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.

Mitochondrial sequencing reveals five separate origins of 'black' Apis mellifera (Hymenoptera: Apidae) in eastern Australian commercial colonies.

PubMed

Oxley, P R; Oldroyd, B P

2009-04-01

Establishment of a closed population honey bee, Apis mellifera L. (Hymenoptera: Apidae), breeding program based on 'black' strains has been proposed for eastern Australia. Long-term success of such a program requires a high level of genetic variance. To determine the likely extent of genetic variation available, 50 colonies from 11 different commercial apiaries were sequenced in the mitochondrial cytochrome oxidase I and II intergenic region. Five distinct and novel mitotypes were identified. No colonies were found with the A. mellifera mellifera mitotype, which is often associated with undesirable feral strains. One group of mitotypes was consistent with a caucasica origin, two with carnica, and two with ligustica. The results suggest that there is sufficient genetic diversity to support a breeding program provided all these five sources were pooled.

Accuracy of Genomic Prediction in a Commercial Perennial Ryegrass Breeding Program.

PubMed

Fè, Dario; Ashraf, Bilal H; Pedersen, Morten G; Janss, Luc; Byrne, Stephen; Roulund, Niels; Lenk, Ingo; Didion, Thomas; Asp, Torben; Jensen, Christian S; Jensen, Just

2016-11-01

The implementation of genomic selection (GS) in plant breeding, so far, has been mainly evaluated in crops farmed as homogeneous varieties, and the results have been generally positive. Fewer results are available for species, such as forage grasses, that are grown as heterogenous families (developed from multiparent crosses) in which the control of the genetic variation is far more complex. Here we test the potential for implementing GS in the breeding of perennial ryegrass ( L.) using empirical data from a commercial forage breeding program. Biparental F and multiparental synthetic (SYN) families of diploid perennial ryegrass were genotyped using genotyping-by-sequencing, and phenotypes for five different traits were analyzed. Genotypes were expressed as family allele frequencies, and phenotypes were recorded as family means. Different models for genomic prediction were compared by using practically relevant cross-validation strategies. All traits showed a highly significant level of genetic variance, which could be traced using the genotyping assay. While there was significant genotype × environment (G × E) interaction for some traits, accuracies were high among F families and between biparental F and multiparental SYN families. We have demonstrated that the implementation of GS in grass breeding is now possible and presents an opportunity to make significant gains for various traits. Copyright © 2016 Crop Science Society of America.

Use of wild genotypes in breeding program increases strawberry fruit sensorial and nutritional quality.

PubMed

Diamanti, Jacopo; Mazzoni, Luca; Balducci, Francesca; Cappelletti, Roberto; Capocasa, Franco; Battino, Maurizio; Dobson, Gary; Stewart, Derek; Mezzetti, Bruno

2014-05-07

This study evaluated 20 advanced selections, derived from a strawberry interspecific backcross program, and their parents for fruit weight, commercial yield, acidity, sugar content, antioxidant capacity, and phenol and anthocyanin contents. Phytochemical profiling analysis was performed to determine the compositional characteristics of the improved selections in comparison with their parents and an important commercial variety ('Elsanta'). Advanced selections showed substantial improvement for agronomic and nutritional quality parameters. From the profiling analysis there was evidence for specific improvements in fruit phytochemical contents; new advanced selections had substantially increased fruit flavonol, anthocyanin, and ellagitannin contents compared to their parent cultivar 'Romina' and, for flavonols and ellagitannins, compared to a standard cultivar 'Elsanta'. Such results confirm that an appropriate breeding program that includes wild strawberry germplasm can produce new strawberry cultivars with a well-defined improvement in fruit nutritional and nutraceutical values.

Assessment of genetic diversity and phylogenetic relationships of Korean native chicken breeds using microsatellite markers

PubMed Central

Seo, Joo Hee; Lee, Jun Heon; Kong, Hong Sik

2017-01-01

Objective This study was conducted to investigate the basic information on genetic structure and characteristics of Korean Native chickens (NC) and foreign breeds through the analysis of the pure chicken populations and commercial chicken lines of the Hanhyup Company which are popular in the NC market, using the 20 microsatellite markers. Methods In this study, the genetic diversity and phylogenetic relationships of 445 NC from five different breeds (NC, Leghorn [LH], Cornish [CS], Rhode Island Red [RIR], and Hanhyup [HH] commercial line) were investigated by performing genotyping using 20 microsatellite markers. Results The highest genetic distance was observed between RIR and LH (18.9%), whereas the lowest genetic distance was observed between HH and NC (2.7%). In the principal coordinates analysis (PCoA) illustrated by the first component, LH was clearly separated from the other groups. The correspondence analysis showed close relationship among individuals belonging to the NC, CS, and HH lines. From the STRUCTURE program, the presence of 5 clusters was detected and it was found that the proportion of membership in the different clusters was almost comparable among the breeds with the exception of one breed (HH), although it was highest in LH (0.987) and lowest in CS (0.578). For the cluster 1 it was high in HH (0.582) and in CS (0.368), while for the cluster 4 it was relatively higher in HH (0.392) than other breeds. Conclusion Our study showed useful genetic diversity and phylogenetic relationship data that can be utilized for NC breeding and development by the commercial chicken industry to meet consumer demands. PMID:28335091

Genetic diversity analysis of two commercial breeds of pigs using genomic and pedigree data.

PubMed

Zanella, Ricardo; Peixoto, Jane O; Cardoso, Fernando F; Cardoso, Leandro L; Biegelmeyer, Patrícia; Cantão, Maurício E; Otaviano, Antonio; Freitas, Marcelo S; Caetano, Alexandre R; Ledur, Mônica C

2016-03-30

Genetic improvement in livestock populations can be achieved without significantly affecting genetic diversity if mating systems and selection decisions take genetic relationships among individuals into consideration. The objective of this study was to examine the genetic diversity of two commercial breeds of pigs. Genotypes from 1168 Landrace (LA) and 1094 Large White (LW) animals from a commercial breeding program in Brazil were obtained using the Illumina PorcineSNP60 Beadchip. Inbreeding estimates based on pedigree (F x) and genomic information using runs of homozygosity (F ROH) and the single nucleotide polymorphisms (SNP) by SNP inbreeding coefficient (F SNP) were obtained. Linkage disequilibrium (LD), correlation of linkage phase (r) and effective population size (N e ) were also estimated. Estimates of inbreeding obtained with pedigree information were lower than those obtained with genomic data in both breeds. We observed that the extent of LD was slightly larger at shorter distances between SNPs in the LW population than in the LA population, which indicates that the LW population was derived from a smaller N e . Estimates of N e based on genomic data were equal to 53 and 40 for the current populations of LA and LW, respectively. The correlation of linkage phase between the two breeds was equal to 0.77 at distances up to 50 kb, which suggests that genome-wide association and selection should be performed within breed. Although selection intensities have been stronger in the LA breed than in the LW breed, levels of genomic and pedigree inbreeding were lower for the LA than for the LW breed. The use of genomic data to evaluate population diversity in livestock animals can provide new and more precise insights about the effects of intense selection for production traits. Resulting information and knowledge can be used to effectively increase response to selection by appropriately managing the rate of inbreeding, minimizing negative effects of inbreeding depression and therefore maintaining desirable levels of genetic diversity.

Genetic diversity and population structure analysis of spinach by single-nucleotide polymorphisms identified through genotyping-by-sequencing.

PubMed

Shi, Ainong; Qin, Jun; Mou, Beiquan; Correll, James; Weng, Yuejin; Brenner, David; Feng, Chunda; Motes, Dennis; Yang, Wei; Dong, Lingdi; Bhattarai, Gehendra; Ravelombola, Waltram

2017-01-01

Spinach (Spinacia oleracea L., 2n = 2x = 12) is an economically important vegetable crop worldwide and one of the healthiest vegetables due to its high concentrations of nutrients and minerals. The objective of this research was to conduct genetic diversity and population structure analysis of a collection of world-wide spinach genotypes using single nucleotide polymorphisms (SNPs) markers. Genotyping by sequencing (GBS) was used to discover SNPs in spinach genotypes. Three sets of spinach genotypes were used: 1) 268 USDA GRIN spinach germplasm accessions originally collected from 30 countries; 2) 45 commercial spinach F1 hybrids from three countries; and 3) 30 US Arkansas spinach cultivars/breeding lines. The results from this study indicated that there was genetic diversity among the 343 spinach genotypes tested. Furthermore, the genetic background in improved commercial F1 hybrids and in Arkansas cultivars/lines had a different structured populations from the USDA germplasm. In addition, the genetic diversity and population structures were associated with geographic origin and germplasm from the US Arkansas breeding program had a unique genetic background. These data could provide genetic diversity information and the molecular markers for selecting parents in spinach breeding programs.

Genetic diversity and population structure analysis of spinach by single-nucleotide polymorphisms identified through genotyping-by-sequencing

PubMed Central

Qin, Jun; Mou, Beiquan; Correll, James; Weng, Yuejin; Brenner, David; Feng, Chunda; Motes, Dennis; Yang, Wei; Dong, Lingdi; Bhattarai, Gehendra; Ravelombola, Waltram

2017-01-01

Spinach (Spinacia oleracea L., 2n = 2x = 12) is an economically important vegetable crop worldwide and one of the healthiest vegetables due to its high concentrations of nutrients and minerals. The objective of this research was to conduct genetic diversity and population structure analysis of a collection of world-wide spinach genotypes using single nucleotide polymorphisms (SNPs) markers. Genotyping by sequencing (GBS) was used to discover SNPs in spinach genotypes. Three sets of spinach genotypes were used: 1) 268 USDA GRIN spinach germplasm accessions originally collected from 30 countries; 2) 45 commercial spinach F1 hybrids from three countries; and 3) 30 US Arkansas spinach cultivars/breeding lines. The results from this study indicated that there was genetic diversity among the 343 spinach genotypes tested. Furthermore, the genetic background in improved commercial F1 hybrids and in Arkansas cultivars/lines had a different structured populations from the USDA germplasm. In addition, the genetic diversity and population structures were associated with geographic origin and germplasm from the US Arkansas breeding program had a unique genetic background. These data could provide genetic diversity information and the molecular markers for selecting parents in spinach breeding programs. PMID:29190770

Genetic divergence for high-molecular weight glutenin subunits (HMW-GS) in indigenous landraces and commercial cultivars of bread wheat of Pakistan.

PubMed

Yasmeen, F; Khurshid, H; Ghafoor, A

2015-05-11

Wheat flour quality is an important consideration in the breeding and development of new cultivars. A strong association between high-molecular weight glutenin subunits (HMW-GS) and bread making quality has resulted in the widespread utilization of HMW-GS in wheat breeding. In this study, we analyzed 242 lines of wheat, including landraces from the provinces of Punjab and Baluchistan, as well as the commercial varieties of Pakistan, to determine allelic variation in the Glu-A1, Glu-B1, and Glu-D1 loci encoding HMW-GS. Higher genetic diversity was observed for HMW-GS in landraces from Baluchistan, followed by landraces collected from Punjab and then commercial varieties. Rare and uncommon subunits were observed in Glu-B1, whereas Glu-A1 was less polymorphic. However, Glu-B1 was the highest contributor to overall diversity (78%), with a total of 31 rare alleles, followed by Glu-D1 (20%) with the high quality 5+10 allele and other variants. Commercial cultivars possessed favorable alleles, potentially from indirect selection for wheat flour quality by the breeders; however, this indirect selection has decreased the pedigree base of commercial cultivars. The allelic combinations, including 2*, 5+10, and 17+18, showing high quality scores were frequent among landraces, indicating their usefulness in future crop improvement and breeding programs.

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.

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.

Sycamore produces viable seed after six years

Treesearch

A. F. Ike

1966-01-01

In the early stages of any tree improvement program it is desirable to know how soon progenies of selected parents can themselves be included in a breeding program. How soon will they produce viable pollen and seed? In the case of sycamore (Platanus occidentalis L.), the information is meager: the Woody- Plant Seed Manual lists the minimum commercial seedbearing age...

50 CFR 13.11 - Application procedures.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Rescue Center Program 50 CFR 23 (1) (1) CITES Registration of Commercial Breeding Operations for Appendix..., POSSESSION, TRANSPORTATION, SALE, PURCHASE, BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS... Conservation Act permits (50 CFR 15); injurious wildlife permits (50 CFR 16); captive-bred wildlife...

50 CFR 13.11 - Application procedures.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Rescue Center Program 50 CFR 23 (1) (1) CITES Registration of Commercial Breeding Operations for Appendix..., POSSESSION, TRANSPORTATION, SALE, PURCHASE, BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS... Conservation Act permits (50 CFR 15); injurious wildlife permits (50 CFR 16); captive-bred wildlife...

50 CFR 13.11 - Application procedures.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Rescue Center Program 50 CFR 23 (1) (1) CITES Registration of Commercial Breeding Operations for Appendix..., POSSESSION, TRANSPORTATION, SALE, PURCHASE, BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS... Conservation Act permits (50 CFR 15); injurious wildlife permits (50 CFR 16); captive-bred wildlife...

50 CFR 13.11 - Application procedures.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Rescue Center Program 50 CFR 23 (1) (1) CITES Registration of Commercial Breeding Operations for Appendix..., POSSESSION, TRANSPORTATION, SALE, PURCHASE, BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS... Conservation Act permits (50 CFR 15); injurious wildlife permits (50 CFR 16); captive-bred wildlife...

A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds.

PubMed

Yang, Songbai; Li, Xiuling; Li, Kui; Fan, Bin; Tang, Zhonglin

2014-01-15

Modern breeding and artificial selection play critical roles in pig domestication and shape the genetic variation of different breeds. China has many indigenous pig breeds with various characteristics in morphology and production performance that differ from those of foreign commercial pig breeds. However, the signatures of selection on genes implying for economic traits between Chinese indigenous and commercial pigs have been poorly understood. We identified footprints of positive selection at the whole genome level, comprising 44,652 SNPs genotyped in six Chinese indigenous pig breeds, one developed breed and two commercial breeds. An empirical genome-wide distribution of Fst (F-statistics) was constructed based on estimations of Fst for each SNP across these nine breeds. We detected selection at the genome level using the High-Fst outlier method and found that 81 candidate genes show high evidence of positive selection. Furthermore, the results of network analyses showed that the genes that displayed evidence of positive selection were mainly involved in the development of tissues and organs, and the immune response. In addition, we calculated the pairwise Fst between Chinese indigenous and commercial breeds (CHN VS EURO) and between Northern and Southern Chinese indigenous breeds (Northern VS Southern). The IGF1R and ESR1 genes showed evidence of positive selection in the CHN VS EURO and Northern VS Southern groups, respectively. In this study, we first identified the genomic regions that showed evidences of selection between Chinese indigenous and commercial pig breeds using the High-Fst outlier method. These regions were found to be involved in the development of tissues and organs, the immune response, growth and litter size. The results of this study provide new insights into understanding the genetic variation and domestication in pigs.

A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds

PubMed Central

2014-01-01

Background Modern breeding and artificial selection play critical roles in pig domestication and shape the genetic variation of different breeds. China has many indigenous pig breeds with various characteristics in morphology and production performance that differ from those of foreign commercial pig breeds. However, the signatures of selection on genes implying for economic traits between Chinese indigenous and commercial pigs have been poorly understood. Results We identified footprints of positive selection at the whole genome level, comprising 44,652 SNPs genotyped in six Chinese indigenous pig breeds, one developed breed and two commercial breeds. An empirical genome-wide distribution of Fst (F-statistics) was constructed based on estimations of Fst for each SNP across these nine breeds. We detected selection at the genome level using the High-Fst outlier method and found that 81 candidate genes show high evidence of positive selection. Furthermore, the results of network analyses showed that the genes that displayed evidence of positive selection were mainly involved in the development of tissues and organs, and the immune response. In addition, we calculated the pairwise Fst between Chinese indigenous and commercial breeds (CHN VS EURO) and between Northern and Southern Chinese indigenous breeds (Northern VS Southern). The IGF1R and ESR1 genes showed evidence of positive selection in the CHN VS EURO and Northern VS Southern groups, respectively. Conclusions In this study, we first identified the genomic regions that showed evidences of selection between Chinese indigenous and commercial pig breeds using the High-Fst outlier method. These regions were found to be involved in the development of tissues and organs, the immune response, growth and litter size. The results of this study provide new insights into understanding the genetic variation and domestication in pigs. PMID:24422716

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.

50 CFR 17.32 - Permits-general.

Code of Federal Regulations, 2014 CFR

2014-10-01

... PLANTS (CONTINUED) ENDANGERED AND THREATENED WILDLIFE AND PLANTS Threatened Wildlife § 17.32 Permits... statement of the applicant's willingness to participate in a cooperative breeding program and to maintain or... demonstrating that such unforeseen circumstances exist, using the best scientific and commercial data available...

50 CFR 17.32 - Permits-general.

Code of Federal Regulations, 2012 CFR

2012-10-01

... PLANTS (CONTINUED) ENDANGERED AND THREATENED WILDLIFE AND PLANTS Threatened Wildlife § 17.32 Permits... statement of the applicant's willingness to participate in a cooperative breeding program and to maintain or... demonstrating that such unforeseen circumstances exist, using the best scientific and commercial data available...

50 CFR 17.32 - Permits-general.

Code of Federal Regulations, 2010 CFR

2010-10-01

... PLANTS (CONTINUED) ENDANGERED AND THREATENED WILDLIFE AND PLANTS Threatened Wildlife § 17.32 Permits... statement of the applicant's willingness to participate in a cooperative breeding program and to maintain or... demonstrating that such unforeseen circumstances exist, using the best scientific and commercial data available...

50 CFR 17.32 - Permits-general.

Code of Federal Regulations, 2011 CFR

2011-10-01

... PLANTS (CONTINUED) ENDANGERED AND THREATENED WILDLIFE AND PLANTS Threatened Wildlife § 17.32 Permits... statement of the applicant's willingness to participate in a cooperative breeding program and to maintain or... demonstrating that such unforeseen circumstances exist, using the best scientific and commercial data available...

50 CFR 17.32 - Permits-general.

Code of Federal Regulations, 2013 CFR

2013-10-01

... PLANTS (CONTINUED) ENDANGERED AND THREATENED WILDLIFE AND PLANTS Threatened Wildlife § 17.32 Permits... statement of the applicant's willingness to participate in a cooperative breeding program and to maintain or... demonstrating that such unforeseen circumstances exist, using the best scientific and commercial data available...

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

Meiotic behavior as a selection tool in silage corn breeding.

PubMed

Souza, V F; Pagliarini, M S; Scapim, C A; Rodovalho, M; Faria, M V

2010-10-19

In breeding programs, commercial hybrids are frequently used as a source of inbred lines to obtain new hybrids. Considering that maize production is dependent on viable gametes, the selection of populations to obtain inbred lines with high meiotic stability could contribute to the formation of new silage corn hybrids adapted to specific region. We evaluated the meiotic stability of five commercial hybrids of silage corn used in southern Brazil with conventional squashing methods. All of them showed meiotic abnormalities. Some abnormalities, such as abnormal chromosome segregation and absence of cytokinesis, occurred in all the genotypes, while others, including cytomixis and abnormal spindle orientation, were found only in some genotypes. The hybrid SG6010 had the lowest mean frequency of abnormal cells (21.27%); the highest frequency was found in the hybrid P30K64 (44.43%). However, the frequency of abnormal meiotic products was much lower in most genotypes, ranging from 7.63% in the hybrid CD304 to 43.86% in Garra. Taking into account the percentage of abnormal meiotic products and, hence, meiotic stability, only the hybrids CD304, P30K64, SG6010, and P30F53 are recommended to be retained in the breeding program to obtain inbred lines to create new hybrids.

Parentage assignment with genomic markers: a major advance for understanding and exploiting genetic variation of quantitative traits in farmed aquatic animals

PubMed Central

Vandeputte, Marc; Haffray, Pierrick

2014-01-01

Since the middle of the 1990s, parentage assignment using microsatellite markers has been introduced as a tool in aquaculture breeding. It now allows close to 100% assignment success, and offered new ways to develop aquaculture breeding using mixed family designs in commercial conditions. Its main achievements are the knowledge and control of family representation and inbreeding, especially in mass spawning species, above all the capacity to estimate reliable genetic parameters in any species and rearing system with no prior investment in structures, and the development of new breeding programs in many species. Parentage assignment should not be seen as a way to replace physical tagging, but as a new way to conceive breeding programs, which have to be optimized with its specific constraints, one of the most important being to well define the number of individuals to genotype to limit costs, maximize genetic gain while minimizing inbreeding. The recent possible shift to (for the moment) more costly single nucleotide polymorphism markers should benefit from future developments in genomics and marker-assisted selection to combine parentage assignment and indirect prediction of breeding values. PMID:25566319

Advances in Japanese pear breeding in Japan

PubMed Central

Saito, Toshihiro

2016-01-01

The Japanese pear (Pyrus pyrifolia Nakai) is one of the most widely grown fruit trees in Japan, and it has been used throughout Japan’s history. The commercial production of pears increased rapidly with the successive discoveries of the chance seedling cultivars ‘Chojuro’ and ‘Nijisseiki’ around 1890, and the development of new cultivars has continued since 1915. The late-maturing, leading cultivars ‘Niitaka’ and ‘Shinko’ were released during the initial breeding stage. Furthermore, systematic breeding by the Horticultural Research Station (currently, NARO Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NIFTS)) began in 1935, which mainly aimed to improve fruit quality by focusing on flesh texture and black spot disease resistance. To date, 22 cultivars have been released, including ‘Kosui’, ‘Hosui’, and ‘Akizuki’, which are current leading cultivars from the breeding program. Four induced mutant cultivars induced by gamma irradiation, which exhibit some resistance to black spot disease, were released from the Institute of Radiation Breeding. Among these cultivars, ‘Gold Nijisseiki’ has become a leading cultivar. Moreover, ‘Nansui’ from the Nagano prefectural institute breeding program was released, and it has also become a leading cultivar. Current breeding objectives at NIFTS mainly combine superior fruit quality with traits related to labor and cost reduction, multiple disease resistance, or self-compatibility. Regarding future breeding, marker-assisted selection for each trait, QTL analyses, genome-wide association studies, and genomic selection analyses are currently in progress. PMID:27069390

Within-farm variability in age structure of breeding-female pigs and reproductive performance on commercial swine breeding farms.

PubMed

Koketsu, Yuzo

2005-03-15

This study investigated relationships between herd age structure and herd productivity in breeding herds; it also investigated a pattern in parity proportions of females over 2 years and its relationship with herd productivity in commercial swine herds. This study was based on data from 148 commercial farms in North America stored in the swine database program at the University of Minnesota. The primary selection criterion was fluctuations in breeding-female pig (female) inventories over a 2-year interval. Productivity measurements and parity proportions of females were extracted from the database. A 24-month time-plot in proportions of Parity 0 and Parities 3-5 females (mid-parity) was charted for each farm. Using these charts, a change in proportions of Parity 0 and mid-parity for each farm was categorized into patterns: FLUCTUATE (Parity 0 and mid-parity proportion lines crossed) or STABLE (the two proportion lines never crossed). Higher proportions of mid-parity sows were correlated with greater pigs weaned per female per year (PWFY; P < 0.01). Farms with a FLUCTUATE (73% of the 148 farms) pattern had lower PWFY than those with a STABLE pattern (P < 0.01). The STABLE farms had higher proportions of mid-parity sows, higher parity at culling, higher frequency of gilt deliveries per year, and lower replacement rate than the FLUCTUATE farms (P < 0.01). In conclusion, maintaining stable subpopulations with mid-parity and Parity 0 are recommended to optimize herd productivity.

Geneva apple rootstock performance in New York state and progress in commercialization

USDA-ARS?s Scientific Manuscript database

A number of new apple rootstocks from the Cornell/USDA apple rootstock breeding project, located at Geneva NY which are resistant to the bacterial disease fire blight (Erwinia amylovora) are rapidly becoming available. Some named rootstock genotypes from this program have previously been tested in s...

Multiple disease resistance to fungal and oomycete pathogens using a recombinant inbred line population in pepper

USDA-ARS?s Scientific Manuscript database

Incorporating disease resistance into cultivars is a primary focus of modern breeding programs. Resistance to pathogens is often introgressed from landrace or wild individuals with poor fruit quality into commercial-quality cultivars. Sites of multiple disease resistance (MDR) are regions or “hotspo...

Tracking the genetic stability of a honeybee breeding program with genetic markers

USDA-ARS?s Scientific Manuscript database

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...

9 CFR 56.3 - Payment of indemnity.

Code of Federal Regulations, 2014 CFR

2014-01-01

... program available to the commercial flock or slaughter plant in part 146 of this chapter; or (3) The....3 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE... described in paragraphs (a)(1) through (a)(3) of this section: (1) The poultry are from a breeding flock...

9 CFR 56.3 - Payment of indemnity.

Code of Federal Regulations, 2012 CFR

2012-01-01

... program available to the commercial flock or slaughter plant in part 146 of this chapter; or (3) The....3 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE... described in paragraphs (a)(1) through (a)(3) of this section: (1) The poultry are from a breeding flock...

9 CFR 56.3 - Payment of indemnity.

Code of Federal Regulations, 2013 CFR

2013-01-01

... program available to the commercial flock or slaughter plant in part 146 of this chapter; or (3) The....3 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE... described in paragraphs (a)(1) through (a)(3) of this section: (1) The poultry are from a breeding flock...

Effect of orange rust on sugarcane breeding program at canal Point

USDA-ARS?s Scientific Manuscript database

Orange rust of sugarcane (Saccharum spp. hybrids), caused by Puccinia kuehnii (W. Krüger) E.J. Butler, appeared in the Western Hemisphere ten years ago. Orange rust substantially reduces yields in susceptible sugarcane genotypes. Majority of the commercial cultivars were susceptible at the time of o...

Update on sensory evaluation of University of Florida strawberry selections

USDA-ARS?s Scientific Manuscript database

The University of Florida strawberry breeding program has evaluated eating quality of fruit from advanced selections using sensory taste panels. Selections FL 05-107, FL 06-38 and FL 09-127 were compared with the commercial cultivars ‘Strawberry Festival’ and FLorida Radiance’ during two consecutive...

Management practices associated with conception rate and service rate of lactating Holstein cows in large, commercial dairy herds.

PubMed

Schefers, J M; Weigel, K A; Rawson, C L; Zwald, N R; Cook, N B

2010-04-01

Data from lactating Holstein cows in herds that participate in a commercial progeny testing program were analyzed to explain management factors associated with herd-average conception and service rates on large commercial dairies. On-farm herd management software was used as the source of data related to production, reproduction, culling, and milk quality for 108 herds. Also, a survey regarding management, facilities, nutrition, and labor was completed on 86 farms. A total of 41 explanatory variables related to management factors and conditions that could affect conception and service rate were considered in this study. Models explaining conception and service rates were developed using a machine learning algorithm for constructing model trees. The most important explanatory variables associated with conception rate were the percentage of repeated inseminations between 4 and 17 d post-artificial insemination, stocking density in the breeding pen, length of the voluntary waiting period, days at pregnancy examination, and somatic cell score. The most important explanatory variables associated with service rate were the number of lactating cows per breeding technician, use of a resynchronization program, utilization of soakers in the holding area during the summer, and bunk space per cow in the breeding pen. The aforementioned models explained 35% and 40% of the observed variation in conception rate and service rate, respectively, and underline the association of herd-level management factors not strictly related to reproduction with herd reproductive performance. Copyright (c) 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds

PubMed Central

Purfield, Deirdre C.; McParland, Sinead; Wall, Eamon; Berry, Donagh P.

2017-01-01

Domestication and the subsequent selection of animals for either economic or morphological features can leave a variety of imprints on the genome of a population. Genomic regions subjected to high selective pressures often show reduced genetic diversity and frequent runs of homozygosity (ROH). Therefore, the objective of the present study was to use 42,182 autosomal SNPs to identify genomic regions in 3,191 sheep from six commercial breeds subjected to selection pressure and to quantify the genetic diversity within each breed using ROH. In addition, the historical effective population size of each breed was also estimated and, in conjunction with ROH, was used to elucidate the demographic history of the six breeds. ROH were common in the autosomes of animals in the present study, but the observed breed differences in patterns of ROH length and burden suggested differences in breed effective population size and recent management. ROH provided a sufficient predictor of the pedigree inbreeding coefficient, with an estimated correlation between both measures of 0.62. Genomic regions under putative selection were identified using two complementary algorithms; the fixation index and hapFLK. The identified regions under putative selection included candidate genes associated with skin pigmentation, body size and muscle formation; such characteristics are often sought after in modern-day breeding programs. These regions of selection frequently overlapped with high ROH regions both within and across breeds. Multiple yet uncharacterised genes also resided within putative regions of selection. This further substantiates the need for a more comprehensive annotation of the sheep genome as these uncharacterised genes may contribute to traits of interest in the animal sciences. Despite this, the regions identified as under putative selection in the current study provide an insight into the mechanisms leading to breed differentiation and genetic variation in meat production. PMID:28463982

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.

Selection for avian immune response: a commercial breeding company challenge.

PubMed

Fulton, J E

2004-04-01

Selection for immune function in the commercial breeding environment is a challenging proposition for commercial breeding companies. Immune response is only one of many traits that are under intensive selection, thus selection pressure needs to be carefully balanced across multiple traits. The selection environment (single bird cages, biosecure facilities, controlled environment) is a very different environment than the commercial production facilities (multiple bird cages, potential disease exposure, variable environment) in which birds are to produce. The testing of individual birds is difficult, time consuming, and expensive. It is essential that the results of any tests be relevant to actual disease or environmental challenge in the commercial environment. The use of genetic markers as indicators of immune function is being explored by breeding companies. Use of genetic markers would eliminate many of the limitations in enhancing immune function currently encountered by commercial breeding companies. Information on genetic markers would allow selection to proceed without subjecting breeding stock to disease conditions and could be done before production traits are measured. These markers could be candidate genes with known interaction or involvement with disease pathology or DNA markers that are closely linked to genetic regions that influence the immune response. The current major limitation to this approach is the paucity of mapped chicken immune response genes and the limited number of DNA markers mapped on the chicken genome. These limitations should be eliminated once the chicken genome is sequenced.

Genetic characterization of commercial honey bee (Hymenoptera: Apidae) populations in the United States by using mitochondrial and microsatellite markers

Treesearch

D. A. Delaney; M.D. Meixner; N.M. Schiff; W.S. Sheppard

2009-01-01

Genetic diversity levels within and between the two commercial breeding areas in theUnited States were analyzed using the DraI restriction fragment length polymorphism of the COICOII mitochondrial region and 10 polymorphic microsatellite loci. The western commercial breeding population (WCBP) and the southeastern commercial...

Unraveling the genetic structure of Brazilian commercial sugarcane cultivars through microsatellite markers

PubMed Central

Manechini, João Ricardo Vieira; da Costa, Juliana Borges; Pereira, Bruna Turcatto; Carlini-Garcia, Luciana Aparecida; Xavier, Mauro Alexandre; Landell, Marcos Guimarães de Andrade

2018-01-01

The Brazilian sugarcane industry plays an important role in the worldwide supply of sugar and ethanol. Investigation into the genetic structure of current commercial cultivars and comparisons to the main ancestor species allow sugarcane breeding programs to better manage crosses and germplasm banks as well as to promote its rational use. In the present study, the genetic structure of a group of Brazilian cultivars currently grown by commercial producers was assessed through microsatellite markers and contrasted with a group of basic germplasm mainly composed of Saccharum officinarum and S. spontaneum accessions. A total of 285 alleles was obtained by a set of 12 SSRs primer pairs that taken together were able to efficiently distinguish and capture the genetic variability of sugarcane commercial cultivars and basic germplasm accessions allowing its application in a fast and cost-effective way for routine cultivar identification and management of sugarcane germplasm banks. Allelic distribution revealed that 97.6% of the cultivar alleles were found in the basic germplasm while 42% of the basic germplasm alleles were absent in cultivars. Of the absent alleles, 3% was exclusive to S. officinarum, 33% to S. spontaneum and 19% to other species/exotic hybrids. We found strong genetic differentiation between the Brazilian commercial cultivars and the two main species (S. officinarum: Φ^ST = 0.211 and S. spontaneum: Φ^ST = 0.216, P<0.001), and significant contribution of the latter in the genetic variability of commercial cultivars. Average dissimilarity within cultivars was 1.2 and 1.4 times lower than that within S. officinarum and S. spontaneum. Genetic divergence found between cultivars and S. spontaneum accessions has practical applications for energy cane breeding programs as the choice of more divergent parents will maximize the frequency of transgressive individuals in the progeny. PMID:29684082

Unraveling the genetic structure of Brazilian commercial sugarcane cultivars through microsatellite markers.

PubMed

Manechini, João Ricardo Vieira; da Costa, Juliana Borges; Pereira, Bruna Turcatto; Carlini-Garcia, Luciana Aparecida; Xavier, Mauro Alexandre; Landell, Marcos Guimarães de Andrade; Pinto, Luciana Rossini

2018-01-01

The Brazilian sugarcane industry plays an important role in the worldwide supply of sugar and ethanol. Investigation into the genetic structure of current commercial cultivars and comparisons to the main ancestor species allow sugarcane breeding programs to better manage crosses and germplasm banks as well as to promote its rational use. In the present study, the genetic structure of a group of Brazilian cultivars currently grown by commercial producers was assessed through microsatellite markers and contrasted with a group of basic germplasm mainly composed of Saccharum officinarum and S. spontaneum accessions. A total of 285 alleles was obtained by a set of 12 SSRs primer pairs that taken together were able to efficiently distinguish and capture the genetic variability of sugarcane commercial cultivars and basic germplasm accessions allowing its application in a fast and cost-effective way for routine cultivar identification and management of sugarcane germplasm banks. Allelic distribution revealed that 97.6% of the cultivar alleles were found in the basic germplasm while 42% of the basic germplasm alleles were absent in cultivars. Of the absent alleles, 3% was exclusive to S. officinarum, 33% to S. spontaneum and 19% to other species/exotic hybrids. We found strong genetic differentiation between the Brazilian commercial cultivars and the two main species (S. officinarum: [Formula: see text] = 0.211 and S. spontaneum: [Formula: see text] = 0.216, P<0.001), and significant contribution of the latter in the genetic variability of commercial cultivars. Average dissimilarity within cultivars was 1.2 and 1.4 times lower than that within S. officinarum and S. spontaneum. Genetic divergence found between cultivars and S. spontaneum accessions has practical applications for energy cane breeding programs as the choice of more divergent parents will maximize the frequency of transgressive individuals in the progeny.

Expression of myogenes in longissimus dorsi muscle during prenatal development in commercial and local Piau pigs.

PubMed

Reis, Evelyze Pinheiro Dos; Paixão, Débora Martins; Brustolini, Otávio José Bernardes; Silva, Fabyano Fonseca E; Silva, Walmir; Araújo, Flávio Marcos Gomes de; Salim, Anna Christina de Matos; Oliveira, Guilherme; Guimarães, Simone Eliza Facioni

2016-01-01

This study used qRT-PCR to examine variation in the expression of 13 myogenes during muscle development in four prenatal periods (21, 40, 70 and 90 days post-insemination) in commercial (the three-way Duroc, Landrace and Large-White cross) and local Piau pig breeds that differ in muscle mass. There was no variation in the expression of the CHD8, EID2B, HIF1AN, IKBKB, RSPO3, SOX7 and SUFU genes at the various prenatal ages or between breeds. The MAP2K1 and RBM24 genes showed similar expression between commercial and Piau pigs but greater expression (p < 0.05) in at least one prenatal period. Pair-wise comparisons of prenatal periods in each breed showed that only the CSRP3, LEF1, MRAS and MYOG genes had higher expression (p < 0.05) in at least one prenatal period in commercial and Piau pigs. Overall, these results identified the LEF1 gene as a primary candidate to account for differences in muscle mass between the pig breeds since activation of this gene may lead to greater myoblast fusion in the commercial breed compared to Piau pigs. Such fusion could explain the different muscularity between breeds in the postnatal periods.

Expression of myogenes in longissimus dorsi muscle during prenatal development in commercial and local Piau pigs

PubMed Central

dos Reis, Evelyze Pinheiro; Paixão, Débora Martins; Brustolini, Otávio José Bernardes; Silva, Fabyano Fonseca e; Silva, Walmir; de Araújo, Flávio Marcos Gomes; Salim, Anna Christina de Matos; Oliveira, Guilherme; Guimarães, Simone Eliza Facioni

2016-01-01

Abstract This study used qRT-PCR to examine variation in the expression of 13 myogenes during muscle development in four prenatal periods (21, 40, 70 and 90 days post-insemination) in commercial (the three-way Duroc, Landrace and Large-White cross) and local Piau pig breeds that differ in muscle mass. There was no variation in the expression of the CHD8, EID2B, HIF1AN, IKBKB, RSPO3, SOX7 and SUFU genes at the various prenatal ages or between breeds. The MAP2K1 and RBM24 genes showed similar expression between commercial and Piau pigs but greater expression (p < 0.05) in at least one prenatal period. Pair-wise comparisons of prenatal periods in each breed showed that only the CSRP3, LEF1, MRAS and MYOG genes had higher expression (p < 0.05) in at least one prenatal period in commercial and Piau pigs. Overall, these results identified the LEF1 gene as a primary candidate to account for differences in muscle mass between the pig breeds since activation of this gene may lead to greater myoblast fusion in the commercial breed compared to Piau pigs. Such fusion could explain the different muscularity between breeds in the postnatal periods. PMID:27801482

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.

Breeding for growth improvement and resistance to multiple pests in Thuja plicata

Treesearch

John H. Russell; Alvin D. Yanchuk

2012-01-01

Western redcedar (Thuja plicata Donn ex D. Don), a member of the Cupressaceae, is an important commercial species in British Columbia (BC) and the Pacific Northwest (PNW), which is prized for its heartwood and its performance as a naturally durable outdoor building material. Although a genetic improvement program has been ongoing for only 15 years...

Genetic diversity in a collection of Saccharum spontaneum genotypes and their contribution to the Louisiana commercial breeding program as revealed using AFLP markers

USDA-ARS?s Scientific Manuscript database

Saccharum spontaneum has been the most important source of wild germpalsm for sugarcane cultivar development in Louisiana, particularly in improving traits such as mosaic virus resistance, vigor, ratooning ability and cold tolerance. A collection of 51 S. spontaneum genotypes maintained at the Sugar...

Genetic characterization of Bombyx mori (Lepidoptera: Bombycidae) breeding and hybrid lines with different geographic origins.

PubMed

Furdui, Emilia M; Mărghitaş, Liviu A; Dezmirean, Daniel S; Paşca, Ioan; Pop, Iulia F; Erler, Silvio; Schlüns, Ellen A

2014-01-01

The domesticated silkworm Bombyx mori L. comprises a large number of geographical breeds and hybrid lines. Knowing the genetic structure of those may provide information to improve the conservation of commercial lines by estimating inbreeding over generations and the consequences of excessive use of those lineages. Here, we analyzed the genetic diversity of seven breeds and eight hybrid lines from Eastern Europe and Asia using highly polymorphic microsatellites markers to determine its genetical impact on their use in global breeding programs. No consistent pattern of deviation from Hardy-Weinberg equilibrium was found for most breed and hybrids; and the absence of a linkage disequilibrium also suggests that the strains are in equilibrium. A principal coordinate analysis revealed a clear separation of two silkworm breeds from the rest: one (IBV) originated from India and the other one (RG90) from Romania/Japan. The tendency of the other breeds from different geographic origins to cluster together in a general mix might be due to similar selection pressures (climate and anthropogenic factors) in different geographic locations. Phylogenetic analyses grouped the different silkworm breeds but not the hybrids according to their geographic origin and confirmed the pattern found in the principal coordinate analysis. © The Author 2014. Published by Oxford University Press on behalf of the Entomological Society of America.

Genetic Characterization of Bombyx mori (Lepidoptera: Bombycidae) Breeding and Hybrid Lines With Different Geographic Origins

PubMed Central

Furdui, Emilia M.; Mărghitaş, Liviu A.; Dezmirean, Daniel S.; Paşca, Ioan; Pop, Iulia F.; Erler, Silvio; Schlüns, Ellen A.

2014-01-01

Abstract The domesticated silkworm Bombyx mori L. comprises a large number of geographical breeds and hybrid lines. Knowing the genetic structure of those may provide information to improve the conservation of commercial lines by estimating inbreeding over generations and the consequences of excessive use of those lineages. Here, we analyzed the genetic diversity of seven breeds and eight hybrid lines from Eastern Europe and Asia using highly polymorphic microsatellites markers to determine its genetical impact on their use in global breeding programs. No consistent pattern of deviation from Hardy–Weinberg equilibrium was found for most breed and hybrids; and the absence of a linkage disequilibrium also suggests that the strains are in equilibrium. A principal coordinate analysis revealed a clear separation of two silkworm breeds from the rest: one (IBV) originated from India and the other one (RG 90 ) from Romania/Japan. The tendency of the other breeds from different geographic origins to cluster together in a general mix might be due to similar selection pressures (climate and anthropogenic factors) in different geographic locations. Phylogenetic analyses grouped the different silkworm breeds but not the hybrids according to their geographic origin and confirmed the pattern found in the principal coordinate analysis. PMID:25502023

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.

Genomic Selection in Commercial Perennial Crops: Applicability and Improvement in Oil Palm (Elaeis guineensis Jacq.).

PubMed

Kwong, Qi Bin; Ong, Ai Ling; Teh, Chee Keng; Chew, Fook Tim; Tammi, Martti; Mayes, Sean; Kulaveerasingam, Harikrishna; Yeoh, Suat Hui; Harikrishna, Jennifer Ann; Appleton, David Ross

2017-06-06

Genomic selection (GS) uses genome-wide markers to select individuals with the desired overall combination of breeding traits. A total of 1,218 individuals from a commercial population of Ulu Remis x AVROS (UR x AVROS) were genotyped using the OP200K array. The traits of interest included: shell-to-fruit ratio (S/F, %), mesocarp-to-fruit ratio (M/F, %), kernel-to-fruit ratio (K/F, %), fruit per bunch (F/B, %), oil per bunch (O/B, %) and oil per palm (O/P, kg/palm/year). Genomic heritabilities of these traits were estimated to be in the range of 0.40 to 0.80. GS methods assessed were RR-BLUP, Bayes A (BA), Cπ (BC), Lasso (BL) and Ridge Regression (BRR). All methods resulted in almost equal prediction accuracy. The accuracy achieved ranged from 0.40 to 0.70, correlating with the heritability of traits. By selecting the most important markers, RR-BLUP B has the potential to outperform other methods. The marker density for certain traits can be further reduced based on the linkage disequilibrium (LD). Together with in silico breeding, GS is now being used in oil palm breeding programs to hasten parental palm selection.

Breeding blueberries for a changing global environment: a review

PubMed Central

Lobos, Gustavo A.; Hancock, James F.

2015-01-01

Today, blueberries are recognized worldwide as one of the foremost health foods, becoming one of the crops with the highest productive and commercial projections. Over the last 100 years, the geographical area where highbush blueberries are grown has extended dramatically into hotter and drier environments. The expansion of highbush blueberry growing into warmer regions will be challenged in the future by increases in average global temperature and extreme fluctuations in temperature and rainfall patterns. Considerable genetic variability exists within the blueberry gene pool that breeders can use to meet these challenges, but traditional selection techniques can be slow and inefficient and the precise adaptations of genotypes often remain hidden. Marker assisted breeding (MAB) and phenomics could aid greatly in identifying those individuals carrying adventitious traits, increasing selection efficiency and shortening the rate of cultivar release. While phenomics have begun to be used in the breeding of grain crops in the last 10 years, their use in fruit breeding programs it is almost non-existent. PMID:26483803

Optimum allocation of test resources and comparison of breeding strategies for hybrid wheat.

PubMed

Longin, C Friedrich H; Mi, Xuefei; Melchinger, Albrecht E; Reif, Jochen C; Würschum, Tobias

2014-10-01

The use of a breeding strategy combining the evaluation of line per se with testcross performance maximizes annual selection gain for hybrid wheat breeding. Recent experimental studies confirmed a high commercial potential for hybrid wheat requiring the design of optimum breeding strategies. Our objectives were to (1) determine the optimum allocation of the type and number of testers, the number of test locations and the number of doubled haploid lines for different breeding strategies, (2) identify the best breeding strategy and (3) elaborate key parameters for an efficient hybrid wheat breeding program. We performed model calculations using the selection gain for grain yield as target variable to optimize the number of lines, testers and test locations in four different breeding strategies. A breeding strategy (BS2) combining the evaluation of line per se performance and general combining ability (GCA) had a far larger annual selection gain across all considered scenarios than a breeding strategy (BS1) focusing only on GCA. In the combined strategy, the production of testcross seed conducted in parallel with the first yield trial for line per se performance (BS2rapid) resulted in a further increase of the annual selection gain. For the current situation in hybrid wheat, this relative superiority of the strategy BS2rapid amounted to 67 % in annual selection gain compared to BS1. Varying a large number of parameters, we identified the high costs for hybrid seed production and the low variance of GCA in hybrid wheat breeding as key parameters limiting selection gain in BS2rapid.

Performance of some Ethiopian fenugreek (Trigonella foenum-graecum L.) germplasm collections as compared with the commercial variety Challa.

PubMed

Fikreselassie, Million

2012-05-01

Systematic breeding efforts on fenugreek have so far been neglected in Ethiopia. For this, 143 random samples of fenugreek accessions along with a commercial variety were used in this study to evaluate the potential of the land races. The field experiment was conducted at Haramaya University research station during 2011 main cropping season. Treatments were arranged in a 12x12 simple lattice design. The highest biomass and seed yielding accessions were generally concentrated more in the categories of yellow and green seed colors. When compared with the commercial variety, above 27% of the tested accessions performed significantly better in terms of seed yield indicating that significant yield gains could be secured by simple selection. However, further evaluation over wider environments is necessary to arrive at conclusive points for such quantitative traits. Green and yellow seeded accessions are widely distributed over all the country and over half of the accessions (63%) had green seed color. High seed yield bearing accessions were those collected from northwest and central part of Ethiopia, while accessions collected from eastern and northwestern Ethiopia were strikingly bold seed size. This variability would provide a basis for improving the crop in breeding program.

Effect of short-term water restriction in hot season on some blood parameters and immune response to Newcastle disease vaccine of local and commercial layers in the late phase of production.

PubMed

Alamer, M A; Ahmed, A S

2012-08-01

Forty-five Hisex commercial layers and forty-five local Saudi breed layers were used to compare and assess the effect of water restriction under hot conditions on blood constituents and immune response to Newcastle disease (ND) vaccine. The trial was divided into three periods: control (7 day), water restriction (14 day) and rehydration (7 day). During water restriction, layers from each breed were divided into three groups that received 0%, 20% and 40% restriction of drinking water relative to the control period. The immune response against ND was affected by breed; it also declined significantly with 40% water restriction 10 days post-restriction. Water restriction did not affect haematocrit value, plasma total protein, albumin, glucose or osmolality, which may not suggest a reduction in plasma volume. However, plasma creatinine increased in both breeds because of water restriction that remained elevated during rehydration. Water restriction increased plasma urea in the local group, while it decreased in the commercial group. Irrespective of rate of water restriction, it can be concluded that the two breeds can withstand up to 40% water restriction during high environmental temperature. However, the local breed may be superior in water conservation in relation to the commercial layers. © 2011 Blackwell Verlag GmbH.

Economic evaluation of progeny-testing and genomic selection schemes for small-sized nucleus dairy cattle breeding programs in developing countries.

PubMed

Kariuki, C M; Brascamp, E W; Komen, H; Kahi, A K; van Arendonk, J A M

2017-03-01

In developing countries minimal and erratic performance and pedigree recording impede implementation of large-sized breeding programs. Small-sized nucleus programs offer an alternative but rely on their economic performance for their viability. We investigated the economic performance of 2 alternative small-sized dairy nucleus programs [i.e., progeny testing (PT) and genomic selection (GS)] over a 20-yr investment period. The nucleus was made up of 453 male and 360 female animals distributed in 8 non-overlapping age classes. Each year 10 active sires and 100 elite dams were selected. Populations of commercial recorded cows (CRC) of sizes 12,592 and 25,184 were used to produce test daughters in PT or to create a reference population in GS, respectively. Economic performance was defined as gross margins, calculated as discounted revenues minus discounted costs following a single generation of selection. Revenues were calculated as cumulative discounted expressions (CDE, kg) × 0.32 (€/kg of milk) × 100,000 (size commercial population). Genetic superiorities, deterministically simulated using pseudo-BLUP index and CDE, were determined using gene flow. Costs were for one generation of selection. Results show that GS schemes had higher cumulated genetic gain in the commercial cow population and higher gross margins compared with PT schemes. Gross margins were between 3.2- and 5.2-fold higher for GS, depending on size of the CRC population. The increase in gross margin was mostly due to a decreased generation interval and lower running costs in GS schemes. In PT schemes many bulls are culled before selection. We therefore also compared 2 schemes in which semen was stored instead of keeping live bulls. As expected, semen storage resulted in an increase in gross margins in PT schemes, but gross margins remained lower than those of GS schemes. We conclude that implementation of small-sized GS breeding schemes can be economically viable for developing countries. The Authors. Published by the Federation of Animal Science Societies and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

Development of crossbreeding high-yield-potential strains for commercial cultivation in the medicinal mushroom Wolfiporia cocos (Higher Basidiomycetes).

PubMed

Xiang, Xiaozhao; Wang, Xiaoxia; Bian, Yinbing; Xu, Zhangyi

2016-07-01

Wolfiporia cocos is a well-known medicinal mushroom, and its dried sclerotia has been widely used as a traditional medicine in China, Japan, and other Asian countries for centuries. However, long-term asexual reproduction of the breeding system in W. cocos results in a current universal degeneration of cultivated strains. To develop a W. cocos breeding program that will benefit commercial cultivation, we previously developed an optimum method for indoor induction of W. cocos fruiting bodies and clarified the nature of preponderant binuclear sexual basidiospores. In this paper, we first show that the majority of W. cocos single-spore isolates cannot form sclerotium in field cultivation. We then investigated the possibility of breeding new strains by crossbreeding. Three types of mating reactions were observed in both intra-strain pairings and inter-strain pairings, and a total of fifty-five hybrids were selected by antagonistic testing and allele-specific polymerase chain reaction (PCR). Field cultivation of hybrids demonstrated that some hybrids can form sclerotium via two cultivated methods. Two new high-yield strains were identified. This report will stimulate new thinking on W. cocos and promote further extensive studies on crossbreeding in W. cocos, a new topic related to the development of more efficient protocols for the discrimination of hybrids in W. cocos.

Nucleotide variability and linkage disequilibrium patterns in the porcine MUC4 gene.

PubMed

Yang, Ming; Yang, Bin; Yan, Xueming; Ouyang, Jing; Zeng, Weihong; Ai, Huashui; Ren, Jun; Huang, Lusheng

2012-07-13

MUC4 is a type of membrane anchored glycoprotein and serves as the major constituent of mucus that covers epithelial surfaces of many tissues such as trachea, colon and cervix. MUC4 plays important roles in the lubrication and protection of the surface epithelium, cell proliferation and differentiation, immune response, cell adhesion and cancer development. To gain insights into the evolution of the porcine MUC4 gene, we surveyed the nucleotide variability and linkage disequilibrium (LD) within this gene in Chinese indigenous breeds and Western commercial breeds. A total of 53 SNPs covering the MUC4 gene were genotyped on 5 wild boars and 307 domestic pigs representing 11 Chinese breeds and 3 Western breeds. The nucleotide variability, haplotype phylogeny and LD extent of MUC4 were analyzed in these breeds. Both Chinese and Western breeds had considerable nucleotide diversity at the MUC4 locus. Western pig breeds like Duroc and Large White have comparable nucleotide diversity as many of Chinese breeds, thus artificial selection for lean pork production have not reduced the genetic variability of MUC4 in Western commercial breeds. Haplotype phylogeny analyses indicated that MUC4 had evolved divergently in Chinese and Western pigs. The dendrogram of genetic differentiation between breeds generally reflected demographic history and geographical distribution of these breeds. LD patterns were unexpectedly similar between Chinese and Western breeds, in which LD usually extended less than 20 kb. This is different from the presumed high LD extent (more than 100 kb) in Western commercial breeds. The significant positive Tajima'D, and Fu and Li's D statistics in a few Chinese and Western breeds implied that MUC4 might undergo balancing selection in domestic breeds. Nevertheless, we cautioned that the significant statistics could be upward biased by SNP ascertainment process. Chinese and Western breeds have similar nucleotide diversity but evolve divergently in the MUC4 region. Western breeds exhibited unusual low LD extent at the MUC4 locus, reflecting the complexity of nucleotide variability of pig genome. The finding suggests that high density (e.g. 1SNP/10 kb) markers are required to capture the underlying causal variants at such regions.

Crisis, Criteria, and Coercion - Beyond Half Measures: The US Marine Corps and Mass Atrocity Response Operations

DTIC Science & Technology

2017-05-25

war is a breeding ground for human atrocities. There exists a large body of scholarship on the relationship between war, politics, and occasions of...considerations are secondary to pursuing political ends. The Responsibility to Protect The seeds of R2P were planted in the late 1990s by humanitarian...respecting commercial shipping. 113 Headquarters, US Marine Corps, Concepts and Programs, 6

Evaluating the sensory properties of unpolished Australian wild rice.

PubMed

Tikapunya, Tiparat; Henry, Robert J; Smyth, Heather

2018-01-01

Australian wild rices are genetically distinct from commercially cultivated rices and present new opportunities for the development of improved rice cultivars. Before use in rice breeding, the eating and cooking properties of Australian wild rice must first be understood as these are key factors in determining rice quality and consumer acceptance. Samples of Australian wild rice (taxa B) were collected and evaluated together with a commercial Canadian wild rice (Zizania aquatic L.), Oryza sativa L.cv. Nipponbare, and selected commercial rices including long grain, medium grain, basmati, red basmati, and red rice. Cooking profiles were established, physical traits were measured and conventional descriptive analysis techniques were used to compare the sensory properties of the unpolished rices. Twenty six descriptors, together with definitions, were developed with a panel of twelve experienced assessors including aroma, flavour, texture and aftertaste attributes. Results reveal that the Australian wild rice had a mild aroma and flavour similar to that of red rice and red basmati but without the lingering aftertaste. In terms of texture, the wild rice was firmer, and somewhat crunchy and chewy rather than soft and fluffy despite requiring a longer cooking time. The sensory, physical and cooking profiles indicate that Australian wild rice has a high potential for commercialization in itself and provides a suitable genetic source for breeding programs, particularly in the coloured rice market. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

Predicting Breed Composition Using Breed Frequencies of 50,000 Markers from the U.S. Meat Animal Research Center 2,000 Bull Project

USDA-ARS?s Scientific Manuscript database

Our objective was to evaluate whether breed composition of crossbred cattle could be predicted using reference breed frequencies of SNP markers on the BovineSNP50 array. Semen DNA samples of over 2,000 bulls from 16 common commercial beef breeds were genotyped using the array and used to estimate cu...

Similar effects of QTL Haplotypes for Bacterial Cold Water Disease resistance across two generations in a commercial rainbow trout breeding population

USDA-ARS?s Scientific Manuscript database

Previously we have demonstrated that genomic selection (GS) for bacterial cold water disease (BCWD) resistance can double the accuracy of traditional pedigree-based selection in a commercial rainbow trout breeding population. The objective of this study was to evaluate the effectiveness of marker ...

Dietary Capsicum and Curcuma longa oleoresins alter the intestinal microbiome and Necrotic Enteritis Severity in three commercial broiler breeds

USDA-ARS?s Scientific Manuscript database

Three commercial broiler breeds were fed from hatch with a diet supplemented with Capsicum and Curcuma longa oleoresins, and co-infected with Eimeria maxima and Clostridium perfringens to induce necrotic enteritis (NE). Pyrotag deep sequencing of bacterial 16S rRNA showed that gut microbiota compos...

Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds.

PubMed

Makina, Sithembile O; Taylor, Jeremy F; van Marle-Köster, Este; Muchadeyi, Farai C; Makgahlela, Mahlako L; MacNeil, Michael D; Maiwashe, Azwihangwisi

2015-01-01

Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40-60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r (2)≥ 0.20 would require about 30,000-50,000 SNPs. However, r (2)≥ 0.20 extended only up to 10-20 kb in the Nguni and Drakensberger and 20-40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.

Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds

PubMed Central

Makina, Sithembile O.; Taylor, Jeremy F.; van Marle-Köster, Este; Muchadeyi, Farai C.; Makgahlela, Mahlako L.; MacNeil, Michael D.; Maiwashe, Azwihangwisi

2015-01-01

Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40–60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r2≥ 0.20 would require about 30,000–50,000 SNPs. However, r2≥ 0.20 extended only up to 10–20 kb in the Nguni and Drakensberger and 20–40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa. PMID:26648975

Optimizing the design of small-sized nucleus breeding programs for dairy cattle with minimal performance recording.

PubMed

Kariuki, C M; Komen, H; Kahi, A K; van Arendonk, J A M

2014-12-01

Dairy cattle breeding programs in developing countries are constrained by minimal and erratic pedigree and performance recording on cows on commercial farms. Small-sized nucleus breeding programs offer a viable alternative. Deterministic simulations using selection index theory were performed to determine the optimum design for small-sized nucleus schemes for dairy cattle. The nucleus was made up of 197 bulls and 243 cows distributed in 8 non-overlapping age classes. Each year 10 sires and 100 dams were selected to produce the next generation of male and female selection candidates. Conception rates and sex ratio were fixed at 0.90 and 0.50, respectively, translating to 45 male and 45 female candidates joining the nucleus per year. Commercial recorded dams provided information for genetic evaluation of selection candidates (bulls) in the nucleus. Five strategies were defined: nucleus records only [within-nucleus dam performance (DP)], progeny records in addition to nucleus records [progeny testing (PT)], genomic information only [genomic selection (GS)], dam performance records in addition to genomic information (GS+DP), and progeny records in addition to genomic information (GS+PT). Alternative PT, GS, GS+DP, and GS+PT schemes differed in the number of progeny per sire and size of reference population. The maximum number of progeny records per sire was 30, and the maximum size of the reference population was 5,000. Results show that GS schemes had higher responses and lower accuracies compared with other strategies, with the higher response being due to shorter generation intervals. Compared with similar sized progeny-testing schemes, genomic-selection schemes would have lower accuracies but these are offset by higher responses per year, which might provide additional incentive for farmers to participate in recording. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Myrciaria dubia, an Amazonian fruit: population structure and its implications for germplasm conservation and genetic improvement.

PubMed

Nunes, C F; Setotaw, T A; Pasqual, M; Chagas, E A; Santos, E G; Santos, D N; Lima, C G B; Cançado, G M A

2017-03-22

Myrciaria dubia (camu-camu) is an Amazon tree that produces a tart fruit with high vitamin C content. It is probably the fruit with the highest vitamin C content among all Brazilian fruit crops and it can be used to supplement daily vitamin C dose. This property has attracted the attention of consumers and, consequently, encouraged fruit farmers to produce it. In order to identify and select potential accessions for commercial exploitation and breeding programs, M. dubia has received considerable research attention. The identification and characterization of genetic diversity, as well as identification of the population structure of accessions preserved in germplasm banks are fundamental for the success of any breeding program. The objective of this study was to evaluate the genetic variability of 10 M. dubia populations obtained from the shores of Reis Lake, located in the municipality of Caracaraí, Roraima, Brazil. Fourteen polymorphic inter simple sequence repeat (ISSR) markers were used to study the population genetic diversity, which resulted in 108 identified alleles. Among the 14 primers, GCV, UBC810, and UBC827 produced the highest number of alleles. The study illustrated the suitability and efficiency of ISSR markers to study the genetic diversity of M. dubia accessions. We also revealed the existence of high genetic variability among both accessions and populations that can be exploited in future breeding programs and conservation activities of this species.

Nucleotide variability and linkage disequilibrium patterns in the porcine MUC4 gene

PubMed Central

2012-01-01

Background MUC4 is a type of membrane anchored glycoprotein and serves as the major constituent of mucus that covers epithelial surfaces of many tissues such as trachea, colon and cervix. MUC4 plays important roles in the lubrication and protection of the surface epithelium, cell proliferation and differentiation, immune response, cell adhesion and cancer development. To gain insights into the evolution of the porcine MUC4 gene, we surveyed the nucleotide variability and linkage disequilibrium (LD) within this gene in Chinese indigenous breeds and Western commercial breeds. Results A total of 53 SNPs covering the MUC4 gene were genotyped on 5 wild boars and 307 domestic pigs representing 11 Chinese breeds and 3 Western breeds. The nucleotide variability, haplotype phylogeny and LD extent of MUC4 were analyzed in these breeds. Both Chinese and Western breeds had considerable nucleotide diversity at the MUC4 locus. Western pig breeds like Duroc and Large White have comparable nucleotide diversity as many of Chinese breeds, thus artificial selection for lean pork production have not reduced the genetic variability of MUC4 in Western commercial breeds. Haplotype phylogeny analyses indicated that MUC4 had evolved divergently in Chinese and Western pigs. The dendrogram of genetic differentiation between breeds generally reflected demographic history and geographical distribution of these breeds. LD patterns were unexpectedly similar between Chinese and Western breeds, in which LD usually extended less than 20 kb. This is different from the presumed high LD extent (more than 100 kb) in Western commercial breeds. The significant positive Tajima’D, and Fu and Li’s D statistics in a few Chinese and Western breeds implied that MUC4 might undergo balancing selection in domestic breeds. Nevertheless, we cautioned that the significant statistics could be upward biased by SNP ascertainment process. Conclusions Chinese and Western breeds have similar nucleotide diversity but evolve divergently in the MUC4 region. Western breeds exhibited unusual low LD extent at the MUC4 locus, reflecting the complexity of nucleotide variability of pig genome. The finding suggests that high density (e.g. 1SNP/10 kb) markers are required to capture the underlying causal variants at such regions. PMID:22793500

Hybrid maize breeding with doubled haploids: II. Optimum type and number of testers in two-stage selection for general combining ability.

PubMed

Longin, C Friedrich H; Utz, H Friedrich; Melchinger, Albrecht E; Reif, Jochen C

2007-02-01

Optimum allocation of test resources is of crucial importance for the efficiency of breeding programs. Our objectives were to (1) determine the optimum allocation of the number of lines, test locations, as well as number and type of testers in hybrid maize breeding using doubled haploids with two breeding strategies for improvement of general combining ability (GCA), (2) compare the maximum selection gain (DeltaG) achievable under both strategies, and (3) give recommendations for the optimum implementation of doubled haploids in commercial hybrid maize breeding. We calculated DeltaG by numerical integration for two two-stage selection strategies with evaluation of (1) testcross performance in both stages (BS1) or (2) line per se performance in the first stage followed by testcross performance in the second stage (BS2). Different assumptions were made regarding the budget, variance components (VCs), and the correlation between line per se performance and GCA. Selection gain for GCA increased with a broader genetic base of the tester. Hence, testers combining a large number of divergent lines are advantageous. However, in applied breeding programs, the use of single- or double-cross testers in the first and inbred testers in the second selection stage may be a good compromise between theoretical and practical requirements. With a correlation between line per se performance and GCA of 0.50, DeltaG for BS1 is about 5% higher than for BS2, if an economic weight of line per se performance is neglected. With increasing economic weight of line per se performance, relative efficiency of BS2 increased rapidly resulting in a superiority of BS2 over BS1 already for an economic weight for line per se performance larger than 0.1. Considering the importance of an economic seed production, an economic weight larger than 0.1 seems realistic indicating the necessity of separate breeding strategies for seed and pollen parent heterotic groups.

Quality assessment of tomato landraces and virus-resistant breeding lines: quick estimation by near infrared reflectance spectroscopy.

PubMed

García-Martínez, Santiago; Gálvez-Sola, Luis N; Alonso, Arantxa; Agulló, Enrique; Rubio, Fernando; Ruiz, Juan J; Moral, Raúl

2012-04-01

Several tomato landraces are very popular in south-eastern Spain for their organoleptic fruit quality, but these cultivars are highly susceptible to several viruses. A breeding programme is being carried out for the introduction of virus resistances into these landraces. In the last steps of our breeding programme a high number of breeding lines must be evaluated for agronomic and organoleptic quality parameters. Near infrared reflectance spectroscopy (NIRS) technology shows considerable promise and is ideally suited to the requirements of breeders. Significant differences between a set of 35 tomato breeding lines, seven landraces and one commercial hybrid were observed for quality and mineral content parameters, suggesting that there are considerable levels of genetic diversity between the cultivar groups studied. Using NIRS on dry samples of tomato constitutes a feasible technique to estimate the content of several minerals (C, N, P, K, Ca, Na, Mn, Mg and Cu) according to the coefficient of determination for calibration (R(2) > 0.90). NIRS estimations of soluble solids content and titratable acidity obtained were considered useful only for general screening purposes. NIRS technology may be a useful tool in the selection of lines coming out of tomato breeding programs, allowing a quick estimation of mineral content. However, the estimation of soluble solids content and titratable acidity by NIRS must be improved. Copyright © 2011 Society of Chemical Industry.

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.

Production of sugarcane and tropical grasses as a renewable energy source. First quarterly report, June 1--August 31, 1977

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

Alexander, A.G.

Research was initiated on the intensive production of sugarcane and other tropical grasses as solar-dried forages. Greenhouse experiments designed to screen candidate clones and to evaluate growth curves were the first to get underway. Chemical growth control tests were also initiated. Plant materials at this stage consist of commercial sugarcane hybrids, progeny from the AES-UPR cane breeding program, Saccharum clones from the species officinarum, spontaneum, sinense, and robustum, Erianthus clones, a commercial tropical forage grass, napier grass, and forms of S. spontaneum plus Arundo donax growing wild in Puerto Rico. Initial stages of cane breeding and progeny selection for themore » high tonnage attribute were begun during August. Foliar tissue analyses for N, P, K, S, and Si were started together-with assays for acid invertase and other components of expanding stem tissue. The first field experiment was initiated during July at the semi-arid Lajas Substation. Four clones (three sugarcane hybrids plus napier grass var. Merker) are being evaluated incident to row spacing and harvest frequency in field-plots.« less

Comparison of Bioactive Compounds and Quality Traits of Breast Meat from Korean Native Ducks and Commercial Ducks.

PubMed

Lee, Hyun Jung; Jayasena, Dinesh D; Kim, Sun Hyo; Kim, Hyun Joo; Heo, Kang Nyung; Song, Ji Eun; Jo, Cheorun

2015-01-01

The aim of this research was to compare the bioactive compound content and quality traits of breast meat from male and female Korean native ducks (KND) and commercial ducks (CD, Cherry Valley). Meat from three 6-wk old birds of each sex from KND and CD were evaluated for carcass and breast weights, pH, color, cooking loss, shear force, and bioactive compound (creatine, carnosine, anserine, betaine, and L-carnitine) content. KND showed significantly higher carcass weights than CD whereas no such difference (p>0.05) was found between male and female ducks. The breed and sex had no significant effects on the breast weight, pH value, and shear force. However, KND had significantly lower cooking loss values than did CD. Creatine, anserine, and L-carnitine contents were significantly higher in KND than in CD and were predominant in female ducks compared to males. The results of this study provide rare information regarding the amounts and the determinants of several bioactive compounds in duck meat, which can be useful for selection and breeding programs, and for popularizing indigenous duck meat.

Towards a Molecular Understanding of the Biosynthesis of Amaryllidaceae Alkaloids in Support of Their Expanding Medical Use

PubMed Central

Takos, Adam M.; Rook, Fred

2013-01-01

The alkaloids characteristically produced by the subfamily Amaryllidoideae of the Amaryllidaceae, bulbous plant species that include well know genera such as Narcissus (daffodils) and Galanthus (snowdrops), are a source of new pharmaceutical compounds. Presently, only the Amaryllidaceae alkaloid galanthamine, an acetylcholinesterase inhibitor used to treat symptoms of Alzheimer’s disease, is produced commercially as a drug from cultivated plants. However, several Amaryllidaceae alkaloids have shown great promise as anti-cancer drugs, but their further clinical development is restricted by their limited commercial availability. Amaryllidaceae species have a long history of cultivation and breeding as ornamental bulbs, and phytochemical research has focussed on the diversity in alkaloid content and composition. In contrast to the available pharmacological and phytochemical data, ecological, physiological and molecular aspects of the Amaryllidaceae and their alkaloids are much less explored and the identity of the alkaloid biosynthetic genes is presently unknown. An improved molecular understanding of Amaryllidaceae alkaloid biosynthesis would greatly benefit the rational design of breeding programs to produce cultivars optimised for the production of pharmaceutical compounds and enable biotechnology based approaches. PMID:23727937

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.

Genetic Map of Mango: A Tool for Mango Breeding

PubMed Central

Kuhn, David N.; Bally, Ian S. E.; Dillon, Natalie L.; Innes, David; Groh, Amy M.; Rahaman, Jordon; Ophir, Ron; Cohen, Yuval; Sherman, Amir

2017-01-01

Mango (Mangifera indica) is an economically and nutritionally important tropical/subtropical tree fruit crop. Most of the current commercial cultivars are selections rather than the products of breeding programs. To improve the efficiency of mango breeding, molecular markers have been used to create a consensus genetic map that identifies all 20 linkage groups in seven mapping populations. Polyembryony is an important mango trait, used for clonal propagation of cultivars and rootstocks. In polyembryonic mango cultivars, in addition to a zygotic embryo, several apomictic embryos develop from maternal tissue surrounding the fertilized egg cell. This trait has been associated with linkage group 8 in our consensus genetic map and has been validated in two of the seven mapping populations. In addition, we have observed a significant association between trait and single nucleotide polymorphism (SNP) markers for the vegetative trait of branch habit and the fruit traits of bloom, ground skin color, blush intensity, beak shape, and pulp color. PMID:28473837

Breeding potential of elite Pee Dee germplasm in Upland cotton breeding programs

USDA-ARS?s Scientific Manuscript database

Successful plant breeding programs begin with parental line selection. Effective parental line selection is facilitated when the breeding potential of candidate parental lines is known. Using topcross families involving germplasm representing eight US public cotton breeding programs, we evaluated th...

50 CFR 15.21 - General application procedures.

Code of Federal Regulations, 2010 CFR

2010-10-01

... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.21 General... purposes only: Scientific research; zoological breeding or display programs; cooperative breeding programs...) A person wishing to obtain a permit under this subpart or approval of cooperative breeding programs...

50 CFR 15.21 - General application procedures.

Code of Federal Regulations, 2011 CFR

2011-10-01

... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.21 General... purposes only: Scientific research; zoological breeding or display programs; cooperative breeding programs...) A person wishing to obtain a permit under this subpart or approval of cooperative breeding programs...

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.

21 CFR 558.185 - Coumaphos.

Code of Federal Regulations, 2013 CFR

2013-04-01

... chapter. (e) Conditions of use—(1) Beef and dairy cattle—(i) Amount. 0.0002 lb. (0.091 gram) per 100 lb... of stress; treatment of colored breeds of commercial layers should be avoided while in production since these breeds appear to be more sensitive to coumaphos than white breeds; as sole medication...

21 CFR 558.185 - Coumaphos.

Code of Federal Regulations, 2011 CFR

2011-04-01

... chapter. (e) Conditions of use—(1) Beef and dairy cattle—(i) Amount. 0.0002 lb. (0.091 gram) per 100 lb... of stress; treatment of colored breeds of commercial layers should be avoided while in production since these breeds appear to be more sensitive to coumaphos than white breeds; as sole medication...

21 CFR 558.185 - Coumaphos.

Code of Federal Regulations, 2012 CFR

2012-04-01

... chapter. (e) Conditions of use—(1) Beef and dairy cattle—(i) Amount. 0.0002 lb. (0.091 gram) per 100 lb... of stress; treatment of colored breeds of commercial layers should be avoided while in production since these breeds appear to be more sensitive to coumaphos than white breeds; as sole medication...

21 CFR 558.185 - Coumaphos.

Code of Federal Regulations, 2014 CFR

2014-04-01

... chapter. (e) Conditions of use—(1) Beef and dairy cattle—(i) Amount. 0.0002 lb. (0.091 gram) per 100 lb... of stress; treatment of colored breeds of commercial layers should be avoided while in production since these breeds appear to be more sensitive to coumaphos than white breeds; as sole medication...

Sugar Beet Breeding - Where are We Going from Here?

USDA-ARS?s Scientific Manuscript database

USDA-Agricultural Research Service plant breeders generally do pre-breeding, but today we will talk a little about what the future holds for new varieties and directions in commercial plant breeding. This presentation is my vision, not a presentation from a seed company, and we will talk about trend...

Reduced neonatal mortality in Meishan piglets: a role for hepatic fatty acids?

PubMed

Fainberg, Hernan P; Bodley, Katherine; Bacardit, Jaume; Li, Dongfang; Wessely, Frank; Mongan, Nigel P; Symonds, Michael E; Clarke, Lynne; Mostyn, Alison

2012-01-01

The Meishan pig breed exhibits increased prolificacy and reduced neonatal mortality compared to commercial breeds, such as the Large White, prompting breeders to introduce the Meishan genotype into commercial herds. Commercial piglets are highly susceptible to hypoglycemia, hypothermia, and death, potentially due to limited lipid stores and/or delayed hepatic metabolic ability. We therefore hypothesized that variation in hepatic development and lipid metabolism could contribute to the differences in neonatal mortality between breeds. Liver samples were obtained from piglets of each breed on days 0, 7, and 21 of postnatal age and subjected to molecular and biochemical analysis. At birth, both breeds exhibited similar hepatic glycogen contents, despite Meishan piglets having significantly lower body weight. The livers from newborn Meishan piglets exhibited increased C18∶1n9C and C20∶1n9 but lower C18∶0, C20∶4n6, and C22∶6n3 fatty acid content. Furthermore, by using an unsupervised machine learning approach, we detected an interaction between C18∶1n9C and glycogen content in newborn Meishan piglets. Bioinformatic analysis could identify unique age-based clusters from the lipid profiles in Meishan piglets that were not apparent in the commercial offspring. Examination of the fatty acid signature during the neonatal period provides novel insights into the body composition of Meishan piglets that may facilitate liver responses that prevent hypoglycaemia and reduce offspring mortality.

50 CFR 15.26 - Approval of cooperative breeding programs.

Code of Federal Regulations, 2011 CFR

2011-10-01

... WILDLIFE AND PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.26 Approval of cooperative breeding programs. Upon receipt of a complete application, the Director... 50 Wildlife and Fisheries 1 2011-10-01 2011-10-01 false Approval of cooperative breeding programs...

Stocking activities for the Arctic charr in Lake Geneva: Genetic effects in space and time.

PubMed

Savary, Romain; Dufresnes, Christophe; Champigneulle, Alexis; Caudron, Arnaud; Dubey, Sylvain; Perrin, Nicolas; Fumagalli, Luca

2017-07-01

Artificial stocking practices are widely used by resource managers worldwide, in order to sustain fish populations exploited by both recreational and commercial activities, but their benefits are controversial. Former practices involved exotic strains, although current programs rather consider artificial breeding of local fishes (supportive breeding). Understanding the complex genetic effects of these management strategies is an important challenge with economic and conservation implications, especially in the context of population declines. In this study, we focus on the declining Arctic charr ( Salvelinus alpinus ) population from Lake Geneva (Switzerland and France), which has initially been restocked with allochtonous fishes in the early eighties, followed by supportive breeding. In this context, we conducted a genetic survey to document the evolution of the genetic diversity and structure throughout the last 50 years, before and after the initiation of hatchery supplementation, using contemporary and historical samples. We show that the introduction of exotic fishes was associated with a genetic bottleneck in the 1980-1990s, a break of Hardy-Weinberg Equilibrium (HWE), a reduction in genetic diversity, an increase in genetic structure among spawning sites, and a change in their genetic composition. Together with better environmental conditions, three decades of subsequent supportive breeding using local fishes allowed to re-establish HWE and the initial levels of genetic variation. However, current spawning sites have not fully recovered their original genetic composition and were extensively homogenized across the lake. Our study demonstrates the drastic genetic consequences of different restocking tactics in a comprehensive spatiotemporal framework and suggests that genetic alteration by nonlocal stocking may be partly reversible through supportive breeding. We recommend that conservation-based programs consider local diversity and implement adequate protocols to limit the genetic homogenization of this Arctic charr population.

Hybrid origin of European commercial pigs examined by an in-depth haplotype analysis on chromosome 1

PubMed Central

Bosse, Mirte; Madsen, Ole; Megens, Hendrik-Jan; Frantz, Laurent A. F.; Paudel, Yogesh; Crooijmans, Richard P. M. A.; Groenen, Martien A. M.

2014-01-01

Although all farm animals have an original source of domestication, a large variety of modern breeds exist that are phenotypically highly distinct from the ancestral wild population. This phenomenon can be the result of artificial selection or gene flow from other sources into the domesticated population. The Eurasian wild boar (Sus scrofa) has been domesticated at least twice in two geographically distinct regions during the Neolithic revolution when hunting shifted to farming. Prior to the establishment of the commercial European pig breeds we know today, some 200 years ago Chinese pigs were imported into Europe to improve local European pigs. Commercial European domesticated pigs are genetically more diverse than European wild boars, although historically the latter represents the source population for domestication. In this study we examine the cause of the higher diversity within the genomes of European commercial pigs compared to their wild ancestors by testing two different hypotheses. In the first hypothesis we consider that European commercial pigs are a mix of different European wild populations as a result of movement throughout Europe, hereby acquiring haplotypes from all over the European continent. As an alternative hypothesis, we examine whether the introgression of Asian haplotypes into European breeds during the Industrial Revolution caused the observed increase in diversity. By using re-sequence data for chromosome 1 of 136 pigs and wild boars, we show that an Asian introgression of about 20% into the genome of European commercial pigs explains the majority of the increase in genetic diversity. These findings confirm that the Asian hybridization, that was used to improve production traits of local breeds, left its signature in the genome of the commercial pigs we know today. PMID:25601878

Dairy sheep production research at the University of Wisconsin-Madison, USA – a review

PubMed Central

2014-01-01

Commercial milking of sheep is a new agricultural industry in the United States starting approximately 30 yr ago. The industry is still small, but it is growing. The majority of the sheep milk is used in the production of specialty cheeses. The United States is the major importer of sheep milk cheeses with 50 to 60% of annual world exports coming to the United States during the past 20 yr. Therefore, there is considerable growth potential for the industry in the United States. The only dairy sheep research flock in North America is located at the Spooner Agricultural Research Station of the University of Wisconsin-Madison. The research program started in 1993 and has been multifaceted; dealing with several areas important to commercial dairy sheep farmers. The East Friesian and Lacaune dairy breeds were compared and introduced to the industry through the research program. Both dairy breeds produced significantly more milk than traditional meat-wool breeds found in the U.S., but the two breeds differed in their production traits. East Friesian-cross ewes produced more lambs and slightly more milk than Lacaune-cross ewes whereas Lacaune-cross ewes produced milk with a higher percentage of fat and protein than East Friesian-cross ewes. Lactation physiology studies have shown that ewes with active corpora lutea have increased milk yields, oxytocin release during milking is required to obtain normal fat percentages in the milk, large udder cisterns of dairy ewes can allow for increased milking intervals, and short daylengths during late pregnancy results in increased milk yield. In the nutrition area, legume-grass pastures and forages with a higher percentage of legume will result in increased milk production. Grazing ewes respond to additional supplementation with increased milk yield, but it is important to match the supplement to the quality of the grazing. Ewes on high quality legume-grass pastures that are high in rumen degradable protein respond with increased milk production to supplements high in energy and/or high in rumen undegraded protein. PMID:24739956

Dairy sheep production research at the University of Wisconsin-Madison, USA - a review.

PubMed

Thomas, David L; Berger, Yves M; McKusick, Brett C; Mikolayunas, Claire M

2014-01-01

Commercial milking of sheep is a new agricultural industry in the United States starting approximately 30 yr ago. The industry is still small, but it is growing. The majority of the sheep milk is used in the production of specialty cheeses. The United States is the major importer of sheep milk cheeses with 50 to 60% of annual world exports coming to the United States during the past 20 yr. Therefore, there is considerable growth potential for the industry in the United States. The only dairy sheep research flock in North America is located at the Spooner Agricultural Research Station of the University of Wisconsin-Madison. The research program started in 1993 and has been multifaceted; dealing with several areas important to commercial dairy sheep farmers. The East Friesian and Lacaune dairy breeds were compared and introduced to the industry through the research program. Both dairy breeds produced significantly more milk than traditional meat-wool breeds found in the U.S., but the two breeds differed in their production traits. East Friesian-cross ewes produced more lambs and slightly more milk than Lacaune-cross ewes whereas Lacaune-cross ewes produced milk with a higher percentage of fat and protein than East Friesian-cross ewes. Lactation physiology studies have shown that ewes with active corpora lutea have increased milk yields, oxytocin release during milking is required to obtain normal fat percentages in the milk, large udder cisterns of dairy ewes can allow for increased milking intervals, and short daylengths during late pregnancy results in increased milk yield. In the nutrition area, legume-grass pastures and forages with a higher percentage of legume will result in increased milk production. Grazing ewes respond to additional supplementation with increased milk yield, but it is important to match the supplement to the quality of the grazing. Ewes on high quality legume-grass pastures that are high in rumen degradable protein respond with increased milk production to supplements high in energy and/or high in rumen undegraded protein.

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.

Dietary Capsicum and Curcuma longa oleoresins increase intestinal microbiome and necrotic enteritis in three commercial broiler breeds.

PubMed

Kim, Ji Eun; Lillehoj, Hyun S; Hong, Yeong Ho; Kim, Geun Bae; Lee, Sung Hyen; Lillehoj, Erik P; Bravo, David M

2015-10-01

Three commercial broiler breeds were fed from hatch with a diet supplemented with Capsicum and Curcuma longa oleoresins, and co-infected with Eimeria maxima and Clostridium perfringens to induce necrotic enteritis (NE). Pyrotag deep sequencing of bacterial 16S rRNA showed that gut microbiota compositions were quite distinct depending on the broiler breed type. In the absence of oleoresin diet, the number of operational taxonomic units (OTUs), was decreased in infected Cobb, and increased in Ross and Hubbard, compared with the uninfected. In the absence of oleoresin diet, all chicken breeds had a decreased Candidatus Arthromitus, while the proportion of Lactobacillus was increased in Cobb, but decreased in Hubbard and Ross. Oleoresin supplementation of infected chickens increased OTUs in Cobb and Ross, but decreased OTUs in Hubbard, compared with unsupplemented/infected controls. Oleoresin supplementation of infected Cobb and Hubbard was associated with an increased percentage of gut Lactobacillus and decreased Selenihalanaerobacter, while Ross had a decreased fraction of Lactobacillus and increased Selenihalanaerobacter, Clostridium, Calothrix, and Geitlerinema. These results suggest that dietary Capsicum/Curcuma oleoresins reduced the negative consequences of NE on body weight and intestinal lesion, in part, through alteration of the gut microbiome in 3 commercial broiler breeds. Published by Elsevier Ltd.

In vitro fermentative capacity of swine large intestine: comparison between native Lantang and commercial Duroc breeds.

PubMed

Cheng, Peng Hui; Liang, Juan Boo; Wu, Yin Bao; Wang, Yan; Tufarelli, Vincenzo; Laudadio, Vito; Liao, Xin Di

2017-08-01

Native Lantang and commercial Duroc pigs were used as animal models to evaluate the differences existing in dietary fiber utilization ability between breeds. Animals were fed the same diet from weaning (4 weeks) to 4 months of age. Neutral detergent fiber (NDF) from wheat bran (as substrate) and fecal samples from the two breeds (as inoculum) were used in an in vitro gas production trial. Results showed that cumulative and maximum gas productions were higher in inocula from Lantang than those from the Duroc breed (P < 0.05). The degradation capacity of NDF for microbiome from Lantang fecal samples were significantly higher compared to Duroc (P < 0.01). The total quantity of short-chain fatty acids and its constituents from the fermentation liquors were different between breeds, suggesting that the dynamic characteristics of fermentation differed between the two breeds. The PCR denaturing gradient gel electrophoresis fingerprint and cluster analysis demonstrated that microbial communities of the two breeds were separated into two clusters and the bacterial community structure of large intestine among the two breed of pigs was different. Our results concluded that Lantang had higher dietary fiber degradation capacity than Duroc pigs, and the higher degradation capacity for the former breed was due to differences in the inherent microbial community in their respective large intestines. © 2016 Japanese Society of Animal Science.

Natural resistance of Sri Lankan village chicken to Salmonella gallinarum infection.

PubMed

Weerasooriya, K M S G; Fernando, P S; Liyanagunawardena, N; Wijewardena, G; Wijemuni, M I; Samarakoon, S A T C

2017-12-01

1. An experiment was conducted to compare the natural resistance of an indigenous breed of local village chickens to Salmonella gallinarum with two commercial breeds: ISA Brown and ISA White layers under experimental conditions. 2. A total of 72 chickens from each of these breeds were randomly distributed to 4 pens to provide equal numbers of two replicate pens maintained as infected and control (uninfected). All chickens in infected groups were inoculated orally with 1 × 10 8 CFU (1 ml dose) of a field isolate of S. gallinarum, at the age of 8 and 16 weeks given over 5 consecutive days. Growth performance, clinical signs, gross pathological lesions and antibody responses were measured. 3. A significantly higher mortality was observed in the brown layers compared with the white layers, and clinical signs and mortality were absent in village chickens. However, a large number of birds with gross lesions and high antibody titres were detected in village chickens, indicating that birds had the disease subclinically. Commercial breeds had a significantly higher body weight, feed intake and feed conversion efficiency. 4. There was a significantly lower proportion of positive reactors in village chickens in the whole-blood agglutination test (35%) compared to brown (100%) and white (90%) layers even after the second inoculation. Uninfected birds were negative in all groups. The indirect enzyme-linked immunosorbent assay confirmed these observations. 5. These results suggest that the indigenous breed had superior natural resistance to S. gallinarum than the commercial breeds.

Selection for Growth Performance in Broiler Chickens Associates with Less Diet Flexibility

PubMed Central

Pauwels, Jana; Coopman, Frank; Cools, An; Michiels, Joris; Fremaut, Dirk; De Smet, Stefaan; Janssens, Geert P. J.

2015-01-01

Global competition for high standard feed-food resources between man and livestock, such as industrial broilers, is a concerning problem. In addition, the low productivity of scavenger chickens in developing countries leaves much to be desired. Changing the ingredients, and therefore, the nutrient composition of feed intake by commercial fed as well as scavenger chickens seems like an obvious solution. In this study, the ability of four broiler chicken breeds to perform on a commercial versus a scavenger diet was tested. The four broiler breeds differed genetically in growth potential. A significant (P < 0.01) negative effect of the scavenger diet on the bodyweight of the fast growing breeds was found and this effect decreased with decreasing growth rate in the other breeds. These differences in bodyweight gain could not be explained by differences in nutrient digestibility but were caused by the lack of ability of the fast growing breeds to increase their feed intake sufficiently. PMID:26042600

Regulating transgenic crops sensibly: lessons from plant breeding, biotechnology and genomics.

PubMed

Bradford, Kent J; Van Deynze, Allen; Gutterson, Neal; Parrott, Wayne; Strauss, Steven H

2005-04-01

The costs of meeting regulatory requirements and market restrictions guided by regulatory criteria are substantial impediments to the commercialization of transgenic crops. Although a cautious approach may have been prudent initially, we argue that some regulatory requirements can now be modified to reduce costs and uncertainty without compromising safety. Long-accepted plant breeding methods for incorporating new diversity into crop varieties, experience from two decades of research on and commercialization of transgenic crops, and expanding knowledge of plant genome structure and dynamics all indicate that if a gene or trait is safe, the genetic engineering process itself presents little potential for unexpected consequences that would not be identified or eliminated in the variety development process before commercialization. We propose that as in conventional breeding, regulatory emphasis should be on phenotypic rather than genomic characteristics once a gene or trait has been shown to be safe.

Whole genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo)

PubMed Central

2012-01-01

Background The turkey (Meleagris gallopavo) is an important agricultural species and the second largest contributor to the world’s poultry meat production. Genetic improvement is attributed largely to selective breeding programs that rely on highly heritable phenotypic traits, such as body size and breast muscle development. Commercial breeding with small effective population sizes and epistasis can result in loss of genetic diversity, which in turn can lead to reduced individual fitness and reduced response to selection. The presence of genomic diversity in domestic livestock species therefore, is of great importance and a prerequisite for rapid and accurate genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome. Results Alignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, which subsequently were used for the analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles. Conclusion The turkey genome is much less diverse with a relatively low frequency of heterozygous SNPs as compared to other livestock species like chicken and pig. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome. All commercial lines appear to share a common origin. Presence of different alleles/haplotypes in the SM population highlights that specific haplotypes have been selected in the modern domesticated turkey. PMID:22891612

50 CFR 15.23 - Permits for zoological breeding or display programs.

Code of Federal Regulations, 2011 CFR

2011-10-01

... OF WILDLIFE AND PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.23 Permits for zoological breeding or display programs. (a) Application requirements for... 50 Wildlife and Fisheries 1 2011-10-01 2011-10-01 false Permits for zoological breeding or display...

50 CFR 15.23 - Permits for zoological breeding or display programs.

Code of Federal Regulations, 2010 CFR

2010-10-01

... OF WILDLIFE AND PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.23 Permits for zoological breeding or display programs. (a) Application requirements for... 50 Wildlife and Fisheries 1 2010-10-01 2010-10-01 false Permits for zoological breeding or display...

Cultivation and breeding of Chinese medicinal plants in Germany.

PubMed

Heuberger, Heidi; Bauer, Rudolf; Friedl, Fritz; Heubl, Günther; Hummelsberger, Josef; Nögel, Rainer; Seidenberger, Rebecca; Torres-Londoño, Paula

2010-12-01

Chinese herbal medicine (CHM) is increasingly used in Germany and Europe. Due to the need for herbal drugs of consistent quality and reliable supply, methods for commercial field cultivation and post-harvest processing under south German conditions have been developed for selected plant species used in CHM since 1999. The project used an interdisciplinary approach covering all aspects from seed sourcing to medicinal application. This paper describes the outcome of the agricultural seed and field experiments, breeding program, botanical and chemical characterization of the experimental material, comparison of experimental and imported herbal material with respect to their pharmaceutical quality, transfer of production methods and plant material to specialized farmers, medicinal application and, finally, information for users along the chain of distribution about the benefits of the locally produced herbal material. © Georg Thieme Verlag KG Stuttgart · New York.

Magnetic fusion commercial power plants

NASA Astrophysics Data System (ADS)

Sheffield, J.

Toroidal magnetic systems present the best opportunity to make a commercial fusion power plant. They offer potential solutions to the main requirements that confront a power plant designer. An ideal system may be postulated in which the coils are a very small part of the cost, and the cost stems primarily from the inescapable components: minimal plasma heating (and sustaining system), tritium breeding blanket, shield, particle input, removal and treatment system, heat transfer system, generators, buildings, and balance of plant. No present system meets the ideal standards; however, toroidal systems contain among them the elements required. Consequently, a logical program may be based upon an evolutionary development, building on the contributions of the tokamak, which has been the mainline of research for a number of years.

Comparison of Bioactive Compounds and Quality Traits of Breast Meat from Korean Native Ducks and Commercial Ducks

PubMed Central

Kim, Sun Hyo; Heo, Kang Nyung

2015-01-01

The aim of this research was to compare the bioactive compound content and quality traits of breast meat from male and female Korean native ducks (KND) and commercial ducks (CD, Cherry Valley). Meat from three 6-wk old birds of each sex from KND and CD were evaluated for carcass and breast weights, pH, color, cooking loss, shear force, and bioactive compound (creatine, carnosine, anserine, betaine, and L-carnitine) content. KND showed significantly higher carcass weights than CD whereas no such difference (p>0.05) was found between male and female ducks. The breed and sex had no significant effects on the breast weight, pH value, and shear force. However, KND had significantly lower cooking loss values than did CD. Creatine, anserine, and L-carnitine contents were significantly higher in KND than in CD and were predominant in female ducks compared to males. The results of this study provide rare information regarding the amounts and the determinants of several bioactive compounds in duck meat, which can be useful for selection and breeding programs, and for popularizing indigenous duck meat. PMID:26761808

Oestrous synchronization, ovarian superovulation and intraspecific transfers from a closed breeding colony of inbred SLA miniature pigs.

PubMed

Arlaud, J J; Baker, L; Williams, R L; French, A J

2010-12-01

The inbred SLA miniature pig is a unique animal model developed for organ transplantation studies and pre-clinical experimental purposes. Reported oestrous synchronization and superovulation treatments were examined in two SLA haplotypes (AA and DD) to allow collection of embryos for both practical embryo transfer and experimental technologies from a closed breeding colony. Pre-puberal miniature pigs were poor responders to oestrous synchronization treatments, while post-puberal sows were equivalent to commercial sows. Following superovulation, the ovulation number (corpora .hemorrhagica) was higher (p < 0.05) in the cycling sows when compared with non-cycling sows. Ovulations were equivalent to commercial pre-puberal gilts and non-cycling sows (p > 0.05). No difference in ovulation number between haplotypes was observed, which differs from the previous report (DD>AA). Collection of zygotes for pronuclear injection was the highest in the non-cycling post-puberal miniature pig group (p < 0.05), although significantly lower when compared with the commercial pig treatment groups (p < 0.05). The incidence of cystic endometrial hyperplasia in our colony was equivalent to rates observed in commercial pigs. Pronuclear visualization following centrifugation was the highest in the non-cycling miniature sow group and approximates to about 25% of ovulations and about half the rate observed in the commercial pigs (50%). Miniature pig embryos transferred between SLA haplotypes and transfer of DD embryos to commercial pigs resulted in live births at a higher efficiency than previously reported. This study demonstrates the feasibility of undertaking assisted reproductive technologies in a closed breeding colony of inbred SLA miniature pigs without compromise to the breeding programmes. © 2009 Blackwell Verlag GmbH.

Comparison of gene expression of Toll-like receptors and cytokines between Piau and Commercial line (Landrace×Large White crossbred) pigs vaccinated against Pasteurella multocida type D.

PubMed

Sousa, Katiene Régia Silva; Ribeiro, André Mauric Frossard; Dantas, Waleska de Melo Ferreira; Oliveira, Leandro Licursi de; Gasparino, Eliane; Guimarães, Simone Eliza Facioni

2017-10-01

We aimed to compare Toll-like receptors (TLR) and cytokines expression in local Piau breed and a Commercial line (Landrace×Large White crossbred) pigs in response to vaccination against Pasteurella multocida type D. Seronegative gilts for Pasteurella multocida type D and Mycoplasma hyopneumoniae were used, from which peripheral blood mononuclear cells (PBMC) were collected in four time points (T0, T1, T2 and T3; before and after each vaccination dose). For bronchoalveolar lavage fluid cells (BALF), we set groups of vaccinated and unvaccinated animals for both genetic groups. Gene expression was evaluated on PBMC and BALF. In PBMC, when we analyzed time points within breeds, significant differences in expression for TLRs and cytokines, except TGFβ, were observed for Commercial animals. For the Piau pigs, only TGFβ showed differential expression. Comparing the expression among genetic groups, the Commercial pigs showed higher expression for TLRs after first vaccination dose, while for IL2, IL6, IL12 and IL13, higher expression was also observed in T3 and IL8 and IL10, in T1 and T3. Still comparing the breeds, the crossbred animals showed higher expression for TNFα in T1 and T2, while for TGFβ only in T2. For gene expression in BALF, vaccinated Commercial pigs showed higher expression of TLR6, TLR10, IL6, IL8, IL10, TNFα and TGFβ genes than vaccinated Piau pigs. The Commercial line pigs showed higher sensitivity to vaccination, while in local Piau breed lower responsiveness, which may partly explain genetic variability in immune response and will let us better understand the tolerance/susceptibility for pasteurellosis. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Review of transgenic crop breeding in China].

PubMed

Huang, Dafang

2015-06-01

The development history and fundamental experience of transgenic crops (Genetically modified crops) breeding in China for near 30 years were reviewed. It was illustrated that a scientific research, development and industrialization system of transgenic crops including gene discovery, transformation, variety breeding, commercialization, application and biosafety assessment has been initially established which was few in number in the world. The research innovative capacity of transgenic cotton, rice and corn has been lifted. The research features as well as relative advantages have been initially formed. The problems and challenges of transgenic crop development were discussed. In addition, three suggestions of promoting commercialization, speeding up implementation of the Major National Project of GM Crops, and enhancing science communication were made.

Development of Elite BPH-Resistant Wide-Spectrum Restorer Lines for Three and Two Line Hybrid Rice.

PubMed

Fan, Fengfeng; Li, Nengwu; Chen, Yunping; Liu, Xingdan; Sun, Heng; Wang, Jie; He, Guangcun; Zhu, Yingguo; Li, Shaoqing

2017-01-01

Hybrid rice has contributed significantly to the world food security. Breeding of elite high-yield, strong-resistant broad-spectrum restorer line is an important strategy for hybrid rice in commercial breeding programs. Here, we developed three elite brown planthopper (BPH)-resistant wide-spectrum restorer lines by pyramiding big-panicle gene Gn8.1 , BPH-resistant genes Bph6 and Bph9 , fertility restorer genes Rf3, Rf4, Rf5 , and Rf6 through molecular marker assisted selection. Resistance analysis revealed that the newly developed restorer lines showed stronger BPH-resistance than any of the single-gene donor parent Luoyang-6 and Luoyang-9. Moreover, the three new restorer lines had broad spectrum recovery capabilities for Honglian CMS, Wild abortive CMS and two-line GMS sterile lines, and higher grain yields than that of the recurrent parent 9,311 under nature field conditions. Importantly, the hybrid crosses also showed good performance for grain yield and BPH-resistance. Thus, the development of elite BPH-resistant wide-spectrum restorer lines has a promising future for breeding of broad spectrum BPH-resistant high-yield varieties.

Goals and hurdles for a successful implementation of genomic selection in breeding programme for selected annual and perennial crops.

PubMed

Jonas, Elisabeth; de Koning, Dirk Jan

Genomic Selection is an important topic in quantitative genetics and breeding. Not only does it allow the full use of current molecular genetic technologies, it stimulates also the development of new methods and models. Genomic selection, if fully implemented in commercial farming, should have a major impact on the productivity of various agricultural systems. But suggested approaches need to be applicable in commercial breeding populations. Many of the published research studies focus on methodologies. We conclude from the reviewed publications, that a stronger focus on strategies for the implementation of genomic selection in advanced breeding lines, introduction of new varieties, hybrids or multi-line crosses is needed. Efforts to find solutions for a better prediction and integration of environmental influences need to continue within applied breeding schemes. Goals of the implementation of genomic selection into crop breeding should be carefully defined and crop breeders in the private sector will play a substantial part in the decision-making process. However, the lack of published results from studies within, or in collaboration with, private companies diminishes the knowledge on the status of genomic selection within applied breeding programmes. Studies on the implementation of genomic selection in plant breeding need to evaluate models and methods with an enhanced emphasis on population-specific requirements and production environments. Adaptation of methods to breeding schemes or changes to breeding programmes for a better integration of genomic selection strategies are needed across species. More openness with a continuous exchange will contribute to successes.

7 CFR 1980.412 - Ineligible loan purposes.

Code of Federal Regulations, 2010 CFR

2010-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control, and/or management of farm and.... (2) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other... capacity of existing competitive commercial or industrial enterprises, unless such financial or other...

7 CFR 1980.412 - Ineligible loan purposes.

Code of Federal Regulations, 2011 CFR

2011-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control, and/or management of farm and.... (2) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other... capacity of existing competitive commercial or industrial enterprises, unless such financial or other...

7 CFR 1980.412 - Ineligible loan purposes.

Code of Federal Regulations, 2014 CFR

2014-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control, and/or management of farm and.... (2) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other... capacity of existing competitive commercial or industrial enterprises, unless such financial or other...

7 CFR 1980.412 - Ineligible loan purposes.

Code of Federal Regulations, 2013 CFR

2013-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control, and/or management of farm and.... (2) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other... capacity of existing competitive commercial or industrial enterprises, unless such financial or other...

7 CFR 1980.412 - Ineligible loan purposes.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control, and/or management of farm and.... (2) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other... capacity of existing competitive commercial or industrial enterprises, unless such financial or other...

Genomic selection using beef commercial carcass phenotypes.

PubMed

Todd, D L; Roughsedge, T; Woolliams, J A

2014-03-01

In this study, an industry terminal breeding goal was used in a deterministic simulation, using selection index methodology, to predict genetic gain in a beef population modelled on the UK pedigree Limousin, when using genomic selection (GS) and incorporating phenotype information from novel commercial carcass traits. The effect of genotype-environment interaction was investigated by including the model variations of the genetic correlation between purebred and commercial cross-bred performance (ρX). Three genomic scenarios were considered: (1) genomic breeding values (GBV)+estimated breeding values (EBV) for existing selection traits; (2) GBV for three novel commercial carcass traits+EBV in existing traits; and (3) GBV for novel and existing traits plus EBV for existing traits. Each of the three scenarios was simulated for a range of training population (TP) sizes and with three values of ρX. Scenarios 2 and 3 predicted substantially higher percentage increases over current selection than Scenario 1. A TP of 2000 sires, each with 20 commercial progeny with carcass phenotypes, and assuming a ρX of 0.7, is predicted to increase gain by 40% over current selection in Scenario 3. The percentage increase in gain over current selection increased with decreasing ρX; however, the effect of varying ρX was reduced at high TP sizes for Scenarios 2 and 3. A further non-genomic scenario (4) was considered simulating a conventional population-wide progeny test using EBV only. With 20 commercial cross-bred progenies per sire, similar gain was predicted to Scenario 3 with TP=5000 and ρX=1.0. The range of increases in genetic gain predicted for terminal traits when using GS are of similar magnitude to those observed after the implementation of BLUP technology in the United Kingdom. It is concluded that implementation of GS in a terminal sire breeding goal, using purebred phenotypes alone, will be sub-optimal compared with the inclusion of novel commercial carcass phenotypes in genomic evaluations.

Genetic diversity, breed composition and admixture of Kenyan domestic pigs.

PubMed

Mujibi, Fidalis Denis; Okoth, Edward; Cheruiyot, Evans K; Onzere, Cynthia; Bishop, Richard P; Fèvre, Eric M; Thomas, Lian; Masembe, Charles; Plastow, Graham; Rothschild, Max

2018-01-01

The genetic diversity of African pigs, whether domestic or wild has not been widely studied and there is very limited published information available. Available data suggests that African domestic pigs originate from different domestication centers as opposed to international commercial breeds. We evaluated two domestic pig populations in Western Kenya, in order to characterize the genetic diversity, breed composition and admixture of the pigs in an area known to be endemic for African swine fever (ASF). One of the reasons for characterizing these specific populations is the fact that a proportion of indigenous pigs have tested ASF virus (ASFv) positive but do not present with clinical symptoms of disease indicating some form of tolerance to infection. Pigs were genotyped using either the porcine SNP60 or SNP80 chip. Village pigs were sourced from Busia and Homabay counties in Kenya. Because bush pigs (Potamochoerus larvatus) and warthogs (Phacochoerus spp.) are known to be tolerant to ASFv infection (exhibiting no clinical symptoms despite infection), they were included in the study to assess whether domestic pigs have similar genomic signatures. Additionally, samples representing European wild boar and international commercial breeds were included as references, given their potential contribution to the genetic make-up of the target domestic populations. The data indicate that village pigs in Busia are a non-homogenous admixed population with significant introgression of genes from international commercial breeds. Pigs from Homabay by contrast, represent a homogenous population with a "local indigenous' composition that is distinct from the international breeds, and clusters more closely with the European wild boar than African wild pigs. Interestingly, village pigs from Busia that tested negative by PCR for ASFv genotype IX, had significantly higher local ancestry (>54%) compared to those testing positive, which contained more commercial breed gene introgression. This may have implication for breed selection and utilization in ASF endemic areas. A genome wide scan detected several regions under preferential selection with signatures for pigs from Busia and Homabay being very distinct. Additionally, there was no similarity in specific genes under selection between the wild pigs and domestic pigs despite having some broad areas under similar selection signatures. These results provide a basis to explore possible genetic determinants underlying tolerance to infection by ASFv genotypes and suggests multiple pathways for genetically mediated ASFv tolerance given the diversity of selection signatures observed among the populations studied.

Development approach to an enterprise-wide medication reconciliation tool in a free-standing pediatric hospital with commercial best-of-breed systems.

PubMed

Yu, Feliciano B; Leising, Scott; Turner, Scott

2007-10-11

Medication reconciliation is essential to providing a safer patient environment during transitions of care in the clinical setting. Current solutions include a mixed-bag of paper and electronic processes. Best-of-breed health information systems architecture poses a specific challenge to organizations that have limited software development resources. Using readily available service-oriented technology, a prototype for an integrated medication reconciliation tool is developed for use in an academic pediatric hospital with commercial systems.

Schemes for Oestrus Synchronization Protocols and Controlled Breeding Programs in Cattle

NASA Astrophysics Data System (ADS)

Sabo, Y. G.; Sandabe, U. K.; Maina, V. A.; Balla, H. G.

Today prostaglandin and progesterone has been found widely used in several schemes of oestrus synchronization and controlled breeding program. Several controlled breeding program, have been developed for synchronizing groups of all open or lactating cows within a breeding group with or without ovarian palpation. Such programs are reviewed in this article which involves extending the luteal phase by treatment with exogenous progesterone such as: progesterone treatment regimes using syncro-mate-B, progesterone releasing intravaginal device, melengesterol acetate-select and melegestrol acetate plus prostaglandin. Also reviewed in the program is the termination of the luteal phase by treatment with prostaglandin or its analogues. These includes, controlled breeding without ovarian palpation such as, the 7-days program; 11-days program, target breeding, ovsynch program, Heat synch, Cosynch and pre synch-ovsynch program. In our opinion full potential of progesterone and prostaglandin for the detection of oestrus and timed artificial insemination should be utilized. This reduces the much labour input employed in previous years. The practitioner of the livestock herd health must-develop strategies for the delivery of this technology to livestock farmers, its use and limitations.

Breeding strategies for north central tree improvement programs

Treesearch

Ronald P. Overton; Hyun Kang

1985-01-01

The rationales and concepts of long-term tree breeding are discussed and compared with those for short-term breeding. A model breeding program is reviewed which maximizes short-term genetic gain for currently important traits and provides genetic resources that can be used effectively in future short-term breeding. The resources of the north-central region are examined...

Historical changes in population structure during rice breeding programs in the northern limits of rice cultivation.

PubMed

Shinada, Hiroshi; Yamamoto, Toshio; Yamamoto, Eiji; Hori, Kiyosumi; Yonemaru, Junichi; Matsuba, Shuichi; Fujino, Kenji

2014-04-01

The rice local population was clearly differentiated into six groups over the 100-year history of rice breeding programs in the northern limit of rice cultivation over the world. Genetic improvements in plant breeding programs in local regions have led to the development of new cultivars with specific agronomic traits under environmental conditions and generated the unique genetic structures of local populations. Understanding historical changes in genome structures and phenotypic characteristics within local populations may be useful for identifying profitable genes and/or genetic resources and the creation of new gene combinations in plant breeding programs. In the present study, historical changes were elucidated in genome structures and phenotypic characteristics during 100-year rice breeding programs in Hokkaido, the northern limit of rice cultivation in the world. We selected 63 rice cultivars to represent the historical diversity of this local population from landraces to the current breeding lines. The results of the phylogenetic analysis demonstrated that these cultivars clearly differentiated into six groups over the history of rice breeding programs. Significant differences among these groups were detected in five of the seven traits, indicating that the differentiation of the Hokkaido rice population into these groups was correlated with these phenotypic changes. These results demonstrated that breeding practices in Hokkaido have created new genetic structures for adaptability to specific environmental conditions and breeding objectives. They also provide a new strategy for rice breeding programs in which such unique genes in local populations in the world can explore the genetic potentials of the local populations.

Influence of Chinese breeds on pork quality of commercial pig lines.

PubMed

Cesar, A S M; Silveira, A C P; Freitas, P F A; Guimarães, E C; Batista, D F A; Torido, L C; Meirelles, F V; Antunes, R C

2010-04-20

We compared carcass and meat quality of pigs from the same sire line and two different dam lines, one that included Chinese breeds and one that did not. Line A consisted of 1/4 Landrace, 1/2 Large White, 1/8 Chinese breeds (Meishan, Fengjing, Jiaxing), and 1/8 Large White, Duroc and Pietrain, and line B consisted of 1/2 Large White and 1/2 Pietrain. The animals (N = 144) were slaughtered at a live weight of 108 kg. Backfat thickness, percentage of lean meat, pH 24 h after slaughter, meat color, percentage of drip loss, and percentage of intramuscular fat were measured and compared using analysis of variance in a completely randomized design; the BioEstat 5.0 test was applied for the comparison of means at a significance level of 5% for all analyses. Backfat was significantly lower for line A (12.78 mm) than for line B (15.90 mm). The pH measured 24 h after slaughter was significantly lower in line A (5.68) compared to line B (5.84). Percent lean meat was significantly higher for line A (61.21%) compared to line B (59.72%). Percentage drip loss was significantly higher in line A (2.73%) than in line B (2.23%). Percentage intramuscular fat and meat color were not significantly different between the lines. The inclusion of Chinese breeds produced a higher percentage of lean meat and reduced fat thickness, along with increased heterosis, which are important characteristics for breeding programs.

QTL mapping of fruit mineral contents provides new chances for molecular breeding of tomato nutritional traits.

PubMed

Capel, Carmen; Yuste-Lisbona, Fernando J; López-Casado, Gloria; Angosto, Trinidad; Heredia, Antonio; Cuartero, Jesús; Fernández-Muñoz, Rafael; Lozano, Rafael; Capel, Juan

2017-05-01

Agronomical characterization of a RIL population for fruit mineral contents allowed for the identification of QTL controlling these fruit quality traits, flanked by co-dominant markers useful for marker-assisted breeding. Tomato quality is a multi-variant attribute directly depending on fruit chemical composition, which in turn determines the benefits of tomato consumption for human health. Commercially available tomato varieties possess limited variability in fruit quality traits. Wild species, such as Solanum pimpinellifolium, could provide different nutritional advantages and can be used for tomato breeding to improve overall fruit quality. Determining the genetic basis of the inheritance of all the traits that contribute to tomato fruit quality will increase the efficiency of the breeding program necessary to take advantage of the wild species variability. A high-density linkage map has been constructed from a recombinant inbred line (RIL) population derived from a cross between tomato Solanum lycopersicum and the wild-relative species S. pimpinellifolium. The RIL population was evaluated for fruit mineral contents during three consecutive growing seasons. The data obtained allowed for the identification of main QTL and novel epistatic interaction among QTL controlling fruit mineral contents on the basis of a multiple-environment analysis. Most of the QTL were flanked by candidate genes providing valuable information for both tomato breeding for new varieties with novel nutritional properties and the starting point to identify the genes underlying these QTL, which will help to reveal the genetic basis of tomato fruit nutritional properties.

Comparison of the amounts of taste-related compounds in raw and cooked meats from broilers and Korean native chickens.

PubMed

Jayasena, Dinesh D; Kim, Sun Hyo; Lee, Hyun Jung; Jung, Samooel; Lee, Jun Heon; Park, Hee Bok; Jo, Cheorun

2014-12-01

This study was aimed at comparing the taste-related compound content in the breast and leg meat from 100-d-old Korean native chickens (KNC-100) and 32-d-old commercial broilers (CB-32) and determining the changes in these compounds during cooking. Cocks from certified meat-type commercial broiler (Ross) and Korean native chicken (Woorimatdag) strains were raised under similar standard commercial conditions, and a total of 10 birds from each breed were slaughtered at 32 and 100 d of age, which represents their market ages, respectively. Raw and cooked meat samples were prepared separately from the breast and leg and analyzed. The KNC-100 showed significantly higher concentrations of inosine 5'-monophosphate, reducing sugars, glutamic acid, linoleic acid, arachidonic acid, and docosahexaenoic acid than CB-32 did. Additionally, significantly higher inosine 5'-monophosphate, cysteine, arachidonic acid, and docosahexaenoic acid concentrations were observed in the breast meat, whereas the leg meat had higher concentration of glutamic acid, oleic acid, and linoleic acid (P < 0.05). Significant depletions in the concentration of all taste-related compounds occurred during the cooking process, except oleic and linoleic acids. We suggest that the higher levels of taste-related compounds present in KNC-100 meat compared with CB-32 meat may result in the unique taste of the former meat, as has been previously reported. In addition, the results of this study may provide useful information for selection and breeding programs. ©2014 Poultry Science Association Inc.

Genome-Wide Specific Selection in Three Domestic Sheep Breeds.

PubMed

Wang, Huihua; Zhang, Li; Cao, Jiaxve; Wu, Mingming; Ma, Xiaomeng; Liu, Zhen; Liu, Ruizao; Zhao, Fuping; Wei, Caihong; Du, Lixin

2015-01-01

Commercial sheep raised for mutton grow faster than traditional Chinese sheep breeds. Here, we aimed to evaluate genetic selection among three different types of sheep breed: two well-known commercial mutton breeds and one indigenous Chinese breed. We first combined locus-specific branch lengths and di statistical methods to detect candidate regions targeted by selection in the three different populations. The results showed that the genetic distances reached at least medium divergence for each pairwise combination. We found these two methods were highly correlated, and identified many growth-related candidate genes undergoing artificial selection. For production traits, APOBR and FTO are associated with body mass index. For meat traits, ALDOA, STK32B and FAM190A are related to marbling. For reproduction traits, CCNB2 and SLC8A3 affect oocyte development. We also found two well-known genes, GHR (which affects meat production and quality) and EDAR (associated with hair thickness) were associated with German mutton merino sheep. Furthermore, four genes (POL, RPL7, MSL1 and SHISA9) were associated with pre-weaning gain in our previous genome-wide association study. Our results indicated that combine locus-specific branch lengths and di statistical approaches can reduce the searching ranges for specific selection. And we got many credible candidate genes which not only confirm the results of previous reports, but also provide a suite of novel candidate genes in defined breeds to guide hybridization breeding.

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.

Increased genetic gains in sheep, beef and dairy breeding programs from using female reproductive technologies combined with optimal contribution selection and genomic breeding values.

PubMed

Granleese, Tom; Clark, Samuel A; Swan, Andrew A; van der Werf, Julius H J

2015-09-14

Female reproductive technologies such as multiple ovulation and embryo transfer (MOET) and juvenile in vitro embryo production and embryo transfer (JIVET) can boost rates of genetic gain but they can also increase rates of inbreeding. Inbreeding can be managed using the principles of optimal contribution selection (OCS), which maximizes genetic gain while placing a penalty on the rate of inbreeding. We evaluated the potential benefits and synergies that exist between genomic selection (GS) and reproductive technologies under OCS for sheep and cattle breeding programs. Various breeding program scenarios were simulated stochastically including: (1) a sheep breeding program for the selection of a single trait that could be measured either early or late in life; (2) a beef breeding program with an early or late trait; and (3) a dairy breeding program with a sex limited trait. OCS was applied using a range of penalties (severe to no penalty) on co-ancestry of selection candidates, with the possibility of using multiple ovulation and embryo transfer (MOET) and/or juvenile in vitro embryo production and embryo transfer (JIVET) for females. Each breeding program was simulated with and without genomic selection. All breeding programs could be penalized to result in an inbreeding rate of 1 % increase per generation. The addition of MOET to artificial insemination or natural breeding (AI/N), without the use of GS yielded an extra 25 to 60 % genetic gain. The further addition of JIVET did not yield an extra genetic gain. When GS was used, MOET and MOET + JIVET programs increased rates of genetic gain by 38 to 76 % and 51 to 81 % compared to AI/N, respectively. Large increases in genetic gain were found across species when female reproductive technologies combined with genomic selection were applied and inbreeding was managed, especially for breeding programs that focus on the selection of traits measured late in life or that are sex-limited. Optimal contribution selection was an effective tool to optimally allocate different combinations of reproductive technologies. Applying a range of penalties to co-ancestry of selection candidates allows a comprehensive exploration of the inbreeding vs. genetic gain space.

Development and Evaluation of Glycine max Germplasm Lines with Quantitative Resistance to Sclerotinia sclerotiorum

PubMed Central

McCaghey, Megan; Willbur, Jaime; Ranjan, Ashish; Grau, Craig R.; Chapman, Scott; Diers, Brian; Groves, Carol; Kabbage, Mehdi; Smith, Damon L.

2017-01-01

Sclerotinia sclerotiorum, the causal agent of Sclerotinia stem rot, is a devastating fungal pathogen of soybean that can cause significant yield losses to growers when environmental conditions are favorable for the disease. The development of resistant varieties has proven difficult. However, poor resistance in commercial cultivars can be improved through additional breeding efforts and understanding the genetic basis of resistance. The objective of this project was to develop soybean germplasm lines that have a high level of Sclerotinia stem rot resistance to be used directly as cultivars or in breeding programs as a source of improved Sclerotinia stem rot resistance. Sclerotinia stem rot-resistant soybean germplasm was developed by crossing two sources of resistance, W04-1002 and AxN-1-55, with lines exhibiting resistance to Heterodera glycines and Cadophora gregata in addition to favorable agronomic traits. Following greenhouse evaluations of 1,076 inbred lines derived from these crosses, 31 lines were evaluated for resistance in field tests during the 2014 field season. Subsequently, 11 Sclerotinia stem rot resistant breeding lines were moved forward for field evaluation in 2015, and seven elite breeding lines were selected and evaluated in the 2016 field season. To better understand resistance mechanisms, a marker analysis was conducted to identify quantitative trait loci linked to resistance. Thirteen markers associated with Sclerotinia stem rot resistance were identified on chromosomes 15, 16, 17, 18, and 19. Our markers confirm previously reported chromosomal regions associated with Sclerotinia stem rot resistance as well as a novel region of chromosome 16. The seven elite germplasm lines were also re-evaluated within a greenhouse setting using a cut petiole technique with multiple S. sclerotiorum isolates to test the durability of physiological resistance of the lines in a controlled environment. This work presents a novel and comprehensive classical breeding method for selecting lines with physiological resistance to Sclerotinia stem rot and a range of agronomic traits. In these studies, we identify four germplasm lines; 91–38, 51–23, SSR51–70, and 52–82B exhibiting a high level of Sclerotinia stem rot resistance combined with desirable agronomic traits, including high protein and oil contents. The germplasm identified in this study will serve as a valuable source of physiological resistance to Sclerotinia stem rot that could be improved through further breeding to generate high-yielding commercial soybean cultivars. PMID:28912790

Breeding and Selection of New Switchgrass Varieties for Increased Biomass Production

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

Taliaferro, C.M.

2003-05-27

Switchgrass breeding and genetics research was conducted from 1992-2002 at the Oklahoma State University as part of the national DOE-Bioenergy Feedstock Development Program (BFDP) effort to develop the species as a bioenergy feedstock crop. The fundamental objective of the program was to implement and conduct a breeding program to increase biomass yield capability in switchgrass and develop cultivars for the central and southern United States. Supporting research objectives included: (1) switchgrass germplasm collection, characterization, and enhancement; (2) elucidation of cytogenetic and breeding behavior; and (3) identification of best breeding procedures.

Peasant friendly plant breeding and the early years of the green revolution in Mexico.

PubMed

Harwood, Jonathan

2009-01-01

Despite their success in boosting cereals production overall, the Green Revolution programs of the 1950s and 1960s were often criticized for failing to achieve their declared aim of alleviating world hunger. Most critics argued that the programs had produced a technology unsuited to the needs of small peasant farmers. This paper explores why such inappropriate technology might have been developed, focusing on the early years of the Rockefeller Foundation's Mexican Agricultural Program (MAP). It shows that some foundation officers as well as agricultural advisors had prior experience of the problems faced by small farmers in the United States and elsewhere. Moreover, the foundation's expressed concern for rural poverty does not appear to have been mere posturing by an organization anxious to be seen as an agent of philanthropy. Furthermore, the program's early work in maize-breeding was well tailored to the conditions of Mexican agriculture. Once the MAP was up and running, however, it became apparent that the task of getting new varieties and cultivation practices to small farmers was going to be difficult. Needing to make some kind of impact quickly, MAP staff chose to concentrate upon projects that were likely to find a rapid uptake. This meant setting aside the needs of peasant farmers to develop high-yielding varieties suited to large commercial farms.

Prevalence and parasitemia of Haemogregarina sp. in Podocnemis expansa (Testudines: Podocnemididae) from the Brazilian Amazon.

PubMed

Picelli, Amanda Maria; de Carvalho, Aluísio Vasconcelos; Viana, Lúcio André; Malvasio, Adriana

2015-01-01

Seventy-five turtles Podocnemis expansa in the Brazilian Amazon were examined for the presence of ectoparasites and hemoparasites. Samplings were performed in three study areas in the state of Tocantins, Brazil. Twenty-five specimens were sampled per study area (a commercial breeding facility, an indigenous subsistence breeding facility and a wild population of the Javaés River). Hemoparasites of the genus Haemogregarina were found in 66% (50/75) of the turtle specimens, and the infections were restricted to the commercial breeding facility and to the wild population of the Javaés River. The mean level of parasitemia was 54/2,000 erythrocytes (2%). There was no correlation between the body condition index of the chelonians and the level of parasitemia, with no significant difference between genders. No leeches were observed during the physical exams in any of the study areas, but the specimens from the commercial breeding facility were in poor physical condition with shell deformities and the presence of a relatively high amount of skin ulcerations, most likely caused by fungi and bacteria. This was the first study to record the occurrence of hemogregarines on a population scale in P. expansa and helps to increase knowledge about hemoparasites in chelonians in Brazil.

Validating selective breeding approaches for disease resistance

USDA-ARS?s Scientific Manuscript database

Selective breeding of rainbow trout at the USDA/ARS National Center for Cool and Cold Water Aquaculture (NCCCWA) in Leetown, West Virginia is designed to accomplish four goals: 1) define commercially important traits such as disease resistance, growth rate, stress response, and feed efficiency; 2) d...

Economic aspects of production of Caiman crocodilus yacare.

PubMed

Carreira, Laura B T; Sabbag, Omar J

2015-03-01

The breeding of crocodilians is still a recent activity in Brazil. Its peak was in the 1990's, but it has gaps in its production, as there are no norms for the commercial breeding of these animals in captivity. However, its economic potential is great, and the search for ecological balance and viability of commercial production has become a challenge among farmers of this activity. Therefor, the objective of the study was to economically analyze the production of Caiman crocodilus yacare on a farm located in Caceres, state of Mato Grosso, identifying relevant items of costs in the activity, as well as the parameters related to the profitability and viability of the activity. The economic results for the breeding of this animal were positive, with profitability ratios higher than 70%.

Actinide management with commercial fast reactors

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

Ohki, Shigeo

The capability of plutonium-breeding and minor-actinide (MA) transmutation in the Japanese commercial sodium-cooled fast reactor offers one of practical solutions for obtaining sustainable energy resources as well as reducing radioactive toxicity and inventory. The reference core design meets the requirement of flexible breeding ratio from 1.03 to 1.2. The MA transmutation amount has been evaluated as 50-100 kg/GW{sub e}y if the MA content in fresh fuel is 3-5 wt%, where about 30-40% of initial MA can be transmuted in the discharged fuel.

50 CFR 15.26 - Approval of cooperative breeding programs.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 1 2014-10-01 2014-10-01 false Approval of cooperative breeding programs. 15.26 Section 15.26 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE... program requested for the exotic bird species, including: (i) A breeding protocol, including a genetic...

50 CFR 15.26 - Approval of cooperative breeding programs.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 50 Wildlife and Fisheries 1 2013-10-01 2013-10-01 false Approval of cooperative breeding programs. 15.26 Section 15.26 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE... program requested for the exotic bird species, including: (i) A breeding protocol, including a genetic...

50 CFR 15.26 - Approval of cooperative breeding programs.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 1 2012-10-01 2012-10-01 false Approval of cooperative breeding programs. 15.26 Section 15.26 Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT OF THE... program requested for the exotic bird species, including: (i) A breeding protocol, including a genetic...

Persian walnut breeding in California

Treesearch

Charles A. Leslie; Gale H. McGranahan

2004-01-01

For over 50 years the University of California Davis Walnut Breeding Program has worked to address the needs of California walnut growers by identifying genetic approaches to problems and developing improved cultivars. The breeding program is a cooperative endeavor that draws on the efforts and resources of university researchers and facilities, USDA germplasm programs...

78 FR 40940 - Lacey Act Implementation Plan; Definitions for Exempt and Regulated Articles

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-09

... plants. Many maricultural products are cultivated on a commercial scale on seaweed farms; however, some...'' definition to require that the plants be ``produced on a commercial scale'' instead. We have also made the... particular traits, through such means as breeding, cloning, or genetic modification. Commercial scale...

Global impact of accelerated plant breeding: Evidence from a meta-analysis on rice breeding.

PubMed

Lenaerts, Bert; de Mey, Yann; Demont, Matty

2018-01-01

Rice breeders in Asia and elsewhere in the world have long overlooked trying to shorten the time it takes to develop new varieties. Plant breeders have proposed a technique called Rapid Generation Advance (RGA) as a way to accelerate the results of public rice breeding programs. However, little is known about RGA's potential impact. Here, we present the first results of a global impact study of RGA. More specifically, we calculated the multiplicator effects of RGA on the research benefits generated by conventional rice breeding programs and applied them to a meta-analysis of selected impact studies in the literature. These insights are a first crucial step in developing a targeted approach for disseminating RGA technology among rice breeders to accelerate the impact of their public rice breeding programs around the world. We show that the additional benefits due to time savings are considerable and offer some insights into the economics of breeding. Our results confirm that the adoption of accelerated breeding would lead to substantial advantages to rice breeding programs and the earlier variety release leads to significant economic benefits to society. This can be important to policy makers when reshaping their public breeding methods and optimising their return on research investments in breeding.

Evaluation of popcorn germplasm for resistance to Sesamia nonagrioides attack.

PubMed

Butrón, A; Sandoya, G; Revilla, P; Ordás, A; Malvar, R A

2005-10-01

Popcorn adapted to Spanish conditions could be an interesting and profitable alternative to field corn. However, little is known about breeding popcorn germplasm for adaptation to Spain. Sesamia nonagrioides Lefèvbre is the main insect pest affecting popcorn quality and yield under Spanish growing conditions. The objectives of the study were the search for sources of resistance to S. nonagrioides among popcorn germplasm and to study the genetics of the resistance to S. nonagrioides attack. Eight breeding populations along with a five-inbred line diallel and two popcorn commercial checks were evaluated under S. nonagrioides infestation in 2 yr. Significant differences were found among general combining ability (GCA) effects for days to silking, S. nonagrioides tunnel length, general appearance of the ear, kernel moisture, and yield. Specific combining ability (SCA) effects were found to be significant for yield and ear damage. Therefore, heterotic patterns among popcorn materials should be taken into account to generate new popcorn hybrids that are not only more productive but also have higher kernel quality. Breeding popcorn populations BSP4APC0 and PSPW1C1 could be base germplasms in a breeding program for obtaining parental inbreds of healthy kernel popcorn hybrids. New inbred lines could be generated from the cross BP1 x BP2 that would have improved GCA and SCA effects for S. nonagrioides resistance when crossed to South American inbreds.

RosBREED: From genomics to DNA-informed breeding in strawberry

USDA-ARS?s Scientific Manuscript database

Angular leaf spot caused by Xanthomonas fragariae is the only major bacterial disease of cultivated strawberry (Fragaria ×ananassa). While this disease may cause reductions of up to 8 % of marketable yield in Florida winter annual production, no resistant cultivars have been commercialized. Wild acc...

78 FR 66686 - Takes of Marine Mammals Incidental to Specified Activities; Seabird and Pinniped Research...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-06

... (other than commercial fishing) within a specified geographical region if: (1) We make certain findings..., but not limited to, migration, breathing, nursing, breeding, feeding, or sheltering [Level B... seabird colonies; observing seabird nesting habitat; restoring nesting burrows; observing breeding...

The contribution of the “SolCAP” project to potato breeding

USDA-ARS?s Scientific Manuscript database

Potato variety development in the US is driven by public sector scientists interacting with state and national grower organizations to test and commercialize new varieties. The processing market drives the breeding focus while disease and insect resistances may have regional importance. Based upon s...

Genomic selection needs to be carefully assessed to meet specific requirements in livestock breeding programs

PubMed Central

Jonas, Elisabeth; de Koning, Dirk-Jan

2015-01-01

Genomic selection is a promising development in agriculture, aiming improved production by exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. It opens opportunities for research, as novel algorithms and lab methodologies are developed. Genomic selection can be applied in many breeds and species. Further research on the implementation of genomic selection (GS) in breeding programs is highly desirable not only for the common good, but also the private sector (breeding companies). It has been projected that this approach will improve selection routines, especially in species with long reproduction cycles, late or sex-limited or expensive trait recording and for complex traits. The task of integrating GS into existing breeding programs is, however, not straightforward. Despite successful integration into breeding programs for dairy cattle, it has yet to be shown how much emphasis can be given to the genomic information and how much additional phenotypic information is needed from new selection candidates. Genomic selection is already part of future planning in many breeding companies of pigs and beef cattle among others, but further research is needed to fully estimate how effective the use of genomic information will be for the prediction of the performance of future breeding stock. Genomic prediction of production in crossbreeding and across-breed schemes, costs and choice of individuals for genotyping are reasons for a reluctance to fully rely on genomic information for selection decisions. Breeding objectives are highly dependent on the industry and the additional gain when using genomic information has to be considered carefully. This review synthesizes some of the suggested approaches in selected livestock species including cattle, pig, chicken, and fish. It outlines tasks to help understanding possible consequences when applying genomic information in breeding scenarios. PMID:25750652

Genomic selection needs to be carefully assessed to meet specific requirements in livestock breeding programs.

PubMed

Jonas, Elisabeth; de Koning, Dirk-Jan

2015-01-01

Genomic selection is a promising development in agriculture, aiming improved production by exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. It opens opportunities for research, as novel algorithms and lab methodologies are developed. Genomic selection can be applied in many breeds and species. Further research on the implementation of genomic selection (GS) in breeding programs is highly desirable not only for the common good, but also the private sector (breeding companies). It has been projected that this approach will improve selection routines, especially in species with long reproduction cycles, late or sex-limited or expensive trait recording and for complex traits. The task of integrating GS into existing breeding programs is, however, not straightforward. Despite successful integration into breeding programs for dairy cattle, it has yet to be shown how much emphasis can be given to the genomic information and how much additional phenotypic information is needed from new selection candidates. Genomic selection is already part of future planning in many breeding companies of pigs and beef cattle among others, but further research is needed to fully estimate how effective the use of genomic information will be for the prediction of the performance of future breeding stock. Genomic prediction of production in crossbreeding and across-breed schemes, costs and choice of individuals for genotyping are reasons for a reluctance to fully rely on genomic information for selection decisions. Breeding objectives are highly dependent on the industry and the additional gain when using genomic information has to be considered carefully. This review synthesizes some of the suggested approaches in selected livestock species including cattle, pig, chicken, and fish. It outlines tasks to help understanding possible consequences when applying genomic information in breeding scenarios.

Simulated selection responses for breeding programs including resistance and resilience to parasites in Creole goats.

PubMed

Gunia, M; Phocas, F; Gourdine, J-L; Bijma, P; Mandonnet, N

2013-02-01

The Creole goat is a local breed used for meat production in Guadeloupe (French West Indies). As in other tropical countries, improvement of parasite resistance is needed. In this study, we compared predicted selection responses for alternative breeding programs with or without parasite resistance and resilience traits. The overall breeding goal included traits for production, reproduction, and parasite resilience and resistance to ensure a balanced selection outcome. The production traits were BW and dressing percentage (DP). The reproduction trait was fertility (FER), which was the number of doe kiddings per mating. The resistance trait was worm fecal egg count (FEC), which is a measurement of the number of gastro-intestinal parasite eggs found in the feces. The resilience trait was the packed cell volume (PCV), which is a measurement of the volume of red blood cells in the blood. Dressing percentage, BW, and FEC were measured at 11 mo of age, which is the mating or selling age. Fertility and PCV were measured on females at each kidding period. The breeding program accounting for the overall breeding goal and a selection index including all traits gave annual selection responses of 800 g for BW, 3.75% for FER, 0.08% for DP, -0.005 ln(eggs/g) for FEC, and 0.28% for PCV. The expected selection responses for BW and DP in this breeding program were reduced by 2% and 6%, respectively, compared with a breeding program not accounting for FEC and PCV. The overall breeding program, proposed for the Creole breed, offers the best breeding strategy in terms of expected selection responses, making it possible to improve all traits together. It offers a good balance between production and adaptation traits and may present some interest for the selection of other goat breeds in the tropics.

Commercial objectives, technology transfer, and systems analysis for fusion power development

NASA Astrophysics Data System (ADS)

Dean, Stephen O.

1988-03-01

Fusion is an essentially inexhaustible source of energy that has the potential for economically attractive commercial applications with excellent safety and environmental characteristics. The primary focus for the fusion-energy development program is the generation of centralstation electricity. Fusion has the potential, however, for many other applications. The fact that a large fraction of the energy released in a DT fusion reaction is carried by high-energy neutrons suggests potentially unique applications. These include breeding of fissile fuels, production of hydrogen and other chemical products, transmutation or “burning” of various nuclear or chemical wastes, radiation processing of materials, production of radioisotopes, food preservation, medical diagnosis and medical treatment, and space power and space propulsion. In addition, fusion R&D will lead to new products and new markets. Each fusion application must meet certain standards of economic and safety and environmental attractiveness. For this reason, economics on the one hand, and safety and environment and licensing on the other hand, are the two primary criteria for setting long-range commercial fusion objectives. A major function of systems analysis is to evaluate the potential of fusion against these objectives and to help guide the fusion R&D program toward practical applications. The transfer of fusion technology and skills from the national laboratories and universities to industry is the key to achieving the long-range objective of commercial fusion applications.

Rapid breeding and varietal replacement are critical to adaptation of cropping systems in the developing world to climate change.

PubMed

Atlin, Gary N; Cairns, Jill E; Das, Biswanath

2017-03-01

Plant breeding is a key mechanism for adaptation of cropping systems to climate change. Much discussion of breeding for climate change focuses on genes with large effects on heat and drought tolerance, but phenology and stress tolerance are highly polygenic. Adaptation will therefore mainly result from continually adjusting allele frequencies at many loci through rapid-cycle breeding that delivers a steady stream of incrementally improved cultivars. This will require access to elite germplasm from other regions, shortened breeding cycles, and multi-location testing systems that adequately sample the target population of environments. The objective of breeding and seed systems serving smallholder farmers should be to ensure that they use varieties developed in the last 10 years. Rapid varietal turnover must be supported by active dissemination of new varieties, and active withdrawal of obsolete ones. Commercial seed systems in temperate regions achieve this through competitive seed markets, but in the developing world, most crops are not served by competitive commercial seed systems, and many varieties date from the end of the Green Revolution (the late 1970s, when the second generation of modern rice and wheat varieties had been widely adopted). These obsolete varieties were developed in a climate different than today's, placing farmers at risk. To reduce this risk, a strengthened breeding system is needed, with freer international exchange of elite varieties, short breeding cycles, high selection intensity, wide-scale phenotyping, and accurate selection supported by genomic technology. Governments need to incentivize varietal release and dissemination systems to continuously replace obsolete varieties.

Application of the aqueous self-cooled blanket concept to fusion reactors

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

Deutsch, L.; Steiner, D.; Embrechts, M.J.

1986-01-01

The development of a reliable, safe, and economically attractive tritium breeding blanket is an essential requirement in the path to commercial fusion power. The primary objective of the recently completed Blanket Comparison and Selection Study (BCSS) was to evaluate previously proposed concepts, and thereby identify a limited number of preferred options that would provide the focus for an R and D program. The water-cooled concepts in the BCSS scored relatively low. We consider it prudent that a promising water-cooled blanket concept be included in this program since nearly all power producing reactors currently rely on water technology. It is inmore » this context that we propose the novel water-cooled blanket concept described herein.« less

RUN1 and REN1 Pyramiding in Grapevine (Vitis vinifera cv. Crimson Seedless) Displays an Improved Defense Response Leading to Enhanced Resistance to Powdery Mildew (Erysiphe necator)

PubMed Central

Agurto, Mario; Schlechter, Rudolf O.; Armijo, Grace; Solano, Esteban; Serrano, Carolina; Contreras, Rodrigo A.; Zúñiga, Gustavo E.; Arce-Johnson, Patricio

2017-01-01

Fungal pathogens are the cause of the most common diseases in grapevine and among them powdery mildew represents a major focus for disease management. Different strategies for introgression of resistance in grapevine are currently undertaken in breeding programs. For example, introgression of several resistance genes (R) from different sources for making it more durable and also strengthening the plant defense response. Taking this into account, we cross-pollinated P09-105/34, a grapevine plant carrying both RUN1 and REN1 pyramided loci of resistance to Erysiphe necator inherited from a pseudo-backcrossing scheme with Muscadinia rotundifolia and Vitis vinifera ‘Dzhandzhal Kara,’ respectively, with the susceptible commercial table grape cv. ‘Crimson Seedless.’ We developed RUN1REN1 resistant genotypes through conventional breeding and identified them by marker assisted selection. The characterization of defense response showed a highly effective defense mechanism against powdery mildew in these plants. Our results reveal that RUN1REN1 grapevine plants display a robust defense response against E. necator, leading to unsuccessful fungal establishment with low penetration rate and poor hypha development. This resistance mechanism includes reactive oxygen species production, callose accumulation, programmed cell death induction and mainly VvSTS36 and VvPEN1 gene activation. RUN1REN1 plants have a great potential as new table grape cultivars with durable complete resistance to E. necator, and are valuable germplasm to be included in grape breeding programs to continue pyramiding with other sources of resistance to grapevine diseases. PMID:28553300

Mary Bidwell Breed: The Educator as Dean.

ERIC Educational Resources Information Center

Fley, Jo Ann; Jaramillo, George R.

1979-01-01

Mary Bidwell Breed predicted that midwestern universities would probably "pass through a stage of educational development in which the liberal arts are entirely feminized, the men are entirely commercialized." We can appreciate how close she came to pinpointing trends which did not begin to be reversed until sixty years later.…

Pentaploid Wheat Hybrids: Applications, Characterisation, and Challenges

PubMed Central

Padmanaban, Sriram; Zhang, Peng; Hare, Ray A.; Sutherland, Mark W.; Martin, Anke

2017-01-01

Interspecific hybridisation between hexaploid and tetraploid wheat species leads to the development of F1 pentaploid hybrids with unique chromosomal constitutions. Pentaploid hybrids derived from bread wheat (Triticum aestivum L.) and durum wheat (Triticum turgidum spp. durum Desf.) crosses can improve the genetic background of either parent by transferring traits of interest. The genetic variability derived from bread and durum wheat and transferred into pentaploid hybrids has the potential to improve disease resistance, abiotic tolerance, and grain quality, and to enhance agronomic characters. Nonetheless, pentaploid wheat hybrids have not been fully exploited in breeding programs aimed at improving crops. There are several potential barriers for efficient pentaploid wheat production, such as low pollen compatibility, poor seed set, failed seedling establishment, and frequent sterility in F1 hybrids. However, most of the barriers can be overcome by careful selection of the parental genotypes and by employing the higher ploidy level genotype as the maternal parent. In this review, we summarize the current research on pentaploid wheat hybrids and analyze the advantages and pitfalls of current methods used to assess pentaploid-derived lines. Furthermore, we discuss current and potential applications in commercial breeding programs and future directions for research into pentaploid wheat. PMID:28367153

Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs.

PubMed

Bosse, Mirte; Lopes, Marcos S; Madsen, Ole; Megens, Hendrik-Jan; Crooijmans, Richard P M A; Frantz, Laurent A F; Harlizius, Barbara; Bastiaansen, John W M; Groenen, Martien A M

2015-12-22

Early pig farmers in Europe imported Asian pigs to cross with their local breeds in order to improve traits of commercial interest. Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds. We propose that the Asian variants are still present because they affect phenotypes that were important for ancient traditional, as well as recent, commercial pig breeding. Genome-wide introgression levels were only weakly correlated with gene content and recombination frequency. However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. Therefore, the Asian alleles are thought to have an effect on phenotypes that were historically under selection. We aimed to estimate the effect of AS in introgressed regions in Large White pigs on the traits of backfat (BF) and litter size. The majority of regions we tested that retained Asian deoxyribonucleic acid (DNA) showed significantly increased BF from the Asian alleles. Our results suggest that the introgression in Large White pigs has been strongly determined by the selective pressure acting upon the introgressed AS. We therefore conclude that human-driven hybridization and selection contributed to the genomic architecture of these commercial pigs. © 2015 The Author(s).

50 CFR 23.62 - What factors are considered in making a finding of not for primarily commercial purposes?

Code of Federal Regulations, 2014 CFR

2014-10-01

... for breeding or artificial propagation is considered to be for primarily commercial purposes. As a... finding of not for primarily commercial purposes? 23.62 Section 23.62 Wildlife and Fisheries UNITED STATES..., SALE, PURCHASE, BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON...

50 CFR 23.62 - What factors are considered in making a finding of not for primarily commercial purposes?

Code of Federal Regulations, 2011 CFR

2011-10-01

... for breeding or artificial propagation is considered to be for primarily commercial purposes. As a... finding of not for primarily commercial purposes? 23.62 Section 23.62 Wildlife and Fisheries UNITED STATES..., SALE, PURCHASE, BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON...

50 CFR 23.62 - What factors are considered in making a finding of not for primarily commercial purposes?

Code of Federal Regulations, 2010 CFR

2010-10-01

... for breeding or artificial propagation is considered to be for primarily commercial purposes. As a... finding of not for primarily commercial purposes? 23.62 Section 23.62 Wildlife and Fisheries UNITED STATES..., SALE, PURCHASE, BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON...

75 FR 53328 - Proposed Information Collection; OMB Control Number 1018-0093; Federal Fish and Wildlife License...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-31

...; hunters; taxidermists; commercial importers/exporters of wildlife and plants; freight forwarders/brokers...). 3-200-33/Export of Artificially 20 303 2 hours 606 Propagated Plants (Multiple Commercial Shipments...-200-65/Registration of 2 2 40 hours 80 Appendix-I Commercial Breeding Operations (CITES). 3-200-66...

50 CFR 23.26 - When is a U.S. or foreign CITES document valid?

Code of Federal Regulations, 2014 CFR

2014-10-01

...) Registered commercial breeding operation for Appendix-I wildlife (i) The operation is included in the... document. (16) Registered commercial nursery for Appendix-I plants The operation is included in the... Secretariat and that the purpose of the import is commercial. (8) The import of a specimen designated as bred...

50 CFR 23.62 - What factors are considered in making a finding of not for primarily commercial purposes?

Code of Federal Regulations, 2013 CFR

2013-10-01

... for breeding or artificial propagation is considered to be for primarily commercial purposes. As a... finding of not for primarily commercial purposes? 23.62 Section 23.62 Wildlife and Fisheries UNITED STATES..., SALE, PURCHASE, BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON...

50 CFR 23.62 - What factors are considered in making a finding of not for primarily commercial purposes?

Code of Federal Regulations, 2012 CFR

2012-10-01

... for breeding or artificial propagation is considered to be for primarily commercial purposes. As a... finding of not for primarily commercial purposes? 23.62 Section 23.62 Wildlife and Fisheries UNITED STATES..., SALE, PURCHASE, BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON...

Expression of Varroa sensitive hygiene (VSH) in commercial VSH honey bees (Hymenoptera: Apidae).

PubMed

Danka, Robert G; Harris, Jeffrey W; Villa, José D

2011-06-01

We tested six commercial sources of honey bees, Apis mellifera L. (Hymenoptera: Apidae), whose breeding incorporated the trait of Varroa sensitive hygiene (VSH). VSH confers resistance to the parasitic mite Varroa destructor Anderson & Trueman by enhancing the ability of the bees to hygienically remove mite-infested brood. VSH production queens (i.e., queens commercially available for use in beekeepers' production colonies) from the six sources were established in colonies which later were measured for VSH. Their responses were compared with those of colonies with three other types of queens, as follows: VSH queens from the selected closed population maintained by USDA-ARS for research and as a source of breeding germplasm, queens from the cooperating commercial distributor of this germplasm, and queens of a commercial, mite-susceptible source. The reduction of mite infestation in brood combs exposed to test colonies for 1 wk differed significantly between groups. On average, colonies with VSH production queens reduced infestation by 44%. This group average was intermediate between the greater removal by pure ARS VSH (76%) and the cooperators' breeding colonies (64%), and the lesser removal by susceptible colonies (7%). VSH production colonies from the different sources had variable expression of hygiene against mites, with average reduced infestations ranging from 22 to 74%. In addition, infertility was high among mites that remained in infested cells in VSH breeder colonies from ARS and the commercial distributor but was lower and more variable in VSH production colonies and susceptible colonies. Commercial VSH production colonies supply mite resistance that generally seems to be useful for beekeeping. Resistance probably could be improved if more VSH drones sources were supplied when VSH production queens are being mated.

The chapter breeding program of the American Chestnut Foundation

Treesearch

Sara Fitzsimmons; Kendra Gurney; William White; Katy McCune

2012-01-01

A unique feature of the American Chestnut Foundation breeding program is the use of volunteers to conduct most of the regional breeding that will help increase genetic diversity and preserve local adaptation in the products of our program. This effort is coordinated by the four authors of this abstract, who are employees of the Foundation. The Foundation has...

Tree improvement in the Pacific Northwest.

Treesearch

R. Johnson

2000-01-01

Advanced-generation tree breeding programs are underway for Douglas-fir and coastal western hemlock. These programs will continue to improve growth rates and other traits. Regardless of whether seeds is from a seed orchard or natural collection, it must be used in its appropriated breeding zone or seed zone. These zones vary by species. Breeding programs are underway...

Optimum allocation of conservation funds and choice of conservation programs for a set of African cattle breeds

PubMed Central

Reist-Marti, Sabine B; Abdulai, Awudu; Simianer, Henner

2006-01-01

Although funds for livestock conservation are limited there is little known about the optimal allocation of conservation funds. A new algorithm was used to allocate Mio US$ 1, 2, 3, 5 or unlimited funds, discounted over 50 years, on 23 African cattle breeds conserved with four different possible conservation programs. Additionally, Mio US$ 1 was preferably allocated to breeds with special traits. The conceptional in situ conservation programs strongly involve breeders and give them part of the responsibility for the conservation of the breed. Therefore, the pure in situ conservation was more efficient than cryoconservation or combined in situ and cryoconservation. The average annual discounted conservation cost for a breed can be as low as US$ 1000 to US$ 4400 depending on the design of the conservation program and the economic situation of the country of conservation. The choice of the breeds and the optimal conservation program and the amount of money allocated to each breed depend on many factors such as the amount of funds available, the conservation potential of each breed, the effects of the conservation program as well as its cost. With Mio US$ 1, 64% of the present diversity could be maintained over 50 years, which is 13% more than would be maintained if no conservation measures were implemented. Special traits could be conserved with a rather small amount of the total funds. Diversity can not be conserved completely, not even with unlimited funds. A maximum of 92% of the present diversity could be conserved with Mio US$ 10, leaving 8% of the diversity to unpredictable happenings. The suggested algorithm proved to be useful for optimal allocation of conservation funds. It allocated the funds optimally among breeds by identifying the most suited conservation program for each breed, also accounting for differences in currency exchange rates between the different countries. PMID:16451794

Genomic selection in a commercial winter wheat population.

PubMed

He, Sang; Schulthess, Albert Wilhelm; Mirdita, Vilson; Zhao, Yusheng; Korzun, Viktor; Bothe, Reiner; Ebmeyer, Erhard; Reif, Jochen C; Jiang, Yong

2016-03-01

Genomic selection models can be trained using historical data and filtering genotypes based on phenotyping intensity and reliability criterion are able to increase the prediction ability. We implemented genomic selection based on a large commercial population incorporating 2325 European winter wheat lines. Our objectives were (1) to study whether modeling epistasis besides additive genetic effects results in enhancement on prediction ability of genomic selection, (2) to assess prediction ability when training population comprised historical or less-intensively phenotyped lines, and (3) to explore the prediction ability in subpopulations selected based on the reliability criterion. We found a 5 % increase in prediction ability when shifting from additive to additive plus epistatic effects models. In addition, only a marginal loss from 0.65 to 0.50 in accuracy was observed using the data collected from 1 year to predict genotypes of the following year, revealing that stable genomic selection models can be accurately calibrated to predict subsequent breeding stages. Moreover, prediction ability was maximized when the genotypes evaluated in a single location were excluded from the training set but subsequently decreased again when the phenotyping intensity was increased above two locations, suggesting that the update of the training population should be performed considering all the selected genotypes but excluding those evaluated in a single location. The genomic prediction ability was substantially higher in subpopulations selected based on the reliability criterion, indicating that phenotypic selection for highly reliable individuals could be directly replaced by applying genomic selection to them. We empirically conclude that there is a high potential to assist commercial wheat breeding programs employing genomic selection approaches.

Estimation of linkage disequilibrium and analysis of genetic diversity in Korean chicken lines.

PubMed

Seo, Dongwon; Lee, Doo Ho; Choi, Nuri; Sudrajad, Pita; Lee, Seung-Hwan; Lee, Jun-Heon

2018-01-01

The development of genetic markers for animal breeding is an effective strategy to reduce the time and cost required to improve economically important traits. To implement genomic selection in the multibreed chicken population of Korea, an understanding of the linkage disequilibrium (LD) status of the target population is essential. In this study, we performed population genetic analyses to investigate LD decay, the effective population size, and breed diversity using 600K high-density single nucleotide polymorphism genotypes of 189 native chickens in 14 lines (including Korean native chicken, imported and adapted purebred and commercial chickens). The results indicated that commercial native chickens have less calculated LD (average, r2 = 0.13-0.26) and purebred native chickens have more calculated LD (average, r2 = 0.24-0.37) across the entire genome. The effective population sizes of the examined lines showed patterns opposite to those of population LD. The phylogeny and admixture analyses showed that commercial and purebred chickens were well distinguished, except for Rhode Island Red (RIR) purebred lines of NC (NIAS_RIR_C) and ND (NIAS_RIR_D). These lines are difficult to distinguish clearly because they originated from the same respective breeds. The results of this study may provide important information for the development of genetic markers that can be used in breeding to improve the economic traits of native chickens.

Estimation of linkage disequilibrium and analysis of genetic diversity in Korean chicken lines

PubMed Central

Seo, Dongwon; Lee, Doo Ho; Choi, Nuri; Sudrajad, Pita; Lee, Seung-Hwan

2018-01-01

The development of genetic markers for animal breeding is an effective strategy to reduce the time and cost required to improve economically important traits. To implement genomic selection in the multibreed chicken population of Korea, an understanding of the linkage disequilibrium (LD) status of the target population is essential. In this study, we performed population genetic analyses to investigate LD decay, the effective population size, and breed diversity using 600K high-density single nucleotide polymorphism genotypes of 189 native chickens in 14 lines (including Korean native chicken, imported and adapted purebred and commercial chickens). The results indicated that commercial native chickens have less calculated LD (average, r2 = 0.13–0.26) and purebred native chickens have more calculated LD (average, r2 = 0.24–0.37) across the entire genome. The effective population sizes of the examined lines showed patterns opposite to those of population LD. The phylogeny and admixture analyses showed that commercial and purebred chickens were well distinguished, except for Rhode Island Red (RIR) purebred lines of NC (NIAS_RIR_C) and ND (NIAS_RIR_D). These lines are difficult to distinguish clearly because they originated from the same respective breeds. The results of this study may provide important information for the development of genetic markers that can be used in breeding to improve the economic traits of native chickens. PMID:29425208

Aspects of sexual precocity and morphometry of uterus, placenta and embryos/fetuses in Piau breed and Commercial line gilts.

PubMed

Montes, José Carlos; Penitente-Filho, Jurandy Mauro; Guimarães, Simone Eliza Facioni; Lopes, Paulo Sávio; Camilo, Breno Soares; Shiomi, Hugo Hideki; Lima, Daniel Araújo; Pinho, Rogério Oliveira; Pereira, Jhonata Vieira Tavares do Nascimento; Okano, Denise Silva; Costa, Karine Assis; Guimarães, José Domingos

2018-01-01

In view of the importance of the genetic material of local breeds in the swine industry and the lack of information about reproductive performance of Piau females, two experiments were conducted to evaluate puberty and sexual maturity as well as the morphometry of embryos/fetuses, placenta and uterus during the first 90 days of gestation in Piau breed and Commercial line gilts. In experiment I, 37 Piau and 25 commercial line gilts were used. From the 120 days of age, detection of estrus was performed using mature boars from the first to third estrus of each gilt. Data regarding to age, body weight and estrus duration were recorded. After third estrus, females were slaughtered and ovaries were collected to determine ovulation rate. In experiment II, 36 Piau and 18 commercial line gilts were distributed into three groups according to the mating: Commercial, commercial line females x commercial line male; cross-mated, Piau females x commercial line male; and Piau, Piau females x Piau male. Gilts were slaughtered at 7, 15, 30, 45, 60 and 90 days of pregnancy. Piau females reached puberty and sexual maturity at the same age as commercial line females, but with lower weight; moreover, Piau group showed negative correlations of birth weight with puberty (-0.27) and sexual maturity (-0.29). Commercial gilts presented higher ovulation rate, weight and length of uterus, and length and thoracic circumference of fetuses. Nevertheless, number of fetuses was similar in all groups at 90 days of gestation suggesting that Piau females present higher survival rates of the conceptuses. The results showed differences between the genetic groups related to fetal and placental development, gestational losses, number of ovulations and uterine development. In addition, an intermediate status of fetal weight was observed in Piau/Commercial line crossbred conceptuses; thus, the selection of Piau females on reproductive traits to be mated with commercial line males would be an alternative to contribute to improvement of intramuscular fat content. Copyright © 2017. Published by Elsevier Inc.

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.

Identification of key ancestors of modern germplasm in a breeding program of maize.

PubMed

Technow, F; Schrag, T A; Schipprack, W; Melchinger, A E

2014-12-01

Probabilities of gene origin computed from the genomic kinships matrix can accurately identify key ancestors of modern germplasms Identifying the key ancestors of modern plant breeding populations can provide valuable insights into the history of a breeding program and provide reference genomes for next generation whole genome sequencing. In an animal breeding context, a method was developed that employs probabilities of gene origin, computed from the pedigree-based additive kinship matrix, for identifying key ancestors. Because reliable and complete pedigree information is often not available in plant breeding, we replaced the additive kinship matrix with the genomic kinship matrix. As a proof-of-concept, we applied this approach to simulated data sets with known ancestries. The relative contribution of the ancestral lines to later generations could be determined with high accuracy, with and without selection. Our method was subsequently used for identifying the key ancestors of the modern Dent germplasm of the public maize breeding program of the University of Hohenheim. We found that the modern germplasm can be traced back to six or seven key ancestors, with one or two of them having a disproportionately large contribution. These results largely corroborated conjectures based on early records of the breeding program. We conclude that probabilities of gene origin computed from the genomic kinships matrix can be used for identifying key ancestors in breeding programs and estimating the proportion of genes contributed by them.

77 FR 19225 - Notice of Availability of Draft Documents for Public Comment Related to a Fishery Conservation...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-30

... behavioral patterns, including breeding, feeding, and sheltering (64 FR 60727, November 8, 1999). ``Harass... breeding, feeding, and sheltering. NMFS may issue permits, under limited circumstances, to allow the take... (Oncorhyncus tshawytscha) are incidentally caught in the commercial shrimp trawl fishery and the recreational...

Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research

USDA-ARS?s Scientific Manuscript database

The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to un...

Red leaf lettuce breeding line with resistance to corky root, 06-810

USDA-ARS?s Scientific Manuscript database

The Agricultural Research Service, United States Department of Agriculture (USDA) announces the release of a breeding line of red leaf lettuce (Lactuca sativa L.), 06-810. The line may be suitable for commercial production, and is suitable for use as a source of resistance to corky root disease in t...

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...

Pup production, abundance, and breeding distribution of northern elephant seals at San Nicolas Island, winter 1981

USGS Publications Warehouse

1985-01-01

A major breeding colony of northern elephant seals, Mirounga angustirostris, occurs on San Nicolas Island, California. Due to commercial hunting, elephant seals were extinct on San Nicolas Island by the end of the 19th century. Subsequent recovery of the population has been well documented (Table 1). Census data collected since 1949 indicate that the colony has been growing rapidly in numbers after breeding began again in the late 1940s.

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.

Salmonella enterica serovar Enteridis (SE) infection in 5 commercial white egg and 3 commercial brown egg strains of laying hens: comparison of SE colonization with immune responsiveness

USDA-ARS?s Scientific Manuscript database

Different chicken breeds have been shown to exhibit varying susceptibility to infection with paratyphoid salmonellae. The current study was undertaken to compare the course of infection with SE in crops and intestines of 5 commercial white egg strains (W1-W5) and 3 commercial brown egg strains (B1-...

Comparing in vitro lymphocyte reactivity to Salmonella enterica serovar Enteridis (SE) antigens 5 commercial white egg and 3 commercial brown egg strains of laying hens following SE infection.

USDA-ARS?s Scientific Manuscript database

Different chicken breeds have been shown to exhibit varying susceptibility to infection with paratyphoid salmonellae. The current study was undertaken to compare the course of infection with SE in crops and intestines of 5 commercial white egg strains (W1-W5) and 3 commercial brown egg strains (B1-...

Salmonella penetration through eggshells of chickens of different genetic backgrounds.

PubMed

Rathgeber, Bruce M; McCarron, Paige; Budgell, Krista L

2013-09-01

Eggs have been identified as a source of salmonellosis, making the transmission of Salmonella to eggs of great concern to the poultry industry. The goal of this experiment was to determine the ability of Salmonella to penetrate the eggshell of 5 different breeds of noncommercial chicken, Barred Plymouth Rock, White Leghorn, Brown Leghorn, Fayoumi, and Light Sussex, and 1 commercial Lohmann LSL-Lite. Egg weight, breaking force, shell weight, and shell thickness measurements were taken for 30 eggs per breed. A 1 cm in diameter hole was cut out from the narrow end of 30 additional eggs per breed. The shells were filled with plate count agar containing tetracycline and 0.1% 2,3,5-triphenyl terazolium chloride and sealed with paraffin wax. Agar-filled eggs were submerged for 1 min in an overnight culture of tetracycline-resistant Salmonella Heidelberg and incubated at 37°C for 40 h. Eggs were candled and visual colonies were counted and reported as cfu per egg and cfu per gram of shell. The SAS mixed model was used to evaluate differences between breeds for egg quality characteristics and the number of cfu per egg and per gram of shell. Commercial layers (62.6 g) and Barred Plymouth Rock (61.5 g) produced the largest eggs, whereas Fayoumi (47.1 g) produced the smallest (P < 0.05). Force to break the shell was lowest (P < 0.05) for Barred Plymouth Rock (3.6 kg) and greatest for the commercial (4.4 kg), White Leghorn (4.4 kg), and Fayoumi (4.2 kg). Bacteria penetrating the shell was lowest (P < 0.05) for Barred Plymouth Rock (10.7 cfu/g) and highest for Light Sussex (27.7 cfu/g) and Brown Leghorn (27.2 cfu/g), with other breeds intermediate. These results indicate that there are breed-specific influences on the ability of an egg to resist Salmonella, which cannot be explained by shell quality measurements. Further investigations are warranted to determine the contributing factors to shell penetration by bacteria. This study highlights the value in maintaining heritage chicken breeds as a genetic resource for the future.

A pre-breeding screening program for transgenic boars based on fluorescence in situ hybridization assay.

PubMed

Bou, Gerelchimeg; Sun, Mingju; Lv, Ming; Zhu, Jiang; Li, Hui; Wang, Juan; Li, Lu; Liu, Zhongfeng; Zheng, Zhong; He, Wenteng; Kong, Qingran; Liu, Zhonghua

2014-08-01

For efficient transgenic herd expansion, only the transgenic animals that possess the ability to transmit transgene into next generation are considered for breeding. However, for transgenic pig, practically lacking a pre-breeding screening program, time, labor and money is always wasted to maintain non-transgenic pigs, low or null transgenic transmission pigs and the related fruitless gestations. Developing a pre-breeding screening program would make the transgenic herd expansion more economical and efficient. In this technical report, we proposed a three-step pre-breeding screening program for transgenic boars simply through combining the fluorescence in situ hybridization (FISH) assay with the common pre-breeding screening workflow. In the first step of screening, combined with general transgenic phenotype analysis, FISH is used to identify transgenic boars. In the second step of screening, combined with conventional semen test, FISH is used to detect transgenic sperm, thus to identify the individuals producing high quality semen and transgenic sperm. In the third step of screening, FISH is used to assess the in vitro fertilization embryos, thus finally to identify the individuals with the ability to produce transgenic embryos. By this three-step screening, the non-transgenic boars and boars with no ability to produce transgenic sperm or transgenic embryos would be eliminated; therefore only those boars could produce transgenic offspring are maintained and used for breeding and herd expansion. It is the first time a systematic pre-breeding screening program is proposed for transgenic pigs. This program might also be applied in other transgenic large animals, and provide an economical and efficient strategy for herd expansion.

Polyploidy creates higher diversity among Cynodon accessions as assessed by molecular markers.

PubMed

Gulsen, Osman; Sever-Mutlu, Songul; Mutlu, Nedim; Tuna, Metin; Karaguzel, Osman; Shearman, Robert C; Riordan, Terrance P; Heng-Moss, Tiffany M

2009-05-01

Developing a better understanding of associations among ploidy level, geographic distribution, and genetic diversity of Cynodon accessions could be beneficial to bermudagrass breeding programs, and would enhance our understanding of the evolutionary biology of this warm season grass species. This study was initiated to: (1) determine ploidy analysis of Cynodon accessions collected from Turkey, (2) investigate associations between ploidy level and diversity, (3) determine whether geographic and ploidy distribution are related to nuclear genome variation, and (4) correlate among four nuclear molecular marker systems for Cynodon accessions' genetic analyses. One hundred and eighty-two Cynodon accessions collected in Turkey from an area south of the Taurus Mountains along the Mediterranean cost and ten known genotypes were genotyped using sequence related amplified polymorphism (SRAP), peroxidase gene polymorphism (POGP), inter-simple sequence repeat (ISSR), and random amplified polymorphic DNA (RAPD). The diploids, triploids, tetraploids, pentaploids, and hexaploids revealed by flow cytometry had a linear present band frequency of 0.36, 0.47, 0.49, 0.52, and 0.54, respectively. Regression analysis explained that quadratic relationship between ploidy level and band frequency was the most explanatory (r = 0.62, P < 0.001). The AMOVA results indicated that 91 and 94% of the total variation resided within ploidy level and provinces, respectively. The UPGMA analysis suggested that commercial bermudagrass cultivars only one-third of the available genetic variation. SRAP, POGP, ISSR, and RAPD markers differed in detecting relationships among the bermudagrass genotypes and rare alleles, suggesting more efficiency of combinatory analysis of molecular marker systems. Elucidating Cynodon accessions' genetic structure can aid to enhance breeding programs and broaden genetic base of commercial cultivars.

Selective breeding of food sized rainbow trout against Flavobacteriosis

USDA-ARS?s Scientific Manuscript database

Selective breeding of rainbow trout is an important component of an integrated fish health management program. The current goals of our selective breeding program are to improve disease resistance, growth and survival in a reuse water environment. To improve these traits, data are recorded on thousa...

Selective breeding of food size rainbow trout against Flavobacteriosis

USDA-ARS?s Scientific Manuscript database

Selective breeding of rainbow trout is an important component of an integrated fish health management program. The current goals of our selective breeding program are to improve disease resistance, growth and survival in a reuse water environment. To improve these traits, data are recorded on thousa...

Leaf physiology and morphology of Castanea dentata (Marsh) Borkh., Castanea mollissima Blume, and three backcross breeding generations planted in the southern Appalachians, USA

Treesearch

Benjamin O. Knapp; G. Geoff Wang; Stacy L Clark; Lauren S. Pile; Scott E. Schlarbaum

2014-01-01

Backcross breeding programs have been used to transfer disease resistance and other traits from one forest tree species to another in order to meet restoration objectives. Evaluating the field performance of such material is critical for determining the success of breeding programs. In eastern North America, The American Chestnut Foundation has a backcross breeding...

A simple language to script and simulate breeding schemes: the breeding scheme language

USDA-ARS?s Scientific Manuscript database

It is difficult for plant breeders to determine an optimal breeding strategy given that the problem involves many factors, such as target trait genetic architecture and breeding resource availability. There are many possible breeding schemes for each breeding program. Although simulation study may b...

Genetic Variants in SDC3 Gene are Significantly Associated with Growth Traits in Two Chinese Beef Cattle Breeds.

PubMed

Huang, Yong-Zhen; Wang, Qin; Zhang, Chun-Lei; Fang, Xing-Tang; Song, En-Liang; Chen, Hong

2016-01-01

Identification of the genes and polymorphisms underlying quantitative traits, and understanding these genes and polymorphisms affect economic growth traits, are important for successful marker-assisted selection and more efficient management strategies in commercial cattle (Bos taurus) population. Syndecan-3 (SDC3), a member of the syndecan family of type I transmembrane heparan sulfate proteoglycans is a novel regulator of feeding behavior and body weight. The aim of this study is to examine the association of the SDC3 polymorphism with growth traits in Chinese Jiaxian and Qinchuan cattle breeds (). Four single nucleotide polymorphisms (SNPs: 1-4) were detected in 555 cows from three Chinese native cattle breeds by means of sequencing pooled DNA samples and polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) methods. We found one SNP (g.28362A > G) in intron and three SNPs (g.30742T > G, g.30821C > T and 33418 A > G) in exons. The statistical analyses indicated that these SNPs of SDC3 gene were associated with bovine body height, body length, chest circumference, and circumference of cannon bone (P < 0.05). The mutant-type variant was superior for growth traits; the heterozygote was associated with higher growth traits compared to wild-type homozygote. Our result confirms the polymorphisms in the SDC3 gene are associated with growth traits that may be used for marker-assisted selection in beef cattle breeding programs.

Ecohealth System Dynamic Model as a Planning Tool for the Reduction of Breeding Sites

NASA Astrophysics Data System (ADS)

Respati, T.; Raksanagara, A.; Djuhaeni, H.; Sofyan, A.; Shandriasti, A.

2017-03-01

Dengue is still one of major health problem in Indonesia. Dengue transmission is influenced by dengue prevention and eradication program, community participation, housing environment and climate. The complexity of the disease coupled with limited resources necessitates different approach for prevention methods that include factors contribute to the transmission. One way to prevent the dengue transmission is by reducing the mosquito’s breeding sites. Four factors suspected to influence breeding sites are dengue prevention and eradication program, community participation, housing environment, and weather condition. In order to have an effective program in reducing the breeding site it is needed to have a model which can predict existence of the breeding sites while the four factors under study are controlled. The objective of this study is to develop an Ecohealth model using system dynamic as a planning tool for the reduction of breeding sites to prevent dengue transmission with regard to dengue prevention and eradication program, community participation, housing environment, and weather condition. The methodology is a mixed method study using sequential exploratory design. The study comprised of 3 stages: first a qualitative study to 14 respondents using in-depth interview and 6 respondents for focus group discussion. The results from the first stage was used to develop entomology and household survey questionnaires for second stage conducted in 2036 households across 12 sub districts in Bandung City. Ecohealth system dynamic model was developed using data from first and second stages. Analyses used are thematic analysis for qualitative data; spatial, generalized estimating equation (GEE) and structural equation modeling for quantitative data; also average mean error (AME) and average variance error (AVE) for dynamic system model validation. System dynamic model showed that the most effective approach to eliminate breeding places was by ensuring the availability of basic sanitation for all houses. Weather factors such as precipitation can be compensated with the eradication of breeding sites activities which is conducted as scheduled and at the same time for the whole areas. Conclusion of this study is that dengue prevention and eradication program, community participation, and housing environment contributed to breeding places elimination influenced the existence of the breeding sites. The availability of basic sanitation and breeding places eradication program done timely and collectively are the most effective approach to eradicate breeding sites. Ecohealth dynamic system model can be used as a tool for the planning of breeding sites eradication program to prevent disease transmissions at city level.

Economic evaluation of genomic selection in small ruminants: a sheep meat breeding program.

PubMed

Shumbusho, F; Raoul, J; Astruc, J M; Palhiere, I; Lemarié, S; Fugeray-Scarbel, A; Elsen, J M

2016-06-01

Recent genomic evaluation studies using real data and predicting genetic gain by modeling breeding programs have reported moderate expected benefits from the replacement of classic selection schemes by genomic selection (GS) in small ruminants. The objectives of this study were to compare the cost, monetary genetic gain and economic efficiency of classic selection and GS schemes in the meat sheep industry. Deterministic methods were used to model selection based on multi-trait indices from a sheep meat breeding program. Decisional variables related to male selection candidates and progeny testing were optimized to maximize the annual monetary genetic gain (AMGG), that is, a weighted sum of meat and maternal traits annual genetic gains. For GS, a reference population of 2000 individuals was assumed and genomic information was available for evaluation of male candidates only. In the classic selection scheme, males breeding values were estimated from own and offspring phenotypes. In GS, different scenarios were considered, differing by the information used to select males (genomic only, genomic+own performance, genomic+offspring phenotypes). The results showed that all GS scenarios were associated with higher total variable costs than classic selection (if the cost of genotyping was 123 euros/animal). In terms of AMGG and economic returns, GS scenarios were found to be superior to classic selection only if genomic information was combined with their own meat phenotypes (GS-Pheno) or with their progeny test information. The predicted economic efficiency, defined as returns (proportional to number of expressions of AMGG in the nucleus and commercial flocks) minus total variable costs, showed that the best GS scenario (GS-Pheno) was up to 15% more efficient than classic selection. For all selection scenarios, optimization increased the overall AMGG, returns and economic efficiency. As a conclusion, our study shows that some forms of GS strategies are more advantageous than classic selection, provided that GS is already initiated (i.e. the initial reference population is available). Optimizing decisional variables of the classic selection scheme could be of greater benefit than including genomic information in optimized designs.

A modern Green Revolution gene for reduced height in wheat.

PubMed

Würschum, Tobias; Langer, Simon M; Longin, C Friedrich H; Tucker, Matthew R; Leiser, Willmar L

2017-12-01

Increases in the yield of wheat during the Green Revolution of the late 20 th century were achieved through the introduction of Reduced height (Rht) dwarfing genes. The Rht-B1 and Rht-D1 loci ensured short stature by limiting the response to the growth-promoting hormone gibberellin, and are now widespread through international breeding programs. Despite this advantage, interference with the plant's response to gibberellin also triggers adverse effects for a range of important agronomic traits, and consequently modern Green Revolution genes are urgently required. In this study, we revisited the genetic control of wheat height using an association mapping approach and a large panel of 1110 worldwide winter wheat cultivars. This led to the identification of a major Rht locus on chromosome 6A, Rht24, which substantially reduces plant height alone as well as in combination with Rht-1b alleles. Remarkably, behind Rht-D1, Rht24 was the second most important locus for reduced height, explaining 15.0% of the genotypic variance and exerting an allele substitution effect of -8.8 cm. Unlike the two Rht-1b alleles, plants carrying Rht24 remain sensitive to gibberellic acid treatment. Rht24 appears in breeding programs from all countries of origin investigated, with increased frequency over the last decades, indicating that wheat breeders have actively selected for this locus. Taken together, this study reveals Rht24 as an important Rht gene of commercial relevance in worldwide wheat breeding. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Characterization of two endoglucanases for the classification of the earthworm, Eisenia fetida Waki.

PubMed

Akazawa, Shin-ichi; Ikarashi, Yuki; Yarimizu, Jun; Yokoyama, Keisuke; Kobayashi, Tomoya; Nakazawa, Hikaru; Ogasawara, Wataru; Morikawa, Yasushi

2016-01-01

Eisenia fetida and Eisenia andrei are vermicomposting species that are used as model animals for testing chemical material toxicology. Eisenia spp. are grown commercially in various fields in Japan. However, these two species have not been classified because it is difficult to distinguish them morphologically; thus, all bred earthworms are called E. fetida. However, it has been proposed that these two species have different expression regulation mechanisms. Here, we classified a sample of earthworms purchased from several farms, confirming that both E. fetida and E. andrei are present in Japanese earthworm breeding programs. We also characterized two highly active endoglucanases (EfEG1 and EfEG2) from the E. fetida Waki strain, which contained strong fibrinolytic enzymes for improving human health. We confirmed that EfEG1 is 1371 bp long and belongs to GHF9. Thus, E. fetida Waki may have commercial application for biomass utilization and as a dietary health supplement.

Genetic relationships among milk production and teat and udder scores in cows sired by seven prominent beef cattle breeds

USDA-ARS?s Scientific Manuscript database

Milk production and teat and udder quality are key components to lifetime cow productivity in commercial beef cattle. Our objective was to determine genetic relationships and breed differences for milk production and teat and udder quality in young and mature cows. Cows (n = 602) were crosses of F...

Green leaf lettuce breeding lines with resistance to corky root, 06-831 and 06-833.

USDA-ARS?s Scientific Manuscript database

The Agricultural Research Service, United States Department of Agriculture (USDA) announces the release of two breeding lines of green leaf lettuce (Lactuca sativa L.). The lines 06-831 and 06-833 look similar to ‘Waldmann’s Green’ and related cultivars. The lines may be suitable for commercial pro...

Rapid development of molecular markers by next-generation sequencing linked to a gene conferring phomopsis stem blight disease resistance for marker-assisted selection in lupin (Lupinus angustifolius L.) breeding.

PubMed

Yang, Huaan; Tao, Ye; Zheng, Zequn; Shao, Di; Li, Zhenzhong; Sweetingham, Mark W; Buirchell, Bevan J; Li, Chengdao

2013-02-01

Selection for phomopsis stem blight disease (PSB) resistance is one of the key objectives in lupin (Lupinus angustifolius L.) breeding programs. A cross was made between cultivar Tanjil (resistant to PSB) and Unicrop (susceptible). The progeny was advanced into F(8) recombinant inbred lines (RILs). The RIL population was phenotyped for PSB disease resistance. Twenty plants from the RIL population representing disease resistance and susceptibility was subjected to next-generation sequencing (NGS)-based restriction site-associated DNA sequencing on the NGS platform Solexa HiSeq2000, which generated 7,241 single nucleotide polymorphisms (SNPs). Thirty-three SNP markers showed the correlation between the marker genotypes and the PSB disease phenotype on the 20 representative plants, which were considered as candidate markers linked to a putative R gene for PSB resistance. Seven candidate markers were converted into sequence-specific PCR markers, which were designated as PhtjM1, PhtjM2, PhtjM3, PhtjM4, PhtjM5, PhtjM6 and PhtjM7. Linkage analysis of the disease phenotyping data and marker genotyping data on a F(8) population containing 187 RILs confirmed that all the seven converted markers were associated with the putative R gene within the genetic distance of 2.1 CentiMorgan (cM). One of the PCR markers, PhtjM3, co-segregated with the R gene. The seven established PCR markers were tested in the 26 historical and current commercial cultivars released in Australia. The numbers of "false positives" (showing the resistance marker allele band but lack of the putative R gene) for each of the seven PCR markers ranged from nil to eight. Markers PhtjM4 and PhtjM7 are recommended in marker-assisted selection for PSB resistance in the Australian national lupin breeding program due to its wide applicability on breeding germplasm and close linkage to the putative R gene. The results demonstrated that application of NGS technology is a rapid and cost-effective approach in development of markers for molecular plant breeding.

Optimization of reproductive management programs using lift chart analysis and cost-sensitive evaluation of classification errors.

PubMed

Shahinfar, Saleh; Guenther, Jerry N; Page, C David; Kalantari, Afshin S; Cabrera, Victor E; Fricke, Paul M; Weigel, Kent A

2015-06-01

The common practice on most commercial dairy farms is to inseminate all cows that are eligible for breeding, while ignoring (or absorbing) the costs associated with semen and labor directed toward low-fertility cows that are unlikely to conceive. Modern analytical methods, such as machine learning algorithms, can be applied to cow-specific explanatory variables for the purpose of computing probabilities of success or failure associated with upcoming insemination events. Lift chart analysis can identify subsets of high fertility cows that are likely to conceive and are therefore appropriate targets for insemination (e.g., with conventional artificial insemination semen or expensive sex-enhanced semen), as well as subsets of low-fertility cows that are unlikely to conceive and should therefore be passed over at that point in time. Although such a strategy might be economically viable, the management, environmental, and financial conditions on one farm might differ widely from conditions on the next, and hence the reproductive management recommendations derived from such a tool may be suboptimal for specific farms. When coupled with cost-sensitive evaluation of misclassified and correctly classified insemination events, the strategy can be a potentially powerful tool for optimizing the reproductive management of individual farms. In the present study, lift chart analysis and cost-sensitive evaluation were applied to a data set consisting of 54,806 insemination events of primiparous Holstein cows on 26 Wisconsin farms, as well as a data set with 17,197 insemination events of primiparous Holstein cows on 3 Wisconsin farms, where the latter had more detailed information regarding health events of individual cows. In the first data set, the gains in profit associated with limiting inseminations to subsets of 79 to 97% of the most fertile eligible cows ranged from $0.44 to $2.18 per eligible cow in a monthly breeding period, depending on days in milk at breeding and milk yield relative to contemporaries. In the second data set, the strategy of inseminating only a subset consisting of 59% of the most fertile cows conferred a gain in profit of $5.21 per eligible cow in a monthly breeding period. These results suggest that, when used with a powerful classification algorithm, lift chart analysis and cost-sensitive evaluation of correctly classified and misclassified insemination events can enhance the performance and profitability of reproductive management programs on commercial dairy farms. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

7 CFR 1980.498 - Business and Industry Disaster Loans.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (4) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1980.490 - Business and industry buydown loans.

Code of Federal Regulations, 2010 CFR

2010-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (3) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1980.498 - Business and Industry Disaster Loans.

Code of Federal Regulations, 2011 CFR

2011-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (4) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1980.490 - Business and industry buydown loans.

Code of Federal Regulations, 2011 CFR

2011-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (3) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1980.498 - Business and Industry Disaster Loans.

Code of Federal Regulations, 2010 CFR

2010-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (4) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1980.498 - Business and Industry Disaster Loans.

Code of Federal Regulations, 2013 CFR

2013-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (4) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1980.498 - Business and Industry Disaster Loans.

Code of Federal Regulations, 2014 CFR

2014-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (4) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1980.490 - Business and industry buydown loans.

Code of Federal Regulations, 2013 CFR

2013-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (3) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1980.490 - Business and industry buydown loans.

Code of Federal Regulations, 2014 CFR

2014-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (3) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1980.490 - Business and industry buydown loans.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm or domestic animals. (3) Other eligible businesses. Eligible types of businesses also include: (i) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

Intellectual property and information controversy(I)

NASA Astrophysics Data System (ADS)

Aoyama, Hirokazu

This paper deals with intellectual property as the results of various intellectual activities such as R & D, and intellectual proprietary rights which protect it. New technology, designs, literary works, computer programs, semiconductor chips, new plant breeding, brands, trading secrets, CI and others, and legislations which protect them are described. Then, the background of the fact that intellectual proprietary rights are emphasized as analyzed. The author points out items as follows; movement toward much larger size of R & D, generation of the areas to be newly protected, trend in enforcement of intellectual property protection, commercialization of intellectual property, trend in software evolution, movement in technological protectionism, and the present status on each item.

Micropropagation systems of Feijoa (Acca sellowiana (O. Berg) Burret).

PubMed

Guerra, Miguel Pedro; Cangahuala-Inocente, Gabriela Claudia; Vesco, Lirio Luiz Dal; Pescador, Rosete; Caprestano, Clarissa Alves

2013-01-01

Acca sellowiana (O. Berg) Burret sin. Feijoa sellowiana (Myrtaceae) is a semiwoody fruit species native to South Brazil, Uruguay, and Argentina; edible fruits are tasty. The naturally occurring populations in Santa Catarina State show high variability in fruit size, color, and other features. A breeding program launched in 1990 resulted in the release of four Brazilian commercial varieties. The conventional clonal propagation methods of this species, such as cutting and grafting, have shown low efficiency. Therefore, tissue culture techniques were developed for mass propagation. This chapter describes several protocols based on organogenesis and somatic embryogenesis. Additional techniques including synthetic seed technology and temporary immersion system are also described.

Effects of insecticides on a phytotelmata-breeding amphibian.

PubMed

Egea-Serrano, Andrés; Solé, Mirco

2017-02-01

Information on the impact of pesticides on amphibian species breeding in phytotelmata (water bodies within plants) is totally lacking. The aim of the present study was to assess the impact of the insecticide malathion on larvae of Phyllodytes luteolus. Individuals were exposed to ecologically relevant concentrations of malathion (commercial formulation) for 16 d under laboratory conditions. Malathion had a lethal effect that allowed the authors to hypothesize that phtytotelmata-breeding species are likely as vulnerable to pollution as pond breeders. Environ Toxicol Chem 2017;36:422-428. © 2016 SETAC. © 2016 SETAC.

50 CFR 15.24 - Permits for cooperative breeding.

Code of Federal Regulations, 2010 CFR

2010-10-01

... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.24 Permits for cooperative breeding. (a) Application requirements for permits for cooperative breeding. Each... 50 Wildlife and Fisheries 1 2010-10-01 2010-10-01 false Permits for cooperative breeding. 15.24...

50 CFR 15.24 - Permits for cooperative breeding.

Code of Federal Regulations, 2011 CFR

2011-10-01

... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.24 Permits for cooperative breeding. (a) Application requirements for permits for cooperative breeding. Each... 50 Wildlife and Fisheries 1 2011-10-01 2011-10-01 false Permits for cooperative breeding. 15.24...

50 CFR 15.24 - Permits for cooperative breeding.

Code of Federal Regulations, 2012 CFR

2012-10-01

... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.24 Permits for cooperative breeding. (a) Application requirements for permits for cooperative breeding. Each... 50 Wildlife and Fisheries 1 2012-10-01 2012-10-01 false Permits for cooperative breeding. 15.24...

At-Sea Distribution and Prey Selection of Antarctic Petrels and Commercial Krill Fisheries.

PubMed

Descamps, Sébastien; Tarroux, Arnaud; Cherel, Yves; Delord, Karine; Godø, Olaf Rune; Kato, Akiko; Krafft, Bjørn A; Lorentsen, Svein-Håkon; Ropert-Coudert, Yan; Skaret, Georg; Varpe, Øystein

2016-01-01

Commercial fisheries may impact marine ecosystems and affect populations of predators like seabirds. In the Southern Ocean, there is an extensive fishery for Antarctic krill Euphausia superba that is projected to increase further. Comparing distribution and prey selection of fishing operations versus predators is needed to predict fishery-related impacts on krill-dependent predators. In this context, it is important to consider not only predators breeding near the fishing grounds but also the ones breeding far away and that disperse during the non-breeding season where they may interact with fisheries. In this study, we first quantified the overlap between the distribution of the Antarctic krill fisheries and the distribution of a krill dependent seabird, the Antarctic petrel Thalassoica antarctica, during both the breeding and non-breeding season. We tracked birds from the world biggest Antarctic petrel colony (Svarthamaren, Dronning Maud Land), located >1000 km from the main fishing areas, during three consecutive seasons. The overall spatial overlap between krill fisheries and Antarctic petrels was limited but varied greatly among and within years, and was high in some periods during the non-breeding season. In a second step, we described the length frequency distribution of Antarctic krill consumed by Antarctic petrels, and compared this with results from fisheries, as well as from diet studies in other krill predators. Krill taken by Antarctic petrels did not differ in size from that taken by trawls or from krill taken by most Antarctic krill predators. Selectivity for specific Antarctic krill stages seems generally low in Antarctic predators. Overall, our results show that competition between Antarctic petrels and krill fisheries is currently likely negligible. However, if krill fisheries are to increase in the future, competition with the Antarctic petrel may occur, even with birds breeding thousands of kilometers away.

At-Sea Distribution and Prey Selection of Antarctic Petrels and Commercial Krill Fisheries

PubMed Central

Descamps, Sébastien; Tarroux, Arnaud; Cherel, Yves; Delord, Karine; Godø, Olaf Rune; Kato, Akiko; Krafft, Bjørn A.; Lorentsen, Svein-Håkon; Ropert-Coudert, Yan; Skaret, Georg; Varpe, Øystein

2016-01-01

Commercial fisheries may impact marine ecosystems and affect populations of predators like seabirds. In the Southern Ocean, there is an extensive fishery for Antarctic krill Euphausia superba that is projected to increase further. Comparing distribution and prey selection of fishing operations versus predators is needed to predict fishery-related impacts on krill-dependent predators. In this context, it is important to consider not only predators breeding near the fishing grounds but also the ones breeding far away and that disperse during the non-breeding season where they may interact with fisheries. In this study, we first quantified the overlap between the distribution of the Antarctic krill fisheries and the distribution of a krill dependent seabird, the Antarctic petrel Thalassoica antarctica, during both the breeding and non-breeding season. We tracked birds from the world biggest Antarctic petrel colony (Svarthamaren, Dronning Maud Land), located >1000 km from the main fishing areas, during three consecutive seasons. The overall spatial overlap between krill fisheries and Antarctic petrels was limited but varied greatly among and within years, and was high in some periods during the non-breeding season. In a second step, we described the length frequency distribution of Antarctic krill consumed by Antarctic petrels, and compared this with results from fisheries, as well as from diet studies in other krill predators. Krill taken by Antarctic petrels did not differ in size from that taken by trawls or from krill taken by most Antarctic krill predators. Selectivity for specific Antarctic krill stages seems generally low in Antarctic predators. Overall, our results show that competition between Antarctic petrels and krill fisheries is currently likely negligible. However, if krill fisheries are to increase in the future, competition with the Antarctic petrel may occur, even with birds breeding thousands of kilometers away. PMID:27533327

Population structure of rice varieties used in Turkish rice breeding programs determined using simple-sequence repeat and inter-primer binding site-retrotransposon data.

PubMed

Cömertpay, G; Baloch, F S; Derya, M; Andeden, E E; Alsaleh, A; Sürek, H; Özkan, H

2016-02-19

Effective breeding programs based on genetic diversity are needed to broaden the genetic basis of rice (Oryza sativa L.) in Turkey. In this study, 81 commercial varieties from seven countries were studied in order to estimate the genomic relationships among them using nine inter-primer binding site (iPBS)-retrotransposon and 17 simple-sequence repeat (SSR) markers. A total of 59 alleles for the SSR markers and 96 bands for the iPBS-retrotransposon markers were detected, with an average of 3.47 and 10.6 per locus, respectively. Each of the varieties could be unequivocally identified by the SSR and iPBS-retrotransposon profiles. The iPBS-retrotransposon- and SSR-based clustering were identical and closely mirrored each other, with a significantly high correlation (r = 0.73). A neighbor-joining cluster based on the combined SSR and iPBS-retrotransposon data divided the rice varieties into three clusters. The population structure was determined using the STRUCTURE software, and three populations (K = 3) were identified among the varieties studied, showing that the diversity harbored by Turkish rice varieties is low. The results indicate that iPBS-retrotransposon markers are a very powerful technique to determine the genetic diversity of rice varieties.

50 CFR 23.51 - What are the requirements for issuing a partially completed CITES document?

Code of Federal Regulations, 2014 CFR

2014-10-01

... captivity or artificially propagated. (D) Appendix-I specimens from registered commercial breeding operations. (E) Appendix-I plants artificially propagated for commercial purposes. (F) Other specimens that..., BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE...

50 CFR 23.51 - What are the requirements for issuing a partially completed CITES document?

Code of Federal Regulations, 2012 CFR

2012-10-01

... captivity or artificially propagated. (D) Appendix-I specimens from registered commercial breeding operations. (E) Appendix-I plants artificially propagated for commercial purposes. (F) Other specimens that..., BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE...

50 CFR 23.51 - What are the requirements for issuing a partially completed CITES document?

Code of Federal Regulations, 2010 CFR

2010-10-01

... captivity or artificially propagated. (D) Appendix-I specimens from registered commercial breeding operations. (E) Appendix-I plants artificially propagated for commercial purposes. (F) Other specimens that..., BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE...

50 CFR 23.51 - What are the requirements for issuing a partially completed CITES document?

Code of Federal Regulations, 2013 CFR

2013-10-01

... captivity or artificially propagated. (D) Appendix-I specimens from registered commercial breeding operations. (E) Appendix-I plants artificially propagated for commercial purposes. (F) Other specimens that..., BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE...

50 CFR 23.51 - What are the requirements for issuing a partially completed CITES document?

Code of Federal Regulations, 2011 CFR

2011-10-01

... captivity or artificially propagated. (D) Appendix-I specimens from registered commercial breeding operations. (E) Appendix-I plants artificially propagated for commercial purposes. (F) Other specimens that..., BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE...

An on-farm trial evaluating the effect of fast and slow growing genotypes on meat quality of chickens reared on a local pasture

USDA-ARS?s Scientific Manuscript database

There has been increasing interest among the consumers for free range and organic poultry in recent years. Even though heritage breed birds grow much slower compared to commercial breeds, many free range producers believe that they are better suited for outdoor production systems. We conducted an on...

75 FR 57426 - Endangered and Threatened Wildlife and Plants; 90-Day Finding on a Petition To Reclassify the U.S...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-21

... requesting scientific and commercial data and other information regarding the U.S. breeding population of...-0067; 92220-1113-0000-C5] Endangered and Threatened Wildlife and Plants; 90-Day Finding on a Petition To Reclassify the U.S. Breeding Population of Wood Storks From Endangered to Threatened AGENCY: Fish...

Danish A.I. field data with sexed semen.

PubMed

Borchersen, S; Peacock, M

2009-01-01

The objective of this study was to compare conception rates, non-return rates and sex ratios of sexed and conventional semen from the same sires in commercial dairy herds in Denmark. The semen was produced from three bulls from each of the three major dairy breeds in Denmark: Holstein, Jersey and Danish Red Dairy Breed (nine bulls total), in order to answer questions on breeds differences in field results. AI was performed by trained technicians using a minimum of 150 doses of sorted sperm and 50 control doses from each bull. During the trial, a total of 2087 doses were used in 63 herds. The trial showed that the conception rate using sorted semen was 5% points lower than with conventional doses for Danish Reds, 7% points for Jerseys, and 12% points for Holsteins. Translating this into non-return rate revealed differences of 10-20% points among bulls. These differences are thought to be a good indicator of what to expect from commercial use of sexed semen. The sex ratios varied from 89% to 93% female calves among breeds, which on average is consistent with the theoretical average sex ratio of 93% females considering the low number of inseminations.

Sensory properties and fatty acids profiles of fermented dry sausages made of pork meat from various breeds

NASA Astrophysics Data System (ADS)

Parunović, N.; Radović, Č.; Savić, R.

2017-09-01

In this study, the parallel examinations on fatty acid profiles and sensory properties of fermented dry sausages are presented. Three types of kulen and sremska sausages were made, which varied depending on the percentage of meat and fat derived from different pig breeds: autochthonous (Swallow-Belly Mangalitsa and Moravka) and commercial (Swedish Landrace). In sausages made from meat of commercial pig breed, the highest cholesterol content was detected. However, sausage made from the Mangalitsa pork meat contained higher levels of monounsaturated fatty acid (MUFA) and unsaturated fatty acid (USFA), and lower saturated fatty acid levels (SFA).The level of polyunsaturated (PUFA) in sausage made of Landrace pork meat was significantly higher than levels in other types. These differences between fatty acids were mostly deriving by higher total n-6 PUFA content. In a sausage made of Mangulitsa meat, the values of atherogenic (IA) and thrombogenic (IT) health lipid indexes are lower. Kulen and sremska sausages made from the Mangalitsa pork meat was superior in terms of colour, odour, taste, after taste and overall acceptability. This study demonstrate that pig breed have an effect on the chemical content, fatty acids profiles and sensory properties of dry fermented sausages.

50 CFR 15.21 - General application procedures.

Code of Federal Regulations, 2013 CFR

2013-10-01

... purposes only: Scientific research; zoological breeding or display programs; cooperative breeding programs...: Office of Management Authority), 4401 N. Fairfax Drive, Room 700, Arlington, VA 22203. Each application...

50 CFR 15.21 - General application procedures.

Code of Federal Regulations, 2012 CFR

2012-10-01

... purposes only: Scientific research; zoological breeding or display programs; cooperative breeding programs...: Office of Management Authority), 4401 N. Fairfax Drive, Room 700, Arlington, VA 22203. Each application...

Selecting loblolly pine parents for seed orchards to minimize the cost of producing pulp

Treesearch

W.J. Lowe; T.D. Byram; F.E. Bridgwater

1999-01-01

Southern pine cooperative breeding programs currently emphasize genetic improvement of growth rates. When a deployment population, typically a seed orchard, is established, there is an opportunity to emphasize traits other than growth rate to maximize the profit of individual cooperators in the breeding program. The authors studied a southeast Texas breeding population...

50 CFR 23.26 - When is a U.S. or foreign CITES document valid?

Code of Federal Regulations, 2010 CFR

2010-10-01

...) Registered commercial breeding operation for Appendix-I wildlife (i) The operation is included in the... document. (16) Registered commercial nursery for Appendix-I plants The operation is included in the... IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE IN ENDANGERED SPECIES OF WILD...

50 CFR 23.36 - What are the requirements for an export permit?

Code of Federal Regulations, 2013 CFR

2013-10-01

... Ginseng Appendix-I Plants Artificially Propagated for Commercial Purposes Biological Specimens Captive... noncommercial purposes. (See § 23.46 for the export of specimens that originated at a commercial breeding... IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE IN ENDANGERED SPECIES OF WILD...

50 CFR 23.36 - What are the requirements for an export permit?

Code of Federal Regulations, 2012 CFR

2012-10-01

... Ginseng Appendix-I Plants Artificially Propagated for Commercial Purposes Biological Specimens Captive... noncommercial purposes. (See § 23.46 for the export of specimens that originated at a commercial breeding... IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE IN ENDANGERED SPECIES OF WILD...

50 CFR 23.26 - When is a U.S. or foreign CITES document valid?

Code of Federal Regulations, 2013 CFR

2013-10-01

...) Registered commercial breeding operation for Appendix-I wildlife (i) The operation is included in the... document. (16) Registered commercial nursery for Appendix-I plants The operation is included in the... IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE IN ENDANGERED SPECIES OF WILD...

50 CFR 23.26 - When is a U.S. or foreign CITES document valid?

Code of Federal Regulations, 2012 CFR

2012-10-01

...) Registered commercial breeding operation for Appendix-I wildlife (i) The operation is included in the... document. (16) Registered commercial nursery for Appendix-I plants The operation is included in the... IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE IN ENDANGERED SPECIES OF WILD...

50 CFR 23.36 - What are the requirements for an export permit?

Code of Federal Regulations, 2010 CFR

2010-10-01

... Ginseng Appendix-I Plants Artificially Propagated for Commercial Purposes Biological Specimens Captive... noncommercial purposes. (See § 23.46 for the export of specimens that originated at a commercial breeding... IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE IN ENDANGERED SPECIES OF WILD...

50 CFR 23.26 - When is a U.S. or foreign CITES document valid?

Code of Federal Regulations, 2011 CFR

2011-10-01

...) Registered commercial breeding operation for Appendix-I wildlife (i) The operation is included in the... document. (16) Registered commercial nursery for Appendix-I plants The operation is included in the... IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE IN ENDANGERED SPECIES OF WILD...

50 CFR 23.36 - What are the requirements for an export permit?

Code of Federal Regulations, 2011 CFR

2011-10-01

... Ginseng Appendix-I Plants Artificially Propagated for Commercial Purposes Biological Specimens Captive... noncommercial purposes. (See § 23.46 for the export of specimens that originated at a commercial breeding... IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE IN ENDANGERED SPECIES OF WILD...

Parasitic helminths of the digestive system of wild boars bred in captivity.

PubMed

da Silva, Diego Silva; Müller, Gertrud

2013-01-01

This study aimed to identify the parasites that inhabit the digestive system of Sus scrofa scrofa from a commercial breeding facility in southern Brazil, and reports the first occurrence of Trichostrongylus colubriformis in wild boars. The gastrointestinal tracts of 40 wild boars from a commercial breeding facility were collected and individualized during slaughter in a cold-storage slaughterhouse. Out of this total, 87.5% were parasitized by the helminths Ascaris suum, Trichostrongylus colubriformis, Oesophagostomum dentatum and Trichuris suis. T. colubriformis presented a prevalence of 45%, mean intensity of 28.4 and mean abundance of 12.8. The data from this study showed that T. colubriformis not only has a capacity to develop in the small intestines of wild boars, but also adapts well to animals raised in captivity, thus representing a possible cause of economic loss in commercial wild boar farming.

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

Genetic diversity and patterns of population structure in Creole goats from the Americas.

PubMed

Ginja, C; Gama, L T; Martínez, A; Sevane, N; Martin-Burriel, I; Lanari, M R; Revidatti, M A; Aranguren-Méndez, J A; Bedotti, D O; Ribeiro, M N; Sponenberg, P; Aguirre, E L; Alvarez-Franco, L A; Menezes, M P C; Chacón, E; Galarza, A; Gómez-Urviola, N; Martínez-López, O R; Pimenta-Filho, E C; da Rocha, L L; Stemmer, A; Landi, V; Delgado-Bermejo, J V

2017-06-01

Biodiversity studies are more efficient when large numbers of breeds belonging to several countries are involved, as they allow for an in-depth analysis of the within- and between-breed components of genetic diversity. A set of 21 microsatellites was used to investigate the genetic composition of 24 Creole goat breeds (910 animals) from 10 countries to estimate levels of genetic variability, infer population structure and understand genetic relationships among populations across the American continent. Three commercial transboundary breeds were included in the analyses to investigate admixture with Creole goats. Overall, the genetic diversity of Creole populations (mean number of alleles = 5.82 ± 1.14, observed heterozygosity = 0.585 ± 0.074) was moderate and slightly lower than what was detected in other studies with breeds from other regions. The Bayesian clustering analysis without prior information on source populations identified 22 breed clusters. Three groups comprised more than one population, namely from Brazil (Azul and Graúna; Moxotó and Repartida) and Argentina (Long and shorthair Chilluda, Pampeana Colorada and Angora-type goat). Substructure was found in Criolla Paraguaya. When prior information on sample origin was considered, 92% of the individuals were assigned to the source population (threshold q ≥ 0.700). Creole breeds are well-differentiated entities (mean coefficient of genetic differentiation = 0.111 ± 0.048, with the exception of isolated island populations). Dilution from admixture with commercial transboundary breeds appears to be negligible. Significant levels of inbreeding were detected (inbreeding coefficient > 0 in most Creole goat populations, P < 0.05). Our results provide a broad perspective on the extant genetic diversity of Creole goats, however further studies are needed to understand whether the observed geographical patterns of population structure may reflect the mode of goat colonization in the Americas. © 2017 Stichting International Foundation for Animal Genetics.

Characterization of the village goat production systems in the rural communities of the Eastern Cape, KwaZulu-Natal, Limpopo and North West Provinces of South Africa.

PubMed

Mdladla, Khanyisile; Dzomba, Edgar Farai; Muchadeyi, Farai Catherine

2017-03-01

Expansion of goat improvement programs requires exploration of the factors that influence the production system and breeding initiatives. Characterization of goat breeds or populations is crucial in providing information on prevalent goat types and their attributes and may suffice as a guideline on conservation, development, and selection for improved productivity. This study investigated the existing village goat production system and phenotypic diversity of the different village populations from four South African provinces. The study further investigated the use of phenotypic attributes to classify goats to breeds or populations. Data was collected from 142 households in 26 villages of the Eastern Cape (n = 2 villages), KwaZulu-Natal (n = 6 villages), Limpopo (n = 13 villages), and North West (n = 5 villages) provinces through a survey. Individual interviews and focus group discussions revealed that the mean goat herd size per household was least in Limpopo at 13.2 ± 12.40 and highest in Eastern Cape (34.18 ± 28.36). Flocks had more (p < 0.05) adults than kids, and the distribution of breeding animals was biased towards does and less bucks. Goats were kept mainly for meat, for selling, and for ritual ceremonies. The goat production system was mainly scavenging. Goat health was a major challenge across households and villages. Qualitative traits such coat, horn, ears, and wattle characteristics were recorded for populations of village goats (n = 319) and a feral Tankwa breed (n = 50). The dominant coat pattern was plain (74.53%) with black as the most common coat color (31.98%). Across breeds, a majority (88.08%) of the goats had horns, and 7.59% had wattles while 56.64% had beard. Adult goats (<3 years; n = 398) were further analyzed for five quantitative traits of chest girth, height, length, and pin bone and there were significant (p < 0.05) breed differences in all. A stepwise discriminatory procedure was used to rank the quantitative traits according to their discriminatory power to separate breeds or populations. Significant traits were then subjected to canonical discriminant analysis for principle component analysis. Based on the quantitative traits, the Tankwa, Xhosa, and Tswana goats formed their own cluster separated from commercial meat type breeds and the Venda and Zulu ecotypes. The discriminant function analysis correctly classified 90.41% of the Zulu goats and 82.93% of the Xhosa village populations. None of the Savanna goats were correctly classified. The study demonstrated diversity in village goat populations and production systems, which would allow for within population selection in genetic improvement programs. The heterogeneity in the phenotypic traits in the village goats is reflective of the role of village production systems in the maintenance of animal diversity in local populations.

Use of an attenuated live Salmonella Typhimurium vaccine on three breeding pig units: A longitudinal observational field study.

PubMed

Davies, R; Gosling, R J; Wales, A D; Smith, R P

2016-06-01

The study examined the effects of a licensed live Salmonella Typhimurium vaccine, administered to sows and gilts on three commercial pig units experiencing clinical salmonellosis associated with S. Typhimurium or its monophasic variant. After vaccination, clinical salmonellosis resolved and shedding of S. Typhimurium declined markedly and persistently on all breeding or breeding-finishing units, during the one- to two-year monitoring period. On two finishing units supplied in part by one of the vaccinated herds, pigs from the vaccinated herd were less likely to shed Salmonella than those from non-vaccinating herds, and Salmonella counts in faeces were also lower from the vaccine-linked animals. Non-Typhimurium Salmonella serovars were isolated typically in fewer than 10% of samples, and showed no clear temporal changes in frequency. Vaccination of dams alone with S. Typhimurium was associated with reduced shedding of closely-related serovars among all age groups in this commercial setting. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

An MSH4 homolog, stpp1, from Pleurotus pulmonarius is a "silver bullet" for resolving problems caused by spores in cultivated mushrooms.

PubMed

Okuda, Yasuhito; Murakami, Shigeyuki; Honda, Yoichi; Matsumoto, Teruyuki

2013-08-01

The enormous number of spores produced by fruiting bodies during cultivation of mushrooms can lead to allergic reactions of workers, reduction of commercial value, spread of mushroom disease, pollution of facilities, and depletion of genetic diversity in natural populations. A cultivar harboring a sporulation-deficient (sporeless) mutation would be very useful for preventing these problems, but sporeless commercial cultivars are very limited in usefulness because sporeless traits are often linked with traits that are unfavorable for commercial cultivation. Thus, identifying a causal gene of a sporeless phenotype not linked to the adverse traits in breeding and cultivation is crucial for the establishment of sporeless breeding using a strategy employing targeting induced local lesions in genomes (TILLING) in cultivated mushrooms. We used a Pleurotus pulmonarius (Fr.) Quél. sporeless strain to identify and characterize the single recessive gene controlling the mutation. The 3,853-bp stpp1 gene encodes a protein of 854 amino acids and belongs to the MutS homolog (MSH) family associated with mismatch repair in DNA synthesis or recombination in meiosis. Gene expression analysis of the fruiting body showed that this gene is strongly expressed in the gills. Phenotypic analysis of disruptants formed by gene targeting suggested a reproducible sporeless phenotype. Mutants deficient in a functional copy of this gene have no unfavorable traits for sporeless cultivar breeding, so this gene will be an extremely useful target for efficient and versatile sporeless breeding in P. pulmonarius and various other cultivated mushrooms.

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.

Predicting cotton yield of small field plots in a cotton breeding program using UAV imagery data

NASA Astrophysics Data System (ADS)

Maja, Joe Mari J.; Campbell, Todd; Camargo Neto, Joao; Astillo, Philip

2016-05-01

One of the major criteria used for advancing experimental lines in a breeding program is yield performance. Obtaining yield performance data requires machine picking each plot with a cotton picker, modified to weigh individual plots. Harvesting thousands of small field plots requires a great deal of time and resources. The efficiency of cotton breeding could be increased significantly while the cost could be decreased with the availability of accurate methods to predict yield performance. This work is investigating the feasibility of using an image processing technique using a commercial off-the-shelf (COTS) camera mounted on a small Unmanned Aerial Vehicle (sUAV) to collect normal RGB images in predicting cotton yield on small plot. An orthonormal image was generated from multiple images and used to process multiple, segmented plots. A Gaussian blur was used to eliminate the high frequency component of the images, which corresponds to the cotton pixels, and used image subtraction technique to generate high frequency pixel images. The cotton pixels were then separated using k-means cluster with 5 classes. Based on the current work, the calculated percentage cotton area was computed using the generated high frequency image (cotton pixels) divided by the total area of the plot. Preliminary results showed (five flights, 3 altitudes) that cotton cover on multiple pre-selected 227 sq. m. plots produce an average of 8% which translate to approximately 22.3 kgs. of cotton. The yield prediction equation generated from the test site was then use on a separate validation site and produced a prediction error of less than 10%. In summary, the results indicate that a COTS camera with an appropriate image processing technique can produce results that are comparable to expensive sensors.

Relationships among and variation within rare breeds of swine.

PubMed

Roberts, K S; Lamberson, W R

2015-08-01

Extinction of rare breeds of livestock threatens to reduce the total genetic variation available for selection in the face of the changing environment and new diseases. Swine breeds facing extinction typically share characteristics such as small size, slow growth rate, and high fat percentage, which limit them from contributing to commercial production. Compounding the risk of loss of variation is the lack of pedigree information for many rare breeds due to inadequate herd books, which increases the chance that producers are breeding closely related individuals. By making genetic data available, producers can make more educated breeding decisions to preserve genetic diversity in future generations, and conservation organizations can prioritize investments in breed preservation. The objective of this study was to characterize genetic variation within and among breeds of swine and prioritize heritage breeds for preservation. Genotypes from the Illumina PorcineSNP60 BeadChip (GeneSeek, Lincoln, NE) were obtained for Guinea, Ossabaw Island, Red Wattle, American Saddleback, Mulefoot, British Saddleback, Duroc, Landrace, Large White, Pietrain, and Tamworth pigs. A whole-genome analysis toolset was used to construct a genomic relationship matrix and to calculate inbreeding coefficients for the animals within each breed. Relatedness and average inbreeding coefficient differed among breeds, and pigs from rare breeds were generally more closely related and more inbred ( < 0.05). A multidimensional scaling diagram was constructed based on the SNP genotypes. Animals within breeds clustered tightly together except for 2 Guinea pigs. Tamworth, Duroc, and Mulefoot tended to not cluster with the other 7 breeds.

Advances and Challenges in Genomic Selection for Disease Resistance.

PubMed

Poland, Jesse; Rutkoski, Jessica

2016-08-04

Breeding for disease resistance is a central focus of plant breeding programs, as any successful variety must have the complete package of high yield, disease resistance, agronomic performance, and end-use quality. With the need to accelerate the development of improved varieties, genomics-assisted breeding is becoming an important tool in breeding programs. With marker-assisted selection, there has been success in breeding for disease resistance; however, much of this work and research has focused on identifying, mapping, and selecting for major resistance genes that tend to be highly effective but vulnerable to breakdown with rapid changes in pathogen races. In contrast, breeding for minor-gene quantitative resistance tends to produce more durable varieties but is a more challenging breeding objective. As the genetic architecture of resistance shifts from single major R genes to a diffused architecture of many minor genes, the best approach for molecular breeding will shift from marker-assisted selection to genomic selection. Genomics-assisted breeding for quantitative resistance will therefore necessitate whole-genome prediction models and selection methodology as implemented for classical complex traits such as yield. Here, we examine multiple case studies testing whole-genome prediction models and genomic selection for disease resistance. In general, whole-genome models for disease resistance can produce prediction accuracy suitable for application in breeding. These models also largely outperform multiple linear regression as would be applied in marker-assisted selection. With the implementation of genomic selection for yield and other agronomic traits, whole-genome marker profiles will be available for the entire set of breeding lines, enabling genomic selection for disease at no additional direct cost. In this context, the scope of implementing genomics selection for disease resistance, and specifically for quantitative resistance and quarantined pathogens, becomes a tractable and powerful approach in breeding programs.

Factors affecting commercial application of embryo technologies in dairy cattle in Europe--a modelling approach.

PubMed

van Arendonk, Johan A M; Bijma, Piter

2003-01-15

Reproductive techniques have a major impact on the structure of breeding programmes, the rate of genetic gain and dissemination of genetic gain in populations. This manuscript reviews the impact of reproductive technologies on the underlying components of genetic gain and inbreeding with special reference to the role of female reproductive technology. Evaluation of alternative breeding schemes should be based on genetic gain while constraining inbreeding. Optimum breeding schemes can be characterised by: decreased importance of sib information; increased accuracy at the expense of intensity; and a factorial mating strategy. If large-scale embryo cloning becomes feasible, this will have a small impact on the rate of genetic gain but will have a large impact on the structure of breeding programmes.

Can functional hologenomics aid tackling current challenges in plant breeding?

PubMed

Nogales, Amaia; Nobre, Tânia; Valadas, Vera; Ragonezi, Carla; Döring, Matthias; Polidoros, Alexios; Arnholdt-Schmitt, Birgit

2016-07-01

Molecular plant breeding usually overlooks the genetic variability that arises from the association of plants with endophytic microorganisms, when looking at agronomic interesting target traits. This source of variability can have crucial effects on the functionality of the organism considered as a whole (the holobiont), and therefore can be selectable in breeding programs. However, seeing the holobiont as a unit for selection and improvement in breeding programs requires novel approaches for genotyping and phenotyping. These should not focus just at the plant level, but also include the associated endophytes and their functional effects on the plant, to make effective desirable trait screenings. The present review intends to draw attention to a new research field on functional hologenomics that if associated with adequate phenotyping tools could greatly increase the efficiency of breeding programs. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

A computational approach to animal breeding.

PubMed

Berger-Wolf, Tanya Y; Moore, Cristopher; Saia, Jared

2007-02-07

We propose a computational model of mating strategies for controlled animal breeding programs. A mating strategy in a controlled breeding program is a heuristic with some optimization criteria as a goal. Thus, it is appropriate to use the computational tools available for analysis of optimization heuristics. In this paper, we propose the first discrete model of the controlled animal breeding problem and analyse heuristics for two possible objectives: (1) breeding for maximum diversity and (2) breeding a target individual. These two goals are representative of conservation biology and agricultural livestock management, respectively. We evaluate several mating strategies and provide upper and lower bounds for the expected number of matings. While the population parameters may vary and can change the actual number of matings for a particular strategy, the order of magnitude of the number of expected matings and the relative competitiveness of the mating heuristics remains the same. Thus, our simple discrete model of the animal breeding problem provides a novel viable and robust approach to designing and comparing breeding strategies in captive populations.

Improving Charging-Breeding Simulations with Space-Charge Effects

NASA Astrophysics Data System (ADS)

Bilek, Ryan; Kwiatkowski, Ania; Steinbrügge, René

2016-09-01

Rare-isotope-beam facilities use Highly Charged Ions (HCI) for accelerators accelerating heavy ions and to improve measurement precision and resolving power of certain experiments. An Electron Beam Ion Trap (EBIT) is able to create HCI through successive electron impact, charge breeding trapped ions into higher charge states. CBSIM was created to calculate successive charge breeding with an EBIT. It was augmented by transferring it into an object-oriented programming language, including additional elements, improving ion-ion collision factors, and exploring the overlap of the electron beam with the ions. The calculation is enhanced with the effects of residual background gas by computing the space charge due to charge breeding. The program assimilates background species, ionizes and charge breeds them alongside the element being studied, and allows them to interact with the desired species through charge exchange, giving fairer overview of realistic charge breeding. Calculations of charge breeding will be shown for realistic experimental conditions. We reexamined the implementation of ionization energies, cross sections, and ion-ion interactions when charge breeding.

50 CFR 224.103 - Special prohibitions for endangered marine mammals.

Code of Federal Regulations, 2010 CFR

2010-10-01

... breeding, nursing, or resting activities, attempts by a whale to shield a calf from a vessel or human...), commercial fishing means taking or harvesting fish or fishery resources to sell, barter, or trade. Commercial... sea lions, shall also apply to the western population of Steller sea lions, which consists of all...

76 FR 61696 - New York State Prohibition of Discharges of Vessel Sewage; Receipt of Petition and Tentative...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-05

..., creeks and wetlands of Lake Ontario support a remarkable diversity of uses--fish spawning areas, breeding grounds, valuable habitats, commercial and recreational boating, and a profusion of recreational resources... described the recreational and commercial vessels that use Lake Ontario, and the pumpout facilities that are...

7 CFR Appendix K to Subpart E of... - Regulations for Loan Guarantees for Disaster Assistance For Rural Business Enterprises

Code of Federal Regulations, 2013 CFR

2013-01-01

...), and disposal or marketing thereof, the raising, housing, feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm and domestic animals. Other eligible uses of loan proceeds under agricultural production include: (1) Commercial nurseries primarily engaged in the...

50 CFR 23.36 - What are the requirements for an export permit?

Code of Federal Regulations, 2014 CFR

2014-10-01

... Ginseng 3-200-34 Appendix-I Plants Artificially Propagated for Commercial Purposes 3-200-33 Biological... noncommercial purposes. (See § 23.46 for the export of specimens that originated at a commercial breeding... IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE IN ENDANGERED SPECIES OF WILD...

7 CFR Appendix K to Subpart E of... - Regulations for Loan Guarantees for Disaster Assistance For Rural Business Enterprises

Code of Federal Regulations, 2012 CFR

2012-01-01

...), and disposal or marketing thereof, the raising, housing, feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm and domestic animals. Other eligible uses of loan proceeds under agricultural production include: (1) Commercial nurseries primarily engaged in the...

7 CFR Appendix K to Subpart E of... - Regulations for Loan Guarantees for Disaster Assistance For Rural Business Enterprises

Code of Federal Regulations, 2014 CFR

2014-01-01

...), and disposal or marketing thereof, the raising, housing, feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm and domestic animals. Other eligible uses of loan proceeds under agricultural production include: (1) Commercial nurseries primarily engaged in the...

7 CFR Appendix K to Subpart E of... - Regulations for Loan Guarantees for Disaster Assistance For Rural Business Enterprises

Code of Federal Regulations, 2011 CFR

2011-01-01

...), and disposal or marketing thereof, the raising, housing, feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm and domestic animals. Other eligible uses of loan proceeds under agricultural production include: (1) Commercial nurseries primarily engaged in the...

7 CFR Appendix K to Subpart E of... - Regulations for Loan Guarantees for Disaster Assistance For Rural Business Enterprises

Code of Federal Regulations, 2010 CFR

2010-01-01

...), and disposal or marketing thereof, the raising, housing, feeding (including commercial custom feedlots), breeding, hatching, control and/or management of farm and domestic animals. Other eligible uses of loan proceeds under agricultural production include: (1) Commercial nurseries primarily engaged in the...

Potential Use of a Weak Ethylene Receptor Mutant, Sletr1-2, as Breeding Material To Extend Fruit Shelf Life of Tomato.

PubMed

Mubarok, Syariful; Okabe, Yoshihiro; Fukuda, Naoya; Ariizumi, Tohru; Ezura, Hiroshi

2015-09-16

Mutations in the ethylene receptor gene (SlETR1), Sletr1-1 and Sletr1-2, are effective in reducing ethylene sensitivity and improving fruit shelf life. In this study the effect of Sletr1-1 and Sletr1-2 mutations was investigated in F1 hybrid lines. These two mutants and control were crossed with four commercial pure-line tomatoes. The Sletr1-1 mutation showed undesirable pleiotropic effects in the F1 hybrid lines. The Sletr1-2 mutation was effective in improving fruit shelf life of F1 hybrid lines for 4-5 days longer. It was also effective in improving fruit firmness without change in fruit size, ethylene production, respiration rate, and total soluble solids or a great reduction in fruit color, lycopene, and β-carotene, although the titratable acidity was increased by Sletr1-2 mutation. These results indicate that the Sletr1-2 mutant allele has the potential to improve fruit shelf life via incorporation in tomato breeding programs.

Breeding design considerations for coastal Douglas-fir.

Treesearch

Randy Johnson

1998-01-01

The basic principles of designing forest tree breeding programs are reviewed for Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) in the Pacific Northwest. Breeding populations are discussed given current and future breeding zone sizes and seed orchard designs. Seed orchard composition is discussed for potential genetic gain and maintaining...

Historical use of cultivars as parents in Florida and Louisiana sugarcane breeding program

USDA-ARS?s Scientific Manuscript database

Sugarcane (Saccharum L. spp. hybrids) growers depend on breeding programs for new, high-yielding cultivars that have resistance to abiotic and biotic stresses, so breeders continually seek out widely adapted, high yielding germplasm to be used as parents for their programs. Cultivars are sometimes u...

For science, love and money: the social worlds of poultry and rabbit breeding in Britain, 1900-1940.

PubMed

Marie, Jenny

2008-12-01

This paper traces the joint histories of poultry and rabbit breeding by fanciers, and for commercial and scientific purposes, in early 20th-century Britain. I show that the histories of the social worlds that bred for these different purposes are intertwined, as are the histories of poultry and rabbit breeding in general. To properly understand the history of scientific breeding we must therefore understand the general context of breeding in which this occurred. In the paper I show that as fancy poultry and rabbits were taken up for scientific research at the start of the 20th century they became scientific specimens and boundary objects between the social worlds. Their existence as boundary objects motivated the social worlds to coordinate their work through translators and trading zones. By the 1930s all three coordination methods were being used simultaneously.

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.

Estimation of genetic diversity in Gute sheep: pedigree and microsatellite analyses of an ancient Swedish breed.

PubMed

Rochus, Christina M; Johansson, Anna M

2017-01-01

Breeds with small population size are in danger of an increased inbreeding rate and loss of genetic diversity, which puts them at risk for extinction. In Sweden there are a number of local breeds, native breeds which have adapted to specific areas in Sweden, for which efforts are being made to keep them pure and healthy over time. One example of such a breed is the Swedish Gute sheep. The objective of this study was to estimate inbreeding and genetic diversity of Swedish Gute sheep. Three datasets were analysed: pedigree information of the whole population, pedigree information for 100 animals of the population, and microsatellite genotypes for 94 of the 100 animals. The average inbreeding coefficient for lambs born during a six year time period (2007-2012) did not increase during that time period. The inbreeding calculated from the entire pedigree (0.038) and for a sample of the population (0.018) was very low. Sheep were more heterozygous at the microsatellite markers than expected (average multilocus heterozygosity and Ritland inbreeding estimates 1.01845 and -0.03931) and five of seven microsatellite markers were not in Hardy Weinberg equilibrium due to heterozygosity excess. The total effective population size estimated from the pedigree information was 155.4 and the average harmonic mean effective population size estimated from microsatellites was 88.3. Pedigree and microsatellite genotype estimations of inbreeding were consistent with a breeding program with the purpose of reducing inbreeding. Our results showed that current breeding programs of the Swedish Gute sheep are consistent with efforts of keeping this breed viable and these breeding programs are an example for other small local breeds in conserving breeds for the future.

Extending RosBREED in the Pacific Northwest for strawberry processing traits: year 1

USDA-ARS?s Scientific Manuscript database

In an effort to implement marker-assisted breeding in Rosaceae, many traits need to be characterized in diverse germplasm. The USDA-NIFA Specialty Crop Research Initiative-funded RosBREED project includes breeding programs of four Rosaceae crops (apple, peach, cherry, and strawberry). Phenotyping ea...

Genetic parameters of linear conformation type traits and their relationship with milk yield throughout lactation in mixed-breed dairy goats.

PubMed

McLaren, A; Mucha, S; Mrode, R; Coffey, M; Conington, J

2016-07-01

Conformation traits are of interest to many dairy goat breeders not only as descriptive traits in their own right, but also because of their influence on production, longevity, and profitability. If these traits are to be considered for inclusion in future dairy goat breeding programs, relationships between them and production traits such as milk yield must be considered. With the increased use of regression models to estimate genetic parameters, an opportunity now exists to investigate correlations between conformation traits and milk yield throughout lactation in more detail. The aims of this study were therefore to (1) estimate genetic parameters for conformation traits in a population of crossbred dairy goats, (2) estimate correlations between all conformation traits, and (3) assess the relationship between conformation traits and milk yield throughout lactation. No information on milk composition was available. Data were collected from goats based on 2 commercial goat farms during August and September in 2013 and 2014. Ten conformation traits, relating to udder, teat, leg, and feet characteristics, were scored on a linear scale (1-9). The overall data set comprised data available for 4,229 goats, all in their first lactation. The population of goats used in the study was created using random crossings between 3 breeds: British Alpine, Saanen, and Toggenburg. In each generation, the best performing animals were selected for breeding, leading to the formation of a synthetic breed. The pedigree file used in the analyses contained sire and dam information for a total of 30,139 individuals. The models fitted relevant fixed and random effects. Heritability estimates for the conformation traits were low to moderate, ranging from 0.02 to 0.38. A range of positive and negative phenotypic and genetic correlations between the traits were observed, with the highest correlations found between udder depth and udder attachment (0.78), teat angle and teat placement (0.70), and back legs and back feet (0.64). The genetic correlations estimated between conformation traits and milk yield across the first lactation demonstrated changes during this period. The majority of correlations estimated between milk yield and the udder and teat traits were negative. Therefore, future breeding programs would benefit from including these traits to ensure that selection for increased productivity is not accompanied by any unwanted change in functional fitness. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

PALLAS BARLEY, A VARIETY PRODUCED BY IONIZING RADIATION: ITS SIGNIFICANCE FOR PLANT BREEDING AND EVOLUTION

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

Borg, G.; Froier, K.f Gustafsson, A.

1959-10-31

Results are reported from plant breeding programs in which mutations induced in barley by irradiation resulted in the development of a variety with characteristics superior to the parents. Good results were also reported in the development of superior varieties of oil rape, white mustard, and pea plants. The usefulness of radiation-induced mutations in plant breeding programs is discussed. (C.H.)

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.

Simple sequence repeat marker loci discovery using SSR primer.

PubMed

Robinson, Andrew J; Love, Christopher G; Batley, Jacqueline; Barker, Gary; Edwards, David

2004-06-12

Simple sequence repeats (SSRs) have become important molecular markers for a broad range of applications, such as genome mapping and characterization, phenotype mapping, marker assisted selection of crop plants and a range of molecular ecology and diversity studies. With the increase in the availability of DNA sequence information, an automated process to identify and design PCR primers for amplification of SSR loci would be a useful tool in plant breeding programs. We report an application that integrates SPUTNIK, an SSR repeat finder, with Primer3, a PCR primer design program, into one pipeline tool, SSR Primer. On submission of multiple FASTA formatted sequences, the script screens each sequence for SSRs using SPUTNIK. The results are parsed to Primer3 for locus-specific primer design. The script makes use of a Web-based interface, enabling remote use. This program has been written in PERL and is freely available for non-commercial users by request from the authors. The Web-based version may be accessed at http://hornbill.cspp.latrobe.edu.au/

Signatures of Diversifying Selection in European Pig Breeds

PubMed Central

Wilkinson, Samantha; Lu, Zen H.; Megens, Hendrik-Jan; Archibald, Alan L.; Haley, Chris; Jackson, Ian J.; Groenen, Martien A. M.; Crooijmans, Richard P. M. A.; Ogden, Rob; Wiener, Pamela

2013-01-01

Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better understand the relationship between genomic composition and phenotypic diversity arising from breed development, the genomes of 13 traditional and commercial European pig breeds were scanned for signatures of diversifying selection using the Porcine60K SNP chip, applying a between-population (differentiation) approach. Signatures of diversifying selection between breeds were found in genomic regions associated with traits related to breed standard criteria, such as coat colour and ear morphology. Amino acid differences in the EDNRB gene appear to be associated with one of these signatures, and variation in the KITLG gene may be associated with another. Other selection signals were found in genomic regions including QTLs and genes associated with production traits such as reproduction, growth, and fat deposition. Some selection signatures were associated with regions showing evidence of introgression from Asian breeds. When the European breeds were compared with wild boar, genomic regions with high levels of differentiation harboured genes related to bone formation, growth, and fat deposition. PMID:23637623

75 FR 46859 - Lacey Act Implementation Plan; Definitions for Exempt and Regulated Articles

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-04

... plants of species grown on a commercial scale. As we propose to define them, these terms would apply to... cultivar. A plant (except a tree) that: (a) Has been developed through selective breeding or other means... concern, while exempting plants grown on a commercial scale. They are also designed to be consistent with...

Earth observations taken during STS-83 mission

NASA Image and Video Library

2016-08-24

STS083-749-084 (4-8 April 1997) --- Laguna Oja De Liebre, Baja, gray whale breeding ground Laguna Oja De Liebre, Baja (Scammons Lagoon) is located on the west coast in the plains of the central Baja. This lagoon and others like it along the Baja coast are used for breeding grounds for the gray whale. One group of gray whales inhabits the Sea of Okhotsk in summer, migrating south in winter then breed off southern Korea. The other summers in the Bering and Chukchi seas and travels south to winter breeding grounds along the coast of Baja California. The gray whale was hunted almost to extinction by 1925 but was placed under complete international protection and since the 1940s has increased in numbers. The white grids seen in the photo are commercial salt ponds.

Methods for shorebird surveys in the Arctic

Treesearch

Jonathan Bart; Susan L. Earnst

2005-01-01

A substantial effort is being made to develop a longterm monitoring program for shorebirds in North American (Brown et al. 2000, Donaldson et al. 2001, Bart et al. this volume). The current program, PRISM (Program for Regional and International Shorebird Monitoring), has four segments: arctic and boreal breeding surveys, temperate breeding surveys, temperate non-...

Integrating molecular tools and conventional approaches in the Oregon State University hazelnut breeding program

Treesearch

Shawn A. Mehlenbacher

2012-01-01

The Oregon State University (OSU) hazelnut breeding program, initiated in 1969, continues to develop new cultivars for the hazelnut industry that combine suitability to the blanched kernel market with resistance to eastern filbert blight (EFB) caused by Anisogramma anomala. Oregon's hazelnut growers support the program through the Oregon...

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.

Future of breeding by genome editing is in the hands of regulators.

PubMed

Jones, Huw D

2015-01-01

We are witnessing the timely convergence of several technologies that together will have significant impact on research, human health and in animal and plant breeding. The exponential increase in genome and expressed sequence data, the ability to compile, analyze and mine these data via sophisticated bioinformatics procedures on high-powered computers, and developments in various molecular and in-vitro cellular techniques combine to underpin novel developments in research and commercial biotechnology. Arguably the most important of these is genome editing which encompasses a suite of site directed nucleases (SDN) that can be designed to cut, or otherwise modify predetermined DNA sequences in the genome and result in targeted insertions, deletions, or other changes for genetic improvement. It is a powerful and adaptive technology for animal and plant science, with huge relevance for plant and animal breeding. But this promise will be realized only if the regulatory oversite is proportionate to the potential hazards and has broad support from consumers, researchers and commercial interests. Despite significant progress in research and development and one genome edited crop close to commercialization, in most regions of the world it still remains unclear how or whether this fledgling technology will be regulated. The various risk management authorities and biotechnology regulators have a unique opportunity to set up a logical, appropriate and workable regulatory framework for gene editing that, unlike the situation for GMOs, would have broad support from stakeholders.

Fruit Phenolic Profiling: A New Selection Criterion in Olive Breeding Programs

PubMed Central

Pérez, Ana G.; León, Lorenzo; Sanz, Carlos; de la Rosa, Raúl

2018-01-01

Olive growing is mainly based on traditional varieties selected by the growers across the centuries. The few attempts so far reported to obtain new varieties by systematic breeding have been mainly focused on improving the olive adaptation to different growing systems, the productivity and the oil content. However, the improvement of oil quality has rarely been considered as selection criterion and only in the latter stages of the breeding programs. Due to their health promoting and organoleptic properties, phenolic compounds are one of the most important quality markers for Virgin olive oil (VOO) although they are not commonly used as quality traits in olive breeding programs. This is mainly due to the difficulties for evaluating oil phenolic composition in large number of samples and the limited knowledge on the genetic and environmental factors that may influence phenolic composition. In the present work, we propose a high throughput methodology to include the phenolic composition as a selection criterion in olive breeding programs. For that purpose, the phenolic profile has been determined in fruits and oils of several breeding selections and two varieties (“Picual” and “Arbequina”) used as control. The effect of three different environments, typical for olive growing in Andalusia, Southern Spain, was also evaluated. A high genetic effect was observed on both fruit and oil phenolic profile. In particular, the breeding selection UCI2-68 showed an optimum phenolic profile, which sums up to a good agronomic performance previously reported. A high correlation was found between fruit and oil total phenolic content as well as some individual phenols from the two different matrices. The environmental effect on phenolic compounds was also significant in both fruit and oil, although the low genotype × environment interaction allowed similar ranking of genotypes on the different environments. In summary, the high genotypic variance and the simplified procedure of the proposed methodology for fruit phenol evaluation seems to be convenient for breeding programs aiming at obtaining new cultivars with improved phenolic profile. PMID:29535752

Fruit Phenolic Profiling: A New Selection Criterion in Olive Breeding Programs.

PubMed

Pérez, Ana G; León, Lorenzo; Sanz, Carlos; de la Rosa, Raúl

2018-01-01

Olive growing is mainly based on traditional varieties selected by the growers across the centuries. The few attempts so far reported to obtain new varieties by systematic breeding have been mainly focused on improving the olive adaptation to different growing systems, the productivity and the oil content. However, the improvement of oil quality has rarely been considered as selection criterion and only in the latter stages of the breeding programs. Due to their health promoting and organoleptic properties, phenolic compounds are one of the most important quality markers for Virgin olive oil (VOO) although they are not commonly used as quality traits in olive breeding programs. This is mainly due to the difficulties for evaluating oil phenolic composition in large number of samples and the limited knowledge on the genetic and environmental factors that may influence phenolic composition. In the present work, we propose a high throughput methodology to include the phenolic composition as a selection criterion in olive breeding programs. For that purpose, the phenolic profile has been determined in fruits and oils of several breeding selections and two varieties ("Picual" and "Arbequina") used as control. The effect of three different environments, typical for olive growing in Andalusia, Southern Spain, was also evaluated. A high genetic effect was observed on both fruit and oil phenolic profile. In particular, the breeding selection UCI2-68 showed an optimum phenolic profile, which sums up to a good agronomic performance previously reported. A high correlation was found between fruit and oil total phenolic content as well as some individual phenols from the two different matrices. The environmental effect on phenolic compounds was also significant in both fruit and oil, although the low genotype × environment interaction allowed similar ranking of genotypes on the different environments. In summary, the high genotypic variance and the simplified procedure of the proposed methodology for fruit phenol evaluation seems to be convenient for breeding programs aiming at obtaining new cultivars with improved phenolic profile.

Does Flooring Substrate Impact Kennel and Dog Cleanliness in Commercial Breeding Facilities?

PubMed

Stella, Judith; Hurt, Moriah; Bauer, Amy; Gomes, Paulo; Ruple, Audrey; Beck, Alan; Croney, Candace

2018-04-21

Evaluation of kennel flooring surfaces is needed to understand their impacts on dog health and well-being. This pilot study aimed to characterize aspects of physical health, kennel cleanliness, and dog body cleanliness on flooring types common in US breeding kennels. Subjects were 118 adult dogs housed on diamond-coated expanded metal (DCEM), polypropylene (POLY), or concrete (CON) flooring at five commercial breeding facilities in Indiana, U.S. Body condition, paw, elbow, and hock health scores were recorded. Each indoor kennel and dog was visually assessed for cleanliness. Kennels were swabbed immediately after cleaning with electrostatic dry cloths and cultured for Escherichia coli . Descriptive statistics were used for analysis. Mean body condition score (BCS), kennel and dog cleanliness scores were all near ideal (3, 1.15, and 1.04, respectively). Thirty-one percent or fewer kennels at each facility were culture-positive for E. coli after cleaning. No serious paw, elbow, or hock problems were identified. Overall, the findings indicate that with appropriate management and regular access to additional surfaces, dog foot health, cleanliness, and kennel cleanliness can be maintained on the flooring types investigated.

Asian fish tapeworm, Khawia japonensis (Yamaguti, 1934), has expanded its European invasive range.

PubMed

Oros, Mikuláš; Barčák, Daniel; Bazsalovicsová, Eva; Hanzelová, Vladimíra

2015-05-01

The invasive fish tapeworm, Khawia japonensis (Yamaguti, 1934) originally described in Japan, is reported for the first time in Slovakia. The tapeworm was found in farmed common carp (Cyprinus carpio L.) from East-Slovakian breeding fish pond. This finding is registered 4 years after the first announcement of this parasite in Europe (Po River Basin in Italy) in 2010 and increases its distribution area within this continent. Morphological characterization of K. japonensis supplemented with DNA sequences of cox1 and ribosomal lsrDNA genes is provided. Specimens from Slovakia phenotypically corresponded with those from feral and farmed carps from China, Vietnam, and Italy. Moreover, 100 and 98.7% identity of partial ribosomal lsrDNA gene and mitochondrial cox1 genes, respectively, were detected with K. japonensis from Japan. The invasive and pathogenic potential of K. japonensis in commercial breeding fisheries and its possible further spread in natural habitats is difficult to estimate for now. As yet, K. japonensis appears to be without a major impact on commercial breeding fisheries, but calls for more attention to the problem of biological invasions.

Inconsistent identification of pit bull-type dogs by shelter staff.

PubMed

Olson, K R; Levy, J K; Norby, B; Crandall, M M; Broadhurst, J E; Jacks, S; Barton, R C; Zimmerman, M S

2015-11-01

Shelter staff and veterinarians routinely make subjective dog breed identification based on appearance, but their accuracy regarding pit bull-type breeds is unknown. The purpose of this study was to measure agreement among shelter staff in assigning pit bull-type breed designations to shelter dogs and to compare breed assignments with DNA breed signatures. In this prospective cross-sectional study, four staff members at each of four different shelters recorded their suspected breed(s) for 30 dogs; there was a total of 16 breed assessors and 120 dogs. The terms American pit bull terrier, American Staffordshire terrier, Staffordshire bull terrier, pit bull, and their mixes were included in the study definition of 'pit bull-type breeds.' Using visual identification only, the median inter-observer agreements and kappa values in pair-wise comparisons of each of the staff breed assignments for pit bull-type breed vs. not pit bull-type breed ranged from 76% to 83% and from 0.44 to 0.52 (moderate agreement), respectively. Whole blood was submitted to a commercial DNA testing laboratory for breed identification. Whereas DNA breed signatures identified only 25 dogs (21%) as pit bull-type, shelter staff collectively identified 62 (52%) dogs as pit bull-type. Agreement between visual and DNA-based breed assignments varied among individuals, with sensitivity for pit bull-type identification ranging from 33% to 75% and specificity ranging from 52% to 100%. The median kappa value for inter-observer agreement with DNA results at each shelter ranged from 0.1 to 0.48 (poor to moderate). Lack of consistency among shelter staff indicated that visual identification of pit bull-type dogs was unreliable. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Optimizing Training Population Size and Genotyping Strategy for Genomic Prediction Using Association Study Results and Pedigree Information. A Case of Study in Advanced Wheat Breeding Lines.

PubMed

Cericola, Fabio; Jahoor, Ahmed; Orabi, Jihad; Andersen, Jeppe R; Janss, Luc L; Jensen, Just

2017-01-01

Wheat breeding programs generate a large amount of variation which cannot be completely explored because of limited phenotyping throughput. Genomic prediction (GP) has been proposed as a new tool which provides breeding values estimations without the need of phenotyping all the material produced but only a subset of it named training population (TP). However, genotyping of all the accessions under analysis is needed and, therefore, optimizing TP dimension and genotyping strategy is pivotal to implement GP in commercial breeding schemes. Here, we explored the optimum TP size and we integrated pedigree records and genome wide association studies (GWAS) results to optimize the genotyping strategy. A total of 988 advanced wheat breeding lines were genotyped with the Illumina 15K SNPs wheat chip and phenotyped across several years and locations for yield, lodging, and starch content. Cross-validation using the largest possible TP size and all the SNPs available after editing (~11k), yielded predictive abilities (rGP) ranging between 0.5-0.6. In order to explore the Training population size, rGP were computed using progressively smaller TP. These exercises showed that TP of around 700 lines were enough to yield the highest observed rGP. Moreover, rGP were calculated by randomly reducing the SNPs number. This showed that around 1K markers were enough to reach the highest observed rGP. GWAS was used to identify markers associated with the traits analyzed. A GWAS-based selection of SNPs resulted in increased rGP when compared with random selection and few hundreds SNPs were sufficient to obtain the highest observed rGP. For each of these scenarios, advantages of adding the pedigree information were shown. Our results indicate that moderate TP sizes were enough to yield high rGP and that pedigree information and GWAS results can be used to greatly optimize the genotyping strategy.

A second generation genetic linkage map of Japanese flounder (Paralichthys olivaceus)

PubMed Central

2010-01-01

Background Japanese flounder (Paralichthys olivaceus) is one of the most economically important marine species in Northeast Asia. Information on genetic markers associated with quantitative trait loci (QTL) can be used in breeding programs to identify and select individuals carrying desired traits. Commercial production of Japanese flounder could be increased by developing disease-resistant fish and improving commercially important traits. Previous maps have been constructed with AFLP markers and a limited number of microsatellite markers. In this study, improved genetic linkage maps are presented. In contrast with previous studies, these maps were built mainly with a large number of codominant markers so they can potentially be used to analyze different families and populations. Results Sex-specific genetic linkage maps were constructed for the Japanese flounder including a total of 1,375 markers [1,268 microsatellites, 105 single nucleotide polymorphisms (SNPs) and two genes]; 1,167 markers are linked to the male map and 1,067 markers are linked to the female map. The lengths of the male and female maps are 1,147.7 cM and 833.8 cM, respectively. Based on estimations of map lengths, the female and male maps covered 79 and 82% of the genome, respectively. Recombination ratio in the new maps revealed F:M of 1:0.7. All linkage groups in the maps presented large differences in the location of sex-specific recombination hot-spots. Conclusions The improved genetic linkage maps are very useful for QTL analyses and marker-assisted selection (MAS) breeding programs for economically important traits in Japanese flounder. In addition, SNP flanking sequences were blasted against Tetraodon nigroviridis (puffer fish) and Danio rerio (zebrafish), and synteny analysis has been carried out. The ability to detect synteny among species or genera based on homology analysis of SNP flanking sequences may provide opportunities to complement initial QTL experiments with candidate gene approaches from homologous chromosomal locations identified in related model organisms. PMID:20937088

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.

Integration of genomic information into sport horse breeding programs for optimization of accuracy of selection.

PubMed

Haberland, A M; König von Borstel, U; Simianer, H; König, S

2012-09-01

Reliable selection criteria are required for young riding horses to increase genetic gain by increasing accuracy of selection and decreasing generation intervals. In this study, selection strategies incorporating genomic breeding values (GEBVs) were evaluated. Relevant stages of selection in sport horse breeding programs were analyzed by applying selection index theory. Results in terms of accuracies of indices (r(TI) ) and relative selection response indicated that information on single nucleotide polymorphism (SNP) genotypes considerably increases the accuracy of breeding values estimated for young horses without own or progeny performance. In a first scenario, the correlation between the breeding value estimated from the SNP genotype and the true breeding value (= accuracy of GEBV) was fixed to a relatively low value of r(mg) = 0.5. For a low heritability trait (h(2) = 0.15), and an index for a young horse based only on information from both parents, additional genomic information doubles r(TI) from 0.27 to 0.54. Including the conventional information source 'own performance' into the before mentioned index, additional SNP information increases r(TI) by 40%. Thus, particularly with regard to traits of low heritability, genomic information can provide a tool for well-founded selection decisions early in life. In a further approach, different sources of breeding values (e.g. GEBV and estimated breeding values (EBVs) from different countries) were combined into an overall index when altering accuracies of EBVs and correlations between traits. In summary, we showed that genomic selection strategies have the potential to contribute to a substantial reduction in generation intervals in horse breeding programs.

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.

A crossbred reference population can improve the response to genomic selection for crossbred performance.

PubMed

Esfandyari, Hadi; Sørensen, Anders Christian; Bijma, Piter

2015-09-29

Breeding goals in a crossbreeding system should be defined at the commercial crossbred level. However, selection is often performed to improve purebred performance. A genomic selection (GS) model that includes dominance effects can be used to select purebreds for crossbred performance. Optimization of the GS model raises the question of whether marker effects should be estimated from data on the pure lines or crossbreds. Therefore, the first objective of this study was to compare response to selection of crossbreds by simulating a two-way crossbreeding program with either a purebred or a crossbred training population. We assumed a trait of interest that was controlled by loci with additive and dominance effects. Animals were selected on estimated breeding values for crossbred performance. There was no genotype by environment interaction. Linkage phase and strength of linkage disequilibrium between quantitative trait loci (QTL) and single nucleotide polymorphisms (SNPs) can differ between breeds, which causes apparent effects of SNPs to be line-dependent. Thus, our second objective was to compare response to GS based on crossbred phenotypes when the line origin of alleles was taken into account or not in the estimation of breeding values. Training on crossbred animals yielded a larger response to selection in crossbred offspring compared to training on both pure lines separately or on both pure lines combined into a single reference population. Response to selection in crossbreds was larger if both phenotypes and genotypes were collected on crossbreds than if phenotypes were only recorded on crossbreds and genotypes on their parents. If both parental lines were distantly related, tracing the line origin of alleles improved genomic prediction, whereas if both parental lines were closely related and the reference population was small, it was better to ignore the line origin of alleles. Response to selection in crossbreeding programs can be increased by training on crossbred genotypes and phenotypes. Moreover, if the reference population is sufficiently large and both pure lines are not very closely related, tracing the line origin of alleles in crossbreds improves genomic prediction.

Distribution of Escherichia coli F4 adhesion phenotypes in pigs of 15 Chinese and Western breeds and a White DurocxErhualian intercross.

PubMed

Yan, Xueming; Huang, Xiang; Ren, Jun; Zou, Zhengzhi; Yang, Shujin; Ouyang, Jing; Zeng, Weihong; Yang, Bin; Xiao, Shijun; Huang, Lusheng

2009-08-01

Diarrhoea in newborn and weaned piglets is mainly caused by enterotoxigenic Escherichia coli (ETEC) with fimbriae F4. To investigate the prevalence of resistance to three fimbrial strains, F4ab, F4ac and F4ad, among Chinese indigenous pigs and Western commercial pigs introduced into China, we determined the ETEC F4 adhesion phenotypes in 292 pure-bred piglets from three Western commercial breeds and 12 Chinese indigenous breeds, and a total of 1093 adult pigs in a White DurocxErhualian intercross, by an in vitro microscopic adhesion assay. All the Tibet and Lantang pigs and a majority of the Erhualian and Rongchang pigs were resistant (nonadherent) to ETEC F4 whereas all the Laiwu pigs and most of the Jiangquhai and Tongcheng pigs were susceptible (adhesive) to at least one of the F4 strains. Yushan Black pigs were uniformly resistant to F4ab, and Jinhua pigs were predominantly resistant to F4ac. Susceptible and resistant animals were observed in the other breeds, indicating that diarrhoea caused by ETEC F4 could be prevalent in these breeds. This study confirmed the existence of eight previously reported F4 adhesion patterns, and supported the assumption that the three F4 receptors are encoded by distinct loci. Expression of the weakly adherent phenotype was observed in six pure-bred piglets and 90 adult F(2)/F(3) animals, and the inheritance of this phenotype and its correlation with susceptibility to disease are still not known.

Addition of a breeding database in the Genome Database for Rosaceae

PubMed Central

Evans, Kate; Jung, Sook; Lee, Taein; Brutcher, Lisa; Cho, Ilhyung; Peace, Cameron; Main, Dorrie

2013-01-01

Breeding programs produce large datasets that require efficient management systems to keep track of performance, pedigree, geographical and image-based data. With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation. The integration of breeding data with other genomic and genetic data is instrumental for the refinement of marker-assisted breeding tools, enhances genetic understanding of important crop traits and maximizes access and utility by crop breeders and allied scientists. Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington State University apple breeding program and subsequently expanded to fit datasets from other Rosaceae breeders. The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data. Breeders can search accessions within the GDR to identify individuals with specific trait combinations. Results from Search by Parentage lists individuals with parents in common and results from Individual Variety pages link to all data available on each chosen individual including pedigree, phenotypic and genotypic information. Genotypic data are searchable by markers and alleles; results are linked to other pages in the GDR to enable the user to access tools such as GBrowse and CMap. This breeding database provides users with the opportunity to search datasets in a fully targeted manner and retrieve and compare performance data from multiple selections, years and sites, and to output the data needed for variety release publications and patent applications. The breeding database facilitates efficient program management. Storing publicly available breeding data in a database together with genomic and genetic data will further accelerate the cross-utilization of diverse data types by researchers from various disciplines. Database URL: http://www.rosaceae.org/breeders_toolbox PMID:24247530

Addition of a breeding database in the Genome Database for Rosaceae.

PubMed

Evans, Kate; Jung, Sook; Lee, Taein; Brutcher, Lisa; Cho, Ilhyung; Peace, Cameron; Main, Dorrie

2013-01-01

Breeding programs produce large datasets that require efficient management systems to keep track of performance, pedigree, geographical and image-based data. With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation. The integration of breeding data with other genomic and genetic data is instrumental for the refinement of marker-assisted breeding tools, enhances genetic understanding of important crop traits and maximizes access and utility by crop breeders and allied scientists. Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington State University apple breeding program and subsequently expanded to fit datasets from other Rosaceae breeders. The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data. Breeders can search accessions within the GDR to identify individuals with specific trait combinations. Results from Search by Parentage lists individuals with parents in common and results from Individual Variety pages link to all data available on each chosen individual including pedigree, phenotypic and genotypic information. Genotypic data are searchable by markers and alleles; results are linked to other pages in the GDR to enable the user to access tools such as GBrowse and CMap. This breeding database provides users with the opportunity to search datasets in a fully targeted manner and retrieve and compare performance data from multiple selections, years and sites, and to output the data needed for variety release publications and patent applications. The breeding database facilitates efficient program management. Storing publicly available breeding data in a database together with genomic and genetic data will further accelerate the cross-utilization of diverse data types by researchers from various disciplines. Database URL: http://www.rosaceae.org/breeders_toolbox.

Perennial plants for biofuel production: bridging genomics and field research.

PubMed

Alves, Alexandre Alonso; Laviola, Bruno G; Formighieri, Eduardo F; Carels, Nicolas

2015-04-01

Development of dedicated perennial crops has been indicated as a strategic action to meet the growing demand for biofuels. Breeding of perennial crops,however, is often time- and resource-consuming. As genomics offers a platform from which to learn more about the relationships of genes and phenotypes,its operational use in the context of breeding programs through strategies such as genomic selection promises to foster the development of perennial crops dedicated to biodiesel production by increasing the efficiency of breeding programs and by shortening the length of the breeding cycles. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

The current status and future of commercial embryo transfer in cattle.

PubMed

Hasler, John F

2003-12-15

A commercially viable cattle embryo transfer (ET) industry was established in North America during the early 1970s, approximately 80 years after the first successful embryo transfer was reported in a mammal. Initially, techniques for recovering and transferring cattle embryos were exclusively surgical. However, by the late 1970s, most embryos were recovered and transferred nonsurgically. Successful cryopreservation of embryos was widespread by the early 1980s, followed by the introduction of embryo splitting, in vitro procedures, direct transfer of frozen embryos and sexing of embryos. The wide spread adoption of ethylene glycol as a cryoprotectant has simplified the thaw-transfer procedures for frozen embryos. The number of embryos recovered annually has not grown appreciably over the last 10 years in North America and Europe; however, there has been significant growth of commercial ET in South America. Within North America, ET activity has been relatively constant in Holstein cattle, whereas there has been a large ET increase in the Angus breed and a concomitant ET decrease in some other beef breeds. Although a number of new technologies have been adopted within the ET industry in the last decade, the basic procedure of superovulation of donor cattle has undergone little improvement over the last 20 years. The export-import of frozen cattle embryos has become a well-established industry, governed by specific health regulations. The international movement of embryos is subject to sudden and dramatic disturbances, as exemplified by the 2001 outbreak of foot and mouth disease in Great Britain. It is probable that there will be an increased influence of animal rights issues on the ET industry in the future. Several companies in North America are currently commercially producing cloned cattle. The sexing of bovine semen with the use of flow cytometry is extremely accurate and moderate pregnancy rates in heifers have been achieved in field trials, but sexed semen currently is available in only a few countries and on an extremely limited basis. As of yet, all programs involving the production of transgenic cattle are experimental in nature.

Achieving Better Buying Power through Acquisition of Open Architecture Software Systems. Volume 2 Understanding Open Architecture Software Systems: Licensing and Security Research and Recommendations

DTIC Science & Technology

2016-01-06

of- breed software components and software products lines (SPLs) that are subject to different IP license and cybersecurity requirements. The... commercially priced closed source software components, to be used in the design, implementation, deployment, and evolution of open architecture (OA... breed software components and software products lines (SPLs) that are subject to different IP license and cybersecurity requirements. The Department

Serosurveillance of Coxiellosis (Q-fever) and Brucellosis in goats in selected provinces of Lao People's Democratic Republic.

PubMed

Burns, Rebekah J L; Douangngeun, Bounlom; Theppangna, Watthana; Khounsy, Syseng; Mukaka, Mavuto; Selleck, Paul W; Hansson, Eric; Wegner, Matthew D; Windsor, Peter A; Blacksell, Stuart D

2018-04-01

Goat raising is a growing industry in Lao People's Democratic Republic, with minimal disease investigation to date, especially zoonoses. This study determined the proportional seropositivity of two zoonotic diseases: Q fever (causative agent Coxiella burnetii) and Brucellosis (Brucella species) in goats across five provinces (Vientiane Capital, Xayaboury, Xiengkhuang, Savannakhet and Attapeu). A total of 1458 goat serum samples were tested using commercial indirect ELISA for both pathogens, plus Rose Bengal agglutination test for Brucellosis. Overall individual seropositivity of C. burnetii was 4.1% and Brucella spp. was 1.4%. A multiple logistic regression model identified that province (Vientiane Capital, p = 0.05), breed (introduced Boer mixed breed, p = 0.006) and age (goats ≥3 years old, p = 0.014) were significant risk factors for C. burnetii seropositivity. The results of the survey indicated that province (Vientiane Capital, p<0.001), breed (introduced Boer mixed breed, p<0.001), production system (commercial, p<0.001), age (adult, p = 0.004), and farm size (large, 0.001) were all significant risk factors seropositivity for Brucella spp. It was concluded that Lao goats have been exposed to both C. burnetii and Brucella spp. however the risk of clinical disease has not yet been determined and there is an urgent need to determine human health risks and economic losses caused by Q fever and Brucellosis.

Serosurveillance of Coxiellosis (Q-fever) and Brucellosis in goats in selected provinces of Lao People’s Democratic Republic

PubMed Central

Burns, Rebekah J. L.; Douangngeun, Bounlom; Theppangna, Watthana; Khounsy, Syseng; Mukaka, Mavuto; Selleck, Paul W.; Hansson, Eric; Wegner, Matthew D.; Windsor, Peter A.

2018-01-01

Goat raising is a growing industry in Lao People’s Democratic Republic, with minimal disease investigation to date, especially zoonoses. This study determined the proportional seropositivity of two zoonotic diseases: Q fever (causative agent Coxiella burnetii) and Brucellosis (Brucella species) in goats across five provinces (Vientiane Capital, Xayaboury, Xiengkhuang, Savannakhet and Attapeu). A total of 1458 goat serum samples were tested using commercial indirect ELISA for both pathogens, plus Rose Bengal agglutination test for Brucellosis. Overall individual seropositivity of C. burnetii was 4.1% and Brucella spp. was 1.4%. A multiple logistic regression model identified that province (Vientiane Capital, p = 0.05), breed (introduced Boer mixed breed, p = 0.006) and age (goats ≥3 years old, p = 0.014) were significant risk factors for C. burnetii seropositivity. The results of the survey indicated that province (Vientiane Capital, p<0.001), breed (introduced Boer mixed breed, p<0.001), production system (commercial, p<0.001), age (adult, p = 0.004), and farm size (large, 0.001) were all significant risk factors seropositivity for Brucella spp. It was concluded that Lao goats have been exposed to both C. burnetii and Brucella spp. however the risk of clinical disease has not yet been determined and there is an urgent need to determine human health risks and economic losses caused by Q fever and Brucellosis. PMID:29649313

‘Norman’ southern highbush blueberry

USDA-ARS?s Scientific Manuscript database

‘Norman’ is the third cultivar released from the University of Arkansas blueberry breeding program, which began in the late 1970s and has involved cooperative efforts with the U.S. Department of Agriculture (USDA). Previous cultivars released from this breeding program were ‘Ozarkblue’ and ‘Summit’....

St. Paul's Pig Pack.

ERIC Educational Resources Information Center

Miller, Penny Folley

1982-01-01

Describes a guinea pig (cavy) breeding and management program developed as part of an elementary school science curriculum. Includes comments on show competitions (sponsored by the American Rabbit Breeders Association) to measure the success of the breeding program and to enable children to experience the business world. (Author/JN)

Expected net present value of pure and mixed sexed semen artificial insemination strategies in dairy heifers.

PubMed

Olynk, N J; Wolf, C A

2007-05-01

Sexed semen has been a long-anticipated tool for dairy farmers to obtain more heifer calves, but challenges exist for integrating sexed semen into commercial dairy farm reproduction programs. The decreased conception rates (CR) experienced with sexed semen make virgin heifers better suited for insemination with sexed semen than lactating dairy cows. This research sought to identify when various sexed semen breeding strategies provided higher expected net present value (NPV) than conventional artificial insemination (AI) breeding schemes, indicating which breeding scheme is advisable under various scenarios. Budgets were developed to calculate the expected NPV of various AI breeding strategies incorporating conventional (non-sexed) and sexed semen. In the base budgets, heifer and bull calf values were held constant at $500 and $110, respectively. The percentage of heifers expected to be born after breeding with conventional and sexed semen used was 49.2 and 90%, respectively. Breeding costs per AI were held constant at $15.00 per AI for conventional semen and $45.00 per AI for sexed semen of approximately the same genetic value. Conventional semen CR of 58 and 65% were used, and an AI submission rate was set at 100%. Breeding strategies with sexed semen were assessed for breakeven heifer calf values and sexed semen costs to obtain a NPV equal to that achieved with conventional semen. Breakeven heifer calf values for pure sexed semen strategies with a constant 58 and 65% base CR in which sexed semen achieved 53% of the base CR are $732.11 and $664.26, respectively. Breakeven sexed semen costs per AI of $17.16 and $22.39, compared with $45.00 per AI, were obtained to obtain a NPV equal to that obtained with pure conventional semen for base CR of 58 and 65%, respectively. The strategy employing purely sexed semen, with base CR of both 58 and 65%, yielded a lower NPV than purely conventional semen in all but the best-case scenario in which sexed semen provides 90% of the CR of conventional semen. Other potential advantages of sexed semen that were not quantified in the scenarios include biosecurity-related concerns, decreased dystocia due to increased numbers of heifer calves, and implications for internal herd growth.

Chemical composition and antioxidant capacity of açaí (Euterpe oleracea) genotypes and commercial pulps.

PubMed

Carvalho, Ana Vânia; Ferreira Ferreira da Silveira, Tayse; Mattietto, Rafaella de Andrade; Padilha de Oliveira, Maria do Socorro; Godoy, Helena Teixeira

2017-03-01

Açaí has been reported to contain many bioactive compounds, including phenolic compounds such as anthocyanins. This study aimed to determine the chemical composition and antioxidant potential of pulps of three different açaí genotypes from the Active Germplasm Bank of Embrapa Eastern Amazon and three commercial açaí pulps from Belém, state of Pará, Brazil. Anthocyanin 3-rutinoside was the major anthocyanin present in freeze-dried açaí pulp samples. The commercial sample C showed the greatest amounts of cyanidin 3-glucoside and cyanidin 3-rutinoside (18 942 and 34 397 µg g -1 respectively). The content of phenolic compounds varied significantly among the commercial and genotype samples, and vanillic acid was found in the highest concentration in the samples studied. All açaí samples showed high DPPH, ORAC and TEAC values, confirming the exceptionally high radical-scavenging capacity of açaí pulp previously reported by other researchers. The commercial samples showed higher antioxidant capacity and higher levels of anthocyanins and non-anthocyanic compounds than those of the genotype samples. Among the genotypes studied, L4P16 stood out for its higher contents of fibre and bioactive compounds and higher antioxidant capacity, indicating that this genotype has great potential for use in plant breeding programs that should be further explored. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Uterine fluid proteins and egg quality characteristics for 2 commercial and 2 heritage laying hen lines in response to manipulation of dietary calcium and vitamin D3.

PubMed

Kaur, Ravinder; Rathgeber, Bruce M; Thompson, Kristen L; Macisaac, Janice

2013-09-01

The aim of this study was to evaluate the quality of eggs from 2 selected commercial strains of laying hens and 2 unselected lines of chickens fed diets with different combinations of Ca and vitamin D and relate it to the profile of uterine proteins and ultrastructure of the shell. A group of 4 chickens was housed in each of 24 cages. The group consisted of one representative from each of the following breeds: Lohmann LSL- Lite, Lohmann Classic-Brown, Fayoumi, and Light Sussex. Six dietary combinations of Ca and vitamin D(3) (3.35%, 2,500 IU; 4.10%, 2,500 IU (control); 4.85%, 2,500 IU; 3.35%, 200 IU; 4.10%, 200 IU; and 4.85%, 200 IU) were randomly assigned to 4 replicate cages for 2 treatment periods (26-29 and 56-59 wk of age). Data were analyzed as a split-plot design with cage as the main plot and hen as the subplot. Egg quality traits were different (P < 0.0001) between commercial and heritage breeds. Lohmann Brown had stronger shells with higher specific gravity compared with other breeds. Both commercial and heritage birds responded to a drop in vitamin D3 level by marked reduction in shell thickness. The SDS-PAGE profiles of uterine fluid samples revealed a decrease (P < 0.05) in 200-, 150-, 116-, and ≤6.5-kDa proteins, whereas proteins with molecular weight (MW) of 80, 55, 52, 45, 42, and 28 kDa increased with bird age. A 36- and 52-kDa protein band was most intense for Fayoumi compared with other breeds. Ultrastructural characteristics showed flattened and deeply etched mammillary caps for Lohmann Brown and the presence of type A and type B bodies between mammillary cones in eggshells from Fayoumi and Lohmann Lite. The negative correlation between ultrastructural characteristics, which decrease with bird age, and the 116-kDa uterine protein band could provide insight into reduced eggshell quality as hens age.

Influence of Honey Bee Genotype and Wintering Method on Wintering Performance of Varroa destructor (Parasitiformes: Varroidae)-Infected Honey Bee (Hymenoptera: Apidae) Colonies in a Northern Climate.

PubMed

Bahreini, Rassol; Currie, Robert W

2015-08-01

The objective of this study was to assess the effectiveness of a cooperative breeding program designed to enhance winter survival of honey bees (Apis mellifera L.) when exposed to high levels of varroa (Varroa destructor Anderson and Trueman) in outdoor-wintered and indoor-wintered colonies. Half of the colonies from selected and unselected stocks were randomly assigned to be treated with late autumn oxalic acid treatment or to be left untreated. Colonies were then randomly assigned to be wintered either indoors (n = 37) or outdoors (n = 40). Late autumn treatment with oxalic acid did not improve wintering performance. However, genotype of bees affected colony survival and the proportion of commercially viable colonies in spring, as indicated by greater rates of colony survival and commercially viable colonies for selected stock (43% survived and 33% were viable) in comparison to unselected stock (19% survived and 9% were viable) across all treatment groups. Indoor wintering improved spring bee population score, proportion of colonies surviving, and proportion of commercially viable colonies relative to outdoor wintering (73% of selected stock and 41% of unselected stock survived during indoor wintering). Selected stock showed better "tolerance" to varroa as the selected stock also maintained higher bee populations relative to unselected stock. However, there was no evidence of "resistance" in selected colonies (reduced mite densities). Collectively, this experiment showed that breeding can improve tolerance to varroa and this can help minimize colony loss through winter and improve colony wintering performance. Overall, colony wintering success of both genotypes of bees was better when colonies were wintered indoors than when colonies were wintered outdoors. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Genetic fingerprinting of potato varieties from the Northwest Potato Variety Development Program

USDA-ARS?s Scientific Manuscript database

The Northwest Potato Variety Development Program using conventional breeding has successfully released more than 40 improved varieties of potato since its inception in 1983. Potato breeders rely primarily on morphological and phenotypic data for selection and breeding of potato cultivars. With the a...

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.

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.

Development of new techniques of using irradiation in the genetic improvement of warm season grasses and an assessment of the genetic and cytogenetic effects. Progress report, November 1, 1977--October 31, 1978. [Pearl millet, Bermuda-grass, and coastcross

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

Hanna, W.W.; Burton, G.W.

1978-05-01

Progress is reported on plant breeding programs for the genetic improvement of warm season grasses using irradiation as a tool. Data are included from studies on alteration of the protein quantity and quality in pearl millet grain by irradiation and mutation breeding; the effects of nitrogen and genotype on pearl millet grain; the effects of seed size on quality in pearl millet; irradiation breeding of sterile triploid turf Bermuda grasses; irradiation breeding of sterile coastcross-1, a forage grass, to increase winter hardiness; use of irradiation to induce resistance to rust disease; and an economic assessment of irradiation-induced mutants for plantmore » breeding programs.« less

Conditional Allele Mouse Planner (CAMP): software to facilitate the planning and design of breeding strategies involving mice with conditional alleles.

PubMed

Hoffert, Jason D; Pisitkun, Trairak; Miller, R Lance

2012-06-01

Transgenic and conditional knockout mouse models play an important role in biomedical research and their use has grown exponentially in the last 5-10 years. Generating conditional knockouts often requires breeding multiple alleles onto the background of a single mouse or group of mice. Breeding these mice depends on parental genotype, litter size, transmission frequency, and the number of breeding rounds. Therefore, a well planned breeding strategy is critical for keeping costs to a minimum. However, designing a viable breeding strategy can be challenging. With so many different variables this would be an ideal task for a computer program. To facilitate this process, we created a Java-based program called Conditional Allele Mouse Planner (CAMP). CAMP is designed to provide an estimate of the number of breeders, amount of time, and costs associated with generating mice of a particular genotype. We provide a description of CAMP, how to use it, and offer it freely as an application.

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.

Applying isozyme analyses in tree-breeding programs

Treesearch

W. T. Adams

1981-01-01

Four examples illustrate the potential for practical use of isozyme analyses in applied breeding programs. These include identifying parent trees and clones, seed sources, and parentage of controlled crosses, and evaluating the effectiveness of different procedures involving open-pollination to produce seed of specific crosses. The improved ability to assess the true...

Initial experiences utilizing exotic landrace germplasm in an upland cotton breeding program

USDA-ARS?s Scientific Manuscript database

A critical objective of plant breeding programs is accessing new sources of genetic variation. In upland cotton, one of the relatively untapped sources of genetic variation is maintained in the USDA-ARS cotton germplasm collection and is the exotic landrace collection. Photoperiod sensitivity is a m...

Increased use of young bulls in dairy cattle breeding programs

USDA-ARS?s Scientific Manuscript database

Availability of genomic evaluations since 2008 has provided many benefits with regard to improving the rate of genetic gain in dairy cattle breeding programs, one of which is a greater accuracy for young animals. As a result, AI organizations have been aggressively promoting young bulls and producer...

Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps

USDA-ARS?s Scientific Manuscript database

Quantitative trait locus (QTL) identification in perennial fruit crops is impeded largely by their lengthy generation time, resulting in costly and labor-intensive maintenance of breeding programs. In a grapevine (genus Vitis) breeding program, although experimental populations are typically unrepli...

Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps

USDA-ARS?s Scientific Manuscript database

Quantitative trait locus (QTL) identification in perennial fruit crops is impeded largely by their lengthy generation time, resulting in costly and labor-intensive maintenance of breeding programs. In a grapevine (genus Vitis) breeding program, although experimental families are typically unreplicat...

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.

Documenting Presence and Movements of Piscivorous Birds along the Illinois River and within the Chicago Area Waterway System

DTIC Science & Technology

2017-07-31

promotional purposes. Citation of trade names does not constitute an official endorsement or approval of the use of such commercial products. All product...15 Figure 7. Breeding home range polygons of Double-Crested Cormorant movements from Baker’s Lake (blue outline) and the TNC Emiquon Preserve (red...48 ERDC/EL TR-17-12 v Figure B1. 95% kernel home range polygons for 14 breeding cormorants from Baker’s Lake, May 26 - July 12

Micropropagation of Phalaenopsis orchids via protocorms and protocorm-like bodies.

PubMed

Paek, Kee Yoeup; Hahn, Eun Joo; Park, So Young

2011-01-01

Phalaenopsis orchids have high economic value in the floriculture industry. Hybridization or cross-pollination in the breeding program have proven to be very reliable techniques for the production of a wide range of successful cultivars with attractive combinations of spray length, bud number, flower color and type, fragrance, seasonality, and compactness. In vitro propagation makes it possible to clonally mass propagate hybrids of commercial value and conserved species. However, in vitro culture technologies are still a challenge because of the slow growth of plantlets, low multiplication rate, poor rooting, and somaclonal variation. Although seed-raised plants can be used for conservation and breeding for the selection of superior features, genetic characteristics including seasonality, inflorescence, flower color, and type are not uniform. In this regard, micropropagation through protocorm-like bodies obtained from germinating embryos and somatic tissues is an important strategy in obtaining genetically stable plants and the improvement of quality. However, not all genotypes of Phalaenopsis respond to the same protocol under the same culture conditions and often result in the development of undesirable characteristics. In this chapter, plantlet production in Phalaenopsis orchids via the culture of protocorms from seeds and protocorm-like bodies from leaf sections and root tips are detailed.

Future of breeding by genome editing is in the hands of regulators

PubMed Central

Jones, Huw D

2015-01-01

ABSTRACT We are witnessing the timely convergence of several technologies that together will have significant impact on research, human health and in animal and plant breeding. The exponential increase in genome and expressed sequence data, the ability to compile, analyze and mine these data via sophisticated bioinformatics procedures on high-powered computers, and developments in various molecular and in-vitro cellular techniques combine to underpin novel developments in research and commercial biotechnology. Arguably the most important of these is genome editing which encompasses a suite of site directed nucleases (SDN) that can be designed to cut, or otherwise modify predetermined DNA sequences in the genome and result in targeted insertions, deletions, or other changes for genetic improvement. It is a powerful and adaptive technology for animal and plant science, with huge relevance for plant and animal breeding. But this promise will be realized only if the regulatory oversight is proportionate to the potential hazards and has broad support from consumers, researchers and commercial interests. Despite significant progress in research and development and one genome edited crop close to commercialization, in most regions of the world it still remains unclear how or whether this fledgling technology will be regulated. The various risk management authorities and biotechnology regulators have a unique opportunity to set up a logical, appropriate and workable regulatory framework for gene editing that, unlike the situation for GMOs, would have broad support from stakeholders. PMID:26930115

Mitigation of inbreeding while preserving genetic gain in genomic breeding programs for outbred plants.

PubMed

Lin, Zibei; Shi, Fan; Hayes, Ben J; Daetwyler, Hans D

2017-05-01

Heuristic genomic inbreeding controls reduce inbreeding in genomic breeding schemes without reducing genetic gain. Genomic selection is increasingly being implemented in plant breeding programs to accelerate genetic gain of economically important traits. However, it may cause significant loss of genetic diversity when compared with traditional schemes using phenotypic selection. We propose heuristic strategies to control the rate of inbreeding in outbred plants, which can be categorised into three types: controls during mate allocation, during selection, and simultaneous selection and mate allocation. The proposed mate allocation measure GminF allocates two or more parents for mating in mating groups that minimise coancestry using a genomic relationship matrix. Two types of relationship-adjusted genomic breeding values for parent selection candidates ([Formula: see text]) and potential offspring ([Formula: see text]) are devised to control inbreeding during selection and even enabling simultaneous selection and mate allocation. These strategies were tested in a case study using a simulated perennial ryegrass breeding scheme. As compared to the genomic selection scheme without controls, all proposed strategies could significantly decrease inbreeding while achieving comparable genetic gain. In particular, the scenario using [Formula: see text] in simultaneous selection and mate allocation reduced inbreeding to one-third of the original genomic selection scheme. The proposed strategies are readily applicable in any outbred plant breeding program.

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.

Tilting at windmills: 20 years of Hippeastrum breeding

USDA-ARS?s Scientific Manuscript database

Hippeastrum Herbert, amaryllis, has yielded popular large-flowered hybrids over a 200-year breeding history, with the Netherlands and South Africa currently dominating the market. The USDA breeding program is now almost ten years old, built upon a ten-year previous history at the University of Flori...

A role for selective contraception of individuals in conservation.

PubMed

Cope, Holly R; Hogg, Carolyn J; White, Peter J; Herbert, Catherine A

2018-06-01

Contraception has an established role in managing overabundant populations and preventing undesirable breeding in zoos. We propose that it can also be used strategically and selectively in conservation to increase the genetic and behavioral quality of the animals. In captive breeding programs, it is becoming increasingly important to maximize the retention of genetic diversity by managing the reproductive contribution of each individual and preventing genetically suboptimal breeding through the use of selective contraception. Reproductive suppression of selected individuals in conservation programs has further benefits of allowing animals to be housed as a group in extensive enclosures without interfering with breeding recommendations, which reduces adaptation to captivity and facilitates the expression of wild behaviors and social structures. Before selective contraception can be incorporated into a breeding program, the most suitable method of fertility control must be selected, and this can be influenced by factors such as species life history, age, ease of treatment, potential for reversibility, and desired management outcome for the individual or population. Contraception should then be implemented in the population following a step-by-step process. In this way, it can provide crucial, flexible control over breeding to promote the physical and genetic health and sustainability of a conservation dependent species held in captivity. For Tasmanian devils (Sarcophilus harrisii), black-flanked rock wallabies (Petrogale lateralis), and burrowing bettongs (Bettongia lesueur), contraception can benefit their conservation by maximizing genetic diversity and behavioral integrity in the captive breeding program, or, in the case of the wallabies and bettongs, by reducing populations to a sustainable size when they become locally overabundant. In these examples, contraceptive duration relative to reproductive life, reversibility, and predictability of the contraceptive agent being used are important to ensure the potential for individuals to reproduce following cessation of contraception, as exemplified by the wallabies when their population crashed and needed females to resume breeding. © 2017 Society for Conservation Biology.

Comprehensive Identification of Sexual Dimorphism-Associated Differentially Expressed Genes in Two-Way Factorial Designed RNA-Seq Data on Japanese Quail (Coturnix coturnix japonica)

PubMed Central

Rodriguez-Zas, Sandra; Oh, Jae-Don; Han, Jae Yong; Lee, Kichoon; Park, Tae Sub; Shin, Sangsu; Jiao Jiao, Zhang; Ghosh, Mrinmoy; Jeong, Dong Kee; Cho, Seoae; Kim, Heebal; Song, Ki-Duk; Lee, Hak-Kyo

2015-01-01

Japanese quail (Coturnix coturnix japonica) reach sexual maturity earlier, breed rapidly and successfully, and cost less and require less space than other birds raised commercially. Given the value of this species for food production and experimental use, more studies are necessary to determine chromosomal regions and genes associated with gender and breed-differentiation. This study employed Trinity and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 4 tissues obtained from 3 different breeding lines of Japanese quail (random bred control, heavy weight, low weight). Differentially expressed genes shared between female and male tissue contrast groups were analyzed to identify genes related to sexual dimorphism as well as potential novel candidate genes for molecular sexing. Several of the genes identified in the present study as significant sex-related genes have been previously found in avian gene expression analyses (NIPBL, UBAP2), and other genes found differentially expressed in this study and not previously associated with sex-related differences may be considered potential candidates for molecular sexing (TERA, MYP0, PPR17, CASQ2). Additionally, other genes likely associated with neuronal and brain development (CHKA, NYAP), as well as body development and size differentiation (ANKRD26, GRP87) in quail were identified. Expression of homeobox protein regulating genes (HXC4, ISL1) shared between our two sex-related contrast groups (Female Brain vs. Male Brain and Ovary vs. Testis) indicates that these genes may regulate sex-specific anatomical development. Results reveal genetic features of the quail breed and could allow for more effective molecular sexing as well as selective breeding for traits important in commercial production. PMID:26418419

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.

Carcass and meat quality characteristics of Churra and Assaf suckling lambs.

PubMed

Mateo, J; Caro, I; Carballo, D E; Gutiérrez-Méndez, N; Arranz, J J; Gutiérrez-Gil, B

2018-05-01

Suckling lamb meat is traditionally produced in Mediterranean Europe. Breed can affect the quality of the lamb carcass and meat. This study is aimed at comparing the carcass and meat quality between suckling lambs from a local and a non-native dairy breed, Churra and Assaf. Churra is included in the Spanish Protected Geographical Indication (PGI) 'Lechazo de Castilla y León', whereas Assaf is not. However, Assaf breeders have requested the inclusion of the breed in the PGI. Carcasses and meat from 16 male lambs (eight Churra and eight Assaf) were used in this study. The lambs were all raised under an intensive rearing system and fed on a milk substitute to minimise maternal influence. The carcasses were evaluated for conformation, fatness, joint and leg tissue proportions and the meat was analysed for composition (i.e. proximate composition, iron, haematin, fatty acids and volatiles) and technological quality traits (i.e. texture, water holding capacity, colour and lipid stability). Churra carcasses were larger than Assaf carcasses. However, the proportions of commercial joints and main tissues did not differ between breeds. Cavity and intermuscular leg fat, but not total leg fat, were higher in Churra carcasses. Churra meat showed a higher proportion of n-6 fatty acids, higher redness and better colour stability during aerobic storage. In contrast, Assaf lamb was more resistant to lipid oxidation after cooking. This is a preliminary study to measure the influence of breed on a wide range of quality characteristics in Churra and Assaf suckling lamb carcass and meat. It may be of relevance for breeders, consumers and food policy makers, setting the basis for future studies that include larger commercial populations.

Evidence for a sex-segregated migration in the humpback whale (Megaptera novaeangliae).

PubMed

Brown, M R; Corkeron, P J; Hale, P T; Schultz, K W; Bryden, M M

1995-02-22

Existing population models for humpback whales assume that all individuals within a population undertake the annual migration from feeding areas in high latitudes to breeding areas in tropical waters. An excess of males was recorded in the commercial whaling catches near breeding areas in the southern hemisphere, but no account of this was taken in developing population models, because it was believed that this bias was a result of whalers selecting against females with young calves. Here we demonstrate that the sex ratio of migrating humpback whales near a breeding area is highly skewed towards males. A biopsy study carried out in 1992 throughout the northward and southward migrations revealed a sex ratio of 2.4 males: 1 female in the population of humpback whales migrating along the east Australian coast (n = 180). A reanalysis of the catches made during commercial whaling in this and other areas of the southern hemisphere gave a sex ratio of the same order. The most plausible explanation, supported by some evidence, is that some females remain in the feeding areas throughout winter. The results reported here show that existing management models require major revision to take account of these findings.

Transformation of fruit trees. Useful breeding tool or continued future prospect?

PubMed

Petri, César; Burgos, Lorenzo

2005-02-01

Regeneration and transformation systems using mature plant material of woody fruit species have to be achieved as a necessary requirement for the introduction of useful genes into specific cultivars and the rapid evaluation of resulting horticultural traits. Although the commercial production of transgenic annual crops is a reality, commercial genetically-engineered fruit trees are still far from common. In most woody fruit species, transformation and regeneration of commercial cultivars are not routine, generally being limited to a few genotypes or to seedlings. The future of genetic transformation as a tool for the breeding of fruit trees requires the development of genotype-independent procedures, based on the transformation of meristematic cells with high regeneration potential and/or the use of regeneration-promoting genes. The public concern with the introduction of antibiotic resistance into food and the restrictions due to new European laws that do not allow deliberate release of plants transformed with antibiotic-resistance genes highlight the development of methods that avoid the use of antibiotic-dependent selection or allow elimination of marker genesfrom the transformed plant as a research priority in coming years.

Biochemical identification of mallard-black duck hybrids through a breeding program and in nature

USGS Publications Warehouse

Morgan, R.P.; Meritt, D.W.; Block, S.B.; Cole, M.

1978-01-01

From 1974 to 1976, a breeding program was used to produce black duck-mallard hybrids for the evaluation of inheritance patterns of serum proteins and esterases. In addition to the initial crosses, a series of matings in 1975 and 1976 were designed to evaluate inheritance patterns in hybrid matings with either black duck or mallards. At the F1 level, hybrids were easily distinguished. However, mallard or black duck crosses with hybrids were detectable as hybrids in only 11.5 - 22.6% of the progeny using serum proteins, and 22.6 - 38.8% using serum esterases. Concurrent with the breeding program, a field survey indicated hybrid frequencies ranging from 4% to 28%.

Oral fluid samples used for PRRSV acclimatization program and sow performance monitoring in endemic PRRS-positive farms.

PubMed

Woonwong, Yonlayong; Kedkovid, Roongtham; Arunorat, Jirapat; Sirisereewan, Chaitawat; Nedumpun, Teerawut; Poonsuk, Korakrit; Panyasing, Yaowalak; Poolperm, Pariwat; Boonsoongnern, Alongkot; Thanawongnuwech, Roongroje

2018-02-01

An effective gilt acclimatization program is one of the most important management strategies for controlling porcine reproductive and respiratory syndrome virus (PRRSV) infection. Recently, oral fluid samples have been used as alternative diagnostic samples for various swine diseases. This study utilized oral fluids for PRRSV monitoring during the gilt acclimatization period in PRRSV endemic farms. The study was performed in two selected commercial breeding herds (farm A and farm B). PRRSV RNA and PRRSV-specific antibodies were monitored using oral fluid and serum samples. Sow performance parameters related to PRRSV infection were recorded and assessed. After PRRSV exposure during acclimatization, viral RNA was demonstrated in oral fluids from 1 to 10 weeks post-exposure (WPE). PRRSV RNA was detected in serum at 1 and 4 WPE in farm A and at 1, 4, 8, and 12 WPE in farm B. Prolonged viremia of gilts from farm B was possibly due to re-infection (within the herd) and later, reproductive problems were found in the breeding herd. The correlation of PRRSV RNA concentration in oral fluids and serum was evident. The S/P ratio values of PRRSV antibodies in oral fluid samples were higher and had similar patterns of antibody responses to the serum samples. The results suggest that the use of oral fluid samples for PRRSV monitoring during gilt acclimatization in endemic farms is effective, convenient, practical, and economical and would be most beneficial when used with other parameters.

BREEDING AND GENETICS SYMPOSIUM: Climate change and selective breeding in aquaculture.

PubMed

Sae-Lim, P; Kause, A; Mulder, H A; Olesen, I

2017-04-01

Aquaculture is the fastest growing food production sector and it contributes significantly to global food security. Based on Food and Agriculture Organization (FAO) of the United Nations, aquaculture production must increase significantly to meet the future global demand for aquatic foods in 2050. According to Intergovernmental Panel on Climate Change (IPCC) and FAO, climate change may result in global warming, sea level rise, changes of ocean productivity, freshwater shortage, and more frequent extreme climate events. Consequently, climate change may affect aquaculture to various extents depending on climatic zones, geographical areas, rearing systems, and species farmed. There are 2 major challenges for aquaculture caused by climate change. First, the current fish, adapted to the prevailing environmental conditions, may be suboptimal under future conditions. Fish species are often poikilothermic and, therefore, may be particularly vulnerable to temperature changes. This will make low sensitivity to temperature more important for fish than for livestock and other terrestrial species. Second, climate change may facilitate outbreaks of existing and new pathogens or parasites. To cope with the challenges above, 3 major adaptive strategies are identified. First, general 'robustness' will become a key trait in aquaculture, whereby fish will be less vulnerable to current and new diseases while at the same time thriving in a wider range of temperatures. Second, aquaculture activities, such as input power, transport, and feed production contribute to greenhouse gas emissions. Selection for feed efficiency as well as defining a breeding goal that minimizes greenhouse gas emissions will reduce impacts of aquaculture on climate change. Finally, the limited adoption of breeding programs in aquaculture is a major concern. This implies inefficient use of resources for feed, water, and land. Consequently, the carbon footprint per kg fish produced is greater than when fish from breeding programs would be more heavily used. Aquaculture should use genetically improved and robust organisms not suffering from inbreeding depression. This will require using fish from well-managed selective breeding programs with proper inbreeding control and breeding goals. Policymakers and breeding organizations should provide incentives to boost selective breeding programs in aquaculture for more robust fish tolerating climatic change.

Genetic conservation in applied tree breeding programs.

Treesearch

R. Johnson; B. St. Clair; S. Lipow

2001-01-01

This paper reviews how population size and structure impacts the maintenance of genetic variation in breeding and gene resource populations. We discuss appropriate population sizes for low frequency alleles and point out some examples of low frequency alleles in the literature. Development of appropriate breeding populations and gene resource populations are discussed...

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...

Using Economics and Genetics To Produce Leaner Pork.

ERIC Educational Resources Information Center

Welch, Mary A., Ed.

1994-01-01

The booklet describes the STAGES (Swine Testing and Genetic Evaluation System) program developed at Purdue University (Indiana), along with the USDA, National Pork Producers Council and swine breed associations. By selecting breeding stock from a coded catalogue developed by STAGES, producers are able to select the best breeding stock for more…

Breeding Perspectives and Programs at East Lansing

USDA-ARS?s Scientific Manuscript database

USDA-ARS sugar beet breeding activities for both Aphanomyces resistance and CMS/O-type conversion at East Lansing reach back to the 1940’s, with variety testing activities at Michigan State University reaching back to circa 1911. Many of those contributions are well known in the sugar beet breeding ...

Increasing the efficiency of traditional cacao breeding using whole genome sequencing information.

USDA-ARS?s Scientific Manuscript database

Unfortunately, 80% of the genotypes from the "hybrid seeds" are unproductive in farmers' fields. In 1999 the USDA and Mars Inc. initiated a Marker Assisted Selection (MAS) program for cacao that has reduces many of the problems in traditional breeding. One limitation of the MAS program is the distan...

Phenotypic evidence suggests a possible major-gene element to weevil resistance in Sitka spruce

Treesearch

John N. King; René I. Alfaro; Peter Ott; Lara vanAkker

2012-01-01

The weevil resistance breeding program against the white pine weevil, Pissodes strobi Peck (Coleoptera: Curculionidae), particularly for Sitka spruce (Picea sitchensis (Bong.) Carr), is arguably one of the most successful pest resistance breeding programs for plantation forest species, and it has done a lot to rehabilitate...

Applying SNP marker technology in the cacao breeding program at the Cocoa Research Institute of Ghana

USDA-ARS?s Scientific Manuscript database

In this investigation 45 parental cacao plants and five progeny derived from the parental stock studied were genotyped using six SNP markers to determine off-types or mislabeled clones and to authenticate crosses made in the Cocoa Research Institute of Ghana (CRIG) breeding program. Investigation wa...

Varieties from the USDA are the foundation of the Florida specialty citrus industry

USDA-ARS?s Scientific Manuscript database

The Florida citrus industry is poised to grow diverse new cultivars from the USDA breeding program, the University of Florida breeding program, and from importation of budwood from new selections from around the world. The top six cultivars of specialty citrus from the USDA (‘Murcott’, ‘Sunburst’, ‘...

The forest and the trees: Applications for molecular markers in the Pecan Breeding Program

USDA-ARS?s Scientific Manuscript database

Inventory specific verification of accession identity is crucial to the function of the National Collection of Genetic Resources (NCGR) for Pecans and Hickories, and is an increasingly important component of the USDA ARS Pecan Breeding Program. The foundation of the NCGR is the living trees maintai...

Developments in amphibian captive breeding and reintroduction programs.

PubMed

Harding, Gemma; Griffiths, Richard A; Pavajeau, Lissette

2016-04-01

Captive breeding and reintroduction remain high profile but controversial conservation interventions. It is important to understand how such programs develop and respond to strategic conservation initiatives. We analyzed the contribution to conservation made by amphibian captive breeding and reintroduction since the launch of the International Union for Conservation of Nature (IUCN) Amphibian Conservation Action Plan (ACAP) in 2007. We assembled data on amphibian captive breeding and reintroduction from a variety of sources including the Amphibian Ark database and the IUCN Red List. We also carried out systematic searches of Web of Science, JSTOR, and Google Scholar for relevant literature. Relative to data collected from 1966 to 2006, the number of species involved in captive breeding and reintroduction projects increased by 57% in the 7 years since release of the ACAP. However, there have been relatively few new reintroductions over this period; most programs have focused on securing captive-assurance populations (i.e., species taken into captivity as a precaution against extinctions in the wild) and conservation-related research. There has been a shift to a broader representation of frogs, salamanders, and caecilians within programs and an increasing emphasis on threatened species. There has been a relative increase of species in programs from Central and South America and the Caribbean, where amphibian biodiversity is high. About half of the programs involve zoos and aquaria with a similar proportion represented in specialist facilities run by governmental or nongovernmental agencies. Despite successful reintroduction often being regarded as the ultimate milestone for such programs, the irreversibility of many current threats to amphibians may make this an impractical goal. Instead, research on captive assurance populations may be needed to develop imaginative solutions to enable amphibians to survive alongside current, emerging, and future threats. © 2015 Society for Conservation Biology.

Prospects and Potential Uses of Genomic Prediction of Key Performance Traits in Tetraploid Potato.

PubMed

Stich, Benjamin; Van Inghelandt, Delphine

2018-01-01

Genomic prediction is a routine tool in breeding programs of most major animal and plant species. However, its usefulness for potato breeding has not yet been evaluated in detail. The objectives of this study were to (i) examine the prospects of genomic prediction of key performance traits in a diversity panel of tetraploid potato modeling additive, dominance, and epistatic effects, (ii) investigate the effects of size and make up of training set, number of test environments and molecular markers on prediction accuracy, and (iii) assess the effect of including markers from candidate genes on the prediction accuracy. With genomic best linear unbiased prediction (GBLUP), BayesA, BayesCπ, and Bayesian LASSO, four different prediction methods were used for genomic prediction of relative area under disease progress curve after a Phytophthora infestans infection, plant maturity, maturity corrected resistance, tuber starch content, tuber starch yield (TSY), and tuber yield (TY) of 184 tetraploid potato clones or subsets thereof genotyped with the SolCAP 8.3k SNP array. The cross-validated prediction accuracies with GBLUP and the three Bayesian approaches for the six evaluated traits ranged from about 0.5 to about 0.8. For traits with a high expected genetic complexity, such as TSY and TY, we observed an 8% higher prediction accuracy using a model with additive and dominance effects compared with a model with additive effects only. Our results suggest that for oligogenic traits in general and when diagnostic markers are available in particular, the use of Bayesian methods for genomic prediction is highly recommended and that the diagnostic markers should be modeled as fixed effects. The evaluation of the relative performance of genomic prediction vs. phenotypic selection indicated that the former is superior, assuming cycle lengths and selection intensities that are possible to realize in commercial potato breeding programs.

Prospects and Potential Uses of Genomic Prediction of Key Performance Traits in Tetraploid Potato

PubMed Central

Stich, Benjamin; Van Inghelandt, Delphine

2018-01-01

Genomic prediction is a routine tool in breeding programs of most major animal and plant species. However, its usefulness for potato breeding has not yet been evaluated in detail. The objectives of this study were to (i) examine the prospects of genomic prediction of key performance traits in a diversity panel of tetraploid potato modeling additive, dominance, and epistatic effects, (ii) investigate the effects of size and make up of training set, number of test environments and molecular markers on prediction accuracy, and (iii) assess the effect of including markers from candidate genes on the prediction accuracy. With genomic best linear unbiased prediction (GBLUP), BayesA, BayesCπ, and Bayesian LASSO, four different prediction methods were used for genomic prediction of relative area under disease progress curve after a Phytophthora infestans infection, plant maturity, maturity corrected resistance, tuber starch content, tuber starch yield (TSY), and tuber yield (TY) of 184 tetraploid potato clones or subsets thereof genotyped with the SolCAP 8.3k SNP array. The cross-validated prediction accuracies with GBLUP and the three Bayesian approaches for the six evaluated traits ranged from about 0.5 to about 0.8. For traits with a high expected genetic complexity, such as TSY and TY, we observed an 8% higher prediction accuracy using a model with additive and dominance effects compared with a model with additive effects only. Our results suggest that for oligogenic traits in general and when diagnostic markers are available in particular, the use of Bayesian methods for genomic prediction is highly recommended and that the diagnostic markers should be modeled as fixed effects. The evaluation of the relative performance of genomic prediction vs. phenotypic selection indicated that the former is superior, assuming cycle lengths and selection intensities that are possible to realize in commercial potato breeding programs. PMID:29563919

The use of integer programming to select bulls across breeding companies with volume price discounts.

PubMed

McConnel, M B; Galligan, D T

2004-10-01

Optimization programs are currently used to aid in the selection of bulls to be used in herd breeding programs. While these programs offer a systematic approach to the problem of semen selection, they ignore the impact of volume discounts. Volume discounts are discounts that vary depending on the number of straws purchased. The dynamic nature of volume discounts means that, in order to be adequately accounted for, they must be considered in the optimization routine. Failing to do this creates a missed economic opportunity because the potential benefits of optimally selecting and combining breeding company discount opportunities are not captured. To address these issues, an integer program was created which used binary decision variables to incorporate the effects of quantity discounts into the optimization program. A consistent set of trait criteria was used to select a group of bulls from 3 sample breeding companies. Three different selection programs were used to select the bulls, 2 traditional methods and the integer method. After the discounts were applied using each method, the integer program resulted in the lowest cost portfolio of bulls. A sensitivity analysis showed that the integer program also resulted in a low cost portfolio when the genetic trait goals were changed to be more or less stringent. In the sample application, a net benefit of the new approach over the traditional approaches was a 12.3 to 20.0% savings in semen cost.

Mutation breeding of ornamental plants using ion beams.

PubMed

Yamaguchi, Hiroyasu

2018-01-01

Ornamental plants that have a rich variety of flower colors and shapes are highly prized in the commercial flower market, and therefore, mutant cultivars that produce different types of flowers while retaining their growth habits are in demand. Furthermore, mutation breeding is well suited for ornamental plants because many species can be easily vegetatively propagated, facilitating the production of spontaneous and induced mutants. The use of ion beams in mutation breeding has rapidly expanded since the 1990s in Japan, with the prospect that more ion beam-specific mutants will be generated. There are currently four irradiation facilities in Japan that provide ion beam irradiation for plant materials. The development of mutant cultivars using ion beams has been attempted on many ornamental plants thus far, and some species have been used to investigate the process of mutagenesis. In addition, progress is being made in clarifying the genetic mechanism for expressing important traits, which will probably result in the development of more efficient mutation breeding methods for ornamental plants. This review not only provides examples of successful mutation breeding results using ion beams, but it also describes research on mutagenesis and compares results of ion beam and gamma ray breeding using ornamental plants.

Cattle genome-wide analysis reveals genetic signatures in trypanotolerant N'Dama.

PubMed

Kim, Soo-Jin; Ka, Sojeong; Ha, Jung-Woo; Kim, Jaemin; Yoo, DongAhn; Kim, Kwondo; Lee, Hak-Kyo; Lim, Dajeong; Cho, Seoae; Hanotte, Olivier; Mwai, Okeyo Ally; Dessie, Tadelle; Kemp, Stephen; Oh, Sung Jong; Kim, Heebal

2017-05-12

Indigenous cattle in Africa have adapted to various local environments to acquire superior phenotypes that enhance their survival under harsh conditions. While many studies investigated the adaptation of overall African cattle, genetic characteristics of each breed have been poorly studied. We performed the comparative genome-wide analysis to assess evidence for subspeciation within species at the genetic level in trypanotolerant N'Dama cattle. We analysed genetic variation patterns in N'Dama from the genomes of 101 cattle breeds including 48 samples of five indigenous African cattle breeds and 53 samples of various commercial breeds. Analysis of SNP variances between cattle breeds using wMI, XP-CLR, and XP-EHH detected genes containing N'Dama-specific genetic variants and their potential associations. Functional annotation analysis revealed that these genes are associated with ossification, neurological and immune system. Particularly, the genes involved in bone formation indicate that local adaptation of N'Dama may engage in skeletal growth as well as immune systems. Our results imply that N'Dama might have acquired distinct genotypes associated with growth and regulation of regional diseases including trypanosomiasis. Moreover, this study offers significant insights into identifying genetic signatures for natural and artificial selection of diverse African cattle breeds.

Mutation breeding of ornamental plants using ion beams

PubMed Central

Yamaguchi, Hiroyasu

2018-01-01

Ornamental plants that have a rich variety of flower colors and shapes are highly prized in the commercial flower market, and therefore, mutant cultivars that produce different types of flowers while retaining their growth habits are in demand. Furthermore, mutation breeding is well suited for ornamental plants because many species can be easily vegetatively propagated, facilitating the production of spontaneous and induced mutants. The use of ion beams in mutation breeding has rapidly expanded since the 1990s in Japan, with the prospect that more ion beam-specific mutants will be generated. There are currently four irradiation facilities in Japan that provide ion beam irradiation for plant materials. The development of mutant cultivars using ion beams has been attempted on many ornamental plants thus far, and some species have been used to investigate the process of mutagenesis. In addition, progress is being made in clarifying the genetic mechanism for expressing important traits, which will probably result in the development of more efficient mutation breeding methods for ornamental plants. This review not only provides examples of successful mutation breeding results using ion beams, but it also describes research on mutagenesis and compares results of ion beam and gamma ray breeding using ornamental plants. PMID:29681749

Does Flooring Substrate Impact Kennel and Dog Cleanliness in Commercial Breeding Facilities?

PubMed Central

Stella, Judith; Hurt, Moriah; Bauer, Amy; Croney, Candace

2018-01-01

Simple Summary It is important to understand how the flooring substrate used in dog housing impacts dog health and well-being. Aspects to consider include paw, elbow, and hock health, the cleanliness of the dog, and the ability of the floors to be cleaned easily and thoroughly. This pilot study assessed the health and cleanliness of 118 dogs housed on three different types of flooring commonly found in commercial breeding kennels. No serious paw, elbow, or hock problems were identified. Thirty-one percent or fewer kennels at each facility were found to have fecal contamination after routine cleaning and the majority of dogs were clean. These findings indicate that a well-managed kennel can maintain clean, healthy dogs on different types of flooring substrates. Abstract Evaluation of kennel flooring surfaces is needed to understand their impacts on dog health and well-being. This pilot study aimed to characterize aspects of physical health, kennel cleanliness, and dog body cleanliness on flooring types common in US breeding kennels. Subjects were 118 adult dogs housed on diamond-coated expanded metal (DCEM), polypropylene (POLY), or concrete (CON) flooring at five commercial breeding facilities in Indiana, U.S. Body condition, paw, elbow, and hock health scores were recorded. Each indoor kennel and dog was visually assessed for cleanliness. Kennels were swabbed immediately after cleaning with electrostatic dry cloths and cultured for Escherichia coli. Descriptive statistics were used for analysis. Mean body condition score (BCS), kennel and dog cleanliness scores were all near ideal (3, 1.15, and 1.04, respectively). Thirty-one percent or fewer kennels at each facility were culture-positive for E. coli after cleaning. No serious paw, elbow, or hock problems were identified. Overall, the findings indicate that with appropriate management and regular access to additional surfaces, dog foot health, cleanliness, and kennel cleanliness can be maintained on the flooring types investigated. PMID:29690514

An 8-Year Breeding Program for Asian Seabass Lates calcarifer: Genetic Evaluation, Experiences, and Challenges.

PubMed

Khang, Pham Van; Phuong, Truong Ha; Dat, Nguyen Khac; Knibb, Wayne; Nguyen, Nguyen Hong

2018-01-01

Selective breeding for marine finfish is challenging due to difficulties in reproduction, larval rearing, and on-growth in captive environments. The farming of Asian seabass ( Lates calcarifer ) has all these problems and our knowledge of the quantitative genetic information (heritability and correlations) of traits necessary for commercial exploitation is poor. The present study was conducted to address this knowledge gap and to provide information that can be applied to sea bass and other aquaculture species. We carried out a comprehensive genetic evaluation for three traits (body weight, total length, and survival) collected from a breeding population for Asian seabass over an eight-year period from 2010 to 2017. Statistical analysis was carried out on 4,567 adult fish at 105, 180, 270, 360, 450, and 570 days post-hatch (dph). The heritabilities (h 2 ) estimated for body weight and length using linear mixed model were moderate to high (0.12 to 0.78 and 0.41 to 0.85, respectively) and they differed between the measurement periods. Survival during grow-out phase was analyzed using threshold logistic and probit models. The heritability estimates for survival rate on the underlying liability scale ( h L 2 ) varied from 0.05 to 0.21. When the observed heritability obtained from the linear mixed model was back-transformed to the liability scale, they were similar but not significant. In addition, we examined effects of genotype by environment (G × E) interaction on body traits. The genetic correlation for body weight between tank and sea cage cultures were high (0.91-0.94) in the first and second rearing periods (180 and 270 dph) but the correlation was decreased to 0.59 ± 0.33 at 360 dph. This suggests that the genotype by environment interaction is important for body traits in this population. Furthermore, the genetic correlations of body weights between different measurement periods were moderate but different from one. This suggests that body weights measured at different time points may be different traits and selection for improved early weight may not capture all genetic expressions in subsequent rearing periods in Asian seabass. Selection of the nucleus in sea cages may produce genotypes that do not perform equally well in tanks, although this deserves further studies to determine a suitable selection environment and optimize the breeding program. This paper discusses challenges encountered during implementation of the selection program for L. calcarifer .

Phylogenetic analysis of different breeds of domestic chickens in selected area of Peninsular Malaysia inferred from partial cytochrome b gene information and RAPD markers.

PubMed

Yap, Fook Choy; Yan, Yap Jin; Loon, Kiung Teh; Zhen, Justina Lee Ning; Kamau, Nelly Warau; Kumaran, Jayaraj Vijaya

2010-10-01

The present investigation was carried out in an attempt to study the phylogenetic analysis of different breeds of domestic chickens in Peninsular Malaysia inferred from partial cytochrome b gene information and random amplified polymorphic DNA (RAPD) markers. Phylogenetic analysis using both neighbor-joining (NJ) and maximum parsimony (MP) methods produced three clusters that encompassed Type-I village chickens, the red jungle fowl subspecies and the Japanese Chunky broilers. The phylogenetic analysis also revealed that majority of the Malaysian commercial chickens were randomly assembled with the Type-II village chickens. In RAPD assay, phylogenetic analysis using neighbor-joining produced six clusters that were completely distinguished based on the locality of chickens. High levels of genetic variations were observed among the village chickens, the commercial broilers, and between the commercial broilers and layer chickens. In this study, it was found that Type-I village chickens could be distinguished from the commercial chickens and Type-II village chickens at the position of the 27th nucleotide of the 351 bp cytochrome b gene. This study also revealed that RAPD markers were unable to differentiate the type of chickens, but it showed the effectiveness of RAPD in evaluating the genetic variation and the genetic relationships between chicken lines and populations.

Calving traits, milk production, body condition, fertility, and survival of Holstein-Friesian and Norwegian Red dairy cattle on commercial dairy farms over 5 lactations.

PubMed

Ferris, C P; Patterson, D C; Gordon, F J; Watson, S; Kilpatrick, D J

2014-01-01

The objective of this study was to compare calving traits, BCS, milk production, fertility, and survival of Holstein-Friesian (HF) and Norwegian Red (NR) dairy cattle in moderate-concentrate input systems. The experiment was conducted on 19 commercial Northern Ireland dairy farms, and involved 221 HF cows and 221 NR cows. Cows completed 5 lactations during the experiment, unless they died or were culled or sold. Norwegian Red cows had a lower calving difficulty score than HF cows when calving for the first and second time, but not for the third and fourth time. At first calving, the incidence of stillbirths for NR cows was 4%, compared with 13% for HF cows, whereas no difference existed between breeds in the proportion of calves born alive when calving for the second time. When calving for the first time, NR cows had a poorer milking temperament than HF cows, whereas milking temperament was unaffected by breed following the second calving. Holstein-Friesian cows had a higher full-lactation milk yield than NR cows, whereas NR cows produced milk with a higher milk fat and protein content. Full-lactation fat + protein yield was unaffected by genotype. Norwegian Red cows had a lower somatic cell score than HF cows during all lactations. Although NR cattle had a higher BCS than the HF cows during lactations 1 and 2, no evidence existed that the 2 genotypes either lost or gained body condition at different rates. Conception rates to first artificial insemination were higher with the NR cows during lactations 1 to 4 (57.8 vs. 40.9%, respectively), with 28.5% of HF cows and 11.8% of NR cows culled as infertile before lactation 6. A greater percentage of NR cows calved for a sixth time compared with HF cows (27.2 vs. 16.3%, respectively). In general, NR cows outperformed HF cows in traits that have been historically included in the NR breeding program. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Managing the rate of increase in average co-ancestry in a rolling front tree breeding strategy.

PubMed

Kerr, R J; McRae, T A; Dutkowski, G W; Tier, B

2015-04-01

In breeding forest trees, as for livestock, the goal is to capture as much genetic gain as possible for the breeding objective, while limiting long- and short-term inbreeding. The Southern Tree Breeding Association (STBA) is responsible for breeding Australia's two main commercial forest tree species and has adopted algorithms and methods commonly used in animal breeding to achieve this balance. Discrete generation breeding is the norm for most tree breeding programmes. However, the STBA uses an overlapping generation strategy, with a new stream of breeding initiated each year. A feature of the species bred by the STBA (Pinus radiata and Eucalyptus globulus) is the long interval (up to 7 years) between when an individual is mated and when its progeny is first assessed in field trials and performance data included in the national performance database. Mate selection methods must therefore recognize the large pool of unmeasured progeny generated over recent years of crossing. In addition, the substantial delay between when an individual is selected in a field trial and when it is clonally copied into a mating facility (breeding arboretum) means that selection and mating must occur as a two-step process. In this article, we describe modifications to preselection and mate selection algorithms that allow unmeasured progeny (juveniles) to be recognized. We also demonstrate that the addition of hypothetical new progeny to the juvenile pool is important for computing the increase in average co-ancestry in the population. Methods outlined in this article may have relevance to animal breeding programmes where between mating and progeny measurement, new rounds of mating are initiated. © 2015 Blackwell Verlag GmbH.

Review of functional markers for improving cooking, eating, and the nutritional qualities of rice

PubMed Central

Lau, Wendy C. P.; Rafii, Mohd Y.; Ismail, Mohd R.; Puteh, Adam; Latif, Mohammad A.; Ramli, Asfaliza

2015-01-01

After yield, quality is one of the most important aspects of rice breeding. Preference for rice quality varies among cultures and regions; therefore, rice breeders have to tailor the quality according to the preferences of local consumers. Rice quality assessment requires routine chemical analysis procedures. The advancement of molecular marker technology has revolutionized the strategy in breeding programs. The availability of rice genome sequences and the use of forward and reverse genetics approaches facilitate gene discovery and the deciphering of gene functions. A well-characterized gene is the basis for the development of functional markers, which play an important role in plant genotyping and, in particular, marker-assisted breeding. In addition, functional markers offer advantages that counteract the limitations of random DNA markers. Some functional markers have been applied in marker-assisted breeding programs and have successfully improved rice quality to meet local consumers’ preferences. Although functional markers offer a plethora of advantages over random genetic markers, the development and application of functional markers should be conducted with care. The decreasing cost of sequencing will enable more functional markers for rice quality improvement to be developed, and application of these markers in rice quality breeding programs is highly anticipated. PMID:26528304

US Residents' Perceptions of Dog Welfare Needs and Canine Welfare Information Sources.

PubMed

Bir, Courtney; Croney, Candace C; Widmar, Nicole J Olynk

2018-06-08

The extent to which welfare needs of breeding dogs are met in commercial dog-breeding kennels is a potential point of controversy. This analysis sought to understand US residents' perceptions and priorities related to dog welfare : by investigating (a) perceptions of breeding-dog welfare needs and (b) perceptions of various nonhuman animal welfare information sources. Using best/worst-choice experiments conducted in an online survey, respondents' choices for most and least important breeding-dog welfare needs (n = 508) and most/least trusted canine welfare information sources (n = 508) were analyzed. The survey sample was targeted to be representative of the US population in terms of gender, age, region of residence, income, and education. The largest preference shares (relatively most important) for breeding-dog welfare needs were for "availability of food and water" (39.2%) and health/veterinary care (18.1%). The largest preference shares (relatively most trusted sources) for welfare information were American Society for the Prevention of Cruelty to Animals, a veterinarian, and American Veterinary Medical Association, with 25.1%, 16.4%, and 14.1% shares, respectively.

Productivity and breeding habitat of loggerhead shrikes in a southwestern urban environment

USGS Publications Warehouse

Boal, C.W.; Estabrook, T.S.; Duerr, A.E.

2003-01-01

Declines in loggerhead shrike (Lanius ludovicianus) populations have been associated in part with habitat loss and degradation, including that resulting from urbanization. We monitored the productivity and examined nesting habitat of loggerhead shrikes nesting in an urban environment in Tucson, Arizona. We located 22 breeding pairs in 1997 and 26 breeding pairs in 1998, with a 72% breeding area reoccupancy between years. Mean fledgling numbers were 2.28/ nesting attempt and 3.11/successful nest. Although some pairs initially failed and renested, 91% and 73% of shrike pairs successfully fledged young in 1997 and 1998, respectively. Mayfield estimates of nesting success were 78% in 1997 and 65% in 1998. Nest sites were characterized by more trees >3 m in height, taller nest trees than those randomly available, and a greater proportion of bare ground surface than at random sites. Shrike breeding territories had lower proportions of residential and commercial development and greater proportions of open areas with low-growing vegetation than randomly available. Some shrikes nested in school playgrounds, residential front yards, and parking lots, if adjacent open space was available.

Genetic relationships between feral cattle from Chirikof Island, Alaska and other breeds.

PubMed

MacNeil, M D; Cronin, M A; Blackburn, H D; Richards, C M; Lockwood, D R; Alexander, L J

2007-06-01

The origin of cattle on Chirikof Island, off the coast of Alaska, is not well documented. We assessed genetic differentiation of cattle isolated on Chirikof Island from several breeds commonly used for commercial production in North America including breeds popularly believed to have contributed to the Chirikof Island population. A set of 34 microsatellite loci was used to genotype Angus, Charolais, Hereford, Highland, Limousin, Red Angus, Salers, Shorthorn, Simmental, Tarentaise and Texas Longhorn cattle sampled from North America and the Chirikof Island population. Resulting F(ST) statistics for these loci ranged from 0.06 to 0.22 and on average, 14% of total genetic variation was between breeds. Whether population structure was modelled as a bifurcating tree or genetic network, Chirikof Island cattle appeared to be unique and strongly differentiated relative to the other breeds that were sampled. Bayesian clustering for multiple-locus assignment to genetic groups indicated low levels of admixture in the Chirikof Island population. Thus, the Chirikof Island population may be a novel genetic resource of some importance for conservation and industry.

The fine-scale genetic structure of the two-spotted spider mite in a commercial greenhouse.

PubMed

Uesugi, R; Kunimoto, Y; Osakabe, Mh

2009-02-01

The fine-scale genetic structure of Tetranychus urticae Koch was studied to estimate local gene flow within a rose tree habitat in a commercial greenhouse using seven microsatellite markers. Two beds of rose trees with different population densities were selected and 18 consecutive quadrats of 1.2 m length were sequentially established in each bed. Heterozygote deficiency was positive within quadrats, which was most likely a result of the Wahlund effect because the mites usually form small breeding colonies. Low population density and frequent inbreeding could also accelerate genetic differentiation among the breeding colonies. A short-range (2.4-3.6 m) positive autocorrelation and clear genetic cline among quadrat populations was detected within a bed. This suggests that gene flow was limited to a short range even if population density was substantially increased. Therefore, large-scale dispersal such as aerial dispersal contributed very little to gene flow in the greenhouse.

Great tits (Parus major) reduce caterpillar damage in commercial apple orchards.

PubMed

Mols, Christel M M; Visser, Marcel E

2007-02-07

Alternative ways to control caterpillar pests and reduce the use of pesticides in apple orchards are in the interest of the environment, farmers and the public. Great tits have already been shown to reduce damage under high caterpillar density when breeding in nest boxes in an experimental apple orchard. We tested whether this reduction also occurs under practical conditions of Integrated Pest Management (IPM), as well as Organic Farming (OF), by setting up an area with nest boxes while leaving a comparable area as a control within 12 commercial orchards. We showed that in IPM orchards, but not in OF orchards, in the areas with breeding great tits, apples had 50% of the caterpillar damage of the control areas. Offering nest boxes to attract insectivorous passerines in orchards can thus lead to more limited pesticide use, thereby adding to the natural biological diversity in an agricultural landscape, while also being economically profitable to the fruit growers.

TILLING for plant breeding.

PubMed

Sharp, Peter; Dong, Chongmei

2014-01-01

TILLING is widely used in plant functional genomics. Mutagenesis and SNP detection is combined to allow for the isolation of mutations in genes of interest. It can also be used as a plant breeding tool, whereby variation in known or candidate genes of interest to breeding programs is generated. Here we describe a simple low-cost TILLING procedure.

Breeding for improved potato nutrition: High amylose starch potatoes show promise as fiber source

USDA-ARS?s Scientific Manuscript database

Potato starch is composed of approximately 75% amylopectin and 25% amylose. We are interested in breeding for higher amylose content, which would increase the fiber content of potato and decrease glycemic index. In order to make progress in a breeding program, we have developed a high throughput ass...

A matter of taste: Improving flavor of fresh potatoes

USDA-ARS?s Scientific Manuscript database

Breeding for improved potato flavor has not been a high priority in US breeding programs. It is a difficult trait to breed for because it cannot be done in a high throughput manner and it requires an understanding of the complex biochemistry of flavor compounds and effects of cooking on those compou...

9 CFR 145.93 - Terminology and classification; flocks and products.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Influenza Clean. This program is intended to be the basis from which the breeding-hatchery industry may conduct a program for the prevention and control of the H5/H7 subtypes of avian influenza. It is intended to determine the presence of the H5/H7 subtypes of avian influenza in meat-type waterfowl breeding...

9 CFR 145.93 - Terminology and classification; flocks and products.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Influenza Clean. This program is intended to be the basis from which the breeding-hatchery industry may conduct a program for the prevention and control of the H5/H7 subtypes of avian influenza. It is intended to determine the presence of the H5/H7 subtypes of avian influenza in meat-type waterfowl breeding...

9 CFR 145.93 - Terminology and classification; flocks and products.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Influenza Clean. This program is intended to be the basis from which the breeding-hatchery industry may conduct a program for the prevention and control of the H5/H7 subtypes of avian influenza. It is intended to determine the presence of the H5/H7 subtypes of avian influenza in meat-type waterfowl breeding...

Validation and Implementation of Marker-Assisted Selection (MAS) for PVY Resistance (Ryadg gene) in a Tetraploid Potato Breeding Program

USDA-ARS?s Scientific Manuscript database

The gene Ryadg from S. tuberosum ssp. andigena provides extreme resistance to PVY. This gene has been mapped to chromosome XI and linked PCR-based DNA markers have been identified. Advanced tetraploid russeted potato clones developed by the U.S. Pacific Northwest Potato Breeding Program with Ryadg P...

Translating science into the next generation meat quality program for Australian lamb.

PubMed

Pethick, D W; Ball, A J; Banks, R G; Gardner, G E; Rowe, J B; Jacob, R H

2014-02-01

This paper introduces a series of papers in the form of a special edition that reports phenotypic analyses done in parallel with genotypic analyses for the Australian Sheep Industry Cooperative Research Centre (Sheep CRC) using data generated from the information nucleus flock (INF). This has allowed new knowledge to be gained of the genetic, environment and management factors that impact on the carcase and eating quality, visual appeal, odour and health attributes of Australian lamb meat. The research described involved close collaboration with commercial partners across the supply chain in the sire breeding as well as the meat processing industries. This approach has enabled timely delivery and adoption of research results to industry in an unprecedented way and provides a good model for future research. © 2013.

Genetic Vulnerability and the Relationship of Commercial Germplasms of Maize in Brazil with the Nested Association Mapping Parents

PubMed Central

Fritsche Neto, Roberto; Granato, Ítalo Stefanine Correia; Sant’Ana, Gustavo César; Morais, Pedro Patric Pinho; Borém, Aluízio

2016-01-01

A few breeding companies dominate the maize (Zea mays L.) hybrid market in Brazil: Monsanto® (35%), DuPont Pioneer® (30%), Dow Agrosciences® (15%), Syngenta® (10%) and Helix Sementes (4%). Therefore, it is important to monitor the genetic diversity in commercial germplasms as breeding practices, registration and marketing of new cultivars can lead to a significant reduction of the genetic diversity. Reduced genetic variation may lead to crop vulnerabilities, food insecurity and limited genetic gains following selection. The aim of this study was to evaluate the genetic vulnerability risk by examining the relationship between the commercial Brazilian maize germplasms and the Nested Association Mapping (NAM) Parents. For this purpose, we used the commercial hybrids with the largest market share in Brazil and the NAM parents. The hybrids were genotyped for 768 single nucleotide polymorphisms (SNPs), using the Illumina Goldengate® platform. The NAM parent genomic data, comprising 1,536 SNPs for each line, were obtained from the Panzea data bank. The population structure, genetic diversity and the correlation between allele frequencies were analyzed. Based on the estimated effective population size and genetic variability, it was found that there is a low risk of genetic vulnerability in the commercial Brazilian maize germplasms. However, the genetic diversity is lower than those found in the NAM parents. Furthermore, the Brazilian germplasms presented no close relations with most NAM parents, except B73. This indicates that B73, or its heterotic group (Iowa Stiff Stalk Synthetic), contributed to the development of the commercial Brazilian germplasms. PMID:27780247

Genetic Vulnerability and the Relationship of Commercial Germplasms of Maize in Brazil with the Nested Association Mapping Parents.

PubMed

Andrade, Luciano Rogério Braatz de; Fritsche Neto, Roberto; Granato, Ítalo Stefanine Correia; Sant'Ana, Gustavo César; Morais, Pedro Patric Pinho; Borém, Aluízio

2016-01-01

A few breeding companies dominate the maize (Zea mays L.) hybrid market in Brazil: Monsanto® (35%), DuPont Pioneer® (30%), Dow Agrosciences® (15%), Syngenta® (10%) and Helix Sementes (4%). Therefore, it is important to monitor the genetic diversity in commercial germplasms as breeding practices, registration and marketing of new cultivars can lead to a significant reduction of the genetic diversity. Reduced genetic variation may lead to crop vulnerabilities, food insecurity and limited genetic gains following selection. The aim of this study was to evaluate the genetic vulnerability risk by examining the relationship between the commercial Brazilian maize germplasms and the Nested Association Mapping (NAM) Parents. For this purpose, we used the commercial hybrids with the largest market share in Brazil and the NAM parents. The hybrids were genotyped for 768 single nucleotide polymorphisms (SNPs), using the Illumina Goldengate® platform. The NAM parent genomic data, comprising 1,536 SNPs for each line, were obtained from the Panzea data bank. The population structure, genetic diversity and the correlation between allele frequencies were analyzed. Based on the estimated effective population size and genetic variability, it was found that there is a low risk of genetic vulnerability in the commercial Brazilian maize germplasms. However, the genetic diversity is lower than those found in the NAM parents. Furthermore, the Brazilian germplasms presented no close relations with most NAM parents, except B73. This indicates that B73, or its heterotic group (Iowa Stiff Stalk Synthetic), contributed to the development of the commercial Brazilian germplasms.

Targeted genotyping-by-sequencing permits cost-effective identification and discrimination of pasture grass species and cultivars.

PubMed

Pembleton, Luke W; Drayton, Michelle C; Bain, Melissa; Baillie, Rebecca C; Inch, Courtney; Spangenberg, German C; Wang, Junping; Forster, John W; Cogan, Noel O I

2016-05-01

A targeted amplicon-based genotyping-by-sequencing approach has permitted cost-effective and accurate discrimination between ryegrass species (perennial, Italian and inter-species hybrid), and identification of cultivars based on bulked samples. Perennial ryegrass and Italian ryegrass are the most important temperate forage species for global agriculture, and are represented in the commercial pasture seed market by numerous cultivars each composed of multiple highly heterozygous individuals. Previous studies have identified difficulties in the use of morphophysiological criteria to discriminate between these two closely related taxa. Recently, a highly multiplexed single nucleotide polymorphism (SNP)-based genotyping assay has been developed that permits accurate differentiation between both species and cultivars of ryegrasses at the genetic level. This assay has since been further developed into an amplicon-based genotyping-by-sequencing (GBS) approach implemented on a second-generation sequencing platform, allowing accelerated throughput and ca. sixfold reduction in cost. Using the GBS approach, 63 cultivars of perennial, Italian and interspecific hybrid ryegrasses, as well as intergeneric Festulolium hybrids, were genotyped. The genetic relationships between cultivars were interpreted in terms of known breeding histories and indistinct species boundaries within the Lolium genus, as well as suitability of current cultivar registration methodologies. An example of applicability to quality assurance and control (QA/QC) of seed purity is also described. Rapid, low-cost genotypic assays provide new opportunities for breeders to more fully explore genetic diversity within breeding programs, allowing the combination of novel unique genetic backgrounds. Such tools also offer the potential to more accurately define cultivar identities, allowing protection of varieties in the commercial market and supporting processes of cultivar accreditation and quality assurance.

Identification of aerenchyma formation-related QTL in barley that can be effective in breeding for waterlogging tolerance.

PubMed

Zhang, Xuechen; Zhou, Gaofeng; Shabala, Sergey; Koutoulis, Anthony; Shabala, Lana; Johnson, Peter; Li, Chengdao; Zhou, Meixue

2016-06-01

Aerenchyma formation after 7 days of waterlogging in commercial potting mixture can be a reliable, fast, and widely utilized approach for the selection of waterlogging tolerant barley genotypes. One major QTL for aerenchyma formation after 7 days of waterlogging treatment was identified and the newly developed markers explained 44 % of the phenotypic variance. This QTL can now be effectively used in barley breeding programs. Waterlogging is one of the important limiting conditions for crop yield and productivity. The main feature of waterlogged soils is oxygen deprivation, due to slow gas diffusion in water. Decreased oxygen content in waterlogged soils leads to the oxygen deficiency in plant tissues, resulting in reduced energy availability for plants. Rapidly induced aerenchyma formation is critical to maintaining adequate oxygen supply and overall waterlogging tolerance in barley. In this study, we have proved that quantifying aerenchyma formation after 7 days of waterlogging in commercial potting mixture can be a reliable, fast, and widely utilised approach for the selection of waterlogging tolerant barley genotypes, which is supported by measurements of redox potential (an indicator of anaerobic conditions). This protocol was also used to identify quantitative trait loci (QTL) in a doubled haploid population of barley from the cross between Yerong (tolerant) and Franklin (sensitive) genotypes. The QTL for aerenchyma formation and root porosity were at the same location as the waterlogging tolerance QTL. Seven new markers were developed and added onto this region on chromosome 4H. One major QTL for aerenchyma formation after 7 days waterlogging treatment explained 44.0 % of the phenotypic variance. This successful QTL for aerenchyma formation can be effectively used in the marker assisted selection to improve waterlogging tolerance in barley.

A WebGIS platform for the monitoring of Farm Animal Genetic Resources (GENMON)

PubMed Central

Flury, Christine; Matasci, Giona; Joerin, Florent; Widmer, Ivo; Joost, Stéphane

2017-01-01

Background In 2007, the Food and Agriculture Organization of the United Nations (FAO) initiated the Global plan of action for Farm Animal Genetic Resources (FAnGR). The main goal of this plan is to reduce further loss of genetic diversity in farm animals, so as to protect and promote the diversity of farm animal resources. An important step to reach this goal is to monitor and prioritize endangered breeds in the context of conservation programs. Methodology/Web portal implementation The GENMON WebGIS platform is able to monitor FAnGR and to evaluate the degree of endangerment of livestock breeds. The system takes into account pedigree and introgression information, the geographical concentration of animals, the cryo-conservation plan and the sustainability of breeding activities based on socio-economic data as well as present and future land use conditions. A multi-criteria decision tool supports the aggregation of the multi-thematic indices mentioned above using the MACBETH method, which is based on a weighted average using satisfaction thresholds. GENMON is a monitoring tool to reach subjective decisions made by a government agency. It relies on open source software and is available at http://lasigsrv2.epfl.ch/genmon-ch. Results/Significance GENMON allows users to upload pedigree-information (animal ID, parents, birthdate, sex, location and introgression) from a specific livestock breed and to define species and/or region-specific weighting parameters and thresholds. The program then completes a pedigree analysis and derives several indices that are used to calculate an integrated score of conservation prioritization for the breeds under investigation. The score can be visualized on a geographic map and allows a fast, intuitive and regional identification of breeds in danger. Appropriate conservation actions and breeding programs can thus be undertaken in order to promote the recovery of the genetic diversity in livestock breeds in need. The use of the platform is illustrated by means of an example based on three local livestock breeds from different species in Switzerland. PMID:28453561

A WebGIS platform for the monitoring of Farm Animal Genetic Resources (GENMON).

PubMed

Duruz, Solange; Flury, Christine; Matasci, Giona; Joerin, Florent; Widmer, Ivo; Joost, Stéphane

2017-01-01

In 2007, the Food and Agriculture Organization of the United Nations (FAO) initiated the Global plan of action for Farm Animal Genetic Resources (FAnGR). The main goal of this plan is to reduce further loss of genetic diversity in farm animals, so as to protect and promote the diversity of farm animal resources. An important step to reach this goal is to monitor and prioritize endangered breeds in the context of conservation programs. The GENMON WebGIS platform is able to monitor FAnGR and to evaluate the degree of endangerment of livestock breeds. The system takes into account pedigree and introgression information, the geographical concentration of animals, the cryo-conservation plan and the sustainability of breeding activities based on socio-economic data as well as present and future land use conditions. A multi-criteria decision tool supports the aggregation of the multi-thematic indices mentioned above using the MACBETH method, which is based on a weighted average using satisfaction thresholds. GENMON is a monitoring tool to reach subjective decisions made by a government agency. It relies on open source software and is available at http://lasigsrv2.epfl.ch/genmon-ch. GENMON allows users to upload pedigree-information (animal ID, parents, birthdate, sex, location and introgression) from a specific livestock breed and to define species and/or region-specific weighting parameters and thresholds. The program then completes a pedigree analysis and derives several indices that are used to calculate an integrated score of conservation prioritization for the breeds under investigation. The score can be visualized on a geographic map and allows a fast, intuitive and regional identification of breeds in danger. Appropriate conservation actions and breeding programs can thus be undertaken in order to promote the recovery of the genetic diversity in livestock breeds in need. The use of the platform is illustrated by means of an example based on three local livestock breeds from different species in Switzerland.

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.

Frequency of five disease-causing genetic mutations in a large mixed-breed dog population (2011–2012)

PubMed Central

Zierath, Sharon; Hughes, Angela M.; Fretwell, Neale; Dibley, Mark

2017-01-01

Background A large and growing number of inherited genetic disease mutations are now known in the dog. Frequencies of these mutations are typically examined within the breed of discovery, possibly in related breeds, but nearly always in purebred dogs. No report to date has examined the frequencies of specific genetic disease mutations in a large population of mixed-breed dogs. Further, veterinarians and dog owners typically dismiss inherited/genetic diseases as possibilities for health problems in mixed-breed dogs, assuming hybrid vigor will guarantee that single-gene disease mutations are not a cause for concern. Therefore, the objective of this study was to screen a large mixed-breed canine population for the presence of mutant alleles associated with five autosomal recessive disorders: hyperuricosuria and hyperuricemia (HUU), cystinuria (CYST), factor VII deficiency (FVIID), myotonia congenita (MYC) and phosphofructokinase deficiency (PKFD). Genetic testing was performed in conjunction with breed determination via the commercially-available Wisdom PanelTM test. Results From a population of nearly 35,000 dogs, homozygous mutant dogs were identified for HUU (n = 57) and FVIID (n = 65). Homozygotes for HUU and FVIID were identified even among dogs with highly mixed breed ancestry. Carriers were identified for all disorders except MYC. HUU and FVIID were of high enough frequency to merit consideration in any mixed-breed dog, while CYST, MYC, and PKFD are vanishingly rare. Conclusions The assumption that mixed-breed dogs do not suffer from single-gene genetic disorders is shown here to be false. Within the diseases examined, HUU and FVIID should remain on any practitioner’s rule-out list, when clinically appropriate, for all mixed-breed dogs, and judicious genetic testing should be performed for diagnosis or screening. Future testing of large mixed-breed dog populations that include additional known canine genetic mutations will refine our knowledge of which genetic diseases can strike mixed-breed dogs. PMID:29166669

Frequency of five disease-causing genetic mutations in a large mixed-breed dog population (2011-2012).

PubMed

Zierath, Sharon; Hughes, Angela M; Fretwell, Neale; Dibley, Mark; Ekenstedt, Kari J

2017-01-01

A large and growing number of inherited genetic disease mutations are now known in the dog. Frequencies of these mutations are typically examined within the breed of discovery, possibly in related breeds, but nearly always in purebred dogs. No report to date has examined the frequencies of specific genetic disease mutations in a large population of mixed-breed dogs. Further, veterinarians and dog owners typically dismiss inherited/genetic diseases as possibilities for health problems in mixed-breed dogs, assuming hybrid vigor will guarantee that single-gene disease mutations are not a cause for concern. Therefore, the objective of this study was to screen a large mixed-breed canine population for the presence of mutant alleles associated with five autosomal recessive disorders: hyperuricosuria and hyperuricemia (HUU), cystinuria (CYST), factor VII deficiency (FVIID), myotonia congenita (MYC) and phosphofructokinase deficiency (PKFD). Genetic testing was performed in conjunction with breed determination via the commercially-available Wisdom PanelTM test. From a population of nearly 35,000 dogs, homozygous mutant dogs were identified for HUU (n = 57) and FVIID (n = 65). Homozygotes for HUU and FVIID were identified even among dogs with highly mixed breed ancestry. Carriers were identified for all disorders except MYC. HUU and FVIID were of high enough frequency to merit consideration in any mixed-breed dog, while CYST, MYC, and PKFD are vanishingly rare. The assumption that mixed-breed dogs do not suffer from single-gene genetic disorders is shown here to be false. Within the diseases examined, HUU and FVIID should remain on any practitioner's rule-out list, when clinically appropriate, for all mixed-breed dogs, and judicious genetic testing should be performed for diagnosis or screening. Future testing of large mixed-breed dog populations that include additional known canine genetic mutations will refine our knowledge of which genetic diseases can strike mixed-breed dogs.

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

Rice Molecular Breeding Laboratories in the Genomics Era: Current Status and Future Considerations

PubMed Central

Collard, Bert C. Y.; Vera Cruz, Casiana M.; McNally, Kenneth L.; Virk, Parminder S.; Mackill, David J.

2008-01-01

Using DNA markers in plant breeding with marker-assisted selection (MAS) could greatly improve the precision and efficiency of selection, leading to the accelerated development of new crop varieties. The numerous examples of MAS in rice have prompted many breeding institutes to establish molecular breeding labs. The last decade has produced an enormous amount of genomics research in rice, including the identification of thousands of QTLs for agronomically important traits, the generation of large amounts of gene expression data, and cloning and characterization of new genes, including the detection of single nucleotide polymorphisms. The pinnacle of genomics research has been the completion and annotation of genome sequences for indica and japonica rice. This information—coupled with the development of new genotyping methodologies and platforms, and the development of bioinformatics databases and software tools—provides even more exciting opportunities for rice molecular breeding in the 21st century. However, the great challenge for molecular breeders is to apply genomics data in actual breeding programs. Here, we review the current status of MAS in rice, current genomics projects and promising new genotyping methodologies, and evaluate the probable impact of genomics research. We also identify critical research areas to “bridge the application gap” between QTL identification and applied breeding that need to be addressed to realize the full potential of MAS, and propose ideas and guidelines for establishing rice molecular breeding labs in the postgenome sequence era to integrate molecular breeding within the context of overall rice breeding and research programs. PMID:18528527

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.

There is room for selection in a small local pig breed when using optimum contribution selection: a simulation study.

PubMed

Gourdine, J L; Sørensen, A C; Rydhmer, L

2012-01-01

Selection progress must be carefully balanced against the conservation of genetic variation in small populations of local breeds. Well-defined breeding programs with specified selection traits are rare in local pig breeds. Given the small population size, the focus is often on the management of genetic diversity. However, in local breeds, optimum contribution selection can be applied to control the rate of inbreeding and to avoid reduced performance in traits with high market value. The aim of this study was to assess the extent to which a breeding program aiming for improved product quality in a small local breed would be feasible. We used stochastic simulations to compare 25 scenarios. The scenarios differed in size of population, selection intensity of boars, type of selection (random selection, truncation selection based on BLUP breeding values, or optimum contribution selection based on BLUP breeding values), and heritability of the selection trait. It was assumed that the local breed is used in an extensive system for a high-meat-quality market. The simulations showed that in the smallest population (300 female reproducers), inbreeding increased by 0.8% when selection was performed at random. With optimum contribution selection, genetic progress can be achieved that is almost as great as that with truncation selection based on BLUP breeding values (0.2 to 0.5 vs. 0.3 to 0.5 genetic SD, P < 0.05), but at a considerably decreased rate of inbreeding (0.7 to 1.2 vs. 2.3 to 5.7%, P < 0.01). This confirmation of the potential utilization of OCS even in small populations is important in the context of sustainable management and the use of animal genetic resources.

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

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.

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.

Developing native Vaccinium crops and cultivars

USDA-ARS?s Scientific Manuscript database

Vaccinium species have long been harvested from the wild. Breeding and cultivar development, however, did not begin until about 1911 in New Jersey with efforts to commercially cultivate northern highbush blueberry (Vaccinium corymbosum). Cultivar development spread to cranberry (V. macrocarpon) and ...

Strategies for selecting and breeding EAB-resistant ash

Treesearch

Jennifer L. Koch; Kathleen Knight; Therese Poland; David W. Carey; Daniel A. Herms; Mary E. Mason

2011-01-01

Breeding for pest resistance in forest trees is a proven approach for managing both native and nonnative insects and diseases. A recent study by the Food and Agriculture Organization of the United Nations reports 255 forest tree breeding programs for insect or disease resistance in 33 diff erent countries (http://www.fao.org/forestry/26445/en/). Advantages to...

Toxoplasmosis in sand cats (Felis margarita) and other animals in the Breeding Centre for Endangered Arabian Wildlife in the United Arab Emirates

USDA-ARS?s Scientific Manuscript database

The Sand cat (Felis margarita) is a small-sized felid occurring in the United Arab Emirates (UAE). The Sand cat captive breeding program at the Breeding Centre for Endangered Arabian Wildlife (BCEAW), Sharjah, UAE, has experienced high newborn mortality rates, and congenital toxoplasmosis was recent...

Monitoring goals and programs of the U.S. Fish and Wildlife Service

Treesearch

John R. Sauer

1993-01-01

The United States Fish and Wildlife Service coordinates several surveys that collect information on the population status of migratory birds in North America. The North American Breeding Bird Survey is the primary source of population information on nongame birds during the breeding season, and waterfowl surveys are conducted during breeding and wintering seasons. The...

Maintenance of a high level of reproductive performance in the beef cow herd.

PubMed

Wiltbank, J N

1983-03-01

To insure a high consistent reproductive program in a cow herd, 90 to 95 per cent of the cows must calve early each year and wean a heavy calf. To accomplish this, the producer should follow these steps: 1. Feed heifers to reach a target weight consistent with their breed. 2. Breed heifers 45 days to a bull known to sire small calves (Longhorn or Jersey or a proven bull within a breed). Also consider cows with Brahman blood to decrease birth weight. 3. Use a 60-day breeding season in the cow herd. 4. Have cows in good to moderate body condition at calving time. 5. Have cows gaining weight three weeks before breeding and during the breeding season. 6. Remove calves for 48 hours at the start of the breeding season. 7. Breed to fertile bulls.

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.

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.

77 FR 25192 - Wild Bird Conservation Act; Receipt of Application for Approval of a Cooperative Breeding Program

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-27

... Conservation Act of 1992 (WBCA). DATES: Written data, comments, or requests for a copy of this application must... to the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Under...-FF09A30000] Wild Bird Conservation Act; Receipt of Application for Approval of a Cooperative Breeding Program...

Genetic diversity, population structure, and correlations between locally adapted zebu and taurine breeds in Brazil using SNP markers.

PubMed

Campos, Bárbara Machado; do Carmo, Adriana Santana; do Egito, Andrea Alves; da Mariante, Arthur Silva; do Albuquerque, Maria Socorro Muaés; de Gouveia, João José Simoni; Malhado, Carlos Henrique Mendes; Verardo, Lucas Lima; da Silva, Marcos Vinícius Gualberto Barbosa; Carneiro, Paulo Luiz Souza

2017-12-01

Genetic diversity is one of the most important issues in studies on conservation of cattle breeds and endangered species. The objective of this study was to estimate the levels of genetic differentiation between locally adapted taurine (Bos taurus taurus) and zebu (Bos taurus indicus) breeds in Brazil, which were genotyped for more than 777,000 SNPs. The fixation index (F ST ), principal component analysis (PCA), and Bayesian clustering were estimated. The F ST highlighted genetic differentiation between taurine and zebu breeds. The taurine lines, Caracu and Caracu Caldeano, had significant genetic differentiation (F ST close to 5%) despite their recent selection for different uses (meat and milk). This genetic variability can be used for conservation of locally adapted animals, as well as for breeding programs on zebu breeds. Introgression of zebu in locally adapted breeds was identified, especially in Curraleiro Pé-Duro breed. The Gyr breed, however, had low breed purity at genomic level due to its very heterogeneous mixing pattern.

Accurate genomic predictions for BCWD resistance in rainbow trout are achieved using low-density SNP panels: Evidence that long-range LD is a major contributing factor.

PubMed

Vallejo, Roger L; Silva, Rafael M O; Evenhuis, Jason P; Gao, Guangtu; Liu, Sixin; Parsons, James E; Martin, Kyle E; Wiens, Gregory D; Lourenco, Daniela A L; Leeds, Timothy D; Palti, Yniv

2018-06-05

Previously accurate genomic predictions for Bacterial cold water disease (BCWD) resistance in rainbow trout were obtained using a medium-density single nucleotide polymorphism (SNP) array. Here, the impact of lower-density SNP panels on the accuracy of genomic predictions was investigated in a commercial rainbow trout breeding population. Using progeny performance data, the accuracy of genomic breeding values (GEBV) using 35K, 10K, 3K, 1K, 500, 300 and 200 SNP panels as well as a panel with 70 quantitative trait loci (QTL)-flanking SNP was compared. The GEBVs were estimated using the Bayesian method BayesB, single-step GBLUP (ssGBLUP) and weighted ssGBLUP (wssGBLUP). The accuracy of GEBVs remained high despite the sharp reductions in SNP density, and even with 500 SNP accuracy was higher than the pedigree-based prediction (0.50-0.56 versus 0.36). Furthermore, the prediction accuracy with the 70 QTL-flanking SNP (0.65-0.72) was similar to the panel with 35K SNP (0.65-0.71). Genomewide linkage disequilibrium (LD) analysis revealed strong LD (r 2  ≥ 0.25) spanning on average over 1 Mb across the rainbow trout genome. This long-range LD likely contributed to the accurate genomic predictions with the low-density SNP panels. Population structure analysis supported the hypothesis that long-range LD in this population may be caused by admixture. Results suggest that lower-cost, low-density SNP panels can be used for implementing genomic selection for BCWD resistance in rainbow trout breeding programs. © 2018 The Authors. This article is a U.S. Government work and is in the public domain in the USA. Journal of Animal Breeding and Genetics published by Blackwell Verlag GmbH.

Development of Commercial Thermo-sensitive Genic Male Sterile Rice Accelerates Hybrid Rice Breeding Using the CRISPR/Cas9-mediated TMS5 Editing System.

PubMed

Zhou, Hai; He, Ming; Li, Jing; Chen, Liang; Huang, Zhifeng; Zheng, Shaoyan; Zhu, Liya; Ni, Erdong; Jiang, Dagang; Zhao, Bingran; Zhuang, Chuxiong

2016-11-22

Hybrid rice breeding offers an important strategy to improve rice production, in which the cultivation of a male sterile line is the key to the success of cross-breeding. CRISPR/Cas9 systems have been widely used in target-site genome editing, whereas their application for crop genetic improvement has been rarely reported. Here, using the CRISPR/Cas9 system, we induced specific mutations in TMS5, which is the most widely applied thermo-sensitive genic male sterility (TGMS) gene in China, and developed new "transgene clean" TGMS lines. We designed 10 target sites in the coding region of TMS5 for targeted mutagenesis using the CRISPR/Cas9 system and assessed the potential rates of on- and off-target effects. Finally, we established the most efficient construct, the TMS5ab construct, for breeding potentially applicable "transgene clean" TGMS lines. We also discussed factors that affect the editing efficiency according to the characteristics of different target sequences. Notably, using the TMS5ab construct, we developed 11 new "transgene clean" TGMS lines with potential applications in hybrid breeding within only one year in both rice subspecies. The application of our system not only significantly accelerates the breeding of sterile lines but also facilitates the exploitation of heterosis.

Breeding of fragrant cyclamen by interspecific hybridization and ion-beam irradiation.

PubMed

Ishizaka, Hiroshi

2018-01-01

Conventional breeding of cyclamen has relied on crossings among Cyclamen persicum cultivars without consideration of the scent of the flowers. Cyclamen purpurascens is a wild species with the most fragrant flowers in the genus Cyclamen. Allodiploid (2 n = 2 x = 41, AB) and allotriploid (2 n = 3 x = 65, AAB) plants have been produced from crosses of diploid and autotetraploid cultivars of C. persicum (2 n = 2 x = 48, AA; 4 x = 96, AAAA) × diploid wild C. purpurascens (2 n = 2 x = 34, BB) by embryo rescue, but are sterile. Fertile allotetraploid (2 n = 4 x = 82, AABB) plants have been produced by chromosome doubling of the sterile allodiploids in vitro . Autotetraploid C. purpurascens (2 n = 4 x = 68, BBBB) has been produced by chromosome doubling of diploid C. purpurascens , and other fertile allotetraploids (2 n = 4 x = 82, AABB) have been produced from crosses of autotetraploid cultivars of C. persicum × autotetraploid C. purpurascens by embryo rescue. Commercial cultivars of fragrant cyclamen have been bred by conventional crosses among the allotetraploids. Mutation breeding using ion-beam irradiation combined with plant tissue culture has resulted in fragrant cyclamens with novel flower colors and pigments. In contrast, allotriploids (AAB) have not been commercialized because of seed sterility and poor ornamental value. The flower colors are determined by anthocyanins and flavonol glycosides or chalcone glucoside, and the fragrances are determined by monoterpenes, sesquiterpenes, phenylpropanoids, or aliphatics. Techniques for the production of fragrant cyclamen and knowledge of flower pigments and volatiles will allow innovation in conventional cyclamen breeding.

Detecting signatures of selection within the Tibetan sheep mitochondrial genome.

PubMed

Niu, Lili; Chen, Xiaoyong; Xiao, Ping; Zhao, Qianjun; Zhou, Jingxuan; Hu, Jiangtao; Sun, Hongxin; Guo, Jiazhong; Li, Li; Wang, Linjie; Zhang, Hongping; Zhong, Tao

2017-11-01

Tibetan sheep, a Chinese indigenous breed, are mainly distributed in plateau and mountain-valley areas at a terrestrial elevation between 2260 and 4100 m. The herd is genetically distinct from the other domestic sheep and undergoes acclimatization to adapt to the hypoxic environment. To date, whether the mitochondrial DNA modification of Tibetan sheep shares the same feature as the other domestic breed remains unknown. In this study, we compared the whole mitogenome sequences from 32 Tibetan sheep, 22 domestic sheep and 24 commercial sheep to identify the selection signatures of hypoxic-tolerant in Tibetan sheep. Nucleotide diversity analysis using the sliding window method showed that the highest level of nucleotide diversity was observed in the control region with a peak value of π = 0.05215, while the lowest π value was detected in the tRNAs region. qPCR results showed that the relative mtDNA copy number in Tibetan sheep was significantly lower than that in Suffolk sheep. None of the mutations in 12S rRNA were fixed in Tibetan sheep, which indicated that there has been less artificial selection in this herd than the other domestic and commercial breeds. Although one site (1277G) might undergo the purifying selection, it was not identified as the breed-specific allele in Tibetan sheep. We proposed that nature selection was the main drive during the domestication of Tibetan sheep and single mutation (or locus) could not reveal the signature of selection as for the high diversity in the mitogenome of Tibetan sheep.

7 CFR 322.21 - Post-entry handling.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Regulations of the Department of Agriculture (Continued) ANIMAL AND PLANT HEALTH INSPECTION SERVICE... restricted organism must move by a bonded commercial carrier directly to a containment facility or apiary... or sterilizing restricted organisms and any breeding materials, pathogens, parasites, containers, or...

7 CFR 322.21 - Post-entry handling.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Regulations of the Department of Agriculture (Continued) ANIMAL AND PLANT HEALTH INSPECTION SERVICE... restricted organism must move by a bonded commercial carrier directly to a containment facility or apiary... or sterilizing restricted organisms and any breeding materials, pathogens, parasites, containers, or...

7 CFR 322.21 - Post-entry handling.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Regulations of the Department of Agriculture (Continued) ANIMAL AND PLANT HEALTH INSPECTION SERVICE... restricted organism must move by a bonded commercial carrier directly to a containment facility or apiary... or sterilizing restricted organisms and any breeding materials, pathogens, parasites, containers, or...

7 CFR 322.21 - Post-entry handling.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Regulations of the Department of Agriculture (Continued) ANIMAL AND PLANT HEALTH INSPECTION SERVICE... restricted organism must move by a bonded commercial carrier directly to a containment facility or apiary... or sterilizing restricted organisms and any breeding materials, pathogens, parasites, containers, or...

7 CFR 322.21 - Post-entry handling.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Regulations of the Department of Agriculture (Continued) ANIMAL AND PLANT HEALTH INSPECTION SERVICE... restricted organism must move by a bonded commercial carrier directly to a containment facility or apiary... or sterilizing restricted organisms and any breeding materials, pathogens, parasites, containers, or...

MEMS based digital transform spectrometers

NASA Astrophysics Data System (ADS)

Geller, Yariv; Ramani, Mouli

2005-09-01

Earlier this year, a new breed of Spectrometers based on Micro-Electro-Mechanical-System (MEMS) engines has been introduced to the commercial market. The use of these engines combined with transform mathematics, produces powerful spectrometers at unprecedented low cost in various spectral regions.

Research in forest genetics and tree breeding at the University of Wisconsin

Treesearch

D.T. Lester

1970-01-01

The genetics and breeding group in the Department of Forestry now has two faculty members and five graduate students. We are now a part of the Plant Breeding and Plant Genetics Group which includes six departments and twenty-six faculty members in an interdepartmental program of graduate teaching and research. Close cooperators are the Department of Plant Pathology at...

National Plant Genome Initiative

DTIC Science & Technology

2004-01-01

trials have also identified new objectives for vegetable breeding programs, expedited by knowledge and tools from crop genomics and farmer demand...The same tools and resources are being applied to develop improved crops and new breeding strategies, as well. With the sequencing of the rice genome...marker-assisted breeding strategies for wheat • Establishment of a comparative cereal genomics database, Gramene, which uses the complete rice

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...

Improved charge breeding efficiency of light ions with an electron cyclotron resonance ion source

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

Vondrasek, R.; Kutsaev, Sergey; Delahaye, P.

2012-11-15

The Californium Rare Isotope Breeder Upgrade is a new radioactive beam facility for the Argonne Tandem Linac Accelerator System (ATLAS). The facility utilizes a {sup 252}Cf fission source coupled with an electron cyclotron resonance ion source to provide radioactive beam species for the ATLAS experimental program. The californium fission fragment distribution provides nuclei in the mid-mass range which are difficult to extract from production targets using the isotope separation on line technique and are not well populated by low-energy fission of uranium. To date the charge breeding program has focused on optimizing these mid-mass beams, achieving high charge breeding efficienciesmore » of both gaseous and solid species including 14.7% for the radioactive species {sup 143}Ba{sup 27+}. In an effort to better understand the charge breeding mechanism, we have recently focused on the low-mass species sodium and potassium which up to present have been difficult to charge breed efficiently. Unprecedented charge breeding efficiencies of 10.1% for {sup 23}Na{sup 7+} and 17.9% for {sup 39}K{sup 10+} were obtained injecting stable Na{sup +} and K{sup +} beams from a surface ionization source.« less

Improved charge breeding efficiency of light ions with an electron cyclotron resonance ion source

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

Vondrasek, R.; Delahaye, P.; Kutsaev, Sergey

2012-11-01

The Californium Rare Isotope Breeder Upgrade is a new radioactive beam facility for the Argonne Tandem Linac Accelerator System (ATLAS). The facility utilizes a 252Cf fission source coupled with an electron cyclotron resonance ion source to provide radioactive beam species for the ATLAS experimental program. The californium fission fragment distribution provides nuclei in the mid-mass range which are difficult to extract from production targets using the isotope separation on line technique and are not well populated by low-energy fission of uranium. To date the charge breeding program has focused on optimizing these mid-mass beams, achieving high charge breeding efficiencies ofmore » both gaseous and solid species including 14.7% for the radioactive species 143Ba27+. In an effort to better understand the charge breeding mechanism, we have recently focused on the low-mass species sodium and potassium which up to present have been difficult to charge breed efficiently. Unprecedented charge breeding efficiencies of 10.1% for 23Na7+ and 17.9% for 39K10+ were obtained injecting stable Na+ and K+ beams from a surface ionization source.« less

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.

Genome-wide scan reveals LEMD3 and WIF1 on SSC5 as the candidates for porcine ear size.

PubMed

Zhang, Longchao; Liang, Jing; Luo, Weizhen; Liu, Xin; Yan, Hua; Zhao, Kebin; Shi, Huibi; Zhang, Yuebo; Wang, Ligang; Wang, Lixian

2014-01-01

The quantitative trait loci (QTL) for porcine ear size was previously reported to mainly focus on SSC5 and SSC7. Recently, a missense mutation, G32E, in PPARD in the QTL interval on SSC7 was identified as the causative mutation for ear size. However, on account of the large interval of QTL, the responsible gene on SSC5 has not been identified. In this study, an intercross population was constructed from the large-eared Minzhu, an indigenous Chinese pig breed, and the Western commercial Large White pig to examine the genetic basis of ear size diversity. A GWAS was performed to detect SNPs significantly associated with ear size. Thirty-five significant SNPs defined a 10.78-Mb (30.14-40.92 Mb) region on SSC5. Further, combining linkage disequilibrium and haplotype sharing analysis, a reduced region of 3.07-Mb was obtained. Finally, by using a selective sweep analysis, a critical region of about 450-kb interval containing two annotated genes LEMD3 and WIF1 was refined in this work. Functional analysis indicated that both represent biological candidates for porcine ear size, with potential application in breeding programs. The two genes could also be used as novel references for further study of the mechanism underlying human microtia.

Signatures of positive selection in East African Shorthorn Zebu: A genome-wide single nucleotide polymorphism analysis

PubMed Central

Bahbahani, Hussain; Clifford, Harry; Wragg, David; Mbole-Kariuki, Mary N; Van Tassell, Curtis; Sonstegard, Tad; Woolhouse, Mark; Hanotte, Olivier

2015-01-01

The small East African Shorthorn Zebu (EASZ) is the main indigenous cattle across East Africa. A recent genome wide SNP analysis revealed an ancient stable African taurine x Asian zebu admixture. Here, we assess the presence of candidate signatures of positive selection in their genome, with the aim to provide qualitative insights about the corresponding selective pressures. Four hundred and twenty-five EASZ and four reference populations (Holstein-Friesian, Jersey, N’Dama and Nellore) were analysed using 46,171 SNPs covering all autosomes and the X chromosome. Following FST and two extended haplotype homozygosity-based (iHS and Rsb) analyses 24 candidate genome regions within 14 autosomes and the X chromosome were revealed, in which 18 and 4 were previously identified in tropical-adapted and commercial breeds, respectively. These regions overlap with 340 bovine QTL. They include 409 annotated genes, in which 37 were considered as candidates. These genes are involved in various biological pathways (e.g. immunity, reproduction, development and heat tolerance). Our results support that different selection pressures (e.g. environmental constraints, human selection, genome admixture constrains) have shaped the genome of EASZ. We argue that these candidate regions represent genome landmarks to be maintained in breeding programs aiming to improve sustainable livestock productivity in the tropics. PMID:26130263

Comparison of growth performance, carcass components, and meat quality between Mos rooster (Galician indigenous breed) and Sasso T-44 line slaughtered at 10 months.

PubMed

Franco, D; Rois, D; Vázquez, J A; Lorenzo, J M

2012-05-01

The aim of this research was to make a full study of the meat from Mos-breed roosters (Spanish indigenous chicken). To achieve this purpose, the type of breed (Mos vs. a hybrid line, Sasso T-44) and the effect of finishing treatment in the last month (corn vs. commercial fodder) on growth performance, carcass and meat quality (physicochemical and textural traits), fatty and amino acid profile, and sensorial description were studied. The finishing feeding effect did not modify the growth, but the differences between genotypes were statistically significant (P < 0.05), in where Sasso T-44 was the genotype that generated the best growths and associated parameters. With regard to carcass characteristics, no significant influences of finishing feeding treatment (P > 0.05) were found, and carcass weight clearly differed between genotypes due to the lower growth rate of Mos roosters. Drumstick, thigh, and wing percentages were greater in Mos breed than in Sasso T-44 birds, whereas breast (15.2%), that is the most highly valued piece of the chicken, was similar for both genotypes. Significant differences in pH, protein, and ash content between genotypes have been found, whereas finishing feeding treatment had an effect on myoglobin and redness index (P < 0.01), showing meat from roosters fed with corn had a higher luminosity. Despite the fact of the slaughtered age of birds, values of shear force were slightly higher than 2 kg (2.11 kg) for both genotypes, thus it can be classified as very tender meat. Mos breed showed a higher percentage of polyunsaturated fatty acids (25.90 vs. 22.74; P < 0.001) and a lower percentage of monounsaturated fatty acids (35.14 vs. 38.95; P < 0.001) than Sasso T-44 chicken muscles. Surprisingly, birds finishing with the corn diet (2 times higher in linolenic acid than fodder) did not increase their polyunsaturated fatty acid level in the breast, obtaining in the Mos breed a polyunsaturated to saturated fatty acid ratio of 0.69. The amino acid profile of the indigenous-breed breast was not similar to that of the commercial-strain breast; besides, finishing feeding treatment had more of an effect on amino acid profile, affecting the majority of amino acids, with the exception of phenylalanine and threonine.

Volatile Compound Profiling by HS-SPME/GC-MS-FID of a Core Olive Cultivar Collection as a Tool for Aroma Improvement of Virgin Olive Oil.

PubMed

García-Vico, Lourdes; Belaj, Angjelina; Sánchez-Ortiz, Araceli; Martínez-Rivas, José M; Pérez, Ana G; Sanz, Carlos

2017-01-14

Virgin olive oil (VOO) is the only food product requiring official sensory analysis to be classified in commercial categories, in which the evaluation of the aroma plays a very important role. The selection of parents, with the aim of obtaining new cultivars with improved oil aroma, is of paramount importance in olive breeding programs. We have assessed the volatile fraction by headspace-solid-phase microextraction/gas chromatography-mass spectrometry-flame ionization detection (HS-SPME/GC-MS-FID) and the deduced aroma properties of VOO from a core set of olive cultivars (Core-36) which possesses most of the genetic diversity found in the World Olive Germplasm Collection (IFAPA Alameda del Obispo) located in Cordoba, Spain. The VOO volatile fractions of Core-36 cultivars display a high level of variability. It is mostly made of compounds produced from polyunsaturated fatty acids through the lipoxygenase pathway, which confirms to be a general characteristic of the olive species ( Olea europaea L.). The main group of volatile compounds in the oils was six straight-chain carbon compounds derived from linolenic acid, some of them being the main contributors to the aroma of the olive oils according to their odor activity values (OAV). The high level of variability found for the volatile fraction of the oils from Core-36 and, therefore, for the aroma odor notes, suggest that this core set may be a very useful tool for the choice of optimal parents in olive breeding programs in order to raise new cultivars with improved VOO aroma.

Variability among Capsicum baccatum accessions from Goiás, Brazil, assessed by morphological traits and molecular markers.

PubMed

Martinez, A L A; Araújo, J S P; Ragassi, C F; Buso, G S C; Reifschneider, F J B

2017-07-06

Capsicum peppers are native to the Americas, with Brazil being a significant diversity center. Capsicum baccatum accessions at Instituto Federal (IF) Goiano represent a portion of the species genetic resources from central Brazil. We aimed to characterize a C. baccatum working collection comprising 27 accessions and 3 commercial cultivars using morphological traits and molecular markers to describe its genetic and morphological variability and verify the occurrence of duplicates. This set included 1 C. baccatum var. praetermissum and 29 C. baccatum var. pendulum with potential for use in breeding programs. Twenty-two morphological descriptors, 57 inter-simple sequence repeat, and 34 random amplified polymorphic DNA markers were used. Genetic distance was calculated through the Jaccard similarity index and genetic variability through cluster analysis using the unweighted pair group method with arithmetic mean, resulting in dendrograms for both morphological analysis and molecular analysis. Genetic variability was found among C. baccatum var. pendulum accessions, and the distinction between the two C. baccatum varieties was evident in both the morphological and molecular analyses. The 29 C. baccatum var. pendulum genotypes clustered in four groups according to fruit type in the morphological analysis. They formed seven groups in the molecular analysis, without a clear correspondence with morphology. No duplicates were found. The results describe the genetic and morphological variability, provide a detailed characterization of genotypes, and discard the possibility of duplicates within the IF Goiano C. baccatum L. collection. This study will foment the use of this germplasm collection in C. baccatum breeding programs.

Comprehensive genotyping of the USA national maize inbred seed bank

PubMed Central

2013-01-01

Background Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world. Results The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits. Conclusions The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity. PMID:23759205

Comprehensive genotyping of the USA national maize inbred seed bank.

PubMed

Romay, Maria C; Millard, Mark J; Glaubitz, Jeffrey C; Peiffer, Jason A; Swarts, Kelly L; Casstevens, Terry M; Elshire, Robert J; Acharya, Charlotte B; Mitchell, Sharon E; Flint-Garcia, Sherry A; McMullen, Michael D; Holland, James B; Buckler, Edward S; Gardner, Candice A

2013-06-11

Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world. The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits. The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity.

Application of DNA fingerprinting to the recovery program of the endangered Puerto Rican parrot

USGS Publications Warehouse

Brock, M.K.; White, B.N.

1992-01-01

The Puerto Rican parrot was reduced to 13 animals in 1975 and as a conservation measure, a captive population was established from a few founders taken from the wild between 1973 and 1983. The number of successful breeding pairs in captivity has been !ow, and the captive breeding program has not been as productive as that of the closely related Hispaniolan parrot. Therefore, a genetic study was initiated to examine the relative levels of relatedness of the captive founders using levels of bandsharing in DNA fingerprints. Unrelated captive founder Puerto Rican parrots had the same average level of bandsharing (0.41) as second-degree relatives of the Hispaniolan parrot (0.38, P > 0,05), with an inbreeding coefficient of 0.04. High levels of bandsharing (>40%) between pairs of males and females correlated with reproductive failure, suggesting that inbreeding depression is partly responsible for the !ow number of' breeding pairs. Consequently, DNA profiling can be used to guide the captive breeding program for the Puerto Rican parrot, and other endangered species, by identifying pairs of males and females with low levels of bandsharing.

The Program for Regional and International Shorebird Monitoring (PRISM)

USGS Publications Warehouse

Bart, J.; Andres, B.; Brown, S.; Donaldson, G.; Harrington, B.; Johnston, V.; Jones, S.; Morrison, R.I.G.; Skagen, S.K.

2005-01-01

This report describes the "Program for Regional and International Shorebird Monitoring" (PRISM). PRISM is being implemented by a Canada-United States Shorebird Monitoring and Assessment Committee formed in 2001 by the Canadian Shorebird Working Group and the U.S. Shorebird Council. PRISM provides a single blueprint for implementing the shorebird conservation plans recently completed in Canada and the United States. The goals of PRISM are to (1) estimate the size of breeding population of 74 shorebird taxa in North America; (2) describe the distribution, abundance, and habitat relationships for each of these taxa; (3) monitor trends in shorebird population size; (4) monitor shorebird numbers at stopover locations, and; (5) assist local managers in meeting their shorebird conservation goals. PRISM has four main components: arctic and boreal breeding surveys, temperate breeding surveys, temperate non-breeding surveys, and neotropical surveys. Progress on, and action items for, each major component are described. The more important major tasks for immediate action are carrying out the northern surveys, conducting regional analyses to design the program of migration counts, and evaluating aerial photographic surveys for migration and winter counts.

Broadening the U.S. alfalfa germplasm base

USDA-ARS?s Scientific Manuscript database

Over 4000 alfalfa (Medicago sativa L.) plant introductions (PIs) exist in the USDA-ARS National Plant Germplasm System (NPGS). NAAIC has discussed/proposed pre-breeding efforts to utilize this germplasm for creating pre-commercial alfalfa germplasm. Funding constraints have been one impediment to th...

9 CFR 93.100 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

...), other than poultry. Commercial birds. Birds which are imported for resale, breeding, public display, or... Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE...: Administrator. The Administrator of the Animal and Plant Health Inspection Service or any other employee of the...

9 CFR 93.100 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

...), other than poultry. Commercial birds. Birds which are imported for resale, breeding, public display, or... Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE...: Administrator. The Administrator of the Animal and Plant Health Inspection Service or any other employee of the...

7 CFR 1951.854 - Ineligible assistance purposes.

Code of Federal Regulations, 2014 CFR

2014-01-01

... raising, housing, feeding, breeding, hatching, control and/or management of farm and domestic animals). Exceptions to this definition are: (i) Aquaculture as identified under eligible purposes. (ii) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1951.854 - Ineligible assistance purposes.

Code of Federal Regulations, 2013 CFR

2013-01-01

... raising, housing, feeding, breeding, hatching, control and/or management of farm and domestic animals). Exceptions to this definition are: (i) Aquaculture as identified under eligible purposes. (ii) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

19 CFR 10.1013 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-04-01

... material for commercial purposes and the properties of which are essentially identical to such other good... both of the Parties” means: (1) Plants and plant products grown, and harvested or gathered, in the..., breeding, raising, trapping, hunting, manufacturing, processing, assembling, or disassembling a good; (p...

19 CFR 10.1013 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-04-01

... material for commercial purposes and the properties of which are essentially identical to such other good... both of the Parties” means: (1) Plants and plant products grown, and harvested or gathered, in the..., breeding, raising, trapping, hunting, manufacturing, processing, assembling, or disassembling a good; (p...

40 CFR 158.2240 - Nontarget organisms.

Code of Federal Regulations, 2014 CFR

2014-07-01

... equipment. (iii) Commercial, institutional and industrial premises and equipment. (iv) Residential and... products, especially preceding or during the breeding season. ii. The pesticide or any of its major... products are stored or accumulated in plant or animal tissues, as indicated by the octanol/water partition...

7 CFR 1951.854 - Ineligible assistance purposes.

Code of Federal Regulations, 2011 CFR

2011-01-01

... raising, housing, feeding, breeding, hatching, control and/or management of farm and domestic animals). Exceptions to this definition are: (i) Aquaculture as identified under eligible purposes. (ii) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

7 CFR 1951.854 - Ineligible assistance purposes.

Code of Federal Regulations, 2012 CFR

2012-01-01

... raising, housing, feeding, breeding, hatching, control and/or management of farm and domestic animals). Exceptions to this definition are: (i) Aquaculture as identified under eligible purposes. (ii) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

9 CFR 79.3 - General restrictions.

Code of Federal Regulations, 2013 CFR

2013-01-01

....3 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE... INCONSISTENT state Moved from CONSISTENT state (a) Sale or other movement of breeding animals, show animals or... must have official individual animal identification. (7) Low-risk commercial sheep Official individual...

9 CFR 79.3 - General restrictions.

Code of Federal Regulations, 2010 CFR

2010-01-01

....3 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE... INCONSISTENT state Moved from CONSISTENT state (a) Sale or other movement of breeding animals, show animals or... must have official individual animal identification. (7) Low-risk commercial sheep Official individual...

9 CFR 93.100 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

...), other than poultry. Commercial birds. Birds which are imported for resale, breeding, public display, or... Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE...: Administrator. The Administrator of the Animal and Plant Health Inspection Service or any other employee of the...

7 CFR 1951.854 - Ineligible assistance purposes.

Code of Federal Regulations, 2010 CFR

2010-01-01

... raising, housing, feeding, breeding, hatching, control and/or management of farm and domestic animals). Exceptions to this definition are: (i) Aquaculture as identified under eligible purposes. (ii) Commercial nurseries primarily engaged in the production of ornamental plants and trees and other nursery products such...

76 FR 70107 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-10

... commercial breeding establishments in Sinaloa and Sonora; (2) derived from poultry that were slaughtered in... number. Animal & Plant Health Inspection Service Title: Importation of Poultry Meat and Other Poultry... and Plant Health Inspection Service (APHIS), is responsible for administering regulations intended to...

9 CFR 93.100 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

...), other than poultry. Commercial birds. Birds which are imported for resale, breeding, public display, or... Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE...: Administrator. The Administrator of the Animal and Plant Health Inspection Service or any other employee of the...

9 CFR 93.100 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

...), other than poultry. Commercial birds. Birds which are imported for resale, breeding, public display, or... Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE...: Administrator. The Administrator of the Animal and Plant Health Inspection Service or any other employee of the...

9 CFR 79.3 - General restrictions.

Code of Federal Regulations, 2012 CFR

2012-01-01

....3 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE... INCONSISTENT state Moved from CONSISTENT state (a) Sale or other movement of breeding animals, show animals or... must have official individual animal identification. (7) Low-risk commercial sheep Official individual...

40 CFR 158.2240 - Nontarget organisms.

Code of Federal Regulations, 2013 CFR

2013-07-01

... equipment. (iii) Commercial, institutional and industrial premises and equipment. (iv) Residential and... products, especially preceding or during the breeding season. ii. The pesticide or any of its major... products are stored or accumulated in plant or animal tissues, as indicated by the octanol/water partition...

9 CFR 79.3 - General restrictions.

Code of Federal Regulations, 2014 CFR

2014-01-01

....3 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE... INCONSISTENT state Moved from CONSISTENT state (a) Sale or other movement of breeding animals, show animals or... must have official individual animal identification. (7) Low-risk commercial sheep Official individual...

19 CFR 10.1013 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-04-01

... material for commercial purposes and the properties of which are essentially identical to such other good... both of the Parties” means: (1) Plants and plant products grown, and harvested or gathered, in the..., breeding, raising, trapping, hunting, manufacturing, processing, assembling, or disassembling a good; (p...

9 CFR 79.3 - General restrictions.

Code of Federal Regulations, 2011 CFR

2011-01-01

....3 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE... INCONSISTENT state Moved from CONSISTENT state (a) Sale or other movement of breeding animals, show animals or... must have official individual animal identification. (7) Low-risk commercial sheep Official individual...

Uniform peanut performance test 2017

USDA-ARS?s Scientific Manuscript database

The Uniform Peanut Performance Tests (UPPT) are designed to evaluate the commercial potential of advanced breeding peanut lines not formally released. The tests are performed in ten locations across the peanut production belt. In this study, 2 controls and 14 entries were evaluated at 8 locations....

Limits to captive breeding of mammals in zoos.

PubMed

Alroy, John

2015-06-01

Captive breeding of mammals in zoos is the last hope for many of the best-known endangered species and has succeeded in saving some from certain extinction. However, the number of managed species selected is relatively small and focused on large-bodied, charismatic mammals that are not necessarily under strong threat and not always good candidates for reintroduction into the wild. Two interrelated and more fundamental questions go unanswered: have the major breeding programs succeeded at the basic level of maintaining and expanding populations, and is there room to expand them? I used published counts of births and deaths from 1970 to 2011 to quantify rates of growth of 118 captive-bred mammalian populations. These rates did not vary with body mass, contrary to strong predictions made in the ecological literature. Most of the larger managed mammalian populations expanded consistently and very few programs failed. However, growth rates have declined dramatically. The decline was predicted by changes in the ratio of the number of individuals within programs to the number of mammal populations held in major zoos. Rates decreased as the ratio of individuals in programs to populations increased. In other words, most of the programs that could exist already do exist. It therefore appears that debates over the general need for captive-breeding programs and the best selection of species are moot. Only a concerted effort could create room to manage a substantially larger number of endangered mammals. © 2015, Society for Conservation Biology.

Can Non-Beak Treated Hens be Kept in Commercial Furnished Cages? Exploring the Effects of Strain and Extra Environmental Enrichment on Behaviour, Feather Cover, and Mortality

PubMed Central

Morrissey, Krysta L. H.; Brocklehurst, Sarah; Baker, Laurence; Widowski, Tina M.; Sandilands, Victoria

2016-01-01

Commercial laying hens are prone to injurious pecking (IP), a common multifactorial problem. A 2 × 2 × 2 factorial design assessed the effects of breed (Lohmann Brown Classic (L) or Hyline Brown (H)), beak treatment (infra-red treated (T) or not (NT)), and environment (extra enrichment (EE) or no extra enrichment (NE)) on mortality, behaviour, feather cover, and beak shape. Hens were allocated to treatments at 16 weeks of age and data were collected every four weeks from age 19 to 71 weeks. Data were analysed in Genstat using mixed models. L hens had higher all and IP-related mortality than H hens (p < 0.003), whilst NT hens had higher mortality than T hens but only due to culling of whole cages (p < 0.001). Feather cover for L hens deteriorated more quickly with age at most body sites than H hens (age × breed × body site p < 0.001). For NT hens, feather cover was worse at most body sites (beak treatment × body site p < 0.001), and worsened more quickly with age (age × beak treatment p = 0.014) than T hens. L and NE hens performed more bird-to-bird pecking than H and EE hens, respectively (breed p = 0.015, enrichment p = 0.032). More damage to mats and ropes was caused by L and NT hens than by H and T hens, respectively (age × breed p < 0.005, beak treatment p < 0.001). Though H hens had fewer mortalities and better feather cover, breed effects may have been influenced by farm management practices, as they may have been better suited to H than L hens. Though EE hens performed less bird-to-bird pecking, the enrichments were less effective at reducing feather cover damage and mortality than expected. PMID:26927190

Can Non-Beak Treated Hens be Kept in Commercial Furnished Cages? Exploring the Effects of Strain and Extra Environmental Enrichment on Behaviour, Feather Cover, and Mortality.

PubMed

Morrissey, Krysta L H; Brocklehurst, Sarah; Baker, Laurence; Widowski, Tina M; Sandilands, Victoria

2016-02-25

Commercial laying hens are prone to injurious pecking (IP), a common multifactorial problem. A 2 × 2 × 2 factorial design assessed the effects of breed (Lohmann Brown Classic (L) or Hyline Brown (H)), beak treatment (infra-red treated (T) or not (NT)), and environment (extra enrichment (EE) or no extra enrichment (NE)) on mortality, behaviour, feather cover, and beak shape. Hens were allocated to treatments at 16 weeks of age and data were collected every four weeks from age 19 to 71 weeks. Data were analysed in Genstat using mixed models. L hens had higher all and IP-related mortality than H hens (p < 0.003), whilst NT hens had higher mortality than T hens but only due to culling of whole cages (p < 0.001). Feather cover for L hens deteriorated more quickly with age at most body sites than H hens (age × breed × body site p < 0.001). For NT hens, feather cover was worse at most body sites (beak treatment × body site p < 0.001), and worsened more quickly with age (age × beak treatment p = 0.014) than T hens. L and NE hens performed more bird-to-bird pecking than H and EE hens, respectively (breed p = 0.015, enrichment p = 0.032). More damage to mats and ropes was caused by L and NT hens than by H and T hens, respectively (age × breed p < 0.005, beak treatment p < 0.001). Though H hens had fewer mortalities and better feather cover, breed effects may have been influenced by farm management practices, as they may have been better suited to H than L hens. Though EE hens performed less bird-to-bird pecking, the enrichments were less effective at reducing feather cover damage and mortality than expected.

Objectives, criteria and methods for using molecular genetic data in priority setting for conservation of animal genetic resources.

PubMed

Boettcher, P J; Tixier-Boichard, M; Toro, M A; Simianer, H; Eding, H; Gandini, G; Joost, S; Garcia, D; Colli, L; Ajmone-Marsan, P

2010-05-01

The genetic diversity of the world's livestock populations is decreasing, both within and across breeds. A wide variety of factors has contributed to the loss, replacement or genetic dilution of many local breeds. Genetic variability within the more common commercial breeds has been greatly decreased by selectively intense breeding programmes. Conservation of livestock genetic variability is thus important, especially when considering possible future changes in production environments. The world has more than 7500 livestock breeds and conservation of all of them is not feasible. Therefore, prioritization is needed. The objective of this article is to review the state of the art in approaches for prioritization of breeds for conservation, particularly those approaches that consider molecular genetic information, and to identify any shortcomings that may restrict their application. The Weitzman method was among the first and most well-known approaches for utilization of molecular genetic information in conservation prioritization. This approach balances diversity and extinction probability to yield an objective measure of conservation potential. However, this approach was designed for decision making across species and measures diversity as distinctiveness. For livestock, prioritization will most commonly be performed among breeds within species, so alternatives that measure diversity as co-ancestry (i.e. also within-breed variability) have been proposed. Although these methods are technically sound, their application has generally been limited to research studies; most existing conservation programmes have effectively primarily based decisions on extinction risk. The development of user-friendly software incorporating these approaches may increase their rate of utilization.

Genetic Distinctiveness of the Herdwick Sheep Breed and Two Other Locally Adapted Hill Breeds of the UK

PubMed Central

Bowles, Dianna; Carson, Amanda; Isaac, Peter

2014-01-01

There is considerable interest in locally adapted breeds of livestock as reservoirs of genetic diversity that may provide important fitness traits for future use in agriculture. In marginal areas, these animals contribute to food security and extract value from land unsuitable for other systems of farming. In England, close to 50% of the national sheep flock is farmed on grassland designated as disadvantaged areas for agricultural production. Many of these areas are in the uplands, where some native breeds of sheep continue to be commercially farmed only in highly localised geographical regions to which they are adapted. This study focuses on three of these breeds, selected for their adaptation to near identical environments and their geographical concentration in regions close to one another. Our objective has been to use retrotyping, microsatellites and single nucleotide polymorphisms to explore the origins of the breeds and whether, despite their similar adaptations and proximity, they are genetically distinctive. We find the three breeds each have a surprisingly different pattern of retrovirus insertions into their genomes compared with one another and with other UK breeds. Uniquely, there is a high incidence of the R0 retrotype in the Herdwick population, characteristic of a primitive genome found previously in very few breeds worldwide and none in the UK mainland. The Herdwick and Rough Fells carry two rare retroviral insertion events, common only in Texels, suggesting sheep populations in the northern uplands have a historical association with the original pin-tail sheep of Texel Island. Microsatellite data and analyses of SNPs associated with RXFP2 (horn traits) and PRLR (reproductive performance traits) also distinguished the three breeds. Significantly, an SNP linked to TMEM154, a locus controlling susceptibility to infection by Maedi-Visna, indicated that all three native hill breeds have a lower than average risk of infection to the lentivirus. PMID:24489968

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.

Genetic diversity of Guangxi chicken breeds assessed with microsatellites and the mitochondrial DNA D-loop region.

PubMed

Liao, Yuying; Mo, Guodong; Sun, Junli; Wei, Fengying; Liao, Dezhong Joshua

2016-05-01

The domestic chicken (Gallus gallus domesticus) is an excellent model for genetic studies of phenotypic diversity. The Guangxi Region of China possesses several native chicken breeds displaying a broad range of phenotypes well adapted to the extreme hot-and-wet environments in the region. We thus evaluated the genetic diversity and relationships among six native chicken populations of the Guangxi region and also evaluated two commercial breeds (Arbor Acres and Roman chickens). We analyzed the sequences of the D-loop region of the mitochondrial DNA (mtDNA) and 18 microsatellite loci of 280 blood samples from six Guangxi native chicken breeds and from Arbor Acres and Roman chickens, and used the neighbor-joining method to construct the phylogenetic tree of these eight breeds. Our results showed that the genetic diversity of Guangxi native breeds was relatively rich. The phylogenetic tree using the unweighed pair-group method with arithmetic means (UPGAM) on microsatellite marks revealed two main clusters. Arbor Acres chicken and Roman chicken were in one cluster, while the Guangxi breeds were in the other cluster. Moreover, the UPGAM tree of Guangxi native breeds based on microsatellite loci was more consistent with the genesis, breeding history, differentiation and location than the mtDNA D-loop region. STRUCTURE analysis further confirmed the genetic structure of Guangxi native breeds in the Neighbor-Net dendrogram. The nomenclature of mtDNA sequence polymorphisms suggests that the Guangxi native chickens are distributed across four clades, but most of them are clustered in two main clades (B and E), with the other haplotypes within the clades A and C. The Guangxi native breeds revealed abundant genetic diversity not only on microsatellite loci but also on mtDNA D-loop region, and contained multiple maternal lineages, including one from China and another from Europe or the Middle East.

Pflanzliche Zellkulturtechniken als Züchtungsschritt am Beispiel Raps

NASA Astrophysics Data System (ADS)

Hoffmann, Franz

1980-06-01

A supplementation of classical plant breeding is now necessary due to the limitations imposed by available genetic variability and the slowness of the method. Therefore, cell culture techniques could play an important role in the future. Using rape seed, in which plants derived from anther culture and in vitro mutagenesis are already field tested, it has been shown that, in this case, somatic genetics is very close to becoming a practical method. For most of the other crop plants, in particular the cereals, no such unconventional breeding techniques have yet been satisfactorily established for commercial use.

Design of an F1 hybrid breeding strategy for ryegrasses based on selection of self-incompatibility locus-specific alleles

PubMed Central

Pembleton, Luke W.; Shinozuka, Hiroshi; Wang, Junping; Spangenberg, German C.; Forster, John W.; Cogan, Noel O. I.

2015-01-01

Relatively modest levels of genetic gain have been achieved in conventional ryegrass breeding when compared to cereal crops such as maize, current estimates indicating an annual improvement of 0.25–0.6% in dry matter production. This property is partially due to an inability to effectively exploit heterosis through the formation of F1 hybrids. Controlled crossing of ryegrass lines from geographically distant origins has demonstrated the occurrence of heterosis, which can result in increases of dry matter production in the order of 25%. Although capture of hybrid vigor offers obvious advantages for ryegrass cultivar production, to date there have been no effective and commercially suitable methods for obtaining high proportions of F1 hybrid seed. Continued advances in fine-scale genetic and physical mapping of the gametophytic self-incompatibility (SI) loci (S and Z) of ryegrasses are likely in the near future to permit the identification of closely linked genetic markers that define locus-specific haplotypes, allowing prediction of allelic variants and hence compatibility between different plant genotypes. Given the availability of such information, a strategy for efficient generation of ryegrass cultivars with a high proportion of F1 hybrid individuals has been simulated, which is suitable for commercial implementation. Through development of two parental pools with restricted diversity at the SI loci, relative crossing compatibility between pools is increased. Based on simulation of various levels of SI allele diversity restriction, the most effective scheme will generate 83.33% F1 hybrids. Results from the study, including the impact of varying flowering time, are discussed along with a proposed breeding design for commercial application. PMID:26442077

Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F1 hybrids of tomato.

PubMed

Ohyama, Akio; Shirasawa, Kenta; Matsunaga, Hiroshi; Negoro, Satomi; Miyatake, Koji; Yamaguchi, Hirotaka; Nunome, Tsukasa; Iwata, Hiroyoshi; Fukuoka, Hiroyuki; Hayashi, Takeshi

2017-08-01

Using newly developed euchromatin-derived genomic SSR markers and a flexible Bayesian mapping method, 13 significant agricultural QTLs were identified in a segregating population derived from a four-way cross of tomato. So far, many QTL mapping studies in tomato have been performed for progeny obtained from crosses between two genetically distant parents, e.g., domesticated tomatoes and wild relatives. However, QTL information of quantitative traits related to yield (e.g., flower or fruit number, and total or average weight of fruits) in such intercross populations would be of limited use for breeding commercial tomato cultivars because individuals in the populations have specific genetic backgrounds underlying extremely different phenotypes between the parents such as large fruit in domesticated tomatoes and small fruit in wild relatives, which may not be reflective of the genetic variation in tomato breeding populations. In this study, we constructed F 2 population derived from a cross between two commercial F 1 cultivars in tomato to extract QTL information practical for tomato breeding. This cross corresponded to a four-way cross, because the four parental lines of the two F 1 cultivars were considered to be the founders. We developed 2510 new expressed sequence tag (EST)-based (euchromatin-derived) genomic SSR markers and selected 262 markers from these new SSR markers and publicly available SSR markers to construct a linkage map. QTL analysis for ten agricultural traits of tomato was performed based on the phenotypes and marker genotypes of F 2 plants using a flexible Bayesian method. As results, 13 QTL regions were detected for six traits by the Bayesian method developed in this study.

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.

An attempt to eradicate Herpesvirus simiae from a rhesus monkey breeding colony.

PubMed

Sauber, J J; Fanton, J W; Harvey, R C; Golden, J G

1992-10-01

In the fall of 1987 an attempt to establish a Herpesvirus simiae (B-virus)-negative rhesus monkey (Macaca mulatta) breeding colony was initiated at the Armstrong Laboratory. A serologic testing program was used to identify all monkeys into groups that were either positive or negative to B-virus based on serologic tests. Segregation of the groups allowed the creation of breeding harems that were exclusively seropositive or -negative to B-virus. Animals that were serologically positive were kept in breeding to maintain infant production levels not unlike those previous to segregation. Decreasing numbers of animals converted to a positive status during the first three serum tests for B-virus in the program. During 1990, an increase in the number of monkeys converting to positive status and the discovery of an indeterminate status demonstrated that latency of B-virus in the rhesus may have the potential to defeat an eradication attempt not conscientiously pursued.

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.

[Breeding of new varieties "zhongchai no. 2" and "zhongchai no. 3" of Bupleurum chinense].

PubMed

Zheng, Tingting; Sui, Chun; Wei, Jianhe; Jin, Yue; Chu, Qinglong; Yang, Chengmin

2010-08-01

To breed new varieties with better uniformity and commercial quality as well as higher saikosaponin contents. The excellent germplasm resources were selected from "zhongchai no. 1" population. Single plant method was applied to get better varieties. All the breeding material was investigated according to morphological characters, agronomic characters and the contents of saikosaponin a and saikosaponin d. The experiments of comparative test and varieties regional test were carried out. The bred new varieties of "zhongchai No. 2" and "zhongchai No. 3" had better uniformity. The dark brown roots ratios of the two varieties were 83.2%, 89.9%, respectively. The contents of saikosaponins (a + d) of the two varieties reached 1.31%, 1.02%, respectively. "zhongchai No. 2" and " zhongchai No. 3" both had the advantages of better uniformity, darker brown roots and higher saikosaponin contents.

Researcher responsibilities and genetic counseling for pure-bred dog populations.

PubMed

Bell, Jerold S

2011-08-01

Breeders of dogs have ethical responsibilities regarding the testing and management of genetic disease. Molecular genetics researchers have their own responsibilities, highlighted in this article. Laboratories offering commercial genetic testing should have proper sample identification and quality control, official test result certificates, clear explanations of test results and reasonably priced testing fees. Providing test results to a publicly-accessible genetic health registry allows breeders and the public to search for health-tested parents to reduce the risk of producing or purchasing affected offspring. Counseling on the testing and elimination of defective genes must consider the effects of genetic selection on the population. Recommendations to breed quality carriers to normal-testing dogs and replacing them with quality normal-testing offspring will help to preserve breeding lines and breed genetic diversity. Copyright © 2011 Elsevier Ltd. All rights reserved.

Prevalence and consequences of chromosomal abnormalities in Canadian commercial swine herds.

PubMed

Quach, Anh T; Revay, Tamas; Villagomez, Daniel A F; Macedo, Mariana P; Sullivan, Alison; Maignel, Laurence; Wyss, Stefanie; Sullivan, Brian; King, W Allan

2016-09-12

Structural chromosome abnormalities are well known as factors that reduce fertility rate in domestic pigs. According to large-scale national cytogenetic screening programs that are implemented in France, it is estimated that new chromosome abnormalities occur at a rate of 0.5 % in fertility-unproven boars. This work aimed at estimating the prevalence and consequences of chromosome abnormalities in commercial swine operations in Canada. We found pig carriers at a frequency of 1.64 % (12 out of 732 boars). Carrier pigs consistently showed lower fertility values. The total number of piglets born for litters from carrier boars was between 4 and 46 % lower than the herd average. Similarly, carrier boars produced litters with a total number of piglets born alive that was between 6 and 28 % lower than the herd average. A total of 12 new structural chromosome abnormalities were identified. Reproductive performance is significantly reduced in sires with chromosome abnormalities. The incidence of such abnormal sires appears relatively high in populations without routine cytogenetic screening such as observed for Canada in this study. Systematic cytogenetic screening of potential breeding boars would minimise the risk of carriers of chromosome aberrations entering artificial insemination centres. This would avoid the large negative effects on productivity for the commercial sow herds and reduce the risk of transmitting abnormalities to future generations in nucleus farms.

Equine viral arteritis in breeding and sport horses in central Spain.

PubMed

Cruz-Lopez, Fatima; Newton, Richard; Sanchez-Rodriguez, Ana; Ireland, Joanne; Mughini-Gras, Lapo; Moreno, Miguel A; Fores, Paloma

2017-12-01

Equine viral arteritis (EVA) may have a high economic impact on breeding stud farms due to the occurrence of EVA-associated abortion outbreaks and the ability of the virus to persist in carrier stallions. While the consequences of EVA in premises with sport horses are usually less severe, the first confirmed outbreak of EVA in Spain occurred in a riding club in Barcelona, but no data on the seroprevalence of EVA in sport horses have been reported in Spain. Given the importance of both Spanish Purebred (SP) breeding horses and sport horses for Spain's equine industry, the aim of this study was to determine and compare the seroprevalence of EVA in these two horse populations in central Spain. Serum samples from 155 SP breeding horses residing in 16 stud farms and 105 sport horses of different breeds housed in 12 riding clubs, collected between September 2011 and November 2013, were tested using a commercial EVA antibody ELISA test with a 100% sensitivity, and confirmed by seroneutralisation (SN) test. EVA seroprevalence in SP breeding horses was higher 21.1% (95% CI 15.3-26.8%) than that in sport horses (6.7%, 95% CI 1.89-11.45%). However, the primary use (breeding vs. sport) was not significantly associated with seropositivity to Equine Arteritis Virus (EAV), suggesting that different management factors do not affect EVA circulation in these two horse populations. Copyright © 2017 Elsevier Ltd. All rights reserved.

A cross-sectional study to estimate prevalence of periodontal disease in a population of dogs (Canis familiaris) in commercial breeding facilities in Indiana and Illinois

PubMed Central

2018-01-01

The objectives of this cross-sectional study were: 1) to estimate the prevalence and characterize the severity of periodontal disease in a population of dogs housed in commercial breeding facilities; 2) to characterize PD preventive care utilized by facility owners; and 3) to assess inter-rater reliability of a visual scoring assessment tool. Adult dogs (N = 445) representing 42 breeds at 24 CB facilities in Indiana and Illinois were assessed. Periodontal disease was scored visually using the American Veterinary Dental Collage 0-IV scale. Inter-rater reliability was assessed on 198 dogs and facility owners were asked to provide information about the preventive care utilized. The overall prevalence of periodontal disease (Grades I-IV) was 86.3% (95% CI: 82.9, 89.3). An ordered logistic regression analysis found age (OR = 1.4; 95% CI 1.24, 1.54; P<0.0001), facility (OR = 1.13; 95% CI 1.09, 1.18; P<0.0001), sex (OR = 1.7; 95% CI 1.12, 2.65; P = 0.013), and non-professional dental scaling (OR = 2.82; 95% CI 1.34, 5.91; P = 0.006) to be statistically significant. Inter-rater reliability analysis found agreement to be 86.2%, with a weighted kappa of 0.4731 (95% CI 0.3847, 0.5615) indicating moderate agreement. Risk of periodontal disease increased with increasing age. Additionally, a trend toward decreasing risk with increasing weight was also found, although it was not statistically significant. The trends identified agree with studies that have evaluated periodontal disease in the companion dog population and do not support the assumption that the dental health of dogs in commercial breeding facilities is worse than that of the population as a whole. Although there were few cases of severe periodontal disease and all facilities employed some type of preventive care in this sample, the large number of dogs with some degree of disease (Grades I-IV) suggests that further investigation of preventive care is warranted. PMID:29346448

A cross-sectional study to estimate prevalence of periodontal disease in a population of dogs (Canis familiaris) in commercial breeding facilities in Indiana and Illinois.

PubMed

Stella, Judith L; Bauer, Amy E; Croney, Candace C

2018-01-01

The objectives of this cross-sectional study were: 1) to estimate the prevalence and characterize the severity of periodontal disease in a population of dogs housed in commercial breeding facilities; 2) to characterize PD preventive care utilized by facility owners; and 3) to assess inter-rater reliability of a visual scoring assessment tool. Adult dogs (N = 445) representing 42 breeds at 24 CB facilities in Indiana and Illinois were assessed. Periodontal disease was scored visually using the American Veterinary Dental Collage 0-IV scale. Inter-rater reliability was assessed on 198 dogs and facility owners were asked to provide information about the preventive care utilized. The overall prevalence of periodontal disease (Grades I-IV) was 86.3% (95% CI: 82.9, 89.3). An ordered logistic regression analysis found age (OR = 1.4; 95% CI 1.24, 1.54; P<0.0001), facility (OR = 1.13; 95% CI 1.09, 1.18; P<0.0001), sex (OR = 1.7; 95% CI 1.12, 2.65; P = 0.013), and non-professional dental scaling (OR = 2.82; 95% CI 1.34, 5.91; P = 0.006) to be statistically significant. Inter-rater reliability analysis found agreement to be 86.2%, with a weighted kappa of 0.4731 (95% CI 0.3847, 0.5615) indicating moderate agreement. Risk of periodontal disease increased with increasing age. Additionally, a trend toward decreasing risk with increasing weight was also found, although it was not statistically significant. The trends identified agree with studies that have evaluated periodontal disease in the companion dog population and do not support the assumption that the dental health of dogs in commercial breeding facilities is worse than that of the population as a whole. Although there were few cases of severe periodontal disease and all facilities employed some type of preventive care in this sample, the large number of dogs with some degree of disease (Grades I-IV) suggests that further investigation of preventive care is warranted.

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.

Variation in the Breeding System of Prunella vulgaris L.

USDA-ARS?s Scientific Manuscript database

Prunella vulgaris (Lamiaceae), commonly known as selfheal, is a perennial herb with a long history of use in traditional medicine. Recent studies have found that P. vulgaris possesses anti-inflammatory, antiviral and anti-bacterial properties, which may lead to increased commercial demand. To date...

Variation in nuclear DNA content and chromosome numbers in blueberry

USDA-ARS?s Scientific Manuscript database

Commercial blueberry production in the U.S. relies on cultivars derived from combinations of different blueberry species. Interspecific hybridization continues to be a vital strategy for blueberry breeding, especially in regards to improving abiotic and biotic stress tolerance to expand the range of...

21 CFR 558.185 - Coumaphos.

Code of Federal Regulations, 2010 CFR

2010-04-01

... FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) ANIMAL DRUGS, FEEDS... under stress, such as those just shipped, dehorned, castrated, or weaned within the last 3 weeks. Do not... conditions of stress; treatment of colored breeds of commercial layers should be avoided while in production...

Advancements in utilizing molecular markers in lettuce breeding

USDA-ARS?s Scientific Manuscript database

Lettuce (Lactuca sativa L.) is globally the most popular commercially produced, leafy vegetable, farmed in moderate climates. Cultivated lettuce is a self-fertilizing, diploid (2n = 2x = 18) species from the family Compositae (Asteraceae). New cultivars of lettuce are developed by combining desirabl...

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.

Breeding nursery tissue collection for possible genomic analysis

USDA-ARS?s Scientific Manuscript database

Phenotyping is considered a major bottleneck in breeding programs. With new genomic technologies, high throughput genotype schemes are constantly being developed. However, every genomic technology requires phenotypic data to inform prediction models generated from the technology. Forage breeders con...

Epigenetics and developmental programming of welfare and production traits in farm animals.

PubMed

Sinclair, K D; Rutherford, K M D; Wallace, J M; Brameld, J M; Stöger, R; Alberio, R; Sweetman, D; Gardner, D S; Perry, V E A; Adam, C L; Ashworth, C J; Robinson, J E; Dwyer, C M

2016-07-21

The concept that postnatal health and development can be influenced by events that occur in utero originated from epidemiological studies in humans supported by numerous mechanistic (including epigenetic) studies in a variety of model species. Referred to as the 'developmental origins of health and disease' or 'DOHaD' hypothesis, the primary focus of large-animal studies until quite recently had been biomedical. Attention has since turned towards traits of commercial importance in farm animals. Herein we review the evidence that prenatal risk factors, including suboptimal parental nutrition, gestational stress, exposure to environmental chemicals and advanced breeding technologies, can determine traits such as postnatal growth, feed efficiency, milk yield, carcass composition, animal welfare and reproductive potential. We consider the role of epigenetic and cytoplasmic mechanisms of inheritance, and discuss implications for livestock production and future research endeavours. We conclude that although the concept is proven for several traits, issues relating to effect size, and hence commercial importance, remain. Studies have also invariably been conducted under controlled experimental conditions, frequently assessing single risk factors, thereby limiting their translational value for livestock production. We propose concerted international research efforts that consider multiple, concurrent stressors to better represent effects of contemporary animal production systems.

Mapping of epistatic quantitative trait loci in four-way crosses.

PubMed

He, Xiao-Hong; Qin, Hongde; Hu, Zhongli; Zhang, Tianzhen; Zhang, Yuan-Ming

2011-01-01

Four-way crosses (4WC) involving four different inbred lines often appear in plant and animal commercial breeding programs. Direct mapping of quantitative trait loci (QTL) in these commercial populations is both economical and practical. However, the existing statistical methods for mapping QTL in a 4WC population are built on the single-QTL genetic model. This simple genetic model fails to take into account QTL interactions, which play an important role in the genetic architecture of complex traits. In this paper, therefore, we attempted to develop a statistical method to detect epistatic QTL in 4WC population. Conditional probabilities of QTL genotypes, computed by the multi-point single locus method, were used to sample the genotypes of all putative QTL in the entire genome. The sampled genotypes were used to construct the design matrix for QTL effects. All QTL effects, including main and epistatic effects, were simultaneously estimated by the penalized maximum likelihood method. The proposed method was confirmed by a series of Monte Carlo simulation studies and real data analysis of cotton. The new method will provide novel tools for the genetic dissection of complex traits, construction of QTL networks, and analysis of heterosis.

Development of Commercial Thermo-sensitive Genic Male Sterile Rice Accelerates Hybrid Rice Breeding Using the CRISPR/Cas9-mediated TMS5 Editing System

PubMed Central

Zhou, Hai; He, Ming; Li, Jing; Chen, Liang; Huang, Zhifeng; Zheng, Shaoyan; Zhu, Liya; Ni, Erdong; Jiang, Dagang; Zhao, Bingran; Zhuang, Chuxiong

2016-01-01

Hybrid rice breeding offers an important strategy to improve rice production, in which the cultivation of a male sterile line is the key to the success of cross-breeding. CRISPR/Cas9 systems have been widely used in target-site genome editing, whereas their application for crop genetic improvement has been rarely reported. Here, using the CRISPR/Cas9 system, we induced specific mutations in TMS5, which is the most widely applied thermo-sensitive genic male sterility (TGMS) gene in China, and developed new “transgene clean” TGMS lines. We designed 10 target sites in the coding region of TMS5 for targeted mutagenesis using the CRISPR/Cas9 system and assessed the potential rates of on- and off-target effects. Finally, we established the most efficient construct, the TMS5ab construct, for breeding potentially applicable “transgene clean” TGMS lines. We also discussed factors that affect the editing efficiency according to the characteristics of different target sequences. Notably, using the TMS5ab construct, we developed 11 new “transgene clean” TGMS lines with potential applications in hybrid breeding within only one year in both rice subspecies. The application of our system not only significantly accelerates the breeding of sterile lines but also facilitates the exploitation of heterosis. PMID:27874087

Current patents and future development underlying marker-assisted breeding in major grain crops.

PubMed

Utomo, Herry S; Linscombe, Steve D

2009-01-01

Genomics and molecular markers provide new tools to assemble and mobilize important traits from different genetic backgrounds, including breeding lines and cultivars from different parts of the world and their related wild ancestors, to improve the quality and yield of the existing commercial cultivars to meet the increasing challenges of global food demand. The basic techniques of marker-assisted breeding, such as isolating DNA, amplifying DNA of interest using publicly available primers, and visualizing DNA fragments using standard polyacrylamid gel, have been described in the literature and, therefore, are available to scientists and breeders without any restrictions. A more sophisticated high-throughput system that includes proprietary chemicals and reagents, parts and equipments, software, and methods or processes, has been a subject of intensive patents and trade secrets. The high-throughput systems offer a more efficient way to discover associated QTLs for traits of economic importance. Therefore, an increasing number of patents of highly valued genes and QTLs is expected. This paper will discuss and review current patents associated with genes and QTLs utilized in marker-assisted breeding in major grain crops. The availability of molecular markers for important agronomic traits combined with more efficient marker detection systems will help reach the full benefit of MAS in the breeding effort to reassemble potential genes and recapture critical genes among the breeding lines that were lost during domestication to help boost crop production worldwide.

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.

Genetic counseling in the era of molecular diagnostics.

PubMed

Traas, Anne M; Casal, Margret; Haskins, Mark; Henthorn, Paula

2006-08-01

Veterinarians with an interest in theriogenology will often be asked by small animal clients for advice concerning hereditary diseases in their breeds. Many new DNA-based tests for analysis of genetic diseases and traits (e.g. coat color) are now available for use by both breeders and veterinarians. With appropriate interpretation, these tests can be invaluable tools in a breeding program. For example, they can be used to produce animals free of specific diseases, to quickly eliminate a disease from an entire breed, or to select for specific traits in breeding stock. Selection strategies that do not take into account maintaining genetic diversity of the breed may be detrimental and reduce the potential for future improvement.

Genomics to feed a switchgrass breeding program

USDA-ARS?s Scientific Manuscript database

Development of improved cultivars is one of three pillars, along with sustainable production and efficient conversion, required for dedicated cellulosic bioenergy crops to succeed. Breeding new cultivars is a long, slow process requiring patience, dedication, and motivation to realize gains and adva...

Pituophis ruthveni (Louisiana pinesnake) Reproduction/breeding phenology

Treesearch

Josh B. Pierce; Craig Rudolph; Christopher A. Melder; Beau B. Gregory

2016-01-01

Determing the reproductive phenology of snakes is important since it marks a time period where snakes are particularly vulnerable to predation. In addition, knowledge of reproductive phenology may help captive breeding programs specify appropriate times to pair snakes for reproduction.

A global threats overview for Numeniini populations: synthesising expert knowledge for a group of declining migratory birds.

USGS Publications Warehouse

Pearce-Higgins, James W.; Brown, Daniel J.; Douglas, David J.T.; Alves, José A.; Bellio, Mariagrazia; Bocher, Pierrick; Buchannan, Graeme M.; Clay, Robert P.; Conklin, Jesse R.; Crockford, Nicola; Dann, Peter; Elts, Jaanus; Friis, Christian; Fuller, Richard A.; Gill, Jennifer A.; Gosbell, Ken; Johnson, James A.; Marquez-Ferrando, Rocio; Masero, José A.; Melville, David S.; Millington, Spike; Minton, Clive; Mundkur, Taej; Nol, Erika; Pehlak, Hannes; Piersma, Theunis; Rogers, Danny I.; Ruthrauff, Daniel R.; Senner, Nathan R.; Nazeer Shah, Junid; Sheldon, Rob D.; Soloviev, Sergej A.; Tomkovich, Pavel S.; Verkuil, Yvonne I.

2017-01-01

The Numeniini is a tribe of 13 wader species (Scolopacidae, Charadriiformes) of which seven are Near Threatened or globally threatened, including two Critically Endangered. To help inform conservation management and policy responses, we present the results of an expert assessment of the threats that members of this taxonomic group face across migratory flyways. Most threats are increasing in intensity, particularly in non-breeding areas, where habitat loss resulting from residential and commercial development, aquaculture, mining, transport, disturbance, problematic invasive species, pollution and climate change were regarded as having the greatest detrimental impact. Fewer threats (mining, disturbance, problematic native species and climate change) were identified as widely affecting breeding areas. Numeniini populations face the greatest number of non-breeding threats in the East Asian-Australasian Flyway, especially those associated with coastal reclamation; related threats were also identified across the Central and Atlantic Americas, and East Atlantic flyways. Threats on the breeding grounds were greatest in Central and Atlantic Americas, East Atlantic and West Asian flyways. Three priority actions were associated with monitoring and research: to monitor breeding population trends (which for species breeding in remote areas may best be achieved through surveys at key non-breeding sites), to deploy tracking technologies to identify migratory connectivity, and to monitor land-cover change across breeding and non-breeding areas. Two priority actions were focused on conservation and policy responses: to identify and effectively protect key non-breeding sites across all flyways (particularly in the East Asian- Australasian Flyway), and to implement successful conservation interventions at a sufficient scale across human-dominated landscapes for species' recovery to be achieved. If implemented urgently, these measures in combination have the potential to alter the current population declines of many Numeniini species and provide a template for the conservation of other groups of threatened species.

A strategy for male sterility facilitated recurrent selection in peach

USDA-ARS?s Scientific Manuscript database

Commercial peach is a highly homozygous self-compatible species with limited diversity. The incorporation of exotic germplasm and breeding of new varieties is hindered by the labor required to generate large segregating populations. Hand pollinations are characterized by a high failure rate with onl...

Marker-assisted selection for resistance to bacterial cold water disease in a commercial rainbow trout breeding population

USDA-ARS?s Scientific Manuscript database

Bacterial cold water disease (BCWD), caused by Flavobacterium psychrophilum, is an endemic and problematic disease in rainbow trout (Oncorhynchus mykiss) aquaculture. Previously, we have identified SNPs (single nucleotide polymorphisms) associated with BCWD resistance in rainbow trout. The objective...

9 CFR 2.35 - Recordkeeping requirements.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Section 2.35 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF... include: (i) The species and breed or type of animal; (ii) The sex; (iii) The date of birth or approximate... commercial or financial information that is privileged or confidential will be governed by applicable...

9 CFR 2.35 - Recordkeeping requirements.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Section 2.35 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF... include: (i) The species and breed or type of animal; (ii) The sex; (iii) The date of birth or approximate... commercial or financial information that is privileged or confidential will be governed by applicable...

9 CFR 56.3 - Payment of indemnity.

Code of Federal Regulations, 2010 CFR

2010-01-01

... are commercial meat-type chickens that are associated with a slaughter plant that slaughters 200,000....3 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE... described in paragraphs (a)(1) through (a)(3) of this section: (1) The poultry are egg-type breeding...

9 CFR 2.35 - Recordkeeping requirements.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Section 2.35 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF... include: (i) The species and breed or type of animal; (ii) The sex; (iii) The date of birth or approximate... commercial or financial information that is privileged or confidential will be governed by applicable...

9 CFR 2.35 - Recordkeeping requirements.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Section 2.35 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF... include: (i) The species and breed or type of animal; (ii) The sex; (iii) The date of birth or approximate... commercial or financial information that is privileged or confidential will be governed by applicable...