid composition). Current breeding programs based on the traditional quantitative approach have achieved appreciable genetic gains for milk yield. In many cases, further selection goals such as milk composition, udder morphology, somatic cell count, and scrapie resistance have been implemented. However, the possibility of including other traits of selective interest is limited by high recording costs. Also, the organizational effort needed to apply the traditional quantitative approach limits the diffusion of current selection programs outside the European Mediterranean area. In this context, the application of selection schemes assisted by molecular information, to improve either traditional dairy traits or traits costly to record, seems to be attractive in dairy sheep. At the moment, the most effective strategy seems to be the strengthening of research projects aimed at finding causal mutations along the genes affecting traits of economic importance. However, genome-wide selection seems to be unfeasible in most dairy sheep breeds.

Impact of reduced marker set estimation of genomic relationship matrices on genomic selection for feed efficiency in Angus cattle.

PubMed

Rolf, Megan M; Taylor, Jeremy F; Schnabel, Robert D; McKay, Stephanie D; McClure, Matthew C; Northcutt, Sally L; Kerley, Monty S; Weaber, Robert L

2010-04-19

Molecular estimates of breeding value are expected to increase selection response due to improvements in the accuracy of selection and a reduction in generation interval, particularly for traits that are difficult or expensive to record or are measured late in life. Several statistical methods for incorporating molecular data into breeding value estimation have been proposed, however, most studies have utilized simulated data in which the generated linkage disequilibrium may not represent the targeted livestock population. A genomic relationship matrix was developed for 698 Angus steers and 1,707 Angus sires using 41,028 single nucleotide polymorphisms and breeding values were estimated using feed efficiency phenotypes (average daily feed intake, residual feed intake, and average daily gain) recorded on the steers. The number of SNPs needed to accurately estimate a genomic relationship matrix was evaluated in this population. Results were compared to estimates produced from pedigree-based mixed model analysis of 862 Angus steers with 34,864 identified paternal relatives but no female ancestors. Estimates of additive genetic variance and breeding value accuracies were similar for AFI and RFI using the numerator and genomic relationship matrices despite fewer animals in the genomic analysis. Bootstrap analyses indicated that 2,500-10,000 markers are required for robust estimation of genomic relationship matrices in cattle. This research shows that breeding values and their accuracies may be estimated for commercially important sires for traits recorded in experimental populations without the need for pedigree data to establish identity by descent between members of the commercial and experimental populations when at least 2,500 SNPs are available for the generation of a genomic relationship matrix.

Simulating a base population in honey bee for molecular genetic studies

PubMed Central

2012-01-01

Background Over the past years, reports have indicated that honey bee populations are declining and that infestation by an ecto-parasitic mite (Varroa destructor) is one of the main causes. Selective breeding of resistant bees can help to prevent losses due to the parasite, but it requires that a robust breeding program and genetic evaluation are implemented. Genomic selection has emerged as an important tool in animal breeding programs and simulation studies have shown that it yields more accurate breeding value estimates, higher genetic gain and low rates of inbreeding. Since genomic selection relies on marker data, simulations conducted on a genomic dataset are a pre-requisite before selection can be implemented. Although genomic datasets have been simulated in other species undergoing genetic evaluation, simulation of a genomic dataset specific to the honey bee is required since this species has a distinct genetic and reproductive biology. Our software program was aimed at constructing a base population by simulating a random mating honey bee population. A forward-time population simulation approach was applied since it allows modeling of genetic characteristics and reproductive behavior specific to the honey bee. Results Our software program yielded a genomic dataset for a base population in linkage disequilibrium. In addition, information was obtained on (1) the position of markers on each chromosome, (2) allele frequency, (3) χ2 statistics for Hardy-Weinberg equilibrium, (4) a sorted list of markers with a minor allele frequency less than or equal to the input value, (5) average r2 values of linkage disequilibrium between all simulated marker loci pair for all generations and (6) average r2 value of linkage disequilibrium in the last generation for selected markers with the highest minor allele frequency. Conclusion We developed a software program that takes into account the genetic and reproductive biology specific to the honey bee and that can be used to constitute a genomic dataset compatible with the simulation studies necessary to optimize breeding programs. The source code together with an instruction file is freely accessible at http://msproteomics.org/Research/Misc/honeybeepopulationsimulator.html PMID:22520469

Simulating a base population in honey bee for molecular genetic studies.

PubMed

Gupta, Pooja; Conrad, Tim; Spötter, Andreas; Reinsch, Norbert; Bienefeld, Kaspar

2012-06-27

Over the past years, reports have indicated that honey bee populations are declining and that infestation by an ecto-parasitic mite (Varroa destructor) is one of the main causes. Selective breeding of resistant bees can help to prevent losses due to the parasite, but it requires that a robust breeding program and genetic evaluation are implemented. Genomic selection has emerged as an important tool in animal breeding programs and simulation studies have shown that it yields more accurate breeding value estimates, higher genetic gain and low rates of inbreeding. Since genomic selection relies on marker data, simulations conducted on a genomic dataset are a pre-requisite before selection can be implemented. Although genomic datasets have been simulated in other species undergoing genetic evaluation, simulation of a genomic dataset specific to the honey bee is required since this species has a distinct genetic and reproductive biology. Our software program was aimed at constructing a base population by simulating a random mating honey bee population. A forward-time population simulation approach was applied since it allows modeling of genetic characteristics and reproductive behavior specific to the honey bee. Our software program yielded a genomic dataset for a base population in linkage disequilibrium. In addition, information was obtained on (1) the position of markers on each chromosome, (2) allele frequency, (3) χ(2) statistics for Hardy-Weinberg equilibrium, (4) a sorted list of markers with a minor allele frequency less than or equal to the input value, (5) average r(2) values of linkage disequilibrium between all simulated marker loci pair for all generations and (6) average r2 value of linkage disequilibrium in the last generation for selected markers with the highest minor allele frequency. We developed a software program that takes into account the genetic and reproductive biology specific to the honey bee and that can be used to constitute a genomic dataset compatible with the simulation studies necessary to optimize breeding programs. The source code together with an instruction file is freely accessible at http://msproteomics.org/Research/Misc/honeybeepopulationsimulator.html.

Estimation of genomic breeding values for milk yield in UK dairy goats.

PubMed

Mucha, S; Mrode, R; MacLaren-Lee, I; Coffey, M; Conington, J

2015-11-01

The objective of this study was to estimate genomic breeding values for milk yield in crossbred dairy goats. The research was based on data provided by 2 commercial goat farms in the UK comprising 590,409 milk yield records on 14,453 dairy goats kidding between 1987 and 2013. The population was created by crossing 3 breeds: Alpine, Saanen, and Toggenburg. In each generation the best performing animals were selected for breeding, and as a result, a synthetic breed was created. The pedigree file contained 30,139 individuals, of which 2,799 were founders. The data set contained test-day records of milk yield, lactation number, farm, age at kidding, and year and season of kidding. Data on milk composition was unavailable. In total 1,960 animals were genotyped with the Illumina 50K caprine chip. Two methods for estimation of genomic breeding value were compared-BLUP at the single nucleotide polymorphism level (BLUP-SNP) and single-step BLUP. The highest accuracy of 0.61 was obtained with single-step BLUP, and the lowest (0.36) with BLUP-SNP. Linkage disequilibrium (r(2), the squared correlation of the alleles at 2 loci) at 50 kb (distance between 2 SNP) was 0.18. This is the first attempt to implement genomic selection in UK dairy goats. Results indicate that the single-step method provides the highest accuracy for populations with a small number of genotyped individuals, where the number of genotyped males is low and females are predominant in the reference population. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Hot topic: Definition and implementation of a breeding value for feed efficiency in dairy cows.

PubMed

Pryce, J E; Gonzalez-Recio, O; Nieuwhof, G; Wales, W J; Coffey, M P; Hayes, B J; Goddard, M E

2015-10-01

A new breeding value that combines the amount of feed saved through improved metabolic efficiency with predicted maintenance requirements is described. The breeding value includes a genomic component for residual feed intake (RFI) combined with maintenance requirements calculated from either a genomic or pedigree estimated breeding value (EBV) for body weight (BW) predicted using conformation traits. Residual feed intake is only available for genotyped Holsteins; however, BW is available for all breeds. The RFI component of the "feed saved" EBV has 2 parts: Australian calf RFI and Australian lactating cow RFI. Genomic breeding values for RFI were estimated from a reference population of 2,036 individuals in a multi-trait analysis including Australian calf RFI (n=843), Australian lactating cow RFI (n=234), and UK and Dutch lactating cow RFI (n=958). In all cases, the RFI phenotypes were deviations from a mean of 0, calculated by correcting dry matter intake for BW, growth, and milk yield (in the case of lactating cows). Single nucleotide polymorphism effects were calculated from the output of genomic BLUP and used to predict breeding values of 4,106 Holstein sires that were genotyped but did not have RFI phenotypes themselves. These bulls already had BW breeding values calculated from type traits, from which maintenance requirements in kilograms of feed per year were inferred. Finally, RFI and the feed required for maintenance (through BW) were used to calculate a feed saved breeding value and expressed as the predicted amount of feed saved per year. Animals that were 1 standard deviation above the mean were predicted to eat 66 kg dry matter less per year at the same level of milk production. In a data set of genotyped Holstein sires, the mean reliability of the feed saved breeding value was 0.37. For Holsteins that are not genotyped and for breeds other than Holsteins, feed saved is calculated using BW only. From April 2015, feed saved has been included as part of the Australian national selection index, the Balanced Performance Index (BPI). Selection on the BPI is expected to lead to modest gains in feed efficiency. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Strategies for Selecting Crosses Using Genomic Prediction in Two Wheat Breeding Programs.

PubMed

Lado, Bettina; Battenfield, Sarah; Guzmán, Carlos; Quincke, Martín; Singh, Ravi P; Dreisigacker, Susanne; Peña, R Javier; Fritz, Allan; Silva, Paula; Poland, Jesse; Gutiérrez, Lucía

2017-07-01

The single most important decision in plant breeding programs is the selection of appropriate crosses. The ideal cross would provide superior predicted progeny performance and enough diversity to maintain genetic gain. The aim of this study was to compare the best crosses predicted using combinations of mid-parent value and variance prediction accounting for linkage disequilibrium (V) or assuming linkage equilibrium (V). After predicting the mean and the variance of each cross, we selected crosses based on mid-parent value, the top 10% of the progeny, and weighted mean and variance within progenies for grain yield, grain protein content, mixing time, and loaf volume in two applied wheat ( L.) breeding programs: Instituto Nacional de Investigación Agropecuaria (INIA) Uruguay and CIMMYT Mexico. Although the variance of the progeny is important to increase the chances of finding superior individuals from transgressive segregation, we observed that the mid-parent values of the crosses drove the genetic gain but the variance of the progeny had a small impact on genetic gain for grain yield. However, the relative importance of the variance of the progeny was larger for quality traits. Overall, the genomic resources and the statistical models are now available to plant breeders to predict both the performance of breeding lines per se as well as the value of progeny from any potential crosses. Copyright © 2017 Crop Science Society of America.

Breeding value prediction for production traits in layer chickens using pedigree or genomic relationships in a reduced animal model.

PubMed

Wolc, Anna; Stricker, Chris; Arango, Jesus; Settar, Petek; Fulton, Janet E; O'Sullivan, Neil P; Preisinger, Rudolf; Habier, David; Fernando, Rohan; Garrick, Dorian J; Lamont, Susan J; Dekkers, Jack C M

2011-01-21

Genomic selection involves breeding value estimation of selection candidates based on high-density SNP genotypes. To quantify the potential benefit of genomic selection, accuracies of estimated breeding values (EBV) obtained with different methods using pedigree or high-density SNP genotypes were evaluated and compared in a commercial layer chicken breeding line. The following traits were analyzed: egg production, egg weight, egg color, shell strength, age at sexual maturity, body weight, albumen height, and yolk weight. Predictions appropriate for early or late selection were compared. A total of 2,708 birds were genotyped for 23,356 segregating SNP, including 1,563 females with records. Phenotypes on relatives without genotypes were incorporated in the analysis (in total 13,049 production records).The data were analyzed with a Reduced Animal Model using a relationship matrix based on pedigree data or on marker genotypes and with a Bayesian method using model averaging. Using a validation set that consisted of individuals from the generation following training, these methods were compared by correlating EBV with phenotypes corrected for fixed effects, selecting the top 30 individuals based on EBV and evaluating their mean phenotype, and by regressing phenotypes on EBV. Using high-density SNP genotypes increased accuracies of EBV up to two-fold for selection at an early age and by up to 88% for selection at a later age. Accuracy increases at an early age can be mostly attributed to improved estimates of parental EBV for shell quality and egg production, while for other egg quality traits it is mostly due to improved estimates of Mendelian sampling effects. A relatively small number of markers was sufficient to explain most of the genetic variation for egg weight and body weight.

Analysis on Reactor Criticality Condition and Fuel Conversion Capability Based on Different Loaded Plutonium Composition in FBR Core

NASA Astrophysics Data System (ADS)

Permana, Sidik; Saputra, Geby; Suzuki, Mitsutoshi; Saito, Masaki

2017-01-01

Reactor criticality condition and fuel conversion capability are depending on the fuel arrangement schemes, reactor core geometry and fuel burnup process as well as the effect of different fuel cycle and fuel composition. Criticality condition of reactor core and breeding ratio capability have been investigated in this present study based on fast breeder reactor (FBR) type for different loaded fuel compositions of plutonium in the fuel core regions. Loaded fuel of Plutonium compositions are based on spent nuclear fuel (SNF) of light water reactor (LWR) for different fuel burnup process and cooling time conditions of the reactors. Obtained results show that different initial fuels of plutonium gives a significant chance in criticality conditions and fuel conversion capability. Loaded plutonium based on higher burnup process gives a reduction value of criticality condition or less excess reactivity. It also obtains more fuel breeding ratio capability or more breeding gain. Some loaded plutonium based on longer cooling time of LWR gives less excess reactivity and in the same time, it gives higher breeding ratio capability of the reactors. More composition of even mass plutonium isotopes gives more absorption neutron which affects to decresing criticality or less excess reactivity in the core. Similar condition that more absorption neutron by fertile material or even mass plutonium will produce more fissile material or odd mass plutonium isotopes to increase the breeding gain of the reactor.

Study on the pollution status and control measures for the livestock and poultry breeding industry in northeastern China.

PubMed

Wang, Hanxi; Xu, Jianling; Liu, Xuejun; Sheng, Lianxi; Zhang, Di; Li, Longwei; Wang, Aixia

2018-02-01

Livestock and poultry breeding industry is one of the main economic pillars of northeastern China. However, the amount of pollutants produced is much higher than that in other parts of China. Through a questionnaire survey, indoor experiment, and outdoor experiment, it was found that the resource utilization rate of livestock and poultry manure in the northeastern region is low, with the pollution of livestock and poultry breeding mainly including air and water pollution. The alarm level of cultivated land and manure is II. While the livestock and poultry breeding is relatively concentrated area, its level is higher than grade II. Based on the pollution status of small farms, biogas can be produced through fermentation, along with the preparation of organic fertilizer, to completely utilize the manure and straw, while obtaining higher economic value, and effectively controlling the pollution from livestock and poultry breeding.

The use of genomic information increases the accuracy of breeding value predictions for sea louse (Caligus rogercresseyi) resistance in Atlantic salmon (Salmo salar).

PubMed

Correa, Katharina; Bangera, Rama; Figueroa, René; Lhorente, Jean P; Yáñez, José M

2017-01-31

Sea lice infestations caused by Caligus rogercresseyi are a main concern to the salmon farming industry due to associated economic losses. Resistance to this parasite was shown to have low to moderate genetic variation and its genetic architecture was suggested to be polygenic. The aim of this study was to compare accuracies of breeding value predictions obtained with pedigree-based best linear unbiased prediction (P-BLUP) methodology against different genomic prediction approaches: genomic BLUP (G-BLUP), Bayesian Lasso, and Bayes C. To achieve this, 2404 individuals from 118 families were measured for C. rogercresseyi count after a challenge and genotyped using 37 K single nucleotide polymorphisms. Accuracies were assessed using fivefold cross-validation and SNP densities of 0.5, 1, 5, 10, 25 and 37 K. Accuracy of genomic predictions increased with increasing SNP density and was higher than pedigree-based BLUP predictions by up to 22%. Both Bayesian and G-BLUP methods can predict breeding values with higher accuracies than pedigree-based BLUP, however, G-BLUP may be the preferred method because of reduced computation time and ease of implementation. A relatively low marker density (i.e. 10 K) is sufficient for maximal increase in accuracy when using G-BLUP or Bayesian methods for genomic prediction of C. rogercresseyi resistance in Atlantic salmon.

Model training across multiple breeding cycles significantly improves genomic prediction accuracy in rye (Secale cereale L.).

PubMed

Auinger, Hans-Jürgen; Schönleben, Manfred; Lehermeier, Christina; Schmidt, Malthe; Korzun, Viktor; Geiger, Hartwig H; Piepho, Hans-Peter; Gordillo, Andres; Wilde, Peer; Bauer, Eva; Schön, Chris-Carolin

2016-11-01

Genomic prediction accuracy can be significantly increased by model calibration across multiple breeding cycles as long as selection cycles are connected by common ancestors. In hybrid rye breeding, application of genome-based prediction is expected to increase selection gain because of long selection cycles in population improvement and development of hybrid components. Essentially two prediction scenarios arise: (1) prediction of the genetic value of lines from the same breeding cycle in which model training is performed and (2) prediction of lines from subsequent cycles. It is the latter from which a reduction in cycle length and consequently the strongest impact on selection gain is expected. We empirically investigated genome-based prediction of grain yield, plant height and thousand kernel weight within and across four selection cycles of a hybrid rye breeding program. Prediction performance was assessed using genomic and pedigree-based best linear unbiased prediction (GBLUP and PBLUP). A total of 1040 S 2 lines were genotyped with 16 k SNPs and each year testcrosses of 260 S 2 lines were phenotyped in seven or eight locations. The performance gap between GBLUP and PBLUP increased significantly for all traits when model calibration was performed on aggregated data from several cycles. Prediction accuracies obtained from cross-validation were in the order of 0.70 for all traits when data from all cycles (N CS  = 832) were used for model training and exceeded within-cycle accuracies in all cases. As long as selection cycles are connected by a sufficient number of common ancestors and prediction accuracy has not reached a plateau when increasing sample size, aggregating data from several preceding cycles is recommended for predicting genetic values in subsequent cycles despite decreasing relatedness over time.

Charge breeding simulations for radioactive ion beam production

DOE Office of Scientific and Technical Information (OSTI.GOV)

Variale, V.; Raino, A. C.; Clauser, T.

2012-02-15

The charge breeding technique is used for radioactive ion beam (RIB) production in order of optimizing the re-acceleration of the radioactive element ions produced by a primary beam in a thick target. Charge breeding is achieved by means of a device capable of increasing the ion charge state from 1+ to a desired value n+. In order to get high intensity RIB, experiments with charge breeding of very high efficiency could be required. To reach this goal, the charge breeding simulation could help to optimize the high charge state production efficiency by finding more proper parameters for the radioactive 1+more » ions. In this paper a device based on an electron beam ion source (EBIS) is considered. In order to study that problem, a code already developed for studying the ion selective containment in an EBIS with RF quadrupoles, BRICTEST, has been modified to simulate the ion charge state breeding rate for different 1+ ion injection conditions. Particularly, the charge breeding simulations for an EBIS with a hollow electron beam have been studied.« less

Single-Nucleotide-Polymorphism-Based Association Mapping of Dog Stereotypes

PubMed Central

Jones, Paul; Chase, Kevin; Martin, Alan; Davern, Pluis; Ostrander, Elaine A.; Lark, Karl G.

2008-01-01

Phenotypic stereotypes are traits, often polygenic, that have been stringently selected to conform to specific criteria. In dogs, Canis familiaris, stereotypes result from breed standards set for conformation, performance (behaviors), etc. As a consequence, phenotypic values measured on a few individuals are representative of the breed stereotype. We used DNA samples isolated from 148 dog breeds to associate SNP markers with breed stereotypes. Using size as a trait to test the method, we identified six significant quantitative trait loci (QTL) on five chromosomes that include candidate genes appropriate to regulation of size (e.g., IGF1, IGF2BP2 SMAD2, etc.). Analysis of other morphological stereotypes, also under extreme selection, identified many additional significant loci. Less well-documented data for behavioral stereotypes tentatively identified loci for herding, pointing, boldness, and trainability. Four significant loci were identified for longevity, a breed characteristic not under direct selection, but inversely correlated with breed size. The strengths and limitations of the approach are discussed as well as its potential to identify loci regulating the within-breed incidence of specific polygenic diseases. PMID:18505865

Prediction of insemination outcomes in Holstein dairy cattle using alternative machine learning algorithms.

PubMed

Shahinfar, Saleh; Page, David; Guenther, Jerry; Cabrera, Victor; Fricke, Paul; Weigel, Kent

2014-02-01

When making the decision about whether or not to breed a given cow, knowledge about the expected outcome would have an economic impact on profitability of the breeding program and net income of the farm. The outcome of each breeding can be affected by many management and physiological features that vary between farms and interact with each other. Hence, the ability of machine learning algorithms to accommodate complex relationships in the data and missing values for explanatory variables makes these algorithms well suited for investigation of reproduction performance in dairy cattle. The objective of this study was to develop a user-friendly and intuitive on-farm tool to help farmers make reproduction management decisions. Several different machine learning algorithms were applied to predict the insemination outcomes of individual cows based on phenotypic and genotypic data. Data from 26 dairy farms in the Alta Genetics (Watertown, WI) Advantage Progeny Testing Program were used, representing a 10-yr period from 2000 to 2010. Health, reproduction, and production data were extracted from on-farm dairy management software, and estimated breeding values were downloaded from the US Department of Agriculture Agricultural Research Service Animal Improvement Programs Laboratory (Beltsville, MD) database. The edited data set consisted of 129,245 breeding records from primiparous Holstein cows and 195,128 breeding records from multiparous Holstein cows. Each data point in the final data set included 23 and 25 explanatory variables and 1 binary outcome for of 0.756 ± 0.005 and 0.736 ± 0.005 for primiparous and multiparous cows, respectively. The naïve Bayes algorithm, Bayesian network, and decision tree algorithms showed somewhat poorer classification performance. An information-based variable selection procedure identified herd average conception rate, incidence of ketosis, number of previous (failed) inseminations, days in milk at breeding, and mastitis as the most effective explanatory variables in predicting pregnancy outcome. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Mercury contamination and stable isotopes reveal variability in foraging ecology of generalist California gulls

USGS Publications Warehouse

Peterson, Sarah; Ackerman, Joshua T.; Eagles-Smith, Collin A.

2017-01-01

Environmental contaminants are a concern for animal health, but contaminant exposure can also be used as a tracer of foraging ecology. In particular, mercury (Hg) concentrations are highly variable among aquatic and terrestrial food webs as a result of habitat- and site-specific biogeochemical processes that produce the bioaccumulative form, methylmercury (MeHg). We used stable isotopes and total Hg (THg) concentrations of a generalist consumer, the California gull (Larus californicus), to examine foraging ecology and illustrate the utility of using Hg contamination as an ecological tracer under certain conditions. We identified four main foraging clusters of gulls during pre-breeding and breeding, using a traditional approach based on light stable isotopes. The foraging cluster with the highest δ15N and δ34S values in gulls (cluster 4) had mean blood THg concentrations 614% (pre-breeding) and 250% (breeding) higher than gulls with the lowest isotope values (cluster 1). Using a traditional approach of stable-isotope mixing models, we showed that breeding birds with a higher proportion of garbage in their diet (cluster 2: 63–82% garbage) corresponded to lower THg concentrations and lower δ15N and δ34S values. In contrast, gull clusters with higher THg concentrations, which were more enriched in 15N and 34S isotopes, consumed a higher proportion of more natural, estuarine prey. δ34S values, which change markedly across the terrestrial to marine habitat gradient, were positively correlated with blood THg concentrations in gulls. The linkage we observed between stable isotopes and THg concentrations suggests that Hg contamination can be used as an additional tool for understanding animal foraging across coastal habitat gradients.

Genetic tests for estimating dairy breed proportion and parentage assignment in East African crossbred cattle.

PubMed

Strucken, Eva M; Al-Mamun, Hawlader A; Esquivelzeta-Rabell, Cecilia; Gondro, Cedric; Mwai, Okeyo A; Gibson, John P

2017-09-12

Smallholder dairy farming in much of the developing world is based on the use of crossbred cows that combine local adaptation traits of indigenous breeds with high milk yield potential of exotic dairy breeds. Pedigree recording is rare in such systems which means that it is impossible to make informed breeding decisions. High-density single nucleotide polymorphism (SNP) assays allow accurate estimation of breed composition and parentage assignment but are too expensive for routine application. Our aim was to determine the level of accuracy achieved with low-density SNP assays. We constructed subsets of 100 to 1500 SNPs from the 735k-SNP Illumina panel by selecting: (a) on high minor allele frequencies (MAF) in a crossbred population; (b) on large differences in allele frequency between ancestral breeds; (c) at random; or (d) with a differential evolution algorithm. These panels were tested on a dataset of 1933 crossbred dairy cattle from Kenya/Uganda and on crossbred populations from Ethiopia (N = 545) and Tanzania (N = 462). Dairy breed proportions were estimated by using the ADMIXTURE program, a regression approach, and SNP-best linear unbiased prediction, and tested against estimates obtained by ADMIXTURE based on the 735k-SNP panel. Performance for parentage assignment was based on opposing homozygotes which were used to calculate the separation value (sv) between true and false assignments. Panels of SNPs based on the largest differences in allele frequency between European dairy breeds and a combined Nelore/N'Dama population gave the best predictions of dairy breed proportion (r 2  = 0.962 to 0.994 for 100 to 1500 SNPs) with an average absolute bias of 0.026. Panels of SNPs based on the highest MAF in the crossbred population (Kenya/Uganda) gave the most accurate parentage assignments (sv = -1 to 15 for 100 to 1500 SNPs). Due to the different required properties of SNPs, panels that did well for breed composition did poorly for parentage assignment and vice versa. A combined panel of 400 SNPs was not able to assign parentages correctly, thus we recommend the use of 200 SNPs either for breed proportion prediction or parentage assignment, independently.

Genetic parameters for milk production traits and breeding goals for Gir dairy cattle in Brazil.

PubMed

Prata, M A; Faro, L E; Moreira, H L; Verneque, R S; Vercesi Filho, A E; Peixoto, M G C D; Cardoso, V L

2015-10-19

To implement an animal breeding program, it is important to define the production circumstances of the animals of interest to determine which traits of economic interest will be selected for the breeding goal. The present study defined breeding goals and proposed selection indices for milk production and quality traits of Gir dairy cattle. First, a bioeconomic model was developed to calculate economic values. The genetic and phenotypic parameters were estimated based on records from 22,468 first-lactation Gir dairy cows and their crosses for which calving occurred between 1970 and 2011. Statistical analyses were carried out for the animal model, with multitrait analyses using the restricted maximum likelihood method. Two situations were created in the present study to define the breeding goals: 1) including only milk yield in the breeding goal (HGL1) and 2) including fat and protein in addition to the milk yield (HGL2). The heritability estimates for milk, protein, and fat production were 0.33 ± 0.02, 0.26 ± 0.02, and 0.24 ± 0.02, respectively. All phenotypic and genetic correlations were highly positive. The economic values for milk, fat, and protein were US$0.18, US$0.27, and US$7.04, respectively. The expected economic responses for HGL2 and for HGL1 were US$126.30 and US$79.82, respectively. These results indicate that milk component traits should be included in a selection index to rank animals evaluated in the National Gir Dairy Breeding Program developed in Brazil.

Efficiency of multi-breed genomic selection for dairy cattle breeds with different sizes of reference population.

PubMed

Hozé, C; Fritz, S; Phocas, F; Boichard, D; Ducrocq, V; Croiseau, P

2014-01-01

Single-breed genomic selection (GS) based on medium single nucleotide polymorphism (SNP) density (~50,000; 50K) is now routinely implemented in several large cattle breeds. However, building large enough reference populations remains a challenge for many medium or small breeds. The high-density BovineHD BeadChip (HD chip; Illumina Inc., San Diego, CA) containing 777,609 SNP developed in 2010 is characterized by short-distance linkage disequilibrium expected to be maintained across breeds. Therefore, combining reference populations can be envisioned. A population of 1,869 influential ancestors from 3 dairy breeds (Holstein, Montbéliarde, and Normande) was genotyped with the HD chip. Using this sample, 50K genotypes were imputed within breed to high-density genotypes, leading to a large HD reference population. This population was used to develop a multi-breed genomic evaluation. The goal of this paper was to investigate the gain of multi-breed genomic evaluation for a small breed. The advantage of using a large breed (Normande in the present study) to mimic a small breed is the large potential validation population to compare alternative genomic selection approaches more reliably. In the Normande breed, 3 training sets were defined with 1,597, 404, and 198 bulls, and a unique validation set included the 394 youngest bulls. For each training set, estimated breeding values (EBV) were computed using pedigree-based BLUP, single-breed BayesC, or multi-breed BayesC for which the reference population was formed by any of the Normande training data sets and 4,989 Holstein and 1,788 Montbéliarde bulls. Phenotypes were standardized by within-breed genetic standard deviation, the proportion of polygenic variance was set to 30%, and the estimated number of SNP with a nonzero effect was about 7,000. The 2 genomic selection (GS) approaches were performed using either the 50K or HD genotypes. The correlations between EBV and observed daughter yield deviations (DYD) were computed for 6 traits and using the different prediction approaches. Compared with pedigree-based BLUP, the average gain in accuracy with GS in small populations was 0.057 for the single-breed and 0.086 for multi-breed approach. This gain was up to 0.193 and 0.209, respectively, with the large reference population. Improvement of EBV prediction due to the multi-breed evaluation was higher for animals not closely related to the reference population. In the case of a breed with a small reference population size, the increase in correlation due to multi-breed GS was 0.141 for bulls without their sire in reference population compared with 0.016 for bulls with their sire in reference population. These results demonstrate that multi-breed GS can contribute to increase genomic evaluation accuracy in small breeds. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Optimizing the creation of base populations for aquaculture breeding programs using phenotypic and genomic data and its consequences on genetic progress.

PubMed

Fernández, Jesús; Toro, Miguel Á; Sonesson, Anna K; Villanueva, Beatriz

2014-01-01

The success of an aquaculture breeding program critically depends on the way in which the base population of breeders is constructed since all the genetic variability for the traits included originally in the breeding goal as well as those to be included in the future is contained in the initial founders. Traditionally, base populations were created from a number of wild strains by sampling equal numbers from each strain. However, for some aquaculture species improved strains are already available and, therefore, mean phenotypic values for economically important traits can be used as a criterion to optimize the sampling when creating base populations. Also, the increasing availability of genome-wide genotype information in aquaculture species could help to refine the estimation of relationships within and between candidate strains and, thus, to optimize the percentage of individuals to be sampled from each strain. This study explores the advantages of using phenotypic and genome-wide information when constructing base populations for aquaculture breeding programs in terms of initial and subsequent trait performance and genetic diversity level. Results show that a compromise solution between diversity and performance can be found when creating base populations. Up to 6% higher levels of phenotypic performance can be achieved at the same level of global diversity in the base population by optimizing the selection of breeders instead of sampling equal numbers from each strain. The higher performance observed in the base population persisted during 10 generations of phenotypic selection applied in the subsequent breeding program.

Defining the breeding goal for a sheep breed including production and functional traits using market data.

PubMed

Theodoridis, A; Ragkos, A; Rose, G; Roustemis, D; Arsenos, G

2017-11-16

In this study, the economic values for production and functional traits of dairy sheep are estimated through the application of a profit function model using farm-level technical and economic data. The traits incorporated in the model were milk production, prolificacy, fertility, milking speed, longevity and mastitis occurrence. The economic values for these traits were derived as the approximate partial derivative of the specified profit function. A sensitivity analysis was also conducted in order to examine how potential changes in input and output prices would affect the breeding goal. The estimated economic values of the traits revealed their economic impact on the definition of the breeding goal for the specified production system. Milk production and fertility had the highest economic values (€40.30 and €20.28 per standard genetic deviation (SDa)), while, mastitis only had a low negative value of -0.57 €/SDa. Therefore, breeding for clinical mastitis will have a minor impact on farm profitability because it affects a small proportion of the flock and has low additive variance. The production traits, which include milk production, prolificacy and milking speed, contributed most to the breeding goal (70.0%), but functional traits still had a considerable share (30.0%). The results of this study highlight the importance of the knowledge of economic values of traits in the design of a breeding program. It is also suggested that the production and functional traits under consideration can be categorized as those which can be efficiently treated through genetic improvement (e.g. milk production and fertility) while others would be better dealt with through managerial interventions (e.g. mastitis occurrence). Also, sub-clinical mastitis that affects a higher proportion of flocks could have a higher contribution to breeding goals.

Differences among breeds and manifestation of heterosis in AI boar sperm output.

PubMed

Smital, J; De Sousa, L L; Mohsen, A

2004-01-01

A total of 271,547 records of semen collections were utilized to appraise sperm characteristics of 3319 boars belonging to eight breeds: Czech Large White (CLW), Czech Landrace (CLA), Prestice Black-Pied (PBP), Czech Meat Pig (CM), Hampshire (HA), Duroc (DC), Pietrain (PN), Large White (LW), and various crosses of these breeds. The data was collected over 8 years (1990-1997) from insemination stations for boars in the Czech Republic. The assessment of sperm output was based on semen volume, number of total spermatozoa and number of viable spermatozoa. A linear model was used for statistical analysis included fixed effects of breed or crossbred combinations, boar within breed or crossbred combinations, year-season, and linear and quadratic regression on age of boars at collection and on interval between collections. The average semen volume of boars ranged from 161 to 349 ml, number of total spermatozoa from 81x10(9) to 119x10(9) and number of viable spermatozoa from 60x10(9) to 86x10(9). The lowest values were detected in DC while the highest were observed in LW. In general, sperm output significantly differed across breeds and their crossbreeds. The highest heterosis effect for semen volume was 30.6% (HA x PN), for number of total spermatozoa 18.2% (HA x PN) and 10.4% for number of viable spermatozoa (CLA x DC). Sperm output varied with season, including high values in autumn and winter and low ones in spring and summer.

Recreation economics to inform migratory species conservation: Case study of the northern pintail

USGS Publications Warehouse

Mattsson, Brady J.; Dubovsky, James A.; Thogmartin, Wayne E.; Bagstad, Kenneth J.; Goldstein, Joshua H.; Loomis, John B.; Diffendorfer, James E.; Semmens, Darius J.; Wiederholt, Ruscena; Lopez-Hoffman, Laura

2018-01-01

Quantification of the economic value provided by migratory species can aid in targeting management efforts and funding to locations yielding the greatest benefits to society and species conservation. Here we illustrate a key step in this process by estimating hunting and birding values of the northern pintail (Anas acuta) within primary breeding and wintering habitats used during the species’ annual migratory cycle in North America. We used published information on user expenditures and net economic values (consumer surplus) for recreational viewing and hunting to determine the economic value of pintail-based recreation in three primary breeding areas and two primary wintering areas. Summed expenditures and consumer surplus for northern pintail viewing were annually valued at $70M, and annual sport hunting totaled $31M (2014 USD). Expenditures for viewing ($42M) were more than twice as high than those for hunting ($18M). Estimates of consumer surplus, defined as the amount consumers are willing to pay above their current expenditures, were $15M greater for viewing ($28M) than for hunting ($13M). We discovered substantial annual consumer surplus ($41M) available for pintail conservation from birders and hunters. We also found spatial differences in economic value among the primary regions used by pintails, with viewing generally valued more in breeding regions than in wintering regions and the reverse being true for hunting. The economic value of pintail-based recreation in the Western wintering region ($26M) exceeded that in any other region by at least a factor of three. Our approach of developing regionally explicit economic values can be extended to other taxonomic groups, and is particularly suitable for migratory game birds because of the availability of large amounts of data. When combined with habitat-linked population models, regionally explicit values could inform development of more effective conservation finance and policy mechanisms to enhance environmental management and societal benefits across the geographically dispersed areas used by migratory species.

Recreation economics to inform migratory species conservation: Case study of the northern pintail.

PubMed

Mattsson, Brady J; Dubovsky, James A; Thogmartin, Wayne E; Bagstad, Kenneth J; Goldstein, Joshua H; Loomis, John B; Diffendorfer, James E; Semmens, Darius J; Wiederholt, Ruscena; López-Hoffman, Laura

2018-01-15

Quantification of the economic value provided by migratory species can aid in targeting management efforts and funding to locations yielding the greatest benefits to society and species conservation. Here we illustrate a key step in this process by estimating hunting and birding values of the northern pintail (Anas acuta) within primary breeding and wintering habitats used during the species' annual migratory cycle in North America. We used published information on user expenditures and net economic values (consumer surplus) for recreational viewing and hunting to determine the economic value of pintail-based recreation in three primary breeding areas and two primary wintering areas. Summed expenditures and consumer surplus for northern pintail viewing were annually valued at $70M, and annual sport hunting totaled $31M (2014 USD). Expenditures for viewing ($42M) were more than twice as high than those for hunting ($18M). Estimates of consumer surplus, defined as the amount consumers are willing to pay above their current expenditures, were $15M greater for viewing ($28M) than for hunting ($13M). We discovered substantial annual consumer surplus ($41M) available for pintail conservation from birders and hunters. We also found spatial differences in economic value among the primary regions used by pintails, with viewing generally valued more in breeding regions than in wintering regions and the reverse being true for hunting. The economic value of pintail-based recreation in the Western wintering region ($26M) exceeded that in any other region by at least a factor of three. Our approach of developing regionally explicit economic values can be extended to other taxonomic groups, and is particularly suitable for migratory game birds because of the availability of large amounts of data. When combined with habitat-linked population models, regionally explicit values could inform development of more effective conservation finance and policy mechanisms to enhance environmental management and societal benefits across the geographically dispersed areas used by migratory species. Copyright © 2017 Elsevier Ltd. All rights reserved.

New breeding objectives and selection indices for the Australian dairy industry.

PubMed

Byrne, T J; Santos, B F S; Amer, P R; Martin-Collado, D; Pryce, J E; Axford, M

2016-10-01

This study comprises an update of the economic values for dairy traits for the Australian industry and the formulation of updated selection indices. An economic model, which calculates partial economic values for each trait individually, was developed to determine the economic implications of selective dairy breeding, based on the effect of trait changes on the profit of commercial dairy farms in Australia. Selection indices were developed from economic values, which were transformed into base economic weights by including the discounted genetic expressions coefficients. Economic weights (in Australian dollars) were 1.79, 6.92, -0.10, -5.44, 8.84, 7.68, 1.07, 4.86, 1.91, 3.51, 4.90, 0.31, 2.03, 2.00, and 0.59, for milk fat (kg), milk protein (kg), milk volume (L), body weight (kg), survival (%), residual survival (%), somatic cell count (cells/mL), fertility (%), mammary system [Australian Breeding Value (ABV) unit], temperament (ABV unit), milking speed (ABV unit), udder depth (%), overall type (%), fore udder attachment (%), and pin set (%), respectively. The updated economic weights presented in this study constituted the basis of the definition for 3 new indices. These indices were developed from combination of bioeconomic principles, patterns of farmer preferences for trait improvements, and desired gains approaches. The 3 indices, Balanced Performance Index, Health Weighted Index, and Type Weighted Index, have been released to the industry. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Application of selection mapping to identify genomic regions associated with dairy production in sheep.

PubMed

Gutiérrez-Gil, Beatriz; Arranz, Juan Jose; Pong-Wong, Ricardo; García-Gámez, Elsa; Kijas, James; Wiener, Pamela

2014-01-01

In Europe, especially in Mediterranean areas, the sheep has been traditionally exploited as a dual purpose species, with income from both meat and milk. Modernization of husbandry methods and the establishment of breeding schemes focused on milk production have led to the development of "dairy breeds." This study investigated selective sweeps specifically related to dairy production in sheep by searching for regions commonly identified in different European dairy breeds. With this aim, genotypes from 44,545 SNP markers covering the sheep autosomes were analysed in both European dairy and non-dairy sheep breeds using two approaches: (i) identification of genomic regions showing extreme genetic differentiation between each dairy breed and a closely related non-dairy breed, and (ii) identification of regions with reduced variation (heterozygosity) in the dairy breeds using two methods. Regions detected in at least two breeds (breed pairs) by the two approaches (genetic differentiation and at least one of the heterozygosity-based analyses) were labeled as core candidate convergence regions and further investigated for candidate genes. Following this approach six regions were detected. For some of them, strong candidate genes have been proposed (e.g. ABCG2, SPP1), whereas some other genes designated as candidates based on their association with sheep and cattle dairy traits (e.g. LALBA, DGAT1A) were not associated with a detectable sweep signal. Few of the identified regions were coincident with QTL previously reported in sheep, although many of them corresponded to orthologous regions in cattle where QTL for dairy traits have been identified. Due to the limited number of QTL studies reported in sheep compared with cattle, the results illustrate the potential value of selection mapping to identify genomic regions associated with dairy traits in sheep.

Application of Selection Mapping to Identify Genomic Regions Associated with Dairy Production in Sheep

PubMed Central

Gutiérrez-Gil, Beatriz; Arranz, Juan Jose; Pong-Wong, Ricardo; García-Gámez, Elsa; Kijas, James; Wiener, Pamela

2014-01-01

In Europe, especially in Mediterranean areas, the sheep has been traditionally exploited as a dual purpose species, with income from both meat and milk. Modernization of husbandry methods and the establishment of breeding schemes focused on milk production have led to the development of “dairy breeds.” This study investigated selective sweeps specifically related to dairy production in sheep by searching for regions commonly identified in different European dairy breeds. With this aim, genotypes from 44,545 SNP markers covering the sheep autosomes were analysed in both European dairy and non-dairy sheep breeds using two approaches: (i) identification of genomic regions showing extreme genetic differentiation between each dairy breed and a closely related non-dairy breed, and (ii) identification of regions with reduced variation (heterozygosity) in the dairy breeds using two methods. Regions detected in at least two breeds (breed pairs) by the two approaches (genetic differentiation and at least one of the heterozygosity-based analyses) were labeled as core candidate convergence regions and further investigated for candidate genes. Following this approach six regions were detected. For some of them, strong candidate genes have been proposed (e.g. ABCG2, SPP1), whereas some other genes designated as candidates based on their association with sheep and cattle dairy traits (e.g. LALBA, DGAT1A) were not associated with a detectable sweep signal. Few of the identified regions were coincident with QTL previously reported in sheep, although many of them corresponded to orthologous regions in cattle where QTL for dairy traits have been identified. Due to the limited number of QTL studies reported in sheep compared with cattle, the results illustrate the potential value of selection mapping to identify genomic regions associated with dairy traits in sheep. PMID:24788864

Assessment of expected breeding values for fertility traits of Murrah buffaloes under subtropical climate.

PubMed

Dash, Soumya; Chakravarty, A K; Singh, Avtar; Shivahre, Pushp Raj; Upadhyay, Arpan; Sah, Vaishali; Singh, K Mahesh

2015-03-01

The aim of the present study was to assess the influence of temperature and humidity prevalent under subtropical climate on the breeding values for fertility traits viz. service period (SP), pregnancy rate (PR) and conception rate (CR) of Murrah buffaloes in National Dairy Research Institute (NDRI) herd. Fertility data on 1379 records of 581 Murrah buffaloes spread over four lactations and climatic parameters viz. dry bulb temperature and relative humidity (RH) spanned over 20 years (1993-2012) were collected from NDRI and Central Soil and Salinity Research Institute, Karnal, India. Monthly average temperature humidity index (THI) values were estimated. Threshold THI value affecting fertility traits was identified by fixed least-squares model analysis. Three zones of non-heat stress, heat stress and critical heat stress zones were developed in a year. The genetic parameters heritability (h(2)) and repeatability (r) of each fertility trait were estimated. Genetic evaluation of Murrah buffaloes was performed in each zone with respect to their expected breeding values (EBV) for fertility traits. Effect of THI was found significant (p<0.001) on all fertility traits with threshold THI value identified as 75. Based on THI values, a year was classified into three zones: Non heat stress zone(THI 56.71-73.21), HSZ (THI 75.39-81.60) and critical HSZ (THI 80.27-81.60). The EBVfor SP, PR, CR were estimated as 138.57 days, 0.362 and 69.02% in non-HSZ while in HSZ EBV were found as 139.62 days, 0.358 and 68.81%, respectively. EBV for SP was increased to 140.92 days and for PR and CR, it was declined to 0.357 and 68.71% in critical HSZ. The negative effect of THI was observed on EBV of fertility traits under the non-HSZ and critical HSZ Thus, the influence of THI should be adjusted before estimating the breeding values for fertility traits in Murrah buffaloes.

Accuracy of genomic selection in European maize elite breeding populations.

PubMed

Zhao, Yusheng; Gowda, Manje; Liu, Wenxin; Würschum, Tobias; Maurer, Hans P; Longin, Friedrich H; Ranc, Nicolas; Reif, Jochen C

2012-03-01

Genomic selection is a promising breeding strategy for rapid improvement of complex traits. The objective of our study was to investigate the prediction accuracy of genomic breeding values through cross validation. The study was based on experimental data of six segregating populations from a half-diallel mating design with 788 testcross progenies from an elite maize breeding program. The plants were intensively phenotyped in multi-location field trials and fingerprinted with 960 SNP markers. We used random regression best linear unbiased prediction in combination with fivefold cross validation. The prediction accuracy across populations was higher for grain moisture (0.90) than for grain yield (0.58). The accuracy of genomic selection realized for grain yield corresponds to the precision of phenotyping at unreplicated field trials in 3-4 locations. As for maize up to three generations are feasible per year, selection gain per unit time is high and, consequently, genomic selection holds great promise for maize breeding programs.

Factors associated with age at slaughter and carcass weight, price, and value of dairy cull cows.

PubMed

Bazzoli, I; De Marchi, M; Cecchinato, A; Berry, D P; Bittante, G

2014-02-01

The sale of cull cows contributes to the overall profit of dairy herds. The objective of this study was to quantify the factors associated with slaughter age (mo), cow carcass weight (kg), price (€/kg of carcass weight), and value (€/head) of dairy cull cows. Data included 20,995 slaughter records in the period from 2003 to 2011 of 5 different breeds: 2 dairy [Holstein Friesian (HF) and Brown Swiss (BS)] and 3 dual-purpose [Simmental (Si), Alpine Grey (AG), and Rendena (Re)]. Associations of breed, age of cow (except when the dependent variable was slaughter age), and year and month of slaughter with slaughter age, carcass weight, price, and value were quantified using a mixed linear model; herd was included as a random effect. The seasonal trends in cow price and value traits were inversely related to the number of cows slaughtered, whereas annual variation in external factors affected market conditions. Relative to BS cows, HF cows were younger at slaughter (73.1 vs. 80.7 mo), yielded slightly lighter carcasses (242 vs. 246 kg), and received a slightly lower price (1.69 vs. 1.73 €/kg) and total value (394 vs. 417 €/head). Dual-purpose breeds were older and heavier and received a much greater price and total value at slaughter (521, 516, and 549 €/head, respectively for Si, Re, and AG) than either dairy breed. Of the dual-purpose cows, Si carcasses were heavier (271 kg), whereas the carcasses of local breeds received a higher price (2.05 and 2.18 €/kg for Re and AG, respectively) and Alpine Grey cows were the oldest at slaughter (93.3 mo). The price per kilogram of cull cow carcasses was greatest for very young cows (i.e., <3 yr of age) and the differential in price and value between younger and older cows was greater in dual-purpose than in dairy breeds. Large differences in cull cow whole carcass value (carcass weight × unit price) among dairy breeds suggest that such a trait could be considered in the breeding objectives of the breeds. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Immunogenetic and population genetic analyses of Iberian cattle.

PubMed

Kidd, K K; Stone, W H; Crimella, C; Carenzi, C; Casati, M; Rognoni, G

1980-01-01

Blood samples were collected from more than 100 animals in each of 2 Spanish cattle breeds (Retinto and De Lidia), 2 Portuguese breeds (Alentejana and Mertolenga), and American Longhorn cattle. All samples for the 4 Iberian breeds were tested for 20 polymorphic systems; American Longhorn were tested for 19 of the 20. For each breed an average inbreeding coefficient was estimated by a comparison of the observed and expected heterozygosity at 7 or 8 codominant systems tested. All breeds had positive values but only 3 breeds had estimates of inbreeding that were statistically significantly different from 0: De Lidia with f = 0.17, Retinto with f = 0.08 and Mertolenga with f = 0.05. The De Lidia breed especially may be suffering from inbreeding depression since this high value is greater than expected if all of the animals were progeny of half-sib matings. Genetic distances were calculated from the gene frequency data on these 5 breeds plus 9 other European breeds. Analyses of these distances show a closely related group of the 4 Iberian breeds and American Longhorn, confirming the close relationships among the Iberian breeds and the Iberian, probably Portuguese, origin of American Longhorn cattle.

A function accounting for training set size and marker density to model the average accuracy of genomic prediction.

PubMed

Erbe, Malena; Gredler, Birgit; Seefried, Franz Reinhold; Bapst, Beat; Simianer, Henner

2013-01-01

Prediction of genomic breeding values is of major practical relevance in dairy cattle breeding. Deterministic equations have been suggested to predict the accuracy of genomic breeding values in a given design which are based on training set size, reliability of phenotypes, and the number of independent chromosome segments ([Formula: see text]). The aim of our study was to find a general deterministic equation for the average accuracy of genomic breeding values that also accounts for marker density and can be fitted empirically. Two data sets of 5'698 Holstein Friesian bulls genotyped with 50 K SNPs and 1'332 Brown Swiss bulls genotyped with 50 K SNPs and imputed to ∼600 K SNPs were available. Different k-fold (k = 2-10, 15, 20) cross-validation scenarios (50 replicates, random assignment) were performed using a genomic BLUP approach. A maximum likelihood approach was used to estimate the parameters of different prediction equations. The highest likelihood was obtained when using a modified form of the deterministic equation of Daetwyler et al. (2010), augmented by a weighting factor (w) based on the assumption that the maximum achievable accuracy is [Formula: see text]. The proportion of genetic variance captured by the complete SNP sets ([Formula: see text]) was 0.76 to 0.82 for Holstein Friesian and 0.72 to 0.75 for Brown Swiss. When modifying the number of SNPs, w was found to be proportional to the log of the marker density up to a limit which is population and trait specific and was found to be reached with ∼20'000 SNPs in the Brown Swiss population studied.

Breeding implications resulting from classification of patellae luxation in dogs.

PubMed

van Grevenhof, E M; Hazewinkel, H A W; Heuven, H C M

2016-08-01

Patellar luxation (PL) is one of the major hereditary orthopaedic abnormalities observed in a variety of dog breeds. When the patellae move sideways out of the trochlear groove, this is called PL. The PL score varies between dogs from normal to very severe. Reducing the prevalence of PL by breeding could prevent surgery, thereby improve welfare. Orthopaedic specialists differentiate between normal and loose patellae, where the patellae can be moved to the edge of the trochlear groove, considering scoring loose patellae as normal in the future. Loose patellae are considered acceptable for breeding so far by the breeding organization. The aim of this study was to analyse the genetic background of PL to decide on the importance of loose patellae when breeding for healthy dogs. Data are available from two dog breeds, that is Flat-coated Retrievers (n = 3808) and Kooiker dogs (n = 794), with a total of 4602 dogs. Results show that loose patellae indicate that dogs are genetically more susceptible to develop PL because family members of the dogs with loose patellae showed more severe PL. In addition, the estimated breeding values for dogs with loose patellae indicate that breeding values of dogs with loose patellae were worse than breeding values obtained for dogs with a normal score. Given these results, it is advised to orthopaedic specialists to continue to score loose patellae as a separate class and to dog breeders to minimize the use of dogs in breeding with a genetically higher susceptibility for PL. © 2015 Blackwell Verlag GmbH.

Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds.

PubMed

Sudrajad, P; Seo, D W; Choi, T J; Park, B H; Roh, S H; Jung, W Y; Lee, S S; Lee, J H; Kim, S; Lee, S H

2017-02-01

The routine collection and use of genomic data are useful for effectively managing breeding programs for endangered populations. Linkage disequilibrium (LD) using high-density DNA markers has been widely used to determine population structures and predict the genomic regions that are associated with economic traits in beef cattle. The extent of LD also provides information about historical events, including past effective population size (N e ), and it allows inferences on the genetic diversity of breeds. The objective of this study was to estimate the LD and N e in three Korean cattle breeds that are genetically similar but have different coat colors (Brown, Brindle and Jeju Black Hanwoo). Brindle and Jeju Black are endangered breeds with small populations, whereas Brown Hanwoo is the main breeding population in Korea. DNA samples from these cattle breeds were genotyped using the Illumina BovineSNP50 Bead Chip. We examined 13 cattle breeds, including European taurines, African taurines and indicines, and hybrids to compare their LD values. Brown Hanwoo consistently had the lowest mean LD compared to Jeju Black, Brindle and the other 13 cattle breeds (0.13, 0.19, 0.21 and 0.15-0.22 respectively). The high LD values of Brindle and Jeju Black contributed to small N e values (53 and 60 respectively), which were distinct from that of Brown Hanwoo (531) for 11 generations ago. The differences in LD and N e for each breed reflect the breeding strategy applied. The N e for these endangered cattle breeds remain low; thus, effort is needed to bring them back to a sustainable tract. © 2016 Stichting International Foundation for Animal Genetics.

Selection against canine hip dysplasia: success or failure?

PubMed

Wilson, Bethany; Nicholas, Frank W; Thomson, Peter C

2011-08-01

Canine hip dysplasia (CHD) is a multifactorial skeletal disorder which is very common in pedigree dogs and represents a huge concern for canine welfare. Control schemes based on selective breeding have been in operation for decades. The aim of these schemes is to reduce the impact of CHD on canine welfare by selecting for reduced radiographic evidence of CHD pathology as assessed by a variety of phenotypes. There is less information regarding the genotypic correlation between these phenotypes and the impact of CHD on canine welfare. Although the phenotypes chosen as the basis for these control schemes have displayed heritable phenotypic variation in many studies, success in achieving improvement in the phenotypes has been mixed. There is significant room for improvement in the current schemes through the use of estimated breeding values (EBVs), which can combine a dog's CHD phenotype with CHD phenotypes of relatives, other phenotypes as they are proven to be genetically correlated with CHD (especially elbow dysplasia phenotypes), and information from genetic tests for population-relevant DNA markers, as such tests become available. Additionally, breed clubs should be encouraged and assisted to formulate rational, evidenced-based breeding recommendations for CHD which suit their individual circumstances and dynamically to adjust the breeding recommendations based on continuous tracking of CHD genetic trends. These improvements can assist in safely and effectively reducing the impact of CHD on pedigree dog welfare. Copyright © 2011 Elsevier Ltd. All rights reserved.

Foraging Strategies of Laysan Albatross Inferred from Stable Isotopes: Implications for Association with Fisheries

PubMed Central

Edwards, Ann E.; Fitzgerald, Shannon M.; Parrish, Julia K.; Klavitter, John L.; Romano, Marc D.

2015-01-01

Fatal entanglement in fishing gear is the leading cause of population decline for albatross globally, a consequence of attraction to bait and fishery discards of commercial fishing operations. We investigated foraging strategies of Laysan albatross (Phoebastria immutabilis), as inferred from nitrogen and carbon isotope values of primary feathers, to determine breeding-related, seasonal, and historic factors that may affect the likelihood of association with Alaskan or Hawaiian longline fisheries. Feather samples were collected from live birds monitored for breeding status and breeding success on Midway Atoll in the northwestern Hawaiian Islands, birds salvaged as fisheries-bycatch, and birds added to museum collections before 1924. During the chick-rearing season (sampled April-May), means and variances of stable isotope values of birds with the highest, most consistent reproductive success were distinct from less productive conspecifics and completely different from birds caught in Hawaiian or Alaskan longline fisheries, suggesting birds with higher multi-annual reproductive success were less likely to associate with these fisheries. Contemporary birds with the highest reproductive success had mean values most similar to historic birds. Values of colony-bound, courting prebreeders were similar to active breeders but distinct from prebreeders caught in Alaskan longline fisheries. During the breeding season, δ15N values were highly variable for both contemporary and historic birds. Although some historic birds exhibited extremely low δ15N values unmatched by contemporary birds (< 11.2‰), others had values as high as the highest fishery-associated contemporary birds. During the non-breeding season (sampled July-September), isotopic variability coalesced into a more narrow set of values for both contemporary and historic birds. Our results suggest that foraging strategies of Laysan albatross are a complex function of season, breeding status, and multi-annual breeding success, factors that likely affect the probability of association with fisheries. PMID:26230731

Contribution of pigment content, myoglobin forms and internal reflectance to the colour of pork loin and ham from pure breed pigs.

PubMed

Lindahl, G; Lundström, K; Tornberg, E

2001-10-01

The colour of loin, M. longissimus dorsi (LD), and ham, M. biceps femoris (BF), from pure breed Hampshire, Swedish Landrace and Swedish Yorkshire pigs was studied. The contribution of the pigment content, the myoglobin forms deoxymyoglobin (Mb), oxymyoglobin (MbO) and metmyoglobin (MetMb) and the internal reflectance to the colour of pork of normal meat quality was evaluated using partial least squares regression (PLS). The colour of LD and BF from the Hampshire breed was more red and yellow and more saturated than the colour of the same muscles from the Swedish Landrace and the Swedish Yorkshire breeds. Furthermore, BF from Hampshire was darker than BF from the other two breeds. These differences in colour were related to the lower pH in Hampshire, resulting in more blooming and in higher internal reflectance, and to the higher pigment content. The colour of BF was darker and more red than the colour of LD within each breed. No colour difference was found between gilts and castrates within each breed. Most of the variation (86-90%) in lightness (L* value), redness (a* value) and yellowness (b* value), chroma (saturation) and hue angle of pork of normal meat quality was explained by the pigment content, myoglobin forms and internal reflectance. The L* value, a* value, chroma and hue angle were influenced by both the pigment content and by the myoglobin forms to almost the same extent, while the internal reflectance was of no significance to these colour parameters. The b* value was influenced most by the myoglobin forms, less by the internal reflectance and almost not at all by the pigment content.

Development of an index to rank dairy females on expected lifetime profit.

PubMed

Kelleher, M M; Amer, P R; Shalloo, L; Evans, R D; Byrne, T J; Buckley, F; Berry, D P

2015-06-01

The objective of this study was to develop an index to rank dairy females on expected profit for the remainder of their lifetime, taking cognizance of both additive and nonadditive genetic merit, permanent environmental effects, and current states of the animal including the most recent calving date and cow parity. The cow own worth (COW) index is intended to be used for culling the expected least profitable females in a herd, as well as inform purchase and pricing decisions for trading of females. The framework of the COW index consisted of the profit accruing from (1) the current lactation, (2) future lactations, and (3) net replacement cost differential. The COW index was generated from estimated performance values (sum of additive genetic merit, nonadditive genetic merit, and permanent environmental effects) of traits, their respective net margin values, and transition probability matrices for month of calving, survival, and somatic cell count; the transition matrices were to account for predicted change in a cow's state in the future. Transition matrices were generated from 3,156,109 lactation records from the Irish national database between the years 2010 and 2013. Phenotypic performance records for 162,981 cows in the year 2012 were used to validate the COW index. Genetic and permanent environmental effects (where applicable) were available for these cows from the 2011 national genetic evaluations and used to calculate the COW index and their national breeding index values (includes only additive genetic effects). Cows were stratified per quartile within herd, based on their COW index value and national breeding index value. The correlation between individual animal COW index value and national breeding index value was 0.65. Month of calving of the cow in her current lactation explained 18% of the variation in the COW index, with the parity of the cow explaining an additional 3 percentage units of the variance in the COW index. Females ranking higher on the COW index yielded more milk and milk solids and calved earlier in the calving season than their lower ranking contemporaries. The difference in phenotypic performance between the best and worst quartiles was larger for cows ranked on COW index than cows ranked on the national breeding index. The COW index is useful to rank females before culling or purchasing decisions on expected profit and is complementary to the national breeding index, which identifies the most suitable females for breeding replacements. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Craniometric Analysis of the Hindbrain and Craniocervical Junction of Chihuahua, Affenpinscher and Cavalier King Charles Spaniel Dogs With and Without Syringomyelia Secondary to Chiari-Like Malformation

PubMed Central

Kiviranta, Anna-Mariam; McFadyen, Angus K.; Jokinen, Tarja S.; La Ragione, Roberto M.; Rusbridge, Clare

2017-01-01

Objectives To characterize and compare the phenotypic variables of the hindbrain and craniocervical junction associated with syringomyelia (SM) in the Chihuahua, Affenpinscher and Cavalier King Charles Spaniel (CKCS). Method Analysis of 273 T1-weighted mid-sagittal DICOM sequences of the hindbrain and craniocervical junction from 99 Chihuahuas, 42 Affenpinschers and 132 CKCSs. The study compared 22 morphometric features (11 lines, eight angles and three ratios) of dogs with and without SM using refined techniques based on previous studies of the Griffon Bruxellois (GB) using Discriminant Function Analysis and ANOVA with post-hoc corrections. Results The analysis identified 14/22 significant traits for SM in the three dog breeds, five of which were identical to those reported for the GB and suggest inclusion of a common aetiology. One ratio, caudal fossa height to the length of the skull base extended to an imaginary point of alignment between the atlas and supraoccipital bones, was common to all three breeds (p values 0.029 to <0.001). Associated with SM were a reduced occipital crest and two acute changes in angulation i) ‘sphenoid flexure’ at the spheno-occipital synchondrosis ii) ‘cervical flexure’ at the foramen magnum allied with medulla oblongata elevation. Comparing dogs with and without SM, each breed had a unique trait: Chihuahua had a smaller angle between the dens, atlas and basioccipital bone (p value < 0.001); Affenpinschers had a smaller distance from atlas to dens (p value 0.009); CKCS had a shorter distance between the spheno-occipital synchondrosis and atlas (p value 0.007). Conclusion The selected morphometries successfully characterised conformational changes in the brain and craniocervical junction that might form the basis of a diagnostic tool for all breeds. The severity of SM involved a spectrum of abnormalities, incurred by changes in both angulation and size that could alter neural parenchyma compliance and/or impede cerebrospinal fluid channels. PMID:28121988

Craniometric Analysis of the Hindbrain and Craniocervical Junction of Chihuahua, Affenpinscher and Cavalier King Charles Spaniel Dogs With and Without Syringomyelia Secondary to Chiari-Like Malformation.

PubMed

Knowler, Susan P; Kiviranta, Anna-Mariam; McFadyen, Angus K; Jokinen, Tarja S; La Ragione, Roberto M; Rusbridge, Clare

2017-01-01

To characterize and compare the phenotypic variables of the hindbrain and craniocervical junction associated with syringomyelia (SM) in the Chihuahua, Affenpinscher and Cavalier King Charles Spaniel (CKCS). Analysis of 273 T1-weighted mid-sagittal DICOM sequences of the hindbrain and craniocervical junction from 99 Chihuahuas, 42 Affenpinschers and 132 CKCSs. The study compared 22 morphometric features (11 lines, eight angles and three ratios) of dogs with and without SM using refined techniques based on previous studies of the Griffon Bruxellois (GB) using Discriminant Function Analysis and ANOVA with post-hoc corrections. The analysis identified 14/22 significant traits for SM in the three dog breeds, five of which were identical to those reported for the GB and suggest inclusion of a common aetiology. One ratio, caudal fossa height to the length of the skull base extended to an imaginary point of alignment between the atlas and supraoccipital bones, was common to all three breeds (p values 0.029 to <0.001). Associated with SM were a reduced occipital crest and two acute changes in angulation i) 'sphenoid flexure' at the spheno-occipital synchondrosis ii) 'cervical flexure' at the foramen magnum allied with medulla oblongata elevation. Comparing dogs with and without SM, each breed had a unique trait: Chihuahua had a smaller angle between the dens, atlas and basioccipital bone (p value < 0.001); Affenpinschers had a smaller distance from atlas to dens (p value 0.009); CKCS had a shorter distance between the spheno-occipital synchondrosis and atlas (p value 0.007). The selected morphometries successfully characterised conformational changes in the brain and craniocervical junction that might form the basis of a diagnostic tool for all breeds. The severity of SM involved a spectrum of abnormalities, incurred by changes in both angulation and size that could alter neural parenchyma compliance and/or impede cerebrospinal fluid channels.

The hydro-chemical and physical conditions of the environment of the immature stages of some species of the simulium (Edwardsellum) damnosum complex (Diptera).

PubMed

Grunewald, J

1976-12-01

Water samples were collected from breeding sites of species of the Simulium (Edwardsellum) damnoslm complex in Upper Volta, Liberia and Cameroon during the dry season; and in Tanzania and Kenya at various seasons during a period of two years. The following 20 factors were analysed at 45 breeding sites: water temperature, current velocity, pH value, conductivity free carbon dioxide, oxygen content, calcium, magnesium, potassium, sodium, alkalinity, chloride, sulphate, nitrite, nitrate, ammonium, phosphate, silicate, total iron and organic substance (consumption of potassium permanganate). A number of notable differences in the chemical composition of the water of the breeding sites of 13 S. damnosum complex species were found, particularly with regard to the pH and conductivity. On the basis of these differences the various species can be divided into three main groups: Group I: 3 species (S. sanctipauli, S. yahense, "Menge"); breeding in sites with pH values always below 7 and conductivity values below 50 mumhos. Group II: 8 species (S. sirbanum, S. sudanense, S. damnosum s.s., S. squamosum, "Sanje", "Nkusi", "Nyamagasani", "Jovi"); breeding in watercourses with neutral, weakly acid or weakly alkaline reactions and conductivity values ranging from 50 to 150 mumhos. Group III: 2 species ("Kibwezi", "Kisiwani"); breeding in watercourses characterized by highly alkaline reactions with pH values between 7.7 and 10 and by conductivity values between 400 and 950 mumhos. The vectors of Onchocerca volvulus are included in group I and II only.

Flock composition, breeding strategies and farmers' traits of interest evaluation of Wollo highland sheep and their F1 crosses.

PubMed

Amare, Tadesse; Goshu, Gebeyehu; Tamir, Berhan

2018-01-01

Sheep production is a major component of the livestock sector in Ethiopia. The country owing to the large population of 30.70 million estimated numbers of sheep in the country and out of which about 72.14% are females, and 27.86% are males with diverse genetic resources. The real value of indigenous breeds was often under-estimated mostly due to their poor appearance and relatively low productivity. Developing countries in most cases opt for exotic breeds to increase animal productivity through crossbreeding or breed substitution without properly investigating the production potential of the indigenous breeds. The main objective of the research was to identify sheep flock composition and structure, farmers' traits of interest and breeding objective of Wollo highland sheep, and their F 1 crossbreed progenies. Smallholder farmers' flock synthesized from breeding ewes, breeding rams, pre-weaned ewe lambs, pre-weaned ram lambs, unproductive ewes, castrated and fattened rams, with the percentage coverage of 29.2, 13.3, 15.5, 16.5, 12.4, and 12.5%, respectively. The maximum number of flock size was 289.0 sheep per flock and higher in the third stratum. The off-take rate percentage of the three strata presented as 21.9% in 1st stratum, 12% in the 2nd stratum, and 16.4% in the 3rd stratum and higher off-take rate recorded in the first stratum. Sheep producer's traits of interest ranked by growth rate (first), body size (second) and marketing value was third rank. Communal breeding (random mating), village based controlled breeding, mixed type and private ram controlled breeding practice were comprised of 39.7, 61.7, 52 and 71.3%, respectively. The percentages of ewes per flock composition were presented as 36.5, 27.1 and 25.5%, respectively in the 3rd stratum, 2nd stratum and 3rd stratum in the order of their importance's. Genetic improvement practices at smallholder sheep producers situation was showing promising outcome with indigenous Washera F 1 crossbred lambs and which designated for weaning rate, body size, marketing age, age at first lambing, good temperament and large litter size in the order of their rank. The contemporary breeding practice tendency indicated that, reduced flock size to improve flock productivity via crossbreeding practices.

Phenotyping of Eggplant Wild Relatives and Interspecific Hybrids with Conventional and Phenomics Descriptors Provides Insight for Their Potential Utilization in Breeding

PubMed Central

Kaushik, Prashant; Prohens, Jaime; Vilanova, Santiago; Gramazio, Pietro; Plazas, Mariola

2016-01-01

Eggplant (Solanum melongena) is related to a large number of wild species that are a source of variation for breeding programmes, in particular for traits related to adaptation to climate change. However, wild species remain largely unexploited for eggplant breeding. Detailed phenotypic characterization of wild species and their hybrids with eggplant may allow identifying promising wild species and information on the genetic control and heterosis of relevant traits. We characterizated six eggplant accessions, 21 accessions of 12 wild species (the only primary genepool species S. insanum and 11 secondary genepool species) and 45 interspecific hybrids of eggplant with wild species (18 with S. insanum and 27 with secondary genepool species) using 27 conventional morphological descriptors and 20 fruit morphometric descriptors obtained with the phenomics tool Tomato Analyzer. Significant differences were observed among cultivated, wild and interspecific hybrid groups for 18 conventional and 18 Tomato Analyzer descriptors, with hybrids generally having intermediate values. Wild species were generally more variable than cultivated accessions and interspecific hybrids displayed intermediate ranges of variation and coefficient of variation (CV) values, except for fruit shape traits in which the latter were the most variable. The multivariate principal components analysis (PCA) reveals a clear separation of wild species and cultivated accessions. Interspecific hybrids with S. insanum plotted closer to cultivated eggplant, while hybrids with secondary genepool species generally clustered together with wild species. Many differences were observed among wild species for traits of agronomic interest, which allowed identifying species of greatest potential interest for eggplant breeding. Heterosis values were positive for most vigor-related traits, while for fruit size values were close to zero for hybrids with S. incanum and highly negative for hybrids with secondary genepool species. Our results allowed the identification of potentially interesting wild species and interspecific hybrids for introgression breeding in eggplant. This is an important step for broadening the genetic base of eggplant and for breeding for adaptation to climate change in this crop. PMID:27242876

Redesigning the exploitation of wheat genetic resources.

PubMed

Longin, C Friedrich H; Reif, Jochen C

2014-10-01

More than half a million wheat genetic resources are resting in gene banks worldwide. Unlocking their hidden favorable genetic diversity for breeding is pivotal for enhancing grain yield potential, and averting future food shortages. Here, we propose exploiting recent advances in hybrid wheat technology to uncover the masked breeding values of wheat genetic resources. The gathered phenotypic information will enable a targeted choice of accessions with high value for pre-breeding among this plethora of genetic resources. We intend to provoke a paradigm shift in pre-breeding strategies for grain yield, moving away from allele mining toward genome-wide selection to bridge the yield gap between genetic resources and elite breeding pools. Copyright © 2014 Elsevier Ltd. All rights reserved.

Considering dominance in reduced single-step genomic evaluations.

PubMed

Ertl, J; Edel, C; Pimentel, E C G; Emmerling, R; Götz, K-U

2018-06-01

Single-step models including dominance can be an enormous computational task and can even be prohibitive for practical application. In this study, we try to answer the question whether a reduced single-step model is able to estimate breeding values of bulls and breeding values, dominance deviations and total genetic values of cows with acceptable quality. Genetic values and phenotypes were simulated (500 repetitions) for a small Fleckvieh pedigree consisting of 371 bulls (180 thereof genotyped) and 553 cows (40 thereof genotyped). This pedigree was virtually extended for 2,407 non-genotyped daughters. Genetic values were estimated with the single-step model and with different reduced single-step models. Including more relatives of genotyped cows in the reduced single-step model resulted in a better agreement of results with the single-step model. Accuracies of genetic values were largest with single-step and smallest with reduced single-step when only the cows genotyped were modelled. The results indicate that a reduced single-step model is suitable to estimate breeding values of bulls and breeding values, dominance deviations and total genetic values of cows with acceptable quality. © 2018 Blackwell Verlag GmbH.

Genetic rescue of an endangered domestic animal through outcrossing with closely related breeds: A case study of the Norwegian Lundehund.

PubMed

Stronen, Astrid V; Salmela, Elina; Baldursdóttir, Birna K; Berg, Peer; Espelien, Ingvild S; Järvi, Kirsi; Jensen, Henrik; Kristensen, Torsten N; Melis, Claudia; Manenti, Tommaso; Lohi, Hannes; Pertoldi, Cino

2017-01-01

Genetic rescue, outcrossing with individuals from a related population, is used to augment genetic diversity in populations threatened by severe inbreeding and extinction. The endangered Norwegian Lundehund dog underwent at least two severe bottlenecks in the 1940s and 1960s that each left only five inbred dogs, and the approximately 1500 dogs remaining world-wide today appear to descend from only two individuals. The Lundehund has a high prevalence of a gastrointestinal disease, to which all remaining dogs may be predisposed. Outcrossing is currently performed with three Nordic Spitz breeds: Norwegian Buhund, Icelandic Sheepdog, and Norrbottenspets. Examination of single nucleotide polymorphism (SNP) genotypes based on 165K loci in 48 dogs from the four breeds revealed substantially lower genetic diversity for the Lundehund (HE 0.035) than for other breeds (HE 0.209-0.284). Analyses of genetic structure with > 15K linkage disequilibrium-pruned SNPs showed four distinct genetic clusters. Pairwise FST values between Lundehund and the candidate breeds were highest for Icelandic Sheepdog, followed by Buhund and Norrbottenspets. We assessed the presence of outlier loci among candidate breeds and examined flanking genome regions (1 megabase) for genes under possible selection to identify potential adaptive differences among breeds; outliers were observed in flanking regions of genes associated with key functions including the immune system, metabolism, cognition and physical development. We suggest crossbreeding with multiple breeds as the best strategy to increase genetic diversity for the Lundehund and to reduce the incidence of health problems. For this project, the three candidate breeds were first selected based on phenotypes and then subjected to genetic investigation. Because phenotypes are often paramount for domestic breed owners, such a strategy could provide a helpful approach for genetic rescue and restoration of other domestic populations at risk, by ensuring the involvement of owners, breeders and managers at the start of the project.

Persistency of accuracy of genomic breeding values for different simulated pig breeding programs in developing countries.

PubMed

Akanno, E C; Schenkel, F S; Sargolzaei, M; Friendship, R M; Robinson, J A B

2014-10-01

Genetic improvement of pigs in tropical developing countries has focused on imported exotic populations which have been subjected to intensive selection with attendant high population-wide linkage disequilibrium (LD). Presently, indigenous pig population with limited selection and low LD are being considered for improvement. Given that the infrastructure for genetic improvement using the conventional BLUP selection methods are lacking, a genome-wide selection (GS) program was proposed for developing countries. A simulation study was conducted to evaluate the option of using 60 K SNP panel and observed amount of LD in the exotic and indigenous pig populations. Several scenarios were evaluated including different size and structure of training and validation populations, different selection methods and long-term accuracy of GS in different population/breeding structures and traits. The training set included previously selected exotic population, unselected indigenous population and their crossbreds. Traits studied included number born alive (NBA), average daily gain (ADG) and back fat thickness (BFT). The ridge regression method was used to train the prediction model. The results showed that accuracies of genomic breeding values (GBVs) in the range of 0.30 (NBA) to 0.86 (BFT) in the validation population are expected if high density marker panels are utilized. The GS method improved accuracy of breeding values better than pedigree-based approach for traits with low heritability and in young animals with no performance data. Crossbred training population performed better than purebreds when validation was in populations with similar or a different structure as in the training set. Genome-wide selection holds promise for genetic improvement of pigs in the tropics. © 2014 Blackwell Verlag GmbH.

Accuracy of estimation of genomic breeding values in pigs using low-density genotypes and imputation.

PubMed

Badke, Yvonne M; Bates, Ronald O; Ernst, Catherine W; Fix, Justin; Steibel, Juan P

2014-04-16

Genomic selection has the potential to increase genetic progress. Genotype imputation of high-density single-nucleotide polymorphism (SNP) genotypes can improve the cost efficiency of genomic breeding value (GEBV) prediction for pig breeding. Consequently, the objectives of this work were to: (1) estimate accuracy of genomic evaluation and GEBV for three traits in a Yorkshire population and (2) quantify the loss of accuracy of genomic evaluation and GEBV when genotypes were imputed under two scenarios: a high-cost, high-accuracy scenario in which only selection candidates were imputed from a low-density platform and a low-cost, low-accuracy scenario in which all animals were imputed using a small reference panel of haplotypes. Phenotypes and genotypes obtained with the PorcineSNP60 BeadChip were available for 983 Yorkshire boars. Genotypes of selection candidates were masked and imputed using tagSNP in the GeneSeek Genomic Profiler (10K). Imputation was performed with BEAGLE using 128 or 1800 haplotypes as reference panels. GEBV were obtained through an animal-centric ridge regression model using de-regressed breeding values as response variables. Accuracy of genomic evaluation was estimated as the correlation between estimated breeding values and GEBV in a 10-fold cross validation design. Accuracy of genomic evaluation using observed genotypes was high for all traits (0.65-0.68). Using genotypes imputed from a large reference panel (accuracy: R(2) = 0.95) for genomic evaluation did not significantly decrease accuracy, whereas a scenario with genotypes imputed from a small reference panel (R(2) = 0.88) did show a significant decrease in accuracy. Genomic evaluation based on imputed genotypes in selection candidates can be implemented at a fraction of the cost of a genomic evaluation using observed genotypes and still yield virtually the same accuracy. On the other side, using a very small reference panel of haplotypes to impute training animals and candidates for selection results in lower accuracy of genomic evaluation.

Multiple trait genetic evaluation of clinical mastitis in three dairy cattle breeds.

PubMed

Govignon-Gion, A; Dassonneville, R; Baloche, G; Ducrocq, V

2016-04-01

In 2010, a routine genetic evaluation on occurrence of clinical mastitis in three main dairy cattle breeds-- Montbéliarde (MO), Normande (NO) and Holstein (HO)--was implemented in France. Records were clinical mastitis events reported by farmers to milk recording technicians and the analyzed trait was the binary variable describing the occurrence of a mastitis case within the first 150 days of the first three lactations. Genetic parameters of clinical mastitis were estimated for the three breeds. Low heritability estimates were found: between 2% and 4% depending on the breed. Despite its low heritability, the trait exhibits genetic variation so efficient genetic improvement is possible. Genetic correlations with other traits were estimated, showing large correlations (often>0.50, in absolute value) between clinical mastitis and somatic cell score (SCS), longevity and some udder traits. Correlation with milk yield was moderate and unfavorable (ρ=0.26 to 0.30). High milking speed was genetically associated with less mastitis in MO (ρ=-0.14) but with more mastitis in HO (ρ=0.18). A two-step approach was implemented for routine evaluation: first, a univariate evaluation based on a linear animal model with permanent environment effect led to pre-adjusted records (defined as records corrected for all non-genetic effects) and associated weights. These data were then combined with similar pre-adjusted records for others traits in a multiple trait BLUP animal model. The combined breeding values for clinical mastitis obtained are the official (published) ones. Mastitis estimated breeding values (EBV) were then combined with SCSs EBV into an udder health index, which receives a weight of 14.5% to 18.5% in the French total merit index (ISU) of the three breeds. Interbull genetic correlations for mastitis occurrence were very high (ρ=0.94) with Nordic countries, where much stricter recording systems exist reflecting a satisfactory quality of phenotypes as reported by the farmers. They were lower (around 0.80) with countries supplying SCS as a proxy for the international evaluation on clinical mastitis.

Genetic diversity and genetic structure of consecutive breeding generations of golden mandarin fish (Siniperca scherzeri Steindachner) using microsatellite markers.

PubMed

Luo, X N; Yang, M; Liang, X F; Jin, K; Lv, L Y; Tian, C X; Yuan, Y C; Sun, J

2015-09-25

In this study, 12 polymorphic microsatellites were inves-tigated to determine the genetic diversity and structure of 5 consecu-tive selected populations of golden mandarin fish (Siniperca scherzeri Steindachner). The total numbers of alleles, average heterozyosity, and average polymorphism information content showed that the genetic diversity of these breeding populations was decreasing. Additionally, pairwise fixation index FST values among populations and Da values in-creased from F1 generation to subsequent generations (FST values from 0.0221-0.1408; Da values from 0.0608-0.1951). Analysis of molecular variance indicated that most genetic variations arise from individuals within populations (about 92.05%), while variation among populations accounted for only 7.95%. The allele frequency of the loci SC75-220 and SC101-222 bp changed regularly in the 5 breeding generations. Their frequencies were gradually increased and showed an enrichment trend, indicating that there may be genetic correlations between these 2 loci and breeding traits. Our study indicated that microsatellite markers are effective for assessing the genetic variability in the golden mandarin fish breeding program.

Defining a breeding objective for Nile tilapia that takes into account the diversity of smallholder production systems.

PubMed

Omasaki, S K; van Arendonk, J A M; Kahi, A K; Komen, H

2016-10-01

In general, livestock and fish farming systems in developing countries tend to be highly diverse in terms of agro-ecological conditions and market orientation. There are no studies that have investigated if and how this diversity translates to varying preferences for breeding objective traits. This is particularly important for breeding programmes that are organized on a national level (e.g. government-supported nucleus breeding programmes). The aim of this study was to investigate whether Nile tilapia farmers with diverse production systems and economic constraints have different preferences for breeding objective traits. The second objective was to derive a consensus breeding goal, using weighted goal programming that could be used for a national breeding programme for Nile tilapia. A survey was conducted among 100 smallholder Nile tilapia farmers in Kenya to obtain preference values for traits of economic importance, by using multiple pairwise comparisons. Individual and group preference values were estimated using analytical hierarchy process. Low-income farmers preferred harvest weight, while medium- and high-income farmers preferred growth rate and survival. Grouping farmers according to market objective (fingerling production or fattening) showed that fingerling producers preferred growth rate and survival, while fattening farmers preferred harvest weight, height and thickness. Weighted goal programming was used to obtain consensus preference values, and these were used to derive desired gains for a breeding goal of a national breeding programme that takes into account the diversity of smallholder production systems. © 2016 Blackwell Verlag GmbH.

Development of a genetic tool for product regulation in the diverse British pig breed market.

PubMed

Wilkinson, Samantha; Archibald, Alan L; Haley, Chris S; Megens, Hendrik-Jan; Crooijmans, Richard P M A; Groenen, Martien A M; Wiener, Pamela; Ogden, Rob

2012-11-15

The application of DNA markers for the identification of biological samples from both human and non-human species is widespread and includes use in food authentication. In the food industry the financial incentive to substituting the true name of a food product with a higher value alternative is driving food fraud. This applies to British pork products where products derived from traditional pig breeds are of premium value. The objective of this study was to develop a genetic assay for regulatory authentication of traditional pig breed-labelled products in the porcine food industry in the United Kingdom. The dataset comprised of a comprehensive coverage of breed types present in Britain: 460 individuals from 7 traditional breeds, 5 commercial purebreds, 1 imported European breed and 1 imported Asian breed were genotyped using the PorcineSNP60 beadchip. Following breed-informative SNP selection, assignment power was calculated for increasing SNP panel size. A 96-plex assay created using the most informative SNPs revealed remarkably high genetic differentiation between the British pig breeds, with an average FST of 0.54 and Bayesian clustering analysis also indicated that they were distinct homogenous populations. The posterior probability of assignment of any individual of a presumed origin actually originating from that breed given an alternative breed origin was > 99.5% in 174 out of 182 contrasts, at a test value of log(LR) > 0. Validation of the 96-plex assay using independent test samples of known origin was successful; a subsequent survey of market samples revealed a high level of breed label conformity. The newly created 96-plex assay using selected markers from the PorcineSNP60 beadchip enables powerful assignment of samples to traditional breed origin and can effectively identify mislabelling, providing a highly effective tool for DNA analysis in food forensics.

Development of a genetic tool for product regulation in the diverse British pig breed market

PubMed Central

2012-01-01

Background The application of DNA markers for the identification of biological samples from both human and non-human species is widespread and includes use in food authentication. In the food industry the financial incentive to substituting the true name of a food product with a higher value alternative is driving food fraud. This applies to British pork products where products derived from traditional pig breeds are of premium value. The objective of this study was to develop a genetic assay for regulatory authentication of traditional pig breed-labelled products in the porcine food industry in the United Kingdom. Results The dataset comprised of a comprehensive coverage of breed types present in Britain: 460 individuals from 7 traditional breeds, 5 commercial purebreds, 1 imported European breed and 1 imported Asian breed were genotyped using the PorcineSNP60 beadchip. Following breed-informative SNP selection, assignment power was calculated for increasing SNP panel size. A 96-plex assay created using the most informative SNPs revealed remarkably high genetic differentiation between the British pig breeds, with an average FST of 0.54 and Bayesian clustering analysis also indicated that they were distinct homogenous populations. The posterior probability of assignment of any individual of a presumed origin actually originating from that breed given an alternative breed origin was > 99.5% in 174 out of 182 contrasts, at a test value of log(LR) > 0. Validation of the 96-plex assay using independent test samples of known origin was successful; a subsequent survey of market samples revealed a high level of breed label conformity. Conclusion The newly created 96-plex assay using selected markers from the PorcineSNP60 beadchip enables powerful assignment of samples to traditional breed origin and can effectively identify mislabelling, providing a highly effective tool for DNA analysis in food forensics. PMID:23150935

Effectiveness of breeding guidelines for reducing the prevalence of syringomyelia.

PubMed

Knowler, S P; McFadyen, A K; Rusbridge, C

Several toy breed dogs are predisposed to syringomyelia (SM), a spinal cord disorder, characterised by fluid-filled cavitation. SM is a complex trait with a moderately high heritability. Selective breeding against SM is confounded by its complex inheritance, its late onset nature and high prevalence in some breeds. This study investigated the early outcome of existing SM breeding guidelines. Six hundred and forty-three dogs, 550 Cavalier King Charles spaniels (CKCS) and 93 Griffon Bruxellois (GB), were identified as having either one (454 dogs) or both parents (189 dogs) with MRI-determined SM status. Offspring without SM were more common when the parents were both clear of SM (SM-free; CKCS 70 per cent, GB 73 per cent). Conversely, offspring with SM were more likely when both parents had SM (SM-affected; CKCS 92 per cent, GB 100 per cent). A mating of one SM-free parent with an SM-affected parent was risky for SM affectedness with 77 per cent of CKCS and 46 per cent of GB offspring being SM-affected. It is recommended that all breeding dogs from breeds susceptible to SM be MRI screened; that the SM status at five years old is established; and all results submitted to a central database that can be used by dog breeders to better enable mate selection based on estimated breeding values.

Population structure of four Thai indigenous chicken breeds.

PubMed

Mekchay, Supamit; Supakankul, Pantaporn; Assawamakin, Anunchai; Wilantho, Alisa; Chareanchim, Wanwisa; Tongsima, Sissades

2014-03-27

In recent years, Thai indigenous chickens have increasingly been bred as an alternative in Thailand poultry market. Due to their popularity, there is a clear need to improve the underlying quality and productivity of these chickens. Studying chicken genetic variation can improve the chicken meat quality as well as conserving rare chicken species. To begin with, a minimal set of molecular markers that can characterize the Thai indigenous chicken breeds is required. Using AFLP-PCR, 30 single nucleotide polymorphisms (SNPs) from Thai indigenous chickens were obtained by DNA sequencing. From these SNPs, we genotyped 465 chickens from 7 chicken breeds, comprising four Thai indigenous chicken breeds--Pradhuhangdum (PD), Luenghangkhao (LK), Dang (DA) and Chee (CH), one wild chicken--the red jungle fowls (RJF), and two commercial chicken breeds--the brown egg layer (BL) and commercial broiler (CB). The chicken genotypes reveal unique genetic structures of the four Thai indigenous chicken breeds. The average expected heterozygosities of PD=0.341, LK=0.357, DA=0.349 and CH=0.373, while the references RJF= 0.327, CB=0.324 and BL= 0.285. The F(ST) values among Thai indigenous chicken breeds vary from 0.051 to 0.096. The F(ST) values between the pairs of Thai indigenous chickens and RJF vary from 0.083 to 0.105 and the FST values between the Thai indigenous chickens and the two commercial chicken breeds vary from 0.116 to 0.221. A neighbour-joining tree of all individual chickens showed that the Thai indigenous chickens were clustered into four groups which were closely related to the wild RJF but far from the commercial breeds. Such commercial breeds were split into two closely groups. Using genetic admixture analysis, we observed that the Thai indigenous chicken breeds are likely to share common ancestors with the RJF, while both commercial chicken breeds share the same admixture pattern. These results indicated that the Thai indigenous chicken breeds may descend from the same ancestors. These indigenous chicken breeds were more closely related to red jungle fowls than those of the commercial breeds. These findings showed that the proposed SNP panel can effectively be used to characterize the four Thai indigenous chickens.

Accuracy of genomic breeding values in multibreed beef cattle populations derived from deregressed breeding values and phenotypes.

PubMed

Weber, K L; Thallman, R M; Keele, J W; Snelling, W M; Bennett, G L; Smith, T P L; McDaneld, T G; Allan, M F; Van Eenennaam, A L; Kuehn, L A

2012-12-01

Genomic selection involves the assessment of genetic merit through prediction equations that allocate genetic variation with dense marker genotypes. It has the potential to provide accurate breeding values for selection candidates at an early age and facilitate selection for expensive or difficult to measure traits. Accurate across-breed prediction would allow genomic selection to be applied on a larger scale in the beef industry, but the limited availability of large populations for the development of prediction equations has delayed researchers from providing genomic predictions that are accurate across multiple beef breeds. In this study, the accuracy of genomic predictions for 6 growth and carcass traits were derived and evaluated using 2 multibreed beef cattle populations: 3,358 crossbred cattle of the U.S. Meat Animal Research Center Germplasm Evaluation Program (USMARC_GPE) and 1,834 high accuracy bull sires of the 2,000 Bull Project (2000_BULL) representing influential breeds in the U.S. beef cattle industry. The 2000_BULL EPD were deregressed, scaled, and weighted to adjust for between- and within-breed heterogeneous variance before use in training and validation. Molecular breeding values (MBV) trained in each multibreed population and in Angus and Hereford purebred sires of 2000_BULL were derived using the GenSel BayesCπ function (Fernando and Garrick, 2009) and cross-validated. Less than 10% of large effect loci were shared between prediction equations trained on (USMARC_GPE) relative to 2000_BULL although locus effects were moderately to highly correlated for most traits and the traits themselves were highly correlated between populations. Prediction of MBV accuracy was low and variable between populations. For growth traits, MBV accounted for up to 18% of genetic variation in a pooled, multibreed analysis and up to 28% in single breeds. For carcass traits, MBV explained up to 8% of genetic variation in a pooled, multibreed analysis and up to 42% in single breeds. Prediction equations trained in multibreed populations were more accurate for Angus and Hereford subpopulations because those were the breeds most highly represented in the training populations. Accuracies were less for prediction equations trained in a single breed due to the smaller number of records derived from a single breed in the training populations.

Population structure and genetic differentiation of livestock guard dog breeds from the Western Balkans.

PubMed

Ceh, E; Dovc, P

2014-08-01

Livestock guard dog (LGD) breeds from the Western Balkans are a good example of how complex genetic diversity pattern observed in dog breeds has been shaped by transition in dog breeding practices. Despite their common geographical origin and relatively recent formal recognition as separate breeds, the Karst Shepherd, Sarplaninac and Tornjak show distinct population dynamics, assessed by pedigree, microsatellite and mtDNA data. We genotyped 493 dogs belonging to five dog breeds using a set of 18 microsatellite markers and sequenced mtDNA from 94 dogs from these breeds. Different demographic histories of the Karst Shepherd and Tornjak breeds are reflected in the pedigree data with the former breed having more unbalanced contributions of major ancestors and a realized effective population size of less than 20 animals. The highest allelic richness was found in Sarplaninac (5.94), followed by Tornjak (5.72), whereas Karst Shepherd dogs exhibited the lowest allelic richness (3.33). Similarly, the highest mtDNA haplotype diversity was found in Sarplaninac, followed by Tornjak and Karst Shepherd, where only one haplotype was found. Based on FST differentiation values and high percentages of animals correctly assigned, all breeds can be considered genetically distinct. However, using microsatellite data, common ancestry between the Karst Shepherd and Sarplaninac could not be reconstructed, despite pedigree and mtDNA evidence of their historical admixture. Using neighbour-joining, STRUCTURE or DAPC methods, Sarplaninac and Caucasian Shepherd breeds could not be separated and additionally showed close proximity in the NeighborNet tree. STRUCTURE analysis of the Tornjak breed demonstrated substructuring, which needs further investigation. Altogether, results of this study show that the official separation of these dog breeds strongly affected the resolution of genetic differentiation and thus suggest that the relationships between breeds are not only determined by breed relatedness, but in small populations even more importantly by stochastic effects. © 2014 Blackwell Verlag GmbH.

Comparison of three-view thoracic radiography and computed tomography for detection of pulmonary nodules in dogs with neoplasia.

PubMed

Armbrust, Laura J; Biller, David S; Bamford, Aubrey; Chun, Ruthanne; Garrett, Laura D; Sanderson, Michael W

2012-05-01

To compare the detection of pulmonary nodules by use of 3-view thoracic radiography and CT in dogs with confirmed neoplasia. Prospective case series. 33 dogs of various breeds. 3 interpreters independently evaluated 3-view thoracic radiography images. The location and size of pulmonary nodules were recorded. Computed tomographic scans of the thorax were obtained and evaluated by a single interpreter. The location, size, margin, internal architecture, and density of pulmonary nodules were recorded. Sensitivity, specificity, positive predictive value, and negative predictive value were calculated for thoracic radiography (with CT as the gold standard). 21 of 33 (64%) dogs had pulmonary nodules or masses detected on CT. Of the dogs that had positive CT findings, 17 of 21 (81%) had pulmonary nodules or masses detected on radiographs by at least 1 interpreter. Sensitivity of radiography ranged from 71% to 95%, and specificity ranged from 67% to 92%. Radiography had a positive predictive value of 83% to 94% and a negative predictive value of 65% to 89%. The 4 dogs that were negative for nodules on thoracic radiography but positive on CT were all large-breed to giant-breed dogs with osteosarcoma. CT was more sensitive than radiography for detection of pulmonary nodules. This was particularly evident in large-breed to giant-breed dogs. Thoracic CT is recommended in large-breed to giant-breed dogs with osteosarcoma if the detection of pulmonary nodules will change treatment.

Serum enzymes levels and influencing factors in three indigenous Ethiopian goat breeds.

PubMed

Tibbo, M; Jibril, Y; Woldemeskel, M; Dawo, F; Aragaw, K; Rege, J E O

2008-12-01

Serum enzymes were studied in 163 apparently healthy goats from three indigenous goat breeds of Ethiopia. The effect of breed, age, sex and season on alanine aminotransferase (ALT) / glutamic pyruvic transaminase (GPT), aspartate aminotransferase (AST) / glutamic oxalacetic transaminases (GOT), alkaline phosphatase (ALP) and acid phosphatase (AcP) levels was assessed. The mean serum enzymes levels of the indigenous Arsi-Bale, Central Highland and Long-eared Somali goat breeds ranged from 14.0-20.2 iu L(-1) for ALT/GPT, from 43.2-49.3 iu L(-1) for AST/GOT, from 83.7-98.8 iu L(-1) for ALP, and from 2.99-4.23 iu L(-1) for AcP, were within the normal range for goats elsewhere. Breed had significant influence on AST/GOT values. Sex had significant effect on ALT/GPT for Arsi-Bale goats with higher values in males than females. Age was significant on all serum enzymes studied in the Arsi-Bale goats and on ALP in the Central Highland goats. Season had significant influence on all serum enzymes except for ALT/GPT in the Arsi-Bale goats. The serum enzyme levels of these indigenous goat breeds can be used as normal reference values for Ethiopian goat breeds adapted to similar agro-ecology and production system.

Single-Step BLUP with Varying Genotyping Effort in Open-Pollinated Picea glauca.

PubMed

Ratcliffe, Blaise; El-Dien, Omnia Gamal; Cappa, Eduardo P; Porth, Ilga; Klápště, Jaroslav; Chen, Charles; El-Kassaby, Yousry A

2017-03-10

Maximization of genetic gain in forest tree breeding programs is contingent on the accuracy of the predicted breeding values and precision of the estimated genetic parameters. We investigated the effect of the combined use of contemporary pedigree information and genomic relatedness estimates on the accuracy of predicted breeding values and precision of estimated genetic parameters, as well as rankings of selection candidates, using single-step genomic evaluation (HBLUP). In this study, two traits with diverse heritabilities [tree height (HT) and wood density (WD)] were assessed at various levels of family genotyping efforts (0, 25, 50, 75, and 100%) from a population of white spruce ( Picea glauca ) consisting of 1694 trees from 214 open-pollinated families, representing 43 provenances in Québec, Canada. The results revealed that HBLUP bivariate analysis is effective in reducing the known bias in heritability estimates of open-pollinated populations, as it exposes hidden relatedness, potential pedigree errors, and inbreeding. The addition of genomic information in the analysis considerably improved the accuracy in breeding value estimates by accounting for both Mendelian sampling and historical coancestry that were not captured by the contemporary pedigree alone. Increasing family genotyping efforts were associated with continuous improvement in model fit, precision of genetic parameters, and breeding value accuracy. Yet, improvements were observed even at minimal genotyping effort, indicating that even modest genotyping effort is effective in improving genetic evaluation. The combined utilization of both pedigree and genomic information may be a cost-effective approach to increase the accuracy of breeding values in forest tree breeding programs where shallow pedigrees and large testing populations are the norm. Copyright © 2017 Ratcliffe et al.

Microsatellite loci analysis for the genetic variability and the parentage test of five dog breeds in South Korea.

PubMed

Kang, Byeong-Teck; Kim, Kyung-Seok; Min, Mi-Sook; Chae, Young-Jin; Kang, Jung-Won; Yoon, Junghee; Choi, Jihye; Seong, Je-Kyung; Park, Han-Chan; An, Junghwa; Lee, Mun-Han; Park, Hee-Myung; Lee, Hang

2009-06-01

To investigate the population structure of five dog breeds in South Korea and to validate polymorphic microsatellite markers for the parentage test, microsatellite loci analyses were conducted for two Korean native dog breeds, Poongsan and Jindo, and three imported dog breeds, German Shepherd, Beagle and Greyhound. Overall genetic diversity was high across all dog breeds (expected heterozygosity range: 0.71 to 0.85), although breeds differed in deviations from Hardy-Weinberg equilibrium (HWE). Significant reduction of heterozygosity in the Poongsan and Greyhound breeds was caused by non-random mating and population substructure within these breeds (the Wahlund effects). The close relationship and high degree of genetic diversity for two Korean native dog breeds were substantial. The mean polymorphism information content value was highest in Jindos (0.82) and Poongsans (0.81), followed by Beagles (0.74), Greyhounds (0.72), and German Shepherds (0.66). Accumulated exclusion power values, as an indication of marker validity for parentage tests, were varied but very high across breeds, 0.9999 for Jindos, Poongsans, and Beagles, 0.9997 for Greyhounds, and 0.9995 for German Shepherds. Taken together, the microsatellite loci investigated in this study can serve as suitable markers for the parentage test and as individual identification to establish a reliable pedigree verification system of dog breeds in South Korea. This study also stresses that the population subdivision within breeds can become an important cause of deviation from HWE in dog breeds.

Unraveling additive from nonadditive effects using genomic relationship matrices.

PubMed

Muñoz, Patricio R; Resende, Marcio F R; Gezan, Salvador A; Resende, Marcos Deon Vilela; de Los Campos, Gustavo; Kirst, Matias; Huber, Dudley; Peter, Gary F

2014-12-01

The application of quantitative genetics in plant and animal breeding has largely focused on additive models, which may also capture dominance and epistatic effects. Partitioning genetic variance into its additive and nonadditive components using pedigree-based models (P-genomic best linear unbiased predictor) (P-BLUP) is difficult with most commonly available family structures. However, the availability of dense panels of molecular markers makes possible the use of additive- and dominance-realized genomic relationships for the estimation of variance components and the prediction of genetic values (G-BLUP). We evaluated height data from a multifamily population of the tree species Pinus taeda with a systematic series of models accounting for additive, dominance, and first-order epistatic interactions (additive by additive, dominance by dominance, and additive by dominance), using either pedigree- or marker-based information. We show that, compared with the pedigree, use of realized genomic relationships in marker-based models yields a substantially more precise separation of additive and nonadditive components of genetic variance. We conclude that the marker-based relationship matrices in a model including additive and nonadditive effects performed better, improving breeding value prediction. Moreover, our results suggest that, for tree height in this population, the additive and nonadditive components of genetic variance are similar in magnitude. This novel result improves our current understanding of the genetic control and architecture of a quantitative trait and should be considered when developing breeding strategies. Copyright © 2014 by the Genetics Society of America.

Application of selection index calculations to determine selection strategies in genomic breeding programs.

PubMed

König, S; Swalve, H H

2009-10-01

The availability of genomic estimated breeding values (GEBV) allows for possible modifications to existing dairy cattle breeding programs. Selection index calculations including genomic and phenotypic observations as index sources were used to determine the optimal number of offspring per genotyped sire with a focus on functional traits and the design of cooperator herds, and to evaluate the importance of a central station test for genotyped bull dams. Evaluation criteria to compare different breeding strategies were correlations between index and aggregate genotype (r(TI)), and the relative selection response percentage (RSR) of an index without single nucleotide polymorphism information in relation to a single nucleotide polymorphism-based index. The number of required daughter records per sire to achieve a predefined r(TI) strongly depends on the accuracy of GEBV (r(mg)) and the heritability of the trait. For a desired r(TI) of 0.8, h(2) = 0.10, and r(mg) = 0.5, at least 57 additional daughters have to be included in the genetic evaluation. Daughter records of genotyped sires are not necessary for optimal scenarios where r(mg) is greater than or equal to r(TI). There still is a substantial need for phenotypic daughter records, especially for low-heritability functional traits and r(mg) < 0.7. Phenotypic records from genotyped potential bull dams have no relevance for increasing r(TI), even with a low value for r(mg) of 0.5. Hence, genomic breeding programs should focus on recording functional traits within progeny groups, preferably in cooperator herds. For low-heritability traits and with r(mg) > 0.7, the RSR of conventional breeding programs was only 10% of RSR from genomic breeding strategies. As shown in scenarios including 2 traits in the index as well as in the aggregate genotype, the availability of highly accurate GEBV for production traits and low-accuracy GEBV for functional traits increased the risk of widening the gap between selection responses in production and functionality. Counteractions are possible, such as via higher economic weights for low-heritability functional traits. Finally, an alternative selection strategy considering only 2 pathways of selection for genotyped male calves and for cow dams was evaluated. This strategy is competitive with a 4-pathway genomic breeding program if the fraction of selected male calves for the artificial insemination program is below 1% and if selection is focused on functionality, thus pointing to substantial insufficiencies caused by low reliabilities of breeding values for cows for such traits in conventional bull dam selection schemes.

Advances in Maize Genomics and Their Value for Enhancing Genetic Gains from Breeding

PubMed Central

Xu, Yunbi; Skinner, Debra J.; Wu, Huixia; Palacios-Rojas, Natalia; Araus, Jose Luis; Yan, Jianbing; Gao, Shibin; Warburton, Marilyn L.; Crouch, Jonathan H.

2009-01-01

Maize is an important crop for food, feed, forage, and fuel across tropical and temperate areas of the world. Diversity studies at genetic, molecular, and functional levels have revealed that, tropical maize germplasm, landraces, and wild relatives harbor a significantly wider range of genetic variation. Among all types of markers, SNP markers are increasingly the marker-of-choice for all genomics applications in maize breeding. Genetic mapping has been developed through conventional linkage mapping and more recently through linkage disequilibrium-based association analyses. Maize genome sequencing, initially focused on gene-rich regions, now aims for the availability of complete genome sequence. Conventional insertion mutation-based cloning has been complemented recently by EST- and map-based cloning. Transgenics and nutritional genomics are rapidly advancing fields targeting important agronomic traits including pest resistance and grain quality. Substantial advances have been made in methodologies for genomics-assisted breeding, enhancing progress in yield as well as abiotic and biotic stress resistances. Various genomic databases and informatics tools have been developed, among which MaizeGDB is the most developed and widely used by the maize research community. In the future, more emphasis should be given to the development of tools and strategic germplasm resources for more effective molecular breeding of tropical maize products. PMID:19688107

Effects of data structure on the estimation of covariance functions to describe genotype by environment interactions in a reaction norm model

PubMed Central

Calus, Mario PL; Bijma, Piter; Veerkamp, Roel F

2004-01-01

Covariance functions have been proposed to predict breeding values and genetic (co)variances as a function of phenotypic within herd-year averages (environmental parameters) to include genotype by environment interaction. The objective of this paper was to investigate the influence of definition of environmental parameters and non-random use of sires on expected breeding values and estimated genetic variances across environments. Breeding values were simulated as a linear function of simulated herd effects. The definition of environmental parameters hardly influenced the results. In situations with random use of sires, estimated genetic correlations between the trait expressed in different environments were 0.93, 0.93 and 0.97 while simulated at 0.89 and estimated genetic variances deviated up to 30% from the simulated values. Non random use of sires, poor genetic connectedness and small herd size had a large impact on the estimated covariance functions, expected breeding values and calculated environmental parameters. Estimated genetic correlations between a trait expressed in different environments were biased upwards and breeding values were more biased when genetic connectedness became poorer and herd composition more diverse. The best possible solution at this stage is to use environmental parameters combining large numbers of animals per herd, while losing some information on genotype by environment interaction in the data. PMID:15339629

Accuracies of genomically estimated breeding values from pure-breed and across-breed predictions in Australian beef cattle.

PubMed

Boerner, Vinzent; Johnston, David J; Tier, Bruce

2014-10-24

The major obstacles for the implementation of genomic selection in Australian beef cattle are the variety of breeds and in general, small numbers of genotyped and phenotyped individuals per breed. The Australian Beef Cooperative Research Center (Beef CRC) investigated these issues by deriving genomic prediction equations (PE) from a training set of animals that covers a range of breeds and crosses including Angus, Murray Grey, Shorthorn, Hereford, Brahman, Belmont Red, Santa Gertrudis and Tropical Composite. This paper presents accuracies of genomically estimated breeding values (GEBV) that were calculated from these PE in the commercial pure-breed beef cattle seed stock sector. PE derived by the Beef CRC from multi-breed and pure-breed training populations were applied to genotyped Angus, Limousin and Brahman sires and young animals, but with no pure-breed Limousin in the training population. The accuracy of the resulting GEBV was assessed by their genetic correlation to their phenotypic target trait in a bi-variate REML approach that models GEBV as trait observations. Accuracies of most GEBV for Angus and Brahman were between 0.1 and 0.4, with accuracies for abattoir carcass traits generally greater than for live animal body composition traits and reproduction traits. Estimated accuracies greater than 0.5 were only observed for Brahman abattoir carcass traits and for Angus carcass rib fat. Averaged across traits within breeds, accuracies of GEBV were highest when PE from the pooled across-breed training population were used. However, for the Angus and Brahman breeds the difference in accuracy from using pure-breed PE was small. For the Limousin breed no reasonable results could be achieved for any trait. Although accuracies were generally low compared to published accuracies estimated within breeds, they are in line with those derived in other multi-breed populations. Thus PE developed by the Beef CRC can contribute to the implementation of genomic selection in Australian beef cattle breeding.

Genomic selection & association mapping in rice: effect of trait genetic architecture, training population composition, marker number & statistical model on accuracy of rice genomic selection in elite, tropical rice breeding

USDA-ARS?s Scientific Manuscript database

Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its ef...

Landscape correlates of breeding bird richness across the United States mid-Atlantic region

USGS Publications Warehouse

Jones, K.B.; Neale, A.C.; Nash, M.S.; Riitters, K.H.; Wickham, J.D.; O'Neill, R. V.; Van Remortel, R. D.

2000-01-01

Using a new set of landscape indicator data generated by the U.S.EPA, and a comprehensive breeding bird database from the National Breeding Bird Survey, we evaluated associations between breeding bird richness and landscape characteristics across the entire mid-Atlantic region of the United States. We evaluated how these relationships varied among different groupings (guilds) of birds based on functional, structural, and compositional aspects of individual species demographics. Forest edge was by far the most important landscape attribute affecting the richness of the lumped specialist and generalist guilds; specialist species richness was negatively associated with forest edge and generalist richness was positively associated with forest edge. Landscape variables (indicators) explained a greater proportion of specialist species richness than the generalist guild (46% and 31%, respectively). The lower value in generalists may reflect freer-scale distributions of open habitat that go undetected by the Landsat satellite, open habitats created by roads (the areas from which breeding bird data are obtained), and the lumping of a wide variety of species into the generalist category. A further breakdown of species into 16 guilds showed considerable variation in the response of breeding birds to landscape conditions; forest obligate species had the strongest association with landscape indicators measured in this study (55% of the total variation explained) and forest generalists and open ground nesters the lowest (17% of the total variation explained). The variable response of guild species richness to landscape pattern suggests that one must consider species' demographics when assessing the consequences of landscape change on breeding birds.Using a new set of landscape indicator data generated by the U.S. EPA, and a comprehensive breeding bird database from the National Breeding Bird Survey, we evaluated associations between breeding bird richness and landscape characteristics across the entire mid-Atlantic region of the United States. We evaluated how these relationships varied among different groupings (guilds) of birds based on functional, structural, and compositional aspects of individual species demographics. Forest edge was by far the most important landscape attribute affecting the richness of the lumped specialist and generalist guilds; specialist species richness was negatively associated with forest edge and generalist richness was positively associated with forest edge. Landscape variables (indicators) explained a greater proportion of specialist species richness than the generalist guild (46% and 31%, respectively). The lower value in generalists may reflect finer-scale distributions of open habitat that go undetected by the Landsat satellite, open habitats created by roads (the areas from which breeding bird data are obtained), and the lumping of a wide variety of species into the generalist category. A further breakdown of species into 16 guilds showed considerable variation in the response of breeding birds to landscape conditions; forest obligate species had the strongest association with landscape indicators measured in this study (55% of the total variation explained) and forest generalists and open ground nesters the lowest (17% of the total variation explained). The variable response of guild species richness to landscape pattern suggests that one must consider species' demographics when assessing the consequences of landscape change on breeding birds.

Comparison of meat quality characteristics and fatty acid composition of finished goat kids from indigenous and dairy breeds.

PubMed

Yalcintan, Hulya; Ekiz, Bulent; Ozcan, Mustafa

2018-03-03

The aim of the study was to compare the certain carcass and meat quality traits and also fatty acid composition of goat kids from indigenous breeds (Gokceada and Hair Goat) and dairy breeds (Saanen and Maltese). A total 40 male kids from Saanen, Gokceada, Maltese and Hair Goat breeds were collected from commercial farms after weaning. Kids were finished for 56 days with grower concentrate and alfalfa hay in the sheepfold until slaughter. Higher mean values were found for Saanen kids in terms of slaughter weight, hot carcass weight and real dressing compared with Maltese, Hair Goat and Gokceada kids under the same intensive conditions. On the other hand, there were no significant differences between breeds in terms of instrumental meat quality traits, except meat colour. Meat from Gokceada and Hair Goat kids had higher lightness and Hue angle values than Saanen kids after 24 h of blooming. High meat redness values were observed for Saanen kids after 0 and 1 h of blooming. Panellist appreciated cooked meat from Saanen and Maltese kids in overall acceptability. If the fatty acid composition of meat was taken into consideration, kids from Saanen and Gokceada breeds displayed better values, because of the lower ƩSFA percentage and higher desirable fatty acids (C18:0 + ΣMUFA + ΣPUFA) percentage than Maltese and Hair Goat kids. Our results indicate that male kids for Saanen which is dairy breed could be assessable for quality goat meat production.

Plant breeding can be made more efficient by having fewer, better crosses.

PubMed

Witcombe, John R; Gyawali, Sanjaya; Subedi, Madhu; Virk, Daljit S; Joshi, Krishna D

2013-02-07

Crop yields have to increase to provide food security for the world's growing population. To achieve these yield increases there will have to be a significant contribution from genetic gains made by conventional plant breeding. However, the breeding process is not efficient because crosses made between parental combinations that fail to produce useful varieties consume over 99% of the resources. We tested in a rice-breeding programme if its efficiency could be improved by using many fewer, but more judiciously chosen crosses than usual. In a 15-year programme in Nepal, with varietal testing also in India and Bangladesh, we made only six crosses that were stringently chosen on complementary parental performance. We evaluated their success by the adoption and official release of the varieties they produced. We then modelled optimum cross number using assumptions based on our experimental results.Four of the six crosses succeeded. This was a fifty-fold improvement over breeding programmes that employ many crosses where only about one, or fewer, crosses in 200 succeed. Based on these results, we modelled the optimum number of crosses by assuming there would be a decline in the reliability of the breeder's prediction of the value of each cross as more crosses were made (because there is progressively less information on the traits of the parents). Fewer-cross programmes were more likely to succeed and did so using fewer resources. Making more crosses reduced the overall probability of success of the breeding programme. The efficiency of national and international breeding programmes would be increased by making fewer crosses among more carefully chosen parents. This would increase the number of higher yielding varieties that are delivered to farmers and hence help to improve food security.

Plant breeding can be made more efficient by having fewer, better crosses

PubMed Central

2013-01-01

Background Crop yields have to increase to provide food security for the world’s growing population. To achieve these yield increases there will have to be a significant contribution from genetic gains made by conventional plant breeding. However, the breeding process is not efficient because crosses made between parental combinations that fail to produce useful varieties consume over 99% of the resources. Results We tested in a rice-breeding programme if its efficiency could be improved by using many fewer, but more judiciously chosen crosses than usual. In a 15-year programme in Nepal, with varietal testing also in India and Bangladesh, we made only six crosses that were stringently chosen on complementary parental performance. We evaluated their success by the adoption and official release of the varieties they produced. We then modelled optimum cross number using assumptions based on our experimental results. Four of the six crosses succeeded. This was a fifty-fold improvement over breeding programmes that employ many crosses where only about one, or fewer, crosses in 200 succeed. Based on these results, we modelled the optimum number of crosses by assuming there would be a decline in the reliability of the breeder’s prediction of the value of each cross as more crosses were made (because there is progressively less information on the traits of the parents). Fewer-cross programmes were more likely to succeed and did so using fewer resources. Making more crosses reduced the overall probability of success of the breeding programme. Conclusions The efficiency of national and international breeding programmes would be increased by making fewer crosses among more carefully chosen parents. This would increase the number of higher yielding varieties that are delivered to farmers and hence help to improve food security. PMID:23391262

Improving production efficiency in the presence of genotype by environment interactions in pig genomic selection breeding programmes.

PubMed

Nirea, K G; Meuwissen, T H E

2017-04-01

We simulated a genomic selection pig breeding schemes containing nucleus and production herds to improve feed efficiency of production pigs that were cross-breed. Elite nucleus herds had access to high-quality feed, and production herds were fed low-quality feed. Feed efficiency in the nucleus herds had a heritability of 0.3 and 0.25 in the production herds. It was assumed the genetic relationships between feed efficiency in the nucleus and production were low (r g  = 0.2), medium (r g  = 0.5) and high (r g  = 0.8). In our alternative breeding schemes, different proportion of production animals were recorded for feed efficiency and genotyped with high-density panel of genetic markers. Genomic breeding value of the selection candidates for feed efficiency was estimated based on three different approaches. In one approach, genomic breeding value was estimated including nucleus animals in the reference population. In the second approach, the reference population was containing a mixture of nucleus and production animals. In the third approach, the reference population was only consisting of production herds. Using a mixture reference population, we generated 40-115% more genetic gain in the production environment as compared to only using nucleus reference population that were fed high-quality feed sources when the production animals were offspring of the nucleus animals. When the production animals were grand offspring of the nucleus animals, 43-104% more genetic gain was generated. Similarly, a higher genetic gain generated in the production environment when mixed reference population was used as compared to only using production animals. This was up to 19 and 14% when the production animals were offspring and grand offspring of nucleus animals, respectively. Therefore, in genomic selection pig breeding programmes, feed efficiency traits could be improved by properly designing the reference population. © 2016 Blackwell Verlag GmbH.

Effect of Particular Breed on the Chemical Composition, Texture, Color, and Sensorial Characteristics of Dry-cured Ham

PubMed Central

Seong, Pil Nam; Park, Kuyng Mi; Kang, Sun Moon; Kang, Geun Ho; Cho, Soo Hyun; Park, Beom Young; Van Ba, Hoa

2014-01-01

The present study demonstrates the impact of specific breed on the characteristics of dry-cured ham. Eighty thighs from Korean native pig (KNP), crossbreed (Landrace×Yorkshire)♀×Duroc♂ (LYD), Berkshire (Ber), and Duroc (Du) pig breeds (n = 10 for each breed) were used for processing of dry-cured ham. The thighs were salted with 6% NaCl (w/w) and 100 ppm NaNO2, and total processing time was 413 days. The effects of breed on the physicochemical composition, texture, color and sensory characteristics were assessed on the biceps femoris muscle of the hams. The results revealed that the highest weight loss was found in the dry-cured ham of LYD breed and the lowest weight loss was found in Ber dry-cured ham. The KNP dry-cured ham contain higher intramuscular fat level than other breed hams (p<0.05). It was observed that the dry-cured ham made from KNP breed had the lowest water activity value and highest salt content, while the LYD dry-cure ham had higher total volatile basic nitrogen content than the Ber and Du hams (p<0.05). Zinc, iron and total monounsaturated fatty acids levels were higher in KNP ham while polyunsaturated fatty acids levels were higher in Du ham when compared to other breed hams (p<0.05). Additionally, the KNP dry-cured ham possessed higher Commission International de l’Eclairage (CIE) a* value, while the Du dry-cured ham had higher L*, CIE b* and hue angle values (p<0.05). Furthermore, breed significantly affected the sensory attributes of dry-cured hams with higher scores for color, aroma and taste found in KNP dry-cured ham as compared to other breed hams (p<0.05). The overall outcome of the study is that the breed has a potential effect on the specific chemical composition, texture, color and sensorial properties of dry-cured hams. These data could be useful for meat processors to select the suitable breeds for economical manufacturing of high quality dry-cured hams. PMID:25083111

Effect of Particular Breed on the Chemical Composition, Texture, Color, and Sensorial Characteristics of Dry-cured Ham.

PubMed

Seong, Pil Nam; Park, Kuyng Mi; Kang, Sun Moon; Kang, Geun Ho; Cho, Soo Hyun; Park, Beom Young; Van Ba, Hoa

2014-08-01

The present study demonstrates the impact of specific breed on the characteristics of dry-cured ham. Eighty thighs from Korean native pig (KNP), crossbreed (Landrace×Yorkshire)♀×Duroc♂ (LYD), Berkshire (Ber), and Duroc (Du) pig breeds (n = 10 for each breed) were used for processing of dry-cured ham. The thighs were salted with 6% NaCl (w/w) and 100 ppm NaNO2, and total processing time was 413 days. The effects of breed on the physicochemical composition, texture, color and sensory characteristics were assessed on the biceps femoris muscle of the hams. The results revealed that the highest weight loss was found in the dry-cured ham of LYD breed and the lowest weight loss was found in Ber dry-cured ham. The KNP dry-cured ham contain higher intramuscular fat level than other breed hams (p<0.05). It was observed that the dry-cured ham made from KNP breed had the lowest water activity value and highest salt content, while the LYD dry-cure ham had higher total volatile basic nitrogen content than the Ber and Du hams (p<0.05). Zinc, iron and total monounsaturated fatty acids levels were higher in KNP ham while polyunsaturated fatty acids levels were higher in Du ham when compared to other breed hams (p<0.05). Additionally, the KNP dry-cured ham possessed higher Commission International de l'Eclairage (CIE) a* value, while the Du dry-cured ham had higher L*, CIE b* and hue angle values (p<0.05). Furthermore, breed significantly affected the sensory attributes of dry-cured hams with higher scores for color, aroma and taste found in KNP dry-cured ham as compared to other breed hams (p<0.05). The overall outcome of the study is that the breed has a potential effect on the specific chemical composition, texture, color and sensorial properties of dry-cured hams. These data could be useful for meat processors to select the suitable breeds for economical manufacturing of high quality dry-cured hams.

Relationships between Podolic cattle breeds assessed by single nucleotide polymorphisms (SNPs) genotyping.

PubMed

Pariset, L; Mariotti, M; Nardone, A; Soysal, M I; Ozkan, E; Williams, J L; Dunner, S; Leveziel, H; Maróti-Agóts, A; Bodò, I; Valentini, A

2010-12-01

Italian Maremmana, Turkish Grey and Hungarian Grey breeds belong to the same Podolic group of cattle, have a similar conformation and recently experienced a similar demographic reduction. The aim of this study was to assess the relationship among the analysed Podolic breeds and to verify whether their genetic state reflects their history. To do so, approximately 100 single nucleotide polymorphisms (SNPs) were genotyped on individuals belonging to these breeds and compared to genotypes of individuals of two Italian beef breeds, Marchigiana and Piemontese, which underwent different selection and migration histories. Population genetic parameters such as allelic frequencies and heterozygosity values were assessed, genetic distances calculated and assignment test performed to evaluate the possibility of recent admixture between the populations. The data show that the physical similarity among the Podolic breeds examined, and particularly between Hungarian Grey and Maremmana cattle that experienced admixture in the recent past, is mainly morphological. The assignment of individuals from genotype data was achieved using Bayesian inference, confirming that the set of chosen SNPs is able to distinguish among the breeds and that the breeds are genetically distinct. Individuals of Turkish Grey breed were clearly assigned to their breed of origin for all clustering alternatives, showing that this breed can be differentiated from the others on the basis of the allelic frequencies. Remarkably, in the Turkish Grey there were differences observed between the population of Enez district, where in situ conservation studies are practised, and that of Bandirma district of Balikesir, where ex situ conservation studies are practised out of the original raising area. In conclusion, this study demonstrates that molecular data could be used to reveal an unbiased view of past events and provide the basis for a rational exploitation of livestock, suggesting appropriate cross-breeding plans based on genetic distance or breeding strategies that include the population structure. © 2010 Blackwell Verlag GmbH.

Preliminary analysis on hybrid vigor in Indonesian indigenous and crossbred cattle population using data from published studies

NASA Astrophysics Data System (ADS)

Prastowo, S.; Widi, TSM; Widyas, N.

2017-04-01

Hybrid vigor or heterosis is the phenomenon where a crossbreed progeny has better performance compared to its parents. Heterosis can be quantified relative to the mid-parents value or relative to one of its parent’s population average by crossing two breeds. Crossbreeding is aimed to increase the production performance of local breeds. According to the Indonesian government policy, crossbreeding program is one of main strategies to achieve meat self-sufficiency. We explore the possibilities observing of heterosis exhibited by crossing Bali and Peranakan Onggole (PO) cattle as local breed with the exotic breed based on the published data. In this paper, growth and reproductive traits from Bali and PO from year 2000-2010 were used for analysis. Moreover, Limousine and Simmental exotic breed data were collected from official information of artificial insemination (AI) centre. Data in growth trait (chest girth, mature weight, weaning weight and yearling weight) in all breeds and their crosses were then analysed using standard heterosis estimation method. Result, shows that crossbred offspring perform better in the growth trait in relative to Bali and PO as local breed. Specifically in Bali crossed with PO, the offspring shown better estimated heterosis effect in yearling weight compared to both parents. Despite heterosis were observed in some traits, careful planning of crossbreeding program is a must in order to avoid the loss of genetic variance.

Population structure of four Thai indigenous chicken breeds

PubMed Central

2014-01-01

Background In recent years, Thai indigenous chickens have increasingly been bred as an alternative in Thailand poultry market. Due to their popularity, there is a clear need to improve the underlying quality and productivity of these chickens. Studying chicken genetic variation can improve the chicken meat quality as well as conserving rare chicken species. To begin with, a minimal set of molecular markers that can characterize the Thai indigenous chicken breeds is required. Results Using AFLP-PCR, 30 single nucleotide polymorphisms (SNPs) from Thai indigenous chickens were obtained by DNA sequencing. From these SNPs, we genotyped 465 chickens from 7 chicken breeds, comprising four Thai indigenous chicken breeds- Pradhuhangdum (PD), Luenghangkhao (LK), Dang (DA) and Chee (CH), one wild chicken - the red jungle fowls (RJF), and two commercial chicken breeds - the brown egg layer (BL) and commercial broiler (CB). The chicken genotypes reveal unique genetic structures of the four Thai indigenous chicken breeds. The average expected heterozygosities of PD= 0.341, LK= 0.357, DA=0.349 and CH= 0.373, while the references RJF= 0.327, CB=0.324 and BL= 0.285. The FST values among Thai indigenous chicken breeds vary from 0.051 to 0.096. The FST values between the pairs of Thai indigenous chickens and RJF vary from 0.083 to 0.105 and the FST values between the Thai indigenous chickens and the two commercial chicken breeds vary from 0.116 to 0.221. A neighbour-joining tree of all individual chickens showed that the Thai indigenous chickens were clustered into four groups which were closely related to the wild RJF but far from the commercial breeds. Such commercial breeds were split into two closely groups. Using genetic admixture analysis, we observed that the Thai indigenous chicken breeds are likely to share common ancestors with the RJF, while both commercial chicken breeds share the same admixture pattern. Conclusion These results indicated that the Thai indigenous chicken breeds may descend from the same ancestors. These indigenous chicken breeds were more closely related to red jungle fowls than those of the commercial breeds. These findings showed that the proposed SNP panel can effectively be used to characterize the four Thai indigenous chickens. PMID:24674423

Applications of population genetics to animal breeding, from wright, fisher and lush to genomic prediction.

PubMed

Hill, William G

2014-01-01

Although animal breeding was practiced long before the science of genetics and the relevant disciplines of population and quantitative genetics were known, breeding programs have mainly relied on simply selecting and mating the best individuals on their own or relatives' performance. This is based on sound quantitative genetic principles, developed and expounded by Lush, who attributed much of his understanding to Wright, and formalized in Fisher's infinitesimal model. Analysis at the level of individual loci and gene frequency distributions has had relatively little impact. Now with access to genomic data, a revolution in which molecular information is being used to enhance response with "genomic selection" is occurring. The predictions of breeding value still utilize multiple loci throughout the genome and, indeed, are largely compatible with additive and specifically infinitesimal model assumptions. I discuss some of the history and genetic issues as applied to the science of livestock improvement, which has had and continues to have major spin-offs into ideas and applications in other areas.

Marker-aided genetic divergence analysis in Brassica.

PubMed

Arunachalam, V; Verma, Shefali; Sujata, V; Prabhu, K V

2005-08-01

Genetic divergence was evaluated in 31 breeding lines from four Brassica species using Mahalanobis' D2. A new method of grouping using D2 values was used to group the 31 lines, based on diagnostic morphological traits (called morphoqts). Isozyme variation of the individual enzymes esterase and glutamate oxaloacetate was quantified by five parameters (called isoqts) developed earlier. Grouping by the same method was also done based on the isoqts, and the grouping by isozymes was compared with that by morphoqts. Overall, there was an agreement of 73% suggesting that isoqts can be used in the choice of parents and also first stage selection of segregants in the laboratory. It was suggested that such an exercise would help to take care of season-bound and field-related problems of breeding. The new isozyme QTs, within lane variance of relative mobility and relative absorption, accounted for about 50% of the total divergence. The utility of the new method and isoqts in cost-effective breeding were highlighted.

Can we use genetic and genomic approaches to identify candidate animals for targeted selective treatment.

PubMed

Laurenson, Yan C S M; Kyriazakis, Ilias; Bishop, Stephen C

2013-10-18

Estimated breeding values (EBV) for faecal egg count (FEC) and genetic markers for host resistance to nematodes may be used to identify resistant animals for selective breeding programmes. Similarly, targeted selective treatment (TST) requires the ability to identify the animals that will benefit most from anthelmintic treatment. A mathematical model was used to combine the concepts and evaluate the potential of using genetic-based methods to identify animals for a TST regime. EBVs obtained by genomic prediction were predicted to be the best determinant criterion for TST in terms of the impact on average empty body weight and average FEC, whereas pedigree-based EBVs for FEC were predicted to be marginally worse than using phenotypic FEC as a determinant criterion. Whilst each method has financial implications, if the identification of host resistance is incorporated into a wider genomic selection indices or selective breeding programmes, then genetic or genomic information may be plausibly included in TST regimes. Copyright © 2013 Elsevier B.V. All rights reserved.

A Novel Non-Invasive Selection Criterion for the Preservation of Primitive Dutch Konik Horses

PubMed Central

May-Davis, Sharon; Shorter, Kathleen; Vermeulen, Zefanja; Butler, Raquel; Koekkoek, Marianne

2018-01-01

The Dutch Konik is valued from a genetic conservation perspective and also for its role in preservation of natural landscapes. The primary management objective for the captive breeding of this primitive horse is to maintain its genetic purity, whilst also maintaining the nature reserves on which they graze. Breeding selection has traditionally been based on phenotypic characteristics consistent with the breed description, and the selection of animals for removal from the breeding program is problematic at times due to high uniformity within the breed, particularly in height at the wither, colour (mouse to grey dun) and presence of primitive markings. With the objective of identifying an additional non-invasive selection criterion with potential uniqueness to the Dutch Konik, this study investigates the anatomic parameters of the distal equine limb, with a specific focus on the relative lengths of the individual splint bones. Post-mortem dissections performed on distal limbs of Dutch Konik (n = 47) and modern domesticated horses (n = 120) revealed significant differences in relation to the length and symmetry of the 2nd and 4th Metacarpals and Metatarsals. Distal limb characteristics with apparent uniqueness to the Dutch Konik are described which could be an important tool in the selection and preservation of the breed. PMID:29389896

Genetic characterization of Russian honey bee stock selected for improved resistance to Varroa destructor.

PubMed

Bourgeois, A Lelania; Rinderer, Thomas E

2009-06-01

Maintenance of genetic diversity among breeding lines is important in selective breeding and stock management. The Russian Honey Bee Breeding Program has strived to maintain high levels of heterozygosity among its breeding lines since its inception in 1997. After numerous rounds of selection for resistance to tracheal and varroa mites and improved honey production, 18 lines were selected as the core of the program. These lines were grouped into three breeding blocks that were crossbred to improve overall heterozygosity levels of the population. Microsatellite DNA data demonstrated that the program has been successful. Heterozygosity and allelic richness values are high and there are no indications of inbreeding among the three blocks. There were significant levels of genetic structure measured among the three blocks. Block C was genetically distinct from both blocks A and B (F(ST) = 0.0238), whereas blocks A and B did not differ from each other (F(ST) = 0.0074). The same pattern was seen for genic (based on numbers of alleles) differentiation. Genetic distance, as measured by chord distance, indicates that all of the 18 lines are equally distant, with minimal clustering. The data indicate that the overall design of the breeding program has been successful in maintaining high levels of diversity and avoiding problems associated with inbreeding.

A Novel Non-Invasive Selection Criterion for the Preservation of Primitive Dutch Konik Horses.

PubMed

May-Davis, Sharon; Brown, Wendy Y; Shorter, Kathleen; Vermeulen, Zefanja; Butler, Raquel; Koekkoek, Marianne

2018-02-01

The Dutch Konik is valued from a genetic conservation perspective and also for its role in preservation of natural landscapes. The primary management objective for the captive breeding of this primitive horse is to maintain its genetic purity, whilst also maintaining the nature reserves on which they graze. Breeding selection has traditionally been based on phenotypic characteristics consistent with the breed description, and the selection of animals for removal from the breeding program is problematic at times due to high uniformity within the breed, particularly in height at the wither, colour (mouse to grey dun) and presence of primitive markings. With the objective of identifying an additional non-invasive selection criterion with potential uniqueness to the Dutch Konik, this study investigates the anatomic parameters of the distal equine limb, with a specific focus on the relative lengths of the individual splint bones. Post-mortem dissections performed on distal limbs of Dutch Konik ( n = 47) and modern domesticated horses ( n = 120) revealed significant differences in relation to the length and symmetry of the 2nd and 4th Metacarpals and Metatarsals. Distal limb characteristics with apparent uniqueness to the Dutch Konik are described which could be an important tool in the selection and preservation of the breed.

Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism

PubMed Central

2009-01-01

The genetic diversity and structure of horses raised in France were investigated using 11 microsatellite markers and 1679 animals belonging to 34 breeds. Between-breed differences explained about ten per cent of the total genetic diversity (Fst = 0.099). Values of expected heterozygosity ranged from 0.43 to 0.79 depending on the breed. According to genetic relationships, multivariate and structure analyses, breeds could be classified into four genetic differentiated groups: warm-blooded, draught, Nordic and pony breeds. Using complementary maximisation of diversity and aggregate diversity approaches, we conclude that particular efforts should be made to conserve five local breeds, namely the Boulonnais, Landais, Merens, Poitevin and Pottok breeds. PMID:19284689

Genetic Correlations Between Carcass Traits And Molecular Breeding Values In Angus Cattle

USDA-ARS?s Scientific Manuscript database

This research elucidated genetic relationships between carcass traits, ultrasound indicator traits, and their respective molecular breeding values (MBV). Animals whose MBV data were used to estimate (co)variance components were not previously used in development of the MBV. Results are presented fo...

Genetic trends for live weight traits reflect breeding strategies in registered Charolais Farms in Mexico.

PubMed

Parra-Bracamonte, G M; Lopez-Villalobos, N; Morris, S T; Sifuentes-Rincón, A M; Lopez-Bustamante, L A

2016-12-01

Genetic trends are commonly used to verify genetic improvement; however, there are few reports on beef cattle in Mexico. Data from 1998 to 2013 from four Charolais bull breeding farms were examined to verify the genetic responses to different breeding management and selection criteria. Analysis included the comparison of regression lines of breeding values for birth (BW), weaning (WW) and yearling weights (YW), and maternal weaning weight (MWW) on the year of birth of the animals. Results revealed differential genetic progress for BW and YW and indicated that the overall analysis may have diluted the perception of genetic progress from the farmer's point of view. The use of breeding values as a tool for selection is effective to achieve genetic progress, even in negatively correlated traits, such as birth weight and yearling weight.

Stakeholder involvement in establishing a milk quality sub-index in dairy cow breeding goals: a Delphi approach.

PubMed

Henchion, M; McCarthy, M; Resconi, V C; Berry, D P; McParland, S

2016-05-01

The relative weighting on traits within breeding goals are generally determined by bio-economic models or profit functions. While such methods have generally delivered profitability gains to producers, and are being expanded to consider non-market values, current approaches generally do not consider the numerous and diverse stakeholders that affect, or are affected, by such tools. Based on principles of respondent anonymity, iteration, controlled feedback and statistical aggregation of feedback, a Delphi study was undertaken to gauge stakeholder opinion of the importance of detailed milk quality traits within an overall dairy breeding goal for profit, with the aim of assessing its suitability as a complementary, participatory approach to defining breeding goals. The questionnaires used over two survey rounds asked stakeholders: (a) their opinion on incorporating an explicit sub-index for milk quality into a national breeding goal; (b) the importance they would assign to a pre-determined list of milk quality traits and (c) the (relative) weighting they would give such a milk quality sub-index. Results from the survey highlighted a good degree of consensus among stakeholders on the issues raised. Similarly, revelation of the underlying assumptions and knowledge used by stakeholders to make their judgements illustrated their ability to consider a range of perspectives when evaluating traits, and to reconsider their answers based on the responses and rationales given by others, which demonstrated social learning. Finally, while the relative importance assigned by stakeholders in the Delphi survey (4% to 10%) and the results of calculations based on selection index theory of the relative emphasis that should be placed on milk quality to halt any deterioration (16%) are broadly in line, the difference indicates the benefit of considering more than one approach to determining breeding goals. This study thus illustrates the role of the Delphi technique, as a complementary approach to traditional approaches, to defining breeding goals. This has implications for how breeding goals will be defined and in determining who should be involved in the decision-making process.

Information-based management mode based on value network analysis for livestock enterprises

NASA Astrophysics Data System (ADS)

Liu, Haoqi; Lee, Changhoon; Han, Mingming; Su, Zhongbin; Padigala, Varshinee Anu; Shen, Weizheng

2018-01-01

With the development of computer and IT technologies, enterprise management has gradually become information-based management. Moreover, due to poor technical competence and non-uniform management, most breeding enterprises show a lack of organisation in data collection and management. In addition, low levels of efficiency result in increasing production costs. This paper adopts 'struts2' in order to construct an information-based management system for standardised and normalised management within the process of production in beef cattle breeding enterprises. We present a radio-frequency identification system by studying multiple-tag anti-collision via a dynamic grouping ALOHA algorithm. This algorithm is based on the existing ALOHA algorithm and uses an improved packet dynamic of this algorithm, which is characterised by a high-throughput rate. This new algorithm can reach a throughput 42% higher than that of the general ALOHA algorithm. With a change in the number of tags, the system throughput is relatively stable.

Genome-enabled prediction models for yield related traits in chickpea

USDA-ARS?s Scientific Manuscript database

Genomic selection (GS) unlike marker-assisted backcrossing (MABC) predicts breeding values of lines using genome-wide marker profiling and allows selection of lines prior to field-phenotyping, thereby shortening the breeding cycle. A collection of 320 elite breeding lines was selected and phenotyped...

Some factors related to eradication action of dengue breeding place at Kota Timu village, subdistrict of Sukakarya in Kota Sabang

NASA Astrophysics Data System (ADS)

Rahmayani, A., Raudhatun Nuzul Z.; Marniati

2017-09-01

According to the Health Department in Kota Sabang, there are 23 patients infected by dengue in 2014. They were nursed in General Hospital and Health Center in Sabang and one child died. To determine the factors related to eradication actions of dengue breeding place, this research is a quantitative research using descriptive analytic with cross sectional design. The population of this research was all housewives in the village of Kuta Timu, subdistrict of Sukakarya in Kota Sabang, and the sample was 33 people. This research was conducted in July 2016. Data were analyzed using SPSS for Windows version 16. The results showed that there is a correlation between education and mother's action in dengue breeding place in the village of Kuta Timu, subdistrict of Sukakarya in Kota Sabang with p value 0.028, and also a correlation between economic status with mother's action in dengue breeding place with p value of 0.009. however, there is no correlation between knowledge with mother's action in dengue breeding place with p value 1.000.

Short communication: Implementation of a breeding value for heat tolerance in Australian dairy cattle.

PubMed

Nguyen, Thuy T T; Bowman, Phil J; Haile-Mariam, Mekonnen; Nieuwhof, Gert J; Hayes, Benjamin J; Pryce, Jennie E

2017-09-01

Excessive ambient temperature and humidity can impair milk production and fertility of dairy cows. Selection for heat-tolerant animals is one possible option to mitigate the effects of heat stress. To enable selection for this trait, we describe the development of a heat tolerance breeding value for Australian dairy cattle. We estimated the direct genomic values of decline in milk, fat, and protein yield per unit increase of temperature-humidity index (THI) using 46,726 single nucleotide polymorphisms and a reference population of 2,236 sires and 11,853 cows for Holsteins and 506 sires and 4,268 cows for Jerseys. This new direct genomic value is the Australian genomic breeding value for heat tolerance (HT ABVg). The components of the HT ABVg are the decline in milk, fat, and protein per unit increase in THI when THI increases above the threshold of 60. These components are weighted by their respective economic values, assumed to be equivalent to the weights applied to milk, fat, and protein yield in the Australian selection indices. Within each breed, the HT ABVg is then standardized to have a mean of 100 and standard deviation (SD) of 5, which is consistent with the presentation of breeding values for many other traits in Australia. The HT ABVg ranged from -4 to +3 SD in Holsteins and -3 to +4 SD in Jerseys. The mean reliabilities of HT ABVg among validation sires, calculated from the prediction error variance and additive genetic variance, were 38% in both breeds. The range in ABVg and their reliability suggests that HT can be improved using genomic selection. There has been a deterioration in the genetic trend of HT, and to moderate the decline it is suggested that the HT ABVg should be included in a multitrait economic index with other traits that contribute to farm profit. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

The accuracies of DNA-based estimates of genetic merit derived from Angus or multibreed beef cattle training populations.

PubMed

Weber, K L; Drake, D J; Taylor, J F; Garrick, D J; Kuehn, L A; Thallman, R M; Schnabel, R D; Snelling, W M; Pollak, E J; Van Eenennaam, A L

2012-12-01

Several organizations have developed prediction models for molecular breeding values (MBV) for quantitative growth and carcass traits in beef cattle using Bovine SNP50 genotypes and phenotypic or EBV data. Molecular breeding values for Angus cattle have been developed by IGENITY, Pfizer Animal Genetics, and a collaboration between researchers from Iowa State University and the University of Missouri-Columbia (ISU/UMC). The U.S. Meat Animal Research Center (USMARC; Clay Center, NE) has also developed MBV for 16 cattle breeds using 2 multibreed populations, the Germplasm Evaluation (GPE) Program and the 2,000 Bull Project (2K(ALL)), and 2 single breed subpopulations of the 2,000 Bull Project, Angus (2K(AN)) and Hereford (2K(HH)). In this study, these MBV were assessed relative to commercial ranch EBV estimated from the progeny phenotypes of Angus bulls naturally mated in multisire breeding pastures to commercial cows: 121 for USMARC MBV, 99 for ISU/UMC MBV, and 29 for IGENITY and Pfizer MBV (selected based on number of progeny carcass records). Five traits were analyzed: weaning weight (WW), HCW, marbling score (MS), rib-eye muscle area (RE), and, for IGENITY and Pfizer only, feedlot ADG. The average accuracies of MBV across traits were 0.38 ± 0.05 for IGENITY, 0.61 ± 0.12 for Pfizer, 0.46 ± 0.12 for ISU/UMC, 0.16 ± 0.04 for GPE, 0.26 ± 0.05 for 2K(ALL), 0.24 ± 0.04 for 2K(AN), and 0.02 ± 0.12 for 2K(HH). Angus-based MBV (IGENITY, Pfizer, ISU/UMC, and 2K(AN)) explained larger proportions of genetic variance in this population than GPE, 2K(ALL), or 2K(HH) MBV for the same traits. In this data set, IGENITY, Pfizer, and ISU/UMC MBV were predictive of realized performance of progeny, and incorporation of that information into national genetic evaluations would be expected to improve EPD accuracy, particularly for young animals.

Novel optimum contribution selection methods accounting for conflicting objectives in breeding programs for livestock breeds with historical migration.

PubMed

Wang, Yu; Bennewitz, Jörn; Wellmann, Robin

2017-05-12

Optimum contribution selection (OCS) is effective for increasing genetic gain, controlling the rate of inbreeding and enables maintenance of genetic diversity. However, this diversity may be caused by high migrant contributions (MC) in the population due to introgression of genetic material from other breeds, which can threaten the conservation of small local populations. Therefore, breeding objectives should not only focus on increasing genetic gains but also on maintaining genetic originality and diversity of native alleles. This study aimed at investigating whether OCS was improved by including MC and modified kinships that account for breed origin of alleles. Three objective functions were considered for minimizing kinship, minimizing MC and maximizing genetic gain in the offspring generation, and we investigated their effects on German Angler and Vorderwald cattle. In most scenarios, the results were similar for Angler and Vorderwald cattle. A significant positive correlation between MC and estimated breeding values of the selection candidates was observed for both breeds, thus traditional OCS would increase MC. Optimization was performed under the condition that the rate of inbreeding did not exceed 1% and at least 30% of the maximum progress was achieved for all other criteria. Although traditional OCS provided the highest breeding values under restriction of classical kinship, the magnitude of MC in the progeny generation was not controlled. When MC were constrained or minimized, the kinship at native alleles increased compared to the reference scenario. Thus, in addition to constraining MC, constraining kinship at native alleles is required to ensure that native genetic diversity is maintained. When kinship at native alleles was constrained, the classical kinship was automatically lowered in most cases and more sires were selected. However, the average breeding value in the next generation was also lower than that obtained with traditional OCS. For local breeds with historical introgressions, current breeding programs should focus on increasing genetic gain and controlling inbreeding, as well as maintaining the genetic originality of the breeds and the diversity of native alleles via the inclusion of MC and kinship at native alleles in the OCS process.

Genetic covariance components within and among linear type traits differ among contrasting beef cattle breeds.

PubMed

Doyle, Jennifer L; Berry, Donagh P; Walsh, Siobhan W; Veerkamp, Roel F; Evans, Ross D; Carthy, Tara R

2018-05-04

Linear type traits describing the skeletal, muscular, and functional characteristics of an animal are routinely scored on live animals in both the dairy and beef cattle industries. Previous studies have demonstrated that genetic parameters for certain performance traits may differ between breeds; no study, however, has attempted to determine if differences exist in genetic parameters of linear type traits among breeds or sexes. Therefore, the objective of the present study was to determine if genetic covariance components for linear type traits differed among five contrasting cattle breeds, and to also investigate if these components differed by sex. A total of 18 linear type traits scored on 3,356 Angus (AA), 31,049 Charolais (CH), 3,004 Hereford (HE), 35,159 Limousin (LM), and 8,632 Simmental (SI) were used in the analysis. Data were analyzed using animal linear mixed models which included the fixed effects of sex of the animal (except in the investigation into the presence of sexual dimorphism), age at scoring, parity of the dam, and contemporary group of herd-date of scoring. Differences (P < 0.05) in heritability estimates, between at least two breeds, existed for 13 out of 18 linear type traits. Differences (P < 0.05) also existed between the pairwise within-breed genetic correlations among the linear type traits. Overall, the linear type traits in the continental breeds (i.e., CH, LM, SI) tended to have similar heritability estimates to each other as well as similar genetic correlations among the same pairwise traits, as did the traits in the British breeds (i.e., AA, HE). The correlation between a linear function of breeding values computed conditional on covariance parameters estimated from the CH breed with a linear function of breeding values computed conditional on covariance parameters estimated from the other breeds was estimated. Replacing the genetic covariance components estimated in the CH breed with those of the LM had least effect but the impact was considerable when the genetic covariance components of the AA were used. Genetic correlations between the same linear type traits in the two sexes were all close to unity (≥0.90) suggesting little advantage in considering these as separate traits for males and females. Results for the present study indicate the potential increase in accuracy of estimated breeding value prediction from considering, at least, the British breed traits separate to continental breed traits.

A preference-based approach to deriving breeding objectives: applied to sheep breeding.

PubMed

Byrne, T J; Amer, P R; Fennessy, P F; Hansen, P; Wickham, B W

2012-05-01

Using internet-based software known as 1000Minds, choice-experiment surveys were administered to experts and farmers from the Irish sheep industry to capture their preferences with respect to the relative importance - represented by part-worth utilities - of target traits in the definition of a breeding objective for sheep in Ireland. Sheep production in Ireland can be broadly separated into lowland and hill farming systems; therefore, each expert was asked to answer the survey first as if he or she were a lowland farmer and second as a hill farmer. In addition to the experts, a group of lowland and a group of hill farmers were surveyed to assess whether, and to what extent, the groups' preferences differ from the experts' preferences. The part-worth utilities obtained from the surveys were converted into relative economic value terms per unit change in each trait. These measures - referred to as 'preference economic values' (pEVs) - were compared with economic values for the traits obtained from bio-economic models. The traits 'value per lamb at the meat processor' and 'lamb survival to slaughter' were revealed as being the two most important traits for the surveyed experts responding as lowland and hill farmers, respectively. In contrast, 'number of foot baths per year for ewes' and 'number of anthelmintic treatments per year for ewes' were the two least important traits. With the exception of 'carcase fat class' (P < 0.05), there were no statistically significant differences in the mean pEVs obtained from the surveyed experts under both the lowland and hill farming scenarios. Compared with the economic values obtained from bio-economic models, the pEVs for 'lambing difficulty' when the experts responded as lowland farmers were higher (P < 0.001); and they were lower (P < 0.001) for 'carcase conformation class', 'carcase fat class' (less negative) and 'ewe mature weight' (less negative) under both scenarios. Compared with surveyed experts, pEVs from lowland farmers differed significantly for 'lambing difficulty', 'lamb survival to slaughter', 'average days to slaughter of lambs', 'number of foot baths per year for ewes', 'number of anthelmintic treatments per year for ewes' and 'ewe mature weight'. Compared with surveyed experts, pEVs from hill farmers differed significantly for 'lambing difficulty', 'average days to slaughter of lambs' and 'number of foot baths per year for ewes'. This study indicates that preference-based tools have the potential to contribute to the definition of breeding objectives where production and price data are not available.

Comparison of composition and quality traits of meat from young finishing bulls from Belgian Blue, Limousin and Aberdeen Angus breeds.

PubMed

Cuvelier, C; Clinquart, A; Hocquette, J F; Cabaraux, J F; Dufrasne, I; Istasse, L; Hornick, J L

2006-11-01

Thirty-six young finishing bulls from three breeds (Belgian Blue, Limousin and Aberdeen Angus) were fattened over five months with finishing diets based either on sugar-beet pulp or on cereals. Nutritional quality traits of meat - fat content and fatty acid composition with emphasis on the n-6 and n-3 polyunsaturated fatty acids - along with some organoleptic quality traits were measured. The Belgian Blue bulls had the lowest intramuscular fat content associated with lower saturated and monounsaturated fatty acid contents. The polyunsaturated fatty acid content did not differ to a large extent between the breeds, the Aberdeen Angus bulls showing slightly higher values. Relative to energy intake, the overall contribution of meat to the n-3 fatty acid recommended intake was small, whatever the breed. By contrast, the contribution of meat to daily fat intake was of greater importance, especially for the Aberdeen Angus bulls. The quality traits of meat varied also according to the breed: compared to the Aberdeen Angus, the Belgian Blue bull meat had the stablest colour, the highest drip and the lowest cooking losses. The meat of Limousin bulls had intermediate characteristics for all the parameters.

Genomic selection in sugar beet breeding populations.

PubMed

Würschum, Tobias; Reif, Jochen C; Kraft, Thomas; Janssen, Geert; Zhao, Yusheng

2013-09-18

Genomic selection exploits dense genome-wide marker data to predict breeding values. In this study we used a large sugar beet population of 924 lines representing different germplasm types present in breeding populations: unselected segregating families and diverse lines from more advanced stages of selection. All lines have been intensively phenotyped in multi-location field trials for six agronomically important traits and genotyped with 677 SNP markers. We used ridge regression best linear unbiased prediction in combination with fivefold cross-validation and obtained high prediction accuracies for all except one trait. In addition, we investigated whether a calibration developed based on a training population composed of diverse lines is suited to predict the phenotypic performance within families. Our results show that the prediction accuracy is lower than that obtained within the diverse set of lines, but comparable to that obtained by cross-validation within the respective families. The results presented in this study suggest that a training population derived from intensively phenotyped and genotyped diverse lines from a breeding program does hold potential to build up robust calibration models for genomic selection. Taken together, our results indicate that genomic selection is a valuable tool and can thus complement the genomics toolbox in sugar beet breeding.

Milk protein concentration, estimated breeding value for fertility, and reproductive performance in lactating dairy cows.

PubMed

Morton, John M; Auldist, Martin J; Douglas, Meaghan L; Macmillan, Keith L

2017-07-01

Milk protein concentration in dairy cows has been positively associated with a range of measures of reproductive performance, and genetic factors affecting both milk protein concentration and reproductive performance may contribute to the observed phenotypic associations. It was of interest to assess whether these beneficial phenotypic associations are accounted for or interact with the effects of estimated breeding values for fertility. The effects of a multitrait estimated breeding value for fertility [the Australian breeding value for daughter fertility (ABV fertility)] on reproductive performance were also of interest. Interactions of milk protein concentration and ABV fertility with the interval from calving date to the start of the herd's seasonally concentrated breeding period were also assessed. A retrospective single cohort study was conducted using data collected from 74 Australian seasonally and split calving dairy herds. Associations between milk protein concentration, ABV fertility, and reproductive performance in Holstein cows were assessed using random effects logistic regression. Between 52,438 and 61,939 lactations were used for analyses of 4 reproductive performance measures. Milk protein concentration was strongly and positively associated with reproductive performance in dairy cows, and this effect was not accounted for by the effects of ABV fertility. Increases in ABV fertility had important additional beneficial effects on the probability of pregnancy by wk 6 and 21 of the herd's breeding period. For cows calved before the start of the breeding period, the effects of increases in both milk protein concentration and ABV fertility were beneficial regardless of their interval from calving to the start of the breeding period. These findings demonstrate the potential for increasing reproductive performance through identifying the causes of the association between milk protein concentration and reproductive performance and then devising management strategies to capitalize on them. Research should be conducted to understand the component of the relationship not captured by ABV fertility. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Changes in animal performance and profitability of Holstein dairy operations after introduction of crossbreeding with Montbéliarde, Normande, and Scandinavian Red.

PubMed

Dezetter, C; Bareille, N; Billon, D; Côrtes, C; Lechartier, C; Seegers, H

2017-10-01

An individual-based mechanistic, stochastic, and dynamic simulation model was developed to assess economic effects resulting from changes in performance for milk yield and solid contents, reproduction, health, and replacement, induced by the introduction of crossbreeding in Holstein dairy operations. Three crossbreeding schemes, Holstein × Montbéliarde, Holstein × Montbéliarde × Normande, and Holstein × Montbéliarde × Scandinavian Red, were implemented in Holstein dairy operations and compared with Holstein pure breeding. Sires were selected based on their estimated breeding value for milk. Two initial operations were simulated according to the prevalence (average or high) of reproductive and health disorders in the lactating herd. Evolution of operations was simulated during 15 yr under 2 alternative managerial goals (constant number of cows or constant volume of milk sold). After 15 yr, breed percentages reached equilibrium for the 2-breed but not for the 3-breed schemes. After 5 yr of simulation, all 3 crossbreeding schemes reduced average milk yield per cow-year compared with the pure Holstein scheme. Changes in other animal performance (milk solid contents, reproduction, udder health, and longevity) were always in favor of crossbreeding schemes. Under an objective of constant number of cows, margin over variable costs in average discounted value over the 15 yr of simulation was slightly increased by crossbreeding schemes, with an average prevalence of disorders up to €32/cow-year. In operations with a high prevalence of disorders, crossbreeding schemes increased the margin over variable costs up to €91/cow-year. Under an objective of constant volume of milk sold, crossbreeding schemes improved margin over variable costs up to €10/1,000L (corresponding to around €96/cow-year) for average prevalence of disorders, and up to €13/1,000L (corresponding to around €117/cow-year) for high prevalence of disorders. Under an objective of constant number of cows, an unfavorable pricing context (milk price vs. concentrates price) increased slightly crossbreeding positive effects on margin over variable costs. Under an objective of constant volume of milk, only very limited changes in differences of margins were found between the breeding schemes. Our results, obtained conditionally to the parameterization values used here, suggest that dairy crossbreeding should be considered as a relevant option for Holstein dairy operations with a production level until 9,000 kg/cow-year in France, and possibly in other countries. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

A two step Bayesian approach for genomic prediction of breeding values.

PubMed

Shariati, Mohammad M; Sørensen, Peter; Janss, Luc

2012-05-21

In genomic models that assign an individual variance to each marker, the contribution of one marker to the posterior distribution of the marker variance is only one degree of freedom (df), which introduces many variance parameters with only little information per variance parameter. A better alternative could be to form clusters of markers with similar effects where markers in a cluster have a common variance. Therefore, the influence of each marker group of size p on the posterior distribution of the marker variances will be p df. The simulated data from the 15th QTL-MAS workshop were analyzed such that SNP markers were ranked based on their effects and markers with similar estimated effects were grouped together. In step 1, all markers with minor allele frequency more than 0.01 were included in a SNP-BLUP prediction model. In step 2, markers were ranked based on their estimated variance on the trait in step 1 and each 150 markers were assigned to one group with a common variance. In further analyses, subsets of 1500 and 450 markers with largest effects in step 2 were kept in the prediction model. Grouping markers outperformed SNP-BLUP model in terms of accuracy of predicted breeding values. However, the accuracies of predicted breeding values were lower than Bayesian methods with marker specific variances. Grouping markers is less flexible than allowing each marker to have a specific marker variance but, by grouping, the power to estimate marker variances increases. A prior knowledge of the genetic architecture of the trait is necessary for clustering markers and appropriate prior parameterization.

Marker-Based Estimates Reveal Significant Non-additive Effects in Clonally Propagated Cassava (Manihot esculenta): Implications for the Prediction of Total Genetic Value and the Selection of Varieties.

PubMed

Wolfe, Marnin D; Kulakow, Peter; Rabbi, Ismail Y; Jannink, Jean-Luc

2016-08-31

In clonally propagated crops, non-additive genetic effects can be effectively exploited by the identification of superior genetic individuals as varieties. Cassava (Manihot esculenta Crantz) is a clonally propagated staple food crop that feeds hundreds of millions. We quantified the amount and nature of non-additive genetic variation for three key traits in a breeding population of cassava from sub-Saharan Africa using additive and non-additive genome-wide marker-based relationship matrices. We then assessed the accuracy of genomic prediction for total (additive plus non-additive) genetic value. We confirmed previous findings based on diallel populations, that non-additive genetic variation is significant for key cassava traits. Specifically, we found that dominance is particularly important for root yield and epistasis contributes strongly to variation in CMD resistance. Further, we showed that total genetic value predicted observed phenotypes more accurately than additive only models for root yield but not for dry matter content, which is mostly additive or for CMD resistance, which has high narrow-sense heritability. We address the implication of these results for cassava breeding and put our work in the context of previous results in cassava, and other plant and animal species. Copyright © 2016 Author et al.

Approximation of reliability of direct genomic breeding values

USDA-ARS?s Scientific Manuscript database

Two methods to efficiently approximate theoretical genomic reliabilities are presented. The first method is based on the direct inverse of the left hand side (LHS) of mixed model equations. It uses the genomic relationship matrix for a small subset of individuals with the highest genomic relationshi...

Feed intake and efficiency of F1 lambs

USDA-ARS?s Scientific Manuscript database

Objective estimates of feed efficiency for progeny of terminal-sire breeds of sheep are needed to improve the value of market lambs. Because recent terminal-sire breed-comparison data are lacking, we determined effects of terminal-sire breed on feed efficiency of F1 lambs. Each year for 3 yr, Columb...

Evaluation of Columbia, USMARC-Composite, Suffolk, and Texel rams at terminal sires in an extensive rangeland production system

USDA-ARS?s Scientific Manuscript database

Crossing proven, superior terminal-sire sheep breeds with well-adapted maternal breeds provide opportunity to increase lamb carcass value, while maintaining acceptable environmental adaptation in crossbred lambs. Large, lean terminal-sire breeds, such as the Suffolk and Columbia, have been typicall...

Integration of DNA marker information into breeding value predictions

USDA-ARS?s Scientific Manuscript database

Calves from seven breeds including 20 herds were genotyped with a reduced DNA marker panel for weaning weight. The marker panel used was derived using USMARC Cycle VII animals. The results from the current study suggest marker effects are not robust across breeds and that methodology exists to integ...

The development of genomics applied to dairy breeding

USDA-ARS?s Scientific Manuscript database

Genomic selection (GS) has profoundly changed dairy cattle breeding in the last decade and can be defined as the use of genomic breeding values (GEBV) in selection programs. The GEBV is the sum of the effects of dense DNA markers across the whole genome, capturing all the quantitative trait loci (QT...

Cow genotyping strategies for genomic selection in small dairy cattle population

USDA-ARS?s Scientific Manuscript database

This study compares how different cow genotyping strategies increase the accuracy of genomic estimated breeding values (EBV) in dairy cattle breeds with low numbers. In these breeds there are few sires with progeny records and genotyping cows can improve the accuracy of genomic EBV. The Guernsey bre...

Genomic selection models double the accuracy of predicted breeding values for bacterial cold water disease resistance compared to a traditional pedigree-based model in rainbow trout aquaculture

USDA-ARS?s Scientific Manuscript database

Previously we have shown that bacterial cold water disease (BCWD) resistance in rainbow trout can be improved using traditional family-based selection, but progress has been limited to exploiting only between-family genetic variation. Genomic selection (GS) is a new alternative enabling exploitation...

Genome-enabled selection doubles the accuracy of predicted breeding values for bacterial cold water disease resistance compared to traditional family-based selection in rainbow trout aquaculture

USDA-ARS?s Scientific Manuscript database

We have shown previously that bacterial cold water disease (BCWD) resistance in rainbow trout can be improved using traditional family-based selection, but progress has been limited to exploiting only between-family genetic variation. Genomic selection (GS) is a new alternative enabling exploitation...

Assessing the relative importance of health and conformation traits in the cavalier king Charles spaniel.

PubMed

Wijnrocx, Katrien; François, Liesbeth; Goos, Peter; Buys, Nadine; Janssens, Steven

2018-01-01

The selection of a future breeding dog is a complicated task, in which disease characteristics and different traits have to be combined and weighed against one another. Truncation selection, that is the exclusion of affected animals, may be very inefficient when selecting on a large number of traits, and may result in a reduction of the genetic diversity in a population or breed. Selection could be facilitated by the use of a selection index that combines multiple traits or breeding values into one score. This however requires a consideration of their relative value according to their economic weight, which is difficult to express in monetary units for health traits. The use of a choice experiment to derive non-market values might be a solution to this problem. This is a pilot study to assess the potential use of choice experiments to ascertain the public preference and relative importance attached to health- and conformation traits in the selection of a Cavalier King Charles spaniel. The focus was on two prevalent disorders, mitral valve disease and syringomyelia, and on several important conformation traits such as muzzle length and eye shape. Based on available prior information, a Bayesian D-optimal design approach was used to develop a choice experiment and the resulting choice sets. Every participant (breeder or owner) in the choice experiment was presented with a total of 17 choice sets, in which at most four traits could vary to reduce the cognitive burden. A total of 114 respondents participated in the choice experiment and results showed that respondents (breeders/owners) current attitudes were directed towards health (syringomyelia and mitral valve disease), followed by eye shape and level of inbreeding. This approach identifies the value breeders and owners attach to certain traits in the breeding objective. The resulting relative weights, represented as the logworths obtained from the choice experiment, could be an alternative to economic weights. They could be implemented as a weight when breeding values are available, but more study on this topic will be necessary. A challenge in this approach is to scale up the experiment with additional traits. Moreover, for other traits, the genetic parameters and correlations should be known first, in order to include them in the health selection index as well.

Considering genetic characteristics in German Holstein breeding programs.

PubMed

Segelke, D; Täubert, H; Reinhardt, F; Thaller, G

2016-01-01

Recently, several research groups have demonstrated that several haplotypes may cause embryonic loss in the homozygous state. Up to now, carriers of genetic disorders were often excluded from mating, resulting in a decrease of genetic gain and a reduced number of sires available for the breeding program. Ongoing research is very likely to identify additional genetic defects causing embryonic loss and calf mortality by genotyping a large proportion of the female cattle population and sequencing key ancestors. Hence, a clear demand is present to develop a method combining selection against recessive defects (e.g., Holstein haplotypes HH1-HH5) with selection for economically beneficial traits (e.g., polled) for mating decisions. Our proposed method is a genetic index that accounts for the allele frequencies in the population and the economic value of the genetic characteristic without excluding carriers from breeding schemes. Fertility phenotypes from routine genetic evaluations were used to determine the economic value per embryo lost. Previous research has shown that embryo loss caused by HH1 and HH2 occurs later than the loss for HH3, HH4, and HH5. Therefore, an economic value of € 97 was used against HH1 and HH2 and € 70 against HH3, HH4, and HH5. For polled, € 7 per polled calf was considered. Minor allele frequencies of the defects ranged between 0.8 and 3.3%. The polled allele has a frequency of 4.1% in the German Holstein population. A genomic breeding program was simulated to study the effect of changing the selection criteria from assortative mating based on breeding values to selecting the females using the genetic index. Selection for a genetic index on the female path is a useful method to control the allele frequencies by reducing undesirable alleles and simultaneously increasing economical beneficial characteristics maintaining most of the genetic gain in production and functional traits. Additionally, we applied the genetic index to real data and found a decrease of the genetic trend for the birth years 1990 to 2006. Since 2010 the genetic index has increased due to a strong increase in the polled frequency. However, further investigation is needed to better understand the biology to determine the correct time of embryo loss and the economic value of fertility disorders. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Prevalence and inheritance of and selection for hip dysplasia in seven breeds of dogs in Sweden and benefit: cost analysis of a screening and control program.

PubMed

Swenson, L; Audell, L; Hedhammar, A

1997-01-15

To determine the prevalence and changes over time in the prevalence of hip dysplasia; to ascertain whether prevalence or severity of hip dysplasia was associated with sex of the dogs, age at which coxofemoral joint status was evaluated, or ancestral background; to determine the effects of selective breeding; and to conduct an economic evaluation of the hip dysplasia program operated by the Swedish Kennel Club. Analysis of radiographic evaluations of coxofemoral joint conformity. 83,229 dogs from 7 breeds registered by the Swedish Kennel Club. All radiographs were scrutinized by a single radiologist (LA), and coxofemoral joint conformation was classified as normal or dysplastic, with the degree of dysplasia classified as 1,2,3, or 4. Decreasing prevalence of hip dysplasia corresponding to selection of breeding stock and high heritabilities was found. Sex differences were documented in 3 of the breeds. This was interpreted as breed differences in the distribution of genes related to hip dysplasia. Economic analyses showed that costs of screening and registration of coxofemoral joints was less than the value of dogs estimated to have been saved from moderate, severe, or very severe hip dysplasia in 6 of the breeds. Documented effects of age suggest that all dogs should be screened at the same age, rather than screening a few dogs at an older, more revealing age. In screening and control programs based on an open registry with access to family records, decreasing prevalence of hip dysplasia can be expected, and related to selection of breeding stock.

Extent of linkage disequilibrium, consistency of gametic phase, and imputation accuracy within and across Canadian dairy breeds.

PubMed

Larmer, S G; Sargolzaei, M; Schenkel, F S

2014-05-01

Genomic selection requires a large reference population to accurately estimate single nucleotide polymorphism (SNP) effects. In some Canadian dairy breeds, the available reference populations are not large enough for accurate estimation of SNP effects for traits of interest. If marker phase is highly consistent across multiple breeds, it is theoretically possible to increase the accuracy of genomic prediction for one or all breeds by pooling several breeds into a common reference population. This study investigated the extent of linkage disequilibrium (LD) in 5 major dairy breeds using a 50,000 (50K) SNP panel and 3 of the same breeds using the 777,000 (777K) SNP panel. Correlation of pair-wise SNP phase was also investigated on both panels. The level of LD was measured using the squared correlation of alleles at 2 loci (r(2)), and the consistency of SNP gametic phases was correlated using the signed square root of these values. Because of the high cost of the 777K panel, the accuracy of imputation from lower density marker panels [6,000 (6K) or 50K] was examined both within breed and using a multi-breed reference population in Holstein, Ayrshire, and Guernsey. Imputation was carried out using FImpute V2.2 and Beagle 3.3.2 software. Imputation accuracies were then calculated as both the proportion of correct SNP filled in (concordance rate) and allelic R(2). Computation time was also explored to determine the efficiency of the different algorithms for imputation. Analysis showed that LD values >0.2 were found in all breeds at distances at or shorter than the average adjacent pair-wise distance between SNP on the 50K panel. Correlations of r-values, however, did not reach high levels (<0.9) at these distances. High correlation values of SNP phase between breeds were observed (>0.94) when the average pair-wise distances using the 777K SNP panel were examined. High concordance rate (0.968-0.995) and allelic R(2) (0.946-0.991) were found for all breeds when imputation was carried out with FImpute from 50K to 777K. Imputation accuracy for Guernsey and Ayrshire was slightly lower when using the imputation method in Beagle. Computing time was significantly greater when using Beagle software, with all comparable procedures being 9 to 13 times less efficient, in terms of time, compared with FImpute. These findings suggest that use of a multi-breed reference population might increase prediction accuracy using the 777K SNP panel and that 777K genotypes can be efficiently and effectively imputed using the lower density 50K SNP panel. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Determination of genetic polymorphism in Guney Karaman local Turkish sheep breed by using STR markers

NASA Astrophysics Data System (ADS)

Karslı, Taki; Balcıoǧlu, Murat Soner

2017-04-01

The objective of this study was to assess genetic diversity of Güney Karaman Turkish local sheep breed. A total of 29 samples were genotyped by using 14 STR markers. All markers were polymorphic. The number of alleles in Güney Karaman sheep breed ranged from 3 to 11 per locus, with a mean of 7.42. The average observed and expected heterozygosity was 0.659 and 0.794, respectively. Mean inbreeding coefficient (Fis) value was found 0.175. The PIC values ranged from 0.569 to 0.860 with a mean of 0.743. The findings of this research demonstrate at moderate level gene diversity and heterozygosity with lower inbreeding in Güney Karaman sheep breed.

Comparison of Bayesian models to estimate direct genomic values in multi-breed commercial beef cattle

USDA-ARS?s Scientific Manuscript database

Background Several studies have examined the accuracy of genomic selection both within and across purebred beef or dairy populations. However, the accuracy of direct genomic breeding values (DGVs) has been less well studied in crossbred or admixed cattle populations. We used a population of 3,240 cr...

Genomic selection for crossbred performance accounting for breed-specific effects.

PubMed

Lopes, Marcos S; Bovenhuis, Henk; Hidalgo, André M; van Arendonk, Johan A M; Knol, Egbert F; Bastiaansen, John W M

2017-06-26

Breed-specific effects are observed when the same allele of a given genetic marker has a different effect depending on its breed origin, which results in different allele substitution effects across breeds. In such a case, single-breed breeding values may not be the most accurate predictors of crossbred performance. Our aim was to estimate the contribution of alleles from each parental breed to the genetic variance of traits that are measured in crossbred offspring, and to compare the prediction accuracies of estimated direct genomic values (DGV) from a traditional genomic selection model (GS) that are trained on purebred or crossbred data, with accuracies of DGV from a model that accounts for breed-specific effects (BS), trained on purebred or crossbred data. The final dataset was composed of 924 Large White, 924 Landrace and 924 two-way cross (F1) genotyped and phenotyped animals. The traits evaluated were litter size (LS) and gestation length (GL) in pigs. The genetic correlation between purebred and crossbred performance was higher than 0.88 for both LS and GL. For both traits, the additive genetic variance was larger for alleles inherited from the Large White breed compared to alleles inherited from the Landrace breed (0.74 and 0.56 for LS, and 0.42 and 0.40 for GL, respectively). The highest prediction accuracies of crossbred performance were obtained when training was done on crossbred data. For LS, prediction accuracies were the same for GS and BS DGV (0.23), while for GL, prediction accuracy for BS DGV was similar to the accuracy of GS DGV (0.53 and 0.52, respectively). In this study, training on crossbred data resulted in higher prediction accuracy than training on purebred data and evidence of breed-specific effects for LS and GL was demonstrated. However, when training was done on crossbred data, both GS and BS models resulted in similar prediction accuracies. In future studies, traits with a lower genetic correlation between purebred and crossbred performance should be included to further assess the value of the BS model in genomic predictions.

Breeding strawberry (Fragaria X ananassa Duch) to increase fruit nutritional quality.

PubMed

Capocasa, F; Diamanti, J; Tulipani, S; Battino, M; Mezzetti, B

2008-01-01

In the last few years the nutritional value of fruit has been widely studied and requested by the consumers, especially for protection against cardiovascular events, cancer and others as well as for the general health benefits it can provide. These benefits can be ascribed mainly to the Total Antioxidant Capacity (TAC) of fruit which is determined by a complex combination of bioactive compounds, generally related to specific characteristics of the genotype and of its interaction with the environment. Strawberry breeding programs are currently used to acquire new varieties improved for specific agronomic (Yield and Size), qualitative (Firmness, Sugars Content and Acidity) and sensorial (Colour and Aroma) characteristics, all combined to increased disease resistance and plant adaptability. Nowadays, besides to all these parameters is necessary to look for the specific bioactive components well known for their effect on human health. This aspect is now highly requested by the consumer. By testing different commercial strawberry varieties, a wide difference among their production and fruit quality, mostly related to their adaptability to the local evaluation conditions, is generally detected. Regarding their nutritional values, only few varieties nowadays differ for their higher phenol content and total antioxidant capacity. By taking into account this knowledge different breeding programs specifically addressed to increase fruit nutritional value, have been started. A first approach is based on the use of inter-specific crosses within wild and cultivated genotypes, so to increase variability for these characters, while the second by considering the intra-specific crosses within cultivars already known for their agronomic behavior and good quality performance. Herewith, we report on the major aspects related to breeding program aimed to increase strawberry fruit nutritional quality and what we can expect for the improvement of consumer acceptability of this fruit.

Short communication: Genotyping of cows to speed up availability of genomic estimated breeding values for direct health traits in Austrian Fleckvieh (Simmental) cattle--genetic and economic aspects.

PubMed

Egger-Danner, C; Schwarzenbacher, H; Willam, A

2014-07-01

The aim of this study was to quantify the impact of genotyping cows with reliable phenotypes for direct health traits on annual monetary genetic gain (AMGG) and discounted profit. The calculations were based on a deterministic approach using ZPLAN software (University of Hohenheim, Stuttgart, Germany). It was assumed that increases in reliability of the total merit index (TMI) of 5, 15, and 25 percentage points were achieved through genotyping 5,000, 25,000, and 50,000 cows, respectively. Costs for phenotyping, genotyping, and genomic estimated breeding values vary between €150 and €20 per cow. The gain in genotyping cows for traits with medium to high heritability is more than for direct health traits with low heritability. The AMGG is increased by 1.5% if the reliability of TMI is 5 percentage points higher (i.e., 5,000 cows genotyped) and 6.53% higher AMGG can be expected when the reliability of TMI is increased by 25 percentage points (i.e., 50,000 cows genotyped). The discounted profit depends not only on the costs of genotyping but also on the population size. This study indicates that genotyping cows with reliable phenotypes is feasible to speed up the availability of genomic estimated breeding values for direct health traits. But, because of the huge amount of valid phenotypes and genotypes needed to establish an efficient genomic evaluation, it is likely that financial constraints will be the main limiting factor for implementation into breeding program such as Fleckvieh Austria. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Long-term selection strategies for complex traits using high-density genetic markers.

PubMed

Kemper, K E; Bowman, P J; Pryce, J E; Hayes, B J; Goddard, M E

2012-08-01

Selection of animals for breeding ranked on estimated breeding value maximizes genetic gain in the next generation but does not necessarily maximize long-term response. An alternative method, as practiced by plant breeders, is to build a desired genotype by selection on specific loci. Maximal long-term response in animal breeding requires selection on estimated breeding values with constraints on coancestry. In this paper, we compared long-term genetic response using either a genotype building or a genomic estimated breeding value (GEBV) strategy for the Australian Selection Index (ASI), a measure of profit. First, we used real marker effects from the Australian Dairy Herd Improvement Scheme to estimate breeding values for chromosome segments (approximately 25 cM long) for 2,650 Holstein bulls. Second, we selected 16 animals to be founders for a simulated breeding program where, between them, founders contain the best possible combination of 2 segments from 2 animals at each position in the genome. Third, we mated founder animals and their descendants over 30 generations with 2 breeding objectives: (1) to create a population with the "ideal genotype," where the best 2 segments from the founders segregate at each position, or (2) obtain the highest possible response in ASI with coancestry lower than that achieved under breeding objective 1. Results show that genotype building achieved the ideal genotype for breeding objective 1 and obtained a large gain in ASI over the current population (+A$864.99). However, selection on overall GEBV had greater short-term response and almost as much long-term gain (+A$820.42). When coancestry was lowered under breeding objective 2, selection on overall GEBV achieved a higher response in ASI than the genotype building strategy. Selection on overall GEBV seems more flexible in its selection decisions and was therefore better able to precisely control coancestry while maximizing ASI. We conclude that selection on overall GEBV while minimizing average coancestry is the more practical strategy for dairy cattle where selection is for highly polygenic traits, the reproductive rate is relatively low, and there is low tolerance of coancestry. The outcome may be different for traits controlled by few loci of relatively large effects or for different species. In contrast to other simulations, our results indicate that response to selection on overall GEBV may continue for several generations. This is because long-term genetic change in complex traits requires favorable changes to allele frequencies for many loci located throughout the genome. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Economic selection index development for Beefmaster cattle II: General-purpose breeding objective.

PubMed

Ochsner, K P; MacNeil, M D; Lewis, R M; Spangler, M L

2017-05-01

An economic selection index was developed for Beefmaster cattle in a general-purpose production system in which bulls are mated to a combination of heifers and mature cows, with resulting progeny retained as replacements or sold at weaning. National average prices from 2010 to 2014 were used to establish income and expenses for the system. Genetic parameters were obtained from the literature. Economic values were estimated by simulating 100,000 animals and approximating the partial derivatives of the profit function by perturbing traits 1 at a time, by 1 unit, while holding the other traits constant at their respective means. Relative economic values for the objective traits calving difficultly direct (CDd), calving difficulty maternal (CDm), weaning weight direct (WWd), weaning weight maternal (WWm), mature cow weight (MW), and heifer pregnancy (HP) were -2.11, -1.53, 18.49, 11.28, -33.46, and 1.19, respectively. Consequently, under the scenario assumed herein, the greatest improvements in profitability could be made by decreasing maintenance energy costs associated with MW followed by improvements in weaning weight. The accuracy of the index lies between 0.218 (phenotypic-based index selection) and 0.428 (breeding values known without error). Implementation of this index would facilitate genetic improvement and increase profitability of Beefmaster cattle operations with a general-purpose breeding objective when replacement females are retained and with weaned calves as the sale end point.

Genome-wide analysis of the diversity and ancestry of Korean dogs.

PubMed

Choi, Bong Hwan; Wijayananda, Hasini I; Lee, Soo Hyun; Lee, Doo Ho; Kim, Jong Seok; Oh, Seok Il; Park, Eung Woo; Lee, Cheul Koo; Lee, Seung Hwan

2017-01-01

There are various hypotheses on dog domestication based on archeological and genetic studies. Although many studies have been conducted on the origin of dogs, the existing literature about the ancestry, diversity, and population structure of Korean dogs is sparse. Therefore, this study is focused on the origin, diversity and population structure of Korean dogs. The study sample comprised four major categories, including non-dogs (coyotes and wolves), ancient, modern and Korean dogs. Selected samples were genotyped using an Illumina CanineHD array containing 173,662 single nucleotide polymorphisms. The genome-wide data were filtered using quality control parameters in PLINK 1.9. Only autosomal chromosomes were used for further analysis. The negative off-diagonal variance of the genetic relationship matrix analysis depicted, the variability of samples in each population. FIS (inbreeding rate within a population) values indicated, a low level of inbreeding within populations, and the patterns were in concordance with the results of Nei's genetic distance analysis. The lowest FST (inbreeding rate between populations) values among Korean and Chinese breeds, using a phylogenetic tree, multi-dimensional scaling, and a TreeMix likelihood tree showed Korean breeds are highly related to Chinese breeds. The Korean breeds possessed a unique and large diversity of admixtures compared with other breeds. The highest and lowest effective population sizes were observed in Korean Jindo Black (485) and Korean Donggyeong White (109), respectively. The historical effective population size of all Korean dogs showed declining trend from the past to present. It is important to take immediate action to protect the Korean dog population while conserving their diversity. Furthermore, this study suggests that Korean dogs have unique diversity and are one of the basal lineages of East Asian dogs, originating from China.

Genome-wide analysis of the diversity and ancestry of Korean dogs

PubMed Central

Lee, Doo Ho; Kim, Jong Seok; Oh, Seok Il; Park, Eung Woo; Lee, Cheul Koo; Lee, Seung Hwan

2017-01-01

There are various hypotheses on dog domestication based on archeological and genetic studies. Although many studies have been conducted on the origin of dogs, the existing literature about the ancestry, diversity, and population structure of Korean dogs is sparse. Therefore, this study is focused on the origin, diversity and population structure of Korean dogs. The study sample comprised four major categories, including non-dogs (coyotes and wolves), ancient, modern and Korean dogs. Selected samples were genotyped using an Illumina CanineHD array containing 173,662 single nucleotide polymorphisms. The genome-wide data were filtered using quality control parameters in PLINK 1.9. Only autosomal chromosomes were used for further analysis. The negative off-diagonal variance of the genetic relationship matrix analysis depicted, the variability of samples in each population. FIS (inbreeding rate within a population) values indicated, a low level of inbreeding within populations, and the patterns were in concordance with the results of Nei’s genetic distance analysis. The lowest FST (inbreeding rate between populations) values among Korean and Chinese breeds, using a phylogenetic tree, multi-dimensional scaling, and a TreeMix likelihood tree showed Korean breeds are highly related to Chinese breeds. The Korean breeds possessed a unique and large diversity of admixtures compared with other breeds. The highest and lowest effective population sizes were observed in Korean Jindo Black (485) and Korean Donggyeong White (109), respectively. The historical effective population size of all Korean dogs showed declining trend from the past to present. It is important to take immediate action to protect the Korean dog population while conserving their diversity. Furthermore, this study suggests that Korean dogs have unique diversity and are one of the basal lineages of East Asian dogs, originating from China. PMID:29182674

[Study of genetic variation in Yakutian cattle (Bos taurus L.) using the prolactin bPRL, growth hormone bGH, and transcription factor bPit-1 genes].

PubMed

Lazebnaia, I V; Lazebnyĭ, O E; Sulimova, G E

2010-03-01

The genetic structure of the Yakutian cattle breed was studied using the following genes: bPRL (RsaI site in exon 3), bGH (AluI site in exon 5), and bPit-1 (HinfI site in exon 6). The values of observed heterozygosity were 0.36 for bPRL, 0.29 for bGH, and 0.16 for bPit-1. These values are within the range of values for this parameter established for a number of Bos taurus breeds. The results obtained show that genetic variation is preserved in this aboriginal Russian breed, despite a catastrophic reduction of the number of animals.

Molecular genetic diversity and maternal origin of Chinese black-bone chicken breeds.

PubMed

Zhu, W Q; Li, H F; Wang, J Y; Shu, J T; Zhu, C H; Song, W T; Song, C; Ji, G G; Liu, H X

2014-04-29

Chinese black-bone chickens are valued for the medicinal properties of their meat in traditional Chinese medicine. We investigated the genetic diversity and systematic evolution of Chinese black-bone chicken breeds. We sequenced the DNA of 520 bp of the mitochondrial cyt b gene of nine Chinese black-bone chicken breeds, including Silky chicken, Jinhu black-bone chicken, Jiangshan black-bone chicken, Yugan black-bone chicken, Wumeng black-bone chicken, Muchuan black-bone chicken, Xingwen black-bone chicken, Dehua black-bone chicken, and Yanjin black-bone chicken. We found 13 haplotypes. Haplotype and nucleotide diversity of the nine black-bone chicken breeds ranged from 0 to 0.78571 and 0.00081 to 0.00399, respectively. Genetic diversity was the richest in Jinhu black-bone chickens and the lowest in Yanjin black-bone chickens. Analysis of phylogenetic trees for all birds constructed based on hyplotypes indicated that the maternal origin of black-bone chickens is predominantly from three subspecies of red jungle fowl. These results provide basic data useful for protection of black-bone chickens and help determine the origin of domestic chickens.

Applications of Population Genetics to Animal Breeding, from Wright, Fisher and Lush to Genomic Prediction

PubMed Central

Hill, William G.

2014-01-01

Although animal breeding was practiced long before the science of genetics and the relevant disciplines of population and quantitative genetics were known, breeding programs have mainly relied on simply selecting and mating the best individuals on their own or relatives’ performance. This is based on sound quantitative genetic principles, developed and expounded by Lush, who attributed much of his understanding to Wright, and formalized in Fisher’s infinitesimal model. Analysis at the level of individual loci and gene frequency distributions has had relatively little impact. Now with access to genomic data, a revolution in which molecular information is being used to enhance response with “genomic selection” is occurring. The predictions of breeding value still utilize multiple loci throughout the genome and, indeed, are largely compatible with additive and specifically infinitesimal model assumptions. I discuss some of the history and genetic issues as applied to the science of livestock improvement, which has had and continues to have major spin-offs into ideas and applications in other areas. PMID:24395822

Accuracies of genomic breeding values in American Angus beef cattle using K-means clustering for cross-validation.

PubMed

Saatchi, Mahdi; McClure, Mathew C; McKay, Stephanie D; Rolf, Megan M; Kim, JaeWoo; Decker, Jared E; Taxis, Tasia M; Chapple, Richard H; Ramey, Holly R; Northcutt, Sally L; Bauck, Stewart; Woodward, Brent; Dekkers, Jack C M; Fernando, Rohan L; Schnabel, Robert D; Garrick, Dorian J; Taylor, Jeremy F

2011-11-28

Genomic selection is a recently developed technology that is beginning to revolutionize animal breeding. The objective of this study was to estimate marker effects to derive prediction equations for direct genomic values for 16 routinely recorded traits of American Angus beef cattle and quantify corresponding accuracies of prediction. Deregressed estimated breeding values were used as observations in a weighted analysis to derive direct genomic values for 3570 sires genotyped using the Illumina BovineSNP50 BeadChip. These bulls were clustered into five groups using K-means clustering on pedigree estimates of additive genetic relationships between animals, with the aim of increasing within-group and decreasing between-group relationships. All five combinations of four groups were used for model training, with cross-validation performed in the group not used in training. Bivariate animal models were used for each trait to estimate the genetic correlation between deregressed estimated breeding values and direct genomic values. Accuracies of direct genomic values ranged from 0.22 to 0.69 for the studied traits, with an average of 0.44. Predictions were more accurate when animals within the validation group were more closely related to animals in the training set. When training and validation sets were formed by random allocation, the accuracies of direct genomic values ranged from 0.38 to 0.85, with an average of 0.65, reflecting the greater relationship between animals in training and validation. The accuracies of direct genomic values obtained from training on older animals and validating in younger animals were intermediate to the accuracies obtained from K-means clustering and random clustering for most traits. The genetic correlation between deregressed estimated breeding values and direct genomic values ranged from 0.15 to 0.80 for the traits studied. These results suggest that genomic estimates of genetic merit can be produced in beef cattle at a young age but the recurrent inclusion of genotyped sires in retraining analyses will be necessary to routinely produce for the industry the direct genomic values with the highest accuracy.

Accuracies of genomic breeding values in American Angus beef cattle using K-means clustering for cross-validation

PubMed Central

2011-01-01

Background Genomic selection is a recently developed technology that is beginning to revolutionize animal breeding. The objective of this study was to estimate marker effects to derive prediction equations for direct genomic values for 16 routinely recorded traits of American Angus beef cattle and quantify corresponding accuracies of prediction. Methods Deregressed estimated breeding values were used as observations in a weighted analysis to derive direct genomic values for 3570 sires genotyped using the Illumina BovineSNP50 BeadChip. These bulls were clustered into five groups using K-means clustering on pedigree estimates of additive genetic relationships between animals, with the aim of increasing within-group and decreasing between-group relationships. All five combinations of four groups were used for model training, with cross-validation performed in the group not used in training. Bivariate animal models were used for each trait to estimate the genetic correlation between deregressed estimated breeding values and direct genomic values. Results Accuracies of direct genomic values ranged from 0.22 to 0.69 for the studied traits, with an average of 0.44. Predictions were more accurate when animals within the validation group were more closely related to animals in the training set. When training and validation sets were formed by random allocation, the accuracies of direct genomic values ranged from 0.38 to 0.85, with an average of 0.65, reflecting the greater relationship between animals in training and validation. The accuracies of direct genomic values obtained from training on older animals and validating in younger animals were intermediate to the accuracies obtained from K-means clustering and random clustering for most traits. The genetic correlation between deregressed estimated breeding values and direct genomic values ranged from 0.15 to 0.80 for the traits studied. Conclusions These results suggest that genomic estimates of genetic merit can be produced in beef cattle at a young age but the recurrent inclusion of genotyped sires in retraining analyses will be necessary to routinely produce for the industry the direct genomic values with the highest accuracy. PMID:22122853

Breeding objectives for sheep should be customised depending on variation in pasture growth across years.

PubMed

Rose, G; Mulder, H A; Thompson, A N; van der Werf, J H J; van Arendonk, J A M

2015-08-01

Breeding programmes for livestock require economic weights for traits that reflect the most profitable animal in a given production system, which affect the response in each trait after selection. The profitability of sheep production systems is affected by changes in pasture growth as well as grain, meat and wool prices between seasons and across years. Annual pasture growth varies between regions within Australia's Mediterranean climate zone from low growth with long periods of drought to high growth with shorter periods of drought. Therefore, the objective of this study was to assess whether breeding objectives need to be adapted for regions, depending on how reliable the pasture growth is across years. We modelled farms with Merino sheep bred for wool and meat in 10 regions in Western Australia. Across these 10 regions, mean annual pasture growth decreased, and the CV of annual pasture growth increased as pasture growth for regions became less reliable. We calculated economic values for nine traits, optimising management across 11 years, including variation for pasture growth and wool, meat and grain prices between and within years from 2002 to 2012. These economic values were used to calculate responses to selection for each trait for the 10 regions. We identified two potential breeding objectives, one for regions with low or high reliability and the other for regions with medium reliability of pasture growth. Breeding objectives for high or low pasture growth reliability had more emphasis on live weight traits and number of lambs weaned. Breeding objectives for medium reliability of pasture growth had more emphasis on decreasing fibre diameter. Relative economic weights for fleece weight did not change across the regions. Regions with low or high pasture reliability had similar breeding objectives and response to selection, because the relationship between the economic values and CV of pasture growth were not linear for live weight traits and the number of lambs weaned. This non-linearity was caused by differences in distribution of pasture growth between regions, particularly during summer and autumn, when ewes were pregnant, with increases in energy requirements affecting the value of lambs weaned. In addition, increasing live weight increased the intake capacity of sheep, which meant that more poor quality pasture could be consumed during summer and autumn, which had more value in regions with low and high pasture reliability. We concluded that breeding values for sheep production systems should be customised depending on the reliability of pasture growth between years.

Evaluation of Columbia, USMARC-Composite, Suffolk, and Texel rams as terminal sires in an extensive rangeland production system: IV. Postfabrication carcass component weights.

PubMed

Mousel, M R; Notter, D R; Leeds, T D; Zerby, H N; Moeller, S J; Lewis, G S

2013-05-01

Postfabrication carcass component weights of 517 crossbred wether lambs were analyzed to evaluate 4 terminal-sire breeds. Wethers were produced over 3 yr from single-sire matings of 22 Columbia, 22 USMARC-Composite (Composite), 21 Suffolk, and 17 Texel rams to adult Rambouillet ewes. Lambs were reared to weaning in an extensive western rangeland production system and finished in a feedlot on a high-energy finishing diet. When wethers reached a mean BW of 54.4, 61.2, or 68.0 kg, they were transported to The Ohio State University abattoir for harvest. After refrigeration for approximately 24 h, chilled carcass weight (CCW) was measured, carcasses were fabricated according to Style A of Institutional Meat Purchase Specifications, and postfabrication weights were recorded. At comparable numbers of days on feed, Suffolk-sired lambs had heavier (P < 0.04) neck, breast, shoulder, foreshank, rack, loin, leg, sirloin, roast-ready rack, trimmed loin, and boneless leg cuts than progeny of the other sire breeds. Boneless sirloins were heavier (P < 0.01) for Suffolk-sired than Composite-sired lambs but did not differ from those for Columbia- or Texel-sired lambs. Columbia- and Suffolk-sired lambs had heavier (P < 0.01) hindshanks than Texel-sired lambs. Suffolk-sired lambs had heavier (P < 0.01) high-value cuts (rack, loin, leg, and sirloin) and trimmed high-value cuts than progeny of the other sire breeds. Cutting loss (CCW - wholesale cut weights) and high-value trimming loss were greatest (P < 0.02) for Suffolk-sired lambs and least for Texel- and Composite-sired lambs. Sire breed did not affect (P > 0.06) flank weight. Data adjusted to comparable CCW reduced the number of significant sire-breed effects and changed sire-breed rankings of carcass component weights, for which sire breeds differed. After adjusting, Suffolk-sired lambs had lighter (P < 0.05) loins than Columbia- and Composite-sired lambs, Composite-sired lambs had heavier (P < 0.05) high-value cuts than Suffolk-sired lambs, and Suffolk- and Columbia-sired lambs had heavier (P < 0.05) necks than Texel-sired lambs. At predicted backfat thickness of 6.6 mm, Composite-sired lambs had a greater (P < 0.05) percentage of high-value cuts than Suffolk-sired lambs before but not after trimming. Producers can use these results to select terminal-sire breeds that will complement their production system and improve lamb value.

Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

PubMed

Spindel, Jennifer; Begum, Hasina; Akdemir, Deniz; Virk, Parminder; Collard, Bertrand; Redoña, Edilberto; Atlin, Gary; Jannink, Jean-Luc; McCouch, Susan R

2015-02-01

Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.

Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines

PubMed Central

Spindel, Jennifer; Begum, Hasina; Akdemir, Deniz; Virk, Parminder; Collard, Bertrand; Redoña, Edilberto; Atlin, Gary; Jannink, Jean-Luc; McCouch, Susan R.

2015-01-01

Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline. PMID:25689273

Molecular characterization of high performance inbred lines of Brazilian common beans.

PubMed

Cardoso, P C B; Veiga, M M; de Menezes, I P P; Valdisser, P A M R; Borba, T C O; Melo, L C; Del Peloso, M J; Brondani, C; Vianello, R P

2013-02-06

The identification of germplasm genetic variability in breeding programs of the common bean (Phaseolus vulgaris) is essential for determining the potential of each combination of parent plants to obtain superior genotypes. The present study aimed to estimated the extent of genetic diversity in 172 lineages and cultivars of the common bean by integrating five tests of value for cultivation and use (VCU) that were conducted over the last eight years by the breeding program of Embrapa Arroz e Feijão in Brazil. Nine multilocus genotyping systems composed of 36 fluorescent microsatellite markers distributed across 11 different chromosomes of the common bean were used, of which 24 were polymorphic in all trials. One hundred and eighty-seven alleles were identified, with an average of 7.79 alleles per locus and an average gene diversity of 0.65. The combined probability of identity for all loci was 1.32 x 10(-16). Lineages that are more genetically divergent between the selection cycles were identified, allowing the breeding program to develop a crossbreed between elite genotypes with a low degree of genetic relatedness. HE values ranged from 0.31 to 0.63, with a large reduction in the genetic base over successive selection cycles. The test showed a significant degree of differentiation (FST = 0.159). Private alleles (26%) were identified and can be directly incorporated into the gene pool of cultivated germplasm, thereby contributing effectively to the expansion of genetic diversity in this bean-breeding program.

An experimental validation of genomic selection in octoploid strawberry

PubMed Central

Gezan, Salvador A; Osorio, Luis F; Verma, Sujeet; Whitaker, Vance M

2017-01-01

The primary goal of genomic selection is to increase genetic gains for complex traits by predicting performance of individuals for which phenotypic data are not available. The objective of this study was to experimentally evaluate the potential of genomic selection in strawberry breeding and to define a strategy for its implementation. Four clonally replicated field trials, two in each of 2 years comprised of a total of 1628 individuals, were established in 2013–2014 and 2014–2015. Five complex yield and fruit quality traits with moderate to low heritability were assessed in each trial. High-density genotyping was performed with the Affymetrix Axiom IStraw90 single-nucleotide polymorphism array, and 17 479 polymorphic markers were chosen for analysis. Several methods were compared, including Genomic BLUP, Bayes B, Bayes C, Bayesian LASSO Regression, Bayesian Ridge Regression and Reproducing Kernel Hilbert Spaces. Cross-validation within training populations resulted in higher values than for true validations across trials. For true validations, Bayes B gave the highest predictive abilities on average and also the highest selection efficiencies, particularly for yield traits that were the lowest heritability traits. Selection efficiencies using Bayes B for parent selection ranged from 74% for average fruit weight to 34% for early marketable yield. A breeding strategy is proposed in which advanced selection trials are utilized as training populations and in which genomic selection can reduce the breeding cycle from 3 to 2 years for a subset of untested parents based on their predicted genomic breeding values. PMID:28090334

Effects of high density on spacing behaviour and reproduction in Akodon azarae: A fencing experiment

NASA Astrophysics Data System (ADS)

Ávila, Belén; Bonatto, Florencia; Priotto, José; Steinmann, Andrea R.

2016-01-01

We studied the short term spacing behavioural responses of Pampean grassland mouse (Akodon azarae) with regard to population density in four 0.25 ha enclosures (two control and two experimental) in the 2011 breeding season. Based on the hypothesis that A. azarae breeding females exhibit spacing behaviour, and breeding males show a fusion spatial response, we tested the following predictions: (1) home range size and intrasexual overlap degree of females are independent of population density values; (2) at high population density, home range size of males decreases and the intrasexual home range overlap degree increases. To determine if female reproductive success decreases at high population density, we analyzed pregnancy rate, size and weight of litters, and period until fecundation in both low and high enclosure population density. We found that both males and females varied their home range size in relation to population density. Although male home ranges were always bigger than those of females in populations with high density, home range sizes of both sexes decreased. Females kept exclusive home ranges independent of density values meanwhile males decreased home range overlap in high breeding density populations. Although females produced litters of similar size in both treatments, weight of litter, pregnant rate and period until fecundation varied in relation to population density. Our results did not support the hypothesis that at high density females of A. azarae exhibit spacing behaviour neither that males exhibit a fusion spatial response.

Genetic conditions of joint Nordic genetic evaluations of lifetime competition performance in warmblood sport horses.

PubMed

Viklund, Å; Furre, S; Eriksson, S; Vangen, O; Philipsson, J

2015-08-01

Breeding programmes for warmblood sport horses are similar in the Nordic countries Sweden, Denmark, Finland and Norway, and stallions of same origin are used. The aim was to investigate whether a joint Nordic genetic evaluation based on lifetime competition performance is feasible and beneficial for breeding competitive sport horses in the Nordic countries. Results for almost 45,000 horses in show jumping and 30,000 horses in dressage were available. The larger populations in Sweden and Denmark contributed with 85% of the results. Heritabilities and genetic correlations between performances in the different countries were estimated, and comparisons of accuracies of estimated breeding values (EBVs) and number of stallions with EBVs based on national or joint data were studied. The heritabilities ranged between 0.25 and 0.42 for show jumping and between 0.14 and 0.55 for dressage. The genetic correlations between competition performances in the Nordic countries were estimated to 0.63-1.00. EBVs based on joint data increased accuracies for EBVs for stallions by 38-81% and increased the number of available stallions with EBVs by 40-288%, compared to EBVs based on national data only. A joint Nordic genetic evaluation for sport horses is recommended. © 2015 Blackwell Verlag GmbH.

Breeding better cultivars, faster: applications of new technologies for the rapid deployment of superior horticultural tree crops

PubMed Central

van Nocker, Steve; Gardiner, Susan E

2014-01-01

Woody perennial plants, including trees that produce fruits and nuts of horticultural value, typically have long breeding cycles, and development and introduction of improved cultivars by plant breeders may require many breeding cycles and dozens of years. However, recent advances in biotechnologies and genomics have the potential to accelerate cultivar development greatly in all crops. This mini-review summarizes approaches to reduce the number and the duration of breeding cycles for horticultural tree crops, and outlines the challenges that remain to implement these into efficient breeding pipelines. PMID:26504538

Latitudinal variation in reproductive strategies by the migratory Louisiana Waterthrush

USGS Publications Warehouse

Mattsson, B.J.; Latta, S.C.; Cooper, R.J.; Mulvihill, R.S.

2011-01-01

We evaluated hypotheses that seek to explain breeding strategies of the Louisiana Waterthrush (Parkesia motacilla) that vary across a latitudinal gradient. On the basis of data from 418 nests of color-banded individuals in southwestern Pennsylvania and 700 km south in the Georgia Piedmont, we found that clutch size in replacement nests and probability of renesting were significantly greater in Pennsylvania (clutch size 4.4; renesting probability 0.66) than in Georgia (clutch size 3.8; renesting probability 0.54). Contrasts of the remaining measures of breeding were not statistically significant, and, in particular, mean daily nest survival in the two study areas was nearly identical (0.974 in Pennsylvania; 0.975 in Georgia). An individual-based model of fecundity (i.e., number of fledged young per adult female), predicted that approximately half of the females in both Pennsylvania and Georgia fledge at least one young, and mean values for fecundity in Pennsylvania and Georgia were 2.28 and 1.91, respectively. On the basis of greater support for the food-limitation hypothesis than for the season-length hypothesis, the trade-off between breeding in a region with more food but making a longer migration may be greater for waterthrushes breeding farther north than for those breeding farther south. ?? The Cooper Ornithological Society 2011.

Breeding synchrony in colonial birds: from local stress to global harmony.

PubMed

Jovani, Roger; Grimm, Volker

2008-07-07

Why and how birds in colonies often breed in striking synchrony is an unsolved question. In colonies, conspecific birds often destroy eggs and kill chicks, either intentionally or not. We propose that social tranquillity at the time of laying can be achieved if a bird's stress level is partly determined by the agitation of its neighbours. Moreover, we propose that this local process, together with environmental cues, can synchronize breeding between neighbours and through a whole colony. We tested our hypotheses using a generic individual-based model where the breeding predisposition of females was updated daily depending on an increase in the photoperiod (positively) and the stress level of neighbours: negatively if they were agitated, and positively otherwise. A female laid her eggs when her stress level fell to a critical value. Even giving only a low relevance to the neighbour's stress level was enough to synchronize the laying date of neighbours and also of a huge colony. Moreover, females bred in a safer environment, which is known from field studies to increase fitness. Our study highlights the power of local adaptive (individual) behaviour to create global (colony) patterns. We argue that collective patterns such as breeding synchrony in colonial birds could have simple adaptive individual-level explanations.

Genomic selection in sugar beet breeding populations

PubMed Central

2013-01-01

Background Genomic selection exploits dense genome-wide marker data to predict breeding values. In this study we used a large sugar beet population of 924 lines representing different germplasm types present in breeding populations: unselected segregating families and diverse lines from more advanced stages of selection. All lines have been intensively phenotyped in multi-location field trials for six agronomically important traits and genotyped with 677 SNP markers. Results We used ridge regression best linear unbiased prediction in combination with fivefold cross-validation and obtained high prediction accuracies for all except one trait. In addition, we investigated whether a calibration developed based on a training population composed of diverse lines is suited to predict the phenotypic performance within families. Our results show that the prediction accuracy is lower than that obtained within the diverse set of lines, but comparable to that obtained by cross-validation within the respective families. Conclusions The results presented in this study suggest that a training population derived from intensively phenotyped and genotyped diverse lines from a breeding program does hold potential to build up robust calibration models for genomic selection. Taken together, our results indicate that genomic selection is a valuable tool and can thus complement the genomics toolbox in sugar beet breeding. PMID:24047500

Potential assessment of genome-wide association study and genomic selection in Japanese pear Pyrus pyrifolia

PubMed Central

Iwata, Hiroyoshi; Hayashi, Takeshi; Terakami, Shingo; Takada, Norio; Sawamura, Yutaka; Yamamoto, Toshiya

2013-01-01

Although the potential of marker-assisted selection (MAS) in fruit tree breeding has been reported, bi-parental QTL mapping before MAS has hindered the introduction of MAS to fruit tree breeding programs. Genome-wide association studies (GWAS) are an alternative to bi-parental QTL mapping in long-lived perennials. Selection based on genomic predictions of breeding values (genomic selection: GS) is another alternative for MAS. This study examined the potential of GWAS and GS in pear breeding with 76 Japanese pear cultivars to detect significant associations of 162 markers with nine agronomic traits. We applied multilocus Bayesian models accounting for ordinal categorical phenotypes for GWAS and GS model training. Significant associations were detected at harvest time, black spot resistance and the number of spurs and two of the associations were closely linked to known loci. Genome-wide predictions for GS were accurate at the highest level (0.75) in harvest time, at medium levels (0.38–0.61) in resistance to black spot, firmness of flesh, fruit shape in longitudinal section, fruit size, acid content and number of spurs and at low levels (<0.2) in all soluble solid content and vigor of tree. Results suggest the potential of GWAS and GS for use in future breeding programs in Japanese pear. PMID:23641189

A proposed selection index for feedlot profitability based on estimated breeding values.

PubMed

van der Westhuizen, R R; van der Westhuizen, J

2009-04-22

It is generally accepted that feed intake and growth (gain) are the most important economic components when calculating profitability in a growth test or feedlot. We developed a single post-weaning growth (feedlot) index based on the economic values of different components. Variance components, heritabilities and genetic correlations for and between initial weight (IW), final weight (FW), feed intake (FI), and shoulder height (SHD) were estimated by multitrait restricted maximum likelihood procedures. The estimated breeding values (EBVs) and the economic values for IW, FW and FI were used in a selection index to estimate a post-weaning or feedlot profitability value. Heritabilities for IW, FW, FI, and SHD were 0.41, 0.40, 0.33, and 0.51, respectively. The highest genetic correlations were 0.78 (between IW and FW) and 0.70 (between FI and FW). EBVs were used in a selection index to calculate a single economical value for each animal. This economic value is an indication of the gross profitability value or the gross test value (GTV) of the animal in a post-weaning growth test. GTVs varied between -R192.17 and R231.38 with an average of R9.31 and a standard deviation of R39.96. The Pearson correlations between EBVs (for production and efficiency traits) and GTV ranged from -0.51 to 0.68. The lowest correlation (closest to zero) was 0.26 between the Kleiber ratio and GTV. Correlations of 0.68 and -0.51 were estimated between average daily gain and GTV and feed conversion ratio and GTV, respectively. These results showed that it is possible to select for GTV. The selection index can benefit feedlotting in selecting offspring of bulls with high GTVs to maximize profitability.

Implications of the difference between true and predicted breeding values for the study of natural selection and micro-evolution.

PubMed

Postma, E

2006-03-01

The ability to predict individual breeding values in natural populations with known pedigrees has provided a powerful tool to separate phenotypic values into their genetic and environmental components in a nonexperimental setting. This has allowed sophisticated analyses of selection, as well as powerful tests of evolutionary change and differentiation. To date, there has, however, been no evaluation of the reliability or potential limitations of the approach. In this article, I address these gaps. In particular, I emphasize the differences between true and predicted breeding values (PBVs), which as yet have largely been ignored. These differences do, however, have important implications for the interpretation of, firstly, the relationship between PBVs and fitness, and secondly, patterns in PBVs over time. I subsequently present guidelines I believe to be essential in the formulation of the questions addressed in studies using PBVs, and I discuss possibilities for future research.

Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data

USDA-ARS?s Scientific Manuscript database

Black raspberry (Rubus occidentalis L.) is a niche fruit crop valued for its flavour and potential health benefits. The improvement of fruit and cane characteristics via molecular breeding technologies has been hindered by the lack of a high-quality reference genome. The recently released draft geno...

The accuracies of DNA-based estimates of genetic merit derived from Angus or multibreed beef cattle training populations

USDA-ARS?s Scientific Manuscript database

Several organizations have developed prediction models for molecular breeding values (MBV) for quantitative growth and carcass traits in beef cattle using BovineSNP50 genotypes and phenotypic or EBV data. MBV for Angus cattle have been developed by IGENITY, Pfizer Animal Genetics, and a collaboratio...

Optimization of genomic selection training populations with a genetic algorithm

USDA-ARS?s Scientific Manuscript database

In this article, we derive a computationally efficient statistic to measure the reliability of estimates of genetic breeding values for a fixed set of genotypes based on a given training set of genotypes and phenotypes. We adopt a genetic algorithm scheme to find a training set of certain size from ...

Genetic approaches refine ex situ lowland tapir (Tapirus terrestris) conservation.

PubMed

Gonçalves da Silva, Anders; Lalonde, Danielle R; Quse, Viviana; Shoemaker, Alan; Russello, Michael A

2010-01-01

Ex situ conservation management remains an important tool in the face of continued habitat loss and global environmental change. Here, we use microsatellite marker variation to evaluate conventional assumptions of pedigree-based ex situ population management and directly inform a captive lowland tapir breeding program within a range country. We found relatively high levels of genetic variation (N(total) = 41; mean H(E) = 0.67 across 10 variable loci) and little evidence for relatedness among founder individuals (N(founders) = 10; mean relatedness = -0.05). Seven of 29 putative parent-offspring relationships were excluded by parentage analysis based on allele sharing, and we identified 2 individuals of high genetic value to the population (mk

Large forest patches promote breeding success of a terrestrial mammal in urban landscapes.

PubMed

Soga, Masashi; Koike, Shinsuke

2013-01-01

Despite a marked increase in the focus toward biodiversity conservation in fragmented landscapes, studies that confirm species breeding success are scarce and limited. In this paper, we asked whether local (area of forest patches) and landscape (amount of suitable habitat surrounding of focal patches) factors affect the breeding success of raccoon dogs (Nyctereutes procyonoides) in Tokyo, Central Japan. The breeding success of raccoon dogs is easy to judge as adults travel with pups during the breeding season. We selected 21 forest patches (3.3-797.8 ha) as study sites. In each forest patch, we used infra-red-triggered cameras for a total of 60 camera days per site. We inspected each photo to determine whether it was of an adult or a pup. Although we found adult raccoon dogs in all 21 forest patches, pups were found only in 13 patches. To estimate probability of occurrence and detection for raccoon in 21 forest fragments, we used single season site occupancy models in PRESENCE program. Model selection based on AIC and model averaging showed that the occupancy probability of pups was positively affected by patch area. This result suggests that large forests improve breeding success of raccoon dogs. A major reason for the low habitat value of small, isolated patches may be the low availability of food sources and the high risk of being killed on the roads in such areas. Understanding the effects of local and landscape parameters on species breeding success may help us to devise and implement effective long-term conservation and management plans.

Genetic Gain and Inbreeding from Genomic Selection in a Simulated Commercial Breeding Program for Perennial Ryegrass.

PubMed

Lin, Zibei; Cogan, Noel O I; Pembleton, Luke W; Spangenberg, German C; Forster, John W; Hayes, Ben J; Daetwyler, Hans D

2016-03-01

Genomic selection (GS) provides an attractive option for accelerating genetic gain in perennial ryegrass () improvement given the long cycle times of most current breeding programs. The present study used simulation to investigate the level of genetic gain and inbreeding obtained from GS breeding strategies compared with traditional breeding strategies for key traits (persistency, yield, and flowering time). Base population genomes were simulated through random mating for 60,000 generations at an effective population size of 10,000. The degree of linkage disequilibrium (LD) in the resulting population was compared with that obtained from empirical studies. Initial parental varieties were simulated to match diversity of current commercial cultivars. Genomic selection was designed to fit into a company breeding program at two selection points in the breeding cycle (spaced plants and miniplot). Genomic estimated breeding values (GEBVs) for productivity traits were trained with phenotypes and genotypes from plots. Accuracy of GEBVs was 0.24 for persistency and 0.36 for yield for single plants, while for plots it was lower (0.17 and 0.19, respectively). Higher accuracy of GEBVs was obtained for flowering time (up to 0.7), partially as a result of the larger reference population size that was available from the clonal row stage. The availability of GEBVs permit a 4-yr reduction in cycle time, which led to at least a doubling and trebling genetic gain for persistency and yield, respectively, than the traditional program. However, a higher rate of inbreeding per cycle among varieties was also observed for the GS strategy. Copyright © 2016 Crop Science Society of America.

Using resampling to assess reliability of audio-visual survey strategies for marbled murrelets at inland forest sites

USGS Publications Warehouse

Jodice, Patrick G.R.; Garman, S.L.; Collopy, Michael W.

2001-01-01

Marbled Murrelets (Brachyramphus marmoratus) are threatened seabirds that nest in coastal old-growth coniferous forests throughout much of their breeding range. Currently, observer-based audio-visual surveys are conducted at inland forest sites during the breeding season primarily to determine nesting distribution and breeding status and are being used to estimate temporal or spatial trends in murrelet detections. Our goal was to assess the feasibility of using audio-visual survey data for such monitoring. We used an intensive field-based survey effort to record daily murrelet detections at seven survey stations in the Oregon Coast Range. We then used computer-aided resampling techniques to assess the effectiveness of twelve survey strategies with varying scheduling and a sampling intensity of 4-14 surveys per breeding season to estimate known means and SDs of murrelet detections. Most survey strategies we tested failed to provide estimates of detection means and SDs that were within A?20% of actual means and SDs. Estimates of daily detections were, however, frequently estimated to within A?50% of field data with sampling efforts of 14 days/breeding season. Additional resampling analyses with statistically generated detection data indicated that the temporal variability in detection data had a great effect on the reliability of the mean and SD estimates calculated from the twelve survey strategies, while the value of the mean had little effect. Effectiveness at estimating multi-year trends in detection data was similarly poor, indicating that audio-visual surveys might be reliably used to estimate annual declines in murrelet detections of the order of 50% per year.

Using multi-species occupancy models in structured decision making on managed lands

USGS Publications Warehouse

Sauer, John R.; Blank, Peter J.; Zipkin, Elise F.; Fallon, Jane E.; Fallon, Frederick W.

2013-01-01

Land managers must balance the needs of a variety of species when manipulating habitats. Structured decision making provides a systematic means of defining choices and choosing among alternative management options; implementation of a structured decision requires quantitative approaches to predicting consequences of management on the relevant species. Multi-species occupancy models provide a convenient framework for making structured decisions when the management objective is focused on a collection of species. These models use replicate survey data that are often collected on managed lands. Occupancy can be modeled for each species as a function of habitat and other environmental features, and Bayesian methods allow for estimation and prediction of collective responses of groups of species to alternative scenarios of habitat management. We provide an example of this approach using data from breeding bird surveys conducted in 2008 at the Patuxent Research Refuge in Laurel, Maryland, evaluating the effects of eliminating meadow and wetland habitats on scrub-successional and woodland-breeding bird species using summed total occupancy of species as an objective function. Removal of meadows and wetlands decreased value of an objective function based on scrub-successional species by 23.3% (95% CI: 20.3–26.5), but caused only a 2% (0.5, 3.5) increase in value of an objective function based on woodland species, documenting differential effects of elimination of meadows and wetlands on these groups of breeding birds. This approach provides a useful quantitative tool for managers interested in structured decision making.

M-mode and two-dimensional echocardiographic reference values for three Hungarian dog breeds: Hungarian Vizsla, Mudi and Hungarian Greyhound.

PubMed

Vörös, Károly; Hetyey, Csaba; Reiczigel, Jeno; Czirok, Gábor Nagy

2009-06-01

The aim of the study was to establish normal reference echocardiographic values for three Hungarian dog breeds, and to determine the potential dependence of intracardiac parameters on body weight, age and gender. M-mode and two-dimensional echocardiography were performed on 95 clinically healthy dogs including 45 Hungarian Vizslas, 28 Mudis and 22 Hungarian Greyhounds. Linear intracardiac measurements included interventricular septal thickness (IVS), left ventricular internal diameter (LVID), left ventricular posterior wall thickness (LVPW) both in systole and diastole, as well as left atrial internal diameter (LAD), and aortic diameter (AOD) in early diastole. Fractional shortening (FS), end-diastolic and end-systolic left ventricular volumes (EDV and ESV), as well as LAD:AOD ratio were calculated from the linear parameters. Mean, range and standard deviation of measurements were calculated for each breed. Body weight positively correlated in all three breeds with all left ventricular dimensions, such as IVS d , IVS s , LVID d , LVIDD s , LVPW d and LVPW s parameters. LA values showed positive correlations to body weight in all three breeds. AOD and LA demonstrated a positive correlation with body weight in Hungarian Vizslas and Mudis, whilst the LAD:AOD ratio was related to body weight only in Mudis. Gender did not correlate with any of the measured echocardiographic parameters in any breeds. In Mudis, a positive correlation was found between the LAD: AOD ratio and age, as well as between the LAD: AOD ratio and E point to septal separation (EPSS).

Endogenous contributions to egg protein formation in lesser scaup Aythya affinis

USGS Publications Warehouse

Cutting, Kyle A.; Hobson, Keith A.; Rotella, Jay J.; Warren, Jeffrey M.; Wainwright-de la Cruz, Susan E.; Takekawa, John Y.

2011-01-01

Lesser scaup Aythya affinis populations have declined throughout the North American continent for the last three decades. It has been hypothesized that the loss and degradation of staging habitats has resulted in reduced female body condition on the breeding grounds and a concomitant decline in productivity. We explored the importance of body (endogenous) reserves obtained prior to arrival on the breeding ground in egg protein formation in southwestern Montana during 2006–2008 using stable-carbon (δ13C) and nitrogen (δ15N) isotope analyses of scaup egg components, female tissue, and local prey items. From arrival on the breeding grounds through the egg-laying period, δ15N values of scaup red blood cells decreased while δ13C values became less variable; a pattern consistent with endogenous tissues equilibrating with local (freshwater) dietary sources. In 2006 and 2008, isotopic values for egg albumen and yolk protein indicated that most (>90%) protein used to produce these components was obtained on the breeding grounds. However, in 2007, a year with an exceptionally warm and dry spring, endogenous reserves contributed on average 41% of yolk and 29% of albumen. Results from this study suggest that female scaup can meet the protein needs of egg production largely from local dietary food sources. This highlights the importance of providing high-quality breeding habitats for scaup. Whether this pattern holds in areas with similar breeding season lengths but longer migration routes, such as those found in the western boreal forest, should be investigated.

Breed-specific reference intervals for assessing thyroid function in seven dog breeds.

PubMed

Hegstad-Davies, Rebecca L; Torres, Sheila M F; Sharkey, Leslie C; Gresch, Sarah C; Muñoz-Zanzi, Claudia A; Davies, Peter R

2015-11-01

Thyroxine (T4), free T4 (FT4), and thyrotropin (TSH) concentrations were measured in serum from 693 healthy representatives from 7 dog breeds (Alaskan Malamute, Collie, English Setter, Golden Retriever, Keeshond, Samoyed, or Siberian Husky) to determine whether breed-specific reference intervals (RIs) are warranted. Veterinarians reviewed the health history, performed a physical examination, and approved laboratory data for the enrolled dogs. Many purebred dogs had T4 and FT4 concentrations that were at, or below, the lower limits previously determined for non-breed-specific RIs. Mean concentrations of T4, FT4, and TSH varied significantly among breeds. The range of mean concentration of T4 (19.7 nmol/L [1.53 µg/dL] in English Setters to 29.0 nmol/L [2.25 µg/dL] in Keeshonds) and FT4 (12.6 pmol/L [0.98 ng/dL] in English Setters to 20.2 pmol/L [1.57 ng/dL] in Samoyeds) was considerable. Median TSH values ranged from 6.10 mIU/L (0.07 ng/mL; Alaskan Malamute and Golden Retriever) to 17.6 mIU/L (0.26 ng/mL; Collie). Mean T4 and FT4 concentrations were higher in females. Increasing age was associated with decreasing T4 and FT4, and increasing TSH concentration. The substantial ranges across breeds of measures of central tendency (mean, median) for all hormones indicate that breed-specific RIs are warranted. RIs encompassing the central 95% of reference values for all breeds combined, and for individual breeds, were calculated using nonparametric (TSH) and robust (T4, FT4) methods. Use of breed-specific RIs in combination with careful attention to the potential for pre-analytical and analytical variability in test results will improve thyroid function assessment in these breeds. © 2015 The Author(s).

Breeding status affects the hormonal and metabolic response to acute stress in a long-lived seabird, the king penguin.

PubMed

Viblanc, Vincent A; Gineste, Benoit; Robin, Jean-Patrice; Groscolas, René

2016-09-15

Stress responses are suggested to physiologically underlie parental decisions promoting the redirection of behaviour away from offspring care when survival is jeopardized (e.g., when facing a predator). Besides this classical view, the "brood-value hypothesis" suggests that parents' stress responses may be adaptively attenuated to increase fitness, ensuring continued breeding when the relative value of the brood is high. Here, we test the brood-value hypothesis in breeding king penguins (Aptenodytes patagonicus), long-lived seabirds for which the energy commitment to reproduction is high. We subjected birds at different breeding stages (courtship, incubation and chick brooding) to an acute 30-min capture stress and measured their hormonal (corticosterone, CORT) and metabolic (non-esterified fatty acid, NEFA) responses to stress. We found that CORT responses were markedly attenuated in chick-brooding birds when compared to earlier stages of breeding (courtship and incubation). In addition, NEFA responses appeared to be rapidly attenuated in incubating and brooding birds, but a progressive increase in NEFA plasma levels in courting birds suggested energy mobilization to deal with the threat. Our results support the idea that stress responses may constitute an important life-history mechanism mediating parental reproductive decisions in relation to their expected fitness outcome. Copyright © 2016 Elsevier Inc. All rights reserved.

Breeding bird use of and nesting success in exotic Russian olive in New Mexico

Treesearch

Scott H. Stoleson; Deborah M. Finch

2001-01-01

The exotic tree, Russian olive (Elaeagnus angustifolia), has invaded riparian zones throughout much of the western Unites States. Although promoted as a useful species for wildlife because of its abundant edible fruit, evidence for its value to breeding birds remains sparse. We compared relative rates of usage, nest success, and cowbird parasitism of birds breeding in...

Economic evaluation of alternative crossbreeding systems involving four breeds of swine. I. The simulation model.

PubMed

McLaren, D G; Buchanan, D S; Williams, J E

1987-10-01

A static, deterministic computer model, programmed in Microsoft Basic for IBM PC and Apple Macintosh computers, was developed to calculate production efficiency (cost per kg of product) for nine alternative types of crossbreeding system involving four breeds of swine. The model simulates efficiencies for four purebred and 60 alternative two-, three- and four-breed rotation, rotaterminal, backcross and static cross systems. Crossbreeding systems were defined as including all purebred, crossbred and commercial matings necessary to maintain a total of 10,000 farrowings. Driving variables for the model are mean conception rate at first service and for an 8-wk breeding season, litter size born, preweaning survival rate, postweaning average daily gain, feed-to-gain ratio and carcass backfat. Predictions are computed using breed direct genetic and maternal effects for the four breeds, plus individual, maternal and paternal specific heterosis values, input by the user. Inputs required to calculate the number of females farrowing in each sub-system include the proportion of males and females replaced each breeding cycle in purebred and crossbred populations, the proportion of male and female offspring in seedstock herds that become breeding animals, and the number of females per boar. Inputs required to calculate the efficiency of terminal production (cost-to-product ratio) for each sub-system include breeding herd feed intake, gilt development costs, feed costs and labor and overhead costs. Crossbreeding system efficiency is calculated as the weighted average of sub-system cost-to-product ratio values, weighting by the number of females farrowing in each sub-system.

Quantitative genetics of taura syndrome resistance in pacific white shrimp (penaeus vannamei): a cure model approach

PubMed Central

2011-01-01

Background In aquaculture breeding, resistance against infectious diseases is commonly assessed as time until death under exposure to a pathogen. For some diseases, a fraction of the individuals may appear as "cured" (non-susceptible), and the resulting survival time may thus be a result of two confounded underlying traits, i.e., endurance (individual hazard) and susceptibility (whether at risk or not), which may be accounted for by fitting a cure survival model. We applied a cure model to survival data of Pacific white shrimp (Penaeus vannamei) challenged with the Taura syndrome virus, which is one of the major pathogens of Panaeid shrimp species. Methods In total, 15,261 individuals of 513 full-sib families from three generations were challenge-tested in 21 separate tests (tanks). All challenge-tests were run until mortality naturally ceased. Time-until-event data were analyzed with a mixed cure survival model using Gibbs sampling, treating susceptibility and endurance as separate genetic traits. Results Overall mortality at the end of test was 28%, while 38% of the population was considered susceptible to the disease. The estimated underlying heritability was high for susceptibility (0.41 ± 0.07), but low for endurance (0.07 ± 0.03). Furthermore, endurance and susceptibility were distinct genetic traits (rg = 0.22 ± 0.25). Estimated breeding values for endurance and susceptibility were only moderately correlated (0.50), while estimated breeding values from classical models for analysis of challenge-test survival (ignoring the cured fraction) were closely correlated with estimated breeding values for susceptibility, but less correlated with estimated breeding values for endurance. Conclusions For Taura syndrome resistance, endurance and susceptibility are apparently distinct genetic traits. However, genetic evaluation of susceptibility based on the cure model showed clear associations with standard genetic evaluations that ignore the cure fraction for these data. Using the current testing design, genetic variation in observed survival time and absolute survival at the end of test were most likely dominated by genetic variation in susceptibility. If the aim is to reduce susceptibility, earlier termination of the challenge-test or back-truncation of the follow-up period should be avoided, as this may shift focus of selection towards endurance rather than susceptibility. PMID:21418636

Enhancing the value of the breeding bird survey: reply to Sauer et al. (2005)

Treesearch

Charles M. Francis; Jonathan Bart; Erica H. Dunn; Kenneth P. Burnham; C. John Ralph

2005-01-01

Bart et al (2004a) proposed several approaches for enhancing the considerable value of the Breeding Bird Survey (BBS). Sauer et al. (2005) critiqued some of these approaches, and emphasized alternative goals for the survey. We agree with many of the suggestions of Sauer et al. (2005); notably that multispecies, large-scale surveys such as the BBS are most valuable for...

An Age-Associated Decline in Thymic Output Differs in Dog Breeds According to Their Longevity.

PubMed

Holder, Angela; Mella, Stephanie; Palmer, Donald B; Aspinall, Richard; Catchpole, Brian

2016-01-01

The age associated decline in immune function is preceded in mammals by a reduction in thymic output. Furthermore, there is increasing evidence of a link between immune competence and lifespan. One approach to determining thymic output is to quantify signal joint T cell receptor excision circles (sj-TRECs), a method which has been developed and used in several mammalian species. Life expectancy and the rate of aging vary in dogs depending upon their breed. In this study, we quantified sj-TRECs in blood samples from dogs of selected breeds to determine whether there was a relationship between longevity and thymic output. In Labrador retrievers, a breed with a median expected lifespan of 11 years, there was an age-associated decline in sj-TREC values, with the greatest decline occurring before 5 years of age, but with sj-TREC still detectable in some geriatric animals, over 13 years of age. In large short-lived breeds (Burnese mountain dogs, Great Danes and Dogue de Bordeaux), the decline in sj-TREC values began earlier in life, compared with small long-lived breeds (Jack Russell terriers and Yorkshire terriers), and the presence of animals with undetectable sj-TRECs occurred at a younger age in the short-lived breeds. The study findings suggest that age-associated changes in canine sj-TRECs are related to breed differences in longevity, and this research highlights the use of dogs as a potential model of immunosenescence.

Accuracy of Predicted Genomic Breeding Values in Purebred and Crossbred Pigs.

PubMed

Hidalgo, André M; Bastiaansen, John W M; Lopes, Marcos S; Harlizius, Barbara; Groenen, Martien A M; de Koning, Dirk-Jan

2015-05-26

Genomic selection has been widely implemented in dairy cattle breeding when the aim is to improve performance of purebred animals. In pigs, however, the final product is a crossbred animal. This may affect the efficiency of methods that are currently implemented for dairy cattle. Therefore, the objective of this study was to determine the accuracy of predicted breeding values in crossbred pigs using purebred genomic and phenotypic data. A second objective was to compare the predictive ability of SNPs when training is done in either single or multiple populations for four traits: age at first insemination (AFI); total number of piglets born (TNB); litter birth weight (LBW); and litter variation (LVR). We performed marker-based and pedigree-based predictions. Within-population predictions for the four traits ranged from 0.21 to 0.72. Multi-population prediction yielded accuracies ranging from 0.18 to 0.67. Predictions across purebred populations as well as predicting genetic merit of crossbreds from their purebred parental lines for AFI performed poorly (not significantly different from zero). In contrast, accuracies of across-population predictions and accuracies of purebred to crossbred predictions for LBW and LVR ranged from 0.08 to 0.31 and 0.11 to 0.31, respectively. Accuracy for TNB was zero for across-population prediction, whereas for purebred to crossbred prediction it ranged from 0.08 to 0.22. In general, marker-based outperformed pedigree-based prediction across populations and traits. However, in some cases pedigree-based prediction performed similarly or outperformed marker-based prediction. There was predictive ability when purebred populations were used to predict crossbred genetic merit using an additive model in the populations studied. AFI was the only exception, indicating that predictive ability depends largely on the genetic correlation between PB and CB performance, which was 0.31 for AFI. Multi-population prediction was no better than within-population prediction for the purebred validation set. Accuracy of prediction was very trait-dependent. Copyright © 2015 Hidalgo et al.

Traditional and modern plant breeding methods with examples in rice (Oryza sativa L.).

PubMed

Breseghello, Flavio; Coelho, Alexandre Siqueira Guedes

2013-09-04

Plant breeding can be broadly defined as alterations caused in plants as a result of their use by humans, ranging from unintentional changes resulting from the advent of agriculture to the application of molecular tools for precision breeding. The vast diversity of breeding methods can be simplified into three categories: (i) plant breeding based on observed variation by selection of plants based on natural variants appearing in nature or within traditional varieties; (ii) plant breeding based on controlled mating by selection of plants presenting recombination of desirable genes from different parents; and (iii) plant breeding based on monitored recombination by selection of specific genes or marker profiles, using molecular tools for tracking within-genome variation. The continuous application of traditional breeding methods in a given species could lead to the narrowing of the gene pool from which cultivars are drawn, rendering crops vulnerable to biotic and abiotic stresses and hampering future progress. Several methods have been devised for introducing exotic variation into elite germplasm without undesirable effects. Cases in rice are given to illustrate the potential and limitations of different breeding approaches.

Phenotypic hip and elbow dysplasia trends in Rottweilers and Labrador retrievers in South Africa (2007-2015): Are we making progress?

PubMed

Kirberger, Robert M

2017-11-22

Canine hip and elbow dysplasia are major orthopaedic problems prevalent the world over, and South Africa is no exception. Hip and elbow dysplasia phenotypic status is certified by a number of different radiographic schemes in the world. South Africa uses the Fédération Cynologique Internationale system to certify hips, and the International Elbow Working Group scheme to certify elbows. One way of reducing these often crippling conditions is by selective breeding using only dogs with no or marginal dysplastic joints. In South Africa, only seven breeds, including the Rottweiler, have breeding restrictions for hip dysplasia. There are no such restrictions for elbow dysplasia. This study assessed the prevalence of hip and elbow dysplasia over a 9-year-period in the Rottweiler and the Labrador retriever in South Africa as evaluated by official national scrutineers. Records from 1148 Rottweilers and 909 Labrador retrievers were obtained and were graded as normal or dysplastic, and numerical values were also evaluated. Data were compared between the two breeds, males and females as well as over time and were compared with similar data of the Orthopaedic Foundation for Animals in the United States. The prevalence values for hip dysplasia in Rottweilers and Labrador retrievers were 22% and 31%, respectively, whereas for elbow dysplasia the values were 39% and 19%, respectively. In Labrador retrievers, this incidence was much higher than in the American population. Rottweiler hip and elbow dysplasia numerical scores significantly improved over time, whereas in Labrador retrievers, only hip dysplasia showed a minor but significant improvement. This study proved that prescribing minimum breeding requirements, as in the Rottweiler in this study, significantly improved the breeding stock, suggesting that minimum hip and elbow breeding requirements should be initiated for all breeds at risk of these often crippling conditions.

Genetic diversity and phylogenetic relationships in local cattle breeds of Senegal based on autosomal microsatellite markers

PubMed Central

Ndiaye, Ndèye Penda; Sow, Adama; Dayo, Guiguigbaza-Kossigan; Ndiaye, Saliou; Sawadogo, Germain Jerôme; Sembène, Mbacké

2015-01-01

Aim: In Senegal, uncontrolled cross-breeding of cattle breeds and changes in production systems are assumed to lead to an increase of gene flow between populations. This might constitute a relevant threat to livestock improvement. Therewith, this study was carried out to assess the current genetic diversity and the phylogenetic relationships of the four native Senegalese cattle breeds (Gobra zebu, Maure zebu, Djakoré, and N’Dama). Methods: Genomic DNA was isolated from blood samples of 120 unrelated animals collected from three agro-ecological areas of Senegal according to their phenotypic traits. Genotyping was done using 11 specific highly polymorphic microsatellite makers recommended by Food and Agriculture Organization. The basic measures of genetic variation and phylogenetic trees were computed using bioinformatics’ software. Results: A total of 115 alleles were identified with a number of alleles (Na) at one locus ranging from 6 to 16. All loci were polymorphic with a mean polymorphic information content of 0.76. The mean allelic richness (Rs) lay within the narrow range of 5.14 in N’Dama taurine to 6.10 in Gobra zebu. While, the expected heterozygosity (HE) per breed was high in general with an overall mean of 0.76±0.04. Generally, the heterozygote deficiency (FIS) of 0.073±0.026 was relatively due to inbreeding among these cattle breeds or the occurrence of population substructure. The high values of allelic and gene diversity showed that Senegalese native cattle breeds represented an important reservoir of genetic variation. The genetic distances and clustering trees concluded that the N’Dama cattle were most distinct among the investigated cattle populations. So, the principal component analyses showed qualitatively that there was an intensive genetic admixture between the Gobra zebu and Maure zebu breeds. Conclusions: The broad genetic diversity in Senegalese cattle breeds will allow for greater opportunities for improvement of productivity and adaptation relative to global changes. For the development of sustainable breeding and crossbreeding programs of Senegalese local breeds, effective management is needed towards genetic selection and transhumance to ensure their long-term survival. PMID:27047188

Prediction of genetic values of quantitative traits with epistatic effects in plant breeding populations.

PubMed

Wang, D; Salah El-Basyoni, I; Stephen Baenziger, P; Crossa, J; Eskridge, K M; Dweikat, I

2012-11-01

Though epistasis has long been postulated to have a critical role in genetic regulation of important pathways as well as provide a major source of variation in the process of speciation, the importance of epistasis for genomic selection in the context of plant breeding is still being debated. In this paper, we report the results on the prediction of genetic values with epistatic effects for 280 accessions in the Nebraska Wheat Breeding Program using adaptive mixed least absolute shrinkage and selection operator (LASSO). The development of adaptive mixed LASSO, originally designed for association mapping, for the context of genomic selection is reported. The results show that adaptive mixed LASSO can be successfully applied to the prediction of genetic values while incorporating both marker main effects and epistatic effects. Especially, the prediction accuracy is substantially improved by the inclusion of two-locus epistatic effects (more than onefold in some cases as measured by cross-validation correlation coefficient), which is observed for multiple traits and planting locations. This points to significant potential in using non-additive genetic effects for genomic selection in crop breeding practices.

Carcase weight and dressing percentage are increased using Australian Sheep Breeding Values for increased weight and muscling and reduced fat depth.

PubMed

Gardner, G E; Williams, A; Ball, A J; Jacob, R H; Refshauge, G; Hocking Edwards, J; Behrendt, R; Pethick, D W

2015-01-01

Pre-slaughter live weight, dressing percentage, and hot standard carcase weight (HCWT) from the 2007, 2008, 2009 and 2010 birth-years of the Information Nucleus Flock Lambs (n=7325) were analysed using linear mixed effects models. Increasing the sire breeding value for post-weaning weight (PWWT), and c-site eye muscle depth (PEMD), and reducing the sire breeding value for fat depth (PFAT) all had positive impacts on HCWT. The magnitude of the PWWT effect was greater in pure bred Merinos compared to Maternal and Terminal sired progeny. The improved HCWT resulting from increased PEMD was entirely due to its impact on improving dressing percentage, given that it had no impact on pre-slaughter live weight. There were marked differences between sire types and dam breeds, with pure-bred Merinos having lower pre-slaughter weight, reduced dressing percentage, and lower HCWT than progeny from Terminal and Maternal sired lambs or progeny from Maternal (1st cross) dams. Copyright © 2014 Elsevier Ltd. All rights reserved.

Relationships among stallion fertility and semen traits using estimated breeding values of German Warmblood stallions.

PubMed

Gottschalk, Maren; Sieme, Harald; Martinsson, Gunilla; Distl, Ottmar

2017-02-01

A high quality of stallion semen is of particular importance for maximum reproductive efficiency. In the present study, we estimated the relationships among estimated breeding values (EBVs) of semen traits and EBVs for the paternal component of the pregnancy rate per estrus cycle (EBV-PAT) for 100 German Warmblood stallions using correlation and general linear model analyses. The most highly correlated sperm quality trait was total number of progressively motile sperm (r = 0.36). EBV-PAT was considered in three classes with stallions 1 SD below (<80), around (80-120), and above (>120) the population mean of 100. The general linear model analysis showed significant effects for EBVs of all semen traits. EBVs of sperm quality traits greater than 100 to 110 were indicative for EBV-PAT greater than 120. Recommendations for breeding soundness examinations on the basis of the assessments of sperm quality traits and estimation of breeding values seem to be an option to support breeders to improve stallion fertility in the present and future stallion generation. Copyright © 2016 Elsevier Inc. All rights reserved.

Domestic estimated breeding values and genomic enhanced breeding values of bulls in comparison with their foreign genomic enhanced breeding values.

PubMed

Přibyl, J; Bauer, J; Čermák, V; Pešek, P; Přibylová, J; Šplíchal, J; Vostrá-Vydrová, H; Vostrý, L; Zavadilová, L

2015-10-01

Estimated breeding values (EBVs) and genomic enhanced breeding values (GEBVs) for milk production of young genotyped Holstein bulls were predicted using a conventional BLUP - Animal Model, a method fitting regression coefficients for loci (RRBLUP), a method utilizing the realized genomic relationship matrix (GBLUP), by a single-step procedure (ssGBLUP) and by a one-step blending procedure. Information sources for prediction were the nation-wide database of domestic Czech production records in the first lactation combined with deregressed proofs (DRP) from Interbull files (August 2013) and domestic test-day (TD) records for the first three lactations. Data from 2627 genotyped bulls were used, of which 2189 were already proven under domestic conditions. Analyses were run that used Interbull values for genotyped bulls only or that used Interbull values for all available sires. Resultant predictions were compared with GEBV of 96 young foreign bulls evaluated abroad and whose proofs were from Interbull method GMACE (August 2013) on the Czech scale. Correlations of predictions with GMACE values of foreign bulls ranged from 0.33 to 0.75. Combining domestic data with Interbull EBVs improved prediction of both EBV and GEBV. Predictions by Animal Model (traditional EBV) using only domestic first lactation records and GMACE values were correlated by only 0.33. Combining the nation-wide domestic database with all available DRP for genotyped and un-genotyped sires from Interbull resulted in an EBV correlation of 0.60, compared with 0.47 when only Interbull data were used. In all cases, GEBVs had higher correlations than traditional EBVs, and the highest correlations were for predictions from the ssGBLUP procedure using combined data (0.75), or with all available DRP from Interbull records only (one-step blending approach, 0.69). The ssGBLUP predictions using the first three domestic lactation records in the TD model were correlated with GMACE predictions by 0.69, 0.64 and 0.61 for milk yield, protein yield and fat yield, respectively.

Genomic selection models double the accuracy of predicted breeding values for bacterial cold water disease resistance compared to a traditional pedigree-based model in rainbow trout aquaculture.

PubMed

Vallejo, Roger L; Leeds, Timothy D; Gao, Guangtu; Parsons, James E; Martin, Kyle E; Evenhuis, Jason P; Fragomeni, Breno O; Wiens, Gregory D; Palti, Yniv

2017-02-01

Previously, we have shown that bacterial cold water disease (BCWD) resistance in rainbow trout can be improved using traditional family-based selection, but progress has been limited to exploiting only between-family genetic variation. Genomic selection (GS) is a new alternative that enables exploitation of within-family genetic variation. We compared three GS models [single-step genomic best linear unbiased prediction (ssGBLUP), weighted ssGBLUP (wssGBLUP), and BayesB] to predict genomic-enabled breeding values (GEBV) for BCWD resistance in a commercial rainbow trout population, and compared the accuracy of GEBV to traditional estimates of breeding values (EBV) from a pedigree-based BLUP (P-BLUP) model. We also assessed the impact of sampling design on the accuracy of GEBV predictions. For these comparisons, we used BCWD survival phenotypes recorded on 7893 fish from 102 families, of which 1473 fish from 50 families had genotypes [57 K single nucleotide polymorphism (SNP) array]. Naïve siblings of the training fish (n = 930 testing fish) were genotyped to predict their GEBV and mated to produce 138 progeny testing families. In the following generation, 9968 progeny were phenotyped to empirically assess the accuracy of GEBV predictions made on their non-phenotyped parents. The accuracy of GEBV from all tested GS models were substantially higher than the P-BLUP model EBV. The highest increase in accuracy relative to the P-BLUP model was achieved with BayesB (97.2 to 108.8%), followed by wssGBLUP at iteration 2 (94.4 to 97.1%) and 3 (88.9 to 91.2%) and ssGBLUP (83.3 to 85.3%). Reducing the training sample size to n = ~1000 had no negative impact on the accuracy (0.67 to 0.72), but with n = ~500 the accuracy dropped to 0.53 to 0.61 if the training and testing fish were full-sibs, and even substantially lower, to 0.22 to 0.25, when they were not full-sibs. Using progeny performance data, we showed that the accuracy of genomic predictions is substantially higher than estimates obtained from the traditional pedigree-based BLUP model for BCWD resistance. Overall, we found that using a much smaller training sample size compared to similar studies in livestock, GS can substantially improve the selection accuracy and genetic gains for this trait in a commercial rainbow trout breeding population.

Whole genome population genetics analysis of Sudanese goats identifies regions harboring genes associated with major traits.

PubMed

Rahmatalla, Siham A; Arends, Danny; Reissmann, Monika; Said Ahmed, Ammar; Wimmers, Klaus; Reyer, Henry; Brockmann, Gudrun A

2017-10-23

Sudan is endowed with a variety of indigenous goat breeds which are used for meat and milk production and which are well adapted to the local environment. The aim of the present study was to determine the genetic diversity and relationship within and between the four main Sudanese breeds of Nubian, Desert, Taggar and Nilotic goats. Using the 50 K SNP chip, 24 animals of each breed were genotyped. More than 96% of high quality SNPs were polymorphic with an average minor allele frequency of 0.3. In all breeds, no significant difference between observed (0.4) and expected (0.4) heterozygosity was found and the inbreeding coefficients (F IS ) did not differ from zero. F st coefficients for the genetic distance between breeds also did not significantly deviate from zero. In addition, the analysis of molecular variance revealed that 93% of the total variance in the examined population can be explained by differences among individuals, while only 7% result from differences between the breeds. These findings provide evidence for high genetic diversity and little inbreeding within breeds on one hand, and low diversity between breeds on the other hand. Further examinations using Nei's genetic distance and STRUCTURE analysis clustered Taggar goats distinct from the other breeds. In a principal component (PC) analysis, PC1 could separate Taggar, Nilotic and a mix of Nubian and Desert goats into three groups. The SNPs that contributed strongly to PC1 showed high F st values in Taggar goat versus the other goat breeds. PCA allowed us to identify target genomic regions which contain genes known to influence growth, development, bone formation and the immune system. The information on the genetic variability and diversity in this study confirmed that Taggar goat is genetically different from the other goat breeds in Sudan. The SNPs identified by the first principal components show high F st values in Taggar goat and allowed to identify candidate genes which can be used in the development of breed selection programs to improve local breeds and find genetic factors contributing to the adaptation to harsh environments.

Breed effect between Mos rooster (Galician indigenous breed) and Sasso T-44 line and finishing feed effect of commercial fodder or corn.

PubMed

Franco, D; Rois, D; Vázquez, J A; Purriños, L; González, R; Lorenzo, J M

2012-02-01

The aim of this research was to study the Mos rooster breed growth performance, carcass, and meat quality. The breed effect (Mos vs. Sasso T-44) and finishing feed in the last month (fodder vs. corn) on animal growth, carcass characteristics, meat quality, and fatty and amino acid profiles were studied using a randomized block design with initial weight as covariance. In total, 80 roosters (n = 30 of Sasso T-44 line and n = 50 of Mos breed) were used. They were separated by breed and allocated to 2 feeding treatment groups (concentrate and corn). Each feeding treatment group consisted of 15 and 25 roosters, for Sasso T-44 line and Mos breed, respectively. Finishing feeding did not affect growth parameters in the 2 genotypes of rooster tested (P > 0.05). Nonetheless, the comparison between both types of roosters led to significant differences in growth parameters (P < 0.05). Regarding carcass characteristics, no significant influences of finishing feeding treatment (P > 0.05) were found, and as expected, carcass weight clearly differed between genotypes due to the lower growth rate of Mos roosters. However, drumstick, thigh, and wing percentages were greater in the Mos breed than in the hybrid line. In color instrumental traits, roosters feeding with corn showed breast meat with significantly (P < 0.001) higher a* and b* values than those of cocks feeding with commercial fodder. Values of shear force were less than 2 kg for both genotypes, thus it can be classified as very tender meat. Finishing with corn significantly increased (P < 0.001) the polyunsaturated fatty acid content in the breast; the Mos breed had a polyunsaturated to saturated fatty acid ratio of 0.73. The amino acid profile of the indigenous breed was not similar to that of the commercial strain. Finishing feeding treatment had a greater influence than breed effect on amino acid profile.

Preselection statistics and Random Forest classification identify population informative single nucleotide polymorphisms in cosmopolitan and autochthonous cattle breeds.

PubMed

Bertolini, F; Galimberti, G; Schiavo, G; Mastrangelo, S; Di Gerlando, R; Strillacci, M G; Bagnato, A; Portolano, B; Fontanesi, L

2018-01-01

Commercial single nucleotide polymorphism (SNP) arrays have been recently developed for several species and can be used to identify informative markers to differentiate breeds or populations for several downstream applications. To identify the most discriminating genetic markers among thousands of genotyped SNPs, a few statistical approaches have been proposed. In this work, we compared several methods of SNPs preselection (Delta, F st and principal component analyses (PCA)) in addition to Random Forest classifications to analyse SNP data from six dairy cattle breeds, including cosmopolitan (Holstein, Brown and Simmental) and autochthonous Italian breeds raised in two different regions and subjected to limited or no breeding programmes (Cinisara, Modicana, raised only in Sicily and Reggiana, raised only in Emilia Romagna). From these classifications, two panels of 96 and 48 SNPs that contain the most discriminant SNPs were created for each preselection method. These panels were evaluated in terms of the ability to discriminate as a whole and breed-by-breed, as well as linkage disequilibrium within each panel. The obtained results showed that for the 48-SNP panel, the error rate increased mainly for autochthonous breeds, probably as a consequence of their admixed origin lower selection pressure and by ascertaining bias in the construction of the SNP chip. The 96-SNP panels were generally more able to discriminate all breeds. The panel derived by PCA-chrom (obtained by a preselection chromosome by chromosome) could identify informative SNPs that were particularly useful for the assignment of minor breeds that reached the lowest value of Out Of Bag error even in the Cinisara, whose value was quite high in all other panels. Moreover, this panel contained also the lowest number of SNPs in linkage disequilibrium. Several selected SNPs are located nearby genes affecting breed-specific phenotypic traits (coat colour and stature) or associated with production traits. In general, our results demonstrated the usefulness of Random Forest in combination to other reduction techniques to identify population informative SNPs.

Object-Based Classification as an Alternative Approach to the Traditional Pixel-Based Classification to Identify Potential Habitat of the Grasshopper Sparrow

NASA Astrophysics Data System (ADS)

Jobin, Benoît; Labrecque, Sandra; Grenier, Marcelle; Falardeau, Gilles

2008-01-01

The traditional method of identifying wildlife habitat distribution over large regions consists of pixel-based classification of satellite images into a suite of habitat classes used to select suitable habitat patches. Object-based classification is a new method that can achieve the same objective based on the segmentation of spectral bands of the image creating homogeneous polygons with regard to spatial or spectral characteristics. The segmentation algorithm does not solely rely on the single pixel value, but also on shape, texture, and pixel spatial continuity. The object-based classification is a knowledge base process where an interpretation key is developed using ground control points and objects are assigned to specific classes according to threshold values of determined spectral and/or spatial attributes. We developed a model using the eCognition software to identify suitable habitats for the Grasshopper Sparrow, a rare and declining species found in southwestern Québec. The model was developed in a region with known breeding sites and applied on other images covering adjacent regions where potential breeding habitats may be present. We were successful in locating potential habitats in areas where dairy farming prevailed but failed in an adjacent region covered by a distinct Landsat scene and dominated by annual crops. We discuss the added value of this method, such as the possibility to use the contextual information associated to objects and the ability to eliminate unsuitable areas in the segmentation and land cover classification processes, as well as technical and logistical constraints. A series of recommendations on the use of this method and on conservation issues of Grasshopper Sparrow habitat is also provided.

Classification and conservation priority of five Deccani sheep ecotypes of Maharashtra, India

PubMed Central

Arora, Reena; Jain, Anand

2017-01-01

Characterization of Indian livestock breeds has mostly been limited to single breed/population focused on either physical description of traditionally recognized breeds/populations or to their genetic description. Usually, morphological and genetic characterization has taken place in isolation. A parallel morphological characterization of genetically identified breeds or genetic characterization of morphologically described breeds is mostly missing, and their conservation priorities have largely been based on solely considering degree of endangerment. This study uses parallel approach based on morphometric and genetic differentiation for classification of five sheep ecotypes of Maharashtra state, and sets their conservation priority using threat parameters, current utilities/merits and contribution to genetic diversity. A total of 1101 animals were described for 7 body measurements for morphometric characterization. From this sample set, 456 animals were genotyped for 25 microsatellite markers for genetic characterization. Conservation priorities were assessed combining genetic and non-genetic factors. All studied traits varied significantly among ecotypes (p<0.05). All morphometric traits exhibited substantial sexual dimorphism except ear length. Males were 42% heavier than females. Madgyal sheep were the largest amongst the five ecotypes. In the stepwise discriminant analysis, all measured traits were significant and were found to have potential discriminatory power. Tail length was the most discriminatory trait. The Mahalanobis distance of the morphological traits between Kolhapuri and Madgyal was maximum (12.07) while the least differentiation was observed between Madgyal and Solapuri (1.50). Discriminant analysis showed that 68.12% sheep were classified into their source population. The Sangamneri sheep showed least assignment error (22%) whilst Solapuri exhibited maximum error level (41%). A total of 407 alleles were observed, with an average of 16.28 alleles per locus. Sufficient levels of genetic diversity were observed in all the ecotypes with observed heterozygosity values exceeding 0.47 and gene diversity values exceeding 0.76. About 6% of the total genetic variation was explained by population differences (FST = 0.059). Pairwise FST values indicated least differentiation between Solapuri and Madgyal (0.025). In terms of genetic distances, Kolhapuri and Lonand were most closely related (Ds = 0.177). The most probable structure clustering of the five studied populations was at K = 5. The study showed a fair congruence between the dendrogram constructed on the basis of Mahalanobis distances and Nei’s as well as Reynolds genetic distances. The findings gave highest conservation priority to Lonand and least to Solapuri ecotype. PMID:28910329

Prediction of Breeding Values for Dairy Cattle Using Artificial Neural Networks and Neuro-Fuzzy Systems

PubMed Central

Shahinfar, Saleh; Mehrabani-Yeganeh, Hassan; Lucas, Caro; Kalhor, Ahmad; Kazemian, Majid; Weigel, Kent A.

2012-01-01

Developing machine learning and soft computing techniques has provided many opportunities for researchers to establish new analytical methods in different areas of science. The objective of this study is to investigate the potential of two types of intelligent learning methods, artificial neural networks and neuro-fuzzy systems, in order to estimate breeding values (EBV) of Iranian dairy cattle. Initially, the breeding values of lactating Holstein cows for milk and fat yield were estimated using conventional best linear unbiased prediction (BLUP) with an animal model. Once that was established, a multilayer perceptron was used to build ANN to predict breeding values from the performance data of selection candidates. Subsequently, fuzzy logic was used to form an NFS, a hybrid intelligent system that was implemented via a local linear model tree algorithm. For milk yield the correlations between EBV and EBV predicted by the ANN and NFS were 0.92 and 0.93, respectively. Corresponding correlations for fat yield were 0.93 and 0.93, respectively. Correlations between multitrait predictions of EBVs for milk and fat yield when predicted simultaneously by ANN were 0.93 and 0.93, respectively, whereas corresponding correlations with reference EBV for multitrait NFS were 0.94 and 0.95, respectively, for milk and fat production. PMID:22991575

The effect of breed and sex on sulfamethazine, enrofloxacin, fenbendazole and flunixin meglumine pharmacokinetic parameters in swine.

PubMed

Howard, J T; Baynes, R E; Brooks, J D; Yeatts, J L; Bellis, B; Ashwell, M S; Routh, P; O'Nan, A T; Maltecca, C

2014-12-01

Drug use in livestock has received increased attention due to welfare concerns and food safety. Characterizing heterogeneity in the way swine populations respond to drugs could allow for group-specific dose or drug recommendations. Our objective was to determine whether drug clearance differs across genetic backgrounds and sex for sulfamethazine, enrofloxacin, fenbendazole and flunixin meglumine. Two sires from each of four breeds were mated to a common sow population. The nursery pigs generated (n = 114) were utilized in a random crossover design. Drugs were administered intravenously and blood collected a minimum of 10 times over 48 h. A non-compartmental analysis of drug and metabolite plasma concentration vs. time profiles was performed. Within-drug and metabolite analysis of pharmacokinetic parameters included fixed effects of drug administration date, sex and breed of sire. Breed differences existed for flunixin meglumine (P-value<0.05; Cl, Vdss ) and oxfendazole (P-value<0.05, AUC0→∞ ). Sex differences existed for oxfendazole (P-value < 0.05; Tmax ) and sulfamethazine (P-value < 0.05, Cl). Differences in drug clearance were seen, and future work will determine the degree of additive genetic variation utilizing a larger population. © 2014 John Wiley & Sons Ltd.

Use of partial least squares regression to impute SNP genotypes in Italian cattle breeds.

PubMed

Dimauro, Corrado; Cellesi, Massimo; Gaspa, Giustino; Ajmone-Marsan, Paolo; Steri, Roberto; Marras, Gabriele; Macciotta, Nicolò P P

2013-06-05

The objective of the present study was to test the ability of the partial least squares regression technique to impute genotypes from low density single nucleotide polymorphisms (SNP) panels i.e. 3K or 7K to a high density panel with 50K SNP. No pedigree information was used. Data consisted of 2093 Holstein, 749 Brown Swiss and 479 Simmental bulls genotyped with the Illumina 50K Beadchip. First, a single-breed approach was applied by using only data from Holstein animals. Then, to enlarge the training population, data from the three breeds were combined and a multi-breed analysis was performed. Accuracies of genotypes imputed using the partial least squares regression method were compared with those obtained by using the Beagle software. The impact of genotype imputation on breeding value prediction was evaluated for milk yield, fat content and protein content. In the single-breed approach, the accuracy of imputation using partial least squares regression was around 90 and 94% for the 3K and 7K platforms, respectively; corresponding accuracies obtained with Beagle were around 85% and 90%. Moreover, computing time required by the partial least squares regression method was on average around 10 times lower than computing time required by Beagle. Using the partial least squares regression method in the multi-breed resulted in lower imputation accuracies than using single-breed data. The impact of the SNP-genotype imputation on the accuracy of direct genomic breeding values was small. The correlation between estimates of genetic merit obtained by using imputed versus actual genotypes was around 0.96 for the 7K chip. Results of the present work suggested that the partial least squares regression imputation method could be useful to impute SNP genotypes when pedigree information is not available.

Prevalence and inheritance of and selection for elbow arthrosis in Bernese mountain dogs and Rottweilers in Sweden and benefit: cost analysis of a screening and control program.

PubMed

Swenson, L; Audell, L; Hedhammar, A

1997-01-15

To determine the prevalence and charges over time in the prevalence of elbow arthrosis in Bernese Mountain Dogs and Rottweilers, to ascertain whether prevalence or severity of elbow arthrosis was associated with sex of the dogs, age at the time of elbow joint examination, or ancestral background, to determine the effects of selective breeding, and to conduct an economic evaluation of the elbow arthrosis program operated by the Swedish Kennel Club. Analysis of radiographic evaluations of elbow joint conformity. 4,515 dogs from 2 breeds registered by the Swedish Kennel Club. All radiographs were scrutinized by a single radiologist (LA), and elbow joint conformation was classified as normal or arthrotic, with the degree of arthrosis classified as 1, 2, or 3. Decreasing prevalence of elbow arthrosis corresponding to selection of breeding stock and high heritabilities was found. Sex differences were documented in both breeds, but with contradictory directions. This was interpreted as breed differences in the distribution of genes related to elbow arthrosis. Economic analyses showed that costs of screening and registration of elbow joints was less than the value of dogs estimated to have been saved from moderate and severe elbow arthrosis in both breeds. Documented effects of age suggest that all dogs should be screened at the same age, rather than screening a few dogs at an older, more revealing age. In screening and control programs based on an open registry with access to family records, decreasing prevalence of elbow arthrosis can be expected, and related to selection of breeding stock.

Estimated breeding values for canine hip dysplasia radiographic traits in a cohort of Australian German Shepherd dogs.

PubMed

Wilson, Bethany J; Nicholas, Frank W; James, John W; Wade, Claire M; Thomson, Peter C

2013-01-01

Canine hip dysplasia (CHD) is a serious and common musculoskeletal disease of pedigree dogs and therefore represents both an important welfare concern and an imperative breeding priority. The typical heritability estimates for radiographic CHD traits suggest that the accuracy of breeding dog selection could be substantially improved by the use of estimated breeding values (EBVs) in place of selection based on phenotypes of individuals. The British Veterinary Association/Kennel Club scoring method is a complex measure composed of nine bilateral ordinal traits, intended to evaluate both early and late dysplastic changes. However, the ordinal nature of the traits may represent a technical challenge for calculation of EBVs using linear methods. The purpose of the current study was to calculate EBVs of British Veterinary Association/Kennel Club traits in the Australian population of German Shepherd Dogs, using linear (both as individual traits and a summed phenotype), binary and ordinal methods to determine the optimal method for EBV calculation. Ordinal EBVs correlated well with linear EBVs (r = 0.90-0.99) and somewhat well with EBVs for the sum of the individual traits (r = 0.58-0.92). Correlation of ordinal and binary EBVs varied widely (r = 0.24-0.99) depending on the trait and cut-point considered. The ordinal EBVs have increased accuracy (0.48-0.69) of selection compared with accuracies from individual phenotype-based selection (0.40-0.52). Despite the high correlations between linear and ordinal EBVs, the underlying relationship between EBVs calculated by the two methods was not always linear, leading us to suggest that ordinal models should be used wherever possible. As the population of German Shepherd Dogs which was studied was purportedly under selection for the traits studied, we examined the EBVs for evidence of a genetic trend in these traits and found substantial genetic improvement over time. This study suggests the use of ordinal EBVs could increase the rate of genetic improvement in this population.

Optimized breeding strategies for multiple trait integration: II. Process efficiency in event pyramiding and trait fixation.

PubMed

Peng, Ting; Sun, Xiaochun; Mumm, Rita H

2014-01-01

Multiple trait integration (MTI) is a multi-step process of converting an elite variety/hybrid for value-added traits (e.g. transgenic events) through backcross breeding. From a breeding standpoint, MTI involves four steps: single event introgression, event pyramiding, trait fixation, and version testing. This study explores the feasibility of marker-aided backcross conversion of a target maize hybrid for 15 transgenic events in the light of the overall goal of MTI of recovering equivalent performance in the finished hybrid conversion along with reliable expression of the value-added traits. Using the results to optimize single event introgression (Peng et al. Optimized breeding strategies for multiple trait integration: I. Minimizing linkage drag in single event introgression. Mol Breed, 2013) which produced single event conversions of recurrent parents (RPs) with ≤8 cM of residual non-recurrent parent (NRP) germplasm with ~1 cM of NRP germplasm in the 20 cM regions flanking the event, this study focused on optimizing process efficiency in the second and third steps in MTI: event pyramiding and trait fixation. Using computer simulation and probability theory, we aimed to (1) fit an optimal breeding strategy for pyramiding of eight events into the female RP and seven in the male RP, and (2) identify optimal breeding strategies for trait fixation to create a 'finished' conversion of each RP homozygous for all events. In addition, next-generation seed needs were taken into account for a practical approach to process efficiency. Building on work by Ishii and Yonezawa (Optimization of the marker-based procedures for pyramiding genes from multiple donor lines: I. Schedule of crossing between the donor lines. Crop Sci 47:537-546, 2007a), a symmetric crossing schedule for event pyramiding was devised for stacking eight (seven) events in a given RP. Options for trait fixation breeding strategies considered selfing and doubled haploid approaches to achieve homozygosity as well as seed chipping and tissue sampling approaches to facilitate genotyping. With selfing approaches, two generations of selfing rather than one for trait fixation (i.e. 'F2 enrichment' as per Bonnett et al. in Strategies for efficient implementation of molecular markers in wheat breeding. Mol Breed 15:75-85, 2005) were utilized to eliminate bottlenecking due to extremely low frequencies of desired genotypes in the population. The efficiency indicators such as total number of plants grown across generations, total number of marker data points, total number of generations, number of seeds sampled by seed chipping, number of plants requiring tissue sampling, and number of pollinations (i.e. selfing and crossing) were considered in comparisons of breeding strategies. A breeding strategy involving seed chipping and a two-generation selfing approach (SC + SELF) was determined to be the most efficient breeding strategy in terms of time to market and resource requirements. Doubled haploidy may have limited utility in trait fixation for MTI under the defined breeding scenario. This outcome paves the way for optimizing the last step in the MTI process, version testing, which involves hybridization of female and male RP conversions to create versions of the converted hybrid for performance evaluation and possible commercial release.

The Predicted Cross Value for Genetic Introgression of Multiple Alleles

PubMed Central

Han, Ye; Cameron, John N.; Wang, Lizhi; Beavis, William D.

2017-01-01

We consider the plant genetic improvement challenge of introgressing multiple alleles from a homozygous donor to a recipient. First, we frame the project as an algorithmic process that can be mathematically formulated. We then introduce a novel metric for selecting breeding parents that we refer to as the predicted cross value (PCV). Unlike estimated breeding values, which represent predictions of general combining ability, the PCV predicts specific combining ability. The PCV takes estimates of recombination frequencies as an input vector and calculates the probability that a pair of parents will produce a gamete with desirable alleles at all specified loci. We compared the PCV approach with existing estimated-breeding-value approaches in two simulation experiments, in which 7 and 20 desirable alleles were to be introgressed from a donor line into a recipient line. Results suggest that the PCV is more efficient and effective for multi-allelic trait introgression. We also discuss how operations research can be used for other crop genetic improvement projects and suggest several future research directions. PMID:28122824

Ranges of North American breeding birds: visualizing long-term population changes in North American breeding birds

USGS Publications Warehouse

Price, Jeff

1995-01-01

These maps show changes in the distribution and abundance patterns of some North American birds for the last 20 years. For each species there are four maps, each representing the average distribution and abundance pattern over the five-year periods 1970-1974, 1975-1979, 1980-1984, and 1985-1989. The maps are based on data collected by the USFWS/CWS Breeding Bird Survey (BBS). Only BBS routes that were run at least once during each of the five-year periods were used (about 1300 routes). The maps were created in the software package Surfer using a kriging technique to interpolate mean relative abundances for areas where no routes were run. On each map, a portion of northeast Canada was blanked out because there were not enough routes to allow for adequate interpolation. All of the maps in this presentation use the same color scale (shown below). The minimum value mapped was 0.5 birds per route, which represents the edge of the species range.

Application of genomic selection in farm animal breeding.

PubMed

Tan, Cheng; Bian, Cheng; Yang, Da; Li, Ning; Wu, Zhen-Fang; Hu, Xiao-Xiang

2017-11-20

Genomic selection (GS) has become a widely accepted method in animal breeding to genetically improve economic traits. With the declining costs of high-density SNP chips and next-generation sequencing, GS has been applied in dairy cattle, swine, poultry and other animals and gained varying degrees of success. Currently, major challenges in GS studies include further reducing the cost of genome-wide SNP genotyping and improving the predictive accuracy of genomic estimated breeding value (GEBV). In this review, we summarize various methods for genome-wide SNP genotyping and GEBV prediction, and give a brief introduction of GS in livestock and poultry breeding. This review will provide a reference for further implementation of GS in farm animal breeding.

[Research progress on breeding standard of medicinal animals and discussion on several key problems].

PubMed

Zhou, Yi-Quan; Qu, Xian-You; Yang, Guang; Li, Jun-de; Su, Yan; Li, Ying

2016-12-01

Medicinal animal breeding standards is regarded as the law to normalize relevant production that can guarantee the quality of traditional Chinese medicine of animal category. The article summarized the medicinal animal resources in our country and the present condition of medicinal animal breeding standards. It considered the current animal breeding standards system was in adequate, not only the quantity of breeding standards, the standard content and index were also uncomprehensive, which is not conducive to the scientific and orderly development and utilization of medicinal animal resources. The article pointed out that the development of the basic standards, environmental control, feed quality, raising management, inspection and quarantine should be included into the medicinal animal breeding standards, and the medicinal animal breeding standards content framework was introduced. Meanwhile, animal welfare, biological safety and file management should be concerned during the process of research. Hope the article has good reference value to medicinal animal breeding standards establishment and production management. Copyright© by the Chinese Pharmaceutical Association.

[Status of traditional Chinese medicine materials seed and seedling breeding bases].

PubMed

Li, Ying; Huang, Lu-Qi; Zhang, Xiao-Bo; Wang, Hui; Cheng, Meng; Zhang, Tian; Yang, Guang

2017-11-01

Seeds and seedlings are the material basis of traditional Chinese medicine materials production, and the construction of traditional Chinese medicine materials seed and seedling breeding bases is beneficial to the production of high-quality traditional Chinese medicine materials. The construction of traditional Chinese medicine materials seed and seedling breeding bases is one of the major topics of Chinese medica resources census pilot. Targets, tasks of traditional Chinese medicine materials seed and seedling breeding bases based on Chinese medica resources census pilot were expounded.Construction progress including hardware construction, germplasm conservation and breeding, procedures and standardsestablishment, social servicesare presented. Development counter measures were proposed for the next step: perfect the standard and system, maintain and strengthen the breeding function, strengthen the cultivation of multi-level talents, explore market development model, joint efforts to deepen services and development. Copyright© by the Chinese Pharmaceutical Association.

Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment Efficiency

PubMed Central

Li, Y. H.; Chu, H. P.; Jiang, Y. N.; Lin, C. Y.; Li, S. H.; Li, K. T.; Weng, G. J.; Cheng, C. C.; Lu, D. J.; Ju, Y. T.

2014-01-01

The Lanyu is a miniature pig breed indigenous to Lanyu Island, Taiwan. It is distantly related to Asian and European pig breeds. It has been inbred to generate two breeds and crossed with Landrace and Duroc to produce two hybrids for laboratory use. Selecting sets of informative genetic markers to track the genetic qualities of laboratory animals and stud stock is an important function of genetic databases. For more than two decades, Lanyu derived breeds of common ancestry and crossbreeds have been used to examine the effectiveness of genetic marker selection and optimal approaches for individual assignment. In this paper, these pigs and the following breeds: Berkshire, Duroc, Landrace and Yorkshire, Meishan and Taoyuan, TLRI Black Pig No. 1, and Kaohsiung Animal Propagation Station Black pig are studied to build a genetic reference database. Nineteen microsatellite markers (loci) provide information on genetic variation and differentiation among studied breeds. High differentiation index (FST) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu’s inbred populations. Inbreeding values (FIS) show that Lanyu and its derived inbred breeds have significant loss of heterozygosity. Individual assignment testing of 352 animals was done with different numbers of microsatellite markers in this study. The testing assigned 99% of the animals successfully into their correct reference populations based on 9 to 14 markers ranking D-scores, allelic number, expected heterozygosity (HE) or FST, respectively. All miss-assigned individuals came from close lineage Lanyu breeds. To improve individual assignment among close lineage breeds, microsatellite markers selected from Lanyu populations with high polymorphic, heterozygosity, FST and D-scores were used. Only 6 to 8 markers ranking HE, FST or allelic number were required to obtain 99% assignment accuracy. This result suggests empirical examination of assignment-error rates is required if discernible levels of co-ancestry exist. In the reference group, optimum assignment accuracy was achievable achieved through a combination of different markers by ranking the heterozygosity, FST and allelic number of close lineage populations. PMID:25049996

Predicting breeding habitat for amphibians: a spatiotemporal analysis across Yellowstone National Park

USGS Publications Warehouse

Bartelt, Paul E.; Gallant, Alisa L.; Klaver, Robert W.; Wright, Christopher K.; Patla, Debra A.; Peterson, Charles R.

2011-01-01

The ability to predict amphibian breeding across landscapes is important for informing land management decisions and helping biologists better understand and remediate factors contributing to declines in amphibian populations. We built geospatial models of likely breeding habitats for each of four amphibian species that breed in Yellowstone National Park (YNP). We used field data collected in 2000-2002 from 497 sites among 16 basins and predictor variables from geospatial models produced from remotely sensed data (e.g., digital elevation model, complex topographic index, landform data, wetland probabililty, and vegetative cover). Except for 31 sites in one basin that were surveyed in both 2000 and 2002, all sites were surveyed once. We used polytomous regression to build statistical models for each species of amphibian from 1) field survey site data only, 2) field data combined with data from geospatial models, and 3) data from geospatial models only. Based on measures of receiver operating characteristic (ROC) scores, models of the second type best explained likely breeding habitat because they contained the most information (ROC values ranged from 0.70 - 0.88). However, models of the third type could be applied to the entire YNP landscape and produced maps that could be verified with reserve field data. Accuracy rates for models built for single years were highly variable, ranging from 0.30 to 0.78. Accuracy rates for models built with data combined from multiple years were higher and less variable, ranging from 0.60 to 0.80. Combining results from the geospatial multiyear models yielded maps of "core" breeding areas (areas with high probability values for all three years) surrounded by areas that scored high for only one or two years, providing an estimate of variability among years. Such information can highlight landscape options for amphibian conservation. For example, our models identify alternative for areas that could be protected for each species, including 6828-10 764 ha for tiger salamanders; 971-3017 ha for western toads; 4732-16 696 ha for boreal chorus frogs; 4940-19 690 hectares for Columbia spotted frogs.

Predicting breeding habitat for amphibians: A spatiotemporal analysis across Yellowstone National Park

USGS Publications Warehouse

Bartelt, Paul E.; Gallant, Alisa L.; Klaver, Robert W.; Wright, C.K.; Patla, Debra A.; Peterson, Charles R.

2011-01-01

The ability to predict amphibian breeding across landscapes is important for informing land management decisions and helping biologists better understand and remediate factors contributing to declines in amphibian populations. We built geospatial models of likely breeding habitats for each of four amphibian species that breed in Yellowstone National Park (YNP). We used field data collected in 2000-2002 from 497 sites among 16 basins and predictor variables from geospatial models produced from remotely sensed data (e.g., digital elevation model, complex topographic index, landform data, wetland probability, and vegetative cover). Except for 31 sites in one basin that were surveyed in both 2000 and 2002, all sites were surveyed once. We used polytomous regression to build statistical models for each species of amphibian from (1) field survey site data only, (2) field data combined with data from geospatial models, and (3) data from geospatial models only. Based on measures of receiver operating characteristic (ROC) scores, models of the second type best explained likely breeding habitat because they contained the most information (ROC values ranged from 0.70 to 0.88). However, models of the third type could be applied to the entire YNP landscape and produced maps that could be verified with reserve field data. Accuracy rates for models built for single years were highly variable, ranging from 0.30 to 0.78. Accuracy rates for models built with data combined from multiple years were higher and less variable, ranging from 0.60 to 0.80. Combining results from the geospatial multiyear models yielded maps of "core" breeding areas (areas with high probability values for all three years) surrounded by areas that scored high for only one or two years, providing an estimate of variability among years. Such information can highlight landscape options for amphibian conservation. For example, our models identify alternative areas that could be protected for each species, including 6828-10 764 ha for tiger salamanders, 971-3017 ha for western toads, 4732-16 696 ha for boreal chorus frogs, and 4940-19 690 ha for Columbia spotted frogs. ?? 2011 by the Ecological Society of America.

Predicting breeding habitat for amphibians: a spatiotemporal analysis across Yellowstone National Park.

PubMed

Bartelt, Paul E; Gallant, Alisa L; Klaver, Robert W; Wright, Chris K; Patla, Debra A; Peterson, Charles R

2011-10-01

The ability to predict amphibian breeding across landscapes is important for informing land management decisions and helping biologists better understand and remediate factors contributing to declines in amphibian populations. We built geospatial models of likely breeding habitats for each of four amphibian species that breed in Yellowstone National Park (YNP). We used field data collected in 2000-2002 from 497 sites among 16 basins and predictor variables from geospatial models produced from remotely sensed data (e.g., digital elevation model, complex topographic index, landform data, wetland probability, and vegetative cover). Except for 31 sites in one basin that were surveyed in both 2000 and 2002, all sites were surveyed once. We used polytomous regression to build statistical models for each species of amphibian from (1) field survey site data only, (2) field data combined with data from geospatial models, and (3) data from geospatial models only. Based on measures of receiver operating characteristic (ROC) scores, models of the second type best explained likely breeding habitat because they contained the most information (ROC values ranged from 0.70 to 0.88). However, models of the third type could be applied to the entire YNP landscape and produced maps that could be verified with reserve field data. Accuracy rates for models built for single years were highly variable, ranging from 0.30 to 0.78. Accuracy rates for models built with data combined from multiple years were higher and less variable, ranging from 0.60 to 0.80. Combining results from the geospatial multiyear models yielded maps of "core" breeding areas (areas with high probability values for all three years) surrounded by areas that scored high for only one or two years, providing an estimate of variability among years. Such information can highlight landscape options for amphibian conservation. For example, our models identify alternative areas that could be protected for each species, including 6828-10 764 ha for tiger salamanders, 971-3017 ha for western toads, 4732-16 696 ha for boreal chorus frogs, and 4940-19 690 ha for Columbia spotted frogs.

Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep.

PubMed

Al-Mamun, Hawlader Abdullah; Clark, Samuel A; Kwan, Paul; Gondro, Cedric

2015-11-24

Knowledge of the genetic structure and overall diversity of livestock species is important to maximise the potential of genome-wide association studies and genomic prediction. Commonly used measures such as linkage disequilibrium (LD), effective population size (N e ), heterozygosity, fixation index (F ST) and runs of homozygosity (ROH) are widely used and help to improve our knowledge about genetic diversity in animal populations. The development of high-density single nucleotide polymorphism (SNP) arrays and the subsequent genotyping of large numbers of animals have greatly increased the accuracy of these population-based estimates. In this study, we used the Illumina OvineSNP50 BeadChip array to estimate and compare LD (measured by r (2) and D'), N e , heterozygosity, F ST and ROH in five Australian sheep populations: three pure breeds, i.e., Merino (MER), Border Leicester (BL), Poll Dorset (PD) and two crossbred populations i.e. F1 crosses of Merino and Border Leicester (MxB) and MxB crossed to Poll Dorset (MxBxP). Compared to other livestock species, the sheep populations that were analysed in this study had low levels of LD and high levels of genetic diversity. The rate of LD decay was greater in Merino than in the other pure breeds. Over short distances (<10 kb), the levels of LD were higher in BL and PD than in MER. Similarly, BL and PD had comparatively smaller N e than MER. Observed heterozygosity in the pure breeds ranged from 0.3 in BL to 0.38 in MER. Genetic distances between breeds were modest compared to other livestock species (highest F ST = 0.063) but the genetic diversity within breeds was high. Based on ROH, two chromosomal regions showed evidence of strong recent selection. This study shows that there is a large range of genome diversity in Australian sheep breeds, especially in Merino sheep. The observed range of diversity will influence the design of genome-wide association studies and the results that can be obtained from them. This knowledge will also be useful to design reference populations for genomic prediction of breeding values in sheep.

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds.

PubMed

Mastrangelo, S; Tolone, M; Di Gerlando, R; Fontanesi, L; Sardina, M T; Portolano, B

2016-05-01

In the local breeds with small population size, one of the most important problems is the increase of inbreeding coefficient (F). High levels of inbreeding lead to reduced genetic diversity and inbreeding depression. The availability of high-density single nucleotide polymorphism (SNP) arrays has facilitated the quantification of F by genomic markers in farm animals. Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes and represent an estimate of the degree of autozygosity at genome-wide level. The current study aims to quantify the genomic F derived from ROH (F ROH) in three local dairy cattle breeds. F ROH values were compared with F estimated from the genomic relationship matrix (F GRM), based on the difference between observed v. expected number of homozygous genotypes (F HOM) and the genomic homozygosity of individual i (F MOL i ). The molecular coancestry coefficient (f MOL ij ) between individuals i and j was also estimated. Individuals of Cinisara (71), Modicana (72) and Reggiana (168) were genotyped with the 50K v2 Illumina BeadChip. Genotypes from 96 animals of Italian Holstein cattle breed were also included in the analysis. We used a definition of ROH as tracts of homozygous genotypes that were >4 Mb. Among breeds, 3661 ROH were identified. Modicana showed the highest mean number of ROH per individual and the highest value of F ROH, whereas Reggiana showed the lowest ones. Differences among breeds existed for the ROH lengths. The individuals of Italian Holstein showed high number of short ROH segments, related to ancient consanguinity. Similar results showed the Reggiana with some extreme animals with segments covering 400 Mb and more of genome. Modicana and Cinisara showed similar results between them with the total length of ROH characterized by the presence of large segments. High correlation was found between F HOM and F ROH ranged from 0.83 in Reggiana to 0.95 in Cinisara and Modicana. The correlations among F ROH and other estimated F coefficients were generally lower ranged from 0.45 (F MOL i -F ROH) in Cinisara to 0.17 (F GRM-F ROH) in Modicana. On the basis of our results, recent inbreeding was observed in local breeds, considering that 16 Mb segments are expected to present inbreeding up to three generations ago. Our results showed the necessity of implementing conservation programs to control the rise of inbreeding and coancestry in the three Italian local dairy cattle breeds.

Genome-association analysis of Korean Holstein milk traits using genomic estimated breeding value.

PubMed

Shin, Donghyun; Lee, Chul; Park, Kyoung-Do; Kim, Heebal; Cho, Kwang-Hyeon

2017-03-01

Holsteins are known as the world's highest-milk producing dairy cattle. The purpose of this study was to identify genetic regions strongly associated with milk traits (milk production, fat, and protein) using Korean Holstein data. This study was performed using single nucleotide polymorphism (SNP) chip data (Illumina BovineSNP50 Beadchip) of 911 Korean Holstein individuals. We inferred each genomic estimated breeding values based on best linear unbiased prediction (BLUP) and ridge regression using BLUPF90 and R. We then performed a genome-wide association study and identified genetic regions related to milk traits. We identified 9, 6, and 17 significant genetic regions related to milk production, fat and protein, respectively. These genes are newly reported in the genetic association with milk traits of Holstein. This study complements a recent Holstein genome-wide association studies that identified other SNPs and genes as the most significant variants. These results will help to expand the knowledge of the polygenic nature of milk production in Holsteins.

Genome-association analysis of Korean Holstein milk traits using genomic estimated breeding value

PubMed Central

Shin, Donghyun; Lee, Chul; Park, Kyoung-Do; Kim, Heebal; Cho, Kwang-hyeon

2017-01-01

Objective Holsteins are known as the world’s highest-milk producing dairy cattle. The purpose of this study was to identify genetic regions strongly associated with milk traits (milk production, fat, and protein) using Korean Holstein data. Methods This study was performed using single nucleotide polymorphism (SNP) chip data (Illumina BovineSNP50 Beadchip) of 911 Korean Holstein individuals. We inferred each genomic estimated breeding values based on best linear unbiased prediction (BLUP) and ridge regression using BLUPF90 and R. We then performed a genome-wide association study and identified genetic regions related to milk traits. Results We identified 9, 6, and 17 significant genetic regions related to milk production, fat and protein, respectively. These genes are newly reported in the genetic association with milk traits of Holstein. Conclusion This study complements a recent Holstein genome-wide association studies that identified other SNPs and genes as the most significant variants. These results will help to expand the knowledge of the polygenic nature of milk production in Holsteins. PMID:26954162

Identifying a breeding habitat of a critically endangered fish, Acheilognathus typus, in a natural river in Japan

NASA Astrophysics Data System (ADS)

Sakata, Masayuki K.; Maki, Nobutaka; Sugiyama, Hideki; Minamoto, Toshifumi

2017-12-01

Freshwater biodiversity has been severely threatened in recent years, and to conserve endangered species, their distribution and breeding habitats need to be clarified. However, identifying breeding sites in a large area is generally difficult. Here, by combining the emerging environmental DNA (eDNA) analysis with subsequent traditional collection surveys, we successfully identified a breeding habitat for the critically endangered freshwater fish Acheilognathus typus in the mainstream of Omono River in Akita Prefecture, Japan, which is one of the original habitats of this species. Based on DNA cytochrome B sequences of A. typus and closely related species, we developed species-specific primers and a probe that were used in real-time PCR for detecting A. typus eDNA. After verifying the specificity and applicability of the primers and probe on water samples from known artificial habitats, eDNA analysis was applied to water samples collected at 99 sites along Omono River. Two of the samples were positive for A. typus eDNA, and thus, small fixed nets and bottle traps were set out to capture adult fish and verify egg deposition in bivalves (the preferred breeding substrate for A. typus) in the corresponding regions. Mature female and male individuals and bivalves containing laid eggs were collected at one of the eDNA-positive sites. This was the first record of adult A. typus in Omono River in 11 years. This study highlights the value of eDNA analysis to guide conventional monitoring surveys and shows that combining both methods can provide important information on breeding sites that is essential for species' conservation.

Identifying a breeding habitat of a critically endangered fish, Acheilognathus typus, in a natural river in Japan.

PubMed

Sakata, Masayuki K; Maki, Nobutaka; Sugiyama, Hideki; Minamoto, Toshifumi

2017-11-14

Freshwater biodiversity has been severely threatened in recent years, and to conserve endangered species, their distribution and breeding habitats need to be clarified. However, identifying breeding sites in a large area is generally difficult. Here, by combining the emerging environmental DNA (eDNA) analysis with subsequent traditional collection surveys, we successfully identified a breeding habitat for the critically endangered freshwater fish Acheilognathus typus in the mainstream of Omono River in Akita Prefecture, Japan, which is one of the original habitats of this species. Based on DNA cytochrome B sequences of A. typus and closely related species, we developed species-specific primers and a probe that were used in real-time PCR for detecting A. typus eDNA. After verifying the specificity and applicability of the primers and probe on water samples from known artificial habitats, eDNA analysis was applied to water samples collected at 99 sites along Omono River. Two of the samples were positive for A. typus eDNA, and thus, small fixed nets and bottle traps were set out to capture adult fish and verify egg deposition in bivalves (the preferred breeding substrate for A. typus) in the corresponding regions. Mature female and male individuals and bivalves containing laid eggs were collected at one of the eDNA-positive sites. This was the first record of adult A. typus in Omono River in 11 years. This study highlights the value of eDNA analysis to guide conventional monitoring surveys and shows that combining both methods can provide important information on breeding sites that is essential for species' conservation.

Genotyping by sequencing for genomic prediction in a soybean breeding population.

PubMed

Jarquín, Diego; Kocak, Kyle; Posadas, Luis; Hyma, Katie; Jedlicka, Joseph; Graef, George; Lorenz, Aaron

2014-08-29

Advances in genotyping technology, such as genotyping by sequencing (GBS), are making genomic prediction more attractive to reduce breeding cycle times and costs associated with phenotyping. Genomic prediction and selection has been studied in several crop species, but no reports exist in soybean. The objectives of this study were (i) evaluate prospects for genomic selection using GBS in a typical soybean breeding program and (ii) evaluate the effect of GBS marker selection and imputation on genomic prediction accuracy. To achieve these objectives, a set of soybean lines sampled from the University of Nebraska Soybean Breeding Program were genotyped using GBS and evaluated for yield and other agronomic traits at multiple Nebraska locations. Genotyping by sequencing scored 16,502 single nucleotide polymorphisms (SNPs) with minor-allele frequency (MAF) > 0.05 and percentage of missing values ≤ 5% on 301 elite soybean breeding lines. When SNPs with up to 80% missing values were included, 52,349 SNPs were scored. Prediction accuracy for grain yield, assessed using cross validation, was estimated to be 0.64, indicating good potential for using genomic selection for grain yield in soybean. Filtering SNPs based on missing data percentage had little to no effect on prediction accuracy, especially when random forest imputation was used to impute missing values. The highest accuracies were observed when random forest imputation was used on all SNPs, but differences were not significant. A standard additive G-BLUP model was robust; modeling additive-by-additive epistasis did not provide any improvement in prediction accuracy. The effect of training population size on accuracy began to plateau around 100, but accuracy steadily climbed until the largest possible size was used in this analysis. Including only SNPs with MAF > 0.30 provided higher accuracies when training populations were smaller. Using GBS for genomic prediction in soybean holds good potential to expedite genetic gain. Our results suggest that standard additive G-BLUP models can be used on unfiltered, imputed GBS data without loss in accuracy.

On the value of the phenotypes in the genomic era.

PubMed

Gonzalez-Recio, O; Coffey, M P; Pryce, J E

2014-12-01

Genetic improvement programs around the world rely on the collection of accurate phenotypic data. These phenotypes have an inherent value that can be estimated as the contribution of an additional record to genetic gain. Here, the contribution of phenotypes to genetic gain was calculated using traditional progeny testing (PT) and 2 genomic selection (GS) strategies that, for simplicity, included either males or females in the reference population. A procedure to estimate the theoretical economic contribution of a phenotype to a breeding program is described for both GS and PT breeding programs through the increment in genetic gain per unit of increase in estimated breeding value reliability obtained when an additional phenotypic record is added. The main factors affecting the value of a phenotype were the economic value of the trait, the number of phenotypic records already available for the trait, and its heritability. Furthermore, the value of a phenotype was affected by several other factors, including the cost of establishing the breeding program and the cost of phenotyping and genotyping. The cost of achieving a reliability of 0.60 was assessed for different reference populations for GS. Genomic reference populations of more sires with small progeny group sizes (e.g., 20 equivalent daughters) had a lower cost than those reference populations with either large progeny group sizes for fewer genotyped sires, or female reference populations, unless the heritability was large and the cost of phenotyping exceeded a few hundred dollars; then, female reference populations were preferable from an economic perspective. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Partition of genetic trends by origin in Landrace and Large-White pigs.

PubMed

Škorput, D; Gorjanc, G; Kasap, A; Luković, Z

2015-10-01

The objective of this study was to analyse the effectiveness of genetic improvement via domestic selection and import for backfat thickness and time on test in a conventional pig breeding programme for Landrace (L) and Large-White (LW) breeds. Phenotype data was available for 25 553 L and 10 432 LW pigs born between 2002 and 2012 from four large-scale farms and 72 family farms. Pedigree information indicated whether each animal was born and registered within the domestic breeding programme or has been imported. This information was used for defining the genetic groups of unknown parents in a pedigree and the partitioning analysis. Breeding values were estimated using a Bayesian analysis of an animal model with and without genetic groups. Such analysis enabled full Bayesian inference of the genetic trends and their partitioning by the origin of germplasm. Estimates of genetic group indicated that imported germplasm was overall better than domestic and substantial changes in estimates of breeding values was observed when genetic group were fitted. The estimated genetic trends in L were favourable and significantly different from zero by the end of the analysed period. Overall, the genetic trends in LW were not different from zero. The relative contribution of imported germplasm to genetic trends was large, especially towards the end of analysed period with 78% and 67% in L and from 50% to 67% in LW. The analyses suggest that domestic breeding activities and sources of imported animals need to be re-evaluated, in particular in LW breed.

Seasonal changes in serum oxidative stress biomarkers in dairy and beef cows in a daytime grazing system.

PubMed

Mirzad, Ahmad Nawid; Tada, Takashi; Ano, Hitoshi; Kobayashi, Ikuo; Yamauchi, Takenori; Katamoto, Hiromu

2018-01-01

This study aims to evaluate the oxidative stress during hot summer season using serum oxidative stress biomarkers and elucidate the effects of serum antioxidant vitamin levels in dairy and beef cows in a daytime grazing system. Blood samples were collected once a month from eight Holstein Friesian (HF) and 10 Japanese Black (JB) cows from November 2013 to October 2014. Serum values of derivatives of reactive oxygen metabolites (d-ROMs) tended to be higher in March in both breeds and those in HF cows were kept at higher (P<0.001) levels than those in JB cows during the study period. Serum levels of biological antioxidant potential (BAP) in both breeds were maintained at almost the same values during study period. The OSI [(d-ROMs/BAP) × 100] values in both breeds showed similar seasonal changes, i. e. increase from December to March and decrease from March to August or September. In addition, the OSI values in HF cows were kept at higher (P<0.01) levels than those in JB cows during the study period. Serum concentrations of α-tocopherol, β-carotene, blood urea nitrogen and total cholesterol showed similar seasonal changes in both breeds, low in the winter and high from spring to summer, which may be attributed to the pasture grass intake. Opposite changes in OSI values and serum concentrations of α-tocopherol and β-carotene indicated that antioxidant vitamin levels could affect oxidative stress status.

Seasonal changes in serum oxidative stress biomarkers in dairy and beef cows in a daytime grazing system

PubMed Central

MIRZAD, Ahmad Nawid; TADA, Takashi; ANO, Hitoshi; KOBAYASHI, Ikuo; YAMAUCHI, Takenori; KATAMOTO, Hiromu

2017-01-01

This study aims to evaluate the oxidative stress during hot summer season using serum oxidative stress biomarkers and elucidate the effects of serum antioxidant vitamin levels in dairy and beef cows in a daytime grazing system. Blood samples were collected once a month from eight Holstein Friesian (HF) and 10 Japanese Black (JB) cows from November 2013 to October 2014. Serum values of derivatives of reactive oxygen metabolites (d-ROMs) tended to be higher in March in both breeds and those in HF cows were kept at higher (P<0.001) levels than those in JB cows during the study period. Serum levels of biological antioxidant potential (BAP) in both breeds were maintained at almost the same values during study period. The OSI [(d-ROMs/BAP) × 100] values in both breeds showed similar seasonal changes, i. e. increase from December to March and decrease from March to August or September. In addition, the OSI values in HF cows were kept at higher (P<0.01) levels than those in JB cows during the study period. Serum concentrations of α-tocopherol, β-carotene, blood urea nitrogen and total cholesterol showed similar seasonal changes in both breeds, low in the winter and high from spring to summer, which may be attributed to the pasture grass intake. Opposite changes in OSI values and serum concentrations of α-tocopherol and β-carotene indicated that antioxidant vitamin levels could affect oxidative stress status. PMID:29142148

Molecular Study of the Amazonian Macabea Cattle History.

PubMed

Vargas, Julio; Landi, Vincenzo; Martínez, Amparo; Gómez, Mayra; Camacho, María Esperanza; Álvarez, Luz Ángela; Aguirre, Lenin; Delgado, Juan Vicente

2016-01-01

Macabea cattle are the only Bos taurus breed that have adapted to the wet tropical conditions of the Amazon. This breed has integrated into the culture of the indigenous Shuar-Asuar nations probably since its origins, being one of the few European zoogenetic resources assimilated by the deep-jungle Amazon communities. Despite its potential for local endogenous sustainable development, this breed is currently endangered. The present study used molecular genetics tools to investigate the within- and between-breeds diversity, in order to characterize the breed population, define its associations with other breeds, and infer its origin and evolution. The within-breed genetic diversity showed high values, as indicated by all genetic parameters, such as the mean number of alleles (MNA = 7.25±2.03), the observed heterozygosity (Ho = 0.72±0.02) and the expected heterozygosity (He = 0.72±0.02). The between-breeds diversity analysis, which included factorial correspondence analysis, Reynolds genetic distance, neighbor-joining analysis, and genetic structure analysis, showed that the Macabea breed belongs to the group of the American Creoles, with a Southern-Spain origin. Our outcomes demonstrated that the Macabea breed has a high level of purity and null influences of exotic cosmopolitan breeds with European or Asiatic origin. This breed is an important zoogenetic resource of Ecuador, with relevant and unique attributes; therefore, there is an urgent need to develop conservation strategies for the Macabea breed.

Molecular Study of the Amazonian Macabea Cattle History

PubMed Central

Vargas, Julio; Martínez, Amparo; Gómez, Mayra; Camacho, María Esperanza; Álvarez, Luz Ángela; Aguirre, Lenin; Delgado, Juan Vicente

2016-01-01

Macabea cattle are the only Bos taurus breed that have adapted to the wet tropical conditions of the Amazon. This breed has integrated into the culture of the indigenous Shuar-Asuar nations probably since its origins, being one of the few European zoogenetic resources assimilated by the deep-jungle Amazon communities. Despite its potential for local endogenous sustainable development, this breed is currently endangered. The present study used molecular genetics tools to investigate the within- and between-breeds diversity, in order to characterize the breed population, define its associations with other breeds, and infer its origin and evolution. The within-breed genetic diversity showed high values, as indicated by all genetic parameters, such as the mean number of alleles (MNA = 7.25±2.03), the observed heterozygosity (Ho = 0.72±0.02) and the expected heterozygosity (He = 0.72±0.02). The between-breeds diversity analysis, which included factorial correspondence analysis, Reynolds genetic distance, neighbor-joining analysis, and genetic structure analysis, showed that the Macabea breed belongs to the group of the American Creoles, with a Southern-Spain origin. Our outcomes demonstrated that the Macabea breed has a high level of purity and null influences of exotic cosmopolitan breeds with European or Asiatic origin. This breed is an important zoogenetic resource of Ecuador, with relevant and unique attributes; therefore, there is an urgent need to develop conservation strategies for the Macabea breed. PMID:27776178

Delayed egg-laying and shortened incubation duration of Arctic-breeding shorebirds coincide with climate cooling.

PubMed

Kwon, Eunbi; English, Willow B; Weiser, Emily L; Franks, Samantha E; Hodkinson, David J; Lank, David B; Sandercock, Brett K

2018-01-01

Biological impacts of climate change are exemplified by shifts in phenology. As the timing of breeding advances, the within-season relationships between timing of breeding and reproductive traits may change and cause long-term changes in the population mean value of reproductive traits. We investigated long-term changes in the timing of breeding and within-season patterns of clutch size, egg volume, incubation duration, and daily nest survival of three shorebird species between two decades. Based on previously known within-season patterns and assuming a warming trend, we hypothesized that the timing of clutch initiation would advance between decades and would be coupled with increases in mean clutch size, egg volume, and daily nest survival rate. We monitored 1,378 nests of western sandpipers, semipalmated sandpipers, and red-necked phalaropes at a subarctic site during 1993-1996 and 2010-2014. Sandpipers have biparental incubation, whereas phalaropes have uniparental incubation. We found an unexpected long-term cooling trend during the early part of the breeding season. Three species delayed clutch initiation by 5 days in the 2010s relative to the 1990s. Clutch size and daily nest survival showed strong within-season declines in sandpipers, but not in phalaropes. Egg volume showed strong within-season declines in one species of sandpiper, but increased in phalaropes. Despite the within-season patterns in traits and shifts in phenology, clutch size, egg volume, and daily nest survival were similar between decades. In contrast, incubation duration did not show within-season variation, but decreased by 2 days in sandpipers and increased by 2 days in phalaropes. Shorebirds demonstrated variable breeding phenology and incubation duration in relation to climate cooling, but little change in nonphenological components of traits. Our results indicate that the breeding phenology of shorebirds is closely associated with the temperature conditions on breeding ground, the effects of which can vary among reproductive traits and among sympatric species.

Genotype imputation from various low-density SNP panels and its impact on accuracy of genomic breeding values in pigs.

PubMed

Grossi, D A; Brito, L F; Jafarikia, M; Schenkel, F S; Feng, Z

2018-04-30

The uptake of genomic selection (GS) by the swine industry is still limited by the costs of genotyping. A feasible alternative to overcome this challenge is to genotype animals using an affordable low-density (LD) single nucleotide polymorphism (SNP) chip panel followed by accurate imputation to a high-density panel. Therefore, the main objective of this study was to screen incremental densities of LD panels in order to systematically identify one that balances the tradeoffs among imputation accuracy, prediction accuracy of genomic estimated breeding values (GEBVs), and genotype density (directly associated with genotyping costs). Genotypes using the Illumina Porcine60K BeadChip were available for 1378 Duroc (DU), 2361 Landrace (LA) and 3192 Yorkshire (YO) pigs. In addition, pseudo-phenotypes (de-regressed estimated breeding values) for five economically important traits were provided for the analysis. The reference population for genotyping imputation consisted of 931 DU, 1631 LA and 2103 YO animals and the remainder individuals were included in the validation population of each breed. A LD panel of 3000 evenly spaced SNPs (LD3K) yielded high imputation accuracy rates: 93.78% (DU), 97.07% (LA) and 97.00% (YO) and high correlations (>0.97) between the predicted GEBVs using the actual 60 K SNP genotypes and the imputed 60 K SNP genotypes for all traits and breeds. The imputation accuracy was influenced by the reference population size as well as the amount of parental genotype information available in the reference population. However, parental genotype information became less important when the LD panel had at least 3000 SNPs. The correlation of the GEBVs directly increased with an increase in imputation accuracy. When genotype information for both parents was available, a panel of 300 SNPs (imputed to 60 K) yielded GEBV predictions highly correlated (⩾0.90) with genomic predictions obtained based on the true 60 K panel, for all traits and breeds. For a small reference population size with no parents on reference population, it is recommended the use of a panel at least as dense as the LD3K and, when there are two parents in the reference population, a panel as small as the LD300 might be a feasible option. These findings are of great importance for the development of LD panels for swine in order to reduce genotyping costs, increase the uptake of GS and, therefore, optimize the profitability of the swine industry.

Effects of correcting missing daily feed intake values on the genetic parameters and estimated breeding values for feeding traits in pigs.

PubMed

Ito, Tetsuya; Fukawa, Kazuo; Kamikawa, Mai; Nikaidou, Satoshi; Taniguchi, Masaaki; Arakawa, Aisaku; Tanaka, Genki; Mikawa, Satoshi; Furukawa, Tsutomu; Hirose, Kensuke

2018-01-01

Daily feed intake (DFI) is an important consideration for improving feed efficiency, but measurements using electronic feeder systems contain many missing and incorrect values. Therefore, we evaluated three methods for correcting missing DFI data (quadratic, orthogonal polynomial, and locally weighted (Loess) regression equations) and assessed the effects of these missing values on the genetic parameters and the estimated breeding values (EBV) for feeding traits. DFI records were obtained from 1622 Duroc pigs, comprising 902 individuals without missing DFI and 720 individuals with missing DFI. The Loess equation was the most suitable method for correcting the missing DFI values in 5-50% randomly deleted datasets among the three equations. Both variance components and heritability for the average DFI (ADFI) did not change because of the missing DFI proportion and Loess correction. In terms of rank correlation and information criteria, Loess correction improved the accuracy of EBV for ADFI compared to randomly deleted cases. These findings indicate that the Loess equation is useful for correcting missing DFI values for individual pigs and that the correction of missing DFI values could be effective for the estimation of breeding values and genetic improvement using EBV for feeding traits. © 2017 The Authors. Animal Science Journal published by John Wiley & Sons Australia, Ltd on behalf of Japanese Society of Animal Science.

Genetic evaluation of mastitis liability and recovery through longitudinal analysis of transition probabilities

PubMed Central

2012-01-01

Background Many methods for the genetic analysis of mastitis use a cross-sectional approach, which omits information on, e.g., repeated mastitis cases during lactation, somatic cell count fluctuations, and recovery process. Acknowledging the dynamic behavior of mastitis during lactation and taking into account that there is more than one binary response variable to consider, can enhance the genetic evaluation of mastitis. Methods Genetic evaluation of mastitis was carried out by modeling the dynamic nature of somatic cell count (SCC) within the lactation. The SCC patterns were captured by modeling transition probabilities between assumed states of mastitis and non-mastitis. A widely dispersed SCC pattern generates high transition probabilities between states and vice versa. This method can model transitions to and from states of infection simultaneously, i.e. both the mastitis liability and the recovery process are considered. A multilevel discrete time survival model was applied to estimate breeding values on simulated data with different dataset sizes, mastitis frequencies, and genetic correlations. Results Correlations between estimated and simulated breeding values showed that the estimated accuracies for mastitis liability were similar to those from previously tested methods that used data of confirmed mastitis cases, while our results were based on SCC as an indicator of mastitis. In addition, unlike the other methods, our method also generates breeding values for the recovery process. Conclusions The developed method provides an effective tool for the genetic evaluation of mastitis when considering the whole disease course and will contribute to improving the genetic evaluation of udder health. PMID:22475575

Sensitivity of breeding values for carcass traits of meat-type quail to changes in dietary (methionine + cystine):lysine ratio using reaction norm models.

PubMed

Miranda, J A; Pires, A V; Abreu, L R A; Mota, L F M; Silva, M A; Bonafé, C M; Lima, H J D; Martins, P G M A

2016-12-01

Our objective was to evaluate changes in breeding values for carcass traits of two meat-type quail (Coturnix coturnix) strains (LF1 and LF2) to changes in the dietary (methionine + cystine):lysine ([Met + Cys]:Lys) ratio due to genotype by environment (G × E) interaction via reaction norm. A total of 7000 records of carcass weight and yield were used for analyses. During the initial phase (from hatching to day 21), five diets with increasing (Met + Cys):Lys ratios (0.61, 0.66, 0.71, 0.76 and 0.81), containing 26.1% crude protein and 2900 kcal ME/kg, were evaluated. Analyses were performed using random regression models that included linear functions of sex (fixed effect) and breeding value (random effect) for carcass weight and yield, without and with heterogeneous residual variance adjustment. Both fixed and random effects were modelled using Legendre polynomials of second order. Genetic variance and heritability estimates were affected by both (Met + Cys):Lys ratio and strain. We observed that a G × E interaction was present, with changes in the breeding value ranking. Therefore, genetic evaluation for carcass traits should be performed under the same (Met + Cys):Lys ratio in which quails are raised. © 2016 Blackwell Verlag GmbH.

Impact of including growth, carcass and feed efficiency traits in the breeding goal for combined milk and beef production systems.

PubMed

Hietala, P; Juga, J

2017-04-01

Improving feed efficiency in dairy cattle could result in more profitable and environmentally sustainable dairy production through lowering feed costs and emissions from dairy farming. In addition, beef production based on dairy herds generates fewer greenhouse gas emissions per unit of meat output than beef production from suckler cow systems. Different scenarios were used to assess the profitability of adding traits, excluded from the current selection index for Finnish Ayrshire, to the breeding goal for combined dairy and beef production systems. The additional breeding goal traits were growth traits (average daily gain of animals in the fattening and rearing periods), carcass traits (fat covering, fleshiness and dressing percentage), mature live weight (LW) of cows and residual feed intake (RFI) traits. A breeding scheme was modeled for Finnish Ayrshire under the current market situation in Finland using the deterministic simulation software ZPLAN+. With the economic values derived for the current production system, the inclusion of growth and carcass traits, while preventing LW increase generated the highest improvement in the discounted profit of the breeding program (3.7%), followed by the scenario where all additional traits were included simultaneously (5.1%). The use of a selection index that included growth and carcass traits excluding LW, increased the profit (0.8%), but reduced the benefits resulted from breeding for beef traits together with LW. A moderate decrease in the profit of the breeding program was obtained when adding only LW to the breeding goal (-3.1%), whereas, adding only RFI traits to the breeding goal resulted in a minor increase in the profit (1.4%). Including beef traits with LW in the breeding goal showed to be the most potential option to improve the profitability of the combined dairy and beef production systems and would also enable a higher rate of self-sufficiency in beef. When considering feed efficiency related traits, the inclusion of LW traits in the breeding goal that includes growth and carcass traits could be more profitable than the inclusion of RFI, because the marginal costs of measuring LW can be expected to be lower than for RFI and it is readily available for selection. In addition, before RFI can be implemented as a breeding objective, the genetic correlations between RFI and other breeding goal traits estimated for the studied population as well as information on the most suitable indicator traits for RFI are needed to assess more carefully the consequences of selecting for RFI.

Fasting energy metabolism of the Yucatan miniature pig.

PubMed

Parsons, A H; Mathieson, K W; Tagliaferro, A R

1990-03-01

The fasting metabolic rates (FMR) of Yucatan miniature swine were determined using an open-circuit indirect respiration calorimeter. Mature nulliparous females had a mean FMR of 93 kcal/kg BW.75 and did not change significantly during the estrous cycle. This value is comparable to that observed in mature domestic swine. The calculated metabolizable energy requirement for maintenance for the Yucatan sow is 116 kcal/kg BW.75. Growing Yucatan boars had FMR of 127, 119 and 101 kcal/kg BW.75 at 15, 21 and 38 weeks of age, respectively, and were similar to values for comparably aged domestic swine. The calculated estimate for the metabolizable energy requirement for maintenance for Yucatan boars ranged from 158 kcal at 15 weeks of age to 126 kcal/kg BW.75 for 38 week old animals. Based on the similarity between the FMR of the Yucatan miniature swine in the present study and values published for standard size commercial hogs, it is concluded that the metabolic rates of these breeds of pig are similar. It is suggested that the daily energy needs of the Yucatan miniature pig may be met using values published for production livestock having similar physiological condition when adjusted for the smaller body size of the Yucatan breed.

Accuracy of genomic selection models in a large population of open-pollinated families in white spruce

PubMed Central

Beaulieu, J; Doerksen, T; Clément, S; MacKay, J; Bousquet, J

2014-01-01

Genomic selection (GS) is of interest in breeding because of its potential for predicting the genetic value of individuals and increasing genetic gains per unit of time. To date, very few studies have reported empirical results of GS potential in the context of large population sizes and long breeding cycles such as for boreal trees. In this study, we assessed the effectiveness of marker-aided selection in an undomesticated white spruce (Picea glauca (Moench) Voss) population of large effective size using a GS approach. A discovery population of 1694 trees representative of 214 open-pollinated families from 43 natural populations was phenotyped for 12 wood and growth traits and genotyped for 6385 single-nucleotide polymorphisms (SNPs) mined in 2660 gene sequences. GS models were built to predict estimated breeding values using all the available SNPs or SNP subsets of the largest absolute effects, and they were validated using various cross-validation schemes. The accuracy of genomic estimated breeding values (GEBVs) varied from 0.327 to 0.435 when the training and the validation data sets shared half-sibs that were on average 90% of the accuracies achieved through traditionally estimated breeding values. The trend was also the same for validation across sites. As expected, the accuracy of GEBVs obtained after cross-validation with individuals of unknown relatedness was lower with about half of the accuracy achieved when half-sibs were present. We showed that with the marker densities used in the current study, predictions with low to moderate accuracy could be obtained within a large undomesticated population of related individuals, potentially resulting in larger gains per unit of time with GS than with the traditional approach. PMID:24781808

Accounting for Genotype-by-Environment Interactions and Residual Genetic Variation in Genomic Selection for Water-Soluble Carbohydrate Concentration in Wheat.

PubMed

Ovenden, Ben; Milgate, Andrew; Wade, Len J; Rebetzke, Greg J; Holland, James B

2018-05-31

Abiotic stress tolerance traits are often complex and recalcitrant targets for conventional breeding improvement in many crop species. This study evaluated the potential of genomic selection to predict water-soluble carbohydrate concentration (WSCC), an important drought tolerance trait, in wheat under field conditions. A panel of 358 varieties and breeding lines constrained for maturity was evaluated under rainfed and irrigated treatments across two locations and two years. Whole-genome marker profiles and factor analytic mixed models were used to generate genomic estimated breeding values (GEBVs) for specific environments and environment groups. Additive genetic variance was smaller than residual genetic variance for WSCC, such that genotypic values were dominated by residual genetic effects rather than additive breeding values. As a result, GEBVs were not accurate predictors of genotypic values of the extant lines, but GEBVs should be reliable selection criteria to choose parents for intermating to produce new populations. The accuracy of GEBVs for untested lines was sufficient to increase predicted genetic gain from genomic selection per unit time compared to phenotypic selection if the breeding cycle is reduced by half by the use of GEBVs in off-season generations. Further, genomic prediction accuracy depended on having phenotypic data from environments with strong correlations with target production environments to build prediction models. By combining high-density marker genotypes, stress-managed field evaluations, and mixed models that model simultaneously covariances among genotypes and covariances of complex trait performance between pairs of environments, we were able to train models with good accuracy to facilitate genetic gain from genomic selection. Copyright © 2018 Ovenden et al.

Linkage disequilibrium, persistence of phase, and effective population size in Spanish local beef cattle breeds assessed through a high-density single nucleotide polymorphism chip.

PubMed

Cañas-Álvarez, J J; Mouresan, E F; Varona, L; Díaz, C; Molina, A; Baro, J A; Altarriba, J; Carabaño, M J; Casellas, J; Piedrafita, J

2016-07-01

Linkage disequilibrium (LD) and persistence of phase are fundamental approaches for exploring the genetic basis of economically important traits in cattle, including the identification of QTL for genomic selection and the estimation of effective population size () to determine the size of the training populations. In this study, we have used the Illumina BovineHD chip in 168 trios of 7 Spanish beef cattle breeds to obtain an overview of the magnitude of LD and the persistence of LD phase through the physical distance between markers. Also, we estimated the time of divergence based on the persistence of the LD phase and calculated past from LD estimates using different alternatives to define the recombination rate. Estimates of average (as a measure of LD) for adjacent markers were close to 0.52 in the 7 breeds and decreased with the distance between markers, although in long distances, some LD still remained (0.07 and 0.05 for markers 200 kb and 1 Mb apart, respectively). A panel with a lower boundary of 38,000 SNP would be necessary to launch a successful within-breed genomic selection program. Persistence of phase, measured as the pairwise correlations between estimates of in 2 breeds at short distances (10 kb), was in the 0.89 to 0.94 range and decreased from 0.33 to 0.52 to a range of 0.01 to 0.08 when marker distance increased from 200 kb to 1 Mb, respectively. The magnitude of the persistence of phase between the Spanish beef breeds was similar to those found in dairy breeds. For across-breed genomic selection, the size of the SNP panels must be in the range of 50,000 to 83,000 SNP. Estimates of past showed values ranging from 26 to 31 for 1 generation ago in all breeds. The divergence among breeds occurred between 129 and 207 generations ago. The results of this study are relevant for the future implementation of within- and across-breed genomic selection programs in the Spanish beef cattle populations. Our results suggest that a reduced subset of the SNP panel would be enough to achieve an adequate precision of the genomic predictions.

Evaluation of Columbia, U.S. Meat Animal Research Center Composite, Suffolk, and Texel rams as terminal sires in an extensive rangeland production system: VI. Measurements of live-lamb and carcass shape and their relationship to carcass yield and value.

PubMed

Notter, D R; Mousel, M R; Leeds, T D; Zerby, H N; Moeller, S J; Lewis, G S; Taylor, J B

2014-05-01

Linear measurements on live lambs and carcasses can be used to characterize sheep breeds and may have value for prediction of carcass yield and value. This study used 512 crossbred lambs produced over 3 yr by mating Columbia, U.S. Meat Animal Research Center (USMARC) Composite, Suffolk, and Texel rams to adult Rambouillet ewes to assess sire-breed differences in live-animal and carcass shape and to evaluate the value of shape measurements as predictors of chilled carcass weight (CCW), weight of high-value cuts (rack, loin, leg, and sirloin; HVW), weight of trimmed high-value cuts (trimmed rack and loin and trimmed, boneless leg and sirloin; TrHVW), and estimated carcass value before (CVal) and after trimming of high-value cuts (TrCVal). Lambs were produced under extensive rangeland conditions, weaned at an average age of 132 d, fed a concentrate diet in a drylot, and harvested in each year in 3 groups at target mean BW of 54, 61, and 68 kg. Canonical discriminant analysis indicated that over 93% of variation among sire breeds was accounted for by the contrast between tall, long, less-thickly muscled breeds with greater BW and CCW (i.e., the Columbia and Suffolk) compared with shorter, more thickly muscled breeds with smaller BW and CCW. After correcting for effects of year, harvest group, sire breed, and shipping BW, linear measurements on live lambs contributed little to prediction of CCW. Similarly, after accounting for effects of CCW, linear measurements on live animals further reduced residual SD (RSD) of dependent variables by 0.2 to 5.7%, with generally positive effects of increasing live leg width and generally negative effects of increasing heart girth. Carcass measurements were somewhat more valuable as predictors of carcass merit. After fitting effects of CCW, additional consideration of carcass shape reduced RSD by 2.1, 3.6, 9.5, and 2.2% for HVW, TrHVW, CVal, and TrCVal, respectively. Effects of increasing carcass leg width were positive for HVW, TrHVW, and TrCVal. We also observed positive effects of increasing carcass length on TrCVal and negative effects of increasing cannon bone length on HVW and CVal. Increasing shoulder width had positive effects on CVal but negative effects on TrHVW. Differences in lamb and carcass shape were significantly associated with carcass yield and value, but the additional accuracy associated with use of these measurements was modest relative to that achieved from use of only shipping BW or CCW.

Risk factor meta-analysis and Bayesian estimation of genetic parameters and breeding values for hypersensibility to cutaneous habronematidosis in donkeys.

PubMed

Navas González, Francisco Javier; Jordana Vidal, Jordi; Camacho Vallejo, María Esperanza; León Jurado, Jose Manuel; de la Haba Giraldo, Manuel Rafael; Barba Capote, Cecilio; Delgado Bermejo, Juan Vicente

2018-03-15

Cutaneous habronematidosis (CH) is a highly prevalent seasonally recurrent skin disease that affects donkeys as a result from the action of spirurid stomach worm larvae. Carrier flies mistakenly deposit these larvae on previous skin lesions or on the moisture of natural orifices, causing distress and inflicting relapsing wounds to the animals. First, we carried out a meta-analysis of the predisposing factors that could condition the development of CH in Andalusian donkeys. Second, basing on the empirical existence of an inter and intrafamilial variation previously addressed by owners, we isolated the genetic background behind the hypersensibility to this parasitological disease. To this aim, we designed a Bayesian linear model (BLM) to estimate the breeding values and genetic parameters for the hypersensibility to CH as a way to infer the potential selection suitability of this trait, seeking the improvement of donkey conservation programs. We studied the historical record of the cases of CH of 765 donkeys from 1984 to 2017. Fixed effects included birth year, birth season, sex, farm/owner, and husbandry system. Age was included as a linear and quadratic covariate. Although the effects of birth season and birth year were statistically non-significant (P > 0.05), their respective interactions with sex and farm/owner were statistically significant (P < 0.01), what translated into an increase of 40.5% in the specificity and of 0.6% of the sensibility of the model designed, when such interactions were included. Our BLM reported highly accurate genetic parameters as suggested by the low error of around 0.005, and the 95% credible interval for the heritability of ±0.0012. The CH hypersensibility heritability was 0.0346. The value of 0.1232 for additive genetic variance addresses a relatively low genetic variation in the Andalusian donkey breed. Our results suggest that farms managed under extensive husbandry conditions are the most protective ones against developing CH. Furthermore, these results provide evidence of the lack of repercussion of other factors such as age or sex. Potentially considering CH hypersensibility as a negative selection aimed goal in donkey breeding programs, may turn into a measure to improve animal welfare indirectly. However, the low heritability value makes it compulsory to control environmental factors to ensure the effectiveness of the breeding measures implemented to obtain individuals that may genetically be less prone to develop the condition. Copyright © 2018 Elsevier B.V. All rights reserved.

Chemical composition and structural characteristics of Arabian camel (Camelus dromedarius) m. longissimus thoracis.

PubMed

Al-Owaimer, A N; Suliman, G M; Sami, A S; Picard, B; Hocquette, J F

2014-03-01

Saudi Arabian camels of four breeds (6 animals per breed) were used to evaluate characteristics and quality of their meat. Chemical composition, fibre cross sectional area, collagen content, muscle metabolism, cooking loss, pH at 24 h post mortem, colour values (except redness) and shear force of Longissimus thoracis (LT) muscle did not differ between the breeds. Elevated pH values and short sarcomeres reduced overall tenderisation, with a difference between myofibril fragmentation index (P<0.001) and sarcomere length (P<0.05) between breeds. A positive correlation was observed between the activities of the mitochondrial enzymes (r>0.49), between the glycolytic activities (PFK and LDH) (r=0.61) and between Myosin Heavy Chain IIa and LDH activity. The intramuscular fat content was positively associated with redness and muscle oxidative metabolism, whereas shear force had a slight positive association with collagen content and muscle glycolytic metabolism and a negative association with muscle oxidative metabolism and muscle fibre area. © 2013.

Carcass measurements and meat quality characteristics of dairy suckling kids compared to an indigenous genotype.

PubMed

Ekiz, Bulent; Ozcan, Mustafa; Yilmaz, Alper; Tölü, Cemil; Savaş, Türker

2010-06-01

Effects of genotype on carcass measurements and meat quality were investigated by using 24 suckling kids from Turkish Saanen, Gokceada and Maltese breeds. Carcass quality characteristics of indigenous kids (Gokceada) were lower than those of dairy type (Turkish Saanen and Maltese) kids. Breed effect on ultimate meat pH, cooking loss, drip loss and Warner Bratzler shear force values were not significant. Meat samples from Turkish Saanen kids had higher redness (at 0, 1 and 24h) and yellowness (at 24h) values than Gokceada kids (P<0.05). Breed had no significant effect on sensory characteristics except flavour intensity. Flavour intensity scores given to meat samples of Maltese kids were higher than those of Turkish Saanen and Gokceada kids (P<0.01). In conclusion, dairy type breeds should be considered for meat production as well, with meat from Maltese kids potentially offering better colour and flavour intensity than that of Turkish Saanen kids. Copyright 2010 Elsevier Ltd. All rights reserved.

Reverse breeding: a novel breeding approach based on engineered meiosis.

PubMed

Dirks, Rob; van Dun, Kees; de Snoo, C Bastiaan; van den Berg, Mark; Lelivelt, Cilia L C; Voermans, William; Woudenberg, Leo; de Wit, Jack P C; Reinink, Kees; Schut, Johan W; van der Zeeuw, Eveline; Vogelaar, Aat; Freymark, Gerald; Gutteling, Evert W; Keppel, Marina N; van Drongelen, Paul; Kieny, Matthieu; Ellul, Philippe; Touraev, Alisher; Ma, Hong; de Jong, Hans; Wijnker, Erik

2009-12-01

Reverse breeding (RB) is a novel plant breeding technique designed to directly produce parental lines for any heterozygous plant, one of the most sought after goals in plant breeding. RB generates perfectly complementing homozygous parental lines through engineered meiosis. The method is based on reducing genetic recombination in the selected heterozygote by eliminating meiotic crossing over. Male or female spores obtained from such plants contain combinations of non-recombinant parental chromosomes which can be cultured in vitro to generate homozygous doubled haploid plants (DHs). From these DHs, complementary parents can be selected and used to reconstitute the heterozygote in perpetuity. Since the fixation of unknown heterozygous genotypes is impossible in traditional plant breeding, RB could fundamentally change future plant breeding. In this review, we discuss various other applications of RB, including breeding per chromosome.

Reverse breeding: a novel breeding approach based on engineered meiosis

PubMed Central

Dirks, Rob; van Dun, Kees; de Snoo, C Bastiaan; van den Berg, Mark; Lelivelt, Cilia L C; Voermans, William; Woudenberg, Leo; de Wit, Jack P C; Reinink, Kees; Schut, Johan W; van der Zeeuw, Eveline; Vogelaar, Aat; Freymark, Gerald; Gutteling, Evert W; Keppel, Marina N; van Drongelen, Paul; Kieny, Matthieu; Ellul, Philippe; Touraev, Alisher; Ma, Hong; de Jong, Hans; Wijnker, Erik

2009-01-01

Reverse breeding (RB) is a novel plant breeding technique designed to directly produce parental lines for any heterozygous plant, one of the most sought after goals in plant breeding. RB generates perfectly complementing homozygous parental lines through engineered meiosis. The method is based on reducing genetic recombination in the selected heterozygote by eliminating meiotic crossing over. Male or female spores obtained from such plants contain combinations of non-recombinant parental chromosomes which can be cultured in vitro to generate homozygous doubled haploid plants (DHs). From these DHs, complementary parents can be selected and used to reconstitute the heterozygote in perpetuity. Since the fixation of unknown heterozygous genotypes is impossible in traditional plant breeding, RB could fundamentally change future plant breeding. In this review, we discuss various other applications of RB, including breeding per chromosome. PMID:19811618

Spatial variation in egg size of a top predator: Interplay of body size and environmental factors?

NASA Astrophysics Data System (ADS)

Louzao, Maite; Igual, José M.; Genovart, Meritxell; Forero, Manuela G.; Hobson, Keith A.; Oro, Daniel

2008-09-01

It is expected that nearby populations are constrained by the same ecological features shaping in turn similarity in their ecological traits. Here, we studied the spatio-temporal variability in egg size among local populations of the critically endangered Balearic shearwater Puffinus mauretanicus, a top marine predator endemic to the western Mediterranean region. Specifically we assessed whether this trait was influenced by maternal body size, as an indicator of a genetic component, and feeding ecology (through stable-carbon and nitrogen-isotope measurements), as an indicator of environmental factors. We found that egg size varied among local populations, an unexpected result at such a small spatial scale. Body size differences at the local population level only partially explained such differences. Blood isotope measurements also differed among local populations. Values of δ 15N suggested inter-population differences in trophic level, showing a similar general pattern with egg size, and suggesting a nutritional link between them whereby egg size was affected by differences in feeding resources and/or behaviour. Values of δ 13C suggested that local populations did not differ in foraging habits with respect to benthic- vs. pelagic-based food-webs. Egg size did not vary among years as did breeding performance, suggesting that a differential temporal window could affect both breeding parameters in relation to food availability. The absence of a relationship between breeding performance and egg size suggested that larger eggs might only confer an advantage during harsh conditions. Alternatively parental quality could greatly affect breeding performance. We showed that inter-population differences in egg size could be influenced by both body size and environmental factors.

Validating the use of intrinsic markers in body feathers to identify inter-individual differences in non-breeding areas of northern fulmars.

PubMed

Quinn, Lucy R; Meharg, Andrew A; van Franeker, Jan A; Graham, Isla M; Thompson, Paul M

Many wildlife studies use chemical analyses to explore spatio-temporal variation in diet, migratory patterns and contaminant exposure. Intrinsic markers are particularly valuable for studying non-breeding marine predators, when direct methods of investigation are rarely feasible. However, any inferences regarding foraging ecology are dependent upon the time scale over which tissues such as feathers are formed. In this study, we validate the use of body feathers for studying non-breeding foraging patterns in a pelagic seabird, the northern fulmar. Analysis of carcasses of successfully breeding adult fulmars indicated that body feathers moulted between September and March, whereas analyses of carcasses and activity patterns suggested that wing feather and tail feather moult occurred during more restricted periods (September to October and September to January, respectively). By randomly sampling relevant body feathers, average values for individual birds were shown to be consistent. We also integrated chemical analyses of body feather with geolocation tracking data to demonstrate that analyses of δ 13 C and δ 15 N values successfully assigned 88 % of birds to one of two broad wintering regions used by breeding adult fulmars from a Scottish study colony. These data provide strong support for the use of body feathers as a tool for exploring non-breeding foraging patterns and diet in wide-ranging, pelagic seabirds.

Effects of incorporating environmental cost and risk aversion on economic values of pig breeding goal traits.

PubMed

Ali, B M; de Mey, Y; Bastiaansen, J W M; Oude Lansink, A G J M

2018-06-01

Economic values (EVs) of traits, accounting for environmental impacts and risk preferences of farmers, are required to design breeding goals that contribute to both economic and environmental sustainability. The objective of this study was to assess the effects of incorporating environmental costs and the risk preferences of farmers on the EVs of pig breeding goal traits. A breeding goal consisting of both sow efficiency and production traits was defined for a typical Brazilian farrow-to-finish pig farm with 1,500 productive sows. A mean-variance utility function was employed for deriving the EVs at finishing pig level assuming fixed slaughter weight. The inclusion of risk and risk aversion reduces the economic weights of sow efficiency traits (17%) while increasing the importance of production traits (7%). For a risk-neutral producer, inclusion of environmental cost reduces the economic importance of sow efficiency traits (3%) while increasing the importance of production traits (1%). Genetic changes of breeding goal traits by their genetic standard deviations reduce emissions of greenhouse gases, and excretions of nitrogen and phosphorus per finished pig by up to 6% while increasing farm profit. The estimated EVs could be used to improve selection criteria and thereby contribute to the sustainability of pig production systems. © 2018 The Authors. Journal of Animal Breeding and Genetics published by Blackwell Verlag GmbH.

Evaluation of Genome-Enabled Selection for Bacterial Cold Water Disease Resistance Using Progeny Performance Data in Rainbow Trout: Insights on Genotyping Methods and Genomic Prediction Models.

PubMed

Vallejo, Roger L; Leeds, Timothy D; Fragomeni, Breno O; Gao, Guangtu; Hernandez, Alvaro G; Misztal, Ignacy; Welch, Timothy J; Wiens, Gregory D; Palti, Yniv

2016-01-01

Bacterial cold water disease (BCWD) causes significant economic losses in salmonid aquaculture, and traditional family-based breeding programs aimed at improving BCWD resistance have been limited to exploiting only between-family variation. We used genomic selection (GS) models to predict genomic breeding values (GEBVs) for BCWD resistance in 10 families from the first generation of the NCCCWA BCWD resistance breeding line, compared the predictive ability (PA) of GEBVs to pedigree-based estimated breeding values (EBVs), and compared the impact of two SNP genotyping methods on the accuracy of GEBV predictions. The BCWD phenotypes survival days (DAYS) and survival status (STATUS) had been recorded in training fish (n = 583) subjected to experimental BCWD challenge. Training fish, and their full sibs without phenotypic data that were used as parents of the subsequent generation, were genotyped using two methods: restriction-site associated DNA (RAD) sequencing and the Rainbow Trout Axiom® 57 K SNP array (Chip). Animal-specific GEBVs were estimated using four GS models: BayesB, BayesC, single-step GBLUP (ssGBLUP), and weighted ssGBLUP (wssGBLUP). Family-specific EBVs were estimated using pedigree and phenotype data in the training fish only. The PA of EBVs and GEBVs was assessed by correlating mean progeny phenotype (MPP) with mid-parent EBV (family-specific) or GEBV (animal-specific). The best GEBV predictions were similar to EBV with PA values of 0.49 and 0.46 vs. 0.50 and 0.41 for DAYS and STATUS, respectively. Among the GEBV prediction methods, ssGBLUP consistently had the highest PA. The RAD genotyping platform had GEBVs with similar PA to those of GEBVs from the Chip platform. The PA of ssGBLUP and wssGBLUP methods was higher with the Chip, but for BayesB and BayesC methods it was higher with the RAD platform. The overall GEBV accuracy in this study was low to moderate, likely due to the small training sample used. This study explored the potential of GS for improving resistance to BCWD in rainbow trout using, for the first time, progeny testing data to assess the accuracy of GEBVs, and it provides the basis for further investigation on the implementation of GS in commercial rainbow trout populations.

Evaluation of Genome-Enabled Selection for Bacterial Cold Water Disease Resistance Using Progeny Performance Data in Rainbow Trout: Insights on Genotyping Methods and Genomic Prediction Models

PubMed Central

Vallejo, Roger L.; Leeds, Timothy D.; Fragomeni, Breno O.; Gao, Guangtu; Hernandez, Alvaro G.; Misztal, Ignacy; Welch, Timothy J.; Wiens, Gregory D.; Palti, Yniv

2016-01-01

Bacterial cold water disease (BCWD) causes significant economic losses in salmonid aquaculture, and traditional family-based breeding programs aimed at improving BCWD resistance have been limited to exploiting only between-family variation. We used genomic selection (GS) models to predict genomic breeding values (GEBVs) for BCWD resistance in 10 families from the first generation of the NCCCWA BCWD resistance breeding line, compared the predictive ability (PA) of GEBVs to pedigree-based estimated breeding values (EBVs), and compared the impact of two SNP genotyping methods on the accuracy of GEBV predictions. The BCWD phenotypes survival days (DAYS) and survival status (STATUS) had been recorded in training fish (n = 583) subjected to experimental BCWD challenge. Training fish, and their full sibs without phenotypic data that were used as parents of the subsequent generation, were genotyped using two methods: restriction-site associated DNA (RAD) sequencing and the Rainbow Trout Axiom® 57 K SNP array (Chip). Animal-specific GEBVs were estimated using four GS models: BayesB, BayesC, single-step GBLUP (ssGBLUP), and weighted ssGBLUP (wssGBLUP). Family-specific EBVs were estimated using pedigree and phenotype data in the training fish only. The PA of EBVs and GEBVs was assessed by correlating mean progeny phenotype (MPP) with mid-parent EBV (family-specific) or GEBV (animal-specific). The best GEBV predictions were similar to EBV with PA values of 0.49 and 0.46 vs. 0.50 and 0.41 for DAYS and STATUS, respectively. Among the GEBV prediction methods, ssGBLUP consistently had the highest PA. The RAD genotyping platform had GEBVs with similar PA to those of GEBVs from the Chip platform. The PA of ssGBLUP and wssGBLUP methods was higher with the Chip, but for BayesB and BayesC methods it was higher with the RAD platform. The overall GEBV accuracy in this study was low to moderate, likely due to the small training sample used. This study explored the potential of GS for improving resistance to BCWD in rainbow trout using, for the first time, progeny testing data to assess the accuracy of GEBVs, and it provides the basis for further investigation on the implementation of GS in commercial rainbow trout populations. PMID:27303436

Genome-wide association and genomic prediction of resistance to viral nervous necrosis in European sea bass (Dicentrarchus labrax) using RAD sequencing.

PubMed

Palaiokostas, Christos; Cariou, Sophie; Bestin, Anastasia; Bruant, Jean-Sebastien; Haffray, Pierrick; Morin, Thierry; Cabon, Joëlle; Allal, François; Vandeputte, Marc; Houston, Ross D

2018-06-08

European sea bass (Dicentrarchus labrax) is one of the most important species for European aquaculture. Viral nervous necrosis (VNN), commonly caused by the redspotted grouper nervous necrosis virus (RGNNV), can result in high levels of morbidity and mortality, mainly during the larval and juvenile stages of cultured sea bass. In the absence of efficient therapeutic treatments, selective breeding for host resistance offers a promising strategy to control this disease. Our study aimed at investigating genetic resistance to VNN and genomic-based approaches to improve disease resistance by selective breeding. A population of 1538 sea bass juveniles from a factorial cross between 48 sires and 17 dams was challenged with RGNNV with mortalities and survivors being recorded and sampled for genotyping by the RAD sequencing approach. We used genome-wide genotype data from 9195 single nucleotide polymorphisms (SNPs) for downstream analysis. Estimates of heritability of survival on the underlying scale for the pedigree and genomic relationship matrices were 0.27 (HPD interval 95%: 0.14-0.40) and 0.43 (0.29-0.57), respectively. Classical genome-wide association analysis detected genome-wide significant quantitative trait loci (QTL) for resistance to VNN on chromosomes (unassigned scaffolds in the case of 'chromosome' 25) 3, 20 and 25 (P < 1e06). Weighted genomic best linear unbiased predictor provided additional support for the QTL on chromosome 3 and suggested that it explained 4% of the additive genetic variation. Genomic prediction approaches were tested to investigate the potential of using genome-wide SNP data to estimate breeding values for resistance to VNN and showed that genomic prediction resulted in a 13% increase in successful classification of resistant and susceptible animals compared to pedigree-based methods, with Bayes A and Bayes B giving the highest predictive ability. Genome-wide significant QTL were identified but each with relatively small effects on the trait. Tests of genomic prediction suggested that incorporating genome-wide SNP data is likely to result in higher accuracy of estimated breeding values for resistance to VNN. RAD sequencing is an effective method for generating such genome-wide SNPs, and our findings highlight the potential of genomic selection to breed farmed European sea bass with improved resistance to VNN.

Genetic diversity of dog breeds: within-breed diversity comparing genealogical and molecular data.

PubMed

Leroy, G; Verrier, E; Meriaux, J C; Rognon, X

2009-06-01

The genetic diversity of 61 dog breeds raised in France was investigated. Genealogical analyses were performed on the pedigree file of the French kennel club. A total of 1514 dogs were also genotyped using 21 microsatellite markers. For animals born from 2001 to 2005, the average coefficient of inbreeding ranged from 0.2% to 8.8% and the effective number of ancestors ranged from 9 to 209, according to the breed. The mean value of heterozygosity was 0.62 over all breeds (range 0.37-0.77). At the breed level, few correlations were found between genealogical and molecular parameters. Kinship coefficients and individual similarity estimators were, however, significantly correlated, with the best mean correlation being found for the Lynch & Ritland estimator (r = 0.43). According to both approaches, it was concluded that special efforts should be made to maintain diversity for three breeds, namely the Berger des Pyrénées, Braque Saint-Germain and Bull Terrier.

Combined prevalence of inherited skeletal disorders in dog breeds in Belgium.

PubMed

Coopman, F; Broeckx, B; Verelst, E; Deforce, D; Saunders, J; Duchateau, L; Verhoeven, G

2014-01-01

Canine hip dysplasia (CHD), canine elbow dysplasia (CED), and humeral head osteochondrosis (HHOC) are inherited traits with uneven incidence in dog breeds. Knowledge of the combined prevalence of these three disorders is necessary to estimate the effect of the currently applied breeding strategies, in order to improve the genetic health of the population. Official screening results of the Belgian National Committee for Inherited Skeletal Disorders (NCSID) revealed that an average of 31.8% (CHD, CED, or both; n = 1273 dogs) and 47.2% (CHD, CED, HHOC, or a combination of these three diseases; n = 250 dogs) of dogs are mildly to severely affected by at least one skeletal disorder. According to the current breeding recommendations in some dog breeds in Belgium, these animals should be restricted (mild signs) or excluded (moderate to severe signs) from breeding. The introduction of genetic parameters, such as estimated breeding values, might create a better approach to gradually reduce the incidence of these complex inherited joint disorders, without compromising genetic population health.

What’s in a Name? Effect of Breed Perceptions & Labeling on Attractiveness, Adoptions & Length of Stay for Pit-Bull-Type Dogs

PubMed Central

Gunter, Lisa M.; Barber, Rebecca T.; Wynne, Clive D. L.

2016-01-01

Previous research has indicated that certain breeds of dogs stay longer in shelters than others. However, exactly how breed perception and identification influences potential adopters' decisions remains unclear. Current dog breed identification practices in animal shelters are often based upon information supplied by the relinquishing owner, or staff determination based on the dog's phenotype. However, discrepancies have been found between breed identification as typically assessed by welfare agencies and the outcome of DNA analysis. In Study 1, the perceived behavioral and adoptability characteristics of a pit-bull-type dog were compared with those of a Labrador Retriever and Border Collie. How the addition of a human handler influenced those perceptions was also assessed. In Study 2, lengths of stay and perceived attractiveness of dogs that were labeled as pit bull breeds were compared to dogs that were phenotypically similar but were labeled as another breed at an animal shelter. The latter dogs were called "lookalikes." In Study 3, we compared perceived attractiveness in video recordings of pit-bull-type dogs and lookalikes with and without breed labels. Lastly, data from an animal shelter that ceased applying breed labeling on kennels were analyzed, and lengths of stay and outcomes for all dog breeds, including pit bulls, before and after the change in labeling practice were compared. In total, these findings suggest that breed labeling influences potential adopters' perceptions and decision-making. Given the inherent complexity of breed assignment based on morphology coupled with negative breed perceptions, removing breed labels is a relatively low-cost strategy that will likely improve outcomes for dogs in animal shelters. PMID:27008213

What's in a Name? Effect of Breed Perceptions & Labeling on Attractiveness, Adoptions & Length of Stay for Pit-Bull-Type Dogs.

PubMed

Gunter, Lisa M; Barber, Rebecca T; Wynne, Clive D L

2016-01-01

Previous research has indicated that certain breeds of dogs stay longer in shelters than others. However, exactly how breed perception and identification influences potential adopters' decisions remains unclear. Current dog breed identification practices in animal shelters are often based upon information supplied by the relinquishing owner, or staff determination based on the dog's phenotype. However, discrepancies have been found between breed identification as typically assessed by welfare agencies and the outcome of DNA analysis. In Study 1, the perceived behavioral and adoptability characteristics of a pit-bull-type dog were compared with those of a Labrador Retriever and Border Collie. How the addition of a human handler influenced those perceptions was also assessed. In Study 2, lengths of stay and perceived attractiveness of dogs that were labeled as pit bull breeds were compared to dogs that were phenotypically similar but were labeled as another breed at an animal shelter. The latter dogs were called "lookalikes." In Study 3, we compared perceived attractiveness in video recordings of pit-bull-type dogs and lookalikes with and without breed labels. Lastly, data from an animal shelter that ceased applying breed labeling on kennels were analyzed, and lengths of stay and outcomes for all dog breeds, including pit bulls, before and after the change in labeling practice were compared. In total, these findings suggest that breed labeling influences potential adopters' perceptions and decision-making. Given the inherent complexity of breed assignment based on morphology coupled with negative breed perceptions, removing breed labels is a relatively low-cost strategy that will likely improve outcomes for dogs in animal shelters.

Sire carcass breeding values affect body composition in lambs - 1. Effects on lean weight and its distribution within the carcass as measured by computed tomography.

PubMed

Anderson, F; Williams, A; Pannier, L; Pethick, D W; Gardner, G E

2015-10-01

Data are obtained from computed tomography scanning of 1665 lambs at locations around Australia. Lambs were progeny of Terminal, Maternal and Merino sires with known Australian Sheep Breeding Values for post weaning c-site eye muscle depth (mm; PEMD) and fat depth (mm; PFAT), and post weaning weight (kg; PWWT). Across the 7.8 unit range of sire PEMD, carcass lean weight increased by 7.7%. This lean was distributed to the saddle section (mid-section) where lean became 3.8% heavier, with fore section lean becoming 3.5% lighter. Reducing sire PFAT across its 5.1 unit range increased carcass lean weight by 9.5%, and distributed lean to the saddle section which was 3.7% heavier. Increasing sire PWWT increased lean at some sites in some years, and on average increased saddle lean by 4% across the 24.7 unit PWWT range. Changes in lean weight and distribution due to selection for carcass breeding values will increase carcass value, particularly through increased weight of high value loin cuts. Copyright © 2015. Published by Elsevier Ltd.

Monitoring changes in the demographic and genealogical structure of the main Spanish local beef breeds.

PubMed

Cañas-Álvarez, J J; Gónzalez-Rodríguez, A; Martín-Collado, D; Avilés, C; Altarriba, J; Baro, J A; De la Fuente, L F; Díaz, C; Molina, A; Varona, L; Piedrafita, J

2014-10-01

Demographic and pedigree analyses describe the structure and dynamics of livestock populations. We studied information recorded in the herdbooks of Asturiana de los Valles (AV; N = 458,806), Avileña-Negra Ibérica (ANI; N = 204,623), Bruna dels Pirineus (BP; N = 62,138), Morucha (Mo; N = 65,350), Pirenaica (Pi; N = 217,428), Retinta (Re; N = 135,300), and Rubia Gallega (RG; N = 235,511) beef breeds from their creation until 2009. All breeds have increased in the number of registered cows in recent years. In all breeds, herds do not behave as isolated entities and a high rate of exchange of breeding males between herds exists. A percentage of herds (12-52%) make some type of selection and sell bulls to other herds. There were large differences in average number of progeny per bull, ranging from 15.6 (AV) to 373.7 animals (RG, with a high incidence of AI). Generation interval estimates ranged from 4.7 (AV) to 7.6 (RG) yr in the sire pathway and from 5.95 (AV) to 7.8 (Mo) yr in the dam pathway. Density of pedigrees varied among breeds, with Pi, ANI, and Re having the more dense pedigrees, with average completeness indexes of more than 96% in the first generation and 80% when 6 generations were considered. A general increase in average inbreeding was observed in all breeds in the years analyzed. For animals born in 2009, average inbreeding coefficients ranged from 0.6 (BP) to 7.2% (Re) when all animals were considered and from 3.6 (Pi) to 17.6% (BP) when only inbred animals were considered. Due to the lack of completeness of pedigrees in most populations, inbreeding coefficients may be considered as a lower bound of the true parameters. The proportion of inbred animals tended to increase in the periods analyzed in all breeds. Differences between inbreeding and coancestry rates (except in RG) suggest the presence of population structure. Effective population size (Ne) based on the inbreeding rate estimated by regression ranged from 43 to 378 for Re and BP, whereas Ne estimates based on coancestry were greater, with a range of 100 for RG to 9,985 for BP. These facts suggest that an adequate mating policy can help to monitor inbreeding so as not to lose genetic variability. Effective number of ancestors in 2009 for 6 of the breeds ranged from 42 (RG) to 220 (AV), with BP having much a greater value, and was lower than was the effective number of founders in all breeds, suggesting the existence of bottlenecks.

Unified method to integrate and blend several, potentially related, sources of information for genetic evaluation.

PubMed

Vandenplas, Jérémie; Colinet, Frederic G; Gengler, Nicolas

2014-09-30

A condition to predict unbiased estimated breeding values by best linear unbiased prediction is to use simultaneously all available data. However, this condition is not often fully met. For example, in dairy cattle, internal (i.e. local) populations lead to evaluations based only on internal records while widely used foreign sires have been selected using internally unavailable external records. In such cases, internal genetic evaluations may be less accurate and biased. Because external records are unavailable, methods were developed to combine external information that summarizes these records, i.e. external estimated breeding values and associated reliabilities, with internal records to improve accuracy of internal genetic evaluations. Two issues of these methods concern double-counting of contributions due to relationships and due to records. These issues could be worse if external information came from several evaluations, at least partially based on the same records, and combined into a single internal evaluation. Based on a Bayesian approach, the aim of this research was to develop a unified method to integrate and blend simultaneously several sources of information into an internal genetic evaluation by avoiding double-counting of contributions due to relationships and due to records. This research resulted in equations that integrate and blend simultaneously several sources of information and avoid double-counting of contributions due to relationships and due to records. The performance of the developed equations was evaluated using simulated and real datasets. The results showed that the developed equations integrated and blended several sources of information well into a genetic evaluation. The developed equations also avoided double-counting of contributions due to relationships and due to records. Furthermore, because all available external sources of information were correctly propagated, relatives of external animals benefited from the integrated information and, therefore, more reliable estimated breeding values were obtained. The proposed unified method integrated and blended several sources of information well into a genetic evaluation by avoiding double-counting of contributions due to relationships and due to records. The unified method can also be extended to other types of situations such as single-step genomic or multi-trait evaluations, combining information across different traits.

Fish genome manipulation and directional breeding.

PubMed

Ye, Ding; Zhu, ZuoYan; Sun, YongHua

2015-02-01

Aquaculture is one of the fastest developing agricultural industries worldwide. One of the most important factors for sustainable aquaculture is the development of high performing culture strains. Genome manipulation offers a powerful method to achieve rapid and directional breeding in fish. We review the history of fish breeding methods based on classical genome manipulation, including polyploidy breeding and nuclear transfer. Then, we discuss the advances and applications of fish directional breeding based on transgenic technology and recently developed genome editing technologies. These methods offer increased efficiency, precision and predictability in genetic improvement over traditional methods.

Comparison of the large muscle group widths of the pelvic limb in seven breeds of dogs.

PubMed

Sabanci, Seyyid Said; Ocal, Mehmet Kamil

2018-05-14

Orthopaedic diseases are common in the pelvic limbs of dogs, and reference values for large muscle groups of the pelvic limb may aid in diagnosis such diseases. As such, the objective of this study was to compare the large muscle groups of the pelvic limb in seven breeds of dogs. A total of 126 dogs from different breeds were included, and the widths of the quadriceps, hamstring and gastrocnemius muscles were measured from images of the lateral radiographies. The width of the quadriceps was not different between the breeds, but the widths of the hamstring and gastrocnemius muscles were significantly different between the breeds. The widest hamstring and gastrocnemius muscles were seen in the Rottweilers and the Boxers, respectively. The narrowest hamstring and gastrocnemius muscles were seen in the Belgian Malinois and the Golden retrievers, respectively. All ratios between the measured muscles differed significantly between the breeds. Doberman pinschers and Belgian Malinois had the highest ratio of gastrocnemius width:hamstring width. Doberman pinschers had also the highest ratio of quadriceps width:hamstring width. German shepherds had the highest ratio of gastrocnemius width:quadriceps width. The lowest ratios of quadriceps width:hamstring width were determined in the German shepherds. The ratios of the muscle widths may be used as reference values to assess muscular atrophy or hypertrophy in cases of bilateral or unilateral orthopaedic diseases of the pelvic limbs. Further studies are required to determine the widths and ratios of the large muscle groups of the pelvic limbs in other dog breeds. © 2018 Blackwell Verlag GmbH.

Economic values of production and functional traits, including residual feed intake, in Finnish milk production.

PubMed

Hietala, P; Wolfová, M; Wolf, J; Kantanen, J; Juga, J

2014-02-01

Improving the feed efficiency of dairy cattle has a substantial effect on the economic efficiency and on the reduction of harmful environmental effects of dairy production through lower feeding costs and emissions from dairy farming. To assess the economic importance of feed efficiency in the breeding goal for dairy cattle, the economic values for the current breeding goal traits and the additional feed efficiency traits for Finnish Ayrshire cattle under production circumstances in 2011 were determined. The derivation of economic values was based on a bioeconomic model in which the profit of the production system was calculated, using the generated steady state herd structure. Considering beef production from dairy farms, 2 marketing strategies for surplus calves were investigated: (A) surplus calves were sold at a young age and (B) surplus calves were fattened on dairy farms. Both marketing strategies were unprofitable when subsidies were not included in the revenues. When subsidies were taken into account, a positive profitability was observed in both marketing strategies. The marginal economic values for residual feed intake (RFI) of breeding heifers and cows were -25.5 and -55.8 €/kg of dry matter per day per cow and year, respectively. The marginal economic value for RFI of animals in fattening was -29.5 €/kg of dry matter per day per cow and year. To compare the economic importance among traits, the standardized economic weight of each trait was calculated as the product of the marginal economic value and the genetic standard deviation; the standardized economic weight expressed as a percentage of the sum of all standardized economic weights was called relative economic weight. When not accounting for subsidies, the highest relative economic weight was found for 305-d milk yield (34% in strategy A and 29% in strategy B), which was followed by protein percentage (13% in strategy A and 11% in strategy B). The third most important traits were calving interval (9%) and mature weight of cows (11%) in strategy A and B, respectively. The sums of the relative economic weights over categories for RFI were 6 and 7% in strategy A and B, respectively. Under production conditions in 2011, the relative economic weights for the studied feed efficiency traits were low. However, it is possible that the relative importance of feed efficiency traits in the breeding goal will increase in the future due to increasing requirements to mitigate the environmental impact of milk production. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

An emperor penguin population estimate: the first global, synoptic survey of a species from space.

PubMed

Fretwell, Peter T; Larue, Michelle A; Morin, Paul; Kooyman, Gerald L; Wienecke, Barbara; Ratcliffe, Norman; Fox, Adrian J; Fleming, Andrew H; Porter, Claire; Trathan, Phil N

2012-01-01

Our aim was to estimate the population of emperor penguins (Aptenodytes fosteri) using a single synoptic survey. We examined the whole continental coastline of Antarctica using a combination of medium resolution and Very High Resolution (VHR) satellite imagery to identify emperor penguin colony locations. Where colonies were identified, VHR imagery was obtained in the 2009 breeding season. The remotely-sensed images were then analysed using a supervised classification method to separate penguins from snow, shadow and guano. Actual counts of penguins from eleven ground truthing sites were used to convert these classified areas into numbers of penguins using a robust regression algorithm.We found four new colonies and confirmed the location of three previously suspected sites giving a total number of emperor penguin breeding colonies of 46. We estimated the breeding population of emperor penguins at each colony during 2009 and provide a population estimate of ~238,000 breeding pairs (compared with the last previously published count of 135,000-175,000 pairs). Based on published values of the relationship between breeders and non-breeders, this translates to a total population of ~595,000 adult birds.There is a growing consensus in the literature that global and regional emperor penguin populations will be affected by changing climate, a driver thought to be critical to their future survival. However, a complete understanding is severely limited by the lack of detailed knowledge about much of their ecology, and importantly a poor understanding of their total breeding population. To address the second of these issues, our work now provides a comprehensive estimate of the total breeding population that can be used in future population models and will provide a baseline for long-term research.

An Emperor Penguin Population Estimate: The First Global, Synoptic Survey of a Species from Space

PubMed Central

Fretwell, Peter T.; LaRue, Michelle A.; Morin, Paul; Kooyman, Gerald L.; Wienecke, Barbara; Ratcliffe, Norman; Fox, Adrian J.; Fleming, Andrew H.; Porter, Claire; Trathan, Phil N.

2012-01-01

Our aim was to estimate the population of emperor penguins (Aptenodytes fosteri) using a single synoptic survey. We examined the whole continental coastline of Antarctica using a combination of medium resolution and Very High Resolution (VHR) satellite imagery to identify emperor penguin colony locations. Where colonies were identified, VHR imagery was obtained in the 2009 breeding season. The remotely-sensed images were then analysed using a supervised classification method to separate penguins from snow, shadow and guano. Actual counts of penguins from eleven ground truthing sites were used to convert these classified areas into numbers of penguins using a robust regression algorithm. We found four new colonies and confirmed the location of three previously suspected sites giving a total number of emperor penguin breeding colonies of 46. We estimated the breeding population of emperor penguins at each colony during 2009 and provide a population estimate of ∼238,000 breeding pairs (compared with the last previously published count of 135,000–175,000 pairs). Based on published values of the relationship between breeders and non-breeders, this translates to a total population of ∼595,000 adult birds. There is a growing consensus in the literature that global and regional emperor penguin populations will be affected by changing climate, a driver thought to be critical to their future survival. However, a complete understanding is severely limited by the lack of detailed knowledge about much of their ecology, and importantly a poor understanding of their total breeding population. To address the second of these issues, our work now provides a comprehensive estimate of the total breeding population that can be used in future population models and will provide a baseline for long-term research. PMID:22514609

Detection of potential mosquito breeding sites based on community sourced geotagged images

NASA Astrophysics Data System (ADS)

Agarwal, Ankit; Chaudhuri, Usashi; Chaudhuri, Subhasis; Seetharaman, Guna

2014-06-01

Various initiatives have been taken all over the world to involve the citizens in the collection and reporting of data to make better and informed data-driven decisions. Our work shows how the geotagged images collected through the general population can be used to combat Malaria and Dengue by identifying and visualizing localities that contain potential mosquito breeding sites. Our method first employs image quality assessment on the client side to reject the images with distortions like blur and artifacts. Each geotagged image received on the server is converted into a feature vector using the bag of visual words model. We train an SVM classifier on a histogram-based feature vector obtained after the vector quantization of SIFT features to discriminate images containing either a small stagnant water body like puddle, or open containers and tires, bushes etc. from those that contain flowing water, manicured lawns, tires attached to a vehicle etc. A geographical heat map is generated by assigning a specific location a probability value of it being a potential mosquito breeding ground of mosquito using feature level fusion or the max approach presented in the paper. The heat map thus generated can be used by concerned health authorities to take appropriate action and to promote civic awareness.

9 CFR 52.3 - Appraisal of swine.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE... § 52.3 Appraisal of swine. (a) Herds of swine and individual breeding sows to be destroyed because they... determined by the meat or breeding value of the animals. Animals may be appraised in groups, provided that...

9 CFR 52.3 - Appraisal of swine.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE... § 52.3 Appraisal of swine. (a) Herds of swine and individual breeding sows to be destroyed because they... determined by the meat or breeding value of the animals. Animals may be appraised in groups, provided that...

Disease evaluations and agronomic traits of advanced peanut breeding lines in 2017

USDA-ARS?s Scientific Manuscript database

Disease evaluations of advanced peanut breeding lines are conducted annually to compare the agronomic traits (crop value, yield, seed grade and characteristics) and disease resistance in cultivars that are currently available or close to being released for the Southwest. In 2017, a total of 19 comm...

Assessing the breeding potential of extra-long staple germplasm in an upland cotton breeding program

USDA-ARS?s Scientific Manuscript database

Fiber quality improvement of upland cotton (Gossypium hirsutum L.) is essential to increase the value and competitiveness of cotton fiber. The closely related allotetraploid species G. barbadense has long been targeted as a source of beneficial fiber quality alleles. Although interspecific hybridiza...

Variation and correlations among European and North American orchardgrass germplasm for herbage yield and nutritive value

USDA-ARS?s Scientific Manuscript database

Efforts to improve water soluble carbohydrate (WSC) concentrations have come to the forefront of perennial forage grass breeding over the last decades. Perennial ryegrass (Lolium perenne L.) breeding has been very successful in developing new cultivars with high WSC and high agronomic performance. ...

Genetic diversity and association mapping of mineral element concentrations in spinach leaves

USDA-ARS?s Scientific Manuscript database

Spinach is one of the healthiest vegetables in the human diet due to its high concentrations of nutrients and mineral elements. Breeding new spinach cultivars with high nutritional value is one of the main goals in spinach breeding programs worldwide, and identification of single nucleotide polymorp...

Farmer views on calving difficulty consequences on dairy and beef farms.

PubMed

Martin-Collado, D; Hely, F; Byrne, T J; Evans, R; Cromie, A R; Amer, P R

2017-02-01

Calving difficulty (CD) is a key functional trait with significant influence on herd profitability and animal welfare. Breeding plays an important role in managing CD both at farm and industry level. An alternative to the economic value approach to determine the CD penalty is to complement the economic models with the analysis of farmer perceived on-farm impacts of CD. The aim of this study was to explore dairy and beef farmer views and perceptions on the economic and non-economic on-farm consequences of CD, to ultimately inform future genetic selection tools for the beef and dairy industries in Ireland. A standardised quantitative online survey was released to all farmers with e-mail addresses on the Irish Cattle Breeding Federation database. In total, 271 farmers completed the survey (173 beef farmers and 98 dairy farmers). Both dairy and beef farmers considered CD a very important issue with economic and non-economic components. However, CD was seen as more problematic by dairy farmers, who mostly preferred to slightly reduce its incidence, than by beef farmers, who tended to support increases in calf value even though it would imply a slight increase in CD incidence. Farm size was found to be related to dairy farmer views of CD with farmers from larger farms considering CD as more problematic than farmers from smaller farms. CD breeding value was reported to be critical for selecting beef sires to mate with either beef or dairy cows, whereas when selecting dairy sires, CD had lower importance than breeding values for other traits. There was considerable variability in the importance farmers give to CD breeding values that could not be explained by the farm type or the type of sire used, which might be related to the farmer non-economic motives. Farmer perceived economic value associated with incremental increases in CD increases substantially as the CD level considered increases. This non-linear relationship cannot be reflected in a standard linear index weighting. The results of this paper provide key underpinning support to the development of non-linear index weightings for CD in Irish national indexes.

Trade-off between mating opportunities and parental care: brood desertion by female Kentish plovers.

PubMed

Székely, T; Cuthill, I C

2000-10-22

Why do some parents care for their young whereas others divorce from their mate and abandon their offspring? This decision is governed by the trade-off between the value of the current breeding event and future breeding prospects. In the precocial Kentish plover Charadrius alexandrinus females frequently, but not always, abandon their broods to be cared for by their mate, and seek new breeding partners within the same season. We have shown previously that females' remating opportunities decline with date in the season, so brood desertion should be particularly favourable for early breeding females. However, the benefits are tempered by the fact that single-parent families have lower survival expectancies than those where the female remains to help the male care for the young. We therefore tested the prediction that increasing the value of the current brood (by brood-size manipulation) should increase the duration of female care early in the season, but that in late breeders, with reduced remating opportunities, desertion and thus the duration of female care should be independent of current brood size. These predictions were fulfilled, indicating that seasonally modulated trade-offs between current brood value and remating opportunities can be important in the desertion decisions of species with flexible patterns of parental care.

Trade-off between mating opportunities and parental care: brood desertion by female Kentish plovers.

PubMed Central

Székely, T; Cuthill, I C

2000-01-01

Why do some parents care for their young whereas others divorce from their mate and abandon their offspring? This decision is governed by the trade-off between the value of the current breeding event and future breeding prospects. In the precocial Kentish plover Charadrius alexandrinus females frequently, but not always, abandon their broods to be cared for by their mate, and seek new breeding partners within the same season. We have shown previously that females' remating opportunities decline with date in the season, so brood desertion should be particularly favourable for early breeding females. However, the benefits are tempered by the fact that single-parent families have lower survival expectancies than those where the female remains to help the male care for the young. We therefore tested the prediction that increasing the value of the current brood (by brood-size manipulation) should increase the duration of female care early in the season, but that in late breeders, with reduced remating opportunities, desertion and thus the duration of female care should be independent of current brood size. These predictions were fulfilled, indicating that seasonally modulated trade-offs between current brood value and remating opportunities can be important in the desertion decisions of species with flexible patterns of parental care. PMID:11416913

Use of microsatellite markers to assign goats to their breeds.

PubMed

Aljumaah, R S; Alobre, M M; Al-Atiyat, R M

2015-08-07

We investigated the potential of 17 microsatellite markers for assigning Saudi goat individuals to their breeds. Three local breeds, Bishi, Jabali, and Tohami were genotyped using these markers, and Somali goats were used as a reference breed. The majority of alleles were shared between the breeds, except for some that were specific to each breed. The Garza-Williamson index was lowest in the Bishi breed, indicating that a recent bottleneck event occurred. The overall results assigned the goat individuals (based on their genotypes) to the same breeds from which they were sampled, except in a few cases. The individuals' genotypes were sufficient to provide a clear distinction between the Somali goat breed and the others. In three factorial dimensions, the results of a correspondence analysis indicated that the total variation for the first and second factors was 48.85 and 31.43%, respectively. Consequently, Jabali, Bishi, and Tohami goats were in separate groups. The Jabali goat was closely related to the Bishi goat. Somali goats were distinguished from each other and from individuals of the other three goat breeds. The markers were successful in assigning individual goats to their breeds, based on the likelihood of a given individual's genotype.

Genetic diversity in German draught horse breeds compared with a group of primitive, riding and wild horses by means of microsatellite DNA markers.

PubMed

Aberle, K S; Hamann, H; Drögemüller, C; Distl, O

2004-08-01

We compared the genetic diversity and distance among six German draught horse breeds to wild (Przewalski's Horse), primitive (Icelandic Horse, Sorraia Horse, Exmoor Pony) or riding horse breeds (Hanoverian Warmblood, Arabian) by means of genotypic information from 30 microsatellite loci. The draught horse breeds included the South German Coldblood, Rhenish German Draught Horse, Mecklenburg Coldblood, Saxon Thuringa Coldblood, Black Forest Horse and Schleswig Draught Horse. Despite large differences in population sizes, the average observed heterozygosity (H(o)) differed little among the heavy horse breeds (0.64-0.71), but was considerably lower than in the Hanoverian Warmblood or Icelandic Horse population. The mean number of alleles (N(A)) decreased more markedly with declining population sizes of German draught horse breeds (5.2-6.3) but did not reach the values of Hanoverian Warmblood (N(A) = 6.7). The coefficient of differentiation among the heavy horse breeds showed 11.6% of the diversity between the heavy horse breeds, as opposed to 21.2% between the other horse populations. The differentiation test revealed highly significant genetic differences among all draught horse breeds except the Mecklenburg and Saxon Thuringa Coldbloods. The Schleswig Draught Horse was the most distinct draught horse breed. In conclusion, the study demonstrated a clear distinction among the German draught horse breeds and even among breeds with a very short history of divergence like Rhenish German Draught Horse and its East German subpopulations Mecklenburg and Saxon Thuringa Coldblood.

Breeding of Acrocomia aculeata using genetic diversity parameters and correlations to select accessions based on vegetative, phenological, and reproductive characteristics.

PubMed

Coser, S M; Motoike, S Y; Corrêa, T R; Pires, T P; Resende, M D V

2016-10-17

Macaw palm (Acrocomia aculeata) is a promising species for use in biofuel production, and establishing breeding programs is important for the development of commercial plantations. The aim of the present study was to analyze genetic diversity, verify correlations between traits, estimate genetic parameters, and select different accessions of A. aculeata in the Macaw Palm Germplasm Bank located in Universidade Federal de Viçosa, to develop a breeding program for this species. Accessions were selected based on precocity (PREC), total spathe (TS), diameter at breast height (DBH), height of the first spathe (HFS), and canopy area (CA). The traits were evaluated in 52 accessions during the 2012/2013 season and analyzed by restricted estimation maximum likelihood/best linear unbiased predictor procedures. Genetic diversity resulted in the formation of four groups by Tocher's clustering method. The correlation analysis showed it was possible to have indirect and early selection for the traits PREC and DBH. Estimated genetic parameters strengthened the genetic variability verified by cluster analysis. Narrow-sense heritability was classified as moderate (PREC, TS, and CA) to high (HFS and DBH), resulting in strong genetic control of the traits and success in obtaining genetic gains by selection. Accuracy values were classified as moderate (PREC and CA) to high (TS, HFS, and DBH), reinforcing the success of the selection process. Selection of accessions for PREC, TS, and HFS by the rank-average method permits selection gains of over 100%, emphasizing the successful use of the accessions in breeding programs and obtaining superior genotypes for commercial plantations.

Estimation of the genetic diversity in tetraploid alfalfa populations based on RAPD markers for breeding purposes.

PubMed

Nagl, Nevena; Taski-Ajdukovic, Ksenija; Barac, Goran; Baburski, Aleksandar; Seccareccia, Ivana; Milic, Dragan; Katic, Slobodan

2011-01-01

Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon's information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA) showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm.

Differential Gene Expression across Breed and Sex in Commercial Pigs Administered Fenbendazole and Flunixin Meglumine

PubMed Central

Howard, Jeremy T.; O’Nan, Audrey T.; Maltecca, Christian; Baynes, Ronald E.; Ashwell, Melissa S.

2015-01-01

Characterizing the variability in transcript levels across breeds and sex in swine for genes that play a role in drug metabolism may shed light on breed and sex differences in drug metabolism. The objective of the study is to determine if there is heterogeneity between swine breeds and sex in transcript levels for genes previously shown to play a role in drug metabolism for animals administered flunixin meglumine or fenbendazole. Crossbred nursery female and castrated male pigs (n = 169) spread across 5 groups were utilized. Sires (n = 15) of the pigs were purebred Duroc, Landrace, Yorkshire or Hampshire boars mated to a common sow population. Animals were randomly placed into the following treatments: no drug (control), flunixin meglumine, or fenbendazole. One hour after the second dosing, animals were sacrificed and liver samples collected. Quantitative Real-Time PCR was used to measure liver gene expression of the following genes: SULT1A1, ABCB1, CYP1A2, CYP2E1, CYP3A22 and CYP3A29. The control animals were used to investigate baseline transcript level differences across breed and sex. Post drug administration transcript differences across breed and sex were investigated by comparing animals administered the drug to the controls. Contrasts to determine fold change were constructed from a model that included fixed and random effects within each drug. Significant (P-value <0.007) basal transcript differences were found across breeds for SULT1A1, CYP3A29 and CYP3A22. Across drugs, significant (P-value <0.0038) transcript differences existed between animals given a drug and controls across breeds and sex for ABCB1, PS and CYP1A2. Significant (P <0.0038) transcript differences across breeds were found for CYP2E1 and SULT1A1 for flunixin meglumine and fenbendazole, respectively. The current analysis found transcript level differences across swine breeds and sex for multiple genes, which provides greater insight into the relationship between flunixin meglumine and fenbendazole and known drug metabolizing genes. PMID:26366864

Differential Gene Expression across Breed and Sex in Commercial Pigs Administered Fenbendazole and Flunixin Meglumine.

PubMed

Howard, Jeremy T; O'Nan, Audrey T; Maltecca, Christian; Baynes, Ronald E; Ashwell, Melissa S

2015-01-01

Characterizing the variability in transcript levels across breeds and sex in swine for genes that play a role in drug metabolism may shed light on breed and sex differences in drug metabolism. The objective of the study is to determine if there is heterogeneity between swine breeds and sex in transcript levels for genes previously shown to play a role in drug metabolism for animals administered flunixin meglumine or fenbendazole. Crossbred nursery female and castrated male pigs (n = 169) spread across 5 groups were utilized. Sires (n = 15) of the pigs were purebred Duroc, Landrace, Yorkshire or Hampshire boars mated to a common sow population. Animals were randomly placed into the following treatments: no drug (control), flunixin meglumine, or fenbendazole. One hour after the second dosing, animals were sacrificed and liver samples collected. Quantitative Real-Time PCR was used to measure liver gene expression of the following genes: SULT1A1, ABCB1, CYP1A2, CYP2E1, CYP3A22 and CYP3A29. The control animals were used to investigate baseline transcript level differences across breed and sex. Post drug administration transcript differences across breed and sex were investigated by comparing animals administered the drug to the controls. Contrasts to determine fold change were constructed from a model that included fixed and random effects within each drug. Significant (P-value <0.007) basal transcript differences were found across breeds for SULT1A1, CYP3A29 and CYP3A22. Across drugs, significant (P-value <0.0038) transcript differences existed between animals given a drug and controls across breeds and sex for ABCB1, PS and CYP1A2. Significant (P <0.0038) transcript differences across breeds were found for CYP2E1 and SULT1A1 for flunixin meglumine and fenbendazole, respectively. The current analysis found transcript level differences across swine breeds and sex for multiple genes, which provides greater insight into the relationship between flunixin meglumine and fenbendazole and known drug metabolizing genes.

Admixture analysis in relation to pedigree studies of introgression in a minority British cattle breed: the Lincoln Red.

PubMed

Bray, T C; Hall, S J G; Bruford, M W

2014-02-01

Investigation of historic population processes using molecular data has been facilitated by the use of approximate Bayesian computation (ABC), which enables the consideration of multiple alternative demographic scenarios. The Lincoln Red cattle breed provides a relatively simple example of two well-documented admixture events. Using molecular data for this breed, we found that structure did not resolve very low (<5% levels) of introgression, possibly due to sampling limitations. We evaluated the performance of two ABC approaches (2BAD and DIYABC) against those of two earlier methodologies, ADMIX and LEADMIX, by comparing their interpretations with the conclusions drawn from herdbook analysis. The ABC methods gave credible values for the proportions of the Lincoln Red genotype that are attributable to Aberdeen Angus and Limousin, although estimates of effective population size and event timing were not realistic. We suggest ABC methods are a valuable supplement to pedigree-based studies but that the accuracy of admixture determination is likely to diminish with increasing complexity of the admixture scenario. © 2013 Blackwell Verlag GmbH.

Genome-wide association analysis for feed efficiency in Angus cattle.

PubMed

Rolf, M M; Taylor, J F; Schnabel, R D; McKay, S D; McClure, M C; Northcutt, S L; Kerley, M S; Weaber, R L

2012-08-01

Estimated breeding values for average daily feed intake (AFI; kg/day), residual feed intake (RFI; kg/day) and average daily gain (ADG; kg/day) were generated using a mixed linear model incorporating genomic relationships for 698 Angus steers genotyped with the Illumina BovineSNP50 assay. Association analyses of estimated breeding values (EBVs) were performed for 41,028 single nucleotide polymorphisms (SNPs), and permutation analysis was used to empirically establish the genome-wide significance threshold (P < 0.05) for each trait. SNPs significantly associated with each trait were used in a forward selection algorithm to identify genomic regions putatively harbouring genes with effects on each trait. A total of 53, 66 and 68 SNPs explained 54.12% (24.10%), 62.69% (29.85%) and 55.13% (26.54%) of the additive genetic variation (when accounting for the genomic relationships) in steer breeding values for AFI, RFI and ADG, respectively, within this population. Evaluation by pathway analysis revealed that many of these SNPs are in genomic regions that harbour genes with metabolic functions. The presence of genetic correlations between traits resulted in 13.2% of SNPs selected for AFI and 4.5% of SNPs selected for RFI also being selected for ADG in the analysis of breeding values. While our study identifies panels of SNPs significant for efficiency traits in our population, validation of all SNPs in independent populations will be necessary before commercialization. © 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics.

DNA-informed breeding of rosaceous crops: promises, progress and prospects

PubMed Central

Peace, Cameron P

2017-01-01

Crops of the Rosaceae family provide valuable contributions to rural economies and human health and enjoyment. Sustained solutions to production challenges and market demands can be met with genetically improved new cultivars. Traditional rosaceous crop breeding is expensive and time-consuming and would benefit from improvements in efficiency and accuracy. Use of DNA information is becoming conventional in rosaceous crop breeding, contributing to many decisions and operations, but only after past decades of solved challenges and generation of sufficient resources. Successes in deployment of DNA-based knowledge and tools have arisen when the ‘chasm’ between genomics discoveries and practical application is bridged systematically. Key steps are establishing breeder desire for use of DNA information, adapting tools to local breeding utility, identifying efficient application schemes, accessing effective services in DNA-based diagnostics and gaining experience in integrating DNA information into breeding operations and decisions. DNA-informed germplasm characterization for revealing identity and relatedness has benefitted many programs and provides a compelling entry point to reaping benefits of genomics research. DNA-informed germplasm evaluation for predicting trait performance has enabled effective reallocation of breeding resources when applied in pioneering programs. DNA-based diagnostics is now expanding from specific loci to genome-wide considerations. Realizing the full potential of this expansion will require improved accuracy of predictions, multi-trait DNA profiling capabilities, streamlined breeding information management systems, strategies that overcome plant-based features that limit breeding progress and widespread training of current and future breeding personnel and allied scientists. PMID:28326185

Genetic diversity and differentiation of five Cuban cattle breeds using 30 microsatellite loci.

PubMed

Acosta, A C; Uffo, O; Sanz, A; Ronda, R; Osta, R; Rodellar, C; Martin-Burriel, I; Zaragoza, P

2013-02-01

Conservation and improvement strategies in farm animals should be based on a combination of genetic and phenotypic characteristics. Genotype data from 30 microsatellites were used to assess the genetic diversity and relationships among five Cuban cattle breeds (Siboney de Cuba, Criollo Cubano, Cebú Cubano, Mambí de Cuba and Taíno de Cuba). All microsatellite markers were highly polymorphic in all the breeds. The expected heterozygosity ranged from 0.67 ± 0.02 in the Taíno de Cuba breed to 0.75 ± 0.02 in the Mambí de Cuba breed, and the observed heterozygosity ranged from 0.66 ± 0.03 in the Cebú Cubano breed to 0.73 ± 0.02 in the Siboney de Cuba breed. The genetic differentiation between the breeds was significant (p < 0.01) based on the infinitesimal model (F(ST)). The exact test for Hardy-Weinberg equilibrium within breeds showed a significant deviation in each breed (p < 0.0003) for one or more loci. The genetic distance and structure analysis showed that a significant amount of genetic variation is maintained in the local cattle population and that all breeds studied could be considered genetically distinct. The Siboney de Cuba and Mambí de Cuba breeds seem to be the most genetically related among the studied five breeds. © 2012 Blackwell Verlag GmbH.

Edible peanut worm ( Sipunculus nudus) in the Beibu Gulf: Resource, aquaculture, ecological impact and counterplan

NASA Astrophysics Data System (ADS)

Li, Junwei; Xie, Xiaoyong; Zhu, Changbo; Guo, Yongjian; Chen, Suwen

2017-10-01

Sipunculus nudus is an important economic species because of its high nutritional and medicinal values. The exploitation and utilization of S. nudus primarily occur in the coastal regions of the Beibu Gulf. However, wild resource of S. nudus is rapidly decreasing because of the overexploitation, which has led to considerable developments of artificial breeding techniques. The cultivation scale of S. nudus has increased in response to successful artificial breeding; however, methods for culturing S. nudus in tidal flats or ponds require further study. Most studies have focused on the breeding, nutrition, medical value and ecological impact of these worms. Studies on the distribution, sediment requirements, nutrition characteristics, breeding techniques and aquaculture ecology of this species are summarized in this paper to promote the development of the aquaculture industry for S. nudus. The high biomass of S. nudus in the Beibu Gulf is positively correlated with the sediment characteristics and water quality of the region. The production of peanut worm has improved to some extent through culturing; however, the nutrient value and ecological environment problems have been observed, which reflect the over exploitation of trace elements and the sediment. These problems will worsen unless they are resolved, and the release of organic materials, nitrogen and phosphorus during harvesting impacts the coastal environment. Moreover, genetic erosion is a potential risk for larvae in artificial breeding programs in tidal flats. Therefore, culturing and collecting methods should be improved and the wild resource conservation should be implemented to promote the sustainable development of the peanut worm.

Prediction of genomic breeding values for dairy traits in Italian Brown and Simmental bulls using a principal component approach.

PubMed

Pintus, M A; Gaspa, G; Nicolazzi, E L; Vicario, D; Rossoni, A; Ajmone-Marsan, P; Nardone, A; Dimauro, C; Macciotta, N P P

2012-06-01

The large number of markers available compared with phenotypes represents one of the main issues in genomic selection. In this work, principal component analysis was used to reduce the number of predictors for calculating genomic breeding values (GEBV). Bulls of 2 cattle breeds farmed in Italy (634 Brown and 469 Simmental) were genotyped with the 54K Illumina beadchip (Illumina Inc., San Diego, CA). After data editing, 37,254 and 40,179 single nucleotide polymorphisms (SNP) were retained for Brown and Simmental, respectively. Principal component analysis carried out on the SNP genotype matrix extracted 2,257 and 3,596 new variables in the 2 breeds, respectively. Bulls were sorted by birth year to create reference and prediction populations. The effect of principal components on deregressed proofs in reference animals was estimated with a BLUP model. Results were compared with those obtained by using SNP genotypes as predictors with either the BLUP or Bayes_A method. Traits considered were milk, fat, and protein yields, fat and protein percentages, and somatic cell score. The GEBV were obtained for prediction population by blending direct genomic prediction and pedigree indexes. No substantial differences were observed in squared correlations between GEBV and EBV in prediction animals between the 3 methods in the 2 breeds. The principal component analysis method allowed for a reduction of about 90% in the number of independent variables when predicting direct genomic values, with a substantial decrease in calculation time and without loss of accuracy. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Potential benefits of genomic selection on genetic gain of small ruminant breeding programs.

PubMed

Shumbusho, F; Raoul, J; Astruc, J M; Palhiere, I; Elsen, J M

2013-08-01

In conventional small ruminant breeding programs, only pedigree and phenotype records are used to make selection decisions but prospects of including genomic information are now under consideration. The objective of this study was to assess the potential benefits of genomic selection on the genetic gain in French sheep and goat breeding designs of today. Traditional and genomic scenarios were modeled with deterministic methods for 3 breeding programs. The models included decisional variables related to male selection candidates, progeny testing capacity, and economic weights that were optimized to maximize annual genetic gain (AGG) of i) a meat sheep breeding program that improved a meat trait of heritability (h(2)) = 0.30 and a maternal trait of h(2) = 0.09 and ii) dairy sheep and goat breeding programs that improved a milk trait of h(2) = 0.30. Values of ±0.20 of genetic correlation between meat and maternal traits were considered to study their effects on AGG. The Bulmer effect was accounted for and the results presented here are the averages of AGG after 10 generations of selection. Results showed that current traditional breeding programs provide an AGG of 0.095 genetic standard deviation (σa) for meat and 0.061 σa for maternal trait in meat breed and 0.147 σa and 0.120 σa in sheep and goat dairy breeds, respectively. By optimizing decisional variables, the AGG with traditional selection methods increased to 0.139 σa for meat and 0.096 σa for maternal traits in meat breeding programs and to 0.174 σa and 0.183 σa in dairy sheep and goat breeding programs, respectively. With a medium-sized reference population (nref) of 2,000 individuals, the best genomic scenarios gave an AGG that was 17.9% greater than with traditional selection methods with optimized values of decisional variables for combined meat and maternal traits in meat sheep, 51.7% in dairy sheep, and 26.2% in dairy goats. The superiority of genomic schemes increased with the size of the reference population and genomic selection gave the best results when nref > 1,000 individuals for dairy breeds and nref > 2,000 individuals for meat breed. Genetic correlation between meat and maternal traits had a large impact on the genetic gain of both traits. Changes in AGG due to correlation were greatest for low heritable maternal traits. As a general rule, AGG was increased both by optimizing selection designs and including genomic information.

Solute accumulation and elastic modulus changes in six radiata pine breeds exposed to drought.

PubMed

De Diego, N; Sampedro, M C; Barrio, R J; Saiz-Fernández, I; Moncaleán, P; Lacuesta, M

2013-01-01

Drought is one of the main abiotic factors that determine forest species growth, survival and productivity. For this reason, knowledge of plant drought response and the identification of physiological traits involved in stress tolerance will be of interest to breeding programs. In this work, several Pinus radiata D. Don breeds from different geographical origins were evaluated along a water stress period (4 weeks) and subsequent rewatering (1 week), showing different responses among them. Leaf water potential (Ψ(leaf)) and osmotic potential decreases were accompanied by a variation in the total relative water content (RWC, %). The most tolerant breeds presented the lowest leaf water potential and RWC at turgor loss point, and showed the lowest elastic modulus (ε) values. A high ε value was a characteristic of a less-drought-tolerant plant and was related to membrane alterations (high electrolyte leakage percentages) that could favor cell water loss. Of the group of solutes that contributed to osmotic adjustment, soluble carbohydrates were the most abundant, although stressed plants also increased their content of free amino acids [mainly proline (Pro) and glutamic acid (Glu), and γ-aminobutyric acid (GABA)] and free polyamines. In addition, the most sensitive breeds had a higher GABA/Glu ratio. After rewatering, Pro and GABA were higher in rehydrated plants than in controls.

Genetic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel

PubMed Central

Makina, Sithembile O.; Muchadeyi, Farai C.; van Marle-Köster, Este; MacNeil, Michael D.; Maiwashe, Azwihangwisi

2014-01-01

Information about genetic diversity and population structure among cattle breeds is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of cattle breeds. This study investigated genetic diversity and the population structure among six cattle breeds in South African (SA) including Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), Bonsmara (n = 44), Angus (n = 31), and Holstein (n = 29). Genetic diversity within cattle breeds was analyzed using three measures of genetic diversity namely allelic richness (AR), expected heterozygosity (He) and inbreeding coefficient (f). Genetic distances between breed pairs were evaluated using Nei's genetic distance. Population structure was assessed using model-based clustering (ADMIXTURE). Results of this study revealed that the allelic richness ranged from 1.88 (Afrikaner) to 1.73 (Nguni). Afrikaner cattle had the lowest level of genetic diversity (He = 0.24) and the Drakensberger cattle (He = 0.30) had the highest level of genetic variation among indigenous and locally-developed cattle breeds. The level of inbreeding was lower across the studied cattle breeds. As expected the average genetic distance was the greatest between indigenous cattle breeds and Bos taurus cattle breeds but the lowest among indigenous and locally-developed breeds. Model-based clustering revealed some level of admixture among indigenous and locally-developed breeds and supported the clustering of the breeds according to their history of origin. The results of this study provided useful insight regarding genetic structure of SA cattle breeds. PMID:25295053

Genetic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel.

PubMed

Makina, Sithembile O; Muchadeyi, Farai C; van Marle-Köster, Este; MacNeil, Michael D; Maiwashe, Azwihangwisi

2014-01-01

Information about genetic diversity and population structure among cattle breeds is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of cattle breeds. This study investigated genetic diversity and the population structure among six cattle breeds in South African (SA) including Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), Bonsmara (n = 44), Angus (n = 31), and Holstein (n = 29). Genetic diversity within cattle breeds was analyzed using three measures of genetic diversity namely allelic richness (AR), expected heterozygosity (He) and inbreeding coefficient (f). Genetic distances between breed pairs were evaluated using Nei's genetic distance. Population structure was assessed using model-based clustering (ADMIXTURE). Results of this study revealed that the allelic richness ranged from 1.88 (Afrikaner) to 1.73 (Nguni). Afrikaner cattle had the lowest level of genetic diversity (He = 0.24) and the Drakensberger cattle (He = 0.30) had the highest level of genetic variation among indigenous and locally-developed cattle breeds. The level of inbreeding was lower across the studied cattle breeds. As expected the average genetic distance was the greatest between indigenous cattle breeds and Bos taurus cattle breeds but the lowest among indigenous and locally-developed breeds. Model-based clustering revealed some level of admixture among indigenous and locally-developed breeds and supported the clustering of the breeds according to their history of origin. The results of this study provided useful insight regarding genetic structure of SA cattle breeds.

Indirect genetic estimates of breeding population size in the polyploid green sturgeon (Acipenser medirostris).

PubMed

Israel, J A; May, B

2010-03-01

The utility of genetic measures for kinship reconstruction in polysomic species is not well evaluated. We developed a framework to test hypotheses about estimating breeding population size indirectly from collections of outmigrating green sturgeon juveniles. We evaluated a polysomic dataset, in allelic frequency and phenotypic formats, from green sturgeon to describe the relationship among known progeny from experimental families. The distributions of relatedness values for kin classes were used for reconstructing green sturgeon pedigrees from juveniles of unknown relationship. We compared three rarefaction functions that described the relationship between the number of kin groups and number of samples in a pedigree to estimate the annual abundance of spawners contributing to the threatened green sturgeon Southern Distinct Population Segment in the upper Sacramento River. Results suggested the estimated abundance of breeding green sturgeon remained roughly constant in the upper Sacramento River over a 5-year period, ranging from 10 to 28 individuals depending on the year and rarefaction method. These results demonstrate an empirical understanding for the distribution of relatedness values among individuals is a benefit for assessing pedigree reconstruction methods and identifying misclassification rates. Monitoring of rare species using these indirect methods is feasible and can provide insight into breeding and ontogenetic behaviour. While this framework was developed for specific application to studying fish populations in a riverscape, the framework could be advanced to improve genetic estimation of breeding population size and to identify important breeding habitats of rare species when combined with finer-scaled sampling of offspring.

Comparison of random regression models with Legendre polynomials and linear splines for production traits and somatic cell score of Canadian Holstein cows.

PubMed

Bohmanova, J; Miglior, F; Jamrozik, J; Misztal, I; Sullivan, P G

2008-09-01

A random regression model with both random and fixed regressions fitted by Legendre polynomials of order 4 was compared with 3 alternative models fitting linear splines with 4, 5, or 6 knots. The effects common for all models were a herd-test-date effect, fixed regressions on days in milk (DIM) nested within region-age-season of calving class, and random regressions for additive genetic and permanent environmental effects. Data were test-day milk, fat and protein yields, and SCS recorded from 5 to 365 DIM during the first 3 lactations of Canadian Holstein cows. A random sample of 50 herds consisting of 96,756 test-day records was generated to estimate variance components within a Bayesian framework via Gibbs sampling. Two sets of genetic evaluations were subsequently carried out to investigate performance of the 4 models. Models were compared by graphical inspection of variance functions, goodness of fit, error of prediction of breeding values, and stability of estimated breeding values. Models with splines gave lower estimates of variances at extremes of lactations than the model with Legendre polynomials. Differences among models in goodness of fit measured by percentages of squared bias, correlations between predicted and observed records, and residual variances were small. The deviance information criterion favored the spline model with 6 knots. Smaller error of prediction and higher stability of estimated breeding values were achieved by using spline models with 5 and 6 knots compared with the model with Legendre polynomials. In general, the spline model with 6 knots had the best overall performance based upon the considered model comparison criteria.

Association between anal sac gland carcinoma and dog leukocyte antigen-DQB1 in the English Cocker Spaniel.

PubMed

Aguirre-Hernández, J; Polton, G; Kennedy, L J; Sargan, D R

2010-12-01

Anal sac gland carcinomas occur frequently in English Cocker Spaniels and, to a lesser extent, in other spaniel breeds. The disease typically presents in dogs aged 8 years or older and frequently metastasises to the local lymph nodes. The association between anal sac gland carcinoma in English Cocker Spaniels and the major histocompatibility complex class II loci (the dog leukocyte antigen loci DLA-DRB1, -DQA1, -DQB1) was investigated in 42 cases and 75 controls. Based on a corrected error rate of 0.017 for each test, the allele distribution in DLA-DRB1 showed no significant difference between cases and controls (P value = 0.019), while a significant difference was obtained for DLA-DQA1 and -DQB1 alleles (P values are 0.010 and 3.3 × 10⁻⁵). The DLA-DQB1*00701 allele was the most common in both cases and controls, but it had a higher frequency among the former (0.89) than in the latter (0.61), while the second most common allele had a higher frequency in the controls (0.23) than in the cases (0.07). Haplotype distributions were also significantly different between the two groups (P value = 1.61 × 10⁻⁴). This is the second disease in English Cocker Spaniels for which the most common DLA-DQB1 allele in the breed has been shown to have a higher frequency in cases than controls, while the second most common allele in the breed (*02001) has a significantly higher frequency in the controls, compared with the cases. © 2010 John Wiley & Sons A/S.

Industry benefits from recent genetic progress in sheep and beef populations.

PubMed

Amer, P R; Nieuwhof, G J; Pollott, G E; Roughsedge, T; Conington, J; Simm, G

2007-11-01

An analytical model that evaluates the benefits from 10 years of genetic improvement over a 20-year time frame was specified. Estimates of recent genetic trends in recorded traits, industry statistics and published estimates of the economic values of trait changes were used to parameterise the model for the UK sheep and beef industries. Despite rates of genetic change in the relevant performance-recorded breeding populations being substantially less than theoretical predictions, the financial benefits of genetic change were substantial. Over 20 years, the benefits from 10 years of genetic progress at recently achieved rates in recorded hill sheep, sheep crossing sire and sheep terminal sire breeding programmes was estimated to be £5.3, £1.0 and £11.5 million, respectively. If dissemination of genetic material is such that these rates of change are also realised across the entire ram breeding industry, the combined benefits would be £110.8 million. For beef cattle, genetic evaluation systems have been operating within all the major breeds for some years with quite widespread use of performance recording, and so genetic trends within the beef breeds were used as predictors of industry genetic change. Benefits from 10 years of genetic progress at recent rates of change, considering a 20-year time frame, in terminal sire beef breeds are expected to be £4.9 million. Benefits from genetic progress for growth and carcass characters in dual-purpose beef breeds were £18.2 million after subtraction of costs associated with a deterioration in calving traits. These benefits may be further offset by unfavourable associated changes in maternal traits. Additional benefits from identification and use of the best animals available from the breeding sector for commercial matings through performance recording and genetic evaluation could not be quantified. When benefits of genetic improvement were expressed on an annual present value basis and compared with lagged annual investment costs to achieve it, the internal rate of return (IRR) on the combined investment in sheep and beef cattle was 32%. Despite a much higher rate of participation in performance recording, the present value of benefits and the IRR were lower for beef cattle than for sheep. The implications of these results for future national and industry investment in genetic improvement infrastructure were discussed.

Effectiveness of a 95 SNP panel for the screening of breed label fraud in the Chinese meat market.

PubMed

Rogberg-Muñoz, A; Wei, S; Ripoli, M V; Guo, B L; Carino, M H; Lirón, J P; Prando, A J; Vaca, R J A; Peral-García, P; Wei, Y M; Giovambattista, G

2016-01-01

Breed assignment has proved to be useful to control meat trade and protect the value of special productions. Meat-related frauds have been detected in China; therefore, 95 SNPs selected from the ISAG core panel were evaluated to develop an automated and technologically updated tool to screen breed label fraud in the Chinese meat market. A total of 271 animals from four Chinese yellow cattle (CYC) populations, six Bos taurus breeds, two Bos indicus and one composite were used. The allocation test distinguished European, Japanese and Zebu breeds, and two Chinese genetic components. It correctly allocated Japanese Black, Zebu and British breeds in 100, 90 and 89% of samples, respectively. CYC evidenced the Zebu, Holstein and Limousin introgression. The test did not detect CYC components in any of the 25 samples from Argentinean butchers. The method could be useful to certify Angus, Hereford and Japanese Black meat, but a modification in the panel would be needed to differentiate other breeds. Copyright © 2015 Elsevier Ltd. All rights reserved.

Genetic evaluation of the breeding population of a valuable reforestation conifer Platycladus orientalis (Cupressaceae)

NASA Astrophysics Data System (ADS)

Jin, Yuqing; Ma, Yongpeng; Wang, Shun; Hu, Xian-Ge; Huang, Li-Sha; Li, Yue; Wang, Xiao-Ru; Mao, Jian-Feng

2016-10-01

Platycladus orientalis, a widespread conifer with long lifespan and significant adaptability. It is much used in reforestation in north China and commonly planted in central Asia. With the increasing demand for plantation forest in central to north China, breeding programs are progressively established for this species. Efficient use of breeding resources requires good understanding of the genetic value of the founder breeding materials. This study investigated the distribution of genetic variation in 192 elite trees collected for the breeding program for the central range of the species. We developed first set of 27 polymorphic EST-derived SSR loci for the species from transcriptome/genome data. After examination of amplification quality, 10 loci were used to evaluate the genetic variation in the breeding population. We found moderate genetic diversity (average He = 0.348) and low population differentiation (Fst = 0.011). Extensive admixture and no significant geographic population structure characterized this set of collections. Our analyses of the diversity and population structure are important steps toward a long-term sustainable deployment of the species and provide valuable genetic information for conservation and breeding applications.

Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed

PubMed Central

Browett, Sam; McHugo, Gillian; Richardson, Ian W.; Magee, David A.; Park, Stephen D. E.; Fahey, Alan G.; Kearney, John F.; Correia, Carolina N.; Randhawa, Imtiaz A. S.; MacHugh, David E.

2018-01-01

Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP array data to evaluate genomic diversity within the Kerry population and between Kerry cattle and other European breeds. Patterns of genetic differentiation and gene flow among breeds using phylogenetic trees with ancestry graphs highlighted historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (Ne) revealed a demographic trend of diminishing Ne over time and that recent estimated Ne values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (FROH) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland. PMID:29520297

Genome-wide population structure and evolutionary history of the Frizarta dairy sheep.

PubMed

Kominakis, A; Hager-Theodorides, A L; Saridaki, A; Antonakos, G; Tsiamis, G

2017-10-01

In the present study, we used genomic data, generated with a medium density single nucleotide polymorphisms (SNP) array, to acquire more information on the population structure and evolutionary history of the synthetic Frizarta dairy sheep. First, two typical measures of linkage disequilibrium (LD) were estimated at various physical distances that were then used to make inferences on the effective population size at key past time points. Population structure was also assessed by both multidimensional scaling analysis and k-means clustering on the distance matrix obtained from the animals' genomic relationships. The Wright's fixation F ST index was also employed to assess herds' genetic homogeneity and to indirectly estimate past migration rates. The Wright's fixation F IS index and genomic inbreeding coefficients based on the genomic relationship matrix as well as on runs of homozygosity were also estimated. The Frizarta breed displays relatively low LD levels with r 2 and |D'| equal to 0.18 and 0.50, respectively, at an average inter-marker distance of 31 kb. Linkage disequilibrium decayed rapidly by distance and persisted over just a few thousand base pairs. Rate of LD decay (β) varied widely among the 26 autosomes with larger values estimated for shorter chromosomes (e.g. β=0.057, for OAR6) and smaller values for longer ones (e.g. β=0.022, for OAR2). The inferred effective population size at the beginning of the breed's formation was as high as 549, was then reduced to 463 in 1981 (end of the breed's formation) and further declined to 187, one generation ago. Multidimensional scaling analysis and k-means clustering suggested a genetically homogenous population, F ST estimates indicated relatively low genetic differentiation between herds, whereas a heat map of the animals' genomic kinship relationships revealed a stratified population, at a herd level. Estimates of genomic inbreeding coefficients suggested that most recent parental relatedness may have been a major determinant of the current effective population size. A denser than the 50k SNP panel may be more beneficial when performing genome wide association studies in the breed.

DNA typing of Pakistani cattle breeds Tharparkar and Red Sindhi by microsatellite markers.

PubMed

Azam, Amber; Babar, Masroor Ellahi; Firyal, Sehrish; Anjum, Aftab Ahmad; Akhtar, Nabeela; Asif, Muhammad; Hussain, Tanveer

2012-02-01

Microsatellite markers are used for any individual identity and breed characterization in animals that is an efficient and successful way of investigation. They are used for multiple purposes as genetic detectors including, rapid mutation rate, high level of polymorphism, and range of variety of microsatellite markers available. A panel of 19 microsatellite markers was developed for breed characterization in Tharparkar and Red Sindhi breeds of cattle in Pakistan. Forty four blood samples of cattle (each breed) were collected from Department of Livestock Management, Sindh Agriculture University, Tandojam, Tando Qaiser, Tharparkar Cattle Farm Nabi sar Road, Umer Kot, Sindh, and Govt. Red Sindhi Cattle Breeding Farm, Tando Muhammad Khan Pakistan. Breed characterization was 100% successful. Average PIC, He and Power of Exclusion values were found to be 0.91, 0.62 and 13.28, respectively. Pattern of allelic frequencies of most of the microsatellite markers were clearly distinct between two breeds. As a result of present study a reliable, efficient and very informative panel of microsatellite markers was successfully developed which was capable to interpret individual identity, forensic cases and breed characterization in cattle. This facility is ready to be provided to local cattle breeder at commercial level for DNA testing of cattle. This study will also be highly helpful for breed conservation of cattle. In addition this study can also become a basis to open up new disciplines of animal forensics in Pakistan.

Assessing metabolomic and chemical diversity of a soybean lineage representing 35 years of breeding

USDA-ARS?s Scientific Manuscript database

Information on crop genotype- and phenotype-metabolite associations can be of value to trait development as well as to food security and safety. The unique study presented here assessed seed metabolomic and ionomic diversity in a soybean lineage representing ~35 years of breeding (launch years 1972-...

Index-in-retrospect and breeding objectives characterizing genetic improvement programs for South African Nguni cattle

USDA-ARS?s Scientific Manuscript database

The objective of the current study was to describe the historical selection applied to Nguni cattle in South Africa. Index-in-retrospect methods were applied to data originating from the National Beef Cattle Improvement Scheme. Data used were estimated breeding values (EBV) for animals born during t...

Genetic parameters and prediction of breeding values in switchgrass bred for bioenergy

USDA-ARS?s Scientific Manuscript database

Estimating genetic parameters is an essential step in breeding by recurrent selection to maximize genetic gains over time. This study evaluated the effects of selection on genetic variation across two successive cycles (C1 and C2) of a ‘Summer’x‘Kanlow’ switchgrass (Panicum virgatum L.) population. ...

Retail colour stability of lamb meat is influenced by breed type, muscle, packaging and iron concentration.

PubMed

Warner, R D; Kearney, G; Hopkins, D L; Jacob, R H

2017-07-01

The longissmus lumborum (LL) and semimembranosus (SM) muscles from 391 lamb carcasses, derived from various breed types, were used to investigate the effect of animal/muscle factors, packaging type [over-wrap (OW) or high oxygen modified atmosphere packaging (MAP O2 )] and duration of display on redness of meat during simulated retail display. Using statistical models the time required (in days) for redness to reach a threshold value of 3.5 (below this is unacceptable) was predicted. High levels of iron in the SM, but not LL, reduced the time for redness to reach 3.5 by 2-2.6days in MAP O2 and 0.5-0.8days in OW. The greater the proportion of Merino breed type, the shorter was the time for redness to reach the value of 3.5, an effect consistent across muscles and packaging types. In summary, breed type, packaging format, muscle and muscle iron levels had a significant impact on colour stability of sheep meat in oxygen-available packaging systems. Copyright © 2017. Published by Elsevier Ltd.

Analysis of genetic and cultural conservation value of three indigenous Croatian cattle breeds in a local and global context.

PubMed

Ramljak, J; Ivanković, A; Veit-Kensch, C E; Förster, M; Medugorac, I

2011-02-01

It is widely accepted that autochthonous cattle breeds can be important genetic resources for unforeseeable environmental conditions in the future. Apart from that, they often represent local culture and tradition and thus assist in the awareness of ethnic identity of a country. In Croatia, there are only three indigenous cattle breeds, Croatian Buša, Slavonian Syrmian Podolian and Istrian Cattle. All of them are threatened but specialized in a particular habitat and production system. We analysed 93 microsatellites in 51 animals of each breed to get thorough information about genetic diversity and population structure. We further set them within an existing frame of additional 16 breeds that have been genotyped for the same marker set and cover a geographical area from the domestication centre near Anatolia, through the Balkan and alpine regions, to the north-west of Europe. The cultural value was evaluated regarding the role in landscape, gastronomy, folklore and handicraft. The overall results recognize Croatian Buša being partly admixed but harbouring an enormous genetic diversity comparable with other traditional unselected Buša breeds in the Anatolian and Balkan areas. The Podolian cattle showed the lowest genetic diversity at the highest genetic distance to all remaining breeds but are playing an important role as part of the cultural landscape and thus contribute to the tourist industry. The genetic diversity of the Istrian cattle was found in the middle range of this study. It is already included in the tourist industry as a local food speciality. Current and future conservation strategies are discussed. © 2010 Blackwell Verlag GmbH.

Can multi-subpopulation reference sets improve the genomic predictive ability for pigs?

PubMed

Fangmann, A; Bergfelder-Drüing, S; Tholen, E; Simianer, H; Erbe, M

2015-12-01

In most countries and for most livestock species, genomic evaluations are obtained from within-breed analyses. To achieve reliable breeding values, however, a sufficient reference sample size is essential. To increase this size, the use of multibreed reference populations for small populations is considered a suitable option in other species. Over decades, the separate breeding work of different pig breeding organizations in Germany has led to stratified subpopulations in the breed German Large White. Due to this fact and the limited number of Large White animals available in each organization, there was a pressing need for ascertaining if multi-subpopulation genomic prediction is superior compared with within-subpopulation prediction in pigs. Direct genomic breeding values were estimated with genomic BLUP for the trait "number of piglets born alive" using genotype data (Illumina Porcine 60K SNP BeadChip) from 2,053 German Large White animals from five different commercial pig breeding companies. To assess the prediction accuracy of within- and multi-subpopulation reference sets, a random 5-fold cross-validation with 20 replications was performed. The five subpopulations considered were only slightly differentiated from each other. However, the prediction accuracy of the multi-subpopulations approach was not better than that of the within-subpopulation evaluation, for which the predictive ability was already high. Reference sets composed of closely related multi-subpopulation sets performed better than sets of distantly related subpopulations but not better than the within-subpopulation approach. Despite the low differentiation of the five subpopulations, the genetic connectedness between these different subpopulations seems to be too small to improve the prediction accuracy by applying multi-subpopulation reference sets. Consequently, resources should be used for enlarging the reference population within subpopulation, for example, by adding genotyped females.

Bayesian Multi-Trait Analysis Reveals a Useful Tool to Increase Oil Concentration and to Decrease Toxicity in Jatropha curcas L.

PubMed Central

Silva Junqueira, Vinícius; de Azevedo Peixoto, Leonardo; Galvêas Laviola, Bruno; Lopes Bhering, Leonardo; Mendonça, Simone; Agostini Costa, Tania da Silveira; Antoniassi, Rosemar

2016-01-01

The biggest challenge for jatropha breeding is to identify superior genotypes that present high seed yield and seed oil content with reduced toxicity levels. Therefore, the objective of this study was to estimate genetic parameters for three important traits (weight of 100 seed, oil seed content, and phorbol ester concentration), and to select superior genotypes to be used as progenitors in jatropha breeding. Additionally, the genotypic values and the genetic parameters estimated under the Bayesian multi-trait approach were used to evaluate different selection indices scenarios of 179 half-sib families. Three different scenarios and economic weights were considered. It was possible to simultaneously reduce toxicity and increase seed oil content and weight of 100 seed by using index selection based on genotypic value estimated by the Bayesian multi-trait approach. Indeed, we identified two families that present these characteristics by evaluating genetic diversity using the Ward clustering method, which suggested nine homogenous clusters. Future researches must integrate the Bayesian multi-trait methods with realized relationship matrix, aiming to build accurate selection indices models. PMID:27281340

Effect of gamma irradiation on nutritional value of dry field beans (Phaseolus vulgaris) for chicks.

PubMed

Reddy, S J; Pubols, M H; McGinnis, J

1979-07-01

The effect of gamma irradiation (60Co) of different varieties and breeding lines of dry field beans (Phaseolus vulgaris) on chick growth was determined using a chick growth assay in which the diet contained approximately 50% beans. Total protein (N X 6.25) in beans was not changed appreciably by irradiation (21 Mrad) but protein solubility in water was decreased. Irradiation increased in vitro enzymatic digestibility of bean protein by pepsin and by a mixture of trypsin, chymotrypsin and peptidase. In the bioassay the diet was formulated to derive half of the total protein (22.6%) from beans. Autoclaved Pinto and Pink beans gave significantly better growth than Red Mexican and White Pea beans. The differences between Red Mexican and White Pea beans were not significant except for Red Mexican breeding line number RS-59. The nutritional value of all varieties of beans, based on chick growth, was significantly improved by gamma irradiation. The irradiation treatment of beans tended to increase nitrogen retention by chicks and decrease uric acid nitrogen excretion in relation to nitrogen intake.

Genomics-assisted breeding in fruit trees.

PubMed

Iwata, Hiroyoshi; Minamikawa, Mai F; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

2016-01-01

Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding.

Genomics-assisted breeding in fruit trees

PubMed Central

Iwata, Hiroyoshi; Minamikawa, Mai F.; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

2016-01-01

Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding. PMID:27069395

Prioritization for conservation of northern European cattle breeds based on analysis of microsatellite data.

PubMed

Tapio, I; Värv, S; Bennewitz, J; Maleviciute, J; Fimland, E; Grislis, Z; Meuwissen, T H E; Miceikiene, I; Olsaker, I; Viinalass, H; Vilkki, J; Kantanen, J

2006-12-01

Northern European indigenous cattle breeds are currently endangered and at a risk of becoming extinct. We analyzed variation at 20 microsatellite loci in 23 indigenous, 3 old imported, and 9 modern commercial cattle breeds that are presently distributed in northern Europe. We measured the breeds' allelic richness and heterozygosity, and studied their genetic relationships with a neighbor-joining tree based on the Chord genetic distance matrix. We used the Weitzman approach and the core set diversity measure of Eding et al. (2002) to quantify the contribution of each breed to the maximum amount of genetic diversity and to identify breeds important for the conservation of genetic diversity. We defined 11 breeds as a "safe set" of breeds (not endangered) and estimated a reduction in genetic diversity if all nonsafe (endangered) breeds were lost. We then calculated the increase in genetic diversity by adding one by one each of the nonsafe breeds to the safe set (the safe-set-plus-one approach). The neighbor-joining tree grouped the northern European cattle breeds into Black-and-White type, Baltic Red, and Nordic cattle groups. Väne cattle, Bohus Poll, and Danish Jersey had the highest relative contribution to the maximum amount of genetic diversity when the diversity was quantified by the Weitzman diversity measure. These breeds not only showed phylogenetic distinctiveness but also low within-population variation. When the Eding et al. method was applied, Eastern Finncattle and Lithuanian White Backed cattle contributed most of the genetic variation. If the loss of the nonsafe set of breeds happens, the reduction in genetic diversity would be substantial (72%) based on the Weitzman approach, but relatively small (1.81%) based on the Eding et al. method. The safe set contained only 66% of the observed microsatellite alleles. The safe-set-plus-one approach indicated that Bohus Poll and Väne cattle contributed most to the Weitzman diversity, whereas the Eastern Finncattle contribution was the highest according to the Eding et al. method. Our results indicate that both methods of Weitzman and Eding et al. recognize the importance of local populations as a valuable resource of genetic variation.

Genomic predictions for crossbreds from all-breed data

USDA-ARS?s Scientific Manuscript database

Genomic predictions of transmitting ability (GPTAs) for crossbred animals were computed from marker effects of 5 dairy breeds weighted by each breed’s genomic contribution to the crossbreds. Estimates of genomic breed composition are labeled breed base representation (BBR) and are reported since May...

Review: Towards the agroecological management of ruminants, pigs and poultry through the development of sustainable breeding programmes. II. Breeding strategies.

PubMed

Phocas, F; Belloc, C; Bidanel, J; Delaby, L; Dourmad, J Y; Dumont, B; Ezanno, P; Fortun-Lamothe, L; Foucras, G; Frappat, B; González-García, E; Hazard, D; Larzul, C; Lubac, S; Mignon-Grasteau, S; Moreno, C R; Tixier-Boichard, M; Brochard, M

2016-11-01

Agroecology uses ecological processes and local resources rather than chemical inputs to develop productive and resilient livestock and crop production systems. In this context, breeding innovations are necessary to obtain animals that are both productive and adapted to a broad range of local contexts and diversity of systems. Breeding strategies to promote agroecological systems are similar for different animal species. However, current practices differ regarding the breeding of ruminants, pigs and poultry. Ruminant breeding is still an open system where farmers continue to choose their own breeds and strategies. Conversely, pig and poultry breeding is more or less the exclusive domain of international breeding companies which supply farmers with hybrid animals. Innovations in breeding strategies must therefore be adapted to the different species. In developed countries, reorienting current breeding programmes seems to be more effective than developing programmes dedicated to agroecological systems that will struggle to be really effective because of the small size of the populations currently concerned by such systems. Particular attention needs to be paid to determining the respective usefulness of cross-breeding v. straight breeding strategies of well-adapted local breeds. While cross-breeding may offer some immediate benefits in terms of improving certain traits that enable the animals to adapt well to local environmental conditions, it may be difficult to sustain these benefits in the longer term and could also induce an important loss of genetic diversity if the initial pure-bred populations are no longer produced. As well as supporting the value of within-breed diversity, we must preserve between-breed diversity in order to maintain numerous options for adaptation to a variety of production environments and contexts. This may involve specific public policies to maintain and characterize local breeds (in terms of both phenotypes and genotypes), which could be used more effectively if they benefited from the scientific and technical resources currently available for more common breeds. Last but not least, public policies need to enable improved information concerning the genetic resources and breeding tools available for the agroecological management of livestock production systems, and facilitate its assimilation by farmers and farm technicians.

Development of Novel SSR Markers for Flax (Linum usitatissimum L.) Using Reduced-Representation Genome Sequencing.

PubMed

Wu, Jianzhong; Zhao, Qian; Wu, Guangwen; Zhang, Shuquan; Jiang, Tingbo

2016-01-01

Flax ( Linum usitatissimum L.) is a major fiber and oil yielding crop grown in northeastern China. Identification of flax molecular markers is a key step toward improving flax yield and quality via marker-assisted breeding. Simple sequence repeat (SSR) markers, which are based on genomic structural variation, are considered the most valuable type of genetic marker for this purpose. In this study, we screened 1574 microsatellites from Linum usitatissimum L. obtained using reduced representation genome sequencing (RRGS) to systematically identify SSR markers. The resulting set of microsatellites consisted mainly of trinucleotide (56.10%) and dinucleotide (35.23%) repeats, with each motif consisting of 5-8 repeats. We then evaluated marker sensitivity and specificity based on samples of 48 flax isolates obtained from northeastern China. Using the new SSR panel, the results demonstrated that fiber flax and oilseed flax varieties clustered into two well separated groups. The novel SSR markers developed in this study show potential value for selection of varieties for use in flax breeding programs.

Characterization of breeding habitats for black and surf scoters in the eastern boreal forest and subarctic regions of Canada

USGS Publications Warehouse

Perry, M.C.; Kidwell, D.M.; Wells, A.M.; Lohnes, E.J.R.; Osenton, P.C.; Altmann, S.H.; Hanson, Alan; Kerekes, Joseph; Paquet, Julie

2006-01-01

We analyzed characteristics of wetland habitats used by breeding black scoters (Melanitta nigra) and surf scoters (M. perspicillata) in the eastern boreal forest and subarctic regions of Canada based on satellite telemetry data collected in the spring and summer. During 2002 and 2004, nine black scoters (four males, five females) were tracked to breeding areas in Quebec, Manitoba, and Northwest Territories. In addition, in 2001?04, seven surf scoters (three males, four females) were tracked to breeding areas in Labrador, Quebec, Northwest Territories, and Nunavut. Based on satellite telemetry data, locations of black and surf scoters in breeding areas were not significantly different in regard to latitude and longitude. Presumed breeding areas were manually plotted on topographic maps and percent cover type and water were estimated. Breeding habitat of black scoters was significantly different than that for surf scoters, with black scoters mainly using open (tundra) areas (44%) and surf scoters using mainly forest areas (66%). Surf scoters presumed breeding areas were at significantly higher elevations than areas used by black scoters. Some breeding areas were associated with islands, but the role of islands for breeding areas is equivocal. These results aid in the identification of potentially critical breeding areas and provide a baseline classification of breeding habitats used by these two species.

Investigating the population structure and genetic differentiation of livestock guard dog breeds.

PubMed

Bigi, D; Marelli, S P; Liotta, L; Frattini, S; Talenti, A; Pagnacco, G; Polli, M; Crepaldi, P

2018-01-14

Livestock guarding dogs are a valuable adjunct to the pastoral community. Having been traditionally selected for their working ability, they fulfil their function with minimal interaction or command from their human owners. In this study, the population structure and the genetic differentiation of three Italian livestock guardian breeds (Sila's Dog, Maremma and Abruzzese Sheepdog and Mannara's Dog) and three functionally and physically similar breeds (Cane Corso, Central Asian Shepherd Dog and Caucasian Shepherd Dog), totalling 179 dogs unrelated at the second generation, were investigated with 18 autosomal microsatellite markers. Values for the number of alleles per locus, observed and expected heterozygosity, Hardy-Weinberg Equilibrium, F stats, Nei's and Reynold's genetic distances, clustering and sub-population formation abilities and individual genetic structures were calculated. Our results show clear breed differentiation, whereby all the considered breeds show reasonable genetic variability despite small population sizes and variable selection schemes. These results provide meaningful data to stakeholders in specific breed and environmental conservation programmes.

Establishment of baseline haematology and biochemistry parameters in wild adult African penguins (Spheniscus demersus).

PubMed

Parsons, Nola J; Schaefer, Adam M; van der Spuy, Stephen D; Gous, Tertius A

2015-03-25

There are few publications on the clinical haematology and biochemistry of African penguins (Spheniscus demersus) and these are based on captive populations. Baseline haematology and serum biochemistry parameters were analysed from 108 blood samples from wild, adult African penguins. Samples were collected from the breeding range of the African penguin in South Africa and the results were compared between breeding region and sex. The haematological parameters that were measured were: haematocrit, haemoglobin, red cell count and white cell count. The biochemical parameters that were measured were: sodium, potassium, chloride, calcium, inorganic phosphate, creatinine, cholesterol, serum glucose, uric acid, bile acid, total serum protein, albumin, aspartate transaminase and creatine kinase. All samples were serologically negative for selected avian diseases and no blood parasites were detected. No haemolysis was present in any of the analysed samples. Male African penguins were larger and heavier than females, with higher haematocrit, haemoglobin and red cell count values, but lower calcium and phosphate values. African penguins in the Eastern Cape were heavier than those in the Western Cape, with lower white cell count and globulin values and a higher albumin/globulin ratio, possibly indicating that birds are in a poorer condition in the Western Cape. Results were also compared between multiple penguin species and with African penguins in captivity. These values for healthy, wild, adult penguins can be used for future health and disease assessments.

Status and trends of the ashy storm-petrel on Southeast Farallon Island, California, based upon capture-recapture analyses

USGS Publications Warehouse

Sydeman, W.J.; Nur, N.; Mclaren, E.B.; McChesney, G.J.

1998-01-01

We conducted a capture-recapture study on the population size and trends of the Ashy Storm-petrel (Oceanodroma homochroa) on Southeast Farallon Island (SEFI), California, based upon data collected in 1971, 1972, and 1992. From March through August, birds were lured to fixed-site sampling locations using taped vocalization playback. Using program JOLLY, we estimated population size and evaluated statistical models using goodness-of-fit and Likelihood Ratio tests. On the southwestern slope of Lighthouse Hill, amidst prime breeding habitat, numbers of breeding birds decreased from 1,271 ?? 140 (?? ?? SE) in 1972 to 710 ?? 117 in 1992, a decline of 44% (approximate 95% CI = 22-66% decline; ?? = -2.8% per annum); for a variety of reasons, we consider this to be the most reliable indicator of population change. In 1971, on a portion of SEFI relatively disjunct from the sampling area in 1972, 2,131 ?? 322 breeding birds were estimated. To produce an overall early 1970s estimate with which to compare to 1992, we summed population estimates from 1971 and 1972. An overall value of 6,461 birds, of which 3,402 (53%) were breeders, was obtained for the early period. In 1992, the overall population in roughly the same area was estimated at 4,284 ?? 409 birds, of which 1,990 ?? 408 (46%) were presumed breeders. These results, encompassing peripheral as well as more centrally located storm-petrel habitat, indicate an overall population decline of 34% and a comparable decline in breeding birds of 42% over the past two decades. However, oceanographic conditions varied between 1971-1972 and 1992, and reduced food availability in 1992 may have influenced colony attendance and breeding effort. Nonetheless, the apparent population decline over the past 20 years suggests that the species warrants management and/or additional protective status.

Ultra-low-density genotype panels for breed assignment of Angus and Hereford cattle.

PubMed

Judge, M M; Kelleher, M M; Kearney, J F; Sleator, R D; Berry, D P

2017-06-01

Angus and Hereford beef is marketed internationally for apparent superior meat quality attributes; DNA-based breed authenticity could be a useful instrument to ensure consumer confidence on premium meat products. The objective of this study was to develop an ultra-low-density genotype panel to accurately quantify the Angus and Hereford breed proportion in biological samples. Medium-density genotypes (13 306 single nucleotide polymorphisms (SNPs)) were available on 54 703 commercial and 4042 purebred animals. The breed proportion of the commercial animals was generated from the medium-density genotypes and this estimate was regarded as the gold-standard breed composition. Ten genotype panels (100 to 1000 SNPs) were developed from the medium-density genotypes; five methods were used to identify the most informative SNPs and these included the Delta statistic, the fixation (F st) statistic and an index of both. Breed assignment analyses were undertaken for each breed, panel density and SNP selection method separately with a programme to infer population structure using the entire 13 306 SNP panel (representing the gold-standard measure). Breed assignment was undertaken for all commercial animals (n=54 703), animals deemed to contain some proportion of Angus based on pedigree (n=5740) and animals deemed to contain some proportion of Hereford based on pedigree (n=5187). The predicted breed proportion of all animals from the lower density panels was then compared with the gold-standard breed prediction. Panel density, SNP selection method and breed all had a significant effect on the correlation of predicted and actual breed proportion. Regardless of breed, the Index method of SNP selection numerically (but not significantly) outperformed all other selection methods in accuracy (i.e. correlation and root mean square of prediction) when panel density was ⩾300 SNPs. The correlation between actual and predicted breed proportion increased as panel density increased. Using 300 SNPs (selected using the global index method), the correlation between predicted and actual breed proportion was 0.993 and 0.995 in the Angus and Hereford validation populations, respectively. When SNP panels optimised for breed prediction in one population were used to predict the breed proportion of a separate population, the correlation between predicted and actual breed proportion was 0.034 and 0.044 weaker in the Hereford and Angus populations, respectively (using the 300 SNP panel). It is necessary to include at least 300 to 400 SNPs (per breed) on genotype panels to accurately predict breed proportion from biological samples.

The Summer Atlas of North American Birds

USGS Publications Warehouse

Price, J.; Droege, S.; Price, A.

1995-01-01

The North American Breeding Bird Survey comprises a network of regularly censussed, road-based survey routes and constitutes the most comprehensive set of data on the relative abundance and population trends of these birds during the summer months. Its value was highlighted in 1989, when the data were used to confirm suspected population declines in a number of species of neotropical migrants breeding in the northeastern United States and Canada. In this book Jeff and Amy Price and Sam Droege have used these data to create detailed, computer-generated maps showing the relative abundance of 450 species that summer in the contiguous United States and southern Canada. Tabular information on distribution hotspots for these, and a further 50 or so species too local in occurrence to map effectively, are also presented. As a data-based survey, the focus of the maps is on places where occurrence has been systematically confirmed over a number of years. As such, the maps provide a baseline for future and more regionally based studies. Supporting chapters provide details on the survey methodology, the mapping procedures used, and some current concerns in North American bird conservation.

Effect of breed on testicular blood flow dynamics in bulls.

PubMed

Junior, Flávio Antônio Barca; Junior, Celso Koetz; Fávaro, Patrícia da Cruz; Pereira, Gabriel Ribas; Morotti, Fábio; Menegassi, Silvio Renato Oliveira; Barcellos, Júlio Otávio Jardim; Seneda, Marcelo Marcondes

2018-05-26

The evaluation of testicular hemodynamics can contribute significantly to the understanding of the thermoregulatory mechanisms and oxygen supply of the testis in domestic animals. The present study aimed to characterize circulatory dynamics using the mean velocity (MV), pulsatility index (PI) and resistive index (RI) of the supratesticular artery in bulls. We evaluated 334 bulls of five different breeds (Nelore, Hereford, Aberdeen Angus, Braford and Brangus) by performing a velocimetry analysis using Doppler ultrasonography. Data were compared by Welch's ANOVA, Games-Howell (post-hoc test) and Spearman correlation with a significance level of 5%. The overall MV of 12.14 ± 0.30 cm/s differed among breeds. In addition, we observed that Brangus bulls showed higher (P < 0.05) MV (16.28 ± 1.02 cm/s) compared to Nelore bulls (8.76 ± 0.40 cm/s). The RI had an overall mean of 0.41 ± 0.01 and differed among breeds. We observed higher (P < 0.05) RI values in Hereford (0.44 ± 0.01) compared to Brangus (0.36 ± 0.02) animals. Overall, the PI values (0.33 ± 0.01) did not differ (P > 0.05) among breeds. The correlation between the PI and RI (0.936; P < 0.001) was high and positive; however, the correlations were low and negative between MV and the PI (-0.228; P < 0.001) and between MV and the RI (-0.270; P < 0.001). We concluded that there are differences in the MV and RI of the bulls' supratesticular arteries among the different evaluated breeds. Moreover, the presented values attributed to blood flow dynamics can serve as parameters in future studies and can be used to identify alternative diagnostic tools for infertility or to understand issues of adaptability in bulls. Copyright © 2018 Elsevier Inc. All rights reserved.

Effect of breed, sex, age and body weight on echocardiographic measurements in the equine species.

PubMed

Al-Haidar, A; Farnir, F; Deleuze, S; Sandersen, C F; Leroux, A A; Borde, L; Cerri, S; Amory, H

2013-08-01

Little is known about the effect of various animal's signalment variables on echocardiographic reference values in the equine species. This study was performed to evaluate the effect of sex, breed, age and body weight (BW) on echocardiographic measurements in the equine species. Echocardiography was performed on 212 ponies or horses of various breeds, aged from 1 day to 37 years old (mean±SD: 7.8 ± 5.8 years), BW 38-890 kg (mean ± SD: 421 ± 133 kg), and free of cardiac disease. Fifty of those animals aged from 2 months to 35 years old (mean ± SD: 11.6 ± 6.4 years old); BW 77-662 kg (mean ± SD: 436 ± 135 kg) were also examined using the pulsed-wave Doppler mode. Standard two-dimensional and M-mode echocardiography were performed on all animals. Standard pulsed-wave Doppler examination of each cardiac valve was performed on the 50 first examined animals. Data were analysed using a general linear model including the effect of sex, age, breed and BW after logarithmic transformation of the data. Therefore, the same analysis was performed separately on animals aged ≤ 2 years-old and on older animals. All dimensional echocardiographic measurements were significantly affected by BW and most of them were significantly affected by breed, but not by sex. Only the aortic and the pulmonary artery internal diameter were significantly affected by age. None of the Doppler measurements were significantly affected by the tested variables. In conclusion, in the equine species, dimensional echocardiographic reference values should be established using regression equations as a function of BW, which could increase the diagnostic value of this leading technique in equine cardiology. Breed could also have an effect on those measurements. Copyright © 2013 Elsevier Ltd. All rights reserved.

Genomic Prediction of Resistance to Pasteurellosis in Gilthead Sea Bream (Sparus aurata) Using 2b-RAD Sequencing

PubMed Central

Palaiokostas, Christos; Ferraresso, Serena; Franch, Rafaella; Houston, Ross D.; Bargelloni, Luca

2016-01-01

Gilthead sea bream (Sparus aurata) is a species of paramount importance to the Mediterranean aquaculture industry, with an annual production exceeding 140,000 metric tons. Pasteurellosis due to the Gram-negative bacterium Photobacterium damselae subsp. piscicida (Phdp) causes significant mortality, especially during larval and juvenile stages, and poses a serious threat to bream production. Selective breeding for improved resistance to pasteurellosis is a promising avenue for disease control, and the use of genetic markers to predict breeding values can improve the accuracy of selection, and allow accurate calculation of estimated breeding values of nonchallenged animals. In the current study, a population of 825 sea bream juveniles, originating from a factorial cross between 67 broodfish (32 sires, 35 dams), were challenged by 30 min immersion with 1 × 105 CFU virulent Phdp. Mortalities and survivors were recorded and sampled for genotyping by sequencing. The restriction-site associated DNA sequencing approach, 2b-RAD, was used to generate genome-wide single nucleotide polymorphism (SNP) genotypes for all samples. A high-density linkage map containing 12,085 SNPs grouped into 24 linkage groups (consistent with the karyotype) was constructed. The heritability of surviving days (censored data) was 0.22 (95% highest density interval: 0.11–0.36) and 0.28 (95% highest density interval: 0.17–0.4) using the pedigree and the genomic relationship matrix respectively. A genome-wide association study did not reveal individual SNPs significantly associated with resistance at a genome-wide significance level. Genomic prediction approaches were tested to investigate the potential of the SNPs obtained by 2b-RAD for estimating breeding values for resistance. The accuracy of the genomic prediction models (r = 0.38–0.46) outperformed the traditional BLUP approach based on pedigree records (r = 0.30). Overall results suggest that major quantitative trait loci affecting resistance to pasteurellosis were not present in this population, but highlight the effectiveness of 2b-RAD genotyping by sequencing for genomic selection in a mass spawning fish species. PMID:27652890

Genome-wide association study using deregressed breeding values for cryptorchidism and scrotal/inguinal hernia in two pig lines.

PubMed

Sevillano, Claudia A; Lopes, Marcos S; Harlizius, Barbara; Hanenberg, Egiel H A T; Knol, Egbert F; Bastiaansen, John W M

2015-03-21

Cryptorchidism and scrotal/inguinal hernia are the most frequent congenital defects in pigs. Identification of genomic regions that control these congenital defects is of great interest to breeding programs, both from an animal welfare point of view as well as for economic reasons. The aim of this genome-wide association study (GWAS) was to identify single nucleotide polymorphisms (SNPs) that are strongly associated with these congenital defects. Genotypes were available for 2570 Large White (LW) and 2272 Landrace (LR) pigs. Breeding values were estimated based on 1 359 765 purebred and crossbred male offspring, using a binary trait animal model. Estimated breeding values were deregressed (DEBV) and taken as the response variable in the GWAS. Heritability estimates were equal to 0.26 ± 0.02 for cryptorchidism and to 0.31 ± 0.01 for scrotal/inguinal hernia. Seven and 31 distinct QTL regions were associated with cryptorchidism in the LW and LR datasets, respectively. The top SNP per region explained between 0.96% and 1.10% and between 0.48% and 2.77% of the total variance of cryptorchidism incidence in the LW and LR populations, respectively. Five distinct QTL regions associated with scrotal/inguinal hernia were detected in both LW and LR datasets. The top SNP per region explained between 1.22% and 1.60% and between 1.15% and 1.46% of the total variance of scrotal/inguinal hernia incidence in the LW and LR populations, respectively. For each trait, we identified one overlapping region between the LW and LR datasets, i.e. a region on SSC8 (Sus scrofa chromosome) between 65 and 73 Mb for cryptorchidism and a region on SSC13 between 34 and 37 Mb for scrotal/inguinal hernia. The use of DEBV in combination with a binary trait model was a powerful approach to detect regions associated with difficult traits such as cryptorchidism and scrotal/inguinal hernia that have a low incidence and for which affected animals are generally not available for genotyping. Several novel QTL regions were detected for cryptorchidism and scrotal/inguinal hernia, and for several previously known QTL regions, the confidence interval was narrowed down.

Economic selection index development for Beefmaster cattle I: Terminal breeding objective.

PubMed

Ochsner, K P; MacNeil, M D; Lewis, R M; Spangler, M L

2017-03-01

The objective of this study was to develop an economic selection index for Beefmaster cattle in a terminal production system where bulls are mated to mature cows with all resulting progeny harvested. National average prices from 2010 to 2014 were used to establish income and expenses for the system. Phenotypic and genetic parameter values among the selection criteria and goal traits were obtained from literature. Economic values were estimated by simulating 100,000 animals and approximating the partial derivatives of the profit function by perturbing traits one at a time, by 1 unit, while holding the other traits constant at their respective means. Relative economic values (REV) for the terminal objective traits HCW, marbling score (MS), ribeye area (REA), 12th-rib fat (FAT), and feed intake (FI) were 91.29, 17.01, 8.38, -7.07, and -29.66, respectively. Consequently, improving the efficiency of beef production is expected to impact profitability greater than improving carcass merit alone. The accuracy of the index lies between 0.338 (phenotypic selection) and 0.503 (breeding values known without error). The application of this index would aid Beefmaster breeders in their sire selection decisions, facilitating genetic improvement for a terminal breeding objective.

On the distance of genetic relationships and the accuracy of genomic prediction in pig breeding.

PubMed

Meuwissen, Theo H E; Odegard, Jorgen; Andersen-Ranberg, Ina; Grindflek, Eli

2014-08-01

With the advent of genomic selection, alternative relationship matrices are used in animal breeding, which vary in their coverage of distant relationships due to old common ancestors. Relationships based on pedigree (A) and linkage analysis (GLA) cover only recent relationships because of the limited depth of the known pedigree. Relationships based on identity-by-state (G) include relationships up to the age of the SNP (single nucleotide polymorphism) mutations. We hypothesised that the latter relationships were too old, since QTL (quantitative trait locus) mutations for traits under selection were probably more recent than the SNPs on a chip, which are typically selected for high minor allele frequency. In addition, A and GLA relationships are too recent to cover genetic differences accurately. Thus, we devised a relationship matrix that considered intermediate-aged relationships and compared all these relationship matrices for their accuracy of genomic prediction in a pig breeding situation. Haplotypes were constructed and used to build a haplotype-based relationship matrix (GH), which considers more intermediate-aged relationships, since haplotypes recombine more quickly than SNPs mutate. Dense genotypes (38 453 SNPs) on 3250 elite breeding pigs were combined with phenotypes for growth rate (2668 records), lean meat percentage (2618), weight at three weeks of age (7387) and number of teats (5851) to estimate breeding values for all animals in the pedigree (8187 animals) using the aforementioned relationship matrices. Phenotypes on the youngest 424 to 486 animals were masked and predicted in order to assess the accuracy of the alternative genomic predictions. Correlations between the relationships and regressions of older on younger relationships revealed that the age of the relationships increased in the order A, GLA, GH and G. Use of genomic relationship matrices yielded significantly higher prediction accuracies than A. GH and G, differed not significantly, but were significantly more accurate than GLA. Our hypothesis that intermediate-aged relationships yield more accurate genomic predictions than G was confirmed for two of four traits, but these results were not statistically significant. Use of estimated genotype probabilities for ungenotyped animals proved to be an efficient method to include the phenotypes of ungenotyped animals.

Ocular biometry by computed tomography in different dog breeds.

PubMed

Chiwitt, Carolin L H; Baines, Stephen J; Mahoney, Paul; Tanner, Andrew; Heinrich, Christine L; Rhodes, Michael; Featherstone, Heidi J

2017-09-01

To (i) correlate B-mode ocular ultrasound (US) and computed tomography (CT) (prospective pilot study), (ii) establish a reliable method to measure the normal canine eye using CT, (iii) establish a reference guide for some dog breeds, (iv) compare eye size between different breeds and breed groups, and (v) investigate the correlation between eye dimensions and body weight, gender, and skull type (retrospective study). B-mode US and CT were performed on ten sheep cadaveric eyes. CT biometry involved 100 adult pure-bred dogs with nonocular and nonorbital disease, representing eleven breeds. Eye length, width, and height were each measured in two of three planes (horizontal, sagittal, and equatorial). B-mode US and CT measurements of sheep cadaveric eyes correlated well (0.70-0.71). The shape of the canine eye was found to be akin to an oblate spheroid (a flattened sphere). A reference guide was established for eleven breeds. Eyes of large breed dogs were significantly larger than those of medium and small breed dogs (P < 0.01), and eyes of medium breed dogs were significantly larger than those of small breed dogs (P < 0.01). Eye size correlated with body weight (0.74-0.82) but not gender or skull type. Computed tomography is a suitable method for biometry of the canine eye, and a reference guide was established for eleven breeds. Eye size correlated with breed size and body weight. Because correlation between B-mode US and CT was shown, the obtained values can be applied in the clinical setting, for example, for the diagnosis of microphthalmos and buphthalmos. © 2016 American College of Veterinary Ophthalmologists.

Breed differences of bull frozen-thawed semen.

PubMed

Ntemka, A; Tsousis, G; Brozos, C; Kiossis, E; Boscos, C M; Tsakmakidis, I A

2016-12-01

The objective of this study was to investigate the quality of frozen-thawed semen from different bull breeds. Commercial frozen-thawed bull semen samples (26 per breed, 130 totally) of five breeds (Holstein [Η], Brown Swiss [BS], Limousin [L], Belgian Blue [BB], Blonde d' Aquitaine [BA]) were used. After thawing, each semen sample was subjected to thermal resistance test (TR) for 0.5 and 1 hr at 38°C and hypo-osmotic swelling test (HOST) for 1 hr at 150 mOsm at 37°C. Additionally, all samples were evaluated at times 0 hr (thawing), 0.5 hr (TR), 1 hr (TR) for kinetics by CASA [progressive, immotile, rapid, medium, slow moving spermatozoa, curvilinear velocity (VCL), average path velocity (VAP), straight line velocity (VSL), linearity (LIN), straightness (STR), beat cross-frequency (BCF), amplitude of lateral head displacement (ALH), wobble (WOB)]. Moreover, directly after thawing, all semen samples were evaluated for morphometry, morphology, viability and DNA fragmentation. Statistical analysis was conducted using a mixed model for repeated measures. The results showed (a) higher VCL after thawing in H, L breeds compared to BB and BA, (b) higher VAP after thawing in L compared to BB, BA, (c) higher values of progressive spermatozoa after TR in H, BS compared to BB, BA, (d) higher values of rapid spermatozoa after thawing and 0.5 hr of TR in H, BS, L compared to BB, BA, (e) lower viability in BA after thawing compared to H, BS, BB, (f) lower morphological abnormalities in H compared to L, BB, (g) higher head length in Η compared to BB. No significant differences were observed in the results from HOST and DNA fragmentation between breeds. In conclusion, quality characteristics of frozen-thawed bull semen are dependent on the breed. Frozen semen from BB and BA breeds should be handled more carefully after thawing, as it is more sensitive to stress. © 2016 Blackwell Verlag GmbH.

Urolithiasis in dogs. II: Breed prevalence, and interrelations of breed, sex, age, and mineral composition.

PubMed

Ling, G V; Franti, C E; Ruby, A L; Johnson, D L

1998-05-01

To analyze selected breed-related data for canine urinary calculi. 11,000 specimens: 5,781 from female dogs, 5,215 from males, and 4 from dogs of unrecorded sex. Information was compiled for all canine urinary calculi submitted between July 1981 and January 1994. Results for a mixed-breed group and 26 of the most common breeds of stone-forming dogs were analyzed. Interrelations of breed, sex, and age of affected dogs and mineral composition of the specimens were determined. Prevalence of 5 specific mineral types was significantly correlated between the sexes of 27 common breed groups: struvite, calcium phosphate (apatite), calcium oxalate, brushite, and urate. Struvite-containing calculi were seen in high proportions in both sexes of 7 breeds, and in low proportions in both sexes of 7 other breeds. Male and female Lhasa Apsos, Cairn Terriers, and 5 other breeds had high proportions of oxalate-containing calculi; values in males were substantially higher. Low numbers of oxalate-containing calculi were seen in both sexes of 7 breeds; Dalmatians had the lowest numbers. Males and females of 6 breeds had high numbers of urate-containing calculi, Dalmatians and English Bulldogs had the highest numbers. Low amounts of urate were found in calculi from males and females of 6 breeds, Samoyeds had the lowest numbers. Highest proportions of cystine-containing calculi were seen in male Dachshunds, English Bulldogs, and Chihuahuas. Males of 8 breeds had no specimens that contained cystine; only 2 such specimens were obtained from females. Prevalence of uroliths differs among breed, age, and sex of affected dogs. Breed, sex, and age of dogs; mineral types of calculi in males versus females; and their anatomic location within the tract are important considerations for clinicians when evaluating risk in dogs with urolithiasis and in identifying areas that need further in-depth applied or clinical investigation, or both.

[Prospects of molecular breeding in medical plants].

PubMed

Ma, Xiao-Jun; Mo, Chang-Ming

2017-06-01

The molecular-assisted breeding, transgenic breeding and molecular designing breeding are three development directions of plant molecular breeding. Base on these three development directions, this paper summarizes developing status and new tendency of research field of genetic linkage mapping, QTL mapping, association mapping, molecular-assisted selections, pollen-mediated transformations, agrobacterium-mediated transformations, particle gun-mediated transformations, genome editing technologies, whole-genome sequencing, transcriptome sequencing, proteome sequencing and varietal molecular designing. The objective and existing problem of medical plant molecular breeding were discussed the prospect of these three molecular breeding technologies application on medical plant molecular breeding was outlooked. Copyright© by the Chinese Pharmaceutical Association.

American woodcock migratory connectivity as indicated by hydrogen isotopes

USGS Publications Warehouse

Sullins, Daniel S.; Conway, Warren C.; Haukos, David A.; Hobson, Keith A.; Wassenaar, Leonard I; Comer, Christopher E.; Hung, I-Kuai

2016-01-01

To identify factors contributing to the long-term decline of American woodcock, a holistic understanding of range-wide population connectivity throughout the annual cycle is needed. We used band recovery data and isotopic composition of primary (P1) and secondary (S13) feathers to estimate population sources and connectivity among natal, early fall, and winter ranges of hunter-harvested juvenile American woodcock. We used P1 feathers from known-origin pre-fledged woodcock (n = 43) to create a hydrogenδ2Hf isoscape by regressing δ2Hf against expected growing-season precipitation (δ2Hp). Modeled δ2Hp values explained 79% of the variance in P1 δ2Hf values, indicating good model fit for estimating woodcock natal origins. However, a poor relationship (r2 = 0.23) between known-origin, S13 δ2Hf values, and expected δ2Hp values precluded assignment of early fall origins. We applied the δ2Hfisoscape to assign natal origins using P1 feathers from 494 hunter-harvested juvenile woodcock in the United States and Canada during 2010–2011 and 2011–2012 hunting seasons. Overall, 64% of all woodcock origins were assigned to the northernmost (>44°N) portion of both the Central and Eastern Management Regions. In the Eastern Region, assignments were more uniformly distributed along the Atlantic coast, whereas in the Central Region, most woodcock were assigned to origins within and north of the Great Lakes region. We compared our origin assignments to spatial coverage of the annual American woodcock Singing Ground Survey (SGS) and evaluated whether the survey effectively encompasses the entire breeding range. When we removed the inadequately surveyed Softwood shield Bird Conservation Region (BCR) from the northern portion of the SGS area, only 48% of juvenile woodcock originated in areas currently surveyed by the SGS. Of the individuals assigned to the northernmost portions of the breeding range, several were harvested in the southern extent of the wintering range. Based upon this latitudinal winter stratification, we examined whether woodcock employed a leapfrog migration strategy. Using δ2Hf values and band-recovery data, we found some support for this migration strategy hypothesis but not as a singular explanation. The large harvest derivation of individuals from the northernmost portions of the breeding range, and the difference in breeding distributions within each Management Region should be considered in future range-wide conservation and harvest management planning for American woodcock. 

Genome-wide investigation of genetic changes during modern breeding of Brassica napus.

PubMed

Wang, Nian; Li, Feng; Chen, Biyun; Xu, Kun; Yan, Guixin; Qiao, Jiangwei; Li, Jun; Gao, Guizhen; Bancroft, Ian; Meng, Jingling; King, Graham J; Wu, Xiaoming

2014-08-01

Considerable genome variation had been incorporated within rapeseed breeding programs over past decades. In past decades, there have been substantial changes in phenotypic properties of rapeseed as a result of extensive breeding effort. Uncovering the underlying patterns of allelic variation in the context of genome organisation would provide knowledge to guide future genetic improvement. We assessed genome-wide genetic changes, including population structure, genetic relatedness, the extent of linkage disequilibrium, nucleotide diversity and genetic differentiation based on F ST outlier detection, for a panel of 472 Brassica napus inbred accessions using a 60 k Brassica Infinium® SNP array. We found genetic diversity varied in different sub-groups. Moreover, the genetic diversity increased from 1950 to 1980 and then remained at a similar level in China and Europe. We also found ~6-10 % genomic regions revealed high F ST values. Some QTLs previously associated with important agronomic traits overlapped with these regions. Overall, the B. napus C genome was found to have more high F ST signals than the A genome, and we concluded that the C genome may contribute more valuable alleles to generate elite traits. The results of this study indicate that considerable genome variation had been incorporated within rapeseed breeding programs over past decades. These results also contribute to understanding the impact of rapeseed improvement on available genome variation and the potential for dissecting complex agronomic traits.

Farm-by-farm analysis of microsatellite, mtDNA and SNP genotype data reveals inbreeding and crossbreeding as threats to the survival of a native Spanish pig breed.

PubMed

Herrero-Medrano, J M; Megens, H J; Crooijmans, R P; Abellaneda, J M; Ramis, G

2013-06-01

The Chato Murciano (CM), a pig breed from the Murcia region in the southeastern region of Spain, is a good model for endangered livestock populations. The remaining populations are bred on approximately 15 small farms, and no herdbook exists. To assess the genetic threats to the integrity and survival of the CM breed, and to aid in designing a conservation program, three genetic marker systems - microsatellites, SNPs and mtDNA - were applied across the majority of the total breeding stock. In addition, mtDNA and SNPs were genotyped in breeds that likely contributed genetically to the current CM gene pool. The analyses revealed the levels of genetic diversity within the range of other European local breeds (H(e) = 0.53). However, when the eight farms that rear at least 10 CM pigs were independently analyzed, high levels of inbreeding were found in some. Despite the evidence for recent crossbreeding with commercial breeds on a few farms, the entire breeding stock remains readily identifiable as CM, facilitating the design of traceability assays. The genetic management of the breed is consistent with farm size, farm owner and presence of other pig breeds on the farm, demonstrating the highly ad hoc nature of current CM breeding. The results of genetic diversity and substructure of the entire breed, as well as admixture and crossbreeding obtained in the present study, provide a benchmark to develop future conservation strategies. Furthermore, this study demonstrates that identifying farm-based practices and farm-based breeding stocks can aid in the design of a sustainable breeding program for minority breeds. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

Accuracy of genomic prediction using deregressed breeding values estimated from purebred and crossbred offspring phenotypes in pigs.

PubMed

Hidalgo, A M; Bastiaansen, J W M; Lopes, M S; Veroneze, R; Groenen, M A M; de Koning, D-J

2015-07-01

Genomic selection is applied to dairy cattle breeding to improve the genetic progress of purebred (PB) animals, whereas in pigs and poultry the target is a crossbred (CB) animal for which a different strategy appears to be needed. The source of information used to estimate the breeding values, i.e., using phenotypes of CB or PB animals, may affect the accuracy of prediction. The objective of our study was to assess the direct genomic value (DGV) accuracy of CB and PB pigs using different sources of phenotypic information. Data used were from 3 populations: 2,078 Dutch Landrace-based, 2,301 Large White-based, and 497 crossbreds from an F1 cross between the 2 lines. Two female reproduction traits were analyzed: gestation length (GLE) and total number of piglets born (TNB). Phenotypes used in the analyses originated from offspring of genotyped individuals. Phenotypes collected on CB and PB animals were analyzed as separate traits using a single-trait model. Breeding values were estimated separately for each trait in a pedigree BLUP analysis and subsequently deregressed. Deregressed EBV for each trait originating from different sources (CB or PB offspring) were used to study the accuracy of genomic prediction. Accuracy of prediction was computed as the correlation between DGV and the DEBV of the validation population. Accuracy of prediction within PB populations ranged from 0.43 to 0.62 across GLE and TNB. Accuracies to predict genetic merit of CB animals with one PB population in the training set ranged from 0.12 to 0.28, with the exception of using the CB offspring phenotype of the Dutch Landrace that resulted in an accuracy estimate around 0 for both traits. Accuracies to predict genetic merit of CB animals with both parental PB populations in the training set ranged from 0.17 to 0.30. We conclude that prediction within population and trait had good predictive ability regardless of the trait being the PB or CB performance, whereas using PB population(s) to predict genetic merit of CB animals had zero to moderate predictive ability. We observed that the DGV accuracy of CB animals when training on PB data was greater than or equal to training on CB data. However, when results are corrected for the different levels of reliabilities in the PB and CB training data, we showed that training on CB data does outperform PB data for the prediction of CB genetic merit, indicating that more CB animals should be phenotyped to increase the reliability and, consequently, accuracy of DGV for CB genetic merit.

A genetic dissection of breed composition and performance enhancement in the Alaskan sled dog

PubMed Central

2010-01-01

Background The Alaskan sled dog offers a rare opportunity to investigate the development of a dog breed based solely on performance, rather than appearance, thus setting the breed apart from most others. Several established breeds, many of which are recognized by the American Kennel Club (AKC), have been introduced into the sled dog population to enhance racing performance. We have used molecular methods to ascertain the constitutive breeds used to develop successful sled dog lines, and in doing so, determined the breed origins of specific performance-related behaviors. One hundred and ninety-nine Alaskan sled dogs were genotyped using 96 microsatellite markers that span the canine genome. These data were compared to that from 141 similarly genotyped purebred dog breeds. Sled dogs were evaluated for breed composition based on a variety of performance phenotypes including speed, endurance and work ethic, and the data stratified based on population structure. Results We observe that the Alaskan sled dog has a unique molecular signature and that the genetic profile is sufficient for identifying dogs bred for sprint versus distance. When evaluating contributions of existing breeds we find that the Alaskan Malamute and Siberian Husky contributions are associated with enhanced endurance; Pointer and Saluki are associated with enhanced speed and the Anatolian Shepherd demonstrates a positive influence on work ethic. Conclusion We have established a genetic breed profile for the Alaskan sled dog, identified profile variance between sprint and distance dogs, and established breeds associated with enhanced performance attributes. These data set the stage for mapping studies aimed at finding genes that are associated with athletic attributes integral to the high performing Alaskan sled dog. PMID:20649949

Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery.

PubMed

Hickey, John M; Chiurugwi, Tinashe; Mackay, Ian; Powell, Wayne

2017-08-30

The rate of annual yield increases for major staple crops must more than double relative to current levels in order to feed a predicted global population of 9 billion by 2050. Controlled hybridization and selective breeding have been used for centuries to adapt plant and animal species for human use. However, achieving higher, sustainable rates of improvement in yields in various species will require renewed genetic interventions and dramatic improvement of agricultural practices. Genomic prediction of breeding values has the potential to improve selection, reduce costs and provide a platform that unifies breeding approaches, biological discovery, and tools and methods. Here we compare and contrast some animal and plant breeding approaches to make a case for bringing the two together through the application of genomic selection. We propose a strategy for the use of genomic selection as a unifying approach to deliver innovative 'step changes' in the rate of genetic gain at scale.

Breeding chorus indices are weakly related to estimated abundance of boreal chorus frogs

Treesearch

Paul Stephen Corn; Erin Muths; Amanda M. Kissel; Rick D. Scherer

2011-01-01

Call surveys used to monitor breeding choruses of anuran amphibians generate index values that are frequently used to represent the number of male frogs present, but few studies have quantified this relationship. We compared abundance of male Boreal Chorus Frogs (Pseudacris maculata), estimated using capture-recapture methods in two populations in Colorado, to call...

Demography of Lewis's Woodpecker, breeding bird densities, and riparian aspen integrity in a grazed landscape

Treesearch

Karen Rachel Newlon

2005-01-01

Aspen (Populus tremuloides) riparian woodlands are extremely limited in distribution throughout the western U.S., yet these habitats have a disproportionate value to breeding birds. Aspen habitats are also considered prime sheep and cattle summer range, particularly in the semiarid Intermountain West. Such concentrated use has raised concern about...

Efficiency of including first-generation information in second-generation ranking and selection: results of computer simulation.

Treesearch

T.Z. Ye; K.J.S. Jayawickrama; G.R. Johnson

2006-01-01

Using computer simulation, we evaluated the impact of using first-generation information to increase selection efficiency in a second-generation breeding program. Selection efficiency was compared in terms of increase in rank correlation between estimated and true breeding values (i.e., ranking accuracy), reduction in coefficient of variation of correlation...

Comparing genomic selection and marker-assisted selection for Fusarium head blight resistance in wheat (Triticum aestivum L.)

USDA-ARS?s Scientific Manuscript database

Genomic selection (GS) and marker-assisted selection (MAS) rely on marker-trait associations and are both routinely used for breeding purposes. Although similar, these two approaches differ in their applications and how markers are used to estimate breeding values. In this study, GS and MAS were com...

Family indices for seed-orchard selection

Treesearch

Gene Namkoong

1966-01-01

Many seed orchard programs include a stage at which clones or seedlings are culled on the basis of progeny tests. Though breeding systems which involve progeny testing differ in efficiency, they all provide information on an individual's breeding value through its own performance and that of parental or seedling relatives. A combined index on any one trait, using...

Acid precipitation and reproductive success of Ambystoma salamanders

Treesearch

F. Harvey Pough; Richard E. Wilson

1976-01-01

The two species of mole salamander that occur in the Ithaca, New York, region (Ambystoma maculatum and A. jeffersonianum) breed in temporary ponds that are formed by accumulation of melted snow and spring rains. Water in many of these pools during the breeding season is acid; pH values as low as 3.5 have been measured. In...

Genetic evaluation of lactation persistency for five breeds of dairy cattle.

PubMed

Cole, J B; Null, D J

2009-05-01

Cows with high lactation persistency tend to produce less milk than expected at the beginning of lactation and more than expected at the end. Best prediction of lactation persistency is calculated as a function of trait-specific standard lactation curves and linear regressions of test-day deviations on days in milk. Because regression coefficients are deviations from a tipping point selected to make yield and lactation persistency phenotypically uncorrelated it should be possible to use 305-d actual yield and lactation persistency to predict yield for lactations with later endpoints. The objectives of this study were to calculate (co)variance components and breeding values for best predictions of lactation persistency of milk (PM), fat (PF), protein (PP), and somatic cell score (PSCS) in breeds other than Holstein, and to demonstrate the calculation of prediction equations for 400-d actual milk yield. Data included lactations from Ayrshire, Brown Swiss, Guernsey (GU), Jersey (JE), and Milking Shorthorn (MS) cows calving since 1997. The number of sires evaluated ranged from 86 (MS) to 3,192 (JE), and mean sire estimated breeding value for PM ranged from 0.001 (Ayrshire) to 0.10 (Brown Swiss); mean estimated breeding value for PSCS ranged from -0.01 (MS) to -0.043 (JE). Heritabilities were generally highest for PM (0.09 to 0.15) and lowest for PSCS (0.03 to 0.06), with PF and PP having intermediate values (0.07 to 0.13). Repeatabilities varied considerably between breeds, ranging from 0.08 (PSCS in GU, JE, and MS) to 0.28 (PM in GU). Genetic correlations of PM, PF, and PP with PSCS were moderate and favorable (negative), indicating that increasing lactation persistency of yield traits is associated with decreases in lactation persistency of SCS, as expected. Genetic correlations among yield and lactation persistency were low to moderate and ranged from -0.55 (PP in GU) to 0.40 (PP in MS). Prediction equations for 400-d milk yield were calculated for each breed by regression of both 305-d yield and 305-d yield and lactation persistency on 400-d yield. Goodness-of-fit was very good for both models, but the addition of lactation persistency to the model significantly improved fit in all cases. Routine genetic evaluations for lactation persistency, as well as the development of prediction equations for several lactation end-points, may provide producers with tools to better manage their herds.

Canine hip dysplasia is predictable by genotyping.

PubMed

Guo, G; Zhou, Z; Wang, Y; Zhao, K; Zhu, L; Lust, G; Hunter, L; Friedenberg, S; Li, J; Zhang, Y; Harris, S; Jones, P; Sandler, J; Krotscheck, U; Todhunter, R; Zhang, Z

2011-04-01

To establish a predictive method using whole genome genotyping for early intervention in canine hip dysplasia (CHD) risk management, for the prevention of the progression of secondary osteoarthritis (OA), and for selective breeding. Two sets of dogs (six breeds) were genotyped with dense SNPs covering the entire canine genome. The first set contained 359 dogs upon which a predictive formula for genomic breeding value (GBV) was derived by using their estimated breeding value (EBV) of the Norberg angle (a measure of CHD) and their genotypes. To investigate how well the formula would work for an individual dog with genotype only (without using EBV), a cross validation was performed by masking the EBV of one dog at a time. The genomic data and the EBV of the remaining dogs were used to predict the GBV for the single dog that was left out. The second set of dogs included 38 new Labrador retriever dogs, which had no pedigree relationship to the dogs in the first set. The cross validation showed a strong correlation (R>0.7) between the EBV and the GBV. The independent validation showed a moderate correlation (R=0.5) between GBV for the Norberg angle and the observed Norberg angle (no EBV was available for the new 38 dogs). Sensitivity, specificity, positive and negative predictive values of the genomic data were all above 70%. Prediction of CHD from genomic data is feasible, and can be applied for risk management of CHD and early selection for genetic improvement to reduce the prevalence of CHD in breeding programs. The prediction can be implemented before maturity, at which age current radiographic screening programs are traditionally applied, and as soon as DNA is available. Copyright © 2010 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Lesser scaup breeding probability and female survival on the yukon flats, Alaska

USGS Publications Warehouse

Martin, K.H.; Lindberg, M.S.; Schmutz, J.A.; Bertram, M.R.

2009-01-01

Information on the ecology of waterfowl breeding in the boreal forest is lacking, despite the boreal region's importance to continental waterfowl populations and to duck species that are currently declining, such as lesser scaup (Aythya affinis). We estimated breeding probability and breeding season survival of female lesser scaup on the Yukon Flats National Wildlife Refuge, Alaska, USA, in 2005 and 2006. We captured and marked 93 lesser scaup with radiotransmitters during prelaying and nesting periods. Although all marked lesser scaup females were paired throughout prelaying and incubation periods, we estimated breeding probability over both years as 0.12 (SE = 0.05, n = 67) using telemetry. Proportion of lesser scaup females undergoing rapid follicle growth at capture in 2006 was 0.46 (SE = 0.11, n = 37), based on concentration of yolk precursors in blood plasma. By combining methods based on telemetry, yolk precursors, and postovulatory follicles, we estimated maximum breeding probability as 0.68 (SE = 0.08, n = 37) in 2006. Notably, breeding probability was positively related to female body mass. Survival of female lesser scaup during the nesting and brood-rearing periods was 0.92 (SE = 0.05) in 2005 and 0.86 (SE = 0.08) in 2006. Our results suggest that breeding probability is lower than expected for lesser scaup. In addition, the implicit assumption of continental duck-monitoring programs that all paired females attempt to breed should be reevaluated. Recruitment estimates based on annual breeding-pair surveys may overestimate productivity of scaup pairs in the boreal forest. ?? The Wildlife Society.

Prioritization based on neutral genetic diversity may fail to conserve important characteristics in cattle breeds.

PubMed

Hall, S J G; Lenstra, J A; Deeming, D C

2012-06-01

Conservation of the intraspecific genetic diversity of livestock species requires protocols that assess between-breed genetic variability and also take into account differences among individuals within breeds. Here, we focus on variation between breeds. Conservation of neutral genetic variation has been seen as promoting, through linkage processes, the retention of useful and potentially useful variation. Using public information on beef cattle breeds, with a total of 165 data sets each relating to a breed comparison of a performance variable, we have tested this paradigm by calculating the correlations between pairwise breed differences in performance and pairwise genetic distances deduced from biochemical and immunological polymorphisms, microsatellites and single-nucleotide polymorphisms. As already observed in floral and faunal biodiversity, significant positive correlations (n=54) were found, but many correlations were non-significant (n=100) or significantly negative (n=11). This implies that maximizing conserved neutral genetic variation with current techniques may conserve breed-level genetic variation in some traits but not in others and supports the view that genetic distance measurements based on neutral genetic variation are not sufficient as a determinant of conservation priority among breeds. © 2011 Blackwell Verlag GmbH.

Association analysis for feet and legs disorders with whole-genome sequence variants in 3 dairy cattle breeds.

PubMed

Wu, Xiaoping; Guldbrandtsen, Bernt; Lund, Mogens Sandø; Sahana, Goutam

2016-09-01

Identification of genetic variants associated with feet and legs disorders (FLD) will aid in the genetic improvement of these traits by providing knowledge on genes that influence trait variations. In Denmark, FLD in cattle has been recorded since the 1990s. In this report, we used deregressed breeding values as response variables for a genome-wide association study. Bulls (5,334 Danish Holstein, 4,237 Nordic Red Dairy Cattle, and 1,180 Danish Jersey) with deregressed estimated breeding values were genotyped with the Illumina Bovine 54k single nucleotide polymorphism (SNP) genotyping array. Genotypes were imputed to whole-genome sequence variants, and then 22,751,039 SNP on 29 autosomes were used for an association analysis. A modified linear mixed-model approach (efficient mixed-model association eXpedited, EMMAX) and a linear mixed model were used for association analysis. We identified 5 (3,854 SNP), 3 (13,642 SNP), and 0 quantitative trait locus (QTL) regions associated with the FLD index in Danish Holstein, Nordic Red Dairy Cattle, and Danish Jersey populations, respectively. We did not identify any QTL that were common among the 3 breeds. In a meta-analysis of the 3 breeds, 4 QTL regions were significant, but no additional QTL region was identified compared with within-breed analyses. Comparison between top SNP locations within these QTL regions and known genes suggested that RASGRP1, LCORL, MOS, and MITF may be candidate genes for FLD in dairy cattle. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Signatures of selection in five Italian cattle breeds detected by a 54K SNP panel.

PubMed

Mancini, Giordano; Gargani, Maria; Chillemi, Giovanni; Nicolazzi, Ezequiel Luis; Marsan, Paolo Ajmone; Valentini, Alessio; Pariset, Lorraine

2014-02-01

In this study we used a medium density panel of SNP markers to perform population genetic analysis in five Italian cattle breeds. The BovineSNP50 BeadChip was used to genotype a total of 2,935 bulls of Piedmontese, Marchigiana, Italian Holstein, Italian Brown and Italian Pezzata Rossa breeds. To determine a genome-wide pattern of positive selection we mapped the F st values against genome location. The highest F st peaks were obtained on BTA6 and BTA13 where some candidate genes are located. We identified selection signatures peculiar of each breed which suggest selection for genes involved in milk or meat traits. The genetic structure was investigated by using a multidimensional scaling of the genetic distance matrix and a Bayesian approach implemented in the STRUCTURE software. The genotyping data showed a clear partitioning of the cattle genetic diversity into distinct breeds if a number of clusters equal to the number of populations were given. Assuming a lower number of clusters beef breeds group together. Both methods showed all five breeds separated in well defined clusters and the Bayesian approach assigned individuals to the breed of origin. The work is of interest not only because it enriches the knowledge on the process of evolution but also because the results generated could have implications for selective breeding programs.

A possible effect of electromagnetic radiation from mobile phone base stations on the number of breeding house sparrows (Passer domesticus).

PubMed

Everaert, Joris; Bauwens, Dirk

2007-01-01

A possible effect of long-term exposure to low-intensity electromagnetic radiation from mobile phone (GSM) base stations on the number of House Sparrows during the breeding season was studied in six residential districts in Belgium. We sampled 150 point locations within the 6 areas to examine small-scale geographic variation in the number of House Sparrow males and the strength of electromagnetic radiation from base stations. Spatial variation in the number of House Sparrow males was negatively and highly significantly related to the strength of electric fields from both the 900 and 1800 MHz downlink frequency bands and from the sum of these bands (Chi(2)-tests and AIC-criteria, P<0.001). This negative relationship was highly similar within each of the six study areas, despite differences among areas in both the number of birds and radiation levels. Thus, our data show that fewer House Sparrow males were seen at locations with relatively high electric field strength values of GSM base stations and therefore support the notion that long-term exposure to higher levels of radiation negatively affects the abundance or behavior of House Sparrows in the wild.

Seroepidemiological survey of pathogenic Yersinia in breeding squirrel monkeys in Japan.

PubMed

Iwata, Taketoshi; Une, Yumi; Lee, Ken-ichi; Nakamura, Shin-ichi; Taniguchi, Takahide; Hayashidani, Hideki

2010-08-01

To investigate the prevalence of antibodies to pathogenic Yersinia in breeding squirrel monkeys, the serum samples of 252 squirrel monkeys from 9 zoological gardens in Japan were tested by ELISA using plasmid-encoded Yersinia outer membrane protein (Yops) as the antigen. The cutoff value was calculated by using the serum samples of the squirrel monkeys from Suriname, where no prevalence of pathogenic Yersinia have been reported. According to the cutoff value, 164 of 252 (65.1%) squirrel monkeys were considered positive against pathogenic Yersinia. These positive monkeys belonged to 8 of the 9 zoological gardens, and the percentage of the seropositive monkeys ranged from 22.2 to 89.4%. Furthermore, in one zoological garden, the positive rate of the squirrel monkeys which were over 1 year old (95.7%) was significantly higher than those which were under 1 year old (23.3%). These results suggested that pathogenic Yersinia is highly prevalent among breeding monkeys in Japan.

Genomic Model with Correlation Between Additive and Dominance Effects.

PubMed

Xiang, Tao; Christensen, Ole Fredslund; Vitezica, Zulma Gladis; Legarra, Andres

2018-05-09

Dominance genetic effects are rarely included in pedigree-based genetic evaluation. With the availability of single nucleotide polymorphism markers and the development of genomic evaluation, estimates of dominance genetic effects have become feasible using genomic best linear unbiased prediction (GBLUP). Usually, studies involving additive and dominance genetic effects ignore possible relationships between them. It has been often suggested that the magnitude of functional additive and dominance effects at the quantitative trait loci are related, but there is no existing GBLUP-like approach accounting for such correlation. Wellmann and Bennewitz showed two ways of considering directional relationships between additive and dominance effects, which they estimated in a Bayesian framework. However, these relationships cannot be fitted at the level of individuals instead of loci in a mixed model and are not compatible with standard animal or plant breeding software. This comes from a fundamental ambiguity in assigning the reference allele at a given locus. We show that, if there has been selection, assigning the most frequent as the reference allele orients the correlation between functional additive and dominance effects. As a consequence, the most frequent reference allele is expected to have a positive value. We also demonstrate that selection creates negative covariance between genotypic additive and dominance genetic values. For parameter estimation, it is possible to use a combined additive and dominance relationship matrix computed from marker genotypes, and to use standard restricted maximum likelihood (REML) algorithms based on an equivalent model. Through a simulation study, we show that such correlations can easily be estimated by mixed model software and accuracy of prediction for genetic values is slightly improved if such correlations are used in GBLUP. However, a model assuming uncorrelated effects and fitting orthogonal breeding values and dominant deviations performed similarly for prediction. Copyright © 2018, Genetics.

Breed relationships facilitate fine-mapping studies: A 7.8-kb deletion cosegregates with Collie eye anomaly across multiple dog breeds

PubMed Central

Parker, Heidi G.; Kukekova, Anna V.; Akey, Dayna T.; Goldstein, Orly; Kirkness, Ewen F.; Baysac, Kathleen C.; Mosher, Dana S.; Aguirre, Gustavo D.; Acland, Gregory M.; Ostrander, Elaine A.

2007-01-01

The features of modern dog breeds that increase the ease of mapping common diseases, such as reduced heterogeneity and extensive linkage disequilibrium, may also increase the difficulty associated with fine mapping and identifying causative mutations. One way to address this problem is by combining data from multiple breeds segregating the same trait after initial linkage has been determined. The multibreed approach increases the number of potentially informative recombination events and reduces the size of the critical haplotype by taking advantage of shortened linkage disequilibrium distances found across breeds. In order to identify breeds that likely share a trait inherited from the same ancestral source, we have used cluster analysis to divide 132 breeds of dog into five primary breed groups. We then use the multibreed approach to fine-map Collie eye anomaly (cea), a complex disorder of ocular development that was initially mapped to a 3.9-cM region on canine chromosome 37. Combined genotypes from affected individuals from four breeds of a single breed group significantly narrowed the candidate gene region to a 103-kb interval spanning only four genes. Sequence analysis revealed that all affected dogs share a homozygous deletion of 7.8 kb in the NHEJ1 gene. This intronic deletion spans a highly conserved binding domain to which several developmentally important proteins bind. This work both establishes that the primary cea mutation arose as a single disease allele in a common ancestor of herding breeds as well as highlights the value of comparative population analysis for refining regions of linkage. PMID:17916641

Avian use of forest habitats in the Pembina Hills of northeastern North Dakota

USGS Publications Warehouse

Faanes, Craig A.; Andrew, Jonathan M.

1983-01-01

North Dakota has the least extensive total area of forested habitats of any of the 50 United States. Although occurring in limited area, forest communities add considerably to the total ecological diversity of the State. The forests of the Pembina Hills region in northeastern North Dakota are one of only three areas large enough to be considered of commercial value. During 1981 we studied the avifauna of the upper valley of the Pembina River in the Pembina Hills. Field work extended from 20 April to 23 July; breeding bird censuses were conducted 7 June to 2 July. Of the 120 bird species recorded during the study period, 79 species were recorded during the breeding season. The total breeding population was estimated at nearly 76,000 breeding pairs. The wood warblers (Parulidae) were the most numerous family, accounting for about 28,000 breeding pairs. The yellow warbler (Dendroica petechia) was the most abundant breeding species, making up 19.4% of the population. American redstart (Setophaga ruticilla) was second in abundance, accounting for 10.5% of the breeding population. Largest breeding densities occurred in the willow (Salix sp.) shrub community. Although supporting the lowest mean breeding density, quaking aspen (Populus tremuloides) forests supported the highest species diversity. First State breeding records were recorded for alder flycatcher (Empidonax alnorum) and golden-winged warbler (Vermivora chrysoptera). Records were obtained for 12 species considered rare or unusual in North Dakota during the breeding season. The status of all species known to have occurred in the study area is described in an annotated species list.

Growth implants reduced tenderness of steaks from steers and heifers with different genetic potentials for growth and marbling.

PubMed

Boles, J A; Boss, D L; Neary, K I; Davis, K C; Tess, M W

2009-01-01

The objective of this study was to evaluate the effect of growth implants on the carcass characteristics and tenderness of steers and heifers with different genetic potentials for growth, lean meat yield production, and marbling. Two experiments were conducted. Experiment 1 evaluated Angus steers sired by bulls with high EPD for retail product yield or marbling. Implant treatment was imposed randomly within sire groups. Loins (Institutional Meat Purchasing Specifications 180) were collected from each carcass and cut into three 2.54-cm steaks aged for 7, 14 and 21 d to evaluate tenderness. The second experiment evaluated steers and heifers of British and Continental breed descent. Steers and heifers were slaughtered after 120 d on feed. Loin sections were collected, and one 2.54-cm steak aged 7 d was used for tenderness analysis. When implants were used in Angus steers, HCW and LM area increased, whereas internal fat and marbling decreased (P < 0.01). In Angus steers, sire type did not affect shear force values of steaks; however, implant use significantly increased shear force values (P < 0.01). Carcasses from cattle of Continental breed descent were significantly heavier than carcasses of British breed descent with larger LM area, slightly less fat, and a reduced yield grade (P < 0.01). Also, steer carcasses were heavier than heifer carcasses with larger LM (P < 0.05), but no effect of sex on fat depth, internal fat, yield grade or marbling was observed. No significant interactions were seen between growth implant and breed or between growth implant and sex for shear force values. Shear force values were significantly less for steaks from steers and heifers of British decent compared with steers and heifers of Continental descent (P < 0.01). Steaks from implanted steers and heifers had significantly (P < 0.01) greater shear force values than steaks from steers and heifers not implanted. Use of growth implants in growing cattle resulted in significantly heavier carcass weights, larger LM area, and reduced internal fat. However, implant use also reduced the amount of marbling along with contributing to reduced tenderness. Complicating the tenderness issue is the increased shear force values reported for heifers as well as steers of Continental breed descent. Use of implants may contribute to tenderness variability because of different animal responses to implants.

Y chromosome haplotype diversity of domestic sheep (Ovis aries) in northern Eurasia.

PubMed

Zhang, Min; Peng, Wei-Feng; Yang, Guang-Li; Lv, Feng-Hua; Liu, Ming-Jun; Li, Wen-Rong; Liu, Yong-Gang; Li, Jin-Quan; Wang, Feng; Shen, Zhi-Qiang; Zhao, Sheng-Guo; Hehua, Eer; Marzanov, Nurbiy; Murawski, Maziek; Kantanen, Juha; Li, Meng-Hua

2014-12-01

Variation in two SNPs and one microsatellite on the Y chromosome was analyzed in a total of 663 rams representing 59 breeds from a large geographic range in northern Eurasia. SNPA-oY1 showed the highest allele frequency (91.55%) across the breeds, whereas SNPG-oY1 was present in only 56 samples. Combined genotypes established seven haplotypes (H4, H5, H6, H7, H8, H12 and H19). H6 dominated in northern Eurasia, and H8 showed the second-highest frequency. H4, which had been earlier reported to be absent in European breeds, was detected in one European breed (Swiniarka), whereas H7, which had been previously identified to be unique to European breeds, was present in two Chinese breeds (Ninglang Black and Large-tailed Han), one Buryatian (Transbaikal Finewool) and two Russian breeds (North Caucasus Mutton-Wool and Kuibyshev). H12, which had been detected only in Turkish breeds, was also found in Chinese breeds in this work. An overall low level of haplotype diversity (median h = 0.1288) was observed across the breeds with relatively higher median values in breeds from the regions neighboring the Near Eastern domestication center of sheep. H6 is the dominant haplotype in northwestern and eastern China, in which the haplotype distribution could be explained by the historical translocations of the H4 and H8 Y chromosomes to China via the Mongol invasions followed by expansions to northwestern and eastern China. Our findings extend previous results of sheep Y chromosomal genetic variability and indicate probably recent paternal gene flows between sheep breeds from distinct major geographic regions. © 2014 Stichting International Foundation for Animal Genetics.

Genetic progress in multistage dairy cattle breeding schemes using genetic markers.

PubMed

Schrooten, C; Bovenhuis, H; van Arendonk, J A M; Bijma, P

2005-04-01

The aim of this paper was to explore general characteristics of multistage breeding schemes and to evaluate multistage dairy cattle breeding schemes that use information on quantitative trait loci (QTL). Evaluation was either for additional genetic response or for reduction in number of progeny-tested bulls while maintaining the same response. The reduction in response in multistage breeding schemes relative to comparable single-stage breeding schemes (i.e., with the same overall selection intensity and the same amount of information in the final stage of selection) depended on the overall selection intensity, the selection intensity in the various stages of the breeding scheme, and the ratio of the accuracies of selection in the various stages of the breeding scheme. When overall selection intensity was constant, reduction in response increased with increasing selection intensity in the first stage. The decrease in response was highest in schemes with lower overall selection intensity. Reduction in response was limited in schemes with low to average emphasis on first-stage selection, especially if the accuracy of selection in the first stage was relatively high compared with the accuracy in the final stage. Closed nucleus breeding schemes in dairy cattle that use information on QTL were evaluated by deterministic simulation. In the base scheme, the selection index consisted of pedigree information and own performance (dams), or pedigree information and performance of 100 daughters (sires). In alternative breeding schemes, information on a QTL was accounted for by simulating an additional index trait. The fraction of the variance explained by the QTL determined the correlation between the additional index trait and the breeding goal trait. Response in progeny test schemes relative to a base breeding scheme without QTL information ranged from +4.5% (QTL explaining 5% of the additive genetic variance) to +21.2% (QTL explaining 50% of the additive genetic variance). A QTL explaining 5% of the additive genetic variance allowed a 35% reduction in the number of progeny tested bulls, while maintaining genetic response at the level of the base scheme. Genetic progress was up to 31.3% higher for schemes with increased embryo production and selection of embryos based on QTL information. The challenge for breeding organizations is to find the optimum breeding program with regard to additional genetic progress and additional (or reduced) cost.

Saving genetic resources of native pigs in Occidental and Oriental countries - practical examples of the characterization and utilization of native pigs in Hungary and Laos.

PubMed

Rátky, Jozsef; Egerszegi, Istvan; Toth, Peter; Keonuchan, Soukanh; Nagai, Takashi; Kikuchi, Kazuhiro; Manabe, Noboru; Brüssow, Klaus-Peter

2013-10-01

Worldwide, only a few "fatty" pig breeds exist with different and/or regional utilization. Using the Hungarian Mangalica, which almost went extinct in Europe and the Lao Moo Lat pig, which still has a large population in South-East Asia as exemples, we wanted to demonstrate that indigenous (fatty) pig breeds may represent both national value and tremendous economic potential. Since these less prolific and less productive breeds cannot contribute to mass production, new market roles and methods should be established for them in the premium segment of pork trading. Thus their preservation and propagation needs the comprehensive collaboration of commercial, governmental actors and researchers. Briefly summarizing the history, we report the current results of reproductive physiology research. The commercial renaissance of Mangalica pigs is indebted to the enthusiastic efforts of basic scientists, pig breeding experts and dedicated Mangalica producers. Scientific achievements were applied to practical breeding and production of delicious pork and processed products, which ultimately made the economic success in the Mangalica sector possible. Both, research on and utilization of endangered (pig) breeds maintain not only breed diversities, but also may improve the livelihood of farmers worldwide.

Development and application of biological technologies in fish genetic breeding.

PubMed

Xu, Kang; Duan, Wei; Xiao, Jun; Tao, Min; Zhang, Chun; Liu, Yun; Liu, ShaoJun

2015-02-01

Fish genetic breeding is a process that remolds heritable traits to obtain neotype and improved varieties. For the purpose of genetic improvement, researchers can select for desirable genetic traits, integrate a suite of traits from different donors, or alter the innate genetic traits of a species. These improved varieties have, in many cases, facilitated the development of the aquaculture industry by lowering costs and increasing both quality and yield. In this review, we present the pertinent literatures and summarize the biological bases and application of selection breeding technologies (containing traditional selective breeding, molecular marker-assisted breeding, genome-wide selective breeding and breeding by controlling single-sex groups), integration breeding technologies (containing cross breeding, nuclear transplantation, germline stem cells and germ cells transplantation, artificial gynogenesis, artificial androgenesis and polyploid breeding) and modification breeding technologies (represented by transgenic breeding) in fish genetic breeding. Additionally, we discuss the progress our laboratory has made in the field of chromosomal ploidy breeding of fish, including distant hybridization, gynogenesis, and androgenesis. Finally, we systematically summarize the research status and known problems associated with each technology.

An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds

PubMed Central

Gutiérrez-Gil, Beatriz; Arranz, Juan J.; Wiener, Pamela

2015-01-01

This review compiles the results of 21 genomic studies of European Bos taurus breeds and thus provides a general picture of the selection signatures in taurine cattle identified by genome-wide selection-mapping scans. By performing a comprehensive summary of the results reported in the literature, we compiled a list of 1049 selection sweeps described across 37 cattle breeds (17 beef breeds, 14 dairy breeds, and 6 dual-purpose breeds), and four different beef-vs.-dairy comparisons, which we subsequently grouped into core selective sweep (CSS) regions, defined as consecutive signals within 1 Mb of each other. We defined a total of 409 CSSs across the 29 bovine autosomes, 232 (57%) of which were associated with a single-breed (Single-breed CSSs), 134 CSSs (33%) were associated with a limited number of breeds (Two-to-Four-breed CSSs) and 39 CSSs (9%) were associated with five or more breeds (Multi-breed CSSs). For each CSS, we performed a candidate gene survey that identified 291 genes within the CSS intervals (from the total list of 5183 BioMart-extracted genes) linked to dairy and meat production, stature, and coat color traits. A complementary functional enrichment analysis of the CSS positional candidates highlighted other genes related to pathways underlying behavior, immune response, and reproductive traits. The Single-breed CSSs revealed an over-representation of genes related to dairy and beef production, this was further supported by over-representation of production-related pathway terms in these regions based on a functional enrichment analysis. Overall, this review provides a comparative map of the selection sweeps reported in European cattle breeds and presents for the first time a characterization of the selection sweeps that are found in individual breeds. Based on their uniqueness, these breed-specific signals could be considered as “divergence signals,” which may be useful in characterizing and protecting livestock genetic diversity. PMID:26029239

Genetic Diversity of Seven Cattle Breeds Inferred Using Copy Number Variations

PubMed Central

Pierce, Magretha D.; Dzama, Kennedy; Muchadeyi, Farai C.

2018-01-01

Copy number variations (CNVs) comprise deletions, duplications, and insertions found within the genome larger than 50 bp in size. CNVs are thought to be primary role-players in breed formation and adaptation. South Africa boasts a diverse ecology with harsh environmental conditions and a broad spectrum of parasites and diseases that pose challenges to livestock production. This has led to the development of composite cattle breeds which combine the hardiness of Sanga breeds and the production potential of the Taurine breeds. The prevalence of CNVs within these respective breeds of cattle and the prevalence of CNV regions (CNVRs) in their diversity, adaptation and production is however not understood. This study therefore aimed to ascertain the prevalence, diversity, and correlations of CNVRs within cattle breeds used in South Africa. Illumina Bovine SNP50 data and PennCNV were utilized to identify CNVRs within the genome of 287 animals from seven cattle breeds representing Sanga, Taurine, Composite, and cross breeds. Three hundred and fifty six CNVRs of between 36 kb to 4.1 Mb in size were identified. The null hypothesis that one CNVR loci is independent of another was tested using the GENEPOP software. One hunded and two and seven of the CNVRs in the Taurine and Sanga/Composite cattle breeds demonstrated a significant (p ≤ 0.05) association. PANTHER overrepresentation analyses of correlated CNVRs demonstrated significant enrichment of a number of biological processes, molecular functions, cellular components, and protein classes. CNVR genetic variation between and within breed group was measured using phiPT which allows intra-individual variation to be suppressed and hence proved suitable for measuring binary CNVR presence/absence data. Estimate PhiPT within and between breed variance was 2.722 and 0.518 respectively. Pairwise population PhiPT values corresponded with breed type, with Taurine Holstein and Angus breeds demonstrating no between breed CNVR variation. Phylogenetic trees were drawn. CNVRs primarily clustered animals of the same breed type together. This study successfully identified, characterized, and analyzed 356 CNVRs within seven cattle breeds. CNVR correlations were evident, with many more correlations being present among the exotic Taurine breeds. CNVR genetic diversity of Sanga, Taurine and Composite breeds was ascertained with breed types exposed to similar selection pressures demonstrating analogous incidences of CNVRs. PMID:29868114

Genomic Selection For Bacterial Cold Water Disease Resistance In Rainbow Trout Reveals Large Within-Family Variation That Cannot Be Exploited In Traditional Family-based Selective Breeding

USDA-ARS?s Scientific Manuscript database

Selective breeding is an effective strategy to improve resistance to specific pathogens, and thus has the potential to mitigate antibiotic use in aquaculture. Large family sizes of aquaculture species permits family-based selective breeding programs, but the need for specific-pathogen-free nucleus p...

Animal breeding strategies can improve meat quality attributes within entire populations.

PubMed

Berry, D P; Conroy, S; Pabiou, T; Cromie, A R

2017-10-01

The contribution of animal breeding to changes in animal performance is well documented across a range of species. Once genetic variation in a trait exists, then breeding to improve the characteristics of that trait is possible, if so desired. Considerable genetic variation exists in a range of meat quality attributes across a range of species. The genetic variation that exists for meat quality is as large as observed for most performance traits; thus, within a well-structured breeding program, rapid genetic gain for meat quality could be possible. The rate of genetic gain can be augmented through the integration of DNA-based technologies into the breeding program; such DNA-based technologies should, however, be based on thousands of DNA markers dispersed across the entire genome. Genetic and genomic technologies can also have beneficial impact outside the farm gate as a tool to segregate carcasses or meat cuts based on expected meat quality features. Copyright © 2017 Elsevier Ltd. All rights reserved.

Phylogenetic relationships of chrysanthemums in Korea based on novel SSR markers.

PubMed

Khaing, A A; Moe, K T; Hong, W J; Park, C S; Yeon, K H; Park, H S; Kim, D C; Choi, B J; Jung, J Y; Chae, S C; Lee, K M; Park, Y J

2013-11-07

Chrysanthemums are well known for their esthetic and medicinal values. Characterization of chrysanthemums is vital for their conservation and management as well as for understanding their genetic relationships. We found 12 simple sequence repeat markers (SSRs) of 100 designed primers to be polymorphic. These novel SSR markers were used to evaluate 95 accessions of chrysanthemums (3 indigenous and 92 cultivated accessions). Two hundred alleles were identified, with an average of 16.7 alleles per locus. KNUCRY-77 gave the highest polymorphic information content value (0.879), while KNUCRY-10 gave the lowest (0.218). Similar patterns of grouping were observed with a distance-based dendrogram developed using PowerMarker and model-based clustering with Structure. Three clusters with some admixtures were identified by model-based clustering. These newly developed SSR markers will be useful for further studies of chrysanthemums, such as taxonomy and marker-assisted selection breeding.

Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle

PubMed Central

2011-01-01

Background 'Selection signatures' delimit regions of the genome that are, or have been, functionally important and have therefore been under either natural or artificial selection. In this study, two different and complementary methods--integrated Haplotype Homozygosity Score (|iHS|) and population differentiation index (FST)--were applied to identify traces of decades of intensive artificial selection for traits of economic importance in modern cattle. Results We scanned the genome of a diverse set of dairy and beef breeds from Germany, Canada and Australia genotyped with a 50 K SNP panel. Across breeds, a total of 109 extreme |iHS| values exceeded the empirical threshold level of 5% with 19, 27, 9, 10 and 17 outliers in Holstein, Brown Swiss, Australian Angus, Hereford and Simmental, respectively. Annotating the regions harboring clustered |iHS| signals revealed a panel of interesting candidate genes like SPATA17, MGAT1, PGRMC2 and ACTC1, COL23A1, MATN2, respectively, in the context of reproduction and muscle formation. In a further step, a new Bayesian FST-based approach was applied with a set of geographically separated populations including Holstein, Brown Swiss, Simmental, North American Angus and Piedmontese for detecting differentiated loci. In total, 127 regions exceeding the 2.5 per cent threshold of the empirical posterior distribution were identified as extremely differentiated. In a substantial number (56 out of 127 cases) the extreme FST values were found to be positioned in poor gene content regions which deviated significantly (p < 0.05) from the expectation assuming a random distribution. However, significant FST values were found in regions of some relevant genes such as SMCP and FGF1. Conclusions Overall, 236 regions putatively subject to recent positive selection in the cattle genome were detected. Both |iHS| and FST suggested selection in the vicinity of the Sialic acid binding Ig-like lectin 5 gene on BTA18. This region was recently reported to be a major QTL with strong effects on productive life and fertility traits in Holstein cattle. We conclude that high-resolution genome scans of selection signatures can be used to identify genomic regions contributing to within- and inter-breed phenotypic variation. PMID:21679429

Acceleration of genetic gain in cattle by reduction of generation interval.

PubMed

Kasinathan, Poothappillai; Wei, Hong; Xiang, Tianhao; Molina, Jose A; Metzger, John; Broek, Diane; Kasinathan, Sivakanthan; Faber, David C; Allan, Mark F

2015-03-02

Genomic selection (GS) approaches, in combination with reproductive technologies, are revolutionizing the design and implementation of breeding programs in livestock species, particularly in cattle. GS leverages genomic readouts to provide estimates of breeding value early in the life of animals. However, the capacity of these approaches for improving genetic gain in breeding programs is limited by generation interval, the average age of an animal when replacement progeny are born. Here, we present a cost-effective approach that combines GS with reproductive technologies to reduce generation interval by rapidly producing high genetic merit calves.

Impact of changes in weight, fat depth, and loin muscle depth on carcass yield and value and implications for selection and pricing of rams from terminal-sire sheep breeds

USDA-ARS?s Scientific Manuscript database

Breeding objectives and selection indexes are necessary to support comprehensive genetic improvement programs. This study used off-test body weights (OTBW) or chilled carcass weights (CCW), ultrasonic measurements of fat depth (USFD, mm), and predicted ultrasound loin muscle depths (USLMD, mm) from ...

Eigen values in epidemic and other bio-inspired models

NASA Astrophysics Data System (ADS)

Supriatna, A. K.; Anggriani, N.; Carnia, E.; Raihan, A.

2017-08-01

Eigen values and the largest eigen value have special roles in many applications. In this paper we will discuss its role in determining the epidemic threshold in which we can determine if an epidemic will decease or blow out eventually. Some examples and their consequences to controling the epidemic are also discusses. Beside the application in epidemic model, the paper also discusses other example of appication in bio-inspired model, such as the backcross breeding for two age classes of local and exotic goats. Here we give some elaborative examples on the use of previous backcross breeding model. Some future direction on the exploration of the relationship between these eigenvalues to different epidemic models and other bio-inspired models are also presented.

[Proportional abundance of culicidae in the urban ecosystem of Havana City].

PubMed

Marquetti, M C; González, D; Aguilera, L; Navarro, A

1999-01-01

Proportional abundance of the four most common mosquito species was determined in six types of breeding places located in Plaza de la Revolución municipality, City of Havana from 1993-1996. Culex quinquifasciatus exhibited values over 0.60 except in tyres and larval traps in 1993 and 1994 whereas Aedes mediovittatus showed similar values in low tanks and artificial reservoirs in 1994 (0.43 and 0.56 respectively). It was also observed that this species prefers larval traps. Aedes aegypti and Culex migripaplpus had the lowest abundance values (0.01). These results allowed us to state that there is a sort of shared use by these species of those reservoirs where they breed and that Culex quinquefasciatus is the predominant one.

The Effects of Pre-slaughter Stress and Season on the Activity of Plasma Creatine Kinase and Mutton Quality from Different Sheep Breeds Slaughtered at a Smallholder Abattoir

PubMed Central

Chulayo, A. Y.; Muchenje, V.

2013-01-01

The objective of the current study was to determine the effect of pre-slaughter stress, season and breed on the activity of plasma creatine kinase (CK) and the quality of mutton. One hundred and seventy-three (173) castrated sheep from Dormer (DM), South African Mutton Merino (SAMM), Dorper (DP) and Blackhead Persian (BP) sheep breeds were used in the study. The animals were grouped according to age-groups as follows: Group 1 (6 to 8 months), Group 2 (9 to 12 months) and Group 3 (13 to 16 months). Blood samples were collected during exsanguinations using disposable vacutainer tubes for CK analysis. Representative samples of the Muscularis longissimuss thoracis et. lumborum (LTL) were collected from 84 castrated sheep, of different breeds (28 per breed) 24 h after slaughter. The following physico-chemical characteristics of mutton were determined; meat pH (pH24), color (L*, a* and b*), thawing and cooking losses and Warner Braztler Shear Force (WBSF). The activity of plasma CK was significantly higher (p<0.001) in summer (1,026.3±105.06) and lower in winter (723.3±77.75). There were higher values for L* (33.7±0.94), b* (11.5±0.48) and WBSF (29.5±1.46) in summer season than in winter season; L* (29.4±0.64), b* (10.2±0.33) and WBSF (21.2±0.99). The activity of plasma CK was influenced by the type of breed with Dormer having the highest (p>0.001) levels (1,358.6±191.08) of CK. South African Mutton Merino had higher values for pH24 (5.9±0.06), L* (34.2±0.97), b* (12.2±0.50) and WBSF (26.8±1.51) and Blackhead Persian had higher values (35.5±2.17) for cooking loss (CL%) than the other breeds. Computed Principal Component Analyses (PCA) on the activity of plasma CK and physico-chemical characteristics of mutton revealed no correlations between these variables. However, positive correlations were observed between pH24, L*, a*, b*, CL% and WBSF. Relationships between pre-slaughter stress, CK activity and physico-chemical characteristics of mutton were also observed. It was therefore concluded that although mutton quality and creatine kinase were not related, pre-slaughter stress, season and breed affected the activity of creatine kinase and mutton quality. PMID:25049767

Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement

PubMed Central

Spindel, J E; Begum, H; Akdemir, D; Collard, B; Redoña, E; Jannink, J-L; McCouch, S

2016-01-01

To address the multiple challenges to food security posed by global climate change, population growth and rising incomes, plant breeders are developing new crop varieties that can enhance both agricultural productivity and environmental sustainability. Current breeding practices, however, are unable to keep pace with demand. Genomic selection (GS) is a new technique that helps accelerate the rate of genetic gain in breeding by using whole-genome data to predict the breeding value of offspring. Here, we describe a new GS model that combines RR-BLUP with markers fit as fixed effects selected from the results of a genome-wide-association study (GWAS) on the RR-BLUP training data. We term this model GS + de novo GWAS. In a breeding population of tropical rice, GS + de novo GWAS outperformed six other models for a variety of traits and in multiple environments. On the basis of these results, we propose an extended, two-part breeding design that can be used to efficiently integrate novel variation into elite breeding populations, thus expanding genetic diversity and enhancing the potential for sustainable productivity gains. PMID:26860200

Genetic diversity and population genetic analysis of bovine MHC class II DRB3.2 locus in three Bos indicus cattle breeds of Southern India.

PubMed

Das, D N; Sri Hari, V G; Hatkar, D N; Rengarajan, K; Saravanan, R; Suryanarayana, V V S; Murthy, L K

2012-12-01

The present study was performed to evaluate the genetic polymorphism of BoLA-DRB3.2 locus in Malnad Gidda, Hallikar and Ongole South Indian Bos indicus cattle breeds, employing the PCR-RFLP technique. In Malnad Gidda population, 37 BoLA-DRB3.2 alleles were detected, including one novel allele DRB3*2503 (GenBank: HM031389) that was observed in the frequency of 1.87%. In Hallikar and Ongole populations, 29 and 21 BoLA-DRB3.2 alleles were identified, respectively. The frequencies of the most common BoLA-DRB3.2 alleles (with allele frequency > 5%), in Malnad Gidda population, were DRB3.2*15 (10.30%), DRB3*5702 (9.35%), DRB3.2*16 (8.41%), DRB3.2*23 (7.01%) and DRB3.2*09 (5.61%). In Hallikar population, the most common alleles were DRB3.2*11 (13.00%), DRB3.2*44 (11.60%), DRB3.2*31 (10.30%), DRB3.2*28 (5.48%) and DRB3.2*51 (5.48%). The most common alleles in Ongole population were DRB3.2*15 (22.50%), DRB3.2*06 (20.00%), DRB3.2*13 (13.30%), DRB3.2*12 (9.17%) and DRB3.2*23 (7.50%). A high degree of heterozygosity observed in Malnad Gidda (H(O) = 0.934, H(E) = 0.955), Hallikar (H(O) = 0.931, H(E) = 0.943) and Ongole (H(O) = 0.800, H(E) = 0.878) populations, along with F(IS) values close to F(IS) zero (Malnad Gidda: F(IS) = 0.0221, Hallikar: F(IS) = 0.0127 and Ongole: F(IS) = 0.0903), yielded nonsignificant P-values with respect to Hardy-Weinberg equilibrium probabilities revealing, no perceptible inbreeding, greater genetic diversity and characteristic population structure being preserved in the three studied cattle populations. The phylogenetic tree constructed based on the frequencies of BoLA-DRB3.2 alleles observed in 10 Bos indicus and Bos taurus cattle breeds revealed distinct clustering of specific Bos indicus cattle breeds, along with unique genetic differentiation observed among them. The results of this study demonstrated that the BoLA-DRB3.2 is a highly polymorphic locus, with significant breed-specific genetic diversities being present amongst the three studied cattle breeds. The population genetics and phylogenetic analysis have revealed pivotal information about the population structure and importance of the presently studied three Bos indicus cattle breeds as unique animal genetic resources, which have to be conserved for maintaining native cattle genetic diversity. © 2012 Blackwell Publishing Ltd.

Mating practices and the dissemination of genetic disorders in domestic animals, based on the example of dog breeding.

PubMed

Leroy, G; Baumung, R

2011-02-01

On the basis of simulations and genealogical data of ten dog breeds, three popular mating practices (popular sire effect, line breeding, close breeding) were investigated along with their effects on the dissemination of genetic disorders. Our results showed that the use of sires in these ten breeds is clearly unbalanced. Depending on the breed, the effective number of sires represented between 33% and 70% of the total number of sires. Mating between close relatives was also found to be quite common, and the percentage of dogs inbred after two generations ranged from 1% to about 8%. A more or less long-term genetic differentiation, linked to line breeding practices, was also emphasized in most breeds. F(IT) index based on gene dropping proved to be efficient in differentiating the effects of the different mating practices, and it ranged from -1.3% to 3.2% when real founders were used to begin a gene dropping process. Simulation results confirmed that the popular sire practice leads to a dissemination of genetic disorders. Under a realistic scenario, regarding the imbalance in the use of sires, the dissemination risk was indeed 4.4 times higher than under random mating conditions. In contrast, line breeding and close breeding practices tend to decrease the risk of the dissemination of genetic disorders. © 2010 The Authors, Animal Genetics © 2010 Stichting International Foundation for Animal Genetics.

The potential of open learning in animal breeding.

PubMed

Lohuis, M M; Lohuis, C T; Petrongolo, R A

1999-07-01

Animal breeding education is presently facing many challenges. These include rapid changes in breeding knowledge and technology, resource and funding restrictions, and altering demographics of the learner and the animal breeding industry. These challenges can be met via an open learning educational format. This nontraditional approach is based on the needs of individual learners, not the interests of the teacher or the institution. An important feature of open learning is its appropriateness for the professional development audience. Delivery methods include interactive distance courses on the Web, computer-assisted learning, and team-based study. The Canadian dairy breeding industry has expressed the need for ongoing professional development to understand and adopt new animal breeding technologies. The University of Guelph responded by delivering a series of animal breeding short courses (Executive Certificate Program in Animal Breeding) to industry decision makers in 1997. A version modified specifically for farmers and breeding industry personnel was offered in 1998. Through the collaboration of experts from various agricultural institutions and the use of a learner-centered format, this professional development initiative was a pedagogical and financial success. This paper describes how the open learning approach differs from traditional university teaching. Using the University of Guelph example in animal breeding professional development, the framework for a successful open learning program will be examined. The best practices for effective adult education will also be identified and discussed within this case study.

Site-directed nucleases: a paradigm shift in predictable, knowledge-based plant breeding.

PubMed

Podevin, Nancy; Davies, Howard V; Hartung, Frank; Nogué, Fabien; Casacuberta, Josep M

2013-06-01

Conventional plant breeding exploits existing genetic variability and introduces new variability by mutagenesis. This has proven highly successful in securing food supplies for an ever-growing human population. The use of genetically modified plants is a complementary approach but all plant breeding techniques have limitations. Here, we discuss how the recent evolution of targeted mutagenesis and DNA insertion techniques based on tailor-made site-directed nucleases (SDNs) provides opportunities to overcome such limitations. Plant breeding companies are exploiting SDNs to develop a new generation of crops with new and improved traits. Nevertheless, some technical limitations as well as significant uncertainties on the regulatory status of SDNs may challenge their use for commercial plant breeding. Copyright © 2013 Elsevier Ltd. All rights reserved.

Twenty years of artificial directional selection have shaped the genome of the Italian Large White pig breed.

PubMed

Schiavo, G; Galimberti, G; Calò, D G; Samorè, A B; Bertolini, F; Russo, V; Gallo, M; Buttazzoni, L; Fontanesi, L

2016-04-01

In this study, we investigated at the genome-wide level if 20 years of artificial directional selection based on boar genetic evaluation obtained with a classical BLUP animal model shaped the genome of the Italian Large White pig breed. The most influential boars of this breed (n = 192), born from 1992 (the beginning of the selection program of this breed) to 2012, with an estimated breeding value reliability of >0.85, were genotyped with the Illumina Porcine SNP60 BeadChip. After grouping the boars in eight classes according to their year of birth, filtered single nucleotide polymorphisms (SNPs) were used to evaluate the effects of time on genotype frequency changes using multinomial logistic regression models. Of these markers, 493 had a PBonferroni  < 0.10. However, there was an increasing number of SNPs with a decreasing level of allele frequency changes over time, representing a continuous profile across the genome. The largest proportion of the 493 SNPs was on porcine chromosome (SSC) 7, SSC2, SSC8 and SSC18 for a total of 204 haploblocks. Functional annotations of genomic regions, including the 493 shifted SNPs, reported a few Gene Ontology terms that might underly the biological processes that contributed to increase performances of the pigs over the 20 years of the selection program. The obtained results indicated that the genome of the Italian Large White pigs was shaped by a directional selection program derived by the application of methodologies assuming the infinitesimal model that captured a continuous trend of allele frequency changes in the boar population. © 2015 Stichting International Foundation for Animal Genetics.

Population size, breeding biology and on-land threats of Cape Verde petrel (Pterodroma feae) in Fogo Island, Cape Verde

PubMed Central

Zango, Laura; Calabuig, Pascual; Stefan, Laura M.; González-Solís, Jacob

2017-01-01

Cape Verde petrel (Pterodroma feae) is currently considered near threatened, but little is known about its population size, breeding biology and on land threats, jeopardizing its management and conservation. To improve this situation, we captured, marked and recaptured (CMR) birds using mist-nets over 10 years; measured and sexed them; monitored up to 14 burrows, deployed GPS devices on breeders and analyzed activity data of geolocators retrieved from breeders in Fogo (Cape Verde). We set cat traps over the colony and investigated their domestic/feral origin by marking domestic cats from a nearby village with transponders, by deploying GPS devices on domestic cats and by performing stable isotope analyses of fur of the trapped and domestic cats. The population of Fogo was estimated to be 293 birds, including immatures (95% CI: 233–254, CMR modelling). Based on geolocator activity data and nest monitoring we determined the breeding phenology of this species and we found biometric differences between sexes. While monitoring breeding performance, we verified a still ongoing cat predation and human harvesting. Overall, data gathered from trapped cats without transponder, cats GPS trips and the distinct isotopic values between domestic and trapped cats suggest cats visiting the colony are of feral origin. GPS tracks from breeders showed birds left and returned to the colony using the sector NE of the islands, where high level of public lights should be avoided specially during the fledging period. Main threats for the Cape Verde petrel in the remaining breeding islands are currently unknown but likely to be similar to Fogo, calling for an urgent assessment of population trends and the control of main threats in all Cape Verde Islands and uplisting its conservation status. PMID:28369105

Population size, breeding biology and on-land threats of Cape Verde petrel (Pterodroma feae) in Fogo Island, Cape Verde.

PubMed

Militão, Teresa; Dinis, Herculano Andrade; Zango, Laura; Calabuig, Pascual; Stefan, Laura M; González-Solís, Jacob

2017-01-01

Cape Verde petrel (Pterodroma feae) is currently considered near threatened, but little is known about its population size, breeding biology and on land threats, jeopardizing its management and conservation. To improve this situation, we captured, marked and recaptured (CMR) birds using mist-nets over 10 years; measured and sexed them; monitored up to 14 burrows, deployed GPS devices on breeders and analyzed activity data of geolocators retrieved from breeders in Fogo (Cape Verde). We set cat traps over the colony and investigated their domestic/feral origin by marking domestic cats from a nearby village with transponders, by deploying GPS devices on domestic cats and by performing stable isotope analyses of fur of the trapped and domestic cats. The population of Fogo was estimated to be 293 birds, including immatures (95% CI: 233-254, CMR modelling). Based on geolocator activity data and nest monitoring we determined the breeding phenology of this species and we found biometric differences between sexes. While monitoring breeding performance, we verified a still ongoing cat predation and human harvesting. Overall, data gathered from trapped cats without transponder, cats GPS trips and the distinct isotopic values between domestic and trapped cats suggest cats visiting the colony are of feral origin. GPS tracks from breeders showed birds left and returned to the colony using the sector NE of the islands, where high level of public lights should be avoided specially during the fledging period. Main threats for the Cape Verde petrel in the remaining breeding islands are currently unknown but likely to be similar to Fogo, calling for an urgent assessment of population trends and the control of main threats in all Cape Verde Islands and uplisting its conservation status.

Genetic parameters for tick count and udder health in commercial and indigenous ewes in South Africa.

PubMed

Cloete, S W P; Cloete, J J E; Scholtz, A J

2016-10-30

The genetics of tick infestation in sheep need study, as host resistance often forms part of integrated pest control programs. Repeated udder health scores, site-specific tick count, mating weight and reproduction records (N=879-1204) were recorded annually from 2010 to 2015 on ewes of the indigenous Namaqua Afrikaner (NA) fat-tailed breed, as well as the commercial Dorper and SA Mutton Merino (SAMM) breeds. Udders were scored subjectively on a 1-5 scale (1 - udder intact and 5 - udder damaged severely) and ticks were counted on three locations. The body sites counted were the head and thoracic limb (HTLTC), udder-pelvic limb (UPLTC) and perineum-breech-tail (PBTTC). These counts were also totaled for a total tick count (TTC). Reproduction traits were number of lambs weaned per ewe lambed and total weight of lamb weaned per ewe lambed. Udder health scores of NA ewes were lower than those of Dorpers, which in turn had lower scores than SAMM ewes. NA ewes had lower values for HTLTC, UPLTC and TTC than the commercial breeds, but higher values for PBTTC than Dorpers. Heritability estimates amounted to 0.26±0.04 for HTLTC, 0.53±0.04 for UPLTC, 0.07±0.06 for PBTTC, 0.44±0.06 for TTC and 0.61±0.03 for udder health score. Animal permanent environment also affected PBTTC (0.14±0.07). Significant genetic correlations were found between the HTLTC and UPLTC (0.47±0.10), UPLTC and udder health score (0.52±0.07), HTLTC and UPLTC (0.24±0.11) as well as UPLTC and PBTTC (-0.44±0.11). Heavier ewes had higher UPLTC (0.38±0.09), TTC (0.33±0.09) and impaired udder health (0.21±0.08). Udder health scores and tick counts at all sites were not related to reproduction traits. The indigenous NA breed outperformed the commercial breeds with lower values for HTLTC, UPLTC, TTC and a better udder health score. Mechanisms contributing to the better performance of the NA breed under pastoral conditions and the scope for selection for tick tolerance within breeds should be studied further. Copyright © 2016 Elsevier B.V. All rights reserved.

Genetic Architecture of Resistance to Stripe Rust in a Global Winter Wheat Germplasm Collection

PubMed Central

Bulli, Peter; Zhang, Junli; Chao, Shiaoman; Chen, Xianming; Pumphrey, Michael

2016-01-01

Virulence shifts in populations of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, are a major challenge to resistance breeding. The majority of known resistance genes are already ineffective against current races of Pst, necessitating the identification and introgression of new sources of resistance. Germplasm core collections that reflect the range of genetic and phenotypic diversity of crop species are ideal platforms for examining the genetic architecture of complex traits such as resistance to stripe rust. We report the results of genetic characterization and genome-wide association analysis (GWAS) for resistance to stripe rust in a core subset of 1175 accessions in the National Small Grains Collection (NSGC) winter wheat germplasm collection, based on genotyping with the wheat 9K single nucleotide polymorphism (SNP) iSelect assay and phenotyping of seedling and adult plants under natural disease epidemics in four environments. High correlations among the field data translated into high heritability values within and across locations. Population structure was evident when accessions were grouped by stripe rust reaction. GWAS identified 127 resistance loci that were effective across at least two environments, including 20 with significant genome-wide adjusted P-values. Based on relative map positions of previously reported genes and QTL, five of the QTL with significant genome-wide adjusted P-values in this study represent potentially new loci. This study provides an overview of the diversity of Pst resistance in the NSGC winter wheat germplasm core collection, which can be exploited for diversification of stripe rust resistance in breeding programs. PMID:27226168

Genetic Architecture of Resistance to Stripe Rust in a Global Winter Wheat Germplasm Collection.

PubMed

Bulli, Peter; Zhang, Junli; Chao, Shiaoman; Chen, Xianming; Pumphrey, Michael

2016-08-09

Virulence shifts in populations of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, are a major challenge to resistance breeding. The majority of known resistance genes are already ineffective against current races of Pst, necessitating the identification and introgression of new sources of resistance. Germplasm core collections that reflect the range of genetic and phenotypic diversity of crop species are ideal platforms for examining the genetic architecture of complex traits such as resistance to stripe rust. We report the results of genetic characterization and genome-wide association analysis (GWAS) for resistance to stripe rust in a core subset of 1175 accessions in the National Small Grains Collection (NSGC) winter wheat germplasm collection, based on genotyping with the wheat 9K single nucleotide polymorphism (SNP) iSelect assay and phenotyping of seedling and adult plants under natural disease epidemics in four environments. High correlations among the field data translated into high heritability values within and across locations. Population structure was evident when accessions were grouped by stripe rust reaction. GWAS identified 127 resistance loci that were effective across at least two environments, including 20 with significant genome-wide adjusted P-values. Based on relative map positions of previously reported genes and QTL, five of the QTL with significant genome-wide adjusted P-values in this study represent potentially new loci. This study provides an overview of the diversity of Pst resistance in the NSGC winter wheat germplasm core collection, which can be exploited for diversification of stripe rust resistance in breeding programs. Copyright © 2016 Bulli et al.

Short communication: casein haplotype variability in sicilian dairy goat breeds.

PubMed

Gigli, I; Maizon, D O; Riggio, V; Sardina, M T; Portolano, B

2008-09-01

In the Mediterranean region, goat milk production is an important economic activity. In the present study, 4 casein genes were genotyped in 5 Sicilian goat breeds to 1) identify casein haplotypes present in the Argentata dell'Etna, Girgentana, Messinese, Derivata di Siria, and Maltese goat breeds; and 2) describe the structure of the Sicilian goat breeds based on casein haplotypes and allele frequencies. In a sample of 540 dairy goats, 67 different haplotypes with frequency >or=0.01 and 27 with frequency >or=0.03 were observed. The most common CSN1S1-CSN2-CSN1S2-CSN3 haplotype for Derivata di Siria and Maltese was FCFB (0.17 and 0.22, respectively), whereas for Argentata dell'Etna, Girgentana and Messinese was ACAB (0.06, 0.23, and 0.10, respectively). According to the haplotype reconstruction, Argentata dell'Etna, Girgentana, and Messinese breeds presented the most favorable haplotype for cheese production, because the casein concentration in milk of these breeds might be greater than that in Derivata di Siria and Maltese breeds. Based on a cluster analysis, the breeds formed 2 main groups: Derivata di Siria, and Maltese in one group, and Argentata dell'Etna and Messinese in the other; the Girgentana breed was between these groups but closer to the latter.

Ability of dairy cows to be inseminated according to breed and genetic merit for production traits under contrasting pasture-based feeding systems.

PubMed

Bedere, N; Disenhaus, C; Ducrocq, V; Leurent-Colette, S; Delaby, L

2017-05-01

Strong genetic selection on production traits is considered to be responsible for the declined ability of dairy cows to ensure reproduction. The present study aimed to quantify the effect of genetic characteristics (breeds and genetic merit for production traits) and feeding systems (FS) on the ability of dairy cows to be inseminated. An experiment was conducted during 9 years on Normande and Holstein cows assigned to contrasted pasture-based FS. Diets were based on maize silage in winter and grazing plus concentrate in spring in the High FS; and on grass silage in winter and grazing with no concentrate during spring in the low FS. Within breed, cows were classified into two genetic groups with similar estimated breeding values (EBV) for milk solids: cows with high EBV for milk yield were included in a Milk-Group and those with high EBV for fat and protein contents were included in a Content-Group. Holstein produced more milk throughout lactation than Normande cows (+2294 kg in the High FS and +1280 kg in the Low FS, P<0.001) and lost more body condition to nadir (-1.00 point in the High FS and -0.80 kg in the Low FS, P<0.001). They also showed a poorer ability to be inseminated because of both a delayed commencement of luteal activity (CLA) and delayed first service (more days from start of the breeding season to first service, DAI1). Cows in the Milk-Group produced more milk than cows in the Content-Group, but milk solids production was similar. Cows in the Content-Group had earlier CLA than cows in the Milk-Group (P<0.01). Genetic group neither affected ovulation detection rate nor DAI1. Within breed and FS, cows with high genetic merit for milk yield had later CLA and DAI1. Cows in the High FS produced more milk and lost less condition to nadir than cows in the Low FS. FS did not affect dairy cows' ability to be inseminated. However, cows with higher milk protein content, and presumably better energy balance, had earlier CLA (P<0.01) and DAI1 (P<0.10). In addition, higher milk yield was associated with poorer ovulation detection rate and oestrus intensity (P<0.05). The study showed that at similar EBV level for milk solids, selection for increased milk fat and protein content resulted in improved cyclicity and similar oestrous expression and submission rates compared with selection for increased milk yield.

Pedigree-based analysis of derivation of genome segments of an elite rice reveals key regions during its breeding.

PubMed

Zhou, Degui; Chen, Wei; Lin, Zechuan; Chen, Haodong; Wang, Chongrong; Li, Hong; Yu, Renbo; Zhang, Fengyun; Zhen, Gang; Yi, Junliang; Li, Kanghuo; Liu, Yaoguang; Terzaghi, William; Tang, Xiaoyan; He, Hang; Zhou, Shaochuan; Deng, Xing Wang

2016-02-01

Analyses of genome variations with high-throughput assays have improved our understanding of genetic basis of crop domestication and identified the selected genome regions, but little is known about that of modern breeding, which has limited the usefulness of massive elite cultivars in further breeding. Here we deploy pedigree-based analysis of an elite rice, Huanghuazhan, to exploit key genome regions during its breeding. The cultivars in the pedigree were resequenced with 7.6× depth on average, and 2.1 million high-quality single nucleotide polymorphisms (SNPs) were obtained. Tracing the derivation of genome blocks with pedigree and information on SNPs revealed the chromosomal recombination during breeding, which showed that 26.22% of Huanghuazhan genome are strictly conserved key regions. These major effect regions were further supported by a QTL mapping of 260 recombinant inbred lines derived from the cross of Huanghuazhan and a very dissimilar cultivar, Shuanggui 36, and by the genome profile of eight cultivars and 36 elite lines derived from Huanghuazhan. Hitting these regions with the cloned genes revealed they include numbers of key genes, which were then applied to demonstrate how Huanghuazhan were bred after 30 years of effort and to dissect the deficiency of artificial selection. We concluded the regions are helpful to the further breeding based on this pedigree and performing breeding by design. Our study provides genetic dissection of modern rice breeding and sheds new light on how to perform genomewide breeding by design. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

[Preface for genome editing special issue].

PubMed

Gu, Feng; Gao, Caixia

2017-10-25

Genome editing technology, as an innovative biotechnology, has been widely used for editing the genome from model organisms, animals, plants and microbes. CRISPR/Cas9-based genome editing technology shows its great value and potential in the dissection of functional genomics, improved breeding and genetic disease treatment. In the present special issue, the principle and application of genome editing techniques has been summarized. The advantages and disadvantages of the current genome editing technology and future prospects would also be highlighted.

Recent advances of microbial breeding via heavy-ion mutagenesis at IMP.

PubMed

Hu, W; Li, W; Chen, J

2017-10-01

Nowadays, the value of heavy-ion mutagenesis has been accepted as a novel powerful mutagen technique to generate new microbial mutants due to its high linear energy transfer and high relative biological effectiveness. This paper briefly reviews recent progress in developing a more efficient mutagenesis technique for microbial breeding using heavy-ion mutagenesis, and also presents the outline of the beam line for microbial breeding in Heavy Ion Research Facility of Lanzhou. Then, new insights into microbial biotechnology via heavy-ion mutagenesis are also further explored. We hope that our concerns will give deep insight into microbial breeding biotechnology via heavy-ion mutagenesis. We also believe that heavy-ion mutagenesis breeding will greatly contribute to the progress of a comprehensive study industrial strain engineering for bioindustry in the future. There is currently a great interest in developing rapid and diverse microbial mutation tool for strain modification. Heavy-ion mutagenesis has been proved as a powerful technology for microbial breeding due to its broad spectrum of mutation phenotypes with high efficiency. In order to deeply understand heavy-ion mutagenesis technology, this paper briefly reviews recent progress in microbial breeding using heavy-ion mutagenesis at IMP, and also presents the outline of the beam line for microbial breeding in Heavy Ion Research Facility of Lanzhou (HIRFL) as well as new insights into microbial biotechnology via heavy-ion mutagenesis. Thus, this work can provide the guidelines to promote the development of novel microbial biotechnology cross-linking heavy-ion mutagenesis breeding that could make breeding process more efficiently in the future. © 2017 The Society for Applied Microbiology.

Effects of parental number and duration of the breeding period on the effective population size and genetic diversity of a captive population of the endangered Tokyo bitterling Tanakia tanago (Teleostei: Cyprinidae).

PubMed

Kubota, Hitoshi; Watanabe, Katsutoshi

2012-01-01

The maintenance of genetic diversity is one of the chief concerns in the captive breeding of endangered species. Using microsatellite and mtDNA markers, we examined the effects of two key variables (parental number and duration of breeding period) on effective population size (N(e) ) and genetic diversity of offspring in an experimental breeding program for the endangered Tokyo bitterling, Tanakia tanago. Average heterozygosity and number of alleles of offspring estimated from microsatellite data increased with parental number in a breeding aquarium, and exhibited higher values for a long breeding period treatment (9 weeks) compared with a short breeding period (3 weeks). Haplotype diversity in mtDNA of offspring decreased with the reduction in parental number, and this tendency was greater for the short breeding period treatment. Genetic estimates of N(e) obtained with two single-sample estimation methods were consistently higher for the long breeding period treatment with the same number of parental fish. Average N(e) /N ratios were ranged from 0.5 to 1.4, and were high especially in the long breeding period with small and medium parental number treatments. Our results suggest that the spawning intervals of females and alternative mating behaviors of males influence the effective size and genetic diversity of offspring in bitterling. To maintain the genetic diversity of captive T. tanago, we recommend that captive breeding programs should be conducted for a sufficiently long period with an optimal level of parental density, as well as using an adequate number of parents. © 2011 Wiley Periodicals, Inc.

Fast genomic predictions via Bayesian G-BLUP and multilocus models of threshold traits including censored Gaussian data.

PubMed

Kärkkäinen, Hanni P; Sillanpää, Mikko J

2013-09-04

Because of the increased availability of genome-wide sets of molecular markers along with reduced cost of genotyping large samples of individuals, genomic estimated breeding values have become an essential resource in plant and animal breeding. Bayesian methods for breeding value estimation have proven to be accurate and efficient; however, the ever-increasing data sets are placing heavy demands on the parameter estimation algorithms. Although a commendable number of fast estimation algorithms are available for Bayesian models of continuous Gaussian traits, there is a shortage for corresponding models of discrete or censored phenotypes. In this work, we consider a threshold approach of binary, ordinal, and censored Gaussian observations for Bayesian multilocus association models and Bayesian genomic best linear unbiased prediction and present a high-speed generalized expectation maximization algorithm for parameter estimation under these models. We demonstrate our method with simulated and real data. Our example analyses suggest that the use of the extra information present in an ordered categorical or censored Gaussian data set, instead of dichotomizing the data into case-control observations, increases the accuracy of genomic breeding values predicted by Bayesian multilocus association models or by Bayesian genomic best linear unbiased prediction. Furthermore, the example analyses indicate that the correct threshold model is more accurate than the directly used Gaussian model with a censored Gaussian data, while with a binary or an ordinal data the superiority of the threshold model could not be confirmed.

Fast Genomic Predictions via Bayesian G-BLUP and Multilocus Models of Threshold Traits Including Censored Gaussian Data

PubMed Central

Kärkkäinen, Hanni P.; Sillanpää, Mikko J.

2013-01-01

Because of the increased availability of genome-wide sets of molecular markers along with reduced cost of genotyping large samples of individuals, genomic estimated breeding values have become an essential resource in plant and animal breeding. Bayesian methods for breeding value estimation have proven to be accurate and efficient; however, the ever-increasing data sets are placing heavy demands on the parameter estimation algorithms. Although a commendable number of fast estimation algorithms are available for Bayesian models of continuous Gaussian traits, there is a shortage for corresponding models of discrete or censored phenotypes. In this work, we consider a threshold approach of binary, ordinal, and censored Gaussian observations for Bayesian multilocus association models and Bayesian genomic best linear unbiased prediction and present a high-speed generalized expectation maximization algorithm for parameter estimation under these models. We demonstrate our method with simulated and real data. Our example analyses suggest that the use of the extra information present in an ordered categorical or censored Gaussian data set, instead of dichotomizing the data into case-control observations, increases the accuracy of genomic breeding values predicted by Bayesian multilocus association models or by Bayesian genomic best linear unbiased prediction. Furthermore, the example analyses indicate that the correct threshold model is more accurate than the directly used Gaussian model with a censored Gaussian data, while with a binary or an ordinal data the superiority of the threshold model could not be confirmed. PMID:23821618

Development of three Drosophila melanogaster strains with different sensitivity to volatile anesthetics.

PubMed

Liu, Jin; Hu, Zhao-yang; Ye, Qi-quan; Dai, Shuo-hua

2009-03-05

The mechanisms of action for volatile anesthetics remain unknown for centuries partly owing to the insufficient or ineffective research models. We designed this study to develop three strains derived from a wild-type Drosophila melanogaster with different sensitivities to volatile anesthetics, which may ultimately facilitate molecular and genetic studies of the mechanism involved. Median effective doses (ED(50)) of sevoflurane in seven-day-old virgin female and male wild-type Drosophila melanogaster were determined. The sensitive males and females of percentile 6 - 10 were cultured for breeding sensitive offspring (S(1)). So did median ones of percentile 48 - 52 for breeding median offspring (M(1)), resistant ones of percentile 91 - 95 for breeding resistant offspring (R(1)). Process was repeated through 31 generations, in the 37th generation, S(37), M(37) and R(37) were used to determine ED(50) for enflurane, isoflurane, sevoflurane, desflurane, halothane, methoxyflurane, chloroform and trichloroethylene, then ED(50) values were correlated with minimum alveolar concentration (MAC) values in human. From a wild-type Drosophila melanogaster we were able to breed three strains with high, median and low sevoflurane requirements. The ratio of sevoflurane requirements of three strains were 1.20:1.00:0.53 for females and 1.22:1.00:0.72 for males. Strains sensitive, median and resistant to sevoflurane were also sensitive, median and resistant to other volatile anesthetics. For eight anesthetics, ED(50) values in three strains correlated directly with MAC values in human. Three Drosophila melanogaster strains with high, median and low sensitivity to volatile anesthetics, but with same hereditary background were developed. The ED(50) are directly correlated with MAC in human for eight volatile anesthetics.

A genome-wide scan for signatures of differential artificial selection in ten cattle breeds.

PubMed

Rothammer, Sophie; Seichter, Doris; Förster, Martin; Medugorac, Ivica

2013-12-21

Since the times of domestication, cattle have been continually shaped by the influence of humans. Relatively recent history, including breed formation and the still enduring enormous improvement of economically important traits, is expected to have left distinctive footprints of selection within the genome. The purpose of this study was to map genome-wide selection signatures in ten cattle breeds and thus improve the understanding of the genome response to strong artificial selection and support the identification of the underlying genetic variants of favoured phenotypes. We analysed 47,651 single nucleotide polymorphisms (SNP) using Cross Population Extended Haplotype Homozygosity (XP-EHH). We set the significance thresholds using the maximum XP-EHH values of two essentially artificially unselected breeds and found up to 229 selection signatures per breed. Through a confirmation process we verified selection for three distinct phenotypes typical for one breed (polledness in Galloway, double muscling in Blanc-Bleu Belge and red coat colour in Red Holstein cattle). Moreover, we detected six genes strongly associated with known QTL for beef or dairy traits (TG, ABCG2, DGAT1, GH1, GHR and the Casein Cluster) within selection signatures of at least one breed. A literature search for genes lying in outstanding signatures revealed further promising candidate genes. However, in concordance with previous genome-wide studies, we also detected a substantial number of signatures without any yet known gene content. These results show the power of XP-EHH analyses in cattle to discover promising candidate genes and raise the hope of identifying phenotypically important variants in the near future. The finding of plausible functional candidates in some short signatures supports this hope. For instance, MAP2K6 is the only annotated gene of two signatures detected in Galloway and Gelbvieh cattle and is already known to be associated with carcass weight, back fat thickness and marbling score in Korean beef cattle. Based on the confirmation process and literature search we deduce that XP-EHH is able to uncover numerous artificial selection targets in subpopulations of domesticated animals.

Rethinking dog domestication by integrating genetics, archeology, and biogeography.

PubMed

Larson, Greger; Karlsson, Elinor K; Perri, Angela; Webster, Matthew T; Ho, Simon Y W; Peters, Joris; Stahl, Peter W; Piper, Philip J; Lingaas, Frode; Fredholm, Merete; Comstock, Kenine E; Modiano, Jaime F; Schelling, Claude; Agoulnik, Alexander I; Leegwater, Peter A; Dobney, Keith; Vigne, Jean-Denis; Vilà, Carles; Andersson, Leif; Lindblad-Toh, Kerstin

2012-06-05

The dog was the first domesticated animal but it remains uncertain when the domestication process began and whether it occurred just once or multiple times across the Northern Hemisphere. To ascertain the value of modern genetic data to elucidate the origins of dog domestication, we analyzed 49,024 autosomal SNPs in 1,375 dogs (representing 35 breeds) and 19 wolves. After combining our data with previously published data, we contrasted the genetic signatures of 121 breeds with a worldwide archeological assessment of the earliest dog remains. Correlating the earliest archeological dogs with the geographic locations of 14 so-called "ancient" breeds (defined by their genetic differentiation) resulted in a counterintuitive pattern. First, none of the ancient breeds derive from regions where the oldest archeological remains have been found. Second, three of the ancient breeds (Basenjis, Dingoes, and New Guinea Singing Dogs) come from regions outside the natural range of Canis lupus (the dog's wild ancestor) and where dogs were introduced more than 10,000 y after domestication. These results demonstrate that the unifying characteristic among all genetically distinct so-called ancient breeds is a lack of recent admixture with other breeds likely facilitated by geographic and cultural isolation. Furthermore, these genetically distinct ancient breeds only appear so because of their relative isolation, suggesting that studies of modern breeds have yet to shed light on dog origins. We conclude by assessing the limitations of past studies and how next-generation sequencing of modern and ancient individuals may unravel the history of dog domestication.

On the additive and dominant variance and covariance of individuals within the genomic selection scope.

PubMed

Vitezica, Zulma G; Varona, Luis; Legarra, Andres

2013-12-01

Genomic evaluation models can fit additive and dominant SNP effects. Under quantitative genetics theory, additive or "breeding" values of individuals are generated by substitution effects, which involve both "biological" additive and dominant effects of the markers. Dominance deviations include only a portion of the biological dominant effects of the markers. Additive variance includes variation due to the additive and dominant effects of the markers. We describe a matrix of dominant genomic relationships across individuals, D, which is similar to the G matrix used in genomic best linear unbiased prediction. This matrix can be used in a mixed-model context for genomic evaluations or to estimate dominant and additive variances in the population. From the "genotypic" value of individuals, an alternative parameterization defines additive and dominance as the parts attributable to the additive and dominant effect of the markers. This approach underestimates the additive genetic variance and overestimates the dominance variance. Transforming the variances from one model into the other is trivial if the distribution of allelic frequencies is known. We illustrate these results with mouse data (four traits, 1884 mice, and 10,946 markers) and simulated data (2100 individuals and 10,000 markers). Variance components were estimated correctly in the model, considering breeding values and dominance deviations. For the model considering genotypic values, the inclusion of dominant effects biased the estimate of additive variance. Genomic models were more accurate for the estimation of variance components than their pedigree-based counterparts.

Genetic diversity, population structure and subdivision of local Balkan pig breeds in Austria, Croatia, Serbia and Bosnia-Herzegovina and its practical value in conservation programs.

PubMed

Druml, Thomas; Salajpal, Kresimir; Dikic, Maria; Urosevic, Miroslav; Grilz-Seger, Gertrud; Baumung, Roswitha

2012-03-01

At present the Croatian Turopolje pig population comprises about 157 breeding animals. In Austria, 324 Turopolje pigs originating from six Croatian founder animals are registered. Multiple bottlenecks have occurred in this population, one major one rather recently and several more older and moderate ones. In addition, it has been subdivided into three subpopulations, one in Austria and two in Croatia, with restricted gene flow. These specificities explain the delicate situation of this endangered Croatian lard-type pig breed. In order to identify candidate breeding animals or gene pools for future conservation breeding programs, we studied the genetic diversity and population structure of this breed using microsatellite data from 197 individuals belonging to five different breeds. The genetic diversity of the Turopolje pig is dramatically low with observed heterozygosities values ranging from 0.38 to 0.57. Split into three populations since 1994, two genetic clusters could be identified: one highly conserved Croatian gene pool in Turopoljski Lug and the"Posavina" gene pool mainly present in the Austrian population. The second Croatian subpopulation in Lonjsko Polje in the Posavina region shows a constant gene flow from the Turopoljski Lug animals. One practical conclusion is that it is necessary to develop a "Posavina" boar line to preserve the "Posavina" gene pool and constitute a corresponding population in Croatia. Animals of the highly inbred herd in Turopoljski Lug should not be crossed with animals of other populations since they represent a specific phenotype-genotype combination. However to increase the genetic diversity of this herd, a program to optimize its sex ratio should be carried out, as was done in the Austrian population where the level of heterozygosity has remained moderate despite its heavy bottleneck in 1994. © 2012 Druml et al; licensee BioMed Central Ltd.

Establishment of the biochemical and endocrine blood profiles in the Majorera and Palmera dairy goat breeds: the effect of feed restriction.

PubMed

Lérias, Joana R; Peña, Raquel; Hernández-Castellano, Lorenzo E; Capote, Juan; Castro, Noemí; Argüello, Anastasio; Araújo, Susana S; Saco, Yolanda; Bassols, Anna; Almeida, André M

2015-11-01

Feed restriction, and seasonal weight loss (SWL), are major setbacks for animal production in the tropics and the Mediterranean. They may be solved through the use of autochthonous breeds particularly well adapted to SWL. It is therefore of major importance to determine markers of tolerance to feed restriction of putative use in animal selection. Two indigenous breeds from the Canary Islands, Palmera and Majorera, are commonly used by dairy goat farmers and, interestingly, have different phenotype characteristics albeit with a common ancestry. Indeed, Majorera is well adapted to feed restriction whereas the Palmera is susceptible to feed restriction. In addition, regardless of their importance in dairy production, there are only a limited number of reports relating to these breeds and, to the best of our knowledge, there is no description of their blood metabolite standard values under control conditions or as affected by feed restriction. In this study we analysed the blood metabolite profiles in Majorera and Palmera goats aiming to establish the differential responses to feed restriction between the two breeds and to characterise their metabolite standard values under control conditions. We observed significant differences in creatinine, urea, non-esterified fatty acids (NEFAs), cholesterol, IGF-1 and T3 due to underfeeding. Furthermore, a PCA analysis, revealed that animals submitted to undernutrition could be distinguished from the control groups, with the formation of three separate clusters (Palmera individuals after 22 d of subnutrition (PE22); Majorera individuals after 22 d of subnutrition (ME22) and animals assigned to control conditions (MC0, MC22, PC0 and PC22)), highlighting different responses of the two breeds to undernutrition.

Environmental, dietary, and hormonal factors in the regulation of seasonal breeding in free-living female Indian rose-ringed parakeets (Psittacula krameri).

PubMed

Sailaja, R; Kotak, V C; Sharp, P J; Schmedemann, R; Haase, E

1988-12-01

The roles of environmental, dietary, and hormonal factors in the timing of seasonal breeding were assessed in free-living female Indian rose-ringed parakeets, Psittacula krameri, in northwest India (22 degrees 2'N, 73 degrees E). The ovaries and oviducts began to enlarge in January, were fully developed in February, and began to regress in March. During this time there was no significant change in the concentration of plasma luteinizing hormone (LH) or estradiol. The concentration of plasma LH decreased (P less than 0.01) at the end of the breeding season. Pair bond formation occurred between September and December and was associated with an increase in levels of plasma LH but no change in plasma estradiol. Concentrations of plasma testosterone (T) and 5 alpha-dihydrotestosterone (5 alpha-DHT) did not vary significantly during the year and were similar to those in males except for higher values of 5 alpha-DHT and lower values of T during the pre- and postbreeding periods, respectively. The similar levels of plasma androgens in both sexes may be related to the equal roles that both sexes play in the defence of their nest holes. An analysis of crop sac contents showed that the birds fed chiefly on pigeon peas (Cajanus cajan) during the breeding season and on cereal grains at other times of the year. It is suggested that pigeon peas provide the extra nutrients, including calcium, required for egg production. Since pigeon peas ripen between November and March, the production of the crop may play a role in the timing of seasonal breeding. A further factor appears to be competition for nest sites. By breeding in winter, the parakeet avoids competing with other species which nest in holes.

Ultrasonographic reproductive tract measures and pelvis measures as predictors of pregnancy failure and anestrus in restricted bred beef heifers.

PubMed

Holm, Dietmar E; Nielen, Mirjam; Jorritsma, Ruurd; Irons, Peter C; Thompson, Peter N

2016-02-01

Previous reports have shown that reproductive tract score (RTS) can predict reproduction outcomes in seasonally bred beef heifers, although the accuracy can vary. Some ultrasonographic measures of the female reproductive tract and pelvis area have also been associated with reproductive outcome in young heifers. The objectives of this study were to determine which transrectal ultrasound or pelvis measures taken at a single examination are independent predictors of reproductive failure and whether the RTS system can be optimized with this information. In this observational study, year-old beef heifers (n = 488) in 2 birth cohorts were followed from just before the first breeding until confirmation of pregnancy. A single pre-breeding examination included body condition score, RTS, ultrasound measures of the reproductive tract (length and diameter of the left and right ovaries, presence and diameter of a CL, largest follicle diameter and left uterus horn diameter) and transverse and vertical diameters of the pelvis. Additional farm records including dam parity, sire, birth weight and birth date, weaning weight, weaning date, prebreeding body weight, AI dates, and semen used were available. Breeding consisted of 50 days of AI, followed 5 to 7 days later by a 42-day bull breeding period. Pregnancy failure was defined as the failure to become pregnant after the AI and bull breeding periods, while anestrus was defined as the failure to be detected in estrus during the 50-day AI period. From the prebreeding data and farm records, independent predictors of pregnancy failure and anestrus were identified using stepwise reduction in multiple logistic regression models. Age at the onset of breeding was the only consistent independent predictor of pregnancy failure and anestrus in both cohorts of this study (P < 0.05). Body condition score, uterus horn diameter, absence of a CL, largest follicle of less than 13 mm, and pelvis area (PA) were the prebreeding examination variables that remained in prognostic models (P < 0.1). Combining either the model based on the 3 remaining ultrasound measures or RTS with PA provided more accurate prognostic models for pregnancy failure and anestrus than using RTS alone (P < 0.05). It is concluded that ultrasound measures have prognostic value for pregnancy failure in restricted bred yearling heifers as a result of their association with anestrus, and that smaller PA has additional prognostic value for poorly performing heifers. Copyright © 2016 Elsevier Inc. All rights reserved.

Estimation of test-day model (co)variance components across breeds using New Zealand dairy cattle data.

PubMed

Vanderick, S; Harris, B L; Pryce, J E; Gengler, N

2009-03-01

In New Zealand, a large proportion of cows are currently crossbreds, mostly Holstein-Friesians (HF) x Jersey (JE). The genetic evaluation system for milk yields is considering the same additive genetic effects for all breeds. The objective was to model different additive effects according to parental breeds to obtain first estimates of correlations among breed-specific effects and to study the usefulness of this type of random regression test-day model. Estimates of (co)variance components for purebred HF and JE cattle in purebred herds were computed by using a single-breed model. This analysis showed differences between the 2 breeds, with a greater variability in the HF breed. (Co)variance components for purebred HF and JE and crossbred HF x JE cattle were then estimated by using a complete multibreed model in which computations of complete across-breed (co)variances were simplified by correlating only eigenvectors for HF and JE random regressions of the same order as obtained from the single-breed analysis. Parameter estimates differed more strongly than expected between the single-breed and multibreed analyses, especially for JE. This could be due to differences between animals and management in purebred and non-purebred herds. In addition, the model used only partially accounted for heterosis. The multibreed analysis showed additive genetic differences between the HF and JE breeds, expressed as genetic correlations of additive effects in both breeds, especially in linear and quadratic Legendre polynomials (respectively, 0.807 and 0.604). The differences were small for overall milk production (0.926). Results showed that permanent environmental lactation curves were highly correlated across breeds; however, intraherd lactation curves were also affected by the breed-environment interaction. This result may indicate the existence of breed-specific competition effects that vary through the different lactation stages. In conclusion, a multibreed model similar to the one presented could optimally use the environmental and genetic parameters and provide breed-dependent additive breeding values. This model could also be a useful tool to evaluate crossbred dairy cattle populations like those in New Zealand. However, a routine evaluation would still require the development of an improved methodology. It would also be computationally very challenging because of the simultaneous presence of a large number of breeds.

Effect of breeding strategy and feeding system on the within-herd variation of lean meat percents in Danish slaughter pigs.

PubMed

Stege, H; Bagger, J; Nielsen, J P; Ersbøll, A K

2011-08-01

In several countries slaughter pigs are paid for individually, according to slaughter weight and lean meat percent (LMP). Production of uniform batches of pigs within the optimal weight and LMP limits will obtain the best price. Therefore, all pigs should have a similar growth rate (average daily gain, ADG) and reach an appropriate slaughter weight within the same time period. LMP may serve as a proxy for ADG since pigs with low LMP have significantly higher ADG than pigs with high LMP and vice versa. Both breeding strategy and feeding system may influence the range of variation among pigs. The aim of this study was to test the two following hypotheses: (1) Herds purchasing breeding gilts have a higher mean value and a lower variation (standard deviation) in LMP than herds producing their own breeding gilts and (2) Herds using restricted feeding of finishers have a higher mean value and a lower variation (standard deviation) in LMP than herds with ad libitum feeding of finishers. The study included 72 herds and a total of 345,132 pigs slaughtered during one year. Among the 72 herds, 40 were home-breeders and 32 purchased breeding gilts from a breeding company. Nineteen herds used restricted feeding, of which 8 (42%) were home-breeders. Fifty-three herds used ad libitum feeding, of which 32 (60%) were home-breeders. Breeding strategy had a significant effect on SDLMP (p=0.003), where purchase of breeding gilts resulted in a significantly lower standard deviation of the monthly LMP compared to home-bred gilts (a difference in median SDLMP of 0.2 percentage points or 8% difference between groups). Feeding system had a significant effect on the meanLMP (p<0.001), with a significantly higher meanLMP in herds using restrictive feeding compared to ad libitum feeding (60.7% versus 60.0%). Restrictive feeding also resulted in a significantly lower SDLMP (p<0.001) compared to ad libitum feeding (2.2% versus 2.5% or a 12% difference between groups). Copyright © 2011 Elsevier B.V. All rights reserved.

Integrated QTL detection for key breeding traits in multiple peach progenies.

PubMed

Hernández Mora, José R; Micheletti, Diego; Bink, Marco; Van de Weg, Eric; Cantín, Celia; Nazzicari, Nelson; Caprera, Andrea; Dettori, Maria Teresa; Micali, Sabrina; Banchi, Elisa; Campoy, José Antonio; Dirlewanger, Elisabeth; Lambert, Patrick; Pascal, Thierry; Troggio, Michela; Bassi, Daniele; Rossini, Laura; Verde, Ignazio; Quilot-Turion, Bénédicte; Laurens, François; Arús, Pere; Aranzana, Maria José

2017-06-06

Peach (Prunus persica (L.) Batsch) is a major temperate fruit crop with an intense breeding activity. Breeding is facilitated by knowledge of the inheritance of the key traits that are often of a quantitative nature. QTLs have traditionally been studied using the phenotype of a single progeny (usually a full-sib progeny) and the correlation with a set of markers covering its genome. This approach has allowed the identification of various genes and QTLs but is limited by the small numbers of individuals used and by the narrow transect of the variability analyzed. In this article we propose the use of a multi-progeny mapping strategy that used pedigree information and Bayesian approaches that supports a more precise and complete survey of the available genetic variability. Seven key agronomic characters (data from 1 to 3 years) were analyzed in 18 progenies from crosses between occidental commercial genotypes and various exotic lines including accessions of other Prunus species. A total of 1467 plants from these progenies were genotyped with a 9 k SNP array. Forty-seven QTLs were identified, 22 coinciding with major genes and QTLs that have been consistently found in the same populations when studied individually and 25 were new. A substantial part of the QTLs observed (47%) would not have been detected in crosses between only commercial materials, showing the high value of exotic lines as a source of novel alleles for the commercial gene pool. Our strategy also provided estimations on the narrow sense heritability of each character, and the estimation of the QTL genotypes of each parent for the different QTLs and their breeding value. The integrated strategy used provides a broader and more accurate picture of the variability available for peach breeding with the identification of many new QTLs, information on the sources of the alleles of interest and the breeding values of the potential donors of such valuable alleles. These results are first-hand information for breeders and a step forward towards the implementation of DNA-informed strategies to facilitate selection of new cultivars with improved productivity and quality.

MHC variability in heritage breeds of chickens.

PubMed

Fulton, J E; Lund, A R; McCarron, A M; Pinegar, K N; Korver, D R; Classen, H L; Aggrey, S; Utterbach, C; Anthony, N B; Berres, M E

2016-02-01

The chicken Major Histocompatibility Complex (MHC) is very strongly associated with disease resistance and thus is a very important region of the chicken genome. Historically, MHC (B locus) has been identified by the use of serology with haplotype specific alloantisera. These antisera can be difficult to produce and frequently cross-react with multiple haplotypes and hence their application is generally limited to inbred and MHC-defined lines. As a consequence, very little information about MHC variability in heritage chicken breeds is available. DNA-based methods are now available for examining MHC variability in these previously uncharacterized populations. A high density SNP panel consisting of 101 SNP that span a 230,000 bp region of the chicken MHC was used to examine MHC variability in 17 heritage populations of chickens from five universities from Canada and the United States. The breeds included 6 heritage broiler lines, 3 Barred Plymouth Rock, 2 New Hampshire and one each of Rhode Island Red, Light Sussex, White Leghorn, Dark Brown Leghorn, and 2 synthetic lines. These heritage breeds contained from one to 11 haplotypes per line. A total of 52 unique MHC haplotypes were found with only 10 of them identical to serologically defined haplotypes. Furthermore, nine MHC recombinants with their respective parental haplotypes were identified. This survey confirms the value of these non-commercially utilized lines in maintaining genetic diversity. The identification of multiple MHC haplotypes and novel MHC recombinants indicates that diversity is being generated and maintained within these heritage populations. © 2016 Poultry Science Association Inc.

Genetic and economic benefits of selection based on performance recording and genotyping in lower tiers of multi-tiered sheep breeding schemes.

PubMed

Santos, Bruno F S; van der Werf, Julius H J; Gibson, John P; Byrne, Timothy J; Amer, Peter R

2017-01-17

Performance recording and genotyping in the multiplier tier of multi-tiered sheep breeding schemes could potentially reduce the difference in the average genetic merit between nucleus and commercial flocks, and create additional economic benefits for the breeding structure. The genetic change in a multiple-trait breeding objective was predicted for various selection strategies that included performance recording, parentage testing and genomic selection. A deterministic simulation model was used to predict selection differentials and the flow of genetic superiority through the different tiers. Cumulative discounted economic benefits were calculated based on trait gains achieved in each of the tiers and considering the extra revenue and associated costs of applying recording, genotyping and selection practices in the multiplier tier of the breeding scheme. Performance recording combined with genomic or parentage information in the multiplier tier reduced the genetic lag between the nucleus and commercial flock by 2 to 3 years. The overall economic benefits of improved performance in the commercial tier offset the costs of recording the multiplier. However, it took more than 18 years before the cumulative net present value of benefits offset the costs at current test prices. Strategies in which recorded multiplier ewes were selected as replacements for the nucleus flock did modestly increase profitability when compared to a closed nucleus structure. Applying genomic selection is the most beneficial strategy if testing costs can be reduced or by genotyping only a proportion of the selection candidates. When the cost of genotyping was reduced, scenarios that combine performance recording with genomic selection were more profitable and reached breakeven point about 10 years earlier. Economic benefits can be generated in multiplier flocks by implementing performance recording in conjunction with either DNA pedigree recording or genomic technology. These recording practices reduce the long genetic lag between the nucleus and commercial flocks in multi-tiered breeding programs. Under current genotyping costs, the time to breakeven was found to be generally very long, although this varied between strategies. Strategies using either genomic selection or DNA pedigree verification were found to be economically viable provided the price paid for the tests is lower than current prices, in the long-term.

Genetic parameters for stayability to consecutive calvings in Zebu cattle.

PubMed

Silva, D O; Santana, M L; Ayres, D R; Menezes, G R O; Silva, L O C; Nobre, P R C; Pereira, R J

2017-12-22

Longer-lived cows tend to be more profitable and the stayability trait is a selection criterion correlated to longevity. An alternative to the traditional approach to evaluate stayability is its definition based on consecutive calvings, whose main advantage is the more accurate evaluation of young bulls. However, no study using this alternative approach has been conducted for Zebu breeds. Therefore, the objective of this study was to compare linear random regression models to fit stayability to consecutive calvings of Guzerá, Nelore and Tabapuã cows and to estimate genetic parameters for this trait in the respective breeds. Data up to the eighth calving were used. The models included the fixed effects of age at first calving and year-season of birth of the cow and the random effects of contemporary group, additive genetic, permanent environmental and residual. Random regressions were modeled by orthogonal Legendre polynomials of order 1 to 4 (2 to 5 coefficients) for contemporary group, additive genetic and permanent environmental effects. Using Deviance Information Criterion as the selection criterion, the model with 4 regression coefficients for each effect was the most adequate for the Nelore and Tabapuã breeds and the model with 5 coefficients is recommended for the Guzerá breed. For Guzerá, heritabilities ranged from 0.05 to 0.08, showing a quadratic trend with a peak between the fourth and sixth calving. For the Nelore and Tabapuã breeds, the estimates ranged from 0.03 to 0.07 and from 0.03 to 0.08, respectively, and increased with increasing calving number. The additive genetic correlations exhibited a similar trend among breeds and were higher for stayability between closer calvings. Even between more distant calvings (second v. eighth), stayability showed a moderate to high genetic correlation, which was 0.77, 0.57 and 0.79 for the Guzerá, Nelore and Tabapuã breeds, respectively. For Guzerá, when the models with 4 or 5 regression coefficients were compared, the rank correlations between predicted breeding values for the intercept were always higher than 0.99, indicating the possibility of practical application of the least parameterized model. In conclusion, the model with 4 random regression coefficients is recommended for the genetic evaluation of stayability to consecutive calvings in Zebu cattle.

Estimation of genetic effects in the presence of multicollinearity in multibreed beef cattle evaluation.

PubMed

Roso, V M; Schenkel, F S; Miller, S P; Schaeffer, L R

2005-08-01

Breed additive, dominance, and epistatic loss effects are of concern in the genetic evaluation of a multibreed population. Multiple regression equations used for fitting these effects may show a high degree of multicollinearity among predictor variables. Typically, when strong linear relationships exist, the regression coefficients have large SE and are sensitive to changes in the data file and to the addition or deletion of variables in the model. Generalized ridge regression methods were applied to obtain stable estimates of direct and maternal breed additive, dominance, and epistatic loss effects in the presence of multicollinearity among predictor variables. Preweaning weight gains of beef calves in Ontario, Canada, from 1986 to 1999 were analyzed. The genetic model included fixed direct and maternal breed additive, dominance, and epistatic loss effects, fixed environmental effects of age of the calf, contemporary group, and age of the dam x sex of the calf, random additive direct and maternal genetic effects, and random maternal permanent environment effect. The degree and the nature of the multicollinearity were identified and ridge regression methods were used as an alternative to ordinary least squares (LS). Ridge parameters were obtained using two different objective methods: 1) generalized ridge estimator of Hoerl and Kennard (R1); and 2) bootstrap in combination with cross-validation (R2). Both ridge regression methods outperformed the LS estimator with respect to mean squared error of predictions (MSEP) and variance inflation factors (VIF) computed over 100 bootstrap samples. The MSEP of R1 and R2 were similar, and they were 3% less than the MSEP of LS. The average VIF of LS, R1, and R2 were equal to 26.81, 6.10, and 4.18, respectively. Ridge regression methods were particularly effective in decreasing the multicollinearity involving predictor variables of breed additive effects. Because of a high degree of confounding between estimates of maternal dominance and direct epistatic loss effects, it was not possible to compare the relative importance of these effects with a high level of confidence. The inclusion of epistatic loss effects in the additive-dominance model did not cause noticeable reranking of sires, dams, and calves based on across-breed EBV. More precise estimates of breed effects as a result of this study may result in more stable across-breed estimated breeding values over the years.

The contribution of efficient production of monozygotic twins to beef cattle breeding

PubMed Central

HASHIYADA, Yutaka

2017-01-01

Production of sires with high breeding potential is indispensable for prompt and reliable breeding using their semen in the cattle industry. Currently, in Japan, we aim to further the production of Japanese black sires via a new breeding system that uses genetically homologous monozygotic twins so that better growth performance and carcass traits can be translated to the increased production of beef with higher economic value. Several studies have reported that monozygotic twins are produced by embryo bisection. On the other hand, with the evolution and stabilization of in vitro fertilization technology, it has become possible to produce multiple monozygotic twin calves from blastomeres separated from a cleavage-stage embryo. This review attempts to clarify breeding practices through revalidation of the factors that affect the production efficiency of monozygotic twin calves by embryo bisection. Furthermore, the establishment of a system for monozygotic twin embryo production via the simplified technique of blastomere separation is reviewed while showing data from our previously performed studies. PMID:29033399

Performance comparison of two efficient genomic selection methods (gsbay & MixP) applied in aquacultural organisms

NASA Astrophysics Data System (ADS)

Su, Hailin; Li, Hengde; Wang, Shi; Wang, Yangfan; Bao, Zhenmin

2017-02-01

Genomic selection is more and more popular in animal and plant breeding industries all around the world, as it can be applied early in life without impacting selection candidates. The objective of this study was to bring the advantages of genomic selection to scallop breeding. Two different genomic selection tools MixP and gsbay were applied on genomic evaluation of simulated data and Zhikong scallop ( Chlamys farreri) field data. The data were compared with genomic best linear unbiased prediction (GBLUP) method which has been applied widely. Our results showed that both MixP and gsbay could accurately estimate single-nucleotide polymorphism (SNP) marker effects, and thereby could be applied for the analysis of genomic estimated breeding values (GEBV). In simulated data from different scenarios, the accuracy of GEBV acquired was ranged from 0.20 to 0.78 by MixP; it was ranged from 0.21 to 0.67 by gsbay; and it was ranged from 0.21 to 0.61 by GBLUP. Estimations made by MixP and gsbay were expected to be more reliable than those estimated by GBLUP. Predictions made by gsbay were more robust, while with MixP the computation is much faster, especially in dealing with large-scale data. These results suggested that both algorithms implemented by MixP and gsbay are feasible to carry out genomic selection in scallop breeding, and more genotype data will be necessary to produce genomic estimated breeding values with a higher accuracy for the industry.

Live weight, conformation, carcass traits and economic values of ram lambs of Red Maasai and Dorper sheep and their crosses.

PubMed

Zonabend König, E; Ojango, J M K; Audho, J; Mirkena, T; Strandberg, E; Okeyo, A M; Philipsson, J

2017-01-01

Meat production is the most important trait in the breeding objectives of sheep production in East Africa. The aim of this study was to investigate breed differences in live weight, conformation, carcass traits and economic values for meat production among Red Maasai and Dorper sheep and their crosses. In total, 88 ram lambs, which were reared at the ILRI experimental station, Kapiti plains Estate in Central Kenya, were used for the study. The lambs were slaughtered at Kenya Meat Commission (KMC) at about 1 year of age. Prior to slaughter, the lambs were weighed, measured and assessed by experienced evaluators, and at the abattoir carcass traits were recorded. Large breed differences were found for most traits. Dorper lambs were heavier at delivery for slaughter and had better carcass grade but lower dressing percentage and fat levels than Red Maasai. Crossbreds were generally better than the parental breeds. Evaluators were willing to pay more for the Dorper lambs for slaughter although carcass weights later were shown not to be higher than for Red Maasai. Evaluators undervalued Red Maasai lambs by 8-13 % compared to Dorper lambs according to the prices quoted per kilogramme live or carcass weight by KMC. Live weight was better than any other live measure in predicting carcass weight. Due to the overall higher ranking of the crossbred lambs for meat production, Dorper may be useful as a terminal sire breed for crossing with Red Maasai ewes.

Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation

PubMed Central

2013-01-01

Background Rapid development of highly saturated genetic maps aids molecular breeding, which can accelerate gain per breeding cycle in woody perennial plants such as Rubus idaeus (red raspberry). Recently, robust genotyping methods based on high-throughput sequencing were developed, which provide high marker density, but result in some genotype errors and a large number of missing genotype values. Imputation can reduce the number of missing values and can correct genotyping errors, but current methods of imputation require a reference genome and thus are not an option for most species. Results Genotyping by Sequencing (GBS) was used to produce highly saturated maps for a R. idaeus pseudo-testcross progeny. While low coverage and high variance in sequencing resulted in a large number of missing values for some individuals, a novel method of imputation based on maximum likelihood marker ordering from initial marker segregation overcame the challenge of missing values, and made map construction computationally tractable. The two resulting parental maps contained 4521 and 2391 molecular markers spanning 462.7 and 376.6 cM respectively over seven linkage groups. Detection of precise genomic regions with segregation distortion was possible because of map saturation. Microsatellites (SSRs) linked these results to published maps for cross-validation and map comparison. Conclusions GBS together with genome-independent imputation provides a rapid method for genetic map construction in any pseudo-testcross progeny. Our method of imputation estimates the correct genotype call of missing values and corrects genotyping errors that lead to inflated map size and reduced precision in marker placement. Comparison of SSRs to published R. idaeus maps showed that the linkage maps constructed with GBS and our method of imputation were robust, and marker positioning reliable. The high marker density allowed identification of genomic regions with segregation distortion in R. idaeus, which may help to identify deleterious alleles that are the basis of inbreeding depression in the species. PMID:23324311

Mixed Model Methods for Genomic Prediction and Variance Component Estimation of Additive and Dominance Effects Using SNP Markers

PubMed Central

Da, Yang; Wang, Chunkao; Wang, Shengwen; Hu, Guo

2014-01-01

We established a genomic model of quantitative trait with genomic additive and dominance relationships that parallels the traditional quantitative genetics model, which partitions a genotypic value as breeding value plus dominance deviation and calculates additive and dominance relationships using pedigree information. Based on this genomic model, two sets of computationally complementary but mathematically identical mixed model methods were developed for genomic best linear unbiased prediction (GBLUP) and genomic restricted maximum likelihood estimation (GREML) of additive and dominance effects using SNP markers. These two sets are referred to as the CE and QM sets, where the CE set was designed for large numbers of markers and the QM set was designed for large numbers of individuals. GBLUP and associated accuracy formulations for individuals in training and validation data sets were derived for breeding values, dominance deviations and genotypic values. Simulation study showed that GREML and GBLUP generally were able to capture small additive and dominance effects that each accounted for 0.00005–0.0003 of the phenotypic variance and GREML was able to differentiate true additive and dominance heritability levels. GBLUP of the total genetic value as the summation of additive and dominance effects had higher prediction accuracy than either additive or dominance GBLUP, causal variants had the highest accuracy of GREML and GBLUP, and predicted accuracies were in agreement with observed accuracies. Genomic additive and dominance relationship matrices using SNP markers were consistent with theoretical expectations. The GREML and GBLUP methods can be an effective tool for assessing the type and magnitude of genetic effects affecting a phenotype and for predicting the total genetic value at the whole genome level. PMID:24498162

Mixed model methods for genomic prediction and variance component estimation of additive and dominance effects using SNP markers.

PubMed

Da, Yang; Wang, Chunkao; Wang, Shengwen; Hu, Guo

2014-01-01

We established a genomic model of quantitative trait with genomic additive and dominance relationships that parallels the traditional quantitative genetics model, which partitions a genotypic value as breeding value plus dominance deviation and calculates additive and dominance relationships using pedigree information. Based on this genomic model, two sets of computationally complementary but mathematically identical mixed model methods were developed for genomic best linear unbiased prediction (GBLUP) and genomic restricted maximum likelihood estimation (GREML) of additive and dominance effects using SNP markers. These two sets are referred to as the CE and QM sets, where the CE set was designed for large numbers of markers and the QM set was designed for large numbers of individuals. GBLUP and associated accuracy formulations for individuals in training and validation data sets were derived for breeding values, dominance deviations and genotypic values. Simulation study showed that GREML and GBLUP generally were able to capture small additive and dominance effects that each accounted for 0.00005-0.0003 of the phenotypic variance and GREML was able to differentiate true additive and dominance heritability levels. GBLUP of the total genetic value as the summation of additive and dominance effects had higher prediction accuracy than either additive or dominance GBLUP, causal variants had the highest accuracy of GREML and GBLUP, and predicted accuracies were in agreement with observed accuracies. Genomic additive and dominance relationship matrices using SNP markers were consistent with theoretical expectations. The GREML and GBLUP methods can be an effective tool for assessing the type and magnitude of genetic effects affecting a phenotype and for predicting the total genetic value at the whole genome level.

Assigning breed origin to alleles in crossbred animals.

PubMed

Vandenplas, Jérémie; Calus, Mario P L; Sevillano, Claudia A; Windig, Jack J; Bastiaansen, John W M

2016-08-22

For some species, animal production systems are based on the use of crossbreeding to take advantage of the increased performance of crossbred compared to purebred animals. Effects of single nucleotide polymorphisms (SNPs) may differ between purebred and crossbred animals for several reasons: (1) differences in linkage disequilibrium between SNP alleles and a quantitative trait locus; (2) differences in genetic backgrounds (e.g., dominance and epistatic interactions); and (3) differences in environmental conditions, which result in genotype-by-environment interactions. Thus, SNP effects may be breed-specific, which has led to the development of genomic evaluations for crossbred performance that take such effects into account. However, to estimate breed-specific effects, it is necessary to know breed origin of alleles in crossbred animals. Therefore, our aim was to develop an approach for assigning breed origin to alleles of crossbred animals (termed BOA) without information on pedigree and to study its accuracy by considering various factors, including distance between breeds. The BOA approach consists of: (1) phasing genotypes of purebred and crossbred animals; (2) assigning breed origin to phased haplotypes; and (3) assigning breed origin to alleles of crossbred animals based on a library of assigned haplotypes, the breed composition of crossbred animals, and their SNP genotypes. The accuracy of allele assignments was determined for simulated datasets that include crosses between closely-related, distantly-related and unrelated breeds. Across these scenarios, the percentage of alleles of a crossbred animal that were correctly assigned to their breed origin was greater than 90 %, and increased with increasing distance between breeds, while the percentage of incorrectly assigned alleles was always less than 2 %. For the remaining alleles, i.e. 0 to 10 % of all alleles of a crossbred animal, breed origin could not be assigned. The BOA approach accurately assigns breed origin to alleles of crossbred animals, even if their pedigree is not recorded.

The effect of dual-hemisphere breeding on stallion fertility.

PubMed

Walbornn, S R; Love, C C; Blanchard, T L; Brinsko, S P; Varner, D D

2017-05-01

Breeding records were analyzed from 24 Thoroughbred stallions that were subjected to dual-hemisphere breeding (DH), including novice (first-year; NOV; n = 11) and experienced (EXP; n = 13) stallions. Fertility variables included seasonal pregnancy rate, pregnancy rate per cycle, and first-cycle pregnancy rate. In addition, values for book size, total number of covers, distribution of mare type (maiden, foaling, and barren) within a stallion's book, cycles per mare, and mare age were examined. Some data were also categorized by mare type (maiden-M, foaling-F, and barren-B). Five separate analyses of the data were performed. For Analyses 1-3, the effects of hemisphere (northern hemisphere [NH] vs. southern hemisphere [SH]) and breeding order (refers to the first [O1] or second [O2] season within the first year of dual-hemisphere breeding) were examined for all stallions (combined group [CG]), NOV stallions only, and EXP stallions only, respectively. Fertility values were generally higher in the SH than the NH (P < 0.05), whereas book size, total number of covers, and cycles per mare were higher in the NH than the SH (P < 0.05). Book size and total covers were negatively correlated to first cycle pregnancy rate (r = -0.57, r = -0.71, respectively; P < 0.05) for NOV stallions. Pregnancy rate per cycle was also negatively correlated with total covers (r = -0.58; P < 0.05) for NOV stallions. Similar trends were noted for Groups CG and EXP, but the relationship was not as marked as for NOV stallions. The fertility of O1 was generally similar to O2 (P > 0.05). For Analysis 4, fertility of DH breeding seasons was compared to single hemisphere (SIN) breeding seasons within the same 16 stallions and was found to be similar between the two groups (P > 0.05). For Analysis 5, the effect of the number of consecutive DH breeding seasons on fertility was examined and was found to remain unchanged (P > 0.05). In summary, no adverse effects of DH breeding on fertility were detected. Fertility was higher when stallions were bred in the SH, as compared to the NH. Potential reasons for higher fertility achieved in the SH were smaller book sizes and better mare reproductive quality. Copyright © 2017. Published by Elsevier Inc.

Contribution of domestic production records, Interbull estimated breeding values, and single nucleotide polymorphism genetic markers to the single-step genomic evaluation of milk production.

PubMed

Přibyl, J; Madsen, P; Bauer, J; Přibylová, J; Simečková, M; Vostrý, L; Zavadilová, L

2013-03-01

Estimated breeding values (EBV) for first-lactation milk production of Holstein cattle in the Czech Republic were calculated using a conventional animal model and by single-step prediction of the genomic enhanced breeding value. Two overlapping data sets of milk production data were evaluated: (1) calving years 1991 to 2006, with 861,429 lactations and 1,918,901 animals in the pedigree and (2) calving years 1991 to 2010, with 1,097,319 lactations and 1,906,576 animals in the pedigree. Global Interbull (Uppsala, Sweden) deregressed proofs of 114,189 bulls were used in the analyses. Reliabilities of Interbull values were equivalent to an average of 8.53 effective records, which were used in a weighted analysis. A total of 1,341 bulls were genotyped using the Illumina BovineSNP50 BeadChip V2 (Illumina Inc., San Diego, CA). Among the genotyped bulls were 332 young bulls with no daughters in the first data set but more than 50 daughters (88.41, on average) with performance records in the second data set. For young bulls, correlations of EBV and genomic enhanced breeding value before and after progeny testing, corresponding average expected reliabilities, and effective daughter contributions (EDC) were calculated. The reliability of prediction pedigree EBV of young bulls was 0.41, corresponding to EDC=10.6. Including Interbull deregressed proofs improved the reliability of prediction by EDC=13.4 and including genotyping improved prediction reliability by EDC=6.2. Total average expected reliability of prediction reached 0.67, corresponding to EDC=30.2. The combination of domestic and Interbull sources for both genotyped and nongenotyped animals is valuable for improving the accuracy of genetic prediction in small populations of dairy cattle. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Genetic diversity in Spanish donkey breeds using microsatellite DNA markers

PubMed Central

Aranguren-Méndez, José; Jordana, Jordi; Gomez, Mariano

2001-01-01

Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (HE) over all the populations varied between 0.637 and 0.684 in this study. The low GST value showed that only 3.6% of the diversity was between breeds (P < 0.01). Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, except HMS5 that showed agreement in all analysed populations. The cumulative exclusion probability (PE) was 0.999 in each breed, suggesting that the loci would be suitable for donkey parentage testing. The constructed dendrogram from the DA distance matrix showed little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse, used as an outgroup. These results confirm the potential use of equine microsatellite loci as a tool for genetic studies in domestic donkey populations, which could also be useful for conservation plans. PMID:11559485

Genetic profile of scrapie codons 146, 211 and 222 in the PRNP gene locus in three breeds of dairy goats.

PubMed

Vouraki, Sotiria; Gelasakis, Athanasios I; Alexandri, Panoraia; Boukouvala, Evridiki; Ekateriniadou, Loukia V; Banos, Georgios; Arsenos, Georgios

2018-01-01

Polymorphisms at PRNP gene locus have been associated with resistance against classical scrapie in goats. Genetic selection on this gene within appropriate breeding programs may contribute to the control of the disease. The present study characterized the genetic profile of codons 146, 211 and 222 in three dairy goat breeds in Greece. A total of 766 dairy goats from seven farms were used. Animals belonged to two indigenous Greek, Eghoria (n = 264) and Skopelos (n = 287) and a foreign breed, Damascus (n = 215). Genomic DNA was extracted from blood samples from individual animals. Polymorphisms were detected in these codons using Real-Time PCR analysis and four different Custom TaqMan® SNP Genotyping Assays. Genotypic, allelic and haplotypic frequencies were calculated based on individual animal genotypes. Chi-square tests were used to examine Hardy-Weinberg equilibrium state and compare genotypic distribution across breeds. Genetic distances among the three breeds, and between these and 30 breeds reared in other countries were estimated based on haplotypic frequencies using fixation index FST with Arlequin v3.1 software; a Neighbor-Joining tree was created using PHYLIP package v3.695. Level of statistical significance was set at P = 0.01. All scrapie resistance-associated alleles (146S, 146D, 211Q and 222K) were detected in the studied population. Significant frequency differences were observed between the indigenous Greek and Damascus breeds. Alleles 222K and 146S had the highest frequency in the two indigenous and the Damascus breed, respectively (ca. 6.0%). The studied breeds shared similar haplotypic frequencies with most South Italian and Turkish breeds but differed significantly from North-Western European, Far East and some USA goat breeds. Results suggest there is adequate variation in the PRNP gene locus to support breeding programs for enhanced scrapie resistance in goats reared in Greece. Genetic comparisons among goat breeds indicate that separate breeding programs should apply to the two indigenous and the imported Damascus breeds.

Genome-wide association study reveals regions associated with gestation length in two pig populations.

PubMed

Hidalgo, A M; Lopes, M S; Harlizius, B; Bastiaansen, J W M

2016-04-01

Reproduction traits, such as gestation length (GLE), play an important role in dam line breeding in pigs. The objective of our study was to identify single nucleotide polymorphisms (SNPs) that are associated with GLE in two pig populations. Genotypes and deregressed breeding values were available for 2081 Dutch Landrace-based (DL) and 2301 Large White-based (LW) pigs. We identified two QTL regions for GLE, one in each population. For DL, three associated SNPs were detected in one QTL region spanning 0.52 Mbp on Sus scrofa chromosome (SSC) 2. For LW, four associated SNPs were detected in one region of 0.14 Mbp on SSC5. The region on SSC2 contains the heparin-binding EGF-like growth factor (HBEGF) gene, which promotes embryo implantation and has been described to be involved in embryo survival throughout gestation. The associated SNP can be used for marker-assisted selection in the studied populations, and further studies of the HBEGF gene are warranted to investigate its role in GLE. © 2015 Stichting International Foundation for Animal Genetics.

Development of Novel SSR Markers for Flax (Linum usitatissimum L.) Using Reduced-Representation Genome Sequencing

PubMed Central

Wu, Jianzhong; Zhao, Qian; Wu, Guangwen; Zhang, Shuquan; Jiang, Tingbo

2017-01-01

Flax (Linum usitatissimum L.) is a major fiber and oil yielding crop grown in northeastern China. Identification of flax molecular markers is a key step toward improving flax yield and quality via marker-assisted breeding. Simple sequence repeat (SSR) markers, which are based on genomic structural variation, are considered the most valuable type of genetic marker for this purpose. In this study, we screened 1574 microsatellites from Linum usitatissimum L. obtained using reduced representation genome sequencing (RRGS) to systematically identify SSR markers. The resulting set of microsatellites consisted mainly of trinucleotide (56.10%) and dinucleotide (35.23%) repeats, with each motif consisting of 5–8 repeats. We then evaluated marker sensitivity and specificity based on samples of 48 flax isolates obtained from northeastern China. Using the new SSR panel, the results demonstrated that fiber flax and oilseed flax varieties clustered into two well separated groups. The novel SSR markers developed in this study show potential value for selection of varieties for use in flax breeding programs. PMID:28133461

Economic weights for maternal traits of sows, including sow longevity.

PubMed

Amer, P R; Ludemann, C I; Hermesch, S

2014-12-01

The objective of this study was to develop a transparent, comprehensive, and flexible model for each trait for the formulation of breeding objectives for sow traits in swine breeding programs. Economic values were derived from submodels considering a typical Australian pig production system. Differences in timing and expressions of traits were accounted for to derive economic weights that were compared on the basis of their relative size after multiplication by their corresponding genetic standard deviation to account for differences in scale and genetic variability present for each trait. The number of piglets born alive had the greatest contribution (27.1%) to a subindex containing only maternal traits, followed by daily gain (maternal; 22.0%) and sow mature weight (15.0%). Other traits considered in the maternal breeding objective were preweaning survival (11.8%), sow longevity (12.5%), gilt age at puberty (8.7%), and piglet survival at birth (3.1%). The economic weights for number of piglets born alive and preweaning piglet survival were found to be highly dependent on the definition of scale of enterprise, with each economic value increasing by approximately 100% when it was assumed that the value of extra output per sow could be captured, rather than assuming a consequent reduction in the number of sows to maintain a constant level of output from a farm enterprise. In the context of a full maternal line index that must account also for the expression of direct genetic traits by the growing piglet progeny of sows, the maternal traits contributed approximately half of the variation in the overall breeding objective. Deployment of more comprehensive maternal line indexes incorporating the new maternal traits described would lead to more balanced selection outcomes and improved survival of pigs. Future work could facilitate evaluation of the economic impacts of desired-gains indexes, which could further improve animal welfare through improved sow and piglet survival. The results justify further development of selection criteria and breeding value prediction systems for a wider range of maternal traits relevant to pig production systems.

Evaluation of approaches for estimating the accuracy of genomic prediction in plant breeding

PubMed Central

2013-01-01

Background In genomic prediction, an important measure of accuracy is the correlation between the predicted and the true breeding values. Direct computation of this quantity for real datasets is not possible, because the true breeding value is unknown. Instead, the correlation between the predicted breeding values and the observed phenotypic values, called predictive ability, is often computed. In order to indirectly estimate predictive accuracy, this latter correlation is usually divided by an estimate of the square root of heritability. In this study we use simulation to evaluate estimates of predictive accuracy for seven methods, four (1 to 4) of which use an estimate of heritability to divide predictive ability computed by cross-validation. Between them the seven methods cover balanced and unbalanced datasets as well as correlated and uncorrelated genotypes. We propose one new indirect method (4) and two direct methods (5 and 6) for estimating predictive accuracy and compare their performances and those of four other existing approaches (three indirect (1 to 3) and one direct (7)) with simulated true predictive accuracy as the benchmark and with each other. Results The size of the estimated genetic variance and hence heritability exerted the strongest influence on the variation in the estimated predictive accuracy. Increasing the number of genotypes considerably increases the time required to compute predictive accuracy by all the seven methods, most notably for the five methods that require cross-validation (Methods 1, 2, 3, 4 and 6). A new method that we propose (Method 5) and an existing method (Method 7) used in animal breeding programs were the fastest and gave the least biased, most precise and stable estimates of predictive accuracy. Of the methods that use cross-validation Methods 4 and 6 were often the best. Conclusions The estimated genetic variance and the number of genotypes had the greatest influence on predictive accuracy. Methods 5 and 7 were the fastest and produced the least biased, the most precise, robust and stable estimates of predictive accuracy. These properties argue for routinely using Methods 5 and 7 to assess predictive accuracy in genomic selection studies. PMID:24314298

Computational strategies for alternative single-step Bayesian regression models with large numbers of genotyped and non-genotyped animals.

PubMed

Fernando, Rohan L; Cheng, Hao; Golden, Bruce L; Garrick, Dorian J

2016-12-08

Two types of models have been used for single-step genomic prediction and genome-wide association studies that include phenotypes from both genotyped animals and their non-genotyped relatives. The two types are breeding value models (BVM) that fit breeding values explicitly and marker effects models (MEM) that express the breeding values in terms of the effects of observed or imputed genotypes. MEM can accommodate a wider class of analyses, including variable selection or mixture model analyses. The order of the equations that need to be solved and the inverses required in their construction vary widely, and thus the computational effort required depends upon the size of the pedigree, the number of genotyped animals and the number of loci. We present computational strategies to avoid storing large, dense blocks of the MME that involve imputed genotypes. Furthermore, we present a hybrid model that fits a MEM for animals with observed genotypes and a BVM for those without genotypes. The hybrid model is computationally attractive for pedigree files containing millions of animals with a large proportion of those being genotyped. We demonstrate the practicality on both the original MEM and the hybrid model using real data with 6,179,960 animals in the pedigree with 4,934,101 phenotypes and 31,453 animals genotyped at 40,214 informative loci. To complete a single-trait analysis on a desk-top computer with four graphics cards required about 3 h using the hybrid model to obtain both preconditioned conjugate gradient solutions and 42,000 Markov chain Monte-Carlo (MCMC) samples of breeding values, which allowed making inferences from posterior means, variances and covariances. The MCMC sampling required one quarter of the effort when the hybrid model was used compared to the published MEM. We present a hybrid model that fits a MEM for animals with genotypes and a BVM for those without genotypes. Its practicality and considerable reduction in computing effort was demonstrated. This model can readily be extended to accommodate multiple traits, multiple breeds, maternal effects, and additional random effects such as polygenic residual effects.

Estimation of genetic parameters and breeding values across challenged environments to select for robust pigs.

PubMed

Herrero-Medrano, J M; Mathur, P K; ten Napel, J; Rashidi, H; Alexandri, P; Knol, E F; Mulder, H A

2015-04-01

Robustness is an important issue in the pig production industry. Since pigs from international breeding organizations have to withstand a variety of environmental challenges, selection of pigs with the inherent ability to sustain their productivity in diverse environments may be an economically feasible approach in the livestock industry. The objective of this study was to estimate genetic parameters and breeding values across different levels of environmental challenge load. The challenge load (CL) was estimated as the reduction in reproductive performance during different weeks of a year using 925,711 farrowing records from farms distributed worldwide. A wide range of levels of challenge, from favorable to unfavorable environments, was observed among farms with high CL values being associated with confirmed situations of unfavorable environment. Genetic parameters and breeding values were estimated in high- and low-challenge environments using a bivariate analysis, as well as across increasing levels of challenge with a random regression model using Legendre polynomials. Although heritability estimates of number of pigs born alive were slightly higher in environments with extreme CL than in those with intermediate levels of CL, the heritabilities of number of piglet losses increased progressively as CL increased. Genetic correlations among environments with different levels of CL suggest that selection in environments with extremes of low or high CL would result in low response to selection. Therefore, selection programs of breeding organizations that are commonly conducted under favorable environments could have low response to selection in commercial farms that have unfavorable environmental conditions. Sows that had experienced high levels of challenge at least once during their productive life were ranked according to their EBV. The selection of pigs using EBV ignoring environmental challenges or on the basis of records from only favorable environments resulted in a sharp decline in productivity as the level of challenge increased. In contrast, selection using the random regression approach resulted in limited change in productivity with increasing levels of challenge. Hence, we demonstrate that the use of a quantitative measure of environmental CL and a random regression approach can be comprehensively combined for genetic selection of pigs with enhanced ability to maintain high productivity in harsh environments.

Evaluation of approaches for estimating the accuracy of genomic prediction in plant breeding.

PubMed

Ould Estaghvirou, Sidi Boubacar; Ogutu, Joseph O; Schulz-Streeck, Torben; Knaak, Carsten; Ouzunova, Milena; Gordillo, Andres; Piepho, Hans-Peter

2013-12-06

In genomic prediction, an important measure of accuracy is the correlation between the predicted and the true breeding values. Direct computation of this quantity for real datasets is not possible, because the true breeding value is unknown. Instead, the correlation between the predicted breeding values and the observed phenotypic values, called predictive ability, is often computed. In order to indirectly estimate predictive accuracy, this latter correlation is usually divided by an estimate of the square root of heritability. In this study we use simulation to evaluate estimates of predictive accuracy for seven methods, four (1 to 4) of which use an estimate of heritability to divide predictive ability computed by cross-validation. Between them the seven methods cover balanced and unbalanced datasets as well as correlated and uncorrelated genotypes. We propose one new indirect method (4) and two direct methods (5 and 6) for estimating predictive accuracy and compare their performances and those of four other existing approaches (three indirect (1 to 3) and one direct (7)) with simulated true predictive accuracy as the benchmark and with each other. The size of the estimated genetic variance and hence heritability exerted the strongest influence on the variation in the estimated predictive accuracy. Increasing the number of genotypes considerably increases the time required to compute predictive accuracy by all the seven methods, most notably for the five methods that require cross-validation (Methods 1, 2, 3, 4 and 6). A new method that we propose (Method 5) and an existing method (Method 7) used in animal breeding programs were the fastest and gave the least biased, most precise and stable estimates of predictive accuracy. Of the methods that use cross-validation Methods 4 and 6 were often the best. The estimated genetic variance and the number of genotypes had the greatest influence on predictive accuracy. Methods 5 and 7 were the fastest and produced the least biased, the most precise, robust and stable estimates of predictive accuracy. These properties argue for routinely using Methods 5 and 7 to assess predictive accuracy in genomic selection studies.

Measurement of Tear Production in English Angora and Dutch Rabbits

PubMed Central

Rajaei, Seyed Mehdi; Rafiee, Siamak Mashhady; Ghaffari, Masoud Selk; Masouleh, Mohammad N; Jamshidian, Mahmoud

2016-01-01

The purpose of this study was to establish normal values for tear production tests in different breeds of domestic rabbits. Healthy adult rabbits (n = 60; 120 eyes) of 2 different breeds (English angora and Dutch; n = 15 of each sex and breed) were used in this study. Tear production was measured by using the 1-min Schirmer tear test (STT), phenol red thread test (PRTT), and endodontic absorbent paper point tear test (EAPTT). In addition, horizontal palpebral fissure length was evaluated as a measure of ocular adnexal dimensions. Tear production (mean ± 1 SD) in English angora rabbits was 5.4 ± 1.6 mm/min according to the STT, 25.0 ± 2.7 mm in 15 s for the PRTT, and 18.8 ± 2.1 mm/min by the EAPTT; in Dutch rabbits, these values were 4.6 ± 1.2 mm/min, 23.6 ± 2.3 mm in 15 s, and 16.9 ± 1.7 mm/min, respectively. Only the EAPTT revealed a significant difference in tear production between English Angora and Dutch rabbits. These results provide reference values for tear production in English Angora and Dutch rabbits according to 3 different quantitative tear film assessment methods. PMID:27025815

Genetic value of herd life adjusted for milk production.

PubMed

Allaire, F R; Gibson, J P

1992-05-01

Cow herd life adjusted for lactational milk production was investigated as a genetic trait in the breeding objective. Under a simple model, the relative economic weight of milk to adjusted herd life on a per genetic standard deviation basis was equal to CVY/dCVL where CVY and CVL are the genetic coefficients of variation of milk production and adjusted herd life, respectively, and d is the depreciation per year per cow divided by the total fixed costs per year per cow. The relative economic value of milk to adjusted herd life at the prices and parameters for North America was about 3.2. An increase of 100-kg milk was equivalent to 2.2 mo of adjusted herd life. Three to 7% lower economic gain is expected when only improved milk production is sought compared with a breeding objective that included both production and adjusted herd life for relative value changed +/- 20%. A favorable economic gain to cost ratio probably exists for herd life used as a genetic trait to supplement milk in the breeding objective. Cow survival records are inexpensive, and herd life evaluations from such records may not extend the generation interval when such an evaluation is used in bull sire selection.

Individual migration timing of common nightingales is tuned with vegetation and prey phenology at breeding sites.

PubMed

Emmenegger, Tamara; Hahn, Steffen; Bauer, Silke

2014-03-21

The timing of migration substantially influences individual fitness. To match peak requirements with peak resource availability, we hypothesized that individual migrants schedule spring migration in close relation to seasonal changes in environmental conditions along the route and particularly, at the breeding destination.To test this hypothesis, we investigated the timing of spring migration in male common nightingales Luscinia megarhynchos, a small Palearctic-African long-distance migrant, by linking spring migration timing to the phenology of local environmental conditions at non-breeding migratory stopover and breeding sites. In particular, we related individual migration decisions (i.e. departure and arrival) of nine males to site-specific vegetation phenology (based on remotely sensed vegetation index) and a proxy of food availability (based on insects' thermal requirements). We found weak relation of departures from non-breeding and no relation of stopover timing with local phenology. However, our results showed that individuals, which departed early from their non-breeding sites and arrived early at the breeding site closely matched spring green-up there. Early arrival at the breeding site meant also a close match with peak food availability for adults and in a time-lagged manner, for offspring. Our findings suggest that male nightingale used cues other than local phenology for their departure decisions from non-breeding grounds and that there is some evidence for equalizing late departures during the course of migration.

Hematologic values of the yucatan miniature pig.

PubMed

Parsons, A H; Wells, R E

1998-01-01

Mean values and ranges for 16 hematological parameters for healthy, young, sexually-mature Yucatan miniature swine are presented. No significant differences were observed between sexes with regard to hemograms. Comparison of observed values with those published in the literature for standard domestic and other breeds of miniature swine reveals no major differences.

Breed distribution and history of canine mdr1-1Δ, a pharmacogenetic mutation that marks the emergence of breeds from the collie lineage

PubMed Central

Neff, Mark W.; Robertson, Kathryn R.; Wong, Aaron K.; Safra, Noa; Broman, Karl W.; Slatkin, Montgomery; Mealey, Katrina L.; Pedersen, Niels C.

2004-01-01

A mutation in the canine multidrug resistance gene, MDR1, has previously been associated with drug sensitivities in two breeds from the collie lineage. We exploited breed phylogeny and reports of drug sensitivity to survey other purebred populations that might be genetically at risk. We found that the same allele, mdr1-1Δ, segregated in seven additional breeds, including two sighthounds that were not expected to share collie ancestry. A mutant haplotype that was conserved among affected breeds indicated that the allele was identical by descent. Based on breed histories and the extent of linkage disequilibrium, we conclude that all dogs carrying mdr1-1Δ are descendants of a dog that lived in Great Britain before the genetic isolation of breeds by registry (ca. 1873). The breed distribution and frequency of mdr1-1Δ have applications in veterinary medicine and selective breeding, whereas the allele's history recounts the emergence of formally recognized breeds from an admixed population of working sheepdogs. PMID:15289602

Breed distribution and history of canine mdr1-1Delta, a pharmacogenetic mutation that marks the emergence of breeds from the collie lineage.

PubMed

Neff, Mark W; Robertson, Kathryn R; Wong, Aaron K; Safra, Noa; Broman, Karl W; Slatkin, Montgomery; Mealey, Katrina L; Pedersen, Niels C

2004-08-10

A mutation in the canine multidrug resistance gene, MDR1, has previously been associated with drug sensitivities in two breeds from the collie lineage. We exploited breed phylogeny and reports of drug sensitivity to survey other purebred populations that might be genetically at risk. We found that the same allele, mdr1-1Delta, segregated in seven additional breeds, including two sighthounds that were not expected to share collie ancestry. A mutant haplotype that was conserved among affected breeds indicated that the allele was identical by descent. Based on breed histories and the extent of linkage disequilibrium, we conclude that all dogs carrying mdr1-1Delta are descendants of a dog that lived in Great Britain before the genetic isolation of breeds by registry (ca. 1873). The breed distribution and frequency of mdr1-1Delta have applications in veterinary medicine and selective breeding, whereas the allele's history recounts the emergence of formally recognized breeds from an admixed population of working sheepdogs.

Supplemental Environmental Assessment (EA) for the Vernal Pool Restoration Project in Wing Infrastructure Development Outlook (WINDO) Implementation Plan EA, Volume 2 Beale Air Force Base, California

DTIC Science & Technology

2010-09-01

Mineral resources include metals, industrial minerals (e.g., aggregate, sand and gravel), oil and gas, and geothermal resources that would be of value...the elderberry shrub ( Sambucus sp.), is not present within the project action area. The proposed project is not likely to adversely affect the bald...impairing essential behavioral patterns, including breeding, feeding, or sheltering. Harass is defined by the Service as an action that creates the

Evaluation of inbreeding in laying hens by applying optimum genetic contribution and gene flow theory.

PubMed

König, S; Tsehay, F; Sitzenstock, F; von Borstel, U U; Schmutz, M; Preisinger, R; Simianer, H

2010-04-01

Due to consistent increases of inbreeding of on average 0.95% per generation in layer populations, selection tools should consider both genetic gain and genetic relationships in the long term. The optimum genetic contribution theory using official estimated breeding values for egg production was applied for 3 different lines of a layer breeding program to find the optimal allocations of hens and sires. Constraints in different scenarios encompassed restrictions related to additive genetic relationships, the increase of inbreeding, the number of selected sires and hens, and the number of selected offspring per mating. All these constraints enabled higher genetic gain up to 10.9% at the same level of additive genetic relationships or in lower relationships at the same gain when compared with conventional selection schemes ignoring relationships. Increases of inbreeding and genetic gain were associated with the number of selected sires. For the lowest level of the allowed average relationship at 10%, the optimal number of sires was 70 and the estimated breeding value for egg production of the selected group was 127.9. At the highest relationship constraint (16%), the optimal number of sires decreased to 15, and the average genetic value increased to 139.7. Contributions from selected sires and hens were used to develop specific mating plans to minimize inbreeding in the following generation by applying a simulated annealing algorithm. The additional reduction of average additive genetic relationships for matings was up to 44.9%. An innovative deterministic approach to estimate kinship coefficients between and within defined selection groups based on gene flow theory was applied to compare increases of inbreeding from random matings with layer populations undergoing selection. Large differences in rates of inbreeding were found, and they underline the necessity to establish selection tools controlling long-term relationships. Furthermore, it was suggested to use optimum genetic contribution theory for conservation schemes or, for example, the experimental line in our study.

Estimates of genetic parameters and eigenvector indices for milk production of Holstein cows.

PubMed

Savegnago, R P; Rosa, G J M; Valente, B D; Herrera, L G G; Carneiro, R L R; Sesana, R C; El Faro, L; Munari, D P

2013-01-01

The objectives of the present study were to estimate genetic parameters of monthly test-day milk yield (TDMY) of the first lactation of Brazilian Holstein cows using random regression (RR), and to compare the genetic gains for milk production and persistency, derived from RR models, using eigenvector indices and selection indices that did not consider eigenvectors. The data set contained monthly TDMY of 3,543 first lactations of Brazilian Holstein cows calving between 1994 and 2011. The RR model included the fixed effect of the contemporary group (herd-month-year of test days), the covariate calving age (linear and quadratic effects), and a fourth-order regression on Legendre orthogonal polynomials of days in milk (DIM) to model the population-based mean curve. Additive genetic and nongenetic animal effects were fit as RR with 4 classes of residual variance random effect. Eigenvector indices based on the additive genetic RR covariance matrix were used to evaluate the genetic gains of milk yield and persistency compared with the traditional selection index (selection index based on breeding values of milk yield until 305 DIM). The heritability estimates for monthly TDMY ranged from 0.12 ± 0.04 to 0.31 ± 0.04. The estimates of additive genetic and nongenetic animal effects correlation were close to 1 at adjacent monthly TDMY, with a tendency to diminish as the time between DIM classes increased. The first eigenvector was related to the increase of the genetic response of the milk yield and the second eigenvector was related to the increase of the genetic gains of the persistency but it contributed to decrease the genetic gains for total milk yield. Therefore, using this eigenvector to improve persistency will not contribute to change the shape of genetic curve pattern. If the breeding goal is to improve milk production and persistency, complete sequential eigenvector indices (selection indices composite with all eigenvectors) could be used with higher economic values for persistency. However, if the breeding goal is to improve only milk yield, the traditional selection index is indicated. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Building the case for a novel teleost model of non-breeding aggression and its neuroendocrine control.

PubMed

Quintana, Laura; Zubizarreta, Lucía; Jalabert, Cecilia; Batista, Gervasio; Perrone, Rossana; Silva, Ana

2016-10-01

In vertebrates, aggression has been traditionally associated with high levels of circulating androgens in breeding males. Nevertheless, the centrality of androgens as primary modulators of aggression is being reconsidered in at least in two particular cases: (1) territorial aggression outside the breeding season, and (2) aggression by females. We are developing the weakly electric fish, Gymnotus omarorum, as a novel, advantageous model system to address these two alternative forms of aggression. This species displays a short, escalated contest, after which a clear hierarchical status emerges. Subordination of individuals involves three sequential decisions: interruptions of their electric discharges, retreats, and chirps. These decisions are influenced by both size asymmetry between contenders and aggression levels of dominants. Both females and males are aggressive, and do not differ in fighting ability nor in the value placed on the resource. Aggression is completely independent of gonadal hormones: dominance status is unrelated to circulating androgen and estrogen levels, and gonadectomy in males does not affect aggression. Nevertheless, estrogenic pathways participate in the modulation of this non-breeding aggression. Our results parallel those put forth in other taxa, heightening the value of G. omarorum as a model to identify commonalities in neuroendrocrine strategies of vertebrate aggression control. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular Genetic Diversity of the Gyeongju Donggyeong Dog in Korea

PubMed Central

LEE, Eun-Woo; CHOI, Seong-Kyoon; CHO, Gil-Jae

2014-01-01

ABSTRACT The present study was conducted to analyze the genetic characteristics of the Donggyeong dog and establish parentage conservation systems for it by using 10 microsatellite markers recommended by the International Society for Animal Genetics (ISAG). A total of 369 dogs from 12 dog breeds including the Donggyeong dog were genotyped using 10 microsatellite loci. The number of alleles per locus varied from 5 to 10 with a mean value of 7.6 in the Donggyeong dog. The observed heterozygosity and expected heterozygosity ranged from 0.4706 to 0.9020 (mean 0.7657) and from 0.4303 to 0.8394 (mean 0.7266), respectively. The total exclusion probability of 10 microsatellite loci was 0.99955. Of the 10 microsatellite markers, the AHT121, AHTh260 and CXX279 markers had relatively high PIC values (≥0.7). This study found that there were specific alleles, 116 allele at AHT121 in the Donggyeong dog when compared with other dog breeds. Also, the results showed two (Korean native dogs and the foreign dog breeds) distinct clusters. The closest distance (0.1184) was observed between the Donggyeong dog and Jindo dog, and the longest distance (0.3435) was observed between the Donggyeong dog and Bulgae. The Korean native dog breeds have comparatively near genetic distances between each other. PMID:25030603

Rethinking dog domestication by integrating genetics, archeology, and biogeography

PubMed Central

Larson, Greger; Karlsson, Elinor K.; Perri, Angela; Webster, Matthew T.; Ho, Simon Y. W.; Peters, Joris; Stahl, Peter W.; Piper, Philip J.; Lingaas, Frode; Fredholm, Merete; Comstock, Kenine E.; Modiano, Jaime F.; Schelling, Claude; Agoulnik, Alexander I.; Leegwater, Peter A.; Dobney, Keith; Vigne, Jean-Denis; Vilà, Carles; Andersson, Leif; Lindblad-Toh, Kerstin

2012-01-01

The dog was the first domesticated animal but it remains uncertain when the domestication process began and whether it occurred just once or multiple times across the Northern Hemisphere. To ascertain the value of modern genetic data to elucidate the origins of dog domestication, we analyzed 49,024 autosomal SNPs in 1,375 dogs (representing 35 breeds) and 19 wolves. After combining our data with previously published data, we contrasted the genetic signatures of 121 breeds with a worldwide archeological assessment of the earliest dog remains. Correlating the earliest archeological dogs with the geographic locations of 14 so-called “ancient” breeds (defined by their genetic differentiation) resulted in a counterintuitive pattern. First, none of the ancient breeds derive from regions where the oldest archeological remains have been found. Second, three of the ancient breeds (Basenjis, Dingoes, and New Guinea Singing Dogs) come from regions outside the natural range of Canis lupus (the dog’s wild ancestor) and where dogs were introduced more than 10,000 y after domestication. These results demonstrate that the unifying characteristic among all genetically distinct so-called ancient breeds is a lack of recent admixture with other breeds likely facilitated by geographic and cultural isolation. Furthermore, these genetically distinct ancient breeds only appear so because of their relative isolation, suggesting that studies of modern breeds have yet to shed light on dog origins. We conclude by assessing the limitations of past studies and how next-generation sequencing of modern and ancient individuals may unravel the history of dog domestication. PMID:22615366

Genetic and economic evaluation of Japanese Black (Wagyu) cattle breeding schemes.

PubMed

Kahi, A K; Hirooka, H

2005-09-01

Deterministic simulation was used to evaluate 10 breeding schemes for genetic gain and profitability and in the context of maximizing returns from investment in Japanese Black cattle breeding. A breeding objective that integrated the cow-calf and feedlot segments was considered. Ten breeding schemes that differed in the records available for use as selection criteria were defined. The schemes ranged from one that used carcass traits currently available to Japanese Black cattle breeders (Scheme 1) to one that also included linear measurements and male and female reproduction traits (Scheme 10). The latter scheme represented the highest level of performance recording. In all breeding schemes, sires were chosen from the proportion selected during the first selection stage (performance testing), modeling a two-stage selection process. The effect on genetic gain and profitability of varying test capacity and number of progeny per sire and of ultrasound scanning of live animals was examined for all breeding schemes. Breeding schemes that selected young bulls during performance testing based on additional individual traits and information on carcass traits from their relatives generated additional genetic gain and profitability. Increasing test capacity resulted in an increase in genetic gain in all schemes. Profitability was optimal in Scheme 2 (a scheme similar to Scheme 1, but selection of young bulls also was based on information on carcass traits from their relatives) to 10 when 900 to 1,000 places were available for performance testing. Similarly, as the number of progeny used in the selection of sires increased, genetic gain first increased sharply and then gradually in all schemes. Profit was optimal across all breeding schemes when sires were selected based on information from 150 to 200 progeny. Additional genetic gain and profitability were generated in each breeding scheme with ultrasound scanning of live animals for carcass traits. Ultrasound scanning of live animals was more important than the addition of any other traits in the selection criteria. These results may be used to provide guidance to Japanese Black cattle breeders.

Effectiveness of controlled internal drug release device treatment to alleviate reproductive seasonality in anestrus lactating or dry Barki and Rahmani ewes during non-breeding season.

PubMed

El-Mokadem, M Y; Nour El-Din, Anm; Ramadan, T A; Rashad, A M; Taha, T A; Samak, M A; Salem, M H

2018-04-01

This study aimed to evaluate the effectiveness of hormonal treatments on ovarian activity and reproductive performance in Barki and Rahmani ewes during non-breeding season. Forty-eight multiparous ewes, 24 Barki and 24 Rahmani ewes were divided into two groups, 12 lactating and 12 dry ewes for each breed. Controlled internal drug release (CIDR) device was inserted in all ewes for 14 days in conjunction with intramuscular 500 IU equine chronic gonadotrophin (eCG) at day of CIDR removal. Data were analysed using PROC MIXED of SAS for repeated measures. Breed, physiological status and days were used as fixed effects and individual ewes as random effects. Barki ewes recorded higher (p < .05) total number of follicles, number of large follicles, serum estradiol concentration and estradiol: progesterone (E 2 :P 4 ) ratio compared to Rahmani ewes. Lactating ewes recorded higher (p < .05) number of small follicles and lower concentration of total antioxidant capacity (TAC) compared to dry ewes. Number and diameter of large follicles recorded the highest (p < .05) values accompanied with disappearance of corpora lutea at day of mating. Serum progesterone concentration recorded lower (p < .05) value at day of mating and the highest (p < .05) value at day 35 after mating. CIDR-eCG protocol induced 100% oestrous behaviour in both breeds, but Rahmani ewes recorded longer (p < .05) oestrous duration compared to Barki. Conception failure was higher (p < .05) in Barki compared to Rahmani ewes. In conclusion, CIDR-eCG protocol was more potent in improving ovarian activity in Barki compared to Rahmani ewes, but this protocol seems to induce hormonal imbalance in Barki ewes that resulted in increasing conception failure compared to Rahmani ewes. © 2017 Blackwell Verlag GmbH.

Effects of transportation during the hot season, breed and electrical stimulation on histochemical and meat quality characteristics of goat longissimus muscle.

PubMed

Kadim, Isam T; Mahgoub, Osman; Al-Marzooqi, Waleed; Khalaf, Samera; Al-Sinawi, Shadia S H; Al-Amri, Issa

2010-06-01

The effects of transportation and electrical stimulation (90 V) on physiological, histochemical and meat quality characteristics of two breeds of Omani goats were assessed. Twenty 1-year-old male goats from each breed (Batina and Dhofari) were divided into two groups: 3 h transported during the hot season (42 degrees C day time temperature) and non-transported. Animals were blood-sampled before loading and prior to slaughter. Electrical stimulation was applied 20 min postmortem to 50% randomly selected carcasses of both breeds. Temperature and pH decline of the Longissimus was monitored. Ultimate pH, shear force, sarcomere length, myofibrillar fragmentation index, expressed juice, cooking loss and colour were measured from samples of Longissimus dorsi muscles. Electrical stimulation and transportation had a significant effect on most biochemical and meat quality characteristics of Longissimus dorsi. The transported goats had higher plasma cortisol (P < 0.01), adrenaline, nor-adrenaline and dopamine concentrations (P < 0.05) than non-transported goats. Electrical stimulation resulted in a significantly (P < 0.05) more rapid muscle pH fall during the first 12 h after slaughter. Muscles from electrically-stimulated carcasses had significantly (P < 0.05) longer sarcomeres, lower shear force value, a lighter colour (higher L* value), higher expressed juice and myofibrillar fragmentation index than those from non-stimulated ones. Meat from transported goats had significantly higher pH, expressed juice and shear force, but contained significantly lower sarcomere length and L* values than non-transported goats. The proportion of the myosin ATPase staining did not change as a function of stimulation, transportation or breed. These results indicated that subjecting goats to transportation for 3 h under high ambient temperatures can generate major physiological and muscle metabolism responses. Electrical stimulation improved quality characteristics of meat from both groups. This indicates that electrical stimulation may reduce detrimental effects of transportation on meat quality of Omani goats.

Breeding objectives for pigs in Kenya. II: economic values incorporating risks in different smallholder production systems.

PubMed

Mbuthia, Jackson Mwenda; Rewe, Thomas Odiwuor; Kahi, Alexander Kigunzu

2015-02-01

This study estimated economic values for production traits (dressing percentage (DP), %; live weight for growers (LWg), kg; live weight for sows (LWs), kg) and functional traits (feed intake for growers (FEEDg), feed intake for sow (FEEDs), preweaning survival rate (PrSR), %; postweaning survival (PoSR), %; sow survival rate (SoSR), %, total number of piglets born (TNB) and farrowing interval (FI), days) under different smallholder pig production systems in Kenya. Economic values were estimated considering two production circumstances: fixed-herd and fixed-feed. Under the fixed-herd scenario, economic values were estimated assuming a situation where the herd cannot be increased due to other constraints apart from feed resources. The fixed-feed input scenario assumed that the herd size is restricted by limitation of feed resources available. In addition to the tradition profit model, a risk-rated bio-economic model was used to derive risk-rated economic values. This model accounted for imperfect knowledge concerning risk attitude of farmers and variance of input and output prices. Positive economic values obtained for traits DP, LWg, LWs, PoSR, PrSR, SoSR and TNB indicate that targeting them in improvement would positively impact profitability in pig breeding programmes. Under the fixed-feed basis, the risk-rated economic values for DP, LWg, LWs and SoSR were similar to those obtained under the fixed-herd situation. Accounting for risks in the EVs did not yield errors greater than ±50 % in all the production systems and basis of evaluation meaning there would be relatively little effect on the real genetic gain of a selection index. Therefore, both traditional and risk-rated models can be satisfactorily used to predict profitability in pig breeding programmes.

Breeds of risk-adjusted fundamentalist strategies in an order-driven market

NASA Astrophysics Data System (ADS)

LiCalzi, Marco; Pellizzari, Paolo

2006-01-01

This paper studies an order-driven stock market where agents have heterogeneous estimates of the fundamental value of the risky asset. The agents are budget-constrained and follow a value-based trading strategy which buys or sells depending on whether the price of the asset is below or above its risk-adjusted fundamental value. This environment generates returns that are remarkably leptokurtic and fat-tailed. By extending the study over a grid of different parameters for the fundamentalist trading strategy, we exhibit the existence of monotone relationships between the bid-ask spread demanded by the agents and several statistics of the returns. We conjecture that this effect, coupled with positive dependence of the risk premium on the volatility, generates positive feedbacks that might explain volatility bursts.

Conservation priorities for the different lines of Dutch Red and White Friesian cattle change when relationships with other breeds are taken into account.

PubMed

Hulsegge, B; Calus, M P L; Oldenbroek, J K; Windig, J J

2017-02-01

From a genetic point of view, the selection of breeds and animals within breeds for conservation in a national gene pool can be based on a maximum diversity strategy. This implies that priority is given to conservation of breeds and animals that diverge most and overlap of conserved diversity is minimized. This study investigated the genetic diversity in the Dutch Red and White Friesian (DFR) cattle breed and its contribution to the total genetic diversity in the pool of the Dutch dairy breeds. All Dutch cattle breeds are clearly distinct, except for Dutch Friesian breed (DF) and DFR and have their own specific genetic identity. DFR has a small but unique contribution to the total genetic diversity of Dutch cattle breeds and is closely related to the Dutch Friesian breed. Seven different lines are distinguished within the DFR breed and all contribute to the diversity of the DFR breed. Two lines show the largest contributions to the genetic diversity in DFR. One of these lines comprises unique diversity both within the breed and across all cattle breeds. The other line comprises unique diversity for the DFR but overlaps with the Holstein Friesian breed. There seems to be no necessity to conserve the other five lines separately, because their level of differentiation is very low. This study illustrates that, when taking conservation decisions for a breed, it is worthwhile to take into account the population structure of the breed itself and the relationships with other breeds. © 2016 Blackwell Verlag GmbH.

Breed base representation in dairy animals of 5 breeds

USDA-ARS?s Scientific Manuscript database

Inheritance of DNA from different dairy breeds can be determined by genotyping, just as individual ancestors such as parents, grandparents, or even great grandparents can be identified correctly in a high percentage of the cases by genotyping even if not reported or reported incorrectly in pedigrees...

Breed-specific incidence rates of canine primary bone tumors — A population based survey of dogs in Norway

PubMed Central

Anfinsen, Kristin P.; Grotmol, Tom; Bruland, Oyvind S.; Jonasdottir, Thora J.

2011-01-01

This is one of few published population-based studies describing breed specific rates of canine primary bone tumors. Incidence rates related to dog breeds could help clarify the impact of etiological factors such as birth weight, growth rate, and adult body weight/height on development of these tumors. The study population consisted of dogs within 4 large/giant breeds; Irish wolfhound (IW), Leonberger (LB), Newfoundland (NF), and Labrador retriever (LR), born between January 1st 1989 and December 31st 1998. Questionnaires distributed to owners of randomly selected dogs — fulfilling the criteria of breed, year of birth, and registration in the Norwegian Kennel Club — constituted the basis for this retrospective, population-based survey. Of the 3748 questionnaires received by owners, 1915 were completed, giving a response rate of 51%. Forty-three dogs had been diagnosed with primary bone tumors, based upon clinical examination and x-rays. The breeds IW and LB, with 126 and 72 cases per 10 000 dog years at risk (DYAR), respectively, had significantly higher incidence rates of primary bone tumors than NF and LR (P < 0.0001). Incidence rates for the latter were 11 and 2 cases per 10 000 DYAR, respectively. Pursuing a search for risk factors other than body size/weight is supported by the significantly different risks of developing primary bone tumors between similarly statured dogs, like NF and LB, observed in this study. Defining these breed-specific incidence rates enables subsequent case control studies, ultimately aiming to identify specific etiological factors for developing primary bone tumors. PMID:22210997

Genetic Variation and Combining Ability Analysis of Bruising Sensitivity in Agaricus bisporus

PubMed Central

Gao, Wei; Baars, Johan J. P.; Dolstra, Oene; Visser, Richard G. F.; Sonnenberg, Anton S. M.

2013-01-01

Advanced button mushroom cultivars that are less sensitive to mechanical bruising are required by the mushroom industry, where automated harvesting still cannot be used for the fresh mushroom market. The genetic variation in bruising sensitivity (BS) of Agaricus bisporus was studied through an incomplete set of diallel crosses to get insight in the heritability of BS and the combining ability of the parental lines used and, in this way, to estimate their breeding value. To this end nineteen homokaryotic lines recovered from wild strains and cultivars were inter-crossed in a diallel scheme. Fifty-one successful hybrids were grown under controlled conditions, and the BS of these hybrids was assessed. BS was shown to be a trait with a very high heritability. The results also showed that brown hybrids were generally less sensitive to bruising than white hybrids. The diallel scheme allowed to estimate the general combining ability (GCA) for each homokaryotic parental line and to estimate the specific combining ability (SCA) of each hybrid. The line with the lowest GCA is seen as the most attractive donor for improving resistance to bruising. The line gave rise to hybrids sensitive to bruising having the highest GCA value. The highest negative SCA possibly indicates heterosis effects for resistance to bruising. This study provides a foundation for estimating breeding value of parental lines to further study the genetic factors underlying bruising sensitivity and other quality-related traits, and to select potential parental lines for further heterosis breeding. The approach of studying combining ability in a diallel scheme was used for the first time in button mushroom breeding. PMID:24116171

Genetic diversity and genomic signatures of selection among cattle breeds from Siberia, eastern and northern Europe.

PubMed

Iso-Touru, T; Tapio, M; Vilkki, J; Kiseleva, T; Ammosov, I; Ivanova, Z; Popov, R; Ozerov, M; Kantanen, J

2016-12-01

Domestication in the near eastern region had a major impact on the gene pool of humpless taurine cattle (Bos taurus). As a result of subsequent natural and artificial selection, hundreds of different breeds have evolved, displaying a broad range of phenotypic traits. Here, 10 Eurasian B. taurus breeds from different biogeographic and production conditions, which exhibit different demographic histories and have been under artificial selection at various intensities, were investigated using the Illumina BovineSNP50 panel to understand their genetic diversity and population structure. In addition, we scanned genomes from eight breeds for signatures of diversifying selection. Our population structure analysis indicated six distinct breed groups, the most divergent being the Yakutian cattle from Siberia. Selection signals were shared (experimental P-value < 0.01) with more than four breeds on chromosomes 6, 7, 13, 16 and 22. The strongest selection signals in the Yakutian cattle were found on chromosomes 7 and 21, where a miRNA gene and genes related to immune system processes are respectively located. In general, genomic regions indicating selection overlapped with known QTL associated with milk production (e.g. on chromosome 19), reproduction (e.g. on chromosome 24) and meat quality (e.g. on chromosome 7). The selection map created in this study shows that native cattle breeds and their genetic resources represent unique material for future breeding. © 2016 Stichting International Foundation for Animal Genetics.

Genetic diversity within and among four South European native horse breeds based on microsatellite DNA analysis: implications for conservation.

PubMed

Solis, A; Jugo, B M; Mériaux, J C; Iriondo, M; Mazón, L I; Aguirre, A I; Vicario, A; Estomba, A

2005-01-01

In the present study, genetic analyses of diversity and differentiation were performed on four Basque-Navarrese semiferal native horse breeds. In total, 417 animals were genotyped for 12 microsatellite markers. Mean heterozygosity was higher than in other horse breeds, surely as a consequence of management. Although the population size of some of these breeds has declined appreciably in the past century, no genetic bottleneck was detected in any of the breeds, possibly because it was not narrow enough to be detectable. In the phylogenetic tree, the Jaca Navarra breed was very similar to the Pottoka, but appeared to stand in an intermediate position between this and the meat breeds. Assuming that Pottoka is the breed less affected by admixture, the others gradually distanced themselves from it through varying influences from outside breeds, among other factors. In a comparative study with other breeds, the French breeds Ardanais, Comtois, and Breton were the closest to the four native breeds. Three different approaches for evaluating the distribution of genetic diversity were applied. The high intrabreed variability of Euskal Herriko Mendiko Zaldia (EHMZ) was pointed out in these analyses. In our opinion, cultural, economic, and scientific factors should also be considered in the management of these horse breeds.

Overlap in genomic variation associated with milk fat composition in Holstein Friesian and Dutch native dual-purpose breeds.

PubMed

Maurice-Van Eijndhoven, M H T; Bovenhuis, H; Veerkamp, R F; Calus, M P L

2015-09-01

The aim of this study was to identify if genomic variations associated with fatty acid (FA) composition are similar between the Holstein-Friesian (HF) and native dual-purpose breeds used in the Dutch dairy industry. Phenotypic and genotypic information were available for the breeds Meuse-Rhine-Yssel (MRY), Dutch Friesian (DF), Groningen White Headed (GWH), and HF. First, the reliability of genomic breeding values of the native Dutch dual-purpose cattle breeds MRY, DF, and GWH was evaluated using single nucleotide polymorphism (SNP) effects estimated in HF, including all SNP or subsets with stronger associations in HF. Second, the genomic variation of the regions associated with FA composition in HF (regions on Bos taurus autosome 5, 14, and 26), were studied in the different breeds. Finally, similarities in genotype and allele frequencies between MRY, DF, GWH, and HF breeds were assessed for specific regions associated with FA composition. On average across the traits, the highest reliabilities of genomic prediction were estimated for GWH (0.158) and DF (0.116) when the 8 to 22 SNP with the strongest association in HF were included. With the same set of SNP, GEBV for MRY were the least reliable (0.022). This indicates that on average only 2 (MRY) to 16% (GWH) of the genomic variation in HF is shared with the native Dutch dual-purpose breeds. The comparison of predicted variances of different regions associated with milk and milk fat composition showed that breeds clearly differed in genomic variation within these regions. Finally, the correlations of allele frequencies between breeds across the 8 to 22 SNP with the strongest association in HF were around 0.8 between the Dutch native dual-purpose breeds, whereas the correlations between the native breeds and HF were clearly lower and around 0.5. There was no consistent relationship between the reliabilities of genomic prediction for a specific breed and the correlation between the allele frequencies of this breed and HF. In conclusion, most of the genomic variation associated with FA composition in the Dutch dual-purpose breeds appears to be breed-specific. Furthermore, the minor allele frequencies of genes having an effect on the milk FA composition in HF were shown to be much smaller in the breeds MRY, DF, and GWH, especially for the MRY breed. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Genome-editing technologies and their potential application in horticultural crop breeding

PubMed Central

Xiong, Jin-Song; Ding, Jing; Li, Yi

2015-01-01

Plant breeding, one of the oldest agricultural activities, parallels human civilization. Many crops have been domesticated to satisfy human's food and aesthetical needs, including numerous specialty horticultural crops such as fruits, vegetables, ornamental flowers, shrubs, and trees. Crop varieties originated through selection during early human civilization. Other technologies, such as various forms of hybridization, mutation, and transgenics, have also been invented and applied to crop breeding over the past centuries. The progress made in these breeding technologies, especially the modern biotechnology-based breeding technologies, has had a great impact on crop breeding as well as on our lives. Here, we first review the developmental process and applications of these technologies in horticultural crop breeding. Then, we mainly describe the principles of the latest genome-editing technologies and discuss their potential applications in the genetic improvement of horticultural crops. The advantages and challenges of genome-editing technologies in horticultural crop breeding are also discussed. PMID:26504570

Comparison of Marker-Based Genomic Estimated Breeding Values and Phenotypic Evaluation for Selection of Bacterial Spot Resistance in Tomato.

PubMed

Liabeuf, Debora; Sim, Sung-Chur; Francis, David M

2018-03-01

Bacterial spot affects tomato crops (Solanum lycopersicum) grown under humid conditions. Major genes and quantitative trait loci (QTL) for resistance have been described, and multiple loci from diverse sources need to be combined to improve disease control. We investigated genomic selection (GS) prediction models for resistance to Xanthomonas euvesicatoria and experimentally evaluated the accuracy of these models. The training population consisted of 109 families combining resistance from four sources and directionally selected from a population of 1,100 individuals. The families were evaluated on a plot basis in replicated inoculated trials and genotyped with single nucleotide polymorphisms (SNP). We compared the prediction ability of models developed with 14 to 387 SNP. Genomic estimated breeding values (GEBV) were derived using Bayesian least absolute shrinkage and selection operator regression (BL) and ridge regression (RR). Evaluations were based on leave-one-out cross validation and on empirical observations in replicated field trials using the next generation of inbred progeny and a hybrid population resulting from selections in the training population. Prediction ability was evaluated based on correlations between GEBV and phenotypes (r g ), percentage of coselection between genomic and phenotypic selection, and relative efficiency of selection (r g /r p ). Results were similar with BL and RR models. Models using only markers previously identified as significantly associated with resistance but weighted based on GEBV and mixed models with markers associated with resistance treated as fixed effects and markers distributed in the genome treated as random effects offered greater accuracy and a high percentage of coselection. The accuracy of these models to predict the performance of progeny and hybrids exceeded the accuracy of phenotypic selection.

PRELIMINARY ANALYSIS OF COMMON LOON GENETIC STRUCTURE IN NORTH AMERICA BASED ON FIVE MICROSATELLITE LOCI

EPA Science Inventory

This study seeks to determine fine-scale genetic structure of Common Loon breeding populations in order to link wintering birds with their breeding regions. Common Loons are large piscivorous birds that breed in lakes of northern North America and Iceland. Loons are highly phil...

The effects of dog breed development on genetic diversity and the relative influences of performance and conformation breeding.

PubMed

Pedersen, N; Liu, H; Theilen, G; Sacks, B

2013-06-01

Genetic diversity was compared among eight dog breeds selected primarily for conformation (Standard Poodle, Italian Greyhound and show English Setter), conformation and performance (Brittany), predominantly performance (German Shorthaired and Wirehaired Pointers) or solely performance (field English Setter and Red Setter). Modern village dogs, which better reflect ancestral genetic diversity, were used as the standard. Four to seven maternal and one to two Y haplotypes were found per breed, with one usually dominant. Diversity of maternal haplotypes was greatest in village dogs, intermediate in performance breeds and lowest in conformation breeds. Maternal haplotype sharing occurred across all breeds, while Y haplotypes were more breed specific. Almost all paternal haplotypes were identified among village dogs, with the exception of the dominant Y haplotype in Brittanys, which has not been identified heretofore. The highest heterozygosity based on 24 autosomal microsatellites was found in village dogs and the lowest in conformation (show) breeds. Principal coordinate analysis indicated that conformation-type breeds were distinct from breeds heavily used for performance, the latter clustering more closely with village dogs. The Brittany, a well-established dual show and field breed, was also genetically intermediate between the conformation and performance breeds. The number of DLA-DRB1 alleles varied from 3 to 10 per breed with extensive sharing. SNPs across the wider DLA region were more frequently homozygous in all pure breeds than in village dogs. Compared with their village dog relatives, all modern breed dogs exhibit reduced genetic diversity. Genetic diversity was even more reduced among breeds under selection for show/conformation. © 2012 Blackwell Verlag GmbH.

Extreme weather and experience influence reproduction in an endangered bird

USGS Publications Warehouse

Reichert, Brian E.; Cattau, Christopher E.; Fletcher, Robert J.; Kendall, William L.; Kitchens, Wiley M.

2012-01-01

Using a 14-year time series spanning large variation in climatic conditions and the entirety of a population's breeding range, we estimated the effects of extreme weather conditions (drought) on the state-specific probabilities of breeding and survival of an endangered bird, the Florida Snail Kite (Rostrhamus sociabilis plumbeus). Our analysis accounted for uncertainty in breeding status assignment, a common source of uncertainty that is often ignored when states are based on field observations. Breeding probabilities in adult kites (>1 year of age) decreased during droughts, whereas the probability of breeding in young kites (1 year of age) tended to increase. Individuals attempting to breed showed no evidence of reduced future survival. Although population viability analyses of this species and other species often implicitly assume that all adults will attempt to breed, we find that breeding probabilities were significantly <1 for all 13 estimable years considered. Our results suggest that experience is an important factor determining whether or not individuals attempt to breed during harsh environmental conditions and that reproductive effort may be constrained by an individual's quality and/or despotic behavior among individuals attempting to breed.

Analysis of relationships between German heavy horse breeds based on pedigree information.

PubMed

Aberle, Kerstin; Wrede, Jörn; Distl, Ottmar

2004-01-01

We analysed the relationship coefficients (R) between the four German heavy horse breeds South German Coldblood, Rhenish German Draught Horse, Schleswig Draught Horse and Black Forest Draught Horse. The relationship coefficient makes it possible to ascertain crossbreeding between the breeds over time, or autonomous developments of the breeds, respectively. The investigation revealed that the relationship coefficients between the German draught horse breeds were very low. The mean relationship coefficients between the four German heavy horse breeds were largest between the South German Coldblood and Schleswig Draught Horse (0.103%), whereas mean relationship coefficients were lowest between the Rhenish German and Black Forest Draught Horse (0.001%). The Rhenish German Draught Horse showed largest relationship coefficients with the Schleswig Draught Horse (0.09%), while the Black Forest Draught Horse was mostly related to the South German Coldblood (0.06%). The results reveal the presence of very few common progenitors of the breeds. The gene flow between the breeds is primarily due to crossbreeding of stallions and, especially, in the Rhenish German Draught Horse population breeding with a few mares from other German draught horse breeds.

Integrating modelling and phenotyping approaches to identify and screen complex traits - Illustration for transpiration efficiency in cereals.

PubMed

Chenu, K; van Oosterom, E J; McLean, G; Deifel, K S; Fletcher, A; Geetika, G; Tirfessa, A; Mace, E S; Jordan, D R; Sulman, R; Hammer, G L

2018-02-21

Following advances in genetics, genomics, and phenotyping, trait selection in breeding is limited by our ability to understand interactions within the plants and with their environments, and to target traits of most relevance for the target population of environments. We propose an integrated approach that combines insights from crop modelling, physiology, genetics, and breeding to identify traits valuable for yield gain in the target population of environments, develop relevant high-throughput phenotyping platforms, and identify genetic controls and their values in production environments. This paper uses transpiration efficiency (biomass produced per unit of water used) as an example of a complex trait of interest to illustrate how the approach can guide modelling, phenotyping, and selection in a breeding program. We believe that this approach, by integrating insights from diverse disciplines, can increase the resource use efficiency of breeding programs for improving yield gains in target populations of environments.

Dog sperm head morphometry: its diversity and evolution.

PubMed

Soler, Carles; Alambiaga, Ana; Martí, Maria A; García-Molina, Almudena; Valverde, Anthony; Contell, Jesús; Campos, Marcos

2017-01-01

Dogs have been under strong artificial selection as a consequence of their relationship with man. Differences between breeds are evident that could be reflected in seminal characteristics. The present study was to evaluate differences in sperm head morphometry between seven well-defined breeds of dog: the British Bulldog, Chihuahua, German Shepherd, Labrador Retriever, Spanish Mastiff, Staffordshire Terrier, and Valencian Rat Hunting dog. Semen samples were obtained by masturbation and smears stained with Diff-Quik. Morphometric analysis (CASA-Morph) produced four size and four shape parameters. Length, Ellipticity, and Elongation showed higher differences between breeds. MANOVA revealed differences among all breeds. Considering the whole dataset, principal component analysis (PCA) showed that PC1 was related to head shape and PC2 to size. Procluster analysis showed the British Bulldog to be the most isolated breed, followed by the German Shepherd. The PCA breed by breed showed the Chihuahua, Labrador Retriever, Spanish Mastiff, and Staffordshire Terrier to have PC1 related to shape and PC2 to size, whereas the British Bulldog, Valencia Rat Hunting dog, and German Shepherd had PC1 related to size and PC2 to shape. The dendrogram for cluster groupings and the distance between them showed the British Bulldog to be separated from the rest of the breeds. Future work on dog semen must take into account the large differences in the breeds' sperm characteristics. The results provide a base for future work on phylogenetic and evolutionary studies of dogs, based on their seminal characteristics.

Perceptions of households on purpose of keeping, trait preference, and production constraints for selected goat types in Ethiopia.

PubMed

Tadesse, Dereje; Urge, Mengistu; Animut, Getachew; Mekasha, Yoseph

2014-02-01

A study was carried out to understand the needs and perception of goat keepers in selected areas of Ethiopia in order to identify the breeding objectives, traits of preference, and production constraints that may be required in designing improvement programs. The study was conducted in three districts (Bati, Meta, and Kebri-Beyah) representing the lowland crop-livestock (LLCL), highland cereal-livestock (HLCL), and pastoral/agropastoral (P/AP) systems, respectively. The study targeted the three goat types (Bati, Hararghe Highland, and Short-eared Somali) found in Ethiopia. Households in all systems considered meat production, milk production, and income generation as major purpose of keeping goats. However, those in the low rainfall and arid environments of P/AP systems gave high ranking to adaptability to harsh environments and also to building social and religious values. In LLCL and HLCL systems, goat skin and manure were more valued than in P/AP systems. Principally, in P/AP systems, the awareness of households to skin utilization and marketing was very low. Despite diverse multiple breeding objectives identified, household breeding practices were affected by constraints related to disease prevalence, feed shortage and water scarcity, and lack of awareness on skin management, utilization, and marketing. Thus, designing and implementing of sustainable goat improvement programs is an overriding priority and should take into account the breeding objectives and knowledge of goat keepers in all production systems. Along with the breed improvement, a strategy should also be devised to enhance the utilization and marketing of goat skin at all levels of production.

Analysis of genetic diversity and phylogenetic relationships among red jungle fowls and Chinese domestic fowls.

PubMed

Bao, WenBin; Chen, GuoHong; Li, BiChun; Wu, XinSheng; Shu, JingTing; Wu, ShengLong; Xu, Qi; Weigend, Steffen

2008-06-01

Genetic diversity and phylogenetic relationships among 568 individuals of two red jungle fowl subspecies (Gallus gallus spadiceus in China and Gallus gallus gallus in Thailand) and 14 Chinese domestic chicken breeds were evaluated with 29 microstaellite loci, the genetic variability within population and genetic differentiation among population were estimated, and then genetic diversity and phylogenetic relationships were analyzed among red jungle fowls and Chinese domestic fowls. A total of 286 alleles were detected in 16 population with 29 microsatellite markers and the average number of the alleles observed in 29 microsatellite loci was 9.86+/-6.36. The overall expected heterozygosity of all population was 0.6708+/-0.0251, and the number of population deviated from Hardy-Weinberg equilibrium per locus ranged from 0 to 7. In the whole population, the average of genetic differentiation among population, measured as FST value, was 16.7% (P<0.001), and all loci contributed significantly (P<0.001) to this differentiation. It can also be seen that the deficit of heterozygotes was very high (0.015) (P<0.01). Reynolds' distance values varied between 0.036 (Xiaoshan chicken-Luyuan chicken pair) and 0.330 (G. gallus gallus-Gushi chicken pair). The Nm value ranged from 0.533 (between G. gallus gallus and Gushi chicken) to 5.833 (between Xiaoshan chicken and Luyuan chicken). An unrooted consensus tree was constructed using the neighbour-joining method and the Reynolds' genetic distance. The heavy-body sized chicken breeds, Luyuan chicken, Xiaoshan chicken, Beijing Fatty chicken, Henan Game chicken, Huainan Partridge and Langshan chicken formed one branch, and it had a close genetic relationship between Xiaoshan chicken-Luyuan chicken pair and Chahua chicken-Tibetan chicken pair. Chahua chicken and Tibetan chicken had closer genetic relationship with these two subspecies of red jungle fowl than other domestic chicken breeds. G. gallus spadiceus showed closer phylogenetic relationship with Chinese domestic chicken breeds than G. gallus gallus. All 29 microstaellite loci in this study showed high levels of polymorphism and significant genetic differentiation was observed among two subspecies of red jungle fowl and 14 Chinese domestic chicken breeds. The evolutional dendrogram is as follows: evolutional breeds-->primitive breeds (Chahua chicken and Tibetan)-->red jungle fowl in China (G. gallus spadiceus)-->red jungle fowl in Thailand (G. gallus gallus). The results supported the theory that the domestic fowls might originate from different subspecies of red jungle fowl and Chinese domestic fowls had independent origin.

Implications of genetic selection on yolk proportion on the dry matter content of eggs in a White Leghorn population.

PubMed

Icken, W; Looft, C; Schellander, K; Cavero, D; Blanco, A; Schmutz, M; Preisinger, R

2014-01-01

1. The responses to genetic selection on yolk proportion as a technique for increasing egg dry matter content, an important criterion for the egg-product industry, was investigated in a pedigree flock of White Leghorn hens. 2. Parents were preselected on high and low yolk proportion from a base population. The absolute estimated breeding value for yolk proportion of both groups differed by 3%. The realised selection difference in dry matter content of eggs between groups was more than 1% in the analysed offspring population. 3. Heritability estimates were moderate and dry matter had a lower heritability (h(2) = 0.39) than yolk proportion (h(2) = 0.44). 4. The genetic correlation between yolk proportion and dry matter content was highly positive (rg = 0.91). Genetic correlations with egg weight were negative and would have to be compensated for in a breeding programme (rg = -0.76 with yolk proportion and rg = -0.64 with dry matter content). The genetic correlation between the laying performance and yolk proportion was rg = 0.28 and close to zero (rg = -0.05) for dry matter content. 5. Easy recording and lower undesirable correlations make yolk proportion more suitable for commercial selection compared with egg dry matter content in layer breeding.