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...

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.

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

PubMed

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

2018-06-02

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

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.

Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds.

PubMed

Yurchenko, Andrey; Yudin, Nikolay; Aitnazarov, Ruslan; Plyusnina, Alexandra; Brukhin, Vladimir; Soloshenko, Vladimir; Lhasaranov, Bulat; Popov, Ruslan; Paronyan, Ivan A; Plemyashov, Kirill V; Larkin, Denis M

2018-01-01

One of the most economically important areas within the Russian agricultural sector is dairy and beef cattle farming contributing about $11 billion to the Russian economy annually. Trade connections, selection and breeding have resulted in the establishment of a number of breeds that are presumably adapted to local climatic conditions. Little however is known about the ancestry and history of Russian native cattle. To address this question, we genotyped 274 individuals from 18 breeds bred in Russia and compared them to 135 additional breeds from around the world that had been genotyped previously. Our results suggest a shared ancestry between most of the Russian cattle and European taurine breeds, apart from a few breeds that shared ancestry with the Asian taurines. The Yakut cattle, belonging to the latter group, was found to be the most diverged breed in the whole combined dataset according to structure results. Haplotype sharing further suggests that the Russian cattle can be divided into four major clusters reflecting ancestral relations with other breeds. Herein, we therefore shed light on to the history of Russian cattle and identified closely related breeds to those from Russia. Our results will facilitate future research on detecting signatures of selection in cattle genomes and eventually inform future genetics-assisted livestock breeding programs in Russia and in other countries.

Using breed composition, breed differences, selection tools, and new technologies to optimize commercial cattle production and allocation of beef cattle in research programs

USDA-ARS?s Scientific Manuscript database

Indicators of breed composition such as hair color and ear length often result in increased or decreased prices of young calves marketed into feedlots. Similarly, feedlot research trials are often initiated with blended cattle from multiple sources with little more than coat color used as a blockin...

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.

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.

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...

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.

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.

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.

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.

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...

Plant breeding for harmony between agriculture and the environment

USDA-ARS?s Scientific Manuscript database

Crop improvements made since the 1950’s coupled with inexpensive agronomic inputs (fertilizers, herbicides, etc.) have resulted in agricultural production that has kept pace with population growth. Breeding programs primarily focus on improving a crop’s environmental adaptability and biotic stress t...

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.

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

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.

Density gradient centrifugation of sperm from a subfertile stallion and effect of seminal plasma addition on fertility.

PubMed

Mari, Gaetano; Castagnetti, Carolina; Rizzato, Giovanni; Mislei, Beatrice; Iacono, Eleonora; Merlo, Barbara

2011-06-01

Stallions are not selected for fertility but for other criteria (pedigree, conformation, performances, progeny), therefore valuable but subfertile stallions with poor semen quality are frequently used in commercial breeding programs. The object of this study was to evaluate whether sperm selection through a silane-coated silica colloid gradient centrifugation, with or without the addition of seminal plasma of a high fertile stallion, could improve the pregnancy rates of an oligospermic valuable stallion in a commercial breeding program. In 2008 breeding season (experiment 1, n=104 mares), simple centrifugation and density gradient centrifugation of the sperm were compared. In 2009 and 2010 breeding seasons (experiment 2, n=125 mares), the effect of the addition of 5% seminal plasma to the extender after sperm selection was evaluated. In all mares deep horn uterine insemination was performed with 1 ml containing 50×10(6) morphologically normal progressive motile spermatozoa, 24-30 h after induction of ovulation with hCG. Pregnancy diagnosis by ultrasonography was performed 14 days following ovulation. Results showed a higher per cycle pregnancy rate (P>0.05) when sperm selection through a density gradient was used (62% vs. 42.3%, exp 1), while the addition of 5% seminal plasma did not influence the outcome (45.9% vs. 47.6%, exp 2) (P>0.05). An age-related decrease in the fertility of the stallion was observed when comparing the results from the different breeding seasons (P<0.05). In conclusion, sperm selection through a discontinuous density gradient enabled a normal per cycle pregnancy rate to be achieved from an oligospermic-subfertile stallion in a commercial breeding program, and no differences were observed regarding the addition of seminal plasma. Copyright © 2011 Elsevier B.V. All rights reserved.

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.

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.

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

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...

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.

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.

Efficiency of including first-generation information in second-generation ranking and selection: results of computer simulation.

Treesearch

T.Z. Ye; K.J.S. Jayawickrama; G.R. Johnson

2006-01-01

Using computer simulation, we evaluated the impact of using first-generation information to increase selection efficiency in a second-generation breeding program. Selection efficiency was compared in terms of increase in rank correlation between estimated and true breeding values (i.e., ranking accuracy), reduction in coefficient of variation of correlation...

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

PubMed

Hietala, P; Juga, J

2017-04-01

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

The genome-wide structure of two economically important indigenous Sicilian cattle breeds.

PubMed

Mastrangelo, S; Saura, M; Tolone, M; Salces-Ortiz, J; Di Gerlando, R; Bertolini, F; Fontanesi, L; Sardina, M T; Serrano, M; Portolano, B

2014-11-01

Genomic technologies, such as high-throughput genotyping based on SNP arrays, provided background information concerning genome structure in domestic animals. The aim of this work was to investigate the genetic structure, the genome-wide estimates of inbreeding, coancestry, effective population size (Ne), and the patterns of linkage disequilibrium (LD) in 2 economically important Sicilian local cattle breeds, Cinisara (CIN) and Modicana (MOD), using the Illumina Bovine SNP50K v2 BeadChip. To understand the genetic relationship and to place both Sicilian breeds in a global context, genotypes from 134 other domesticated bovid breeds were used. Principal component analysis showed that the Sicilian cattle breeds were closer to individuals of Bos taurus taurus from Eurasia and formed nonoverlapping clusters with other breeds. Between the Sicilian cattle breeds, MOD was the most differentiated, whereas the animals belonging to the CIN breed showed a lower value of assignment, the presence of substructure, and genetic links with the MOD breed. The average molecular inbreeding and coancestry coefficients were moderately high, and the current estimates of Ne were low in both breeds. These values indicated a low genetic variability. Considering levels of LD between adjacent markers, the average r(2) in the MOD breed was comparable to those reported for others cattle breeds, whereas CIN showed a lower value. Therefore, these results support the need of more dense SNP arrays for a high-power association mapping and genomic selection efficiency, particularly for the CIN cattle breed. Controlling molecular inbreeding and coancestry would restrict inbreeding depression, the probability of losing beneficial rare alleles, and therefore the risk of extinction. The results generated from this study have important implications for the development of conservation and/or selection breeding programs in these 2 local cattle breeds.

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...

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...

Hybrid wheat: quantitative genetic parameters and consequences for the design of breeding programs.

PubMed

Longin, Carl Friedrich Horst; Gowda, Manje; Mühleisen, Jonathan; Ebmeyer, Erhard; Kazman, Ebrahim; Schachschneider, Ralf; Schacht, Johannes; Kirchhoff, Martin; Zhao, Yusheng; Reif, Jochen Christoph

2013-11-01

Commercial heterosis for grain yield is present in hybrid wheat but long-term competiveness of hybrid versus line breeding depends on the development of heterotic groups to improve hybrid prediction. Detailed knowledge of the amount of heterosis and quantitative genetic parameters are of paramount importance to assess the potential of hybrid breeding. Our objectives were to (1) examine the extent of midparent, better-parent and commercial heterosis in a vast population of 1,604 wheat (Triticum aestivum L.) hybrids and their parental elite inbred lines and (2) discuss the consequences of relevant quantitative parameters for the design of hybrid wheat breeding programs. Fifteen male lines were crossed in a factorial mating design with 120 female lines, resulting in 1,604 of the 1,800 potential single-cross hybrid combinations. The hybrids, their parents, and ten commercial wheat varieties were evaluated in multi-location field experiments for grain yield, plant height, heading time and susceptibility to frost, lodging, septoria tritici blotch, yellow rust, leaf rust, and powdery mildew at up to five locations. We observed that hybrids were superior to the mean of their parents for grain yield (10.7 %) and susceptibility to frost (-7.2 %), leaf rust (-8.4 %) and septoria tritici blotch (-9.3 %). Moreover, 69 hybrids significantly (P < 0.05) outyielded the best commercial inbred line variety underlining the potential of hybrid wheat breeding. The estimated quantitative genetic parameters suggest that the establishment of reciprocal recurrent selection programs is pivotal for a successful long-term hybrid wheat breeding.

Differences in innate and adaptive immune response traits of Pahari (Indian non-descript indigenous breed) and Jersey crossbred cattle.

PubMed

Verma, Subhash; Thakur, Aneesh; Katoch, Shailja; Shekhar, Chander; Wani, Aasim Habib; Kumar, Sandeep; Dohroo, Shweta; Singh, Geetanjali; Sharma, Mandeep

2017-10-01

Cattle are an integral part of the largely agrarian economy of India. Indigenous breeds of cattle comprise about 80% of total cattle population of the country and contribute significantly to the overall milk production. There are 40 recognized indigenous breeds of cattle and a number of uncharacterized non-descript cattle. Pahari cattle of Himachal Pradesh in Northern India are one such non-descript indigenous breed. Here we describe a comprehensive evaluation of haematobiochemical parameters and innate and adaptive immune response traits of Pahari cattle and a comparison with Jersey crossbred cattle. The study shows demonstrable differences in the two breeds with respect to some innate and adaptive immunological traits. This is a first attempt to characterize immune response traits of Pahari cattle and the results of the study provide an understanding of breed differences in immune status of cattle which could be useful for their breeding and conservations programs. Copyright © 2017 Elsevier B.V. All rights reserved.

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...

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 of tomorrow's chickens to improve well-being.

PubMed

Cheng, H-W

2010-04-01

Chickens, as well as other animals, have the ability to change their behavior (behavioral plasticity) and physiology (physiological plasticity) based on the costs and benefits to fit their environment (adaptation). Through natural selection, the population preserves and accumulates traits that are beneficial and rejects those that are detrimental in their prevailing environments. The surviving populations are able to contribute more genes associated with beneficial traits for increased fitness to subsequent generations. Natural selection is slow but constant; working over multiple generations, the changes to the population often appear silent or undetectable at a given point in history. Chickens were domesticated from the wild red jungle fowl. The principle of domestication of chickens, as well as other farm animals, by humans is similar to that of natural selection: selecting the best animals with the highest survivability and reproducibility (artificial selection). Compared with natural selection, the process of artificial selection is motivated by human needs and acts more rapidly with more visible results over a short time period. This process has been further accelerated following the development of current breeding programs and the emergence of specialized breeding companies. A laying hen, for example, produces more than 300 hundred eggs a year, whereas a jungle fowl lays 4 to 6 eggs in a year. During the domestication process, chickens retained their capability to adapt to their housing environments, which is usually achieved by genetic changes occurring with each subsequent generation. Genes control the behavioral, physiological, immunological, and psychological responses of animals to stressors, including environmental stimulations. With advances in understanding of genetic mediation of animal physiology and behavior and the discovery of the genome sequences of many species, animal production breeding programs can be improved in both speed and efficiency. Modern chicken breeding programs have the potential to be operated successfully in the breeding of tomorrow's chickens with high production efficiency and optimal welfare, resulting from resistance to stress, disease, or both.

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.

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.

Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breed

PubMed Central

2010-01-01

Background Decisions to initiate conservation programmes need to account for extant variability, diversity loss and cultural and economic aspects. Molecular markers were used to investigate if putative Algarvia animals could be identified for use as progenitors in a breeding programme to recover this nearly extinct breed. Methods 46 individuals phenotypically representative of Algarvia cattle were genotyped for 27 microsatellite loci and compared with 11 Portuguese autochthonous and three imported breeds. Genetic distances and factorial correspondence analyses (FCA) were performed to investigate the relationship among Algarvia and related breeds. Assignment tests were done to identify representative individuals of the breed. Y chromosome and mtDNA analyses were used to further characterize Algarvia animals. Gene- and allelic-based conservation analyses were used to determine breed contributions to overall genetic diversity. Results Genetic distance and FCA results confirmed the close relationship between Algarvia and southern Portuguese breeds. Assignment tests without breed information classified 17 Algarvia animals in this cluster with a high probability (q > 0.95). With breed information, 30 cows and three bulls were identified (q > 0.95) that could be used to reconstitute the Algarvia breed. Molecular and morphological results were concordant. These animals showed intermediate levels of genetic diversity (MNA = 6.0 ± 1.6, Rt = 5.7 ± 1.4, Ho = 0.63 ± 0.19 and He = 0.69 ± 0.10) relative to other Portuguese breeds. Evidence of inbreeding was also detected (Fis = 0.083, P < 0.001). The four Algarvia bulls had Y-haplotypes H6Y2 and H11Y2, common in Portuguese cattle. The mtDNA composition showed prevalence of T3 matrilines and presence of the African-derived T1a haplogroup. This analysis confirmed the genetic proximity of Algarvia and Garvonesa breeds (Fst = 0.028, P > 0.05). Algarvia cattle provide an intermediate contribution (CB = 6.18, CW = -0.06 and D1 = 0.50) to the overall gene diversity of Portuguese cattle. Algarvia and seven other autochthonous breeds made no contribution to the overall allelic diversity. Conclusions Molecular analyses complemented previous morphological findings to identify 33 animals that can be considered remnants of the Algarvia breed. Results of genetic diversity and conservation analyses provide objective information to establish a management program to reconstitute the Algarvia breed. PMID:20540741

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.

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

PubMed

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

2016-07-01

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

Genomic diversity and population structure of three autochthonous Greek sheep breeds assessed with genome-wide DNA arrays.

PubMed

Michailidou, S; Tsangaris, G; Fthenakis, G C; Tzora, A; Skoufos, I; Karkabounas, S C; Banos, G; Argiriou, A; Arsenos, G

2018-06-01

In the present study, genome-wide genotyping was applied to characterize the genetic diversity and population structure of three autochthonous Greek breeds: Boutsko, Karagouniko and Chios. Dairy sheep are among the most significant livestock species in Greece numbering approximately 9 million animals which are characterized by large phenotypic variation and reared under various farming systems. A total of 96 animals were genotyped with the Illumina's OvineSNP50K microarray beadchip, to study the population structure of the breeds and develop a specialized panel of single-nucleotide polymorphisms (SNPs), which could distinguish one breed from the others. Quality control on the dataset resulted in 46,125 SNPs, which were used to evaluate the genetic structure of the breeds. Population structure was assessed through principal component analysis (PCA) and admixture analysis, whereas inbreeding was estimated based on runs of homozygosity (ROHs) coefficients, genomic relationship matrix inbreeding coefficients (F GRM ) and patterns of linkage disequilibrium (LD). Associations between SNPs and breeds were analyzed with different inheritance models, to identify SNPs that distinguish among the breeds. Results showed high levels of genetic heterogeneity in the three breeds. Genetic distances among breeds were modest, despite their different ancestries. Chios and Karagouniko breeds were more genetically related to each other compared to Boutsko. Analysis revealed 3802 candidate SNPs that can be used to identify two-breed crosses and purebred animals. The present study provides, for the first time, data on the genetic background of three Greek indigenous dairy sheep breeds as well as a specialized marker panel that can be applied for traceability purposes as well as targeted genetic improvement schemes and conservation programs.

Genetic Parameters and the Impact of Off-Types for Theobroma cacao L. in a Breeding Program in Brazil

PubMed Central

DuVal, Ashley; Gezan, Salvador A.; Mustiga, Guiliana; Stack, Conrad; Marelli, Jean-Philippe; Chaparro, José; Livingstone, Donald; Royaert, Stefan; Motamayor, Juan C.

2017-01-01

Breeding programs of cacao (Theobroma cacao L.) trees share the many challenges of breeding long-living perennial crops, and genetic progress is further constrained by both the limited understanding of the inheritance of complex traits and the prevalence of technical issues, such as mislabeled individuals (off-types). To better understand the genetic architecture of cacao, in this study, 13 years of phenotypic data collected from four progeny trials in Bahia, Brazil were analyzed jointly in a multisite analysis. Three separate analyses (multisite, single site with and without off-types) were performed to estimate genetic parameters from statistical models fitted on nine important agronomic traits (yield, seed index, pod index, % healthy pods, % pods infected with witches broom, % of pods other loss, vegetative brooms, diameter, and tree height). Genetic parameters were estimated along with variance components and heritabilities from the multisite analysis, and a trial was fingerprinted with low-density SNP markers to determine the impact of off-types on estimations. Heritabilities ranged from 0.37 to 0.64 for yield and its components and from 0.03 to 0.16 for disease resistance traits. A weighted index was used to make selections for clonal evaluation, and breeding values estimated for the parental selection and estimation of genetic gain. The impact of off-types to breeding progress in cacao was assessed for the first time. Even when present at <5% of the total population, off-types altered selections by 48%, and impacted heritability estimations for all nine of the traits analyzed, including a 41% difference in estimated heritability for yield. These results show that in a mixed model analysis, even a low level of pedigree error can significantly alter estimations of genetic parameters and selections in a breeding program. PMID:29250097

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...

Identification of breeding objectives for Begait goat in western Tigray, North Ethiopia.

PubMed

Abraham, Hagos; Gizaw, Solomon; Urge, Mengistu

2018-06-21

A sound breeding objective is the basis for genetic improvement in overall economic merit of farm animals. Begait goat is one of the identified breeds in Ethiopia, which is a multipurpose breed as it serves as source of cash income and source of food (meat and milk). Despite its importance, no formal breeding objectives exist for Begait goat. The objective of the present study was to identify breeding objectives for the breed through two approaches: using own-flock ranking experiment and developing deterministic bio-economic models as a preliminary step towards designing sustainable breeding programs for the breed. In the own-flock ranking experiment, a total of 45 households were visited at their homesteads and were asked to select, with reasons, the first best, second best, third best, and the most inferior does from their own flock. Age, previous reproduction, and production information of the identified animals were inquired; live body weight and some linear body measurements were taken. The bio-economic model included performance traits (weights, daily weight gain, kidding interval, litter size, milk yield, kid mortality, pregnancy, and replacement rates) and economic (revenue and costs) parameters. It was observed that there was close agreement between the farmers' ranking and bio-economic model results. In general, the results of the present study indicated that Begait goat owners could improve performance of their goats and profitability of their farms by selecting for 6-month weight, litter size, pre-weaning kid survival rate, and milk yield.

Genetic diversity and differentiation of exotic and American commercial cattle breeds raised in Brazil.

PubMed

Brasil, B S A F; Coelho, E G A; Drummond, M G; Oliveira, D A A

2013-11-18

The Brazilian cattle population is mainly composed of breeds of zebuine origin and their American derivatives. Comprehensive knowledge about the genetic diversity of these populations is fundamental for animal breeding programs and the conservation of genetic resources. This study aimed to assess the phylogenetic relationships, levels of genetic diversity, and patterns of taurine/zebuine admixture among 9 commercial cattle breeds raised in Brazil. Analysis of DNA polymorphisms was performed on 2965 animals using the 11 microsatellite markers recommended by the International Society of Animal Genetics. High genetic diversity was detected in all breeds, even though significant inbreeding was observed within some. Differences among the breeds accounted for 14.72% of the total genetic variability, and genetic differentiation was higher among taurine than among zebuine cattle. Of note, Nelore cattle presented with high levels of admixture, which is consistent with the history of frequent gene flow during the establishment of this breed in Brazil. Furthermore, significant genetic variability was partitioned within the commercial cattle breeds formed in America, which, therefore, comprise important resources of genetic diversity in the tropics. The genetic characterization of these important Brazilian breeds may now facilitate the development of management and breeding programs for these populations.

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

PubMed

Wang, Yu; Bennewitz, Jörn; Wellmann, Robin

2017-05-12

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

Efficient Breeding by Genomic Mating.

PubMed

Akdemir, Deniz; Sánchez, Julio I

2016-01-01

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

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...

Genome-wide investigation of genetic changes during modern breeding of Brassica napus.

PubMed

Wang, Nian; Li, Feng; Chen, Biyun; Xu, Kun; Yan, Guixin; Qiao, Jiangwei; Li, Jun; Gao, Guizhen; Bancroft, Ian; Meng, Jingling; King, Graham J; Wu, Xiaoming

2014-08-01

Considerable genome variation had been incorporated within rapeseed breeding programs over past decades. In past decades, there have been substantial changes in phenotypic properties of rapeseed as a result of extensive breeding effort. Uncovering the underlying patterns of allelic variation in the context of genome organisation would provide knowledge to guide future genetic improvement. We assessed genome-wide genetic changes, including population structure, genetic relatedness, the extent of linkage disequilibrium, nucleotide diversity and genetic differentiation based on F ST outlier detection, for a panel of 472 Brassica napus inbred accessions using a 60 k Brassica Infinium® SNP array. We found genetic diversity varied in different sub-groups. Moreover, the genetic diversity increased from 1950 to 1980 and then remained at a similar level in China and Europe. We also found ~6-10 % genomic regions revealed high F ST values. Some QTLs previously associated with important agronomic traits overlapped with these regions. Overall, the B. napus C genome was found to have more high F ST signals than the A genome, and we concluded that the C genome may contribute more valuable alleles to generate elite traits. The results of this study indicate that considerable genome variation had been incorporated within rapeseed breeding programs over past decades. These results also contribute to understanding the impact of rapeseed improvement on available genome variation and the potential for dissecting complex agronomic traits.

A Qualitative Evidence of the Breeding Sites of Anopheles arabiensis Patton (Diptera: Culicidae) in and Around Kassala Town, Eastern Sudan

PubMed Central

Hamza, Asma Mahmoud; El Rayah, El Amin

2016-01-01

Anopheles arabiensis Patton (Diptera: Culicidae) is considered the most efficient malaria vector in eastern Sudan. This study aims to characterize the breeding sites of An. arabiensis throughout the year in and around Kassala town, eastern Sudan. Diverse larval habitat types were visited and characterized based on the habitat type and chemical composition. Mosquito larvae were found in many diverse habitats. During the rainy season, rain pools and water bodies created by the seasonal Gash River serve as the main breeding sites. In the dry season, irrigation canals, seepage from water pipes, neglected wells, artificial containers, and man-made ditches serve as the main breeding sites. Breeding water showed a pH of 7.9 and a low concentration of the total dissolved salts. The results of this study may be considered in planning and implementing larval control programs in the area. PMID:27547039

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.

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

PubMed

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

2015-10-19

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

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

PubMed Central

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

2013-01-01

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

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...

High genetic diversity of Jatropha curcas assessed by ISSR.

PubMed

Díaz, B G; Argollo, D M; Franco, M C; Nucci, S M; Siqueira, W J; de Laat, D M; Colombo, C A

2017-05-31

Jatropha curcas L. is a highly promising oilseed for sustainable production of biofuels and bio-kerosene due to its high oil content and excellent quality. However, it is a perennial and incipiently domesticated species with none stable cultivar created until now despite genetic breeding programs in progress in several countries. Knowledge of the genetic structure and diversity of the species is a necessary step for breeding programs. The molecular marker can be used as a tool for speed up the process. This study was carried out to assess genetic diversity of a germplasm bank represented by J. curcas accessions from different provenance beside interspecific hybrid and backcrosses generated by IAC breeding programs using inter-simple sequence repeat markers. The molecular study revealed 271 bands of which 98.9% were polymorphic with an average of 22.7 polymorphic bands per primer. Genetic diversity of the germplasm evaluated was slightly higher than other germplasm around the world and ranged from 0.55 to 0.86 with an average of 0.59 (Jaccard index). Cluster analysis (UPGMA) revealed no clear grouping as to the geographical origin of accessions, consistent with genetic structure analysis using the Structure software. For diversity analysis between groups, accessions were divided into eight groups by origin. Nei's genetic distance between groups was 0.14. The results showed the importance of Mexican accessions, congeneric wild species, and interspecific hybrids for conservation and development of new genotypes in breeding programs.

Genomic selection in sugar beet breeding populations.

PubMed

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

2013-09-18

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

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.

The reproductive endocrinology and behavior of Vancouver Island marmot (Marmota vancouverensis).

PubMed

Keeley, T; Goodrowe, K L; Graham, L; Howell, C; MacDonald, S E

2012-01-01

The Vancouver Island marmot (Marmota vancouverensis; VIM) is one of North America's most endangered species with fewer than 150 individuals remaining in the wild. A captive breeding program was established across four facilities in Canada as an insurance population and source of animals for reintroduction to the wild. The purpose of this study was to gather information about the basic reproductive biology and behavior of this species, which is essential to improve captive breeding programs. Regular fecal samples were obtained from adult female (n = 14) and male (n = 10) marmots, 2 years of age and older, over 1-3 breeding seasons (2-3 months duration posthibernation) for steroid hormone analysis. Enzyme immunoassays were validated for quantifying fecal testosterone metabolite concentrations for males, and fecal estrogen and progesterone metabolite concentrations for females. Results indicated that fecal progesterone metabolite concentrations can be used to monitor ovulation and pregnancy. Behavioral monitoring through infrared video surveillance was conducted in four breeding pairs over a 2-year period (n = 7 behavioral profiles). Breeding behaviors correlated strongly with changes in reproductive endocrine profiles. A high frequency of play behavior or "wrestling" was observed in conjunction with breeding activity before an elevation in progesterone metabolite concentrations. Impending parturition was associated with increased aggression and exclusion of the male from the maternal nestbox as well as an increase in nesting activity. Observational data combined with hormonal analysis suggest that female VIMs are induced ovulators and that multiple breeding attempts may be required for ovulation and conception. Gestation appears to be approximately 34 days from peak breeding activity (32 days from estimated ovulation). Fecal testosterone concentrations suggest that testicular activity is seasonal with the reproductive activity occurring immediately posthibernation. Monitoring breeding behavior is a useful means of indicating estrus, conception and pregnancy, which can also be supported by the hormonal analysis of daily fecal samples of individual animals. © 2011 Wiley Periodicals, Inc.

Genomic selection in sugar beet breeding populations

PubMed Central

2013-01-01

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

Factors influencing breeding success, ovarian cyclicity, and cub survival in zoo-managed tigers (Panthera tigris).

PubMed

Saunders, Sarah P; Harris, Tara; Traylor-Holzer, Kathy; Beck, Karen Goodrowe

2014-01-10

Understanding factors that influence reproduction and offspring survival in zoo populations is critical for management of threatened and endangered species. Examination of long-term data (1989-2011) compiled from the Association of Zoos and Aquarium's zoo-managed tiger breeding program provides the basis for a more thorough understanding of reproduction and scientifically based decisions for effective population management in this endangered felid. Biological and management-related factors that could influence tiger breeding success and cub survival were evaluated using logistic mixed models. Breeding success improved with female age until approximately age five, then declined thereafter. Experienced female breeders had greater breeding success than inexperienced females. Litter size was most predictive of cub survival, with average-sized litters (3-4 cubs) experiencing the highest proportional survival. Management-related factors, such as whether the breeding institution had a recent tiger litter and whether both animals were already located at the same institution, also influenced breeding success and cub survival. These results highlight the importance of institutional husbandry experience and the need to retain knowledge through staff turnovers to achieve optimal reproductive success. Using fecal estrogen data, frequency of ovarian cyclicity and mean cycle length did not differ by female age or parity; thus, lack of cyclicity and/or increased cycle duration are not likely explanations for declining breeding success with age. These results provide valuable reproductive information that should improve scientific management of zoo-based tiger populations. Copyright © 2013 Elsevier B.V. All rights reserved.

Correlation, path analysis and heritability estimation for agronomic traits contribute to yield on soybean

NASA Astrophysics Data System (ADS)

Sulistyo, A.; Purwantoro; Sari, K. P.

2018-01-01

Selection is a routine activity in plant breeding programs that must be done by plant breeders in obtaining superior plant genotypes. The use of appropriate selection criteria will determine the effectiveness of selection activities. The purpose of this study was to analysis the inheritable agronomic traits that contribute to soybean yield. A total of 91 soybean lines were planted in Muneng Experimental Station, Probolinggo District, East Java Province, Indonesia in 2016. All soybean lines were arranged in randomized complete block design with two replicates. Correlation analysis, path analysis and heritability estimation were performed on days to flowering, days to maturing, plant height, number of branches, number of fertile nodes, number of filled pods, weight of 100 seeds, and yield to determine selection criteria on soybean breeding program. The results showed that the heritability value of almost all agronomic traits observed is high except for the number of fertile nodes with low heritability. The result of correlation analysis shows that days to flowering, plant height and number of fertile nodes have positive correlation with seed yield per plot (0.056, 0.444, and 0.100, respectively). In addition, path analysis showed that plant height and number of fertile nodes have highest positive direct effect on soybean yield. Based on this result, plant height can be selected as one of selection criteria in soybean breeding program to obtain high yielding soybean variety.

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.

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.

Simulating a base population in honey bee for molecular genetic studies

PubMed Central

2012-01-01

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

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

PubMed

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

2017-03-10

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

‘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)

Behavioral profiles of dog breeds.

PubMed

Hart, B L; Miller, M F

1985-06-01

Breed behavior profiles were obtained by a method that was quantitative and free of personal biases. The profiles concerned 13 traits, eg, excitability, snapping at children, watchdog barking, and affection demand, which are of interest to people wanting dogs as pets. Authorities for the development of the profiles were 48 small animal veterinarians and 48 obedience judges, randomly selected from directories so as to represent equally men and women, and eastern, central, and western geographic regions of the United States. Each authority was asked to rank on each of the behavioral traits a list of 7 breeds chosen randomly from a list of 56 breeds. The data were analyzed in a custom-designed computer program that pooled the data and then ranked all 56 breeds on the basis of the 13 traits. The results indicated that some behavioral traits discriminate between breeds better than others. An examination of sample profiles indicated the feasibility of developing a statistically meaningful behavioral profile that integrates comparative rankings of several authorities balanced as to representation of geographic location, sex, and type of experience with dogs.

Productive performance of the dairy cattle Girolando breed mediated by the fat-related genes DGAT1 and LEP and their polymorphisms.

PubMed

Cardoso, S R; Queiroz, L B; Goulart, V Alonso; Mourão, G B; Benedetti, E; Goulart, L R

2011-12-01

Candidate genes have been associated with milk production in bovines, such as the diacylglycerol O-acyltransferase 1 (DGAT1) and leptin (LEP); however, they have not been simultaneously investigated nor have been evaluated in the Brazilian Girolando breed (Gir×Holstein, backcrossed to Holstein). Our aim was to determine the influence of fat-related genes, DGAT1 and LEP, and their polymorphisms on performance traits of milk production in the Girolando breed. Results indicated that the K allele of the DGAT1 gene showed a significant association with total and average daily milk production with additive effect. The LEP gene showed that the A allele and its homozygote are highly prevalent and almost fixed in this population and may have been favorably selected during backcrossing for the origin of this breed. The important impact of the K allele of the DGAT1 gene on milk production corroborates the initiative of performing marker-assisted selections with this gene in breeding programs of the Girolando breed. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

PubMed

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

2014-10-10

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

Genomic Selection in Plant Breeding: Methods, Models, and Perspectives.

PubMed

Crossa, José; Pérez-Rodríguez, Paulino; Cuevas, Jaime; Montesinos-López, Osval; Jarquín, Diego; de Los Campos, Gustavo; Burgueño, Juan; González-Camacho, Juan M; Pérez-Elizalde, Sergio; Beyene, Yoseph; Dreisigacker, Susanne; Singh, Ravi; Zhang, Xuecai; Gowda, Manje; Roorkiwal, Manish; Rutkoski, Jessica; Varshney, Rajeev K

2017-11-01

Genomic selection (GS) facilitates the rapid selection of superior genotypes and accelerates the breeding cycle. In this review, we discuss the history, principles, and basis of GS and genomic-enabled prediction (GP) as well as the genetics and statistical complexities of GP models, including genomic genotype×environment (G×E) interactions. We also examine the accuracy of GP models and methods for two cereal crops and two legume crops based on random cross-validation. GS applied to maize breeding has shown tangible genetic gains. Based on GP results, we speculate how GS in germplasm enhancement (i.e., prebreeding) programs could accelerate the flow of genes from gene bank accessions to elite lines. Recent advances in hyperspectral image technology could be combined with GS and pedigree-assisted breeding. Copyright © 2017 Elsevier Ltd. All rights reserved.

Signatures of selection in five Italian cattle breeds detected by a 54K SNP panel.

PubMed

Mancini, Giordano; Gargani, Maria; Chillemi, Giovanni; Nicolazzi, Ezequiel Luis; Marsan, Paolo Ajmone; Valentini, Alessio; Pariset, Lorraine

2014-02-01

In this study we used a medium density panel of SNP markers to perform population genetic analysis in five Italian cattle breeds. The BovineSNP50 BeadChip was used to genotype a total of 2,935 bulls of Piedmontese, Marchigiana, Italian Holstein, Italian Brown and Italian Pezzata Rossa breeds. To determine a genome-wide pattern of positive selection we mapped the F st values against genome location. The highest F st peaks were obtained on BTA6 and BTA13 where some candidate genes are located. We identified selection signatures peculiar of each breed which suggest selection for genes involved in milk or meat traits. The genetic structure was investigated by using a multidimensional scaling of the genetic distance matrix and a Bayesian approach implemented in the STRUCTURE software. The genotyping data showed a clear partitioning of the cattle genetic diversity into distinct breeds if a number of clusters equal to the number of populations were given. Assuming a lower number of clusters beef breeds group together. Both methods showed all five breeds separated in well defined clusters and the Bayesian approach assigned individuals to the breed of origin. The work is of interest not only because it enriches the knowledge on the process of evolution but also because the results generated could have implications for selective breeding programs.

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.

Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness

PubMed Central

Bink, Marco CAM; van Heerwaarden, Joost; Chancerel, Emilie; Boury, Christophe; Lesur, Isabelle; Isik, Fikret; Bouffier, Laurent; Plomion, Christophe

2016-01-01

Background Increasing our understanding of the genetic architecture of complex traits, through analyses of genotype-phenotype associations and of the genes/polymorphisms accounting for trait variation, is crucial, to improve the integration of molecular markers into forest tree breeding. In this study, two full-sib families and one breeding population of maritime pine were used to identify quantitative trait loci (QTLs) for height growth and stem straightness, through linkage analysis (LA) and linkage disequilibrium (LD) mapping approaches. Results The populations used for LA consisted of two unrelated three-generation full-sib families (n = 197 and n = 477). These populations were assessed for height growth or stem straightness and genotyped for 248 and 217 markers, respectively. The population used for LD mapping consisted of 661 founders of the first and second generations of the breeding program. This population was phenotyped for the same traits and genotyped for 2,498 single-nucleotide polymorphism (SNP) markers corresponding to 1,652 gene loci. The gene-based reference genetic map of maritime pine was used to localize and compare the QTLs detected by the two approaches, for both traits. LA identified three QTLs for stem straightness and two QTLs for height growth. The LD study yielded seven significant associations (P ≤ 0.001): four for stem straightness and three for height growth. No colocalisation was found between QTLs identified by LA and SNPs detected by LD mapping for the same trait. Conclusions This study provides the first comparison of LA and LD mapping approaches in maritime pine, highlighting the complementary nature of these two approaches for deciphering the genetic architecture of two mandatory traits of the breeding program. PMID:27806077

Twenty years of artificial directional selection have shaped the genome of the Italian Large White pig breed.

PubMed

Schiavo, G; Galimberti, G; Calò, D G; Samorè, A B; Bertolini, F; Russo, V; Gallo, M; Buttazzoni, L; Fontanesi, L

2016-04-01

In this study, we investigated at the genome-wide level if 20 years of artificial directional selection based on boar genetic evaluation obtained with a classical BLUP animal model shaped the genome of the Italian Large White pig breed. The most influential boars of this breed (n = 192), born from 1992 (the beginning of the selection program of this breed) to 2012, with an estimated breeding value reliability of >0.85, were genotyped with the Illumina Porcine SNP60 BeadChip. After grouping the boars in eight classes according to their year of birth, filtered single nucleotide polymorphisms (SNPs) were used to evaluate the effects of time on genotype frequency changes using multinomial logistic regression models. Of these markers, 493 had a PBonferroni  < 0.10. However, there was an increasing number of SNPs with a decreasing level of allele frequency changes over time, representing a continuous profile across the genome. The largest proportion of the 493 SNPs was on porcine chromosome (SSC) 7, SSC2, SSC8 and SSC18 for a total of 204 haploblocks. Functional annotations of genomic regions, including the 493 shifted SNPs, reported a few Gene Ontology terms that might underly the biological processes that contributed to increase performances of the pigs over the 20 years of the selection program. The obtained results indicated that the genome of the Italian Large White pigs was shaped by a directional selection program derived by the application of methodologies assuming the infinitesimal model that captured a continuous trend of allele frequency changes in the boar population. © 2015 Stichting International Foundation for Animal Genetics.

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...

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.

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.

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.

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...

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.

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.

Sugarcane Genotype Selection on Muck and Sand Soils in Florida — a Case for Dedicated Environments

USDA-ARS?s Scientific Manuscript database

Traditionally, the cooperative sugarcane (Saccharum spp.) breeding program located at Canal Point has selected genotypes exclusively on muck soils in the early to middle stages of the program. Only about 0.20% of genotypes are ever tested on sand, resulting in the possibility that many sand-adapted ...

Sugarcane Genotype Selection on Muck and Sand Soils in Florida — a Case for Dedicated Environments

USDA-ARS?s Scientific Manuscript database

Traditionally, the cooperative sugarcane breeding program at Canal Point, Florida has selected genotypes exclusively on muck soils in the early to middle stages of the program, resulting in the possibility that many genotypes adapted to sand soils are discarded. The objective of this study was to de...

Population Structure and Genomic Breed Composition in an Angus-Brahman Crossbred Cattle Population.

PubMed

Gobena, Mesfin; Elzo, Mauricio A; Mateescu, Raluca G

2018-01-01

Crossbreeding is a common strategy used in tropical and subtropical regions to enhance beef production, and having accurate knowledge of breed composition is essential for the success of a crossbreeding program. Although pedigree records have been traditionally used to obtain the breed composition of crossbred cattle, the accuracy of pedigree-based breed composition can be reduced by inaccurate and/or incomplete records and Mendelian sampling. Breed composition estimation from genomic data has multiple advantages including higher accuracy without being affected by missing, incomplete, or inaccurate records and the ability to be used as independent authentication of breed in breed-labeled beef products. The present study was conducted with 676 Angus-Brahman crossbred cattle with genotype and pedigree information to evaluate the feasibility and accuracy of using genomic data to determine breed composition. We used genomic data in parametric and non-parametric methods to detect population structure due to differences in breed composition while accounting for the confounding effect of close familial relationships. By applying principal component analysis (PCA) and the maximum likelihood method of ADMIXTURE to genomic data, it was possible to successfully characterize population structure resulting from heterogeneous breed ancestry, while accounting for close familial relationships. PCA results offered additional insight into the different hierarchies of genetic variation structuring. The first principal component was strongly correlated with Angus-Brahman proportions, and the second represented variation within animals that have a relatively more extended Brangus lineage-indicating the presence of a distinct pattern of genetic variation in these cattle. Although there was strong agreement between breed proportions estimated from pedigree and genetic information, there were significant discrepancies between these two methods for certain animals. This was most likely due to inaccuracies in the pedigree-based estimation of breed composition, which supported the case for using genomic information to complement and/or replace pedigree information when estimating breed composition. Comparison with a supervised analysis where purebreds are used as the training set suggest that accurate predictions can be achieved even in the absence of purebred population information.

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%.

Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds.

PubMed

Onzima, R B; Upadhyay, M R; Mukiibi, R; Kanis, E; Groenen, M A M; Crooijmans, R P M A

2018-02-01

Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium-density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (H O ) and expected (H E ) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub-structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f 4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within-breed diversity and heterozygote advantage in crossbreeding schemes. © 2018 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.

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.

Low Impact of Avian Pox on Captive-Bred Houbara Bustard Breeding Performance.

PubMed

Le Loc'h, Guillaume; Souley, Mam-Noury Amadou; Bertagnoli, Stéphane; Paul, Mathilde C

2017-01-01

Avian pox, a disease caused by avipoxviruses, is a major cause of decline of some endangered bird species. While its impact has been assessed in several species in the wild, effects of the disease in conservation breeding have never been studied. Houbara bustard species ( Chlamydotis undulata and Chlamydotis macqueenii ), whose populations declined in the last decades, have been captive bred for conservation purposes for more than 20 years. While mortality and morbidity induced by avipoxviruses can be controlled by appropriate management, the disease might still affect bird breeding performance and jeopardize the production objectives of conservation programs. Impacts of the disease was studied during two outbreaks in captive-bred juvenile Houbara bustards in Morocco in 2009-2010 and 2010-2011, by modeling the effect of the disease on individual breeding performance (male display and female egg production) of 2,797 birds during their first breeding season. Results showed that the impact of avian pox on the ability of birds to reproduce and on the count of displays or eggs is low and mainly non-significant. The absence of strong impact compared to what could be observed in other species in the wild may be explained by the controlled conditions provided by captivity, especially the close veterinary monitoring of each bird. Those results emphasize the importance of individual management to prevent major disease emergence and their effects in captive breeding of endangered species.

New World cattle show ancestry from multiple independent domestication events

PubMed Central

McTavish, Emily Jane; Decker, Jared E.; Schnabel, Robert D.; Taylor, Jeremy F.; Hillis, David M.

2013-01-01

Previous archeological and genetic research has shown that modern cattle breeds are descended from multiple independent domestication events of the wild aurochs (Bos primigenius) ∼10,000 y ago. Two primary areas of domestication in the Middle East/Europe and the Indian subcontinent resulted in taurine and indicine lines of cattle, respectively. American descendants of cattle brought by European explorers to the New World beginning in 1493 generally have been considered to belong to the taurine lineage. Our analyses of 47,506 single nucleotide polymorphisms show that these New World cattle breeds, as well as many related breeds of cattle in southern Europe, actually exhibit ancestry from both the taurine and indicine lineages. In this study, we show that, although European cattle are largely descended from the taurine lineage, gene flow from African cattle (partially of indicine origin) contributed substantial genomic components to both southern European cattle breeds and their New World descendants. New World cattle breeds, such as Texas Longhorns, provide an opportunity to study global population structure and domestication in cattle. Following their introduction into the Americas in the late 1400s, semiferal herds of cattle underwent between 80 and 200 generations of predominantly natural selection, as opposed to the human-mediated artificial selection of Old World breeding programs. Our analyses of global cattle breed population history show that the hybrid ancestry of New World breeds contributed genetic variation that likely facilitated the adaptation of these breeds to a novel environment. PMID:23530234

Genome-Wide Association Mapping for Yield and Other Agronomic Traits in an Elite Breeding Population of Tropical Rice (Oryza sativa)

PubMed Central

Lalusin, Antonio; Borromeo, Teresita; Gregorio, Glenn; Hernandez, Jose; Virk, Parminder; Collard, Bertrand; McCouch, Susan R.

2015-01-01

Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models. PMID:25785447

Feasibility of pedigree recording and genetic selection in village sheep flocks of smallholder farmers.

PubMed

Gizaw, Solomon; Goshme, Shenkute; Getachew, Tesfaye; Haile, Aynalem; Rischkowsky, Barbara; van Arendonk, Johan; Valle-Zárate, Anne; Dessie, Tadelle; Mwai, Ally Okeyo

2014-06-01

Pedigree recording and genetic selection in village flocks of smallholder farmers have been deemed infeasible by researchers and development workers. This is mainly due to the difficulty of sire identification under uncontrolled village breeding practices. A cooperative village sheep-breeding scheme was designed to achieve controlled breeding and implemented for Menz sheep of Ethiopia in 2009. In this paper, we evaluated the reliability of pedigree recording in village flocks by comparing genetic parameters estimated from data sets collected in the cooperative village and in a nucleus flock maintained under controlled breeding. Effectiveness of selection in the cooperative village was evaluated based on trends in breeding values over generations. Heritability estimates for 6-month weight recorded in the village and the nucleus flock were very similar. There was an increasing trend over generations in average estimated breeding values for 6-month weight in the village flocks. These results have a number of implications: the pedigree recorded in the village flocks was reliable; genetic parameters, which have so far been estimated based on nucleus data sets, can be estimated based on village recording; and appreciable genetic improvement could be achieved in village sheep selection programs under low-input smallholder farming systems.

Lesser scaup breeding probability and female survival on the yukon flats, Alaska

USGS Publications Warehouse

Martin, K.H.; Lindberg, M.S.; Schmutz, J.A.; Bertram, M.R.

2009-01-01

Information on the ecology of waterfowl breeding in the boreal forest is lacking, despite the boreal region's importance to continental waterfowl populations and to duck species that are currently declining, such as lesser scaup (Aythya affinis). We estimated breeding probability and breeding season survival of female lesser scaup on the Yukon Flats National Wildlife Refuge, Alaska, USA, in 2005 and 2006. We captured and marked 93 lesser scaup with radiotransmitters during prelaying and nesting periods. Although all marked lesser scaup females were paired throughout prelaying and incubation periods, we estimated breeding probability over both years as 0.12 (SE = 0.05, n = 67) using telemetry. Proportion of lesser scaup females undergoing rapid follicle growth at capture in 2006 was 0.46 (SE = 0.11, n = 37), based on concentration of yolk precursors in blood plasma. By combining methods based on telemetry, yolk precursors, and postovulatory follicles, we estimated maximum breeding probability as 0.68 (SE = 0.08, n = 37) in 2006. Notably, breeding probability was positively related to female body mass. Survival of female lesser scaup during the nesting and brood-rearing periods was 0.92 (SE = 0.05) in 2005 and 0.86 (SE = 0.08) in 2006. Our results suggest that breeding probability is lower than expected for lesser scaup. In addition, the implicit assumption of continental duck-monitoring programs that all paired females attempt to breed should be reevaluated. Recruitment estimates based on annual breeding-pair surveys may overestimate productivity of scaup pairs in the boreal forest. ?? The Wildlife Society.

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

PubMed

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

2015-02-01

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

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

PubMed Central

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

2015-01-01

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

A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes

PubMed Central

2012-01-01

Background Carcass fatness is an important trait in most pig breeding programs. Following market requests, breeding plans for fresh pork consumption are usually designed to reduce carcass fat content and increase lean meat deposition. However, the Italian pig industry is mainly devoted to the production of Protected Designation of Origin dry cured hams: pigs are slaughtered at around 160 kg of live weight and the breeding goal aims at maintaining fat coverage, measured as backfat thickness to avoid excessive desiccation of the hams. This objective has shaped the genetic pool of Italian heavy pig breeds for a few decades. In this study we applied a selective genotyping approach within a population of ~ 12,000 performance tested Italian Large White pigs. Within this population, we selectively genotyped 304 pigs with extreme and divergent backfat thickness estimated breeding value by the Illumina PorcineSNP60 BeadChip and performed a genome wide association study to identify loci associated to this trait. Results We identified 4 single nucleotide polymorphisms with P≤5.0E-07 and additional 119 ones with 5.0E-07

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

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

PubMed

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

2012-11-01

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

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...

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.

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.

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

Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia

PubMed Central

2010-01-01

Background Identification of global livestock diversity hotspots and their importance in diversity maintenance is essential for making global conservation efforts. We screened 52 sheep breeds from the Eurasian subcontinent with 20 microsatellite markers. By estimating and weighting differently within- and between-breed genetic variation our aims were to identify genetic diversity hotspots and prioritize the importance of each breed for conservation, respectively. In addition we estimated how important within-species diversity hotspots are in livestock conservation. Results Bayesian clustering analysis revealed three genetic clusters, termed Nordic, Composite and Fat-tailed. Southern breeds from close to the region of sheep domestication were more variable, but less genetically differentiated compared with more northern populations. Decreasing weight for within-breed diversity component led to very high representation of genetic clusters or regions containing more diverged breeds, but did not increase phenotypic diversity among the high ranked breeds. Sampling populations throughout 14 regional groups was suggested for maximized total genetic diversity. Conclusions During initial steps of establishing a livestock conservation program populations from the diversity hot-spot area are the most important ones, but for the full design our results suggested that approximately equal population presentation across environments should be considered. Even in this case, higher per population emphasis in areas of high diversity is appropriate. The analysis was based on neutral data, but we have no reason to think the general trend is limited to this type of data. However, a comprehensive valuation of populations should balance production systems, phenotypic traits and available genetic information, and include consideration of probability of success. PMID:20698974

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.

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.

Production objectives, trait and breed preferences of farmers keeping N'Dama, Fulani Zebu and crossbred cattle and implications for breeding programs.

PubMed

Traoré, S A; Markemann, A; Reiber, C; Piepho, H P; Valle Zárate, A

2017-04-01

Many local livestock breeds in developing countries are being replaced by exotic breeds, leading to a loss of genetic resources. In southern Mali, for the past two decades, a trend towards increasing crossbreeding between the trypanotolerant N'Dama cattle and the trypano-susceptible Fulani Zebu cattle has been taking place. A survey with 160 farmers owning a cattle herd was carried out in southern Mali to investigate their production objectives, as well as trait and breed preferences and correlated socio-economic determinants in order to understand farmers' breeding decisions and to identify comparative advantages of three breed groups (N'Dama, Fulani Zebu and crossbreds) raised in the study area. Data were analyzed using an exploded logit model. The reasons for raising cattle, as well as trait and breed preferences reflected the multiple objectives of the farmers. Draught power and savings were the most important production objectives. Productive traits were ranked highest; farmers reported large body size as the most preferred trait, followed by fertility, draught ability and milk yield. Crossbreds were the favored breed group. Breed preferences were mainly explained by 'resistance to disease' for N'Dama cattle and 'high market price' for Fulani Zebu and crossbred cattle. Production objectives, trait and breed preferences were mainly influenced by farmer group (local farmers and settled transhumants). Local farmers put comparatively more emphasis on livestock functions linked to crop production such as draught power. They had a higher preference for traction ability as a selection trait and preferred N'Dama over Fulani Zebu cattle. Settled transhumants emphasized milk yield as a selection trait and preferred Fulani Zebu over N'Dama. The results indicate that the trend towards more crossbreeding will continue putting the N'Dama breed under high risk of genetic dilution in southern Mali. The N'Dama cattle remain a valuable breed due to their adaptive traits such as disease and drought tolerance and their good traction ability, fulfilling the diverse objectives of local farmers. Crossbreeding was found to be a promising breeding strategy, which might contribute to the maintenance of the local breed, provided that breeding schemes are thoroughly planned and organized.

Cornell University remote sensing program. [New York

NASA Technical Reports Server (NTRS)

Liang, T.; Mcnair, A. J.; Philipson, W. R. (Principal Investigator)

1978-01-01

The author has identified the following significant results. Available aerial photographs were used to characterize mosquito breeding sites in Oswego County, New York. Numerous wetlands are contained within this county; this area is the only inland area in North America to have confirmed outbreaks of eastern equine encephalitis. This photocharacterization of primary mosquito breeding sites will be used to develop effective spraying. Large scale color and color infrared aerial photographs were used to assess changes in aquatic vegetation that accompanied phosphorus reduction in an eutrophic lake in New York.

Etiopathogenesis of Canine Hip Dysplasia, Prevalence, and Genetics.

PubMed

King, Michael D

2017-07-01

First identified in 1935, canine hip dysplasia is thought to be the most common orthopedic condition diagnosed in the dog. It is most prevalent in large and giant breed dogs, with a complex polygenic mode of inheritance, and relatively low heritability. External factors including caloric intake when growing have a significant effect on phenotypic expression. Initial joint laxity progresses to osteoarthritis due to subluxation and abnormal wearing. Selective breeding programs to attempt to decrease prevalence have shown modest results so far. Copyright © 2017 Elsevier Inc. All rights reserved.

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...

Predicting extractives content of Eucalyptus bosistoana F. Muell. Heartwood from stem cores by near infrared spectroscopy

NASA Astrophysics Data System (ADS)

Li, Yanjie; Altaner, Clemens

2018-06-01

Time and resource are the restricting factors for the wider use of chemical information of wood in tree breeding programs. NIR offers an advantage over wet-chemical analysis in these aspects and is starting to be used for tree breeding. This work describes the development of a NIR-based assessment of extractive content in heartwood of E. bosistoana, which does not require milling and conditioning of the samples. This was achieved by applying the signal processing algorithms (external parameter orthogonalisation (EPO) and significance multivariate correlation (sMC)) to spectra obtained from solid wood cores, which were able to correct for moisture content, grain direction and sample form. The accuracy of extractive content predictions was further improved by variable selection, resulting in a root mean square error of 1.27%. Considering the range of extractive content in E. bosistoana heartwood of 1.3 to 15.0%, the developed NIR calibration has the potential to be used in an E. bosistoana breeding program or to assess the special variation in extractive content throughout a stem.

Temporal Dynamics and Spatial Patterns of Aedes aegypti Breeding Sites, in the Context of a Dengue Control Program in Tartagal (Salta Province, Argentina).

PubMed

Espinosa, Manuel; Weinberg, Diego; Rotela, Camilo H; Polop, Francisco; Abril, Marcelo; Scavuzzo, Carlos Marcelo

2016-05-01

Since 2009, Fundación Mundo Sano has implemented an Aedes aegypti Surveillance and Control Program in Tartagal city (Salta Province, Argentina). The purpose of this study was to analyze temporal dynamics of Ae. aegypti breeding sites spatial distribution, during five years of samplings, and the effect of control actions over vector population dynamics. Seasonal entomological (larval) samplings were conducted in 17,815 fixed sites in Tartagal urban area between 2009 and 2014. Based on information of breeding sites abundance, from satellite remote sensing data (RS), and by the use of Geographic Information Systems (GIS), spatial analysis (hotspots and cluster analysis) and predictive model (MaxEnt) were performed. Spatial analysis showed a distribution pattern with the highest breeding densities registered in city outskirts. The model indicated that 75% of Ae. aegypti distribution is explained by 3 variables: bare soil coverage percentage (44.9%), urbanization coverage percentage(13.5%) and water distribution (11.6%). This results have called attention to the way entomological field data and information from geospatial origin (RS/GIS) are used to infer scenarios which could then be applied in epidemiological surveillance programs and in the determination of dengue control strategies. Predictive maps development constructed with Ae. aegypti systematic spatiotemporal data, in Tartagal city, would allow public health workers to identify and target high-risk areas with appropriate and timely control measures. These tools could help decision-makers to improve health system responses and preventive measures related to vector control.

Temporal Dynamics and Spatial Patterns of Aedes aegypti Breeding Sites, in the Context of a Dengue Control Program in Tartagal (Salta Province, Argentina)

PubMed Central

Espinosa, Manuel; Weinberg, Diego; Rotela, Camilo H.; Polop, Francisco; Abril, Marcelo; Scavuzzo, Carlos Marcelo

2016-01-01

Background Since 2009, Fundación Mundo Sano has implemented an Aedes aegypti Surveillance and Control Program in Tartagal city (Salta Province, Argentina). The purpose of this study was to analyze temporal dynamics of Ae. aegypti breeding sites spatial distribution, during five years of samplings, and the effect of control actions over vector population dynamics. Methodology/Principal Findings Seasonal entomological (larval) samplings were conducted in 17,815 fixed sites in Tartagal urban area between 2009 and 2014. Based on information of breeding sites abundance, from satellite remote sensing data (RS), and by the use of Geographic Information Systems (GIS), spatial analysis (hotspots and cluster analysis) and predictive model (MaxEnt) were performed. Spatial analysis showed a distribution pattern with the highest breeding densities registered in city outskirts. The model indicated that 75% of Ae. aegypti distribution is explained by 3 variables: bare soil coverage percentage (44.9%), urbanization coverage percentage(13.5%) and water distribution (11.6%). Conclusions/Significance This results have called attention to the way entomological field data and information from geospatial origin (RS/GIS) are used to infer scenarios which could then be applied in epidemiological surveillance programs and in the determination of dengue control strategies. Predictive maps development constructed with Ae. aegypti systematic spatiotemporal data, in Tartagal city, would allow public health workers to identify and target high-risk areas with appropriate and timely control measures. These tools could help decision-makers to improve health system responses and preventive measures related to vector control. PMID:27223693

Contribution of research to management and recovery of the roseate tern: review of a twelve-year project

USGS Publications Warehouse

Nisbet, I.C.T.; Spendelow, J.A.

1999-01-01

The Northwest Atlantic population of the Roseate Tern (Sterna dougallii) is largely confined to a small breeding area along the northeast coast of the USA between 40? and 42?N. This population was listed as endangered in the USA in 1987 because it was dangerously concentrated into a few breeding sites (85% on two islands in the 1980s). The nesting population in the area from Long Island, New York to Cape Cod, Massachusetts has been studied intensively since 1987, in conjunction with a program of management of the breeding colonies. This paper summarizes the results of the research program and discusses the extent to which it has contributed to effective management. The regional population now numbers about 4,000 breeding pairs and has been increasing slowly since 1987, except between 1991 and 1992 when it declined by about 17%. This decline was probably caused by Hurricane `Bob' in August 1991. Roseate Terns have specialized foraging habits and are concentrated into a small number of foraging areas near the nesting colonies. The historically important breeding sites were taken over by large gulls between 1930 and 1972. Many of the terns moved to less suitable sites near the mainland, where they are subject to predation by mainland-based predators. Despite this, Roseate Terns breed with high success at many sites. The sex-ratio is skewed towards females; about 12% of nests are attended by female-female pairs. The annual adult survival rate (0.83) is unusually low for a seabird. Most mortality occurs away from the breeding grounds, but the winter quarters remained unknown until one roost site was found in Brazil in 1995-1997. A major management goal has been to restore former colony-sites by eliminating nesting gulls, but the success of some of these projects has been questionable because they may have attracted birds to sites with higher levels of predation. Although the research has yielded important information about the biology and demography of the species, it has taken longer than expected to obtain and analyze data from multiple sites on this long-lived species. Most work has been carried out at breeding sites: critical studies on feeding ecology and winter ecology have been hampered by insufficient funding and the paucity of self-motivated biologists. Hence, the program has not yet provided all the keys to restoring the population.

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

Breed and trait preferences of Sheko cattle keepers in southwestern Ethiopia.

PubMed

Desta, Takele Taye; Ayalew, Workneh; Hegde, B P

2011-04-01

Like their smallholder subsistence counterparts in developing countries, breed and trait preferences of Sheko cattle keepers have broad perspectives. Our study has documented breed and trait preferences of Sheko cattle keepers in southwestern Ethiopia--the natural breeding tract of Sheko cattle. Our results showed that due to their multifunctionality, cattle are the most preferred livestock species. Overall, farmers showed slightly more preference to local Zebus over Sheko breed. This is due to voracious feeding behavior of Sheko cattle, which make them less preferable in the face of worsening feed shortage, and due to aggressive temperament of Sheko cattle. This is despite Sheko's outperforming potential over local Zebus in their milk production, draft power, and hardiness. At trait level, overall milk production was consistently reported as the most preferred trait followed by fertility and traction. This trait preference rank has matched with the reported frequency count ranks for Sheko cattle use. However, breed preference rank has not matched with reported trait preference ranks because Sheko excels local Zebus in all the three most preferred traits, but it was ranked second. Therefore, to minimize these conflicting interests, breed management plans for Sheko cattle should target on strategies that help to solve feed shortage problem and to improve feeding practices, and on selection of less aggressive Sheko cattle. Therefore, these strategies should be considered in line with Sheko cattle conservation and genetic improvement programs.

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.

Genetic variation and comparison of orchardgrass (Dactylis glomerata L.) cultivars and wild accessions as revealed by SSR markers.

PubMed

Xie, W G; Lu, X F; Zhang, X Q; Huang, L K; Cheng, L

2012-02-24

Orchardgrass is a highly variable, perennial forage grass that is cultivated throughout temperate and subtropical regions of the world. Despite its economic importance, the genetic relationship and distance among and within cultivars are largely unknown but would be of great interest for breeding programs. We investigated the molecular variation and structure of cultivar populations, compared the level of genetic diversity among cultivars (Baoxing, Anba, Bote, and Kaimo), subspecies (Dactylis glomerata ssp Woronowii) and advanced breeding line (YA02-116) to determine whether there is still sufficient genetic diversity within presently used cultivars for future breeding progress in China. Twenty individuals were analyzed from each of six accessions using SSR markers; 114 easily scored bands were generated from 15 SSR primer pairs, with an average of 7.6 alleles per locus. The polymorphic rate was 100% among the 120 individuals, reflecting a high degree of genetic diversity. Among the six accessions, the highest genetic diversity was observed in Kaimo (H = 0.2518; I = 0.3916; P = 87.3%) and 02-116 had a lower level of genetic diversity (H = 0.1806; I = 0.2788; P = 58.73%) compared with other cultivars tested. An of molecular variance revealed a much larger genetic variation within accessions (65%) than between them (35%). This observation suggests that these cultivars have potential for providing rich genetic resource for further breeding program. Furthermore, the study also indicated that Chinese orchardgrass breeding has involved strong selection for adaptation to forage production, which may result in restricted genetic base of orchardgrass cultivar.

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.

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.

The GCP molecular marker toolkit, an instrument for use in breeding food security crops.

PubMed

Van Damme, Veerle; Gómez-Paniagua, Humberto; de Vicente, M Carmen

2011-12-01

Crop genetic resources carry variation useful for overcoming the challenges of modern agriculture. Molecular markers can facilitate the selection of agronomically important traits. The pervasiveness of genomics research has led to an overwhelming number of publications and databases, which are, nevertheless, scattered and hence often difficult for plant breeders to access, particularly those in developing countries. This situation separates them from developed countries, which have better endowed programs for developing varieties. To close this growing knowledge gap, we conducted an intensive literature review and consulted with more than 150 crop experts on the use of molecular markers in the breeding program of 19 food security crops. The result was a list of effectively used and highly reproducible sequence tagged site (STS), simple sequence repeat (SSR), single nucleotide polymorphism (SNP), and sequence characterized amplified region (SCAR) markers. However, only 12 food crops had molecular markers suitable for improvement. That is, marker-assisted selection is not yet used for Musa spp., coconut, lentils, millets, pigeonpea, sweet potato, and yam. For the other 12 crops, 214 molecular markers were found to be effectively used in association with 74 different traits. Results were compiled as the GCP Molecular Marker Toolkit, a free online tool that aims to promote the adoption of molecular approaches in breeding activities.

Crocodilian perivitelline membrane-bound sperm detection.

PubMed

Augustine, Lauren

2017-05-01

Advanced reproductive technologies (ART's) are often employed with various taxa to enhance captive breeding programs and maintain genetic diversity. Perivitelline membrane-bound (PVM-bound) sperm detection has previously been demonstrated in avian and chelonian species as a useful technique for breeding management. In the absence of embryotic development within an egg, this technique can detect the presence of sperm trapped on the oocyte membrane confirming breeding, male reproductive status, and pair compatibility. PVM-bound sperm were successfully detected in three clutches of Cuban crocodile (Crocodylus rhombifer) eggs at the Smithsonian's National Zoological Park (NZP) for the first time in any crocodilian species. PVM-bound sperm were detected in fresh and incubated C. rhombifer eggs, as well as eggs that were developing (banded) and those that were not (not banded). The results of this study showed significant differences in average sperm densities per egg between clutches (p = 0.001). Additionally, there was not a significant difference within clutches between eggs that banded and those that did not band (Clutch A, p = 0.505; Clutch B, p = 0.665; Clutch C, p = 0.266). The results of this study demonstrate the necessity to microscopically examine eggs that do not develop (do not band), to determine if sperm is present, which can help animal managers problem solve reproductive shortcomings. PVM-bound sperm detection could be a useful technique in assessing crocodilian breeding programs, as well as have potential uses in studies assessing sperm storage, artificial insemination, and artificial incubation. This article is a U.S. Government work and is in the public domain in the USA.

Factors affecting the outcome of artificial insemination using cryopreserved spermatozoa in the giant panda (Ailuropoda melanoleuca).

PubMed

Huang, Yan; Li, Desheng; Zhou, Yingmin; Zhou, Qiang; Li, Rengui; Wang, Chengdong; Huang, Zhi; Hull, Vanessa; Zhang, Hemin

2012-01-01

Artificial insemination (AI) is an important component of captive breeding programs for endangered species, such as the giant panda. The panda has been the subject of increasingly successful captive breeding programs involving a compilation of assisted breeding techniques, including AI using cryopreserved spermatozoa. AI implementation is currently hampered by a lack of understanding of the factors that may cause failure. We investigated factors influencing the probability of success of AI for 14 giant panda females housed at the China Center for Research and Conservation of the Giant Panda (CCRCGP) inseminated in a total of 20 instances using cryopreserved spermatozoa from 11 males currently residing in 6 different captive breeding institutions. One of the pandas was the oldest giant panda female to ever successfully conceive from AI (20.5 years old). The success of AI was significantly affected by the timing of AI in relationship to both timing of peak urinary estrogen of the female and percent decline in urinary estrogen between the peak level and the first AI attempt. Our results suggest that the window for successful AI in giant pandas may be narrower than previously suspected, although individual differences in rates of decline in urinary estrogen may reflect some degree of variation in this crucial window across females. Our results are consistent with recent research on pandas and other species that demonstrates the efficacy of cryopreserved spermatozoa for AI and highlights the need for more in-depth analysis of factors related to female physiology that may influence its success. © 2011 Wiley Periodicals, Inc.

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

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.

Individual Quality Explains Variation in Reproductive Success Better than Territory Quality in a Long-Lived Territorial Raptor

PubMed Central

Zabala, Jabi; Zuberogoitia, Iñigo

2014-01-01

Evolution by natural selection depends on the relationship between individual traits and fitness. Variation in individual fitness can result from habitat (territory) quality and individual variation. Individual quality and specialization can have a deep impact on fitness, yet in most studies on territorial species the quality of territory and individuals are confused. We aimed to determine if variation in breeding success is better explained by territories, individual quality or a combination of both. We analysed the number of fledglings and the breeding quality index (the difference between the number of fledglings of an individual/breeding pair and the average number of fledglings of the monitored territories in the same year) as part of a long term (16 years) peregrine falcon (Falco peregrinus) monitoring program with identification of individuals. Using individual and territory identities as correlates of quality, we built Generalised Linear Models with Mixed effects, in which random factors depicted different hypotheses for sources of variation (territory/individual quality) in the reproductive success of unique breeding pairs, males and females, and assessed their performance. Most evidence supported the hypothesis that variation in breeding success is explained by individual identity, particularly male identity, rather than territory. There is also some evidence for inter year variations in the breeding success of females and a territory effect in the case of males. We argue that, in territorial species, individual quality is a major source of variation in breeding success, often masked by territory. Future ecological and conservation studies on habitat use should consider and include the effect of individuals, in order to avoid misleading results. PMID:24599280

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.

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.

Optimization of Swine Breeding Programs Using Genomic Selection with ZPLAN+

PubMed Central

Lopez, B. M.; Kang, H. S.; Kim, T. H.; Viterbo, V. S.; Kim, H. S.; Na, C. S.; Seo, K. S.

2016-01-01

The objective of this study was to evaluate the present conventional selection program of a swine nucleus farm and compare it with a new selection strategy employing genomic enhanced breeding value (GEBV) as the selection criteria. The ZPLAN+ software was employed to calculate and compare the genetic gain, total cost, return and profit of each selection strategy. The first strategy reflected the current conventional breeding program, which was a progeny test system (CS). The second strategy was a selection scheme based strictly on genomic information (GS1). The third scenario was the same as GS1, but the selection by GEBV was further supplemented by the performance test (GS2). The last scenario was a mixture of genomic information and progeny tests (GS3). The results showed that the accuracy of the selection index of young boars of GS1 was 26% higher than that of CS. On the other hand, both GS2 and GS3 gave 31% higher accuracy than CS for young boars. The annual monetary genetic gain of GS1, GS2 and GS3 was 10%, 12%, and 11% higher, respectively, than that of CS. As expected, the discounted costs of genomic selection strategies were higher than those of CS. The costs of GS1, GS2 and GS3 were 35%, 73%, and 89% higher than those of CS, respectively, assuming a genotyping cost of $120. As a result, the discounted profit per animal of GS1 and GS2 was 8% and 2% higher, respectively, than that of CS while GS3 was 6% lower. Comparison among genomic breeding scenarios revealed that GS1 was more profitable than GS2 and GS3. The genomic selection schemes, especially GS1 and GS2, were clearly superior to the conventional scheme in terms of monetary genetic gain and profit. PMID:26954222

Combining US and Brazilian microsatellite data for a meta-analysis of sheep (Ovis aries) breed diversity: facilitating the FAO Global Plan of Action for Conserving Animal Genetic Resources.

PubMed

Paiva, Samuel Rezende; Mariante, Arthur da Silva; Blackburn, Harvey D

2011-01-01

Microsatellites are commonly used to understand genetic diversity among livestock populations. Nevertheless, most studies have involved the processing of samples in one laboratory or with common standards across laboratories. Our objective was to identify an approach to facilitate the merger of microsatellite data for cross-country comparison of genetic resources when samples were not evaluated in a single laboratory. Eleven microsatellites were included in the analysis of 13 US and 9 Brazilian sheep breeds (N = 706). A Bayesian approach was selected and evaluated with and without a shared set of samples analyzed by each country. All markers had a posterior probability of greater than 0.5, which was higher than predicted as reasonable by the software used. Sensitivity analysis indicated no difference between results with or without shared samples. Cluster analysis showed breeds to be partitioned by functional groups of hair, meat, or wool types (K = 7 and 12 of STRUCTURE). Cross-country comparison of hair breeds indicated substantial genetic distances and within breed variability. The selected approach can facilitate the merger and analysis of microsatellite data for cross-country comparison and extend the utility of previously collected molecular markers. In addition, the result of this type of analysis can be used in new and existing conservation programs.

Binucleation to breed new plant species adaptable to their environments

PubMed Central

Moustafa, Khaled

2015-01-01

Classical plant breeding approaches may fall short to breed new plant species of high environmental and ecological interests. Biotechnological and genetic manipulations, on the other hand, may hold more effective capabilities to circumvent the limitations of sexual incompatibility and conventional breeding programs. Given that plant cells encompass multiple copies of organellar genomes (mitochondrial and plastidial genomes), an important question could be raised about whether an artificial attempt to duplicate the nuclear genome might also be conceivable through a binucleation approach (generating plant cells with 2 nuclei from 2 different plant species) for potential production of new polyploidies that would characterize new plant species. Since the complexities of plant genomes are the result of multiple genome duplications, an artificial binucleation approach would thus be of some interest to eventually varying plant genomes and producing new polyploidy from related or distal plant species. Here, I discuss the potentiality of such an approach to engineer binucleated plant cells as a germ of new plant species to fulfill some environmental applications such as increasing the biodiversity and breeding new species adaptable to harsh environmental stresses and increasing green surfaces to reduce atmospheric pollutions in arid lands with poor vegetation. PMID:26322577

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.

Conservation of indigenous cattle genetic resources in Southern Africa's smallholder areas: turning threats into opportunities - A review.

PubMed

Nyamushamba, G B; Mapiye, C; Tada, O; Halimani, T E; Muchenje, V

2017-05-01

The current review focuses on characterization and conservation efforts vital for the development of breeding programmes for indigenous beef cattle genetic resources in Southern Africa. Indigenous African cattle breeds were identified and characterized using information from refereed journals, conference papers and research reports. Results of this current review reviewed that smallholder beef cattle production in Southern Africa is extensive and dominated by indigenous beef cattle strains adaptable to the local environment. The breeds include Nguni, Mashona, Tuli, Malawi Zebu, Bovino de Tete, Angoni, Landim, Barotse, Twsana and Ankole. These breeds have important functions ranging from provision of food and income to socio-economic, cultural and ecological roles. They also have adaptive traits ranging from drought tolerant, resistance to ticks and tick borne diseases, heat tolerance and resistance to trypanosomosis. Stakeholders in the conservation of beef cattle were also identified and they included farmers, national government, research institutes and universities as well as breeding companies and societies in Southern Africa. Research efforts made to evaluate threats and opportunities of indigenous beef cattle production systems, assess the contribution of indigenous cattle to household food security and income, genetically and phenotypically characterize and conserve indigenous breeds, and develop breeding programs for smallholder beef production are highlighted. Although smallholder beef cattle production in the smallholder farming systems contributes substantially to household food security and income, their productivity is hindered by several constraints that include high prevalence of diseases and parasites, limited feed availability and poor marketing. The majority of the African cattle populations remain largely uncharacterized although most of the indigenous cattle breeds have been identified.

Disaggregating sorghum yield reductions under warming scenarios exposes narrow genetic diversity in US breeding programs

PubMed Central

Tack, Jesse; Lingenfelser, Jane; Jagadish, S. V. Krishna

2017-01-01

Historical adaptation of sorghum production to arid and semiarid conditions has provided promise regarding its sustained productivity under future warming scenarios. Using Kansas field-trial sorghum data collected from 1985 to 2014 and spanning 408 hybrid cultivars, we show that sorghum productivity under increasing warming scenarios breaks down. Through extensive regression modeling, we identify a temperature threshold of 33 °C, beyond which yields start to decline. We show that this decline is robust across both field-trial and on-farm data. Moderate and higher warming scenarios of 2 °C and 4 °C resulted in roughly 17% and 44% yield reductions, respectively. The average reduction across warming scenarios from 1 to 5 °C is 10% per degree Celsius. Breeding efforts over the last few decades have developed high-yielding cultivars with considerable variability in heat resilience, but even the most tolerant cultivars did not offer much resilience to warming temperatures. This outcome points to two concerns regarding adaption to global warming, the first being that adaptation will not be as simple as producers’ switching among currently available cultivars and the second being that there is currently narrow genetic diversity for heat resilience in US breeding programs. Using observed flowering dates and disaggregating heat-stress impacts, both pre- and postflowering stages were identified to be equally important for overall yields. These findings suggest the adaptation potential for sorghum under climate change would be greatly facilitated by introducing wider genetic diversity for heat resilience into ongoing breeding programs, and that there should be additional efforts to improve resilience during the preflowering phase. PMID:28808013

Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs.

PubMed

Marsden, Clare D; Ortega-Del Vecchyo, Diego; O'Brien, Dennis P; Taylor, Jeremy F; Ramirez, Oscar; Vilà, Carles; Marques-Bonet, Tomas; Schnabel, Robert D; Wayne, Robert K; Lohmueller, Kirk E

2016-01-05

Population bottlenecks, inbreeding, and artificial selection can all, in principle, influence levels of deleterious genetic variation. However, the relative importance of each of these effects on genome-wide patterns of deleterious variation remains controversial. Domestic and wild canids offer a powerful system to address the role of these factors in influencing deleterious variation because their history is dominated by known bottlenecks and intense artificial selection. Here, we assess genome-wide patterns of deleterious variation in 90 whole-genome sequences from breed dogs, village dogs, and gray wolves. We find that the ratio of amino acid changing heterozygosity to silent heterozygosity is higher in dogs than in wolves and, on average, dogs have 2-3% higher genetic load than gray wolves. Multiple lines of evidence indicate this pattern is driven by less efficient natural selection due to bottlenecks associated with domestication and breed formation, rather than recent inbreeding. Further, we find regions of the genome implicated in selective sweeps are enriched for amino acid changing variants and Mendelian disease genes. To our knowledge, these results provide the first quantitative estimates of the increased burden of deleterious variants directly associated with domestication and have important implications for selective breeding programs and the conservation of rare and endangered species. Specifically, they highlight the costs associated with selective breeding and question the practice favoring the breeding of individuals that best fit breed standards. Our results also suggest that maintaining a large population size, rather than just avoiding inbreeding, is a critical factor for preventing the accumulation of deleterious variants.

Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs

PubMed Central

Marsden, Clare D.; Ortega-Del Vecchyo, Diego; O’Brien, Dennis P.; Taylor, Jeremy F.; Ramirez, Oscar; Vilà, Carles; Marques-Bonet, Tomas; Schnabel, Robert D.; Wayne, Robert K.; Lohmueller, Kirk E.

2016-01-01

Population bottlenecks, inbreeding, and artificial selection can all, in principle, influence levels of deleterious genetic variation. However, the relative importance of each of these effects on genome-wide patterns of deleterious variation remains controversial. Domestic and wild canids offer a powerful system to address the role of these factors in influencing deleterious variation because their history is dominated by known bottlenecks and intense artificial selection. Here, we assess genome-wide patterns of deleterious variation in 90 whole-genome sequences from breed dogs, village dogs, and gray wolves. We find that the ratio of amino acid changing heterozygosity to silent heterozygosity is higher in dogs than in wolves and, on average, dogs have 2–3% higher genetic load than gray wolves. Multiple lines of evidence indicate this pattern is driven by less efficient natural selection due to bottlenecks associated with domestication and breed formation, rather than recent inbreeding. Further, we find regions of the genome implicated in selective sweeps are enriched for amino acid changing variants and Mendelian disease genes. To our knowledge, these results provide the first quantitative estimates of the increased burden of deleterious variants directly associated with domestication and have important implications for selective breeding programs and the conservation of rare and endangered species. Specifically, they highlight the costs associated with selective breeding and question the practice favoring the breeding of individuals that best fit breed standards. Our results also suggest that maintaining a large population size, rather than just avoiding inbreeding, is a critical factor for preventing the accumulation of deleterious variants. PMID:26699508

[Genetic improvement of cotton varieties in Huang-Huai region in China since 1950's. III. Improvement on agronomy properties, disease resistance and stability].

PubMed

Jiang, B G; Kong, F L; Zhang, Q Y; Yang, F X; Jiang, R Q

2000-01-01

Data from a set of 5-location and 2-year experiments on 10 representative historical cotton varieties and the data of Huang-Huai Regional Cotton Trials from 1973 to 1996 were analyzed to estimate the effects of genetic improvement in agronomy properties, disease resistance and stability of cotton in Huang-Huai Region in China. The results indicated that a great genetic progress of earliness and disease resistance had been achieved by breeding programs since 1950's. The maturity was shortened 3-5 days; The rate of preforst yield was increased about 7 percentages. The problem of resistance to Fususium wilt has been solved and the resistance to Verticillum wilt was improving. Some progress in stability of cotton varieties also has been achieved by breeding programs since 1950.

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

PubMed

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

2017-10-23

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

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...

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.

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.

The first 50 years of the North American Breeding Bird Survey

USGS Publications Warehouse

Sauer, John; Ziolkowski, David; Pardieck, Keith L.; Smith, Adam C.; Hudson, Marie-Anne R.; Rodriguez, Vicente; Berlanga, Humberto; Niven, Daniel; Link, William

2017-01-01

The vision of Chandler (Chan) S. Robbins for a continental-scale omnibus survey of breeding birds led to the development of the North American Breeding Bird Survey (BBS). Chan was uniquely suited to develop the BBS. His position as a government scientist had given him experience with designing and implementing continental-scale surveys, his research background made him an effective advocate of the need for a survey to monitor pesticide effects on birds, and his prominence in the birding community gave him connections to infrastructure—a network of qualified volunteer birders who could conduct roadside surveys with standardized point counts. Having started in the eastern United States and the Atlantic provinces of Canada in 1966, the BBS now provides population change information for ∼546 species in the continental United States and Canada, and recently initiated routes in Mexico promise to greatly expand the areas and species covered by the survey. Although survey protocols have remained unchanged for 50 years, the BBS remains relevant in a changing world. Several papers that follow in this Special Section of The Condor: Ornithological Advances review how the BBS has been applied to conservation assessments, especially in combination with other large-scale survey data. A critical feature of the BBS program is an active research program into field and analytical methods to enhance the quality of the count data and to control for factors that influence detectability. Papers in the Special Section also present advances in BBS analyses that improve the utility of this expanding and sometimes controversial survey. In this Perspective, we introduce the Special Section by reviewing the history of the BBS, describing current analyses, and providing summary trend results for all species, highlighting 3 groups of conservation concern: grassland-breeding birds, aridland-breeding birds, and aerial insectivorous birds.

Comparative ecophysiology of a critically endangered (CR) ectotherm: Implications for conservation management.

PubMed

Currylow, Andrea F T; Mandimbihasina, Angelo; Gibbons, Paul; Bekarany, Ernest; Stanford, Craig B; Louis, Edward E; Crocker, Daniel E

2017-01-01

Captive breeding is a vital conservation tool for many endangered species programs. It is often a last resort when wild animal population numbers drop to below critical minimums for natural reproduction. However, critical ecophysiological information of wild counterparts may not be well documented or understood, leading to years of minimal breeding successes. We collected endocrine and associated ecological data on a critically endangered ectotherm concurrently in the wild and in captivity over several years. We tracked plasma concentrations of steroid stress and reproductive hormones, body condition, activity, and environmental parameters in three populations (one wild and two geographically distinct captive) of ploughshare tortoise (Astrochelys yniphora). Hormone profiles along with environmental and behavioral data are presented and compared. We show that animals have particular seasonal environmental requirements that can affect annual reproduction, captivity affects reproductive state, and sociality may be required at certain times of the year for breeding to be successful. Our data suggest that changes in climatic conditions experienced by individuals, either due to decades-long shifts or hemispheric differences when translocated from their native range, can stifle breeding success for several years while the animals physiologically acclimatize. We also found that captivity affects stress (plasma corticosterone) and body condition of adults and juveniles differently and seasonally. Our results indicate that phenotypic plasticity in reproduction and behavior is related to environmental cues in long-lived ectotherms, and detailed ecophysiological data should be used when establishing and improving captive husbandry conditions for conservation breeding programs. Further, considering the recent revelation of this tortoises' possible extirpation from the wild, these data are critically opportune and may be key to the survival of this species.

Comparative ecophysiology of a critically endangered (CR) ectotherm: Implications for conservation management

PubMed Central

Mandimbihasina, Angelo; Gibbons, Paul; Bekarany, Ernest; Stanford, Craig B.; Louis, Edward E.; Crocker, Daniel E.

2017-01-01

Captive breeding is a vital conservation tool for many endangered species programs. It is often a last resort when wild animal population numbers drop to below critical minimums for natural reproduction. However, critical ecophysiological information of wild counterparts may not be well documented or understood, leading to years of minimal breeding successes. We collected endocrine and associated ecological data on a critically endangered ectotherm concurrently in the wild and in captivity over several years. We tracked plasma concentrations of steroid stress and reproductive hormones, body condition, activity, and environmental parameters in three populations (one wild and two geographically distinct captive) of ploughshare tortoise (Astrochelys yniphora). Hormone profiles along with environmental and behavioral data are presented and compared. We show that animals have particular seasonal environmental requirements that can affect annual reproduction, captivity affects reproductive state, and sociality may be required at certain times of the year for breeding to be successful. Our data suggest that changes in climatic conditions experienced by individuals, either due to decades-long shifts or hemispheric differences when translocated from their native range, can stifle breeding success for several years while the animals physiologically acclimatize. We also found that captivity affects stress (plasma corticosterone) and body condition of adults and juveniles differently and seasonally. Our results indicate that phenotypic plasticity in reproduction and behavior is related to environmental cues in long-lived ectotherms, and detailed ecophysiological data should be used when establishing and improving captive husbandry conditions for conservation breeding programs. Further, considering the recent revelation of this tortoises’ possible extirpation from the wild, these data are critically opportune and may be key to the survival of this species. PMID:28813439

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

PubMed

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

2014-10-01

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

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.

Comparing methods of ploidy estimation in potato.

USDA-ARS?s Scientific Manuscript database

Ploidy manipulation and the resulting need for rapid ploidy screening is an important part of a potato research and breeding program. Determining ploidy by counting chromosomes or measuring DNA in individual cells is definitive, but takes time, technical skills and equipment. We tested three predi...

Levels of maternal care in dogs affect adult offspring temperament

NASA Astrophysics Data System (ADS)

Foyer, Pernilla; Wilsson, Erik; Jensen, Per

2016-01-01

Dog puppies are born in a state of large neural immaturity; therefore, the nervous system is sensitive to environmental influences early in life. In primates and rodents, early experiences, such as maternal care, have been shown to have profound and lasting effects on the later behaviour and physiology of offspring. We hypothesised that this would also be the case for dogs with important implications for the breeding of working dogs. In the present study, variation in the mother-offspring interactions of German Shepherd dogs within the Swedish breeding program for military working dogs was studied by video recording 22 mothers with their litters during the first three weeks postpartum. The aim was to classify mothers with respect to their level of maternal care and to investigate the effect of this care on pup behaviour in a standardised temperament test carried out at approximately 18 months of age. The results show that females differed consistently in their level of maternal care, which significantly affected the adult behaviour of the offspring, mainly with respect to behaviours classified as Physical and Social Engagement, as well as Aggression. Taking maternal quality into account in breeding programs may therefore improve the process of selecting working dogs.

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

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.

Insight into the genetic composition of South African Sanga cattle using SNP data from cattle breeds worldwide.

PubMed

Makina, Sithembile O; Whitacre, Lindsey K; Decker, Jared E; Taylor, Jeremy F; MacNeil, Michael D; Scholtz, Michiel M; van Marle-Köster, Este; Muchadeyi, Farai C; Makgahlela, Mahlako L; Maiwashe, Azwihangwisi

2016-11-15

Understanding the history of cattle breeds is important because it provides the basis for developing appropriate selection and breed improvement programs. In this study, patterns of ancestry and admixture in Afrikaner, Nguni, Drakensberger and Bonsmara cattle of South Africa were investigated. We used 50 K single nucleotide polymorphism genotypes that were previously generated for the Afrikaner (n = 36), Nguni (n = 50), Drakensberger (n = 47) and Bonsmara (n = 44) breeds, and for 394 reference animals representing European taurine, African taurine, African zebu and Bos indicus. Our findings support previous conclusions that Sanga cattle breeds are composites between African taurine and Bos indicus. Among these breeds, the Afrikaner breed has significantly diverged from its ancestral forebears, probably due to genetic drift and selection to meet breeding objectives of the breed society that enable registration. The Nguni, Drakensberger and Bonsmara breeds are admixed, perhaps unintentionally in the case of Nguni and Drakensberger, but certainly by design in the case of Bonsmara, which was developed through crossbreeding between the Afrikaner, Hereford and Shorthorn breeds. We established patterns of admixture and ancestry for South African Sanga cattle breeds, which provide a basis for developing appropriate strategies for their genetic improvement.

The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies.

PubMed

Muñoz-Amatriaín, María; Cuesta-Marcos, Alfonso; Endelman, Jeffrey B; Comadran, Jordi; Bonman, John M; Bockelman, Harold E; Chao, Shiaoman; Russell, Joanne; Waugh, Robbie; Hayes, Patrick M; Muehlbauer, Gary J

2014-01-01

New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and spike row number (an inflorescence architecture trait). Different patterns of linkage disequilibrium (LD) were found across the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The genotype data were used to define 'mini-core' sets of accessions capturing the majority of the allelic diversity present in the core collection. These 'mini-core' sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide association studies (GWAS) of 'hull cover', 'spike row number', and 'heading date' demonstrate the utility of the core collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections.

Diversity of macro- and micronutrients in the seeds of lentil landraces.

PubMed

Karaköy, Tolga; Erdem, Halil; Baloch, Faheem S; Toklu, Faruk; Eker, Selim; Kilian, Benjamin; Özkan, Hakan

2012-01-01

Increasing the amount of bioavailable mineral elements in plant foods would help to improve the nutritional status of populations in developing countries. Legume seeds have the potential to provide many essential nutrients. It is important to have information on genetic variations among different lentil populations so that plant breeding programs can use new varieties in cross-breeding programs. The main objective of this study was to characterize the micro- and macronutrient concentrations of lentil landraces seeds collected from South-Eastern Turkey. We found impressive variation in the micro- and macroelement concentrations in 39 lentil landraces and 7 cultivars. We investigated the relationships of traits by correlation analysis and principal component analysis (PCA). The concentrations of several minerals, particularly Zn, were positively correlated with other minerals, suggesting that similar pathways or transporters control the uptake and transport of these minerals. Some genotypes had high mineral and protein content and potential to improve the nutritional value of cultivated lentil. Cross-breeding of numerous lentil landraces from Turkey with currently cultivated varieties could improve the levels of micro- and macronutrients of lentil and may contribute to the worldwide lentil quality breeding program.

Cost and accuracy of advanced breeding trial designs in apple

PubMed Central

Harshman, Julia M; Evans, Kate M; Hardner, Craig M

2016-01-01

Trialing advanced candidates in tree fruit crops is expensive due to the long-term nature of the planting and labor-intensive evaluations required to make selection decisions. How closely the trait evaluations approximate the true trait value needs balancing with the cost of the program. Designs of field trials of advanced apple candidates in which reduced number of locations, the number of years and the number of harvests per year were modeled to investigate the effect on the cost and accuracy in an operational breeding program. The aim was to find designs that would allow evaluation of the most additional candidates while sacrificing the least accuracy. Critical percentage difference, response to selection, and correlated response were used to examine changes in accuracy of trait evaluations. For the quality traits evaluated, accuracy and response to selection were not substantially reduced for most trial designs. Risk management influences the decision to change trial design, and some designs had greater risk associated with them. Balancing cost and accuracy with risk yields valuable insight into advanced breeding trial design. The methods outlined in this analysis would be well suited to other horticultural crop breeding programs. PMID:27019717

Trends in genome-wide and region-specific genetic diversity in the Dutch-Flemish Holstein-Friesian breeding program from 1986 to 2015.

PubMed

Doekes, Harmen P; Veerkamp, Roel F; Bijma, Piter; Hiemstra, Sipke J; Windig, Jack J

2018-04-11

In recent decades, Holstein-Friesian (HF) selection schemes have undergone profound changes, including the introduction of optimal contribution selection (OCS; around 2000), a major shift in breeding goal composition (around 2000) and the implementation of genomic selection (GS; around 2010). These changes are expected to have influenced genetic diversity trends. Our aim was to evaluate genome-wide and region-specific diversity in HF artificial insemination (AI) bulls in the Dutch-Flemish breeding program from 1986 to 2015. Pedigree and genotype data (~ 75.5 k) of 6280 AI-bulls were used to estimate rates of genome-wide inbreeding and kinship and corresponding effective population sizes. Region-specific inbreeding trends were evaluated using regions of homozygosity (ROH). Changes in observed allele frequencies were compared to those expected under pure drift to identify putative regions under selection. We also investigated the direction of changes in allele frequency over time. Effective population size estimates for the 1986-2015 period ranged from 69 to 102. Two major breakpoints were observed in genome-wide inbreeding and kinship trends. Around 2000, inbreeding and kinship levels temporarily dropped. From 2010 onwards, they steeply increased, with pedigree-based, ROH-based and marker-based inbreeding rates as high as 1.8, 2.1 and 2.8% per generation, respectively. Accumulation of inbreeding varied substantially across the genome. A considerable fraction of markers showed changes in allele frequency that were greater than expected under pure drift. Putative selected regions harboured many quantitative trait loci (QTL) associated to a wide range of traits. In consecutive 5-year periods, allele frequencies changed more often in the same direction than in opposite directions, except when comparing the 1996-2000 and 2001-2005 periods. Genome-wide and region-specific diversity trends reflect major changes in the Dutch-Flemish HF breeding program. Introduction of OCS and the shift in breeding goal were followed by a drop in inbreeding and kinship and a shift in the direction of changes in allele frequency. After introduction of GS, rates of inbreeding and kinship increased substantially while allele frequencies continued to change in the same direction as before GS. These results provide insight in the effect of breeding practices on genomic diversity and emphasize the need for efficient management of genetic diversity in GS schemes.

Early generation selection results from a two year, six location study

USDA-ARS?s Scientific Manuscript database

In potato breeding programs, early generation selections are rarely evaluated in multiple environments because of limited seed quantities. By the time seed quantities are available, few clones remain from the original population. The purpose of this study was to allow multiple locations to select ...

Characterization of saccharum species germplasm for starch content

USDA-ARS?s Scientific Manuscript database

The renewed interest in wild Saccharum species germplasm across sugarcane breeding programs has been necessitated by the need to widen the genetic base of breeding populations. Modern sugarcane cultivars were derived from inter-specific hybridization between S. officinarum and S. spontaneum. Very fe...

50 CFR 13.11 - Application procedures.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Rescue Center Program 50 CFR 23 No fee CITES Registration of Commercial Breeding Operations for Appendix—I Wildlife 50 CFR 23 100 —Renewal of Registration of Commercial Breeding Operations for Appendix-I..., POSSESSION, TRANSPORTATION, SALE, PURCHASE, BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS...

Routine DNA testing

USDA-ARS?s Scientific Manuscript database

Routine DNA testing. It’s done once you’ve Marker-Assisted Breeding Pipelined promising Qantitative Trait Loci within your own breeding program and thereby established the performance-predictive power of each DNA test for your germplasm under your conditions. By then you are ready to screen your par...

Lettuce and spinach breeding

USDA-ARS?s Scientific Manuscript database

Lettuce and spinach production is beset by numerous biotic an abiotic challenges. This report to the California Leafy Greens Research Program annual meeting provides an update by the ‘Genetic Enhancement of Lettuce, Spinach, Melon, and Related Species’ project at Salinas on the genetics and breeding...

Peptide biomarkers used for the selective breeding of a complex polygenic trait in honey bees.

PubMed

Guarna, M Marta; Hoover, Shelley E; Huxter, Elizabeth; Higo, Heather; Moon, Kyung-Mee; Domanski, Dominik; Bixby, Miriam E F; Melathopoulos, Andony P; Ibrahim, Abdullah; Peirson, Michael; Desai, Suresh; Micholson, Derek; White, Rick; Borchers, Christoph H; Currie, Robert W; Pernal, Stephen F; Foster, Leonard J

2017-08-21

We present a novel way to select for highly polygenic traits. For millennia, humans have used observable phenotypes to selectively breed stronger or more productive livestock and crops. Selection on genotype, using single-nucleotide polymorphisms (SNPs) and genome profiling, is also now applied broadly in livestock breeding programs; however, selection on protein/peptide or mRNA expression markers has not yet been proven useful. Here we demonstrate the utility of protein markers to select for disease-resistant hygienic behavior in the European honey bee (Apis mellifera L.). Robust, mechanistically-linked protein expression markers, by integrating cis- and trans- effects from many genomic loci, may overcome limitations of genomic markers to allow for selection. After three generations of selection, the resulting marker-selected stock outperformed an unselected benchmark stock in terms of hygienic behavior, and had improved survival when challenged with a bacterial disease or a parasitic mite, similar to bees selected using a phenotype-based assessment for this trait. This is the first demonstration of the efficacy of protein markers for industrial selective breeding in any agricultural species, plant or animal.

Conservation of indigenous cattle genetic resources in Southern Africa’s smallholder areas: turning threats into opportunities — A review

PubMed Central

Nyamushamba, G. B.; Mapiye, C.; Tada, O.; Halimani, T. E.; Muchenje, V.

2017-01-01

The current review focuses on characterization and conservation efforts vital for the development of breeding programmes for indigenous beef cattle genetic resources in Southern Africa. Indigenous African cattle breeds were identified and characterized using information from refereed journals, conference papers and research reports. Results of this current review reviewed that smallholder beef cattle production in Southern Africa is extensive and dominated by indigenous beef cattle strains adaptable to the local environment. The breeds include Nguni, Mashona, Tuli, Malawi Zebu, Bovino de Tete, Angoni, Landim, Barotse, Twsana and Ankole. These breeds have important functions ranging from provision of food and income to socio-economic, cultural and ecological roles. They also have adaptive traits ranging from drought tolerant, resistance to ticks and tick borne diseases, heat tolerance and resistance to trypanosomosis. Stakeholders in the conservation of beef cattle were also identified and they included farmers, national government, research institutes and universities as well as breeding companies and societies in Southern Africa. Research efforts made to evaluate threats and opportunities of indigenous beef cattle production systems, assess the contribution of indigenous cattle to household food security and income, genetically and phenotypically characterize and conserve indigenous breeds, and develop breeding programs for smallholder beef production are highlighted. Although smallholder beef cattle production in the smallholder farming systems contributes substantially to household food security and income, their productivity is hindered by several constraints that include high prevalence of diseases and parasites, limited feed availability and poor marketing. The majority of the African cattle populations remain largely uncharacterized although most of the indigenous cattle breeds have been identified. PMID:27004814

Sources of variation and genetic profile of spontaneous, out-of-season ovulatory activity in the Chios sheep

PubMed Central

Avdi, Melpomeni; Banos, Georgios; Kouttos, Athanasios; Bodin, Loys; Chemineau, Philippe

2003-01-01

Organising the breeding plan of a seasonally breeding species, such as sheep, presents a challenge to farmers and the industry as a whole, since both economical and biological considerations need to be carefully balanced. Understanding the breeding activity of individual animals becomes a prerequisite for a successful breeding program. This study set out to investigate the sources of variation and the genetic profile of the spontaneous, out-of-season ovulatory activity of ewes of the Chios dairy sheep breed in Greece. The definition of the trait was based on blood progesterone levels, measured before exposing the ewes to rams, which marks the onset of the usual breeding season. Data were 707 records, taken over two consecutive years, of 435 ewes kept at the Agricultural Research Station of Chalkidiki in northern Greece. When all available pedigree was included, the total number of animals involved was 1068. On average, 29% of all ewes exhibited spontaneous, out-of-season ovulatory activity, with no substantial variation between the years. Significant sources of systematic variation were the ewe age and live weight, and the month of previous lambing. Older, heavier ewes, that had lambed early the previous autumn, exhibited more frequent activity. Heritability estimates were 0.216 (± 0.084) with a linear and 0.291 with a threshold model. The latter better accounts for the categorical nature of the trait. The linear model repeatability was 0.230 (± 0.095). The results obtained in this study support the notion that spontaneous out-of-season ovulatory activity can be considered in the development of a breeding plan for the Chios sheep breed. PMID:12605851

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

PubMed

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

2017-11-16

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

Genetic diversity, population structure and subdivision of local Balkan pig breeds in Austria, Croatia, Serbia and Bosnia-Herzegovina and its practical value in conservation programs.

PubMed

Druml, Thomas; Salajpal, Kresimir; Dikic, Maria; Urosevic, Miroslav; Grilz-Seger, Gertrud; Baumung, Roswitha

2012-03-01

At present the Croatian Turopolje pig population comprises about 157 breeding animals. In Austria, 324 Turopolje pigs originating from six Croatian founder animals are registered. Multiple bottlenecks have occurred in this population, one major one rather recently and several more older and moderate ones. In addition, it has been subdivided into three subpopulations, one in Austria and two in Croatia, with restricted gene flow. These specificities explain the delicate situation of this endangered Croatian lard-type pig breed. In order to identify candidate breeding animals or gene pools for future conservation breeding programs, we studied the genetic diversity and population structure of this breed using microsatellite data from 197 individuals belonging to five different breeds. The genetic diversity of the Turopolje pig is dramatically low with observed heterozygosities values ranging from 0.38 to 0.57. Split into three populations since 1994, two genetic clusters could be identified: one highly conserved Croatian gene pool in Turopoljski Lug and the"Posavina" gene pool mainly present in the Austrian population. The second Croatian subpopulation in Lonjsko Polje in the Posavina region shows a constant gene flow from the Turopoljski Lug animals. One practical conclusion is that it is necessary to develop a "Posavina" boar line to preserve the "Posavina" gene pool and constitute a corresponding population in Croatia. Animals of the highly inbred herd in Turopoljski Lug should not be crossed with animals of other populations since they represent a specific phenotype-genotype combination. However to increase the genetic diversity of this herd, a program to optimize its sex ratio should be carried out, as was done in the Austrian population where the level of heterozygosity has remained moderate despite its heavy bottleneck in 1994. © 2012 Druml et al; licensee BioMed Central Ltd.

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

PubMed

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

2014-02-01

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

From phenotyping towards breeding strategies: using in vivo indicator traits and genetic markers to improve meat quality in an endangered pig breed.

PubMed

Biermann, A D M; Yin, T; König von Borstel, U U; Rübesam, K; Kuhn, B; König, S

2015-06-01

In endangered and local pig breeds of small population sizes, production has to focus on alternative niche markets with an emphasis on specific product and meat quality traits to achieve economic competiveness. For designing breeding strategies on meat quality, an adequate performance testing scheme focussing on phenotyped selection candidates is required. For the endangered German pig breed 'Bunte Bentheimer' (BB), no breeding program has been designed until now, and no performance testing scheme has been implemented. For local breeds, mainly reared in small-scale production systems, a performance test based on in vivo indicator traits might be a promising alternative in order to increase genetic gain for meat quality traits. Hence, the main objective of this study was to design and evaluate breeding strategies for the improvement of meat quality within the BB breed using in vivo indicator traits and genetic markers. The in vivo indicator trait was backfat thickness measured by ultrasound (BFiv), and genetic markers were allele variants at the ryanodine receptor 1 (RYR1) locus. In total, 1116 records of production and meat quality traits were collected, including 613 in vivo ultrasound measurements and 713 carcass and meat quality records. Additionally, 700 pigs were genotyped at the RYR1 locus. Data were used (1) to estimate genetic (co)variance components for production and meat quality traits, (2) to estimate allele substitution effects at the RYR1 locus using a selective genotyping approach and (3) to evaluate breeding strategies on meat quality by combining results from quantitative-genetic and molecular-genetic approaches. Heritability for the production trait BFiv was 0.27, and 0.48 for backfat thickness measured on carcass. Estimated heritabilities for meat quality traits ranged from 0.14 for meat brightness to 0.78 for the intramuscular fat content (IMF). Genetic correlations between BFiv and IMF were higher than estimates based on carcass backfat measurements (0.39 v. 0.25). The presence of the unfavorable n allele was associated with increased electric conductivity, paler meat and higher drip loss. The allele substitution effect on IMF was unfavorable, indicating lower IMF when the n allele is present. A breeding strategy including the phenotype (BFiv) combined with genetic marker information at the RYR1 locus from the selection candidate, resulted in a 20% increase in accuracy and selection response when compared with a breeding strategy without genetic marker information.

We Made Your Bed, Why Won’t You Lie in It? Food Availability and Disease May Affect Reproductive Output of Reintroduced Frogs

PubMed Central

Valdez, Jose; Stockwell, Michelle; Fardell, Loren; Clulow, Simon; Clulow, John; Mahony, Michael

2016-01-01

Mitigation to offset the impacts of land development is becoming increasingly common, with reintroductions and created habitat programs used as key actions. However, numerous reviews cite high rates of poor success from these programs, and a need for improved monitoring and scientific testing to evaluate outcomes and improve management actions. We conducted extensive monitoring of a released population of endangered green and golden bell frogs, Litoria aurea, within a created habitat, as well as complementary surveys of a surrounding wild population. We then compared differences between the created habitat and natural ponds where extant frogs either bred or didn’t breed in order to determine factors that contributed to the breeding failure within the created habitat. We evaluated differences of L. aurea abundance, abundance of other fauna, vegetation, water quality, habitat structure, invasive fish, and disease between the three pond types (created habitat, breeding ponds, non-breeding ponds). We discovered that vegetation and invertebrate diversity were low within the created habitat, potentially reducing energy and nutritional resources required for breeding. Also, a greater proportion of frogs in the created habitat were carrying the chytrid fungal pathogen, Batrachochytrium dendrobatidis, compared to the wild populations. In addition to causing the potentially fatal disease, chytridiomycosis, this pathogen has been shown to reduce reproductive functioning in male L. aurea, and subsequently may have reduced reproductive activities in the created habitat. Conspecific attraction, pond hydrology, and aquatic vegetation may also have had some influence on breeding behaviours, whilst the presence of the invasive mosquitofish, Gambusia holbrooki, and heterospecific tadpoles were unlikely to have deterred L. aurea from breeding within the created habitat. Through the use of scientific testing and monitoring, this study is able to make recommendations for future amphibian breed and release programs, and suggests planting a diversity of plant species to attract invertebrates, creating some permanent ponds, connecting habitat with existing populations, trialling artificial mating calls, and following recommendations to reduce the prevalence of disease within the population. PMID:27463095

Root Traits and Phenotyping Strategies for Plant Improvement

PubMed Central

Paez-Garcia, Ana; Motes, Christy M.; Scheible, Wolf-Rüdiger; Chen, Rujin; Blancaflor, Elison B.; Monteros, Maria J.

2015-01-01

Roots are crucial for nutrient and water acquisition and can be targeted to enhance plant productivity under a broad range of growing conditions. A current challenge for plant breeding is the limited ability to phenotype and select for desirable root characteristics due to their underground location. Plant breeding efforts aimed at modifying root traits can result in novel, more stress-tolerant crops and increased yield by enhancing the capacity of the plant for soil exploration and, thus, water and nutrient acquisition. Available approaches for root phenotyping in laboratory, greenhouse and field encompass simple agar plates to labor-intensive root digging (i.e., shovelomics) and soil boring methods, the construction of underground root observation stations and sophisticated computer-assisted root imaging. Here, we summarize root architectural traits relevant to crop productivity, survey root phenotyping strategies and describe their advantages, limitations and practical value for crop and forage breeding programs. PMID:27135332

Root Traits and Phenotyping Strategies for Plant Improvement.

PubMed

Paez-Garcia, Ana; Motes, Christy M; Scheible, Wolf-Rüdiger; Chen, Rujin; Blancaflor, Elison B; Monteros, Maria J

2015-06-15

Roots are crucial for nutrient and water acquisition and can be targeted to enhance plant productivity under a broad range of growing conditions. A current challenge for plant breeding is the limited ability to phenotype and select for desirable root characteristics due to their underground location. Plant breeding efforts aimed at modifying root traits can result in novel, more stress-tolerant crops and increased yield by enhancing the capacity of the plant for soil exploration and, thus, water and nutrient acquisition. Available approaches for root phenotyping in laboratory, greenhouse and field encompass simple agar plates to labor-intensive root digging (i.e., shovelomics) and soil boring methods, the construction of underground root observation stations and sophisticated computer-assisted root imaging. Here, we summarize root architectural traits relevant to crop productivity, survey root phenotyping strategies and describe their advantages, limitations and practical value for crop and forage breeding programs.

Genetic characterization of four native Italian shepherd dog breeds and analysis of their relationship to cosmopolitan dog breeds using microsatellite markers.

PubMed

Bigi, D; Marelli, S P; Randi, E; Polli, M

2015-12-01

Very little research into genetic diversity of Italian native dog breeds has been carried out so far. In this study we aimed to estimate and compare the genetic diversity of four native Italian shepherd dog breeds: the Maremma, Bergamasco, Lupino del Gigante and Oropa shepherds. Therefore, some cosmopolitan dog breeds, which have been widely raised in Italy for a long time past, have also been considered to check possible influence of these dog populations on the Italian autochthonous breeds considered here. A total of 212 individuals, belonging to 10 different dog breeds, were sampled and genotyped using 18 autosomal microsatellite loci. We analyzed the genetic diversity of these breeds, within breed diversity, breed relationship and population structure. The 10 breeds considered in this study were clearly genetically differentiated from each other, regardless of current population sizes and the onset of separate breeding history. The level of genetic diversity explained 20% of the total genetic variation. The level of H E found here is in agreement with that found by other studies. The native Italian breeds showed generally higher genetic diversity compared with the long established, well-defined cosmopolitan dog breeds. As the Border Collie seems closer to the Italian breeds than the other cosmopolitan shepherd dogs considered here, a possible utilization of this breed to improve working performance in Italian traditional working shepherd dogs cannot be ignored. The data and information found here can be utilized in the organization of conservation programs planned to reduce inbreeding and to minimize loss of genetic variability.

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

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

PubMed

Soga, Masashi; Koike, Shinsuke

2013-01-01

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

Membrane proteins associated with sperm-oocyte interaction: A proteomic comparison between Kedah Kelantan (Bos indicus) and Mafriwal (Bos taurus × Bos indicus) sperm

NASA Astrophysics Data System (ADS)

Ashrafzadeh, Ali; Nathan, Sheila; Othman, Iekhsan; Yee, Tee Ting; Karsani, Saiful Anuar

2013-11-01

Production performance of European cattle breeds has significantly improved through various breeding programs. However, European breeds are more susceptible to heat stress compared to zebu cattle (Bos indicus) as their conception rate can range between 20 to 30% in hot seasons compared to winter. To identify cattle sperm proteins associated with zebu cattle higher fertility and heat tolerance in tropical environments, we utilised a proteomics-based approach to compare sperm from the highly fertile Malaysian indigenous breed, Kedah Kelantan (Bos indicus), with sperm from the sub-fertile crossbreed, Mafriwal (Bos taurus × Bos indicus). Frozen semen of three high performance bulls from each breed was processed to obtain live and pure sperm. Proteins were separated and gel bands were processed by in-gel tryptic digestion. For each breed, mass spectrometry data was acquired over 11 replicates. The analyzed data identified peptides with different expression levels (99% confidence level) and protein identification was determined by targeted MS/MS. Among the identified proteins associated with sperm-oocyte interaction, two proteins were up-regulated in Kedah Kelantan sperm and 7 proteins were up-regulated in or specific to Mafriwal. Our results suggest that the higher fertility of zebu cattle in tropical areas may not be related to more efficient sperm-oocyte interaction. Further analysis of the other regulated proteins in these two breeds may contribute further knowledge on the physiological reason/s for higher fertility and heat tolerance of Zebu cattle in tropical areas.

Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia.

PubMed

Tapio, Miika; Ozerov, Mikhail; Tapio, Ilma; Toro, Miguel A; Marzanov, Nurbiy; Cinkulov, Mirjana; Goncharenko, Galina; Kiselyova, Tatyana; Murawski, Maziek; Kantanen, Juha

2010-08-10

Identification of global livestock diversity hotspots and their importance in diversity maintenance is essential for making global conservation efforts. We screened 52 sheep breeds from the Eurasian subcontinent with 20 microsatellite markers. By estimating and weighting differently within- and between-breed genetic variation our aims were to identify genetic diversity hotspots and prioritize the importance of each breed for conservation, respectively. In addition we estimated how important within-species diversity hotspots are in livestock conservation. Bayesian clustering analysis revealed three genetic clusters, termed Nordic, Composite and Fat-tailed. Southern breeds from close to the region of sheep domestication were more variable, but less genetically differentiated compared with more northern populations. Decreasing weight for within-breed diversity component led to very high representation of genetic clusters or regions containing more diverged breeds, but did not increase phenotypic diversity among the high ranked breeds. Sampling populations throughout 14 regional groups was suggested for maximized total genetic diversity. During initial steps of establishing a livestock conservation program populations from the diversity hot-spot area are the most important ones, but for the full design our results suggested that approximately equal population presentation across environments should be considered. Even in this case, higher per population emphasis in areas of high diversity is appropriate. The analysis was based on neutral data, but we have no reason to think the general trend is limited to this type of data. However, a comprehensive valuation of populations should balance production systems, phenotypic traits and available genetic information, and include consideration of probability of success.

Cryopreservation of apple (Malus spp.): development, progress and future prospects

USDA-ARS?s Scientific Manuscript database

Apple (Malus sp.) is one of the most economically important temperate fruit crops. Wild Malus genetic resources and existing cultivars provide valuable genes for breeding new elite cultivars and rootstocks through traditional and biotechnological breeding programs. Over the last three decades, great...

Pedigree reconstruction with genome-wide markers in potato

USDA-ARS?s Scientific Manuscript database

Reliable pedigree information facilitates a scientific approach to breeding, but errors can be introduced in many stages of a breeding program. Our objective was to use single nucleotide polymorphisms (SNPs) to check the pedigree records of elite North American potato germplasm. A population of 635 ...

Postweaning nutritional programming of ovarian development in beef heifers

USDA-ARS?s Scientific Manuscript database

From weaning to breeding, nutritional management of replacement females is critical to their lifetime productivity. Traditionally, cereal grains have been used to develop replacement heifers to enter the breeding system at a younger age. Overfeeding heifers decreases the number of calves weaned, w...

Post-weaning nutritional programming of ovarian development in beef heifers

USDA-ARS?s Scientific Manuscript database

From weaning to breeding, the nutritional management of replacement females is critical to their lifetime productivity. Traditionally, cereal grains have been used to develop replacement heifers to enter the breeding system at a younger age. However, overfeeding heifers decreased number of calves ...

The Effect of Weight Loss on the Muscle Proteome in the Damara, Dorper and Australian Merino Ovine Breeds

PubMed Central

Almeida, André M.; Palhinhas, Rui G.; Kilminster, Tanya; Scanlon, Timothy; van Harten, Sofia; Milton, John; Blache, Dominique; Greeff, Johan; Oldham, Chris; Coelho, Ana Varela; Cardoso, Luís Alfaro

2016-01-01

Seasonal Weight Loss (SWL) is an important constraint, limiting animal production in the Tropics and the Mediterranean. As a result, the study of physiological and biochemical mechanisms by which domestic animal breeds respond to SWL is important to those interested in animal breeding and the improvement thereof. To that end, the study of the proteome has been instrumental in gathering important information on physiological mechanisms, including those underlying SWL. In spite of that, little information is available concerning physiological mechanisms of SWL in production animals. The objective of this study was to determine differential protein expression in the muscle of three different breeds of sheep, the Australian Merino, the Dorper and the Damara, each showing different levels of tolerance to weight loss (low, medium and high, respectively). Per breed, two experimental groups were established, one labeled “Growth” and the other labeled “Restricted.” After forty-two days of dietary treatment, all animals were euthanized. Muscle samples were then taken. Total protein was extracted from the muscle, then quantified and two-dimensional gel electrophoresis were conducted using 24 cm pH 3–10 immobiline dry strips and colloidal coomassie staining. Gels were analyzed using Samespots® software and spots of interest were in-gel digested with trypsin. The isolated proteins were identified using MALDI-TOF/TOF. Results indicated relevant differences between breeds; several proteins are suggested as putative biomarkers of tolerance to weight loss: Desmin, Troponin T, Phosphoglucomutase and the Histidine Triad nucleotide-binding protein 1. This information is of relevance to and of possible use in selection programs aiming towards ruminant animal production in regions prone to droughts and weight loss. PMID:26828937

Effects of wildlife forestry on abundance of breeding birds in bottomland hardwood forests of Louisiana

USGS Publications Warehouse

Norris, Jennifer L.; Chamberlain, Michael J.; Twedt, Daniel J.

2009-01-01

Effects of silvicultural activities on birds are of increasing interest because of documented national declines in breeding bird populations for some species and the potential that these declines are in part due to changes in forest habitat. Silviculturally induced disturbances have been advocated as a means to achieve suitable forest conditions for priority wildlife species in bottomland hardwood forests. We evaluated how silvicultural activities on conservation lands in bottomland hardwood forests of Louisiana, USA, influenced species-specific densities of breeding birds. Our data were from independent studies, which used standardized point-count surveys for breeding birds in 124 bottomland hardwood forest stands on 12 management areas. We used Program DISTANCE 5.0, Release 2.0 (Thomas et al. 2006) to estimate density for 43 species with > 50 detections. For 36 of those species we compared density estimates among harvest regimes (individual selection, group selection, extensive harvest, and no harvest). We observed 10 species with similar densities in those harvest regimes compared with densities in stands not harvested. However, we observed 10 species that were negatively impacted by harvest with greater densities in stands not harvested, 9 species with greater densities in individual selection stands, 4 species with greater densities in group selection stands, and 4 species with greater densities in stands receiving an extensive harvest (e.g., > 40% canopy removal). Differences in intensity of harvest influenced densities of breeding birds. Moreover, community-wide avian conservation values of stands subjected to individual and group selection, and stands not harvested, were similar to each other and greater than that of stands subjected to extensive harvest that removed > 40% canopy cover. These results have implications for managers estimating breeding bird populations, in addition to predicting changes in bird communities as a result of prescribed and future forest management practices.

Genomic Tools in Cowpea Breeding Programs: Status and Perspectives

PubMed Central

Boukar, Ousmane; Fatokun, Christian A.; Huynh, Bao-Lam; Roberts, Philip A.; Close, Timothy J.

2016-01-01

Cowpea is one of the most important grain legumes in sub-Saharan Africa (SSA). It provides strong support to the livelihood of small-scale farmers through its contributions to their nutritional security, income generation and soil fertility enhancement. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. The low productivity of cowpea is attributable to numerous abiotic and biotic constraints. The abiotic stress factors comprise drought, low soil fertility, and heat while biotic constraints include insects, diseases, parasitic weeds, and nematodes. Cowpea farmers also have limited access to quality seeds of improved varieties for planting. Some progress has been made through conventional breeding at international and national research institutions in the last three decades. Cowpea improvement could also benefit from modern breeding methods based on molecular genetic tools. A number of advances in cowpea genetic linkage maps, and quantitative trait loci associated with some desirable traits such as resistance to Striga, Macrophomina, Fusarium wilt, bacterial blight, root-knot nematodes, aphids, and foliar thrips have been reported. An improved consensus genetic linkage map has been developed and used to identify QTLs of additional traits. In order to take advantage of these developments single nucleotide polymorphism (SNP) genotyping is being streamlined to establish an efficient workflow supported by genotyping support service (GSS)-client interactions. About 1100 SNPs mapped on the cowpea genome were converted by LGC Genomics to KASP assays. Several cowpea breeding programs have been exploiting these resources to implement molecular breeding, especially for MARS and MABC, to accelerate cowpea variety improvement. The combination of conventional breeding and molecular breeding strategies, with workflow managed through the CGIAR breeding management system (BMS), promises an increase in the number of improved varieties available to farmers, thereby boosting cowpea production and productivity in SSA. PMID:27375632

9 CFR 51.20 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... for the Administrator. Affected herd/flock. Any herd or flock in which any cattle, bison, breeding... results. Any test used for cattle and bison under the APHIS official brucellosis eradication program (see... 0.3 or lower. Complement fixation test (CF) If reading is 2+:20 dilution. (3) Any cattle, bison, or...

9 CFR 51.20 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... for the Administrator. Affected herd/flock. Any herd or flock in which any cattle, bison, breeding... results. Any test used for cattle and bison under the APHIS official brucellosis eradication program (see... 0.3 or lower. Complement fixation test (CF) If reading is 2+:20 dilution. (3) Any cattle, bison, or...

9 CFR 51.20 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... for the Administrator. Affected herd/flock. Any herd or flock in which any cattle, bison, breeding... results. Any test used for cattle and bison under the APHIS official brucellosis eradication program (see... 0.3 or lower. Complement fixation test (CF) If reading is 2+:20 dilution. (3) Any cattle, bison, or...

Batrachochytrium dendrobatidis in amphibians confiscated from illegal wildlife trade and used in an ex situ breeding program in Brazil.

PubMed

De Paula, C D; Pacífico-Assis, E C; Catão-Dias, J L

2012-03-20

This paper describes an outbreak of chytridiomycosis affecting a group of Dendrobates tinctorius, a Neotropical anuran species, confiscated from the illegal wildlife trade and housed in a private zoo in Brazil as part of an ex situ breeding program. We examined histological sections of the skin of 30 D. tinctorius and 20 Adelphobates galactonotus individuals. Twenty D. tinctorius (66.7%) and none of the A. galactonotus were positive for Batrachochytrium dendrobatidis (Bd). Multiple development stages of Bd infection were observed. The reasons for the inter-specific difference in the rate of infection could not be determined, and further studies are advised. Because the examined population consisted of confiscated frogs, detailed epidemiological aspects could not be investigated, and the source of the fungus remains uncertain. The existence of ex situ amphibian populations is important for protecting species at higher risk in the wild, and ex situ amphibian conservation and breeding programs in Brazil may be established using confiscated frogs as founders. However, this paper alerts these programs to the urgency of strict quarantine procedures to prevent the introduction of potential pathogens, particularly Bd, into ex situ conservation programs.

Deriving Temporal Height Information for Maize Breeding

NASA Astrophysics Data System (ADS)

Malambo, L.; Popescu, S. C.; Murray, S.; Sheridan, R.; Richardson, G.; Putman, E.

2016-12-01

Phenotypic data such as height provide useful information to crop breeders to better understand their field experiments and associated field variability. However, the measurement of crop height in many breeding programs is done manually which demands significant effort and time and does not scale well when large field experiments are involved. Through structure from motion (SfM) techniques, small unmanned aerial vehicles (sUAV) or drones offer tremendous potential for generating crop height data and other morphological data such as canopy area and biomass in cost-effective and efficient way. We present results of an on-going UAV application project aimed at generating temporal height metrics for maize breeding at the Texas A&M AgriLife Research farm in Burleson County, Texas. We outline the activities involved from the drone aerial surveys, image processing and generation of crop height metrics. The experimental period ran from April (planting) through August (harvest) 2016 and involved 36 maize hybrids replicated over 288 plots ( 1.7 Ha). During the time, crop heights were manually measured per plot at weekly intervals. Corresponding aerial flights were carried out using a DJI Phantom 3 Professional UAV at each interval and images captured processed into point clouds and image mosaics using Pix4D (Pix4D SA; Lausanne, Switzerland) software. LiDAR data was also captured at two intervals (05/06 and 07/29) to provide another source of height information. To obtain height data per plot from SfM point clouds and LiDAR data, percentile height metrics were then generated using FUSION software. Results of the comparison between SfM and field measurement height show high correlation (R2 > 0.7), showing that use of sUAV can replace laborious manual height measurement and enhance plant breeding programs. Similar results were also obtained from the comparison of SfM and LiDAR heights. Outputs of this project are helping plant breeders at Texas A&M automate routine height measurements in maize and quickly make actionable decisions and discover new hybrids.

Citrus breeding, genetics and genomics in Japan

PubMed Central

Omura, Mitsuo; Shimada, Takehiko

2016-01-01

Citrus is one of the most cultivated fruits in the world, and satsuma mandarin (Citrus unshiu Marc.) is a major cultivated citrus in Japan. Many excellent cultivars derived from satsuma mandarin have been released through the improvement of mandarins using a conventional breeding method. The citrus breeding program is a lengthy process owing to the long juvenility, and it is predicted that marker-assisted selection (MAS) will overcome the obstacle and improve the efficiency of conventional breeding methods. To promote citrus molecular breeding in Japan, a genetic mapping was initiated in 1987, and the experimental tools and resources necessary for citrus functional genomics have been developed in relation to the physiological analysis of satsuma mandarin. In this paper, we review the progress of citrus breeding and genome researches in Japan and report the studies on genetic mapping, expression sequence tag cataloguing, and molecular characterization of breeding characteristics, mainly in terms of the metabolism of bio-functional substances as well as factors relating to, for example, fruit quality, disease resistance, polyembryony, and flowering. PMID:27069387

Effectors as tools in disease resistance breeding against biotrophic, hemibiotrophic, and necrotrophic plant pathogens.

PubMed

Vleeshouwers, Vivianne G A A; Oliver, Richard P

2014-03-01

One of most important challenges in plant breeding is improving resistance to the plethora of pathogens that threaten our crops. The ever-growing world population, changing pathogen populations, and fungicide resistance issues have increased the urgency of this task. In addition to a vital inflow of novel resistance sources into breeding programs, the functional characterization and deployment of resistance also needs improvement. Therefore, plant breeders need to adopt new strategies and techniques. In modern resistance breeding, effectors are emerging as tools to accelerate and improve the identification, functional characterization, and deployment of resistance genes. Since genome-wide catalogues of effectors have become available for various pathogens, including biotrophs as well as necrotrophs, effector-assisted breeding has been shown to be successful for various crops. "Effectoromics" has contributed to classical resistance breeding as well as for genetically modified approaches. Here, we present an overview of how effector-assisted breeding and deployment is being exploited for various pathosystems.

Breeding season survival and breeding incidence of female Mottled Ducks on the upper Texas gulf coast

USGS Publications Warehouse

Rigby, Elizabeth A.; Haukos, David A.

2012-01-01

Previous Mottled Duck (Anas fulvigula) studies suggested that high female breeding season survival may be caused by low nesting effort, but few breeding season estimates of survival associated with nesting effort exist on the western Gulf Coast. Here, breeding season survival (N = 40) and breeding incidence (N = 39) were estimated for female Mottled Ducks on the upper Texas coast, 2006–2008. Females were fitted with backpack radio transmitters and visually relocated every 3–4 days. Weekly survival was estimated using the Known Fate procedure of program MARK with breeding incidence estimated as the annual proportion of females observed nesting or with broods. The top-ranked survival model included a body mass covariate and held weekly female survival constant across weeks and years (SW = 0.986, SE = 0.006). When compared to survival across the entire year estimated from previous band recovery and age ratio analysis, survival rate during the breeding season did not differ. Breeding incidence was well below 100% in all years and highly variable among years (15%–63%). Breeding season survival and breeding incidence were similar to estimates obtained with implant transmitters from the mid-coast of Texas. The greatest breeding incidence for both studies occurred when drought indices indicated average environmental moisture during the breeding season. The observed combination of low breeding incidence and high breeding season survival support the hypothesis of a trade-off between the ecological cost of nesting effort and survival for Mottled Duck females. Habitat cues that trigger nesting are unknown and should be investigated.

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

PubMed Central

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

2015-01-01

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

Crossing eastern cottonwood in the greenhouse

Treesearch

R. E. Farmer; W. L. Nance

1968-01-01

Eastern cottonwood (Populus deltoides Bartr.) is the subject of breeding programs designed to develop planting stock with potential for rapid growth, desirable wood properties, and pest resistance (4). Techniques for making controlled crosses within the species are essential to breeding, and their development constitutes an early phase of genetics...

New Brahman breed improvement program at STARS

USDA-ARS?s Scientific Manuscript database

At the USDA, ARS, Subtropical Agricultural Research Station (STARS) in Brooksville, Florida we have initiated a new ambitious research project that many believe will have a positive influence on the Brahman breed. This research was developed from a meeting held at STARS that included past and prese...

Lessons from Cotton: Research Projects Following Development of a Community-based Genotyping Array

USDA-ARS?s Scientific Manuscript database

High-throughput, cost-effective genotyping arrays provide a standardized resource for plant breeding communities that can be used for a wide range of applications at a suitable pace for integrating pertinent information into breeding programs. Traditionally, crop research communities will target dev...

Can genomics boost productivity of orphan crops?

USDA-ARS?s Scientific Manuscript database

Advances in genomics over the past 20 years have enhanced the precision and efficiency of breeding programs in many temperate cereal crops. One of the first applications of genomics-assisted breeding has been the introgression of loci for resistance to biotic stresses or major quantitative trait loc...

Genomic selection for Bacterial Cold Water Disease resistance in rainbow trout

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...

Inheritance of rainbow trout Oncorhynchus mykiss spleen size and correlation with bacterial cold water disease resistance

USDA-ARS?s Scientific Manuscript database

Infectious disease causes substantial loss in aquaculture and selective breeding for increased innate resistance offers an attractive strategy for controlling disease. In 2005, the NCCCWA implemented a selective breeding program to increase rainbow trout survival following challenge with Flavobacte...

Decision analysis for conservation breeding: Maximizing production for reintroduction of whooping cranes

USGS Publications Warehouse

Smith, Des H.V.; Converse, Sarah J.; Gibson, Keith; Moehrenschlager, Axel; Link, William A.; Olsen, Glenn H.; Maguire, Kelly

2011-01-01

Captive breeding is key to management of severely endangered species, but maximizing captive production can be challenging because of poor knowledge of species breeding biology and the complexity of evaluating different management options. In the face of uncertainty and complexity, decision-analytic approaches can be used to identify optimal management options for maximizing captive production. Building decision-analytic models requires iterations of model conception, data analysis, model building and evaluation, identification of remaining uncertainty, further research and monitoring to reduce uncertainty, and integration of new data into the model. We initiated such a process to maximize captive production of the whooping crane (Grus americana), the world's most endangered crane, which is managed through captive breeding and reintroduction. We collected 15 years of captive breeding data from 3 institutions and used Bayesian analysis and model selection to identify predictors of whooping crane hatching success. The strongest predictor, and that with clear management relevance, was incubation environment. The incubation period of whooping crane eggs is split across two environments: crane nests and artificial incubators. Although artificial incubators are useful for allowing breeding pairs to produce multiple clutches, our results indicate that crane incubation is most effective at promoting hatching success. Hatching probability increased the longer an egg spent in a crane nest, from 40% hatching probability for eggs receiving 1 day of crane incubation to 95% for those receiving 30 days (time incubated in each environment varied independently of total incubation period). Because birds will lay fewer eggs when they are incubating longer, a tradeoff exists between the number of clutches produced and egg hatching probability. We developed a decision-analytic model that estimated 16 to be the optimal number of days of crane incubation needed to maximize the number of offspring produced. These results show that using decision-analytic tools to account for uncertainty in captive breeding can improve the rate at which such programs contribute to wildlife reintroductions. 

General parity between trio and pairwise breeding of laboratory mice in static caging.

PubMed

Kedl, Ross M; Wysocki, Lawrence J; Janssen, William J; Born, Willi K; Rosenbaum, Matthew D; Granowski, Julia; Kench, Jennifer A; Fong, Derek L; Switzer, Lisa A; Cruse, Margaret; Huang, Hua; Jakubzick, Claudia V; Kosmider, Beata; Takeda, Katsuyuki; Stranova, Thomas J; Klumm, Randal C; Delgado, Christine; Tummala, Saigiridhar; De Langhe, Stijn; Cambier, John; Haskins, Katherine; Lenz, Laurel L; Curran-Everett, Douglas

2014-11-15

Changes made in the 8th edition of the Guide for the Care and Use of Laboratory Animals included new recommendations for the amount of space for breeding female mice. Adopting the new recommendations required, in essence, the elimination of trio breeding practices for all institutions. Both public opinion and published data did not readily support the new recommendations. In response, the National Jewish Health Institutional Animal Care and Use Committee established a program to directly compare the effects of breeding format on mouse pup survival and growth. Our study showed an overall parity between trio and pairwise breeding formats on the survival and growth of the litters, suggesting that the housing recommendations for breeding female mice as stated in the current Guide for the Care and Use of Laboratory Animals should be reconsidered. Copyright © 2014 by The American Association of Immunologists, Inc.

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.

Combining Breeding Bird Survey and distance sampling to estimate density of migrant and breeding birds

USGS Publications Warehouse

Somershoe, S.G.; Twedt, D.J.; Reid, B.

2006-01-01

We combined Breeding Bird Survey point count protocol and distance sampling to survey spring migrant and breeding birds in Vicksburg National Military Park on 33 days between March and June of 2003 and 2004. For 26 of 106 detected species, we used program DISTANCE to estimate detection probabilities and densities from 660 3-min point counts in which detections were recorded within four distance annuli. For most species, estimates of detection probability, and thereby density estimates, were improved through incorporation of the proportion of forest cover at point count locations as a covariate. Our results suggest Breeding Bird Surveys would benefit from the use of distance sampling and a quantitative characterization of habitat at point count locations. During spring migration, we estimated that the most common migrant species accounted for a population of 5000-9000 birds in Vicksburg National Military Park (636 ha). Species with average populations of 300 individuals during migration were: Blue-gray Gnatcatcher (Polioptila caerulea), Cedar Waxwing (Bombycilla cedrorum), White-eyed Vireo (Vireo griseus), Indigo Bunting (Passerina cyanea), and Ruby-crowned Kinglet (Regulus calendula). Of 56 species that bred in Vicksburg National Military Park, we estimated that the most common 18 species accounted for 8150 individuals. The six most abundant breeding species, Blue-gray Gnatcatcher, White-eyed Vireo, Summer Tanager (Piranga rubra), Northern Cardinal (Cardinalis cardinalis), Carolina Wren (Thryothorus ludovicianus), and Brown-headed Cowbird (Molothrus ater), accounted for 5800 individuals.

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

PubMed

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

2012-06-27

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

Visualization of Genome Diversity in German Shepherd Dogs.

PubMed

Mortlock, Sally-Anne; Booth, Rachel; Mazrier, Hamutal; Khatkar, Mehar S; Williamson, Peter

2015-01-01

A loss of genetic diversity may lead to increased disease risks in subpopulations of dogs. The canine breed structure has contributed to relatively small effective population size in many breeds and can limit the options for selective breeding strategies to maintain diversity. With the completion of the canine genome sequencing project, and the subsequent reduction in the cost of genotyping on a genomic scale, evaluating diversity in dogs has become much more accurate and accessible. This provides a potential tool for advising dog breeders and developing breeding programs within a breed. A challenge in doing this is to present complex relationship data in a form that can be readily utilized. Here, we demonstrate the use of a pipeline, known as NetView, to visualize the network of relationships in a subpopulation of German Shepherd Dogs.

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

PubMed

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

2012-08-01

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

Top 5 exotic clones for potato breeding

USDA-ARS?s Scientific Manuscript database

Wild and cultivated relatives of potato feature prominently in breeding programs. In this short article, I describe five exotic clones that have promising traits for the future of the US potato industry. They include M6, an inbred line of S. chacoense that provides a source of genes for self-compati...

Population analysis of 60 worldwide cattle breeds using high-density (700k)SNP genotyping

USDA-ARS?s Scientific Manuscript database

Genetic differences associated with speciation, breed formation, or local adaptation can help inform efforts to preserve and to effectively utilize individuals in selection programs as well as assist in accurately identifying genomic region’s importance through genome-wide association studies. To th...

Cross-transferability of SSR markers in Osmanthus

USDA-ARS?s Scientific Manuscript database

Developing a molecular tool kit for hybrid breeding of Osmanthus species and related genera is an important step in creating a systematic breeding program for this species. To date, molecular resources have been aimed solely at O. fragrans with little work to develop markers for other species and cu...

Selection efficiency for raspberry postharvest shelf life affected by storage temperature and harvest season

USDA-ARS?s Scientific Manuscript database

Improved postharvest quality is an important goal for fresh-market raspberry breeding programs. To determine if warm or cold storage following harvest would better facilitate the breeding selection process for the assessment of postharvest decay and bleed, pesticide-free fruit from cultivars and bre...

Utilization of a major brown rust resistance gene in sugarcane breeding

USDA-ARS?s Scientific Manuscript database

Brown rust, caused by Puccinia melanocephala has had devastating effects on sugarcane (Saccharum spp.) breeding programs and on commercial production. The discovery of Bru1, a major gene conferring resistance to brown rust represented a substantial breakthrough and markers for the detection of Bru1 ...

Breeding FHB-resistant soft winter wheat: progress and prospects

USDA-ARS?s Scientific Manuscript database

Soft winter wheat (Triticum aestivum L.) breeding programs in the US have used two general approaches to developing FHB-resistant cultivars: 1) incorporation of Fhb1 plus other minor QTL from Asian wheat cultivars and their derivatives and 2) reliance on resistance native to the soft winter wheat ge...

Temperate non-breeding surveys - a key to shorebird conservation

Treesearch

Sue Thomas

2005-01-01

Completion of the United States and Canadian shorebird conservation plans recently identified and prioritized shorebird monitoring, management, and conservation needs in the Western Hemisphere. We present an emerging approach to monitor shorebird use of temperate non-breeding areas under the Program for Regional and International Shorebird Monitoring (PRISM). This...

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

Code of Federal Regulations, 2012 CFR

2012-10-01

... education protocol that provides information on educational materials on the ecology and/or conservation... self-sustaining population of the exotic bird species in captivity; (iii) A statement on efforts to... the population from which the exotic bird was or would be removed; (4) Whether the breeding or display...

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

Code of Federal Regulations, 2014 CFR

2014-10-01

... education protocol that provides information on educational materials on the ecology and/or conservation... self-sustaining population of the exotic bird species in captivity; (iii) A statement on efforts to... the population from which the exotic bird was or would be removed; (4) Whether the breeding or display...

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

Code of Federal Regulations, 2013 CFR

2013-10-01

... education protocol that provides information on educational materials on the ecology and/or conservation... self-sustaining population of the exotic bird species in captivity; (iii) A statement on efforts to... the population from which the exotic bird was or would be removed; (4) Whether the breeding or display...

Feeding & Management of Dairy Calves & Heifers. Teacher's Guide.

ERIC Educational Resources Information Center

Bjoraker, Walt

This guide is designed to assist postsecondary and secondary teachers of agriculture in their use of the University of Wisconsin bulletin "Raising Dairy Replacements" in their dairy science instructional program. Eight lessons are provided in this unit: breeding decisions, management of cows from breeding to calving, care at calving time, the…

Breeding black walnuts in the age of genomics

Treesearch

Mark V. Coggeshall; Jeanne Romero-Severson

2013-01-01

Molecular markers have been used in several walnut species to help reconstruct breeding program pedigrees, to characterize genetic structure in natural Juglans populations, to determine the impact of different timber harvest scenarios on residual levels of genetic diversity, and to quantify the effects of interspecific hybridization on subsequent...

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

USDA-ARS?s Scientific Manuscript database

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

GGE analysis of ratooning ability in Louisiana sugarcane breeding

USDA-ARS?s Scientific Manuscript database

Ratooning ability is an important sugarcane growth habit that affects profitability. Ratooning ability is the ability of sugarcane to regrow after harvesting and it is measured in this research as the percentage of second ratoon of a trait to plant cane. In sugarcane breeding programs, it is time co...

Development of the first consensus genetic map of intermediate wheatgrass (Thinopyrum intermedium) using genotyping-by-sequencing

USDA-ARS?s Scientific Manuscript database

Intermediate wheatgrass (Thinopyrum intermedium) has been identified as a candidate for domestication and improvement as a perennial grain, forage, and biofuel crop by several active breeding programs. To accelerate this process using genomics-assisted breeding, efficient genotyping methods and gen...

QTLs detected for individual sugars and soluble solids content in apple

USDA-ARS?s Scientific Manuscript database

Sweetness is one of the most important fruit quality traits in breeding programs, determining the overall quality and flavor-perception of apples. Selecting for this trait using conventional breeding methods is challenging due to the complexity of its genetic control. In order to improve the efficie...

What's the latest on USDA citrus scion breeding?

USDA-ARS?s Scientific Manuscript database

In its 120 year history, the USDA citrus scion breeding program has provided the mainstays of the Florida specialty citrus industry. In the last few years, the USDA has released US Early Pride mandarin, US Seedless Pineapple sweet orange and most recently, US Furr/US Furr-ST mandarin. Clearly huangl...

Towards the elucidation of the cytoplasmic diversity of North American Grape Breeding Programs

USDA-ARS?s Scientific Manuscript database

Plants have an intriguing tripartite genetic system: Nuclear genome × Mitochondria × Plastids, and their interactions may impact germplasm breeding. In grapevine, the study of cytoplasmic genomes has been limited, and their role with respect to grapevine germplasm diversity has not been elucidated y...

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

USDA-ARS?s Scientific Manuscript database

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

USE OF NEUTRON IRRADIATIONS IN THE BROOKHAVEN MUTATIONS PROGRAM

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

Miksche, J.P.; Shapiro, S.

1963-01-01

Many plant species were irradiated with x rays, thermal and fast neutrons, andd gamma radiation during the past 10 yr of the cooperative mutations program and adjunct mutation breeding program. Four major concepts and/ or approaches related to the use of mutagenic agents in plant breeding that have evolved are discussed. It was concluded that outcrossing between treated and nontreated populations must be reckoned with, and consequently the two populations should be separated before a true measure of mutation induction can be ascertained; chromosome rearrangement studies are useful, with particular emphasis on inducing disease resistance; work concerned with tissue reorgandizationmore » and rearrangement as related to chimera production and basic understanding of tissue ontogeny, particularly with fruit crops andd horticultural crops is promising; and the effectiveness of responses of plant tissues to neutrons and other mutagenic agents is extremely variable and more basic work is needed before the full potentialities of mutation breeding as a tool in crop improvement can be appreciated. (auth)« less

Genomic Regions in Local Endangered Sheep Encode Potentially Favorable Genes.

PubMed

Moioli, Bianca; Steri, Roberto; Catillo, Gennaro

2018-01-02

The economic evaluation of farm animal genetic resources plays a key role in developing conservation programs. However, to date, the link between diversity as assessed by neutral genetic markers and the functional diversity is not yet understood. Two genome-wide comparisons, using over 44,000 Single Nucleotide Polymorphisms, identified the markers with the highest difference in allele frequency between the Alpago endangered breed and two clusters, composed of four specialized dairy sheep, and four meat breeds respectively. The genes in proximity of these markers were mapped to known pathways of the Gene Ontology to determine which ones were most represented. Our results indicated that the differences of the Alpago breed from the more productive sheep rely upon genes involved in cellular defense and repair mechanisms. A higher number of different markers and genes were detected in the comparison with the specialized dairy sheep. These genes play a role in complex biological processes: metabolic, homeostatic, neurological system, and macromolecular organization; such processes may possibly explain the evolution of gene function as a result of selection to improve milk yield.

Potential of gene drives with genome editing to increase genetic gain in livestock breeding programs.

PubMed

Gonen, Serap; Jenko, Janez; Gorjanc, Gregor; Mileham, Alan J; Whitelaw, C Bruce A; Hickey, John M

2017-01-04

This paper uses simulation to explore how gene drives can increase genetic gain in livestock breeding programs. Gene drives are naturally occurring phenomena that cause a mutation on one chromosome to copy itself onto its homologous chromosome. We simulated nine different breeding and editing scenarios with a common overall structure. Each scenario began with 21 generations of selection, followed by 20 generations of selection based on true breeding values where the breeder used selection alone, selection in combination with genome editing, or selection with genome editing and gene drives. In the scenarios that used gene drives, we varied the probability of successfully incorporating the gene drive. For each scenario, we evaluated genetic gain, genetic variance [Formula: see text], rate of change in inbreeding ([Formula: see text]), number of distinct quantitative trait nucleotides (QTN) edited, rate of increase in favourable allele frequencies of edited QTN and the time to fix favourable alleles. Gene drives enhanced the benefits of genome editing in seven ways: (1) they amplified the increase in genetic gain brought about by genome editing; (2) they amplified the rate of increase in the frequency of favourable alleles and reduced the time it took to fix them; (3) they enabled more rapid targeting of QTN with lesser effect for genome editing; (4) they distributed fixed editing resources across a larger number of distinct QTN across generations; (5) they focussed editing on a smaller number of QTN within a given generation; (6) they reduced the level of inbreeding when editing a subset of the sires; and (7) they increased the efficiency of converting genetic variation into genetic gain. Genome editing in livestock breeding results in short-, medium- and long-term increases in genetic gain. The increase in genetic gain occurs because editing increases the frequency of favourable alleles in the population. Gene drives accelerate the increase in allele frequency caused by editing, which results in even higher genetic gain over a shorter period of time with no impact on inbreeding.

The Collaborative Cross at Oak Ridge National Laboratory: developing a powerful resource for systems genetics

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

Chesler, Elissa J; Branstetter, Lisa R; Churchill, Gary A

2008-01-01

Complex traits and disease co-morbidity in humans and in model organisms are the result of naturally occurring polymorphisms that interact with each other and with the environment. To ensure the availability of the resources needed to investigate biomolecular networks and ultimately systems level phenotypes, we have initiated breeding of a new genetic reference population of mice, the Collaborative Cross. This population has been designed to optimally support systems genetics analysis. Its novel and important features include high levels of genetic diversity, a large population size to ensure sufficient power in high-dimensional studies, and high mapping precision through accumulation of independentmore » recombination events. Implementation of the Collaborative Cross has been in progress at the Oak Ridge National Laboratory (ORNL) since May 2005. This is achieved through a software assisted breeding program with fully traceable lineages, performed in a uniform environment. Currently, there are 650 lines in production with almost 200 lines over seven generations of inbreeding. Retired breeders enter a high-throughput phenotyping protocol and DNA samples are banked for analysis of recombination history, allele loss, and population structure. Herein we present a progress report of the Collaborative Cross breeding program at ORNL and a description of the kinds of investigations that this resource will support.« less

Gynogenic plant regeneration from unpollinated flower explants of Eragrostis tef (Zuccagni) Trotter.

PubMed

Gugsa, Likyelesh; Sarial, Ashok K; Lörz, Horst; Kumlehn, Jochen

2006-12-01

Tef [Eragrostis tef (Zucc.) Trotter] is the most important cereal in Ethiopia. In its wild relative E. mexicana, regeneration of six green plants resulted from culture of 121 non-pollinated immature pistils. In the allotetraploid crop species tef, however, only callus and root formation was obtained by this method. By contrast, immature spikelets and panicle segments of E. tef proved amenable to gynogenic plant regeneration. Upon step-wise optimization of the protocol, efficient plant formation was achieved in all three cultivars tested. In cv. DZ-01-196, culture of 1305 immature spikelets resulted in formation of 159 green plants. Flow cytometric analysis revealed (di)haploid, triploid, tetraploid and octoploid regenerants, from which the vast majority was tetraploid. Tef-breeding programs will likely benefit substantially from efficient generation of true-breeding plants.

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

PubMed

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

2013-02-06

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

Genome Properties and Prospects of Genomic Prediction of Hybrid Performance in a Breeding Program of Maize

PubMed Central

Technow, Frank; Schrag, Tobias A.; Schipprack, Wolfgang; Bauer, Eva; Simianer, Henner; Melchinger, Albrecht E.

2014-01-01

Maize (Zea mays L.) serves as model plant for heterosis research and is the crop where hybrid breeding was pioneered. We analyzed genomic and phenotypic data of 1254 hybrids of a typical maize hybrid breeding program based on the important Dent × Flint heterotic pattern. Our main objectives were to investigate genome properties of the parental lines (e.g., allele frequencies, linkage disequilibrium, and phases) and examine the prospects of genomic prediction of hybrid performance. We found high consistency of linkage phases and large differences in allele frequencies between the Dent and Flint heterotic groups in pericentromeric regions. These results can be explained by the Hill–Robertson effect and support the hypothesis of differential fixation of alleles due to pseudo-overdominance in these regions. In pericentromeric regions we also found indications for consistent marker–QTL linkage between heterotic groups. With prediction methods GBLUP and BayesB, the cross-validation prediction accuracy ranged from 0.75 to 0.92 for grain yield and from 0.59 to 0.95 for grain moisture. The prediction accuracy of untested hybrids was highest, if both parents were parents of other hybrids in the training set, and lowest, if none of them were involved in any training set hybrid. Optimizing the composition of the training set in terms of number of lines and hybrids per line could further increase prediction accuracy. We conclude that genomic prediction facilitates a paradigm shift in hybrid breeding by focusing on the performance of experimental hybrids rather than the performance of parental lines in testcrosses. PMID:24850820

The polyploidy and its key role in plant breeding.

PubMed

Sattler, Mariana Cansian; Carvalho, Carlos Roberto; Clarindo, Wellington Ronildo

2016-02-01

This article provides an up-to-date review concerning from basic issues of polyploidy to aspects regarding the relevance and role of both natural and artificial polyploids in plant breeding programs. Polyploidy is a major force in the evolution of both wild and cultivated plants. Polyploid organisms often exhibit increased vigor and, in some cases, outperform their diploid relatives in several aspects. This remarkable superiority of polyploids has been the target of many plant breeders in the last century, who have induced polyploidy and/or used natural polyploids in many ways to obtain increasingly improved plant cultivars. Some of the most important consequences of polyploidy for plant breeding are the increment in plant organs ("gigas" effect), buffering of deleterious mutations, increased heterozygosity, and heterosis (hybrid vigor). Regarding such features as tools, cultivars have been generated with higher yield levels, improving the product quality and increasing the tolerance to both biotic and abiotic stresses. In some cases, when the crossing between two species is not possible because of differences in ploidy level, polyploids can be used as a bridge for gene transferring between them. In addition, polyploidy often results in reduced fertility due to meiotic errors, allowing the production of seedless varieties. On the other hand, the genome doubling in a newly formed sterile hybrid allows the restoration of its fertility. Based on these aspects, the present review initially concerns the origin, frequency and classification of the polyploids, progressing to show the revolution promoted by the discovery of natural polyploids and polyploidization induction in the breeding program status of distinct crops.

Blight-resistant American chestnut trees: selection of progeny from a breeding program

Treesearch

Shiv Hiremath; Kirsten Lehtoma; Fred Hebard

2007-01-01

Introduction of the fungus Cryphonectria parasitica into North America in early 1900s resulted in the demise of the American chestnut, which was once the most dominant forest tree in the eastern United States. While the American chestnut (Castanea dentate) is susceptible, its counterpart from Asia, the Chinese chestnut, is...

Deployment of deer-resistant western redcedar (Thuja plicata)

Treesearch

John Russell

2008-01-01

Protecting planted western redcedar (Thuja plicata) seedlings from deer browse in the Pacific Northwest and British Columbia is estimated to cost up to CAN$ 25 million annually. Recent studies linking deer browse and needle monoterpenes has resulted in the initiation of a breeding program for deer-resistant western redcedar at Cowichan Lake Research...

The use of remote sensing in mosquito control

NASA Technical Reports Server (NTRS)

1973-01-01

The technology of remote sensing, developed by the space program for identification of surface features from the vantage point of an aircraft or satellite, has substantial application in precisely locating mosquito breeding grounds. Preliminary results of the NASA technology working cooperatively with a city government agency in solving this problem are discussed.

Improved method for reliable HMW-GS identification by RP-HPLC and SDS-PAGE in common wheat cultivars

USDA-ARS?s Scientific Manuscript database

The accurate identification of alleles for high-molecular weight glutenins (HMW-GS) is critical for wheat breeding programs targeting end-use quality. RP-HPLC methods were optimized for separation of HMW-GS, resulting in enhanced resolution of 1By and 1Dx subunits. Statistically significant differe...

Effect of genetic European taurine ancestry on milk yield of Ankole-Holstein crossbred dairy cattle in mixed smallholders system of Burundi highlands.

PubMed

Manirakiza, J; Hatungumukama, G; Thévenon, S; Gautier, M; Besbes, B; Flori, L; Detilleux, J

2017-10-01

Different breeding systems associated with specific bovine genetic resources have coexisted in Burundi. To prepare for the development of a national action plan for the improvement of bovine genetic resources in Burundi, we aimed at performing genetic characterization of Ankole and Ankole × European crossbred individuals and assessing the effect of European ancestry on milk productivity of cows kept under the mixed crops livestock system. To that end, we genotyped 37 Ankole and 138 crossbred individuals on 42 636 SNPs and combined these genotypes with those from 21 cattle breeds, representative of the bovine genetic diversity. We also measured milk yield not suckled and estimated suckled milk. Given the results, we confirmed the indicine × African taurine admixed origin of the Ankole in Burundi and showed that crossbred individuals present a high proportion of European ancestry (i.e. 57% on average). As the proportion of European ancestry increased, milk yield increased by 0.03 ± 0.01 l/day, at a lower extent than expected. We also observed that breeders were unable to correctly evaluate the European proportion in their livestock. Our results may provide useful information for objective dairy breeding in Burundi. As an example, an ex-situ conservation program of Ankole within the framework of value chains is proposed as an accompanying strategy to improve the sustainability of the crossbreeding program. © 2017 Stichting International Foundation for Animal Genetics.

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

Identification of smallholder farmers and pastoralists' preferences for sheep breeding traits: choice model approach.

PubMed

Duguma, G; Mirkena, T; Haile, A; Okeyo, A M; Tibbo, M; Rischkowsky, B; Sölkner, J; Wurzinger, M

2011-12-01

Identification of breeding objective traits pertinent to specific production environments with the involvement of target beneficiaries is crucial to the success of a breed improvement program. A choice experiment was conducted in four locations representing different production systems and agro-ecologies that are habitat to four indigenous sheep breeds (Afar, Bonga, Horro and Menz) of Ethiopia with the objective of identifying farmers'/pastoralists' preferences for sheep breeding traits. Following a synthesis of secondary information and diagnostic surveys, two communities per location consisting of 60 households each having at least four breeding ewes were identified. Producers' priority attributes used in the choice sets were identified through in-depth production system studies conducted from December 2007 to March 2008. On the basis of prior information, four to seven attributes were used to design choice sets with different profiles in order to capture results that mimic real life of the different communities. The attributes and levels chosen for the sheep profile were as follows: body size (large/small), coat color (brown/white/black), tail type (good/bad) for both rams and ewes; horn (polled/horned) and libido (active/poor) for rams; and lambing interval (three lambings in 2 years/two lambings in 2 years time), mothering ability (good mother/bad mother), twinning rate (twin bearer/single bearer) and milk yield (two cups per milking/one cup per milking) for ewes. A fractional factorial design was implemented to construct the alternatives included in the choice sets. The design resulted in a randomized selection of 48 sheep profiles (24 sets) for both sexes, which were grouped into four blocks with six choice sets each. An individual respondent was presented with one of the four blocks to make his/her choices. Results indicate that producers' trait preferences were heterogeneous except for body size in rams and mothering ability in ewes where nearly homogeneous preferences were investigated. In the pastoral production system, attention was given to coat color of both breeding rams and ewes, favoring brown and white colors over black. Ram libido influenced producers' decisions in Bonga, Horro and Menz areas. The influence of milk yield and twinning on respondents' decision making was high in Afar and Horro, respectively. Breeders in all areas attempt to combine production and reproduction traits as well as they can in order to maximize benefits from their sheep. The elicited measurable objective traits were used to design alternative community-based sheep breeding plans for the four indigenous sheep breeds in their production environments that have been implemented since.

Non-invasive monitoring of reproductive and stress hormones in the endangered red panda (Ailurus fulgens fulgens).

PubMed

Beaulah Budithi, Neema Raja; Kumar, Vinod; Yalla, Suneel Kumar; Rai, Upashna; Umapathy, Govindhaswamy

2016-09-01

The red panda (Ailurus fulgens fulgens) is classified as endangered due to its declining population, habitat fragmentation and poaching. Efforts are being made to breed them in captivity as part of nationwide conservation breeding program. This study aimed to standardize Enzyme immunoassays (EIAs) to monitor reproductive (Progesterone metabolite, Testosterone) and stress hormone (Cortisol) in red panda. For this purpose, we collected 1471 faecal samples from four females and one male over a period of one year from Padmaja Naidu Himalayan Zoological Park, Darjeeling, India. HPLC confirmed the presence of immunoreactive 5α-pregnan-3α-ol-20-one, testosterone and cortisol metabolites in faecal samples. Using 5α-pregnan-3α-ol-20-one EIA, we were able to monitor reproduction and detect pregnancy in one of the females, which successfully conceived and delivered during the study period. We were also able to monitor testosterone and cortisol in faecal samples of the red panda. Faecal testosterone levels were found in higher concentration in breeding season than in non-breeding season. Faecal cortisol concentrations showed a negative relationship with ambient temperature and peaked during winter months in all animals. Standardization of EIAs and faecal hormone monitoring would facilitate red panda conservation breeding programs in India and elsewhere. Copyright © 2016 Elsevier B.V. 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.

Mammary gland and milk fatty acid composition of two dairy goat breeds under feed-restriction.

PubMed

Palma, Mariana; Alves, Susana P; Hernández-Castellano, Lorenzo E; Capote, Juan; Castro, Noemí; Argüello, Anastasio; Matzapetakis, Manolis; Bessa, Rui J B; de Almeida, André M

2017-08-01

Goat dairy products are an important source of animal protein in the tropics. During the dry season, pasture scarcity leads animals to lose up to 40% of their body weight, a condition known as Seasonal Weight Loss (SWL) that is one of the major constraints in ruminant production. Breeds with high tolerance to SWL are relevant to understand the physiological responses to pasture scarcity so they could be used in programs for animal breeding. In the Canary Islands there are two dairy goat breeds with different levels of tolerance to SWL: the Palmera, susceptible to SWL; and the Majorera, tolerant to SWL. Fat is one of the milk components most affected by environmental and physiological conditions. This study hypothesises that feed-restriction affects Majorera and Palmera breeds differently, leading to different fatty acid profiles in the mammary gland and milk. An interaction between breed and feed-restriction was observed in the mammary gland. Feed-restriction was associated with an increase in oleic acid and a decrease in palmitic acid percentage in the Palmera breed whereas no differences were observed in the Majorera breed. Palmitic and oleic acids together constituted around 60% of the total fatty acids identified, which suggests that Palmera breed is more susceptible to SWL. In milk, feed-restriction affected both breeds similarly. Regarding the interaction of the breed with the treatment, we also observed similar responses in both breeds, but this influence affects only around 2% of the total fatty acids. In general, Majorera breed is more tolerant to feed-restriction.

Waterbird nest monitoring program in San Francisco Bay (2005-10)

USGS Publications Warehouse

Ackerman, Joshua T.; Herzog, Mark P.

2012-01-01

Historically, Forster’s Terns (Sterna forsteri), American Avocets (Recurvirostra americana), and Black-necked Stilts (Himantopus mexicanus) were uncommon residents of San Francisco Bay, California (Grinnell and others, 1918; Grinnell and Wythe, 1927; Sibley, 1952). Presently, however, avocets and stilts are the two most abundant breeding shorebirds in San Francisco Bay (Stenzel and others, 2002; Rintoul and others, 2003). More than 4,000 avocets and 1,000 stilts, roughly 20 percent of their San Francisco Bay wintering populations, breed within the estuary, making San Francisco Bay the largest breeding area for these species on the Pacific Coast (Stenzel and others, 2002; Rintoul and others, 2003). Forster’s Terns were first observed breeding in the San Francisco Bay in 1948 (110 nests); they had increased to over 4000 individuals by the 1980s (Sibley, 1952; Gill, 1977; Harvey and others, 1992; Carter and others, 1990) and were estimated at 2000–3000 for 1998–2002; (Strong and others, 2004).It is hypothesized that the relatively large size of the current waterbird breeding populations is a result of the creation of artificial salt evaporation ponds from the 1930s through the 1950s (Gill, 1977; Goals Project, 1999). Until recently, these salt ponds and associated islands used by waterbirds for nesting have been managed relatively similarly and have supported large breeding waterbird populations. Recently, the South Bay Salt Pond Restoration Project has implemented plans to convert 50–90 percent of the 15,000 acres of salt ponds in the South San Francisco Bay back to tidal marsh habitat. Therefore, there is concern that the Restoration Project, while benefiting other native species, could negatively influence local breeding populations of waterbirds that are reliant on salt pond habitats for both breeding and foraging. A primary goal of the South Bay Salt Pond Restoration Project is to maintain current breeding waterbird populations (South Bay Salt Pond Long-Term Restoration Project, 2004); thus, specific efforts are planned to ensure that the Restoration Project enhances the habitats of the remaining salt ponds for breeding waterbirds.Here, we provide a summary of nesting ecology data for Forster’s Terns, American Avocets, and Black-necked Stilts, collected from 2005 to 2010 in the areas of the South Bay Salt Pond Restoration Project, including lands managed by the Don Edwards San Francisco Bay National Wildlife Refuge and Eden Landing Ecological Reserve. These results provide baseline conditions for breeding waterbirds prior to implementation of most restoration actions and can be used to both guide future restoration actions as well as to determine the effect of the South Bay Salt Pond Restoration Project on breeding waterbirds. It is imperative to continue to collect nesting waterbird data annually to assess the response of birds to the South Bay Salt Pond Restoration Project.

A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation

PubMed Central

2013-01-01

Background Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior varieties of Douglas-fir (vars. menziesii and glauca) are native to North America, the coastal variety is also widely planted for timber production in Europe, New Zealand, Australia, and Chile. Our main goal was to develop a SNP resource large enough to facilitate genomic selection in Douglas-fir breeding programs. To accomplish this, we developed a 454-based reference transcriptome for coastal Douglas-fir, annotated and evaluated the quality of the reference, identified putative SNPs, and then validated a sample of those SNPs using the Illumina Infinium genotyping platform. Results We assembled a reference transcriptome consisting of 25,002 isogroups (unique gene models) and 102,623 singletons from 2.76 million 454 and Sanger cDNA sequences from coastal Douglas-fir. We identified 278,979 unique SNPs by mapping the 454 and Sanger sequences to the reference, and by mapping four datasets of Illumina cDNA sequences from multiple seed sources, genotypes, and tissues. The Illumina datasets represented coastal Douglas-fir (64.00 and 13.41 million reads), interior Douglas-fir (80.45 million reads), and a Yakima population similar to interior Douglas-fir (8.99 million reads). We assayed 8067 SNPs on 260 trees using an Illumina Infinium SNP genotyping array. Of these SNPs, 5847 (72.5%) were called successfully and were polymorphic. Conclusions Based on our validation efficiency, our SNP database may contain as many as ~200,000 true SNPs, and as many as ~69,000 SNPs that could be genotyped at ~20,000 gene loci using an Infinium II array—more SNPs than are needed to use genomic selection in tree breeding programs. Ultimately, these genomic resources will enhance Douglas-fir breeding and allow us to better understand landscape-scale patterns of genetic variation and potential responses to climate change. PMID:23445355

Establishment of American chestnuts (Castanea dentata) bred for blight (Cryphonectria parasitica ) resistance: influence of breeding and nursery grading

Treesearch

Stacy L. Clark; Scott E. Schlarbaum; Arnold M. Saxton; Frederick V. Hebard

2016-01-01

European and American chestnut species (Castanea) have been decimated by exotic species, most notably chestnut blight (Cryphonectria parasitica), since the early nineteenth century. Backcross breeding programs that transfer blight disease resistance from Chinese chestnut (C. mollissima) into American...

Sustaining the future of plant breeding: The critical role of the USDA-ARS National Plant Germplasm System

USDA-ARS?s Scientific Manuscript database

Plant breeders require genetic diversity in their breeding programs to develop cultivars that are productive, nutritious, tolerant of biotic and abiotic stresses, and make efficient use of water and fertilizer. The USDA-ARS National Plant Germplasm System (NPGS) is a major source for global plant ge...

Dissecting genotype × environment interactions and trait correlations present in the Pee Dee cotton germplasm collection following seventy years of plant breeding

USDA-ARS?s Scientific Manuscript database

Genotype × environment interactions and trait correlations significantly impact efforts to develop high yield, high quality, and environmentally stable Upland cotton (Gossypium hirsutum L.) cultivars. Knowledge of both can and should be used to design optimal breeding programs and effective selectio...

Tandem selection for fusiform rust sisease resistance to develop a clonal elite breeding population of loblolly pine

Treesearch

Steve McKeand; Saul Garcia; Josh Steiger; Jim Grissom; Ross Whetten; Fikret Isik

2012-01-01

The elite breeding populations of loblolly pine (Pinus taeda L.) in the North Carolina State University Cooperative Tree Improvement Program are intensively managed for short-term genetic gain. Fusiform rust disease, caused by the fungus Cronartium quercuum f. sp. fusiforme, is the most economically...

Proceedings of the symposium on isozymes of North American forest trees and forest insects; July 27, 1979; Berkeley, California

Treesearch

M. Thompson Conkle

1981-01-01

These 10 symposium papers discuss gene resource management, basic genetics, genetic variation between and within tree species, genetic variability and growth, comparisons of tree life history characteristics, genetic variation in forest insects, breeding systems, and applied uses of isozymes in breeding programs.

Development and integration of an SSR-based molecular identity database into sugarcane breeding program

USDA-ARS?s Scientific Manuscript database

Sugarcane breeding is very difficult and it takes 12 to 14 years to develop a new cultivar for commercial production. This is because sugarcane varieties are highly polyploid, inter-specific hybrids with 100 to 130 chromosomes that may vary across geographical areas. Other obstacles/constraints incl...

Index-in-retrospect and breeding objectives characterizing genetic improvement programs for South African Nguni cattle

USDA-ARS?s Scientific Manuscript database

The objective of the current study was to describe the historical selection applied to Nguni cattle in South Africa. Index-in-retrospect methods were applied to data originating from the National Beef Cattle Improvement Scheme. Data used were estimated breeding values (EBV) for animals born during t...

Biobanking genetic resources: Challenges and implementation at the USDA National Animal Germplasm Program

USDA-ARS?s Scientific Manuscript database

There is adequate infrastructure in the US to identify and acquire germplasm from the major beef and dairy cattle and swine breeds. However, when we venture outside these species the same tasks become more difficult because of a lack of breed associations, databases that include genotypic and pheno...

Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers

USDA-ARS?s Scientific Manuscript database

Knowledge of germplasm diversity and relationships among elite breeding materials is fundamentally important in crop improvement. We genotyped 450 maize lines developed and/or widely used by CIMMYT breeding programs both in Kenya and Zimbabwe using 1065 SNP markers to (i) investigate population stru...

Rebuilding Hawaii’s Anthurium germplasm collection for cultivar and species preservation, breeding, and biotechnological research

USDA-ARS?s Scientific Manuscript database

Anthurium is the third most important floriculture crop in Hawaii, grown mainly as a cut flower. The University of Hawaii (UH) has a well-established anthurium breeding program since 1950, with a germplasm collection assembled from backyard growers, hobbyists, researchers and collection trips from c...

Honey bee stock genotypes do not affect the level of physiological responses to chalkbrood fungus, Ascosphaera apis.

USDA-ARS?s Scientific Manuscript database

Breeding honey bees (Apis mellifera) for physiological resistance to diseases is a highly desirable and environmentally safe approach to increasing colony survival. Selection of desirable traits is a critical element of any breeding program. In this study we investigate whether honey bee stocks dif...

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

Treesearch

Jennifer Myszewski; Thomas Byram; Floyd Bridgwater

2006-01-01

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

What can be Learned from Silage Breeding Programs?

NASA Astrophysics Data System (ADS)

Lorenz, Aaron J.; Coors, James G.

Improving the quality of cellulosic ethanol feedstocks through breeding and genetic manipulation could significantly impact the economics of this industry. Attaining this will require comprehensive and rapid characterization of large numbers of samples. There are many similarities between improving corn silage quality for dairy production and improving feedstock quality for cellulosic ethanol. It was our objective to provide insight into what is needed for genetic improvement of cellulosic feedstocks by reviewing the development and operation of a corn silage breeding program. We discuss the evolving definition of silage quality and relate what we have learned about silage quality to what is needed for measuring and improving feedstock quality. In addition, repeatability estimates of corn stover traits are reported for a set of hybrids. Repeatability of theoretical ethanol potential measured by near-infrared spectroscopy is high, suggesting that this trait may be easily improved through breeding. Just as cell wall digestibility has been factored into the latest measurements of silage quality, conversion efficiency should be standardized and included in indices of feedstock quality to maximize overall, economical energy availability.

Genome engineering in ornamental plants: Current status and future prospects.

PubMed

Kishi-Kaboshi, Mitsuko; Aida, Ryutaro; Sasaki, Katsutomo

2018-03-13

Ornamental plants, like roses, carnations, and chrysanthemums, are economically important and are sold all over the world. In addition, numerous cut and garden flowers add colors to homes and gardens. Various strategies of plant breeding have been employed to improve traits of many ornamental plants. These approaches span from conventional techniques, such as crossbreeding and mutation breeding, to genetically modified plants. Recently, genome editing has become available as an efficient means for modifying traits in plant species. Genome editing technology is useful for genetic analysis and is poised to become a common breeding method for ornamental plants. In this review, we summarize the benefits and limitations of conventional breeding techniques and genome editing methods and discuss their future potential to accelerate the rate breeding programs in ornamental plants. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

The Effects of Both Recent and Long-Term Selection and Genetic Drift Are Readily Evident in North American Barley Breeding Populations

PubMed Central

Poets, Ana M.; Mohammadi, Mohsen; Seth, Kiran; Wang, Hongyun; Kono, Thomas J. Y.; Fang, Zhou; Muehlbauer, Gary J.; Smith, Kevin P.; Morrell, Peter L.

2015-01-01

Barley was introduced to North America ∼400 yr ago but adaptation to modern production environments is more recent. Comparisons of allele frequencies among growth habits and spike (inflorescence) types in North America indicate that significant genetic differentiation has accumulated in a relatively short evolutionary time span. Allele frequency differentiation is greatest among barley with two-row vs. six-row spikes, followed by spring vs. winter growth habit. Large changes in allele frequency among breeding programs suggest a major contribution of genetic drift and linked selection on genetic variation. Despite this, comparisons of 3613 modern North American cultivated barley breeding lines that differ for spike-type and growth habit permit the discovery of 142 single nucleotide polymorphism (SNP) outliers putatively linked to targets of selection. For example, SNPs within the Cbf4, Ppd-H1, and Vrn-H1 loci, which have previously been associated with agronomically adaptive phenotypes, are identified as outliers. Analysis of extended haplotype sharing identifies genomic regions shared within and among breeding populations, suggestive of a number of genomic regions subject to recent selection. Finally, we are able to identify recent bouts of gene flow between breeding populations that could point to the sharing of agronomically adaptive variation. These results are supported by pedigrees and breeders’ understanding of germplasm sharing. PMID:26715093

A Review of Microsatellite Markers and Their Applications in Rice Breeding Programs to Improve Blast Disease Resistance

PubMed Central

Miah, Gous; Rafii, Mohd Y.; Ismail, Mohd R.; Puteh, Adam B.; Rahim, Harun A.; Islam, Kh. Nurul; Latif, Mohammad Abdul

2013-01-01

Over the last few decades, the use of molecular markers has played an increasing role in rice breeding and genetics. Of the different types of molecular markers, microsatellites have been utilized most extensively, because they can be readily amplified by PCR and the large amount of allelic variation at each locus. Microsatellites are also known as simple sequence repeats (SSR), and they are typically composed of 1–6 nucleotide repeats. These markers are abundant, distributed throughout the genome and are highly polymorphic compared with other genetic markers, as well as being species-specific and co-dominant. For these reasons, they have become increasingly important genetic markers in rice breeding programs. The evolution of new biotypes of pests and diseases as well as the pressures of climate change pose serious challenges to rice breeders, who would like to increase rice production by introducing resistance to multiple biotic and abiotic stresses. Recent advances in rice genomics have now made it possible to identify and map a number of genes through linkage to existing DNA markers. Among the more noteworthy examples of genes that have been tightly linked to molecular markers in rice are those that confer resistance or tolerance to blast. Therefore, in combination with conventional breeding approaches, marker-assisted selection (MAS) can be used to monitor the presence or lack of these genes in breeding populations. For example, marker-assisted backcross breeding has been used to integrate important genes with significant biological effects into a number of commonly grown rice varieties. The use of cost-effective, finely mapped microsatellite markers and MAS strategies should provide opportunities for breeders to develop high-yield, blast resistance rice cultivars. The aim of this review is to summarize the current knowledge concerning the linkage of microsatellite markers to rice blast resistance genes, as well as to explore the use of MAS in rice breeding programs aimed at improving blast resistance in this species. We also discuss the various advantages, disadvantages and uses of microsatellite markers relative to other molecular marker types. PMID:24240810

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

PubMed

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

2016-05-01

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

The risk of Aedes aegypti breeding and premises condition in South Mexico.

PubMed

Manrique-Saide, Pablo; Davies, Clive R; Coleman, Paul G; Che-Mendoza, Azael; Dzul-Manzanilla, Felipe; Barrera-Pérez, Mario; Hernández-Betancourt, Silvia; Ayora-Talavera, Guadalupe; Pinkus-Rendón, Miguel; Burciaga-Zúñiga, Pierre; Sánchez Tejeda, Gustavo; Arredondo-Jiménez, Juan I

2013-12-01

A recent innovation instrumented for the Dengue Prevention and Control program in Mexico is the use of the premises condition index (PCI) as an indicator of risk for the vector Aedes aegypti infestation in dengue-endemic localities of Mexico. This paper addresses whether further improvements for the dengue control program could be made if the prevalence and productivity of Ae. aegypti populations could be reliably predicted using PCI at the household level, as well as medium-sized neighborhoods. We evaluated the use of PCI to predict the infestation with Aedes aegypti (breeding sites and immature productivity) in Merida, Mexico. The study consisted of a cross-sectional survey based on a cluster-randomized sampling design. We analyzed the statistical association between Aedes infestation and PCI, the extent to which the 3 components of PCI (house maintenance, and tidiness and shading of the patio) contributed to the association between PCI and infestation and whether infestation in a given premises was also affected by the PCI of the surrounding ones. Premises with the lowest PCI had significantly lower Aedes infestation and productivity; and as PCI scores increased infestation levels also tended to increase. Household PCI was significantly associated with Ae. aegypti breeding, largely due to the effect of patio untidiness and patio shade. The mean PCI within the surroundings premises also had a significant and independent explanatory power to predict the risk for infestation, in addition to individual PCI. This is the 1st study in Mexico showing evidence that premises condition as measured by the PCI is related to Ae. aegypti breeding sites and immature productivity. Results suggest that PCI could be used to streamline surveys to inform control efforts at least where Ae. aegypti breeds outdoors, as in Merida. The effect of individual premises, neighborhood condition, and the risk of Aedes infestation imply that the risk for dengue vector infestation can only be minimized by the mass effect at the community level.

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

PubMed

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

2014-08-29

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

Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.

PubMed Central

2012-01-01

Background In the last 30 years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting task to identify highly polymorphic and closely linked molecular markers for a target trait for molecular marker-assisted selection. The next-generation sequencing (NGS) technology is far more powerful than any existing generic DNA fingerprinting methods in generating DNA markers. In this study, we employed a grain legume crop Lupinus angustifolius (lupin) as a test case, and examined the utility of an NGS-based method of RAD (restriction-site associated DNA) sequencing as DNA fingerprinting for rapid, cost-effective marker development tagging a disease resistance gene for molecular breeding. Results Twenty informative plants from a cross of RxS (disease resistant x susceptible) in lupin were subjected to RAD single-end sequencing by multiplex identifiers. The entire RAD sequencing products were resolved in two lanes of the 16-lanes per run sequencing platform Solexa HiSeq2000. A total of 185 million raw reads, approximately 17 Gb of sequencing data, were collected. Sequence comparison among the 20 test plants discovered 8207 SNP markers. Filtration of DNA sequencing data with marker identification parameters resulted in the discovery of 38 molecular markers linked to the disease resistance gene Lanr1. Five randomly selected markers were converted into cost-effective, simple PCR-based markers. Linkage analysis using marker genotyping data and disease resistance phenotyping data on a F8 population consisting of 186 individual plants confirmed that all these five markers were linked to the R gene. Two of these newly developed sequence-specific PCR markers, AnSeq3 and AnSeq4, flanked the target R gene at a genetic distance of 0.9 centiMorgan (cM), and are now replacing the markers previously developed by a traditional DNA fingerprinting method for marker-assisted selection in the Australian national lupin breeding program. Conclusions We demonstrated that more than 30 molecular markers linked to a target gene of agronomic trait of interest can be identified from a small portion (1/8) of one sequencing run on HiSeq2000 by applying NGS based RAD sequencing in marker development. The markers developed by the strategy described in this study are all co-dominant SNP markers, which can readily be converted into high throughput multiplex format or low-cost, simple PCR-based markers desirable for large scale marker implementation in plant breeding programs. The high density and closely linked molecular markers associated with a target trait help to overcome a major bottleneck for implementation of molecular markers on a wide range of germplasm in breeding programs. We conclude that application of NGS based RAD sequencing as DNA fingerprinting is a very rapid and cost-effective strategy for marker development in molecular plant breeding. The strategy does not require any prior genome knowledge or molecular information for the species under investigation, and it is applicable to other plant species. PMID:22805587

Economic comparison of natural service and timed artificial insemination breeding programs in dairy cattle.

PubMed

Lima, F S; De Vries, A; Risco, C A; Santos, J E P; Thatcher, W W

2010-09-01

The objective was to compare the costs of natural service (NS) and timed artificial insemination (TAI) as breeding programs for dairy cows. Both programs were directly compared in a field study from November 2006 to March 2008. Reproductive results in that study were similar and served as inputs for this study. A herd budget accounting for all costs and revenues was created. Net cost during the field study for the NS program was $100.49/cow per year and for the TAI program was $67.80/cow per year, unadjusted for differences in voluntary waiting period for first insemination (VWP) and pregnancy rates (PR). After inclusion of the differences in VWP and PR, the economic advantage of the TAI program was $9.73/cow per year. Costs per day a cow was eligible for insemination were estimated at $1.45 for the NS program and $1.06 for the TAI program. Sensitivity analysis revealed that if the marginal feed cost increased to $5/hundredweight (cwt; 1 cwt=45.36kg), the advantage of TAI increased to $48.32/cow per year. In addition, higher milk prices and greater genetic progress increased the advantage of TAI. When semen price increased from $6 to $22, the NS program had an economic advantage of $33.29/cow per year. If each NS bull was replaced by an additional cow, the advantage of the TAI program was $60.81/cow per year. Setting the PR for both programs at 18% and the VWP at 80 d resulted in an advantage of $37.87/cow per year for the TAI program. In conclusion, any advantage of TAI depended greatly on cost to feed bulls, semen price, and genetic merit of semen. Copyright (c) 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Intrabreed Stratification Related to Divergent Selection Regimes in Purebred Dogs May Affect the Interpretation of Genetic Association Studies

PubMed Central

Chang, Melanie L.; Yokoyama, Jennifer S.; Branson, Nick; Dyer, Donna J.; Hitte, Christophe; Overall, Karen L.

2009-01-01

Until recently, canine genetic research has not focused on population structure within breeds, which may confound the results of case–control studies by introducing spurious correlations between phenotype and genotype that reflect population history. Intrabreed structure may exist when geographical origin or divergent selection regimes influence the choices of potential mates for breeding dogs. We present evidence for intrabreed stratification from a genome-wide marker survey in a sample of unrelated dogs. We genotyped 76 Border Collies, 49 Australian Shepherds, 17 German Shepherd Dogs, and 17 Portuguese Water Dogs for our primary analyses using Affymetrix Canine v2.0 single-nucleotide polymorphism (SNP) arrays. Subsets of autosomal markers were examined using clustering algorithms to facilitate assignment of individuals to populations and estimation of the number of populations represented in the sample. SNPs passing stringent quality control filters were employed for explicitly phylogenetic analyses reconstructing relationships between individuals using maximum parsimony and Bayesian methods. We used simulation studies to explore the possible effects of intrabreed stratification on genome-wide association studies. These analyses demonstrate significant stratification in at least one of our primary breeds of interest, the Border Collie. Demographic and pedigree data suggest that this population substructure may result from geographic isolation or divergent selection regimes practiced by breeders with different breeding program goals. Simulation studies indicate that such stratification could result in false discovery rates significant enough to confound genome-wide association analyses. Intrabreed stratification should be accounted for when designing and interpreting the results of case–control association studies using purebred dogs.

Microsatellite based genetic diversity and population structure of the endangered Spanish Guadarrama goat breed

PubMed Central

Serrano, Magdalena; Calvo, Jorge H; Martínez, Marta; Marcos-Carcavilla, Ane; Cuevas, Javier; González, Carmen; Jurado, Juan J; de Tejada, Paloma Díez

2009-01-01

Background Assessing genetic biodiversity and population structure of minor breeds through the information provided by neutral molecular markers, allows determination of their extinction risk and to design strategies for their management and conservation. Analysis of microsatellite loci is known to be highly informative in the reconstruction of the historical processes underlying the evolution and differentiation of animal populations. Guadarrama goat is a threatened Spanish breed which actual census (2008) consists of 3057 females and 203 males distributed in 22 populations more or less isolated. The aim of this work is to study the genetic status of this breed through the analysis of molecular data from 10 microsatellites typed in historic and actual live animals. Results The mean expected heterozygosity across loci within populations ranged from 0.62 to 0.77. Genetic differentiation measures were moderate, with a mean FST of 0.074, GST of 0.081 and RST of 0.085. Percentages of variation among and within populations were 7.5 and 92.5, respectively. Bayesian clustering analyses pointed out a population subdivision in 16 clusters, however, no correlation between geographical distances and genetic differences was found. Management factors such as the limited exchange of animals between farmers (estimated gene flow Nm = 3.08) mostly due to sanitary and social constraints could be the major causes affecting Guadarrama goat population subdivision. Conclusion Genetic diversity measures revealed a good status of biodiversity in the Guadarrama goat breed. Since diseases are the first cause affecting the census in this breed, population subdivision would be an advantage for its conservation. However, to maintain private alleles present at low frequencies in such small populations minimizing the inbreeding rate, it would necessitate some mating designs of animals carrying such alleles among populations. The systematic use of molecular markers will facilitate the comprehensive management of these populations, which in combination with the actual breeding program to increase milk yield, will constitute a good strategy to preserve the breed. PMID:19785776

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-01-01

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

Genetic potential of common bean progenies obtained by different breeding methods evaluated in various environments.

PubMed

Pontes Júnior, V A; Melo, P G S; Pereira, H S; Melo, L C

2016-09-02

Grain yield is strongly influenced by the environment, has polygenic and complex inheritance, and is a key trait in the selection and recommendation of cultivars. Breeding programs should efficiently explore the genetic variability resulting from crosses by selecting the most appropriate method for breeding in segregating populations. The goal of this study was to evaluate and compare the genetic potential of common bean progenies of carioca grain for grain yield, obtained by different breeding methods and evaluated in different environments. Progenies originating from crosses between lines and CNFC 7812 and CNFC 7829 were replanted up to the F 7 generation using three breeding methods in segregating populations: population (bulk), bulk within F 2 progenies, and single-seed descent (SSD). Fifteen F 8 progenies per method, two controls (BRS Estilo and Perola), and the parents were evaluated in a 7 x 7 simple lattice design, with plots of two 4-m rows. The tests were conducted in 10 environments in four States of Brazil and in three growing seasons in 2009 and 2010. Genetic parameters including genetic variance, heritability, variance of interaction, and expected selection gain were estimated. Genetic variability among progenies and the effect of progeny-environment interactions were determined for the three methods. The breeding methods differed significantly due to the effects of sampling procedures on the progenies and due to natural selection, which mainly affected the bulk method. The SSD and bulk methods provided populations with better estimates of genetic parameters and more stable progenies that were less affected by interaction with the environment.

Fasciola hepatica in goats from north-western Spain: Risk factor analysis using a capture ELISA.

PubMed

Pérez-Creo, Ana; Díaz, Pablo; López, Ceferino; Béjar, Juan Pablo; Martínez-Sernández, Victoria; Panadero, Rosario; Díez-Baños, Pablo; Ubeira, Florencio M; Morrondo, Patrocinio

2016-02-01

In order to study the seroprevalence of Fasciola hepatica infection in goats from north-western Spain, a total of 603 serum samples from 47 herds were tested using a capture ELISA (MM3-SERO). The identification of risk factors was assessed by a mixed-effects logistic regression analysis. The results showed that F. hepatica is widespread in this area with 57.4% of the herds and 22.7% of the animals testing positive. Breed and age were identified as determining factors for caprine F. hepatica infection. Seroprevalence in cross-bred animals was significantly higher than in the autochthonous Cabra Galega breed. A significantly higher seroprevalence was observed in older animals. The use of locally adapted breeds and the implementation of suitable management practices could provide a substantial improvement over the current F. hepatica control measures carried out in goat herds and should be considered when designing new F. hepatica control programs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Progress at the TITAN-EBIT

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

Klawitter, R.; Alanssari, M.; Frekers, D.

2015-01-09

Precision mass measurements of short-lived isotopes provide insight into a wide array of physics, including nuclear structure, nucleosynthesis, and tests of the Standard Model. The precision of Penning trap mass spectrometry (PTMS) measurements is limited by the lifetime of the isotopes of interest, but scales proportionally with their charge state q, making highly charged ions attractive for mass measurements of nuclides far from stability. TITAN, TRIUMF's Ion Trap(s) for Atomic and Nuclear science, is currently the only setup in the world coupling an EBIT to a rare isotope facility for the purpose of PTMS. Charge breeding ions for Penning trapmore » mass spectrometry, however, entails specific set of challenges. To make use of its potential, efficiencies have to be high, breeding times have to be short and the ion energy spread has to be small. An overview of the TITAN facility and charge-breeding program is given, current and future developments are highlighted and some selected results are presented.« less

Mating programs including genomic relationships

USDA-ARS?s Scientific Manuscript database

Computer mating programs have helped breeders minimize pedigree inbreeding and avoid recessive defects by mating animals with parents that have fewer common ancestors. With genomic selection, breed associations, AI organizations, and on-farm software providers could use new programs to minimize geno...

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

PubMed

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

2017-07-01

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

Long-term on-farm participatory maize breeding by stratified mass selection retains molecular diversity while improving agronomic performance.

PubMed

Alves, Mara Lisa; Belo, Maria; Carbas, Bruna; Brites, Cláudia; Paulo, Manuel; Mendes-Moreira, Pedro; Brites, Carla; Bronze, Maria do Rosário; Šatović, Zlatko; Vaz Patto, Maria Carlota

2018-02-01

Modern maize breeding programs gave rise to genetically uniform varieties that can affect maize's capacity to cope with increasing climate unpredictability. Maize populations, genetically more heterogeneous, can evolve and better adapt to a broader range of edaphic-climatic conditions. These populations usually suffer from low yields; it is therefore desirable to improve their agronomic performance while maintaining their valuable diversity levels. With this objective, a long-term participatory breeding/on-farm conservation program was established in Portugal. In this program, maize populations were subject to stratified mass selection. This work aimed to estimate the effect of on-farm stratified mass selection on the agronomic performance, quality, and molecular diversity of two historical maize populations. Multilocation field trials, comparing the initial populations with the derived selection cycles, showed that this selection methodology led to agronomic improvement for one of the populations. The molecular diversity analysis, using microsatellites, revealed that overall genetic diversity in both populations was maintained throughout selection. The comparison of quality parameters between the initial populations and the derived selection cycles was made using kernel from a common-garden experiment. This analysis showed that the majority of the quality traits evaluated progressed erratically over time. In conclusion, this breeding approach, through simple and low-cost methodologies, proved to be an alternative strategy for genetic resources' on-farm conservation.

On the value of the phenotypes in the genomic era.

PubMed

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

2014-12-01

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

Forensic assays of ricin: development of snp assays to generate precise genetic signatures for mixed genotypes found in ricin preparations

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

Jackson, Paul J.; Hill, Karen K.

2009-11-09

The results outlined in this report provide the information for needed to apply a SNP-based forensic analysis to diverse ricin preparations. The same methods could be useful in castor breeding programs that seek to reduce or eliminate ricin in oil-producing R. communis cultivars.

nalyses of rhizoctonia screening nursery results over 15 selected years from 1980 to 2015

USDA-ARS?s Scientific Manuscript database

The USDA-ARS has had a research program at Fort Collins focused on breeding for resistance to Rhizoctonia crown and root rot (Rcrr) since the late 1950s. By 1980, current resistant and susceptible checks were in use. All individual roots from each plot were lifted and rated on a disease index (DI)...

Development of the PCAD Model to Assess Biological Significance of Acoustic Disturbance

DTIC Science & Technology

2014-09-30

Katie McHugh from the Sarasota Dolphin Research Program compiled data on breathing rates of known dead or rescued individuals (N = 10). RESULTS...Biology 217:1485-1495. Maxwell, S. M., E. L. Hazen, S. J. Bograd, B. S. Halpern, G. A. Breed, B. Nickel , N. M. Teutschel, L. B. Crowder, S. Benson, P. H

Genotype by environment interaction and the use of unbalanced historical data for genomic selection in an international wheat breeding program

USDA-ARS?s Scientific Manuscript database

Genomic selection (GS) offers breeders the possibility of using historic data and unbalanced breeding trials to form training populations for predicting the performance of new lines. However, in using datasets that are unbalanced over time and space, there is increasing exposure to particular genoty...

A 100-year review: Methods and impact of genetic selection in dairy cattle—From daughter–dam comparisons to deep learning algorithms

USDA-ARS?s Scientific Manuscript database

In the early 1900s, breed society herdbooks had been established, and milk recording programs were in their infancy. Farmers were interested in improving the productivity of dairy cattle, but the foundations of population genetics, quantitative genetics, and animal breeding had not yet been laid. Li...

Putative resistance gene markers associated with quantitative trait loci for fire blight resistance in Malus 'Robusta 5' accessions

USDA-ARS?s Scientific Manuscript database

Breeding of fire blight resistant scions and rootstocks is a goal of several international apple breeding programs, as options are limited for management of this destructive disease caused by the bacterial pathogen Erwinia amylovora. A broad, large effect QTL for fire blight resistance has been pre...

Breed effects and genetic parameter estimates for calving difficulty and birth weight in a multi-breed population

USDA-ARS?s Scientific Manuscript database

Birth weight (BWT) and calving difficulty (CD) were recorded on 4,579 first parity females from the Germplasm Evaluation (GPE) program at the U.S. Meat Animal Research Center (USMARC). Both traits were analyzed using a bivariate animal model with direct and maternal effects. Calving difficulty was...

Early generation selection at multiple locations may identify potato parents that produce more widely adapted progency

USDA-ARS?s Scientific Manuscript database

Potato production in the eastern U.S. occurs over a wide range of environments from Maine to Florida; many of these states do not have a breeding program. Initial selections are usually made at the breeding location for more than two years before undergoing evaluation elsewhere, at which point, few...

Identification of quantitative trait loci (QTL) for fruit quality traits and number of weeks of flowering in the cultivated strawberry

USDA-ARS?s Scientific Manuscript database

Fruit quality traits and dayneutrality are two major foci of several strawberry breeding programs. The identification of quantitative trait loci (QTL) and molecular markers linked to these traits could improve breeding efficiency. In this work, an F1 population derived from the cross ‘Delmarvel’ × ...

50 CFR 15.24 - Permits for cooperative breeding.

Code of Federal Regulations, 2014 CFR

2014-10-01

... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.24 Permits..., at the time of the application, the exotic bird is still in the wild, has already been removed from the wild, or was bred in captivity; (2) If the exotic bird is still in the wild or was taken from the...

50 CFR 15.24 - Permits for cooperative breeding.

Code of Federal Regulations, 2013 CFR

2013-10-01

... PLANTS WILD BIRD CONSERVATION ACT Permits and Approval of Cooperative Breeding Programs § 15.24 Permits..., at the time of the application, the exotic bird is still in the wild, has already been removed from the wild, or was bred in captivity; (2) If the exotic bird is still in the wild or was taken from the...

The first research plantings of third-generation, third-backcross American chestnut (Castanea dentata) in the southeastern United States

Treesearch

Stacy Clark; S.E. Schlarbaum; F,V Saxton

2014-01-01

Production of American chestnut (Castanea dentata) resistant to the chestnut blight fungus (Cryphonectria parasitica) is being conducted currently through traditional breeding and genetic transformation. Sufficient material for field testing is currently available from The American Chestnut Foundation’s backcross breeding program. We planted approximately 4500 chestnut...

Background on the development of a nonfunded cooperative agreement between USDA’s Agricultural Research Service (ARS) and the Council on Dairy Cattle Breeding (CDCB)

USDA-ARS?s Scientific Manuscript database

Dairy producers, dairy record providers, breed associations, artificial-insemination companies, and the Animal Improvement Programs Laboratory, which is part of USDA’s Agricultural Research Service (ARS) in Beltsville, Maryland, have collaborated for many decades to provide the dairy industry with i...

Seroprevalence of antibodies to Toxoplasma gondii in Gordon's wild cat (Felis silvestris gordoni) in the Middle East

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 until recently been severely compromised by very high newborn mortality rates. Tw...

Breeding trees resistant to insects and diseases: putting theory into application

Treesearch

Richard A. Sniezko; Jennifer Koch

2017-01-01

Tree species world-wide are under increasing threat from diseases and insects, many of which are non-native. The integrity of our natural, urban and plantation forest ecosystems, and the services they provide are seriously imperiled. Breeding programs that harness the natural genetic resistance within tree species can provide a durable solution to these threats. In...

Family indices for seed-orchard selection

Treesearch

Gene Namkoong

1966-01-01

Many seed orchard programs include a stage at which clones or seedlings are culled on the basis of progeny tests. Though breeding systems which involve progeny testing differ in efficiency, they all provide information on an individual's breeding value through its own performance and that of parental or seedling relatives. A combined index on any one trait, using...

Breeding graft-compatible Douglas-fir rootstocks (Pseudotsuga menziesii (Mirb.) Franco).

Treesearch

D.L. Copes

1999-01-01

A study encompassing 24 years was conducted to determine if a breeding program could produce highly graft-compatible rootstocks. Twenty-seven trees of apparent high graft compatibility were selected and crossed to produce 226 control-pollinated families. Seedlings were grown, field planted, and grafted with test scions. Graft unions from field tests were evaluated...

QTL for bacterial cold water disease resistance and spleen size are located on rainbow trout chromosome Omy19

USDA-ARS?s Scientific Manuscript database

Selective breeding of aquatic animals for improved disease resistance has become a major focus in aquaculture, although little is known about underlying QTL or correlated traits. At the National Center for Cool and Cold Water Aquaculture (NCCCWA), we have pursued a selective breeding program with t...

Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness.

PubMed

Bartholomé, Jérôme; Bink, Marco Cam; van Heerwaarden, Joost; Chancerel, Emilie; Boury, Christophe; Lesur, Isabelle; Isik, Fikret; Bouffier, Laurent; Plomion, Christophe

2016-01-01

Increasing our understanding of the genetic architecture of complex traits, through analyses of genotype-phenotype associations and of the genes/polymorphisms accounting for trait variation, is crucial, to improve the integration of molecular markers into forest tree breeding. In this study, two full-sib families and one breeding population of maritime pine were used to identify quantitative trait loci (QTLs) for height growth and stem straightness, through linkage analysis (LA) and linkage disequilibrium (LD) mapping approaches. The populations used for LA consisted of two unrelated three-generation full-sib families (n = 197 and n = 477). These populations were assessed for height growth or stem straightness and genotyped for 248 and 217 markers, respectively. The population used for LD mapping consisted of 661 founders of the first and second generations of the breeding program. This population was phenotyped for the same traits and genotyped for 2,498 single-nucleotide polymorphism (SNP) markers corresponding to 1,652 gene loci. The gene-based reference genetic map of maritime pine was used to localize and compare the QTLs detected by the two approaches, for both traits. LA identified three QTLs for stem straightness and two QTLs for height growth. The LD study yielded seven significant associations (P ≤ 0.001): four for stem straightness and three for height growth. No colocalisation was found between QTLs identified by LA and SNPs detected by LD mapping for the same trait. This study provides the first comparison of LA and LD mapping approaches in maritime pine, highlighting the complementary nature of these two approaches for deciphering the genetic architecture of two mandatory traits of the breeding program.

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

PubMed

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

2015-01-01

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

Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery.

PubMed

Hickey, John M; Chiurugwi, Tinashe; Mackay, Ian; Powell, Wayne

2017-08-30

The rate of annual yield increases for major staple crops must more than double relative to current levels in order to feed a predicted global population of 9 billion by 2050. Controlled hybridization and selective breeding have been used for centuries to adapt plant and animal species for human use. However, achieving higher, sustainable rates of improvement in yields in various species will require renewed genetic interventions and dramatic improvement of agricultural practices. Genomic prediction of breeding values has the potential to improve selection, reduce costs and provide a platform that unifies breeding approaches, biological discovery, and tools and methods. Here we compare and contrast some animal and plant breeding approaches to make a case for bringing the two together through the application of genomic selection. We propose a strategy for the use of genomic selection as a unifying approach to deliver innovative 'step changes' in the rate of genetic gain at scale.

A rapid method to increase the number of F₁ plants in pea (Pisum sativum) breeding programs.

PubMed

Espósito, M A; Almirón, P; Gatti, I; Cravero, V P; Anido, F S L; Cointry, E L

2012-08-16

In breeding programs, a large number of F₂ individuals are required to perform the selection process properly, but often few such plants are available. In order to obtain more F₂ seeds, it is necessary to multiply the F₁ plants. We developed a rapid, efficient and reproducible protocol for in vitro shoot regeneration and rooting of seeds using 6-benzylaminopurine. To optimize shoot regeneration, basic medium contained Murashige and Skoog (MS) salts with or without B5 Gamborg vitamins and different concentrations of 6-benzylaminopurine (25, 50 and 75 μM) using five genotypes. We found that modified MS (B5 vitamins + 25 μM 6-benzylaminopurine) is suitable for in vitro shoot regeneration of pea. Thirty-eight hybrid combinations were transferred onto selected medium to produce shoots that were used for root induction on MS medium supplemented with α-naphthalene-acetic acid. Elongated shoots were developed from all hybrid genotypes. This procedure can be used in pea breeding programs and will allow working with a large number of plants even when the F₁ plants produce few seeds.

The Spring of Systems Biology-Driven Breeding.

PubMed

Lavarenne, Jérémy; Guyomarc'h, Soazig; Sallaud, Christophe; Gantet, Pascal; Lucas, Mikaël

2018-05-12

Genetics and molecular biology have contributed to the development of rationalized plant breeding programs. Recent developments in both high-throughput experimental analyses of biological systems and in silico data processing offer the possibility to address the whole gene regulatory network (GRN) controlling a given trait. GRN models can be applied to identify topological features helping to shortlist potential candidate genes for breeding purposes. Time-series data sets can be used to support dynamic modelling of the network. This will enable a deeper comprehension of network behaviour and the identification of the few elements to be genetically rewired to push the system towards a modified phenotype of interest. This paves the way to design more efficient, systems biology-based breeding strategies. Copyright © 2018 Elsevier Ltd. All rights reserved.

Introgression and pyramiding into common bean market class fabada of genes conferring resistance to anthracnose and potyvirus.

PubMed

Ferreira, Juan José; Campa, Ana; Pérez-Vega, Elena; Rodríguez-Suárez, Cristina; Giraldez, Ramón

2012-03-01

Anthracnose and bean common mosaic (BCM) are considered major diseases in common bean crop causing severe yield losses worldwide. This work describes the introgression and pyramiding of genes conferring genetic resistance to BCM and anthracnose local races into line A25, a bean genotype classified as market class fabada. Resistant plants were selected using resistance tests or combining resistance tests and marker-assisted selection. Lines A252, A321, A493, Sanilac BC6-Are, and BRB130 were used as resistance sources. Resistance genes to anthracnose (Co-2 ( C ), Co-2 ( A252 ) and Co-3/9) and/or BCM (I and bc-3) were introgressed in line A25 through six parallel backcrossing programs, and six breeding lines showing a fabada seed phenotype were obtained after six backcross generations: line A1258 from A252; A1231 from A321; A1220 from A493; A1183 and A1878 from Sanilac BC6-Are; and line A2418 from BRB130. Pyramiding of different genes were developed using the pedigree method from a single cross between lines obtained in the introgression step: line A1699 (derived from cross A1258 × A1220), A2438 (A1220 × A1183), A2806 (A1878 × A2418), and A3308 (A1699 × A2806). A characterization based on eight morpho-agronomic traits revealed a limited differentiation among the obtained breeding lines and the recurrent line A25. However, using a set of seven molecular markers linked to the loci used in the breeding programs it was possible to differentiate the 11 fabada lines. Considering the genetic control of the resistance in resistant donor lines, the observed segregations in the last backcrossing generation, the reaction against the pathogens, and the expression of the molecular markers it was also possible to infer the genotype conferring resistance in the ten fabada breeding lines obtained. As a result of these breeding programs, genetic resistance to three anthracnose races controlled by genes included in clusters Co-2 and Co-3/9, and genetic resistance to BCM controlled by genotype I + bc-3 was combined in the fabada line A3308.

Considering genetic characteristics in German Holstein breeding programs.

PubMed

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

2016-01-01

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

Genome properties and prospects of genomic prediction of hybrid performance in a breeding program of maize.

PubMed

Technow, Frank; Schrag, Tobias A; Schipprack, Wolfgang; Bauer, Eva; Simianer, Henner; Melchinger, Albrecht E

2014-08-01

Maize (Zea mays L.) serves as model plant for heterosis research and is the crop where hybrid breeding was pioneered. We analyzed genomic and phenotypic data of 1254 hybrids of a typical maize hybrid breeding program based on the important Dent × Flint heterotic pattern. Our main objectives were to investigate genome properties of the parental lines (e.g., allele frequencies, linkage disequilibrium, and phases) and examine the prospects of genomic prediction of hybrid performance. We found high consistency of linkage phases and large differences in allele frequencies between the Dent and Flint heterotic groups in pericentromeric regions. These results can be explained by the Hill-Robertson effect and support the hypothesis of differential fixation of alleles due to pseudo-overdominance in these regions. In pericentromeric regions we also found indications for consistent marker-QTL linkage between heterotic groups. With prediction methods GBLUP and BayesB, the cross-validation prediction accuracy ranged from 0.75 to 0.92 for grain yield and from 0.59 to 0.95 for grain moisture. The prediction accuracy of untested hybrids was highest, if both parents were parents of other hybrids in the training set, and lowest, if none of them were involved in any training set hybrid. Optimizing the composition of the training set in terms of number of lines and hybrids per line could further increase prediction accuracy. We conclude that genomic prediction facilitates a paradigm shift in hybrid breeding by focusing on the performance of experimental hybrids rather than the performance of parental lines in test crosses. Copyright © 2014 by the Genetics Society of America.

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.

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.

Speed breeding is a powerful tool to accelerate crop research and breeding.

PubMed

Watson, Amy; Ghosh, Sreya; Williams, Matthew J; Cuddy, William S; Simmonds, James; Rey, María-Dolores; Asyraf Md Hatta, M; Hinchliffe, Alison; Steed, Andrew; Reynolds, Daniel; Adamski, Nikolai M; Breakspear, Andy; Korolev, Andrey; Rayner, Tracey; Dixon, Laura E; Riaz, Adnan; Martin, William; Ryan, Merrill; Edwards, David; Batley, Jacqueline; Raman, Harsh; Carter, Jeremy; Rogers, Christian; Domoney, Claire; Moore, Graham; Harwood, Wendy; Nicholson, Paul; Dieters, Mark J; DeLacy, Ian H; Zhou, Ji; Uauy, Cristobal; Boden, Scott A; Park, Robert F; Wulff, Brande B H; Hickey, Lee T

2018-01-01

The growing human population and a changing environment have raised significant concern for global food security, with the current improvement rate of several important crops inadequate to meet future demand 1 . This slow improvement rate is attributed partly to the long generation times of crop plants. Here, we present a method called 'speed breeding', which greatly shortens generation time and accelerates breeding and research programmes. Speed breeding can be used to achieve up to 6 generations per year for spring wheat (Triticum aestivum), durum wheat (T. durum), barley (Hordeum vulgare), chickpea (Cicer arietinum) and pea (Pisum sativum), and 4 generations for canola (Brassica napus), instead of 2-3 under normal glasshouse conditions. We demonstrate that speed breeding in fully enclosed, controlled-environment growth chambers can accelerate plant development for research purposes, including phenotyping of adult plant traits, mutant studies and transformation. The use of supplemental lighting in a glasshouse environment allows rapid generation cycling through single seed descent (SSD) and potential for adaptation to larger-scale crop improvement programs. Cost saving through light-emitting diode (LED) supplemental lighting is also outlined. We envisage great potential for integrating speed breeding with other modern crop breeding technologies, including high-throughput genotyping, genome editing and genomic selection, accelerating the rate of crop improvement.

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

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

PubMed

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

2017-02-01

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

PrP genotype frequencies and risk evaluation for scrapie in dairy sheep breeds from southern Italy.

PubMed

Martemucci, Giovanni; Iamartino, Daniela; Blasi, Michele; D'Alessandro, Angela Gabriella

2015-12-01

Concerns regarding scrapie in sheep breeding have increased in the last few decades. The present study was carried out in dairy sheep breeds from southern Italy. In order to find breeding animals resistant to scrapie, the PrP genes of 1,205 animals from entire flocks of dairy native Apulian Leccese and Altamurana breeds, and Sicilian Comisana breed, were analysed for polymorphisms at codons 136, 154, and 171 related to scrapie resistance/susceptibility. The Altamurana breed was considered as two populations (Alt-Cav and Alt-Cra-Zoe), based on presumed cross-breeding. A total of five alleles and ten different genotypes were found. The ARQ allele was predominant for all breeds followed by ARR, the most resistant allele to scrapie, which was highly prevalent in Comisana (50%) and in native Alt-Cav (42.4%). The VRQ allele, associated with the highest susceptibility to scrapie, was detected at not negligeable levels in allocthonous Comisana (3.5%), at a low frequency (0.2%) in native Leccese and Alt-Cra-Zoe, while it was absent in Alt-Cav. The frequencies of PrP genotypes with a very low susceptibility risk to scrapie (R1) was higher in Comisana and Alt-Cav. The most susceptible genotype, ARQ/VRQ, was found only in Comisana. Within the Altamurana breed, there were notable differences between Alt-Cav and Alt-Cra-Zoe sheep. The Alt-Cav was characterised by the absence of VRQ and AHQ alleles and by the higher frequency of the ARR/ARR genotype (18.7%). Breeding programs, mainly in endangered breeds such as Altamurana, should be conducted gradually, combining resistance to scrapie, maintenance of genetic variability, and production. Copyright © 2015 Elsevier B.V. All rights reserved.

Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data

PubMed Central

Petersen, Jessica L.; Mickelson, James R.; Cothran, E. Gus; Andersson, Lisa S.; Axelsson, Jeanette; Bailey, Ernie; Bannasch, Danika; Binns, Matthew M.; Borges, Alexandre S.; Brama, Pieter; da Câmara Machado, Artur; Distl, Ottmar; Felicetti, Michela; Fox-Clipsham, Laura; Graves, Kathryn T.; Guérin, Gérard; Haase, Bianca; Hasegawa, Telhisa; Hemmann, Karin; Hill, Emmeline W.; Leeb, Tosso; Lindgren, Gabriella; Lohi, Hannes; Lopes, Maria Susana; McGivney, Beatrice A.; Mikko, Sofia; Orr, Nicholas; Penedo, M. Cecilia T; Piercy, Richard J.; Raekallio, Marja; Rieder, Stefan; Røed, Knut H.; Silvestrelli, Maurizio; Swinburne, June; Tozaki, Teruaki; Vaudin, Mark; M. Wade, Claire; McCue, Molly E.

2013-01-01

Horses were domesticated from the Eurasian steppes 5,000–6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection. PMID:23383025

Tomato as a Source of Carotenoids and Polyphenols Targeted to Cancer Prevention

PubMed Central

Martí, Raúl; Roselló, Salvador; Cebolla-Cornejo, Jaime

2016-01-01

A diet rich in vegetables has been associated with a reduced risk of many diseases related to aging and modern lifestyle. Over the past several decades, many researches have pointed out the direct relation between the intake of bioactive compounds present in tomato and a reduced risk of suffering different types of cancer. These bioactive constituents comprise phytochemicals such as carotenoids and polyphenols. The direct intake of these chemoprotective molecules seems to show higher efficiencies when they are ingested in its natural biological matrix than when they are ingested isolated or in dietary supplements. Consequently, there is a growing trend for improvement of the contents of these bioactive compounds in foods. The control of growing environment and processing conditions can ensure the maximum potential accumulation or moderate the loss of bioactive compounds, but the best results are obtained developing new varieties via plant breeding. The modification of single steps of metabolic pathways or their regulation via conventional breeding or genetic engineering has offered excellent results in crops such as tomato. In this review, we analyse the potential of tomato as source of the bioactive constituents with cancer-preventive properties and the result of modern breeding programs as a strategy to increase the levels of these compounds in the diet. PMID:27331820

Mating programs including genomic relationships and dominance effects

USDA-ARS?s Scientific Manuscript database

Computer mating programs have helped breeders minimize pedigree inbreeding and avoid recessive defects by mating animals with parents that have fewer common ancestors. With genomic selection, breed associations, AI organizations, and on-farm software providers could use new programs to minimize geno...

Evaluating Methods of Updating Training Data in Long-Term Genomewide Selection

PubMed Central

Neyhart, Jeffrey L.; Tiede, Tyler; Lorenz, Aaron J.; Smith, Kevin P.

2017-01-01

Genomewide selection is hailed for its ability to facilitate greater genetic gains per unit time. Over breeding cycles, the requisite linkage disequilibrium (LD) between quantitative trait loci and markers is expected to change as a result of recombination, selection, and drift, leading to a decay in prediction accuracy. Previous research has identified the need to update the training population using data that may capture new LD generated over breeding cycles; however, optimal methods of updating have not been explored. In a barley (Hordeum vulgare L.) breeding simulation experiment, we examined prediction accuracy and response to selection when updating the training population each cycle with the best predicted lines, the worst predicted lines, both the best and worst predicted lines, random lines, criterion-selected lines, or no lines. In the short term, we found that updating with the best predicted lines or the best and worst predicted lines resulted in high prediction accuracy and genetic gain, but in the long term, all methods (besides not updating) performed similarly. We also examined the impact of including all data in the training population or only the most recent data. Though patterns among update methods were similar, using a smaller but more recent training population provided a slight advantage in prediction accuracy and genetic gain. In an actual breeding program, a breeder might desire to gather phenotypic data on lines predicted to be the best, perhaps to evaluate possible cultivars. Therefore, our results suggest that an optimal method of updating the training population is also very practical. PMID:28315831

Major advances in globalization and consolidation of the artificial insemination industry.

PubMed

Funk, D A

2006-04-01

The artificial insemination (AI) industry in the United States has gone through many consolidations, mergers, and acquisitions over the past 25 yr. There are 5 major AI companies in the United States today: 3 large cooperatives, 1 private company, and 1 public company. The latter 2 have majority ownership outside of the United States. The AI industry in the United States progeny-tests more than 1,000 Holstein young sires per year. Because healthy, mature dairy bulls are capable of producing well over 100,000 straws of frozen semen per year, only a relatively small number of bulls are needed to breed the world's population of dairy cows. Most AI companies in the United States do not own many, if any, females and tend to utilize the same maternal families in their breeding programs. Little differences exist among the selection programs of the AI companies in the United States. The similarity of breeding programs and the extreme semen-production capabilities of bulls have contributed to difficulties the AI companies have had in developing genetically different product lines. Exports of North American Holstein genetics increased steadily from the 1970s into the 1990s because of the perceived superiority of North American Holsteins for dairy traits compared with European strains, especially for production. The breeding industry moved towards international genetic evaluations of bulls in the 1990s, with the International Bull Evaluation Service (Interbull) in Sweden coordinating the evaluations. The extensive exchange of elite genetics has led to a global dairy genetics industry with bulls that are closely related, and the average inbreeding level for the major dairy breeds continues to increase. Genetic markers have been used extensively and successfully by the industry for qualitative traits, especially for recessive genetic disorders, but markers have had limited impact for quantitative traits. Selection emphasis continues to migrate away from production traits and towards nonproduction traits, especially towards health and fitness traits. Specifically, fertility has arguably become the major breeding and management issue facing dairy farmers today. Some producers have implemented crossbreeding programs in an effort to capitalize on heterosis, and crossbreeding will almost certainly need to be a bigger part of the AI companies business in the years ahead.

Genome-wide association study for identifying loci that affect fillet yield, carcass, and body weight traits in rainbow trout (Oncorhynchus mykiss)

USDA-ARS?s Scientific Manuscript database

Fillet yield (FY, %) is an economically important trait in rainbow trout aquaculture that affects production efficiency. Despite that, FY has not received much attention in breeding programs because it is difficult to measure on a large number of fish and it cannot be directly measured on breeding c...

Exploring pima and upland cross-combinations to identify fusarium oxysporum f. sp. vasinfectum race 4 resistant cottons by combining ability of superior cultivars

USDA-ARS?s Scientific Manuscript database

A cotton breeding program strives to identify the best performance cultivars or breeding lines which can be used as parents in crosses. Multi-cross combinations provide the means of performance of each parent and assess the combining ability or productivity of parents through the hybridization proce...

Walnut genetic improvement at the start of a new century

Treesearch

Keith E. Woeste; James R. McKenna

2004-01-01

Since the early 1960s, researchers in programs to improve black walnut for timber have struggled to meet some basic breeding objectives. Promising avenues of research had been identified by the early 1950s, and conventional methods to breed forest trees were widely adopted as suitable for walnut. Progress has been slow however, due to practical problems related to...

Regional breeding bird monitoring in Western Great Lakes National Forests

Treesearch

JoAnn Hanowski; Jim Lind; Nick Danz; Gerald Niemi; Tim Jones

2005-01-01

We established breeding bird monitoring programs in three National Forests in northern Minnesota (Superior and Chippewa in 1991) and northern Wisconsin (Chequamegon in 1992). A total of 134, 169, and 132 stands (1,272 survey points) have been surveyed annually in these forests through 2002. We examined trends in relative abundance for 53 species in the Chequamegon, 51...

Identification of genomic region controlling resistance to aflatoxin contamination in a peanut recombinant inbred line population (Tifrunner XGT-C20)

USDA-ARS?s Scientific Manuscript database

In peanut, limited genetic variation for disease resistance is available in breeding programs necessitating the identification of stable resistance sources for use in cultivar development. ‘Tifrunner’ is a runner cultivar while ‘GT-C20’ is a Spanish-type breeding line with resistance to aflatoxin co...

Impact of changes in weight, fat depth, and loin muscle depth on carcass yield and value and implications for selection and pricing of rams from terminal-sire sheep breeds

USDA-ARS?s Scientific Manuscript database

Breeding objectives and selection indexes are necessary to support comprehensive genetic improvement programs. This study used off-test body weights (OTBW) or chilled carcass weights (CCW), ultrasonic measurements of fat depth (USFD, mm), and predicted ultrasound loin muscle depths (USLMD, mm) from ...

Inter- and intraspecific grafting and breeding of five-needle pines

Treesearch

Clifford E. Ahlgren

1970-01-01

The forest tree improvement work at the Center was started in 1949 with the introduction of some of Dr. Riker's grafted eastern white pine selections. Subsequently a program of selecting, grafting, breeding and testing for resistance was begun. The work was initiated at Basswood Lake (15 miles NE of Ely, Minnesota) rather than elsewhere on a more accessible site...

A Strategy for the Third Breeding Cycle of Loblolly Pine in the Southeastern U.S.

Treesearch

S.E. McKeand; F.E. Bridgwater

1998-01-01

A strategy for the North Carolina State University - Industry Cooperative Tree Improvement Program's third-cycle breeding for loblolly pine (Pinus taeda L.) was developed to provide genetic gain in the short-term as well as to maintain genetic diversity so that long-term genetic gains will also be possible. Our strategy will be to manage a...

Integration of selective breeding and vaccination to improve disease resistance in aquaculture: Application to control bacterial cold water disease

USDA-ARS?s Scientific Manuscript database

Bacterial cold water disease (BCWD) is a frequent cause of elevated mortality in rainbow trout and the development of effective control strategies is a priority within the U.S. A goal of the NCCCWA breeding program is to produce germplasm with superior growth and survival following exposure to infe...

Captive-breeding of captive and wild-reared Gunnison sage-grouse.

PubMed

Apa, Anthony D; Wiechman, Lief A

2016-01-01

Gunnison sage-grouse (Centrocercus minimus) distribution in North America has decreased over historical accounts and has received federal protection under the Endangered Species Act. We investigated captive-breeding of a captive-flock of Gunnison sage-grouse created from individuals reared in captivity from wild-collected eggs we artificially incubated. We also introduced wild-reared individuals into captivity. Our captive-flock successfully bred and produced fertile eggs. We controlled the timing and duration of male-female breeding interactions and facilitated a semi-natural mating regime. Males established a strutting ground in captivity that females attended for mate selection. In 2010, we allowed females to establish eight nests, incubate, and hatch eggs. Females in captivity were more successful incubating nests than raising broods. Although there are many technical, financial, and logistic issues associated with captive-breeding, we recommend that federal biologists and managers work collaboratively with state wildlife agencies and consider developing a captive-flock as part of a comprehensive conservation strategy for a conservation-reliant species like the Gunnison sage-grouse. The progeny produced from a captive-rearing program could assist in the recovery if innovative approaches to translocation are part of a comprehensive proactive conservation program. © 2015 Wiley Periodicals, Inc.

Male and female breeding strategies in a cooperative primate.

PubMed

Yamamoto, Maria Emilia; Araujo, Arrilton; Arruda, Maria de Fatima; Lima, Ana Karinne Moreira; Siqueira, Jose de Oliveira; Hattori, Wallisen Tadashi

2014-11-01

Marmosets are cooperative breeders organized as extended family groups, but breeding is generally restricted to a single pair. Breeding competition is fierce in female marmosets; males, on the other hand, show low levels of intragroup aggression. We investigated male and female breeding strategies and the resulting reproductive output in 9 wild groups. Reproductive output, tenure of breeding animals, identification of the breeding system, breeding position replacements, migration and infanticide were recorded; also, we recorded grooming and aggression. Replacement of the breeding male or female was observed on nine occasions. On four occasions, the son of the breeding male inherited the breeding post, but we never observed inheritance of a breeding post by a daughter. Mostly, females attained a breeding post by immigrating to a group that had a breeding vacancy. Our results showed that Callithrix jacchus males and females use different strategies to attain a breeding position and maintain it for as long as possible. These strategies prolong the tenure of the breeding position, which is the best way to produce a large number of offspring. This article is part of a Special Issue entitled: Neotropical Behaviour. Copyright © 2014 Elsevier B.V. All rights reserved.

Frequency and distribution of 152 genetic disease variants in over 100,000 mixed breed and purebred dogs

PubMed Central

Anderson, Heidi; Davison, Stephen; Hughes, Angela M.; Bouirmane, Julia; Lindqvist, Johan; Lytle, Katherine M.; Ganesan, Balasubramanian; Ottka, Claudia; Ruotanen, Päivi; Forman, Oliver P.; Fretwell, Neale; Cole, Cynthia A.; Lohi, Hannes

2018-01-01

Knowledge on the genetic epidemiology of disorders in the dog population has implications for both veterinary medicine and sustainable breeding. Limited data on frequencies of genetic disease variants across breeds exists, and the disease heritage of mixed breed dogs remains poorly explored to date. Advances in genetic screening technologies now enable comprehensive investigations of the canine disease heritage, and generate health-related big data that can be turned into action. We pursued population screening of genetic variants implicated in Mendelian disorders in the largest canine study sample examined to date by examining over 83,000 mixed breed and 18,000 purebred dogs representing 330 breeds for 152 known variants using a custom-designed beadchip microarray. We further announce the creation of MyBreedData (www.mybreeddata.com), an online updated inherited disorder prevalence resource with its foundation in the generated data. We identified the most prevalent, and rare, disease susceptibility variants across the general dog population while providing the first extensive snapshot of the mixed breed disease heritage. Approximately two in five dogs carried at least one copy of a tested disease variant. Most disease variants are shared by both mixed breeds and purebreds, while breed- or line-specificity of others is strongly suggested. Mixed breed dogs were more likely to carry a common recessive disease, whereas purebreds were more likely to be genetically affected with one, providing DNA-based evidence for hybrid vigor. We discovered genetic presence of 22 disease variants in at least one additional breed in which they were previously undescribed. Some mutations likely manifest similarly independently of breed background; however, we emphasize the need for follow up investigations in each case and provide a suggested validation protocol for broader consideration. In conclusion, our study provides unique insight into genetic epidemiology of canine disease risk variants, and their relevance for veterinary medicine, breeding programs and animal welfare. PMID:29708978

Frequency and distribution of 152 genetic disease variants in over 100,000 mixed breed and purebred dogs.

PubMed

Donner, Jonas; Anderson, Heidi; Davison, Stephen; Hughes, Angela M; Bouirmane, Julia; Lindqvist, Johan; Lytle, Katherine M; Ganesan, Balasubramanian; Ottka, Claudia; Ruotanen, Päivi; Kaukonen, Maria; Forman, Oliver P; Fretwell, Neale; Cole, Cynthia A; Lohi, Hannes

2018-04-01

Knowledge on the genetic epidemiology of disorders in the dog population has implications for both veterinary medicine and sustainable breeding. Limited data on frequencies of genetic disease variants across breeds exists, and the disease heritage of mixed breed dogs remains poorly explored to date. Advances in genetic screening technologies now enable comprehensive investigations of the canine disease heritage, and generate health-related big data that can be turned into action. We pursued population screening of genetic variants implicated in Mendelian disorders in the largest canine study sample examined to date by examining over 83,000 mixed breed and 18,000 purebred dogs representing 330 breeds for 152 known variants using a custom-designed beadchip microarray. We further announce the creation of MyBreedData (www.mybreeddata.com), an online updated inherited disorder prevalence resource with its foundation in the generated data. We identified the most prevalent, and rare, disease susceptibility variants across the general dog population while providing the first extensive snapshot of the mixed breed disease heritage. Approximately two in five dogs carried at least one copy of a tested disease variant. Most disease variants are shared by both mixed breeds and purebreds, while breed- or line-specificity of others is strongly suggested. Mixed breed dogs were more likely to carry a common recessive disease, whereas purebreds were more likely to be genetically affected with one, providing DNA-based evidence for hybrid vigor. We discovered genetic presence of 22 disease variants in at least one additional breed in which they were previously undescribed. Some mutations likely manifest similarly independently of breed background; however, we emphasize the need for follow up investigations in each case and provide a suggested validation protocol for broader consideration. In conclusion, our study provides unique insight into genetic epidemiology of canine disease risk variants, and their relevance for veterinary medicine, breeding programs and animal welfare.

Can non-breeding be a cost of breeding dispersal?

USGS Publications Warehouse

Danchin, E.; Cam, E.

2002-01-01

Breeding habitat selection and dispersal are crucial processes that affect many components of fitness. Breeding dispersal entails costs, one of which has been neglected: dispersing animals may miss breeding opportunities because breeding dispersal requires finding a new nesting site and mate, two time- and energy-consuming activities. Dispersers are expected to be prone to non-breeding. We used the kittiwake (Rissa tridactyla) to test whether breeding dispersal influences breeding probability. Breeding probability was associated with dispersal, in that both were negatively influenced by private information (previous individual reproductive success) and public information (average reproductive success of conspecifics) about patch quality. Furthermore, the probability of skipping breeding was 1.7 times higher in birds that settled in a new patch relative to those that remained on the same patch. Finally, non-breeders that resumed breeding were 4.4 times more likely to disperse than birds that bred in successive years. Although private information may influence breeding probability directly, the link between breeding probability and public information may be indirect, through the influence of public information on breeding dispersal, non-breeding thus being a cost of dispersal. These results support the hypothesis that dispersal may result in not being able to breed. More generally, non-breeding (which can be interpreted as an extreme form of breeding failure) may reveal costs of various previous activities. Because monitoring the non-breeding portion of a population is difficult, non-breeders have been neglected in many studies of reproduction trade-offs.

Analysis of Time-Dependent Tritium Breeding Capability of Water Cooled Ceramic Breeder Blanket for CFETR

NASA Astrophysics Data System (ADS)

Gao, Fangfang; Zhang, Xiaokang; Pu, Yong; Zhu, Qingjun; Liu, Songlin

2016-08-01

Attaining tritium self-sufficiency is an important mission for the Chinese Fusion Engineering Testing Reactor (CFETR) operating on a Deuterium-Tritium (D-T) fuel cycle. It is necessary to study the tritium breeding ratio (TBR) and breeding tritium inventory variation with operation time so as to provide an accurate data for dynamic modeling and analysis of the tritium fuel cycle. A water cooled ceramic breeder (WCCB) blanket is one candidate of blanket concepts for the CFETR. Based on the detailed 3D neutronics model of CFETR with the WCCB blanket, the time-dependent TBR and tritium surplus were evaluated by a coupling calculation of the Monte Carlo N-Particle Transport Code (MCNP) and the fusion activation code FISPACT-2007. The results indicated that the TBR and tritium surplus of the WCCB blanket were a function of operation time and fusion power due to the Li consumption in breeder and material activation. In addition, by comparison with the results calculated by using the 3D neutronics model and employing the transfer factor constant from 1D to 3D, it is noted that 1D analysis leads to an over-estimation for the time-dependent tritium breeding capability when fusion power is larger than 1000 MW. supported by the National Magnetic Confinement Fusion Science Program of China (Nos. 2013GB108004, 2015GB108002, and 2014GB119000), and by National Natural Science Foundation of China (No. 11175207)

Microsatellite Variations of Elite Setaria Varieties Released during Last Six Decades in China.

PubMed

Jia, Guanqing; Liu, Xiaotong; Schnable, James C; Niu, Zhengang; Wang, Chunfang; Li, Yuhui; Wang, Shujun; Wang, Suying; Liu, Jinrong; Guo, Erhu; Zhi, Hui; Diao, Xianmin

2015-01-01

Crop improvement is a multifaceted micro-evolutionary process, involving changes in breeding approaches, planting configurations and consumption preferences of human beings. Recent research has started to identify the specific genes or genomic regions correlate to improved agronomic traits, however, an apparent blank between the genetic structure of crop elite varieties and their improving histories in diverse modern breeding programs is still in existence. Foxtail millet (Setaria italica) was one of the earliest cereal crops to be domesticated and served as a staple crop for early civilizations in China, where it is still widely grown today. In the present trial, a panel of foxtail millet elite varieties, which were released in the last sixty years in different geographical regions of China, was characterized using microsatellite markers (SSRs). A clear separation of two subpopulations corresponding to the two eco-geographical regions of foxtail millet production in China was identified by the dataset, which also indicated that in more recently released elite varieties, large quantities of accessions have been transferred from spring-sowing to summer-sowing ecotypes, likely as a result of breeding response to planting configurations. An association mapping study was conducted to identify loci controlling traits of major agronomic interest. Furthermore, selective sweeps involved in improvement of foxtail millet were identified as multi-diverse minor effect loci controlling different agronomic traits during the long-term improvement of elite varieties. Our results highlight the effect of transition of planting configuration and breeding preference on genetic evolvement of crop species.

Microsatellite Variations of Elite Setaria Varieties Released during Last Six Decades in China

PubMed Central

Schnable, James C.; Niu, Zhengang; Wang, Chunfang; Li, Yuhui; Wang, Shujun; Wang, Suying; Liu, Jinrong; Guo, Erhu; Zhi, Hui; Diao, Xianmin

2015-01-01

Crop improvement is a multifaceted micro-evolutionary process, involving changes in breeding approaches, planting configurations and consumption preferences of human beings. Recent research has started to identify the specific genes or genomic regions correlate to improved agronomic traits, however, an apparent blank between the genetic structure of crop elite varieties and their improving histories in diverse modern breeding programs is still in existence. Foxtail millet (Setaria italica) was one of the earliest cereal crops to be domesticated and served as a staple crop for early civilizations in China, where it is still widely grown today. In the present trial, a panel of foxtail millet elite varieties, which were released in the last sixty years in different geographical regions of China, was characterized using microsatellite markers (SSRs). A clear separation of two subpopulations corresponding to the two eco-geographical regions of foxtail millet production in China was identified by the dataset, which also indicated that in more recently released elite varieties, large quantities of accessions have been transferred from spring-sowing to summer-sowing ecotypes, likely as a result of breeding response to planting configurations. An association mapping study was conducted to identify loci controlling traits of major agronomic interest. Furthermore, selective sweeps involved in improvement of foxtail millet were identified as multi-diverse minor effect loci controlling different agronomic traits during the long-term improvement of elite varieties. Our results highlight the effect of transition of planting configuration and breeding preference on genetic evolvement of crop species. PMID:25932649

Toward responsible stock enhancement: broadcast spawning dynamics and adaptive genetic management in white seabass aquaculture.

PubMed

Gruenthal, Kristen M; Drawbridge, Mark A

2012-06-01

The evolutionary effects captive-bred individuals that can have on wild conspecifics are necessary considerations for stock enhancement programs, but breeding protocols are often developed without the knowledge of realized reproductive behavior. To help fill that gap, parentage was assigned to offspring produced by a freely mating group of 50 white seabass (Atractoscion nobilis), a representative broadcast spawning marine finfish cultured for conservation. Similar to the well-known and closely related red drum (Sciaenops ocellatus), A. nobilis exhibited large variation in reproductive success. More males contributed and contributed more equally than females within and among spawns in a mating system best described as lottery polygyny. Two females produced 27% of the seasonal offspring pool and female breeding effective size averaged 1.85 per spawn and 12.38 seasonally, whereas male breeding effective size was higher (6.42 and 20.87, respectively), with every male contributing 1-7% of offspring. Further, females batch spawned every 1-5 weeks, while males displayed continuous reproductive readiness. Sex-specific mating strategies resulted in multiple successful mate pairings and a breeding effective to census size ratio of ≥0.62. Understanding a depleted species' mating system allowed management to more effectively utilize parental genetic variability for culture, but the fitness consequences of long-term stocking can be difficult to address.

Germplasm-regression-combined (GRC) marker-trait association identification in plant breeding: a challenge for plant biotechnological breeding under soil water deficit conditions.

PubMed

Ruan, Cheng-Jiang; Xu, Xue-Xuan; Shao, Hong-Bo; Jaleel, Cheruth Abdul

2010-09-01

In the past 20 years, the major effort in plant breeding has changed from quantitative to molecular genetics with emphasis on quantitative trait loci (QTL) identification and marker assisted selection (MAS). However, results have been modest. This has been due to several factors including absence of tight linkage QTL, non-availability of mapping populations, and substantial time needed to develop such populations. To overcome these limitations, and as an alternative to planned populations, molecular marker-trait associations have been identified by the combination between germplasm and the regression technique. In the present preview, the authors (1) survey the successful applications of germplasm-regression-combined (GRC) molecular marker-trait association identification in plants; (2) describe how to do the GRC analysis and its differences from mapping QTL based on a linkage map reconstructed from the planned populations; (3) consider the factors that affect the GRC association identification, including selections of optimal germplasm and molecular markers and testing of identification efficiency of markers associated with traits; and (4) finally discuss the future prospects of GRC marker-trait association analysis used in plant MAS/QTL breeding programs, especially in long-juvenile woody plants when no other genetic information such as linkage maps and QTL are available.

Genetic analysis of prolactin gene in Pakistani cattle.

PubMed

Uddin, Raza Mohy; Babar, Masroor Ellahi; Nadeem, Asif; Hussain, Tanveer; Ahmad, Shakil; Munir, Sadia; Mehboob, Riffat; Ahmad, Fridoon Jawad

2013-10-01

Prolactin (PRL) is a polypeptide hormone, secreted mainly by the anterior pituitary gland. It is involved in many endocrine activities. The key functions of PRL are related to reproduction and lactation in mammals. To ascertain the presence of polymorphisms in the bovine PRL gene (bPRL), the bPRL gene was sequenced. Five mutations were identified in exonic region and eleven in associated intronic regions in 100 cattle from four Pakistani cattle breeds. Haplotype of predicted amino acid changes represent a common alteration at codon 222 from R-Arginine into K-Lysine in all four breeds. Significant statistical variations were observed in the distribution of single nucleotide polymorphism (SNP) in various cattle populations. However, on basis of present study, an association of these SNPs with milk performance traits in four Pakistani cow breeds cannot be truly replicated but at least can be effective DNA markers for some of the breeds studied. Linkage analysis between these SNPs on larger populations can be useful for the association with milk production traits. Furthermore, present study may be used for marker-assisted selection and management in cattle breeding program in local cattle breeds.

Species hybridization in the genus Pinus

Treesearch

Peter W. Garrett

1979-01-01

Results of a breeding program in which a large number of pine species were tested indicate that a number of species and hybrids may be useful in the northeastern United States. Austrian black pine x Japanese black pine and hybrids containing Japanese red pine all had good growth rates. While none of the soft pines grew faster than eastern white pine, a number of...

How well can captive breeding programs conserve biodiversity? A review of salmonids

PubMed Central

Fraser, Dylan J

2008-01-01

Captive breeding programs are increasingly being initiated to prevent the imminent extinction of endangered species and/or populations. But how well can they conserve genetic diversity and fitness, or re-establish self-sustaining populations in the wild? A review of these complex questions and related issues in salmonid fishes reveals several insights and uncertainties. Most programs can maintain genetic diversity within populations over several generations, but available research suggests the loss of fitness in captivity can be rapid, its magnitude probably increasing with the duration in captivity. Over the long-term, there is likely tremendous variation between (i) programs in their capacity to maintain genetic diversity and fitness, and (ii) species or even intraspecific life-history types in both the severity and manner of fitness-costs accrued. Encouragingly, many new theoretical and methodological approaches now exist for current and future programs to potentially reduce these effects. Nevertheless, an unavoidable trade-off exists between conserving genetic diversity and fitness in certain instances, such as when captive-bred individuals are temporarily released into the wild. Owing to several confounding factors, there is also currently little evidence that captive-bred lines of salmonids can or cannot be reintroduced as self-sustaining populations. Most notably, the root causes of salmonid declines have not been mitigated where captive breeding programs exist. Little research has also addressed under what conditions an increase in population abundance due to captive-rearing might offset fitness reductions induced in captivity. Finally, more empirical investigation is needed to evaluate the genetic/fitness benefits and risks associated with (i) maintaining captive broodstocks as either single or multiple populations within one or more facilities, (ii) utilizing cryopreservation or surrogate broodstock technologies, and (iii) adopting other alternatives to captive-rearing such as translocations to new habitats. Management recommendations surrounding these issues are proposed, with the aim of facilitating meta-analyses and more general principles or guidelines for captive-breeding. These include the need for the following: (i) captive monitoring to involve, a priori, greater application of hypothesis testing through the use of well-designed experiments and (ii) improved documentation of procedures adopted by specific programs for reducing the loss of genetic diversity and fitness. PMID:25567798

Complex Admixture Preceded and Followed the Extinction of Wisent in the Wild

PubMed Central

Hartmann, Stefanie; Paijmans, Johanna L. A.; Taron, Ulrike; Xenikoudakis, Georgios; Cahill, James A.; Heintzman, Peter D.; Shapiro, Beth; Baryshnikov, Gennady; Bunevich, Aleksei N.; Crees, Jennifer J.; Dobosz, Roland; Manaserian, Ninna; Okarma, Henryk; Tokarska, Małgorzata; Turvey, Samuel T.; Wójcik, Jan M.; Żyła, Waldemar; Szymura, Jacek M.; Hofreiter, Michael

2017-01-01

Retracing complex population processes that precede extreme bottlenecks may be impossible using data from living individuals. The wisent (Bison bonasus), Europe’s largest terrestrial mammal, exemplifies such a population history, having gone extinct in the wild but subsequently restored by captive breeding efforts. Using low coverage genomic data from modern and historical individuals, we investigate population processes occurring before and after this extinction. Analysis of aligned genomes supports the division of wisent into two previously recognized subspecies, but almost half of the genomic alignment contradicts this population history as a result of incomplete lineage sorting and admixture. Admixture between subspecies populations occurred prior to extinction and subsequently during the captive breeding program. Admixture with the Bos cattle lineage is also widespread but results from ancient events rather than recent hybridization with domestics. Our study demonstrates the huge potential of historical genomes for both studying evolutionary histories and for guiding conservation strategies. PMID:28007976

Recovery of Native Genetic Background in Admixed Populations Using Haplotypes, Phenotypes, and Pedigree Information – Using Cika Cattle as a Case Breed

PubMed Central

Simčič, Mojca; Smetko, Anamarija; Sölkner, Johann; Seichter, Doris; Gorjanc, Gregor; Kompan, Dragomir; Medugorac, Ivica

2015-01-01

The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which potentially have had direct or indirect historical contribution to the genetic makeup of the breed of interest. PMID:25923207

Genetic diversity and relationships among six local cattle populations in semi-arid areas assessed by a bovine medium-density single nucleotide polymorphism data.

PubMed

Boushaba, N; Boujenane, I; Moazami-Goudarzi, K; Flori, L; Saïdi-Mehtar, N; Tabet-Aoul, N; Laloë, D

2018-06-18

The local cattle populations belonging to the 'Brune de l'Atlas' cattle in Algeria and Morocco are potential resources in terms of genetic diversity and socioeconomic prevalence and their characterization is an essential step in any program designed to conserve genetic diversity. Our objectives were to assess the genetic diversity, the population structure and relationships among four Algerian cattle breeds, the Biskra, Cheurfa, Chelifienne and Guelmoise and of two Moroccan, the Oulmès-Zaër and Tidili by genotyping 50 309 single nucleotide polymorphism in 203 unrelated animals. A low population structure was observed across breeds with pairwise F ST values ranging from 0.008 to 0.043, suggesting a high level of gene flow. These data were combined with the available data on cattle populations representative of Europe (EUT), West African taurine (WAT) and zebu (ZEB). Principle Components Analysis was carried out which revealed that the Maghrebin populations are closer to the EUT/ZEB population than to the WAT. Structure analysis confirmed this mixed origin of the Maghrebin cattle populations. We also detected the influence of zebu breeds in Cheurfa and Guelmoise populations. This study provides the first information about genetic diversity within and between Algerian and Moroccan cattle populations and gives a detailed description of their genetic structure and relationships according to their historical origins. This study revealed that several combined effects contributed to shape the genetic diversity of the six Maghrebin populations studied: (i) gene flow among local breeds, (ii) the recent introgression of European breeds in local Algerian breeds and (iii) the traditional management systems. The results of this study will primarily assist policy makers and livestock keepers to make useful decisions for improvement of genetic resources while ensuring the preservation and conservation of local breeds in Algeria and Morocco.

Genomic-based-breeding tools for tropical maize improvement.

PubMed

Chakradhar, Thammineni; Hindu, Vemuri; Reddy, Palakolanu Sudhakar

2017-12-01

Maize has traditionally been the main staple diet in the Southern Asia and Sub-Saharan Africa and widely grown by millions of resource poor small scale farmers. Approximately, 35.4 million hectares are sown to tropical maize, constituting around 59% of the developing worlds. Tropical maize encounters tremendous challenges besides poor agro-climatic situations with average yields recorded <3 tones/hectare that is far less than the average of developed countries. On the contrary to poor yields, the demand for maize as food, feed, and fuel is continuously increasing in these regions. Heterosis breeding introduced in early 90 s improved maize yields significantly, but genetic gains is still a mirage, particularly for crop growing under marginal environments. Application of molecular markers has accelerated the pace of maize breeding to some extent. The availability of array of sequencing and genotyping technologies offers unrivalled service to improve precision in maize-breeding programs through modern approaches such as genomic selection, genome-wide association studies, bulk segregant analysis-based sequencing approaches, etc. Superior alleles underlying complex traits can easily be identified and introgressed efficiently using these sequence-based approaches. Integration of genomic tools and techniques with advanced genetic resources such as nested association mapping and backcross nested association mapping could certainly address the genetic issues in maize improvement programs in developing countries. Huge diversity in tropical maize and its inherent capacity for doubled haploid technology offers advantage to apply the next generation genomic tools for accelerating production in marginal environments of tropical and subtropical world. Precision in phenotyping is the key for success of any molecular-breeding approach. This article reviews genomic technologies and their application to improve agronomic traits in tropical maize breeding has been reviewed in detail.

Understanding crop genetic diversity under modern plant breeding.

PubMed

Fu, Yong-Bi

2015-11-01

Maximizing crop yield while at the same time minimizing crop failure for sustainable agriculture requires a better understanding of the impacts of plant breeding on crop genetic diversity. This review identifies knowledge gaps and shows the need for more research into genetic diversity changes under plant breeding. Modern plant breeding has made a profound impact on food production and will continue to play a vital role in world food security. For sustainable agriculture, a compromise should be sought between maximizing crop yield under changing climate and minimizing crop failure under unfavorable conditions. Such a compromise requires better understanding of the impacts of plant breeding on crop genetic diversity. Efforts have been made over the last three decades to assess crop genetic diversity using molecular marker technologies. However, these assessments have revealed some temporal diversity patterns that are largely inconsistent with our perception that modern plant breeding reduces crop genetic diversity. An attempt was made in this review to explain such discrepancies by examining empirical assessments of crop genetic diversity and theoretical investigations of genetic diversity changes over time under artificial selection. It was found that many crop genetic diversity assessments were not designed to assess diversity impacts from specific plant breeding programs, while others were experimentally inadequate and contained technical biases from the sampling of cultivars and genomes. Little attention has been paid to theoretical investigations on crop genetic diversity changes from plant breeding. A computer simulation of five simplified breeding schemes showed the substantial effects of plant breeding on the retention of heterozygosity over generations. It is clear that more efforts are needed to investigate crop genetic diversity in space and time under plant breeding to achieve sustainable crop production.

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

PubMed

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

2018-03-15

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

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

Epidemiology of ocular disorders presumed to be inherited in three small Italian dog breeds in Italy.

PubMed

Guandalini, Adolfo; Di Girolamo, Nicola; Corvi, Roberta; Santillo, Daniele; Andreani, Valentina; Pinzo, Barbara

2017-12-28

To describe the prevalence and the types of eye disorders that are known or presumed to be inherited (KP-HED) in three small Italian dog breeds. Three small Italian dog breeds: Maltese, Bolognese, and Italian Greyhound. All dogs of the breeds selected for this prospective observational study that underwent a complete ophthalmic examination between 1994 and 2015 were included. General and proportional KP-HED prevalence with 95% confidence intervals were reported. Three hundred and six of 462 dogs were affected by at least one KP-HED (66.2%; 95% CI: 61.8%-70.4%). In the entire population, the five most common KP-HED were cataract (n = 122; rate on the total number of KP-HED: 31.4%), entropion (n = 56; 14.4%), keratoconjunctivitis sicca (n = 33; 8.5%), retinal dysplasia (n = 24; 6.2%), and persistent pupillary membrane (iris to iris) (n = 21; 5.4%). The most common KP-HED in each breed were cataracts in the Maltese (35.1%) and in the Bolognese (24.2%), and presentation of vitreous in the anterior chamber in the Italian Greyhound (46.7%). Clinicians should be aware of KP-HED that commonly affect three small Italian dog breeds. Breed standards should be reconsidered, and breeding programs should be directed at limiting such disorders. © 2017 American College of Veterinary Ophthalmologists.

Marker-assisted selection in plant breeding for salinity tolerance.

PubMed

Ashraf, M; Akram, N A; Mehboob-Ur-Rahman; Foolad, M R

2012-01-01

Marker-assisted selection (MAS) is the process of using morphological, biochemical, or DNA markers as indirect selection criteria for selecting agriculturally important traits in crop breeding. This process is used to improve the effectiveness or efficiency of selection for the traits of interest in breeding programs. The significance of MAS as a tool for crop improvement has been extensively investigated in different crop -species and for different traits. The use of MAS for manipulating simple/qualitative traits is straightforward and has been well reported. However, MAS for the improvement of complex/polygenic traits, including plant tolerance/resistance to abiotic stresses, is more complicated, although its usefulness has been recognized. With the recent advances in marker technology, including high-throughput genotyping of plants, together with the development of nested association mapping populations, it is expected that the utility of MAS for breeding for stress tolerance traits will increase. In this chapter, we describe the basic procedure for using MAS in crop breeding for salt tolerance.

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

PubMed Central

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

2015-01-01

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

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.

Non-invasive assessment of reproductive status and stress in captive Asian elephants in three south Indian zoos.

PubMed

Kumar, Vinod; Palugulla Reddy, Vivekananda; Kokkiligadda, Adiseshu; Shivaji, Sisinthy; Umapathy, Govindhaswamy

2014-05-15

Asian elephants in captivity need immediate attention to be bred so as to meet the increasing demand for captive elephants and to overcome the dependence on supplementing the captive stock with wild animals. Unfortunately, captive breeding programs across the globe have met with limited success and therefore more effort is needed to improve breeding in captivity. Endocrine profiling of reproductive hormones (progestagens and androgens) and the stress hormone (glucocorticoids) could facilitate better management and breeding strategies. In the present study, we investigated reproductive and stress physiology of 12 captive Asian elephants for 10-27 months using a non-invasive method based on steroid analysis of 1700 elephant dung samples. Most of the elephants were cycling regularly. Males during musth showed increased fecal androgen metabolite concentrations and exhibited a slight increase in fecal glucocorticoid metabolite levels. Elephants used in public festivals and processions showed significantly increased in faecal glucocorticoid metabolite levels. The results indicate that captive elephants require periodic health care, better husbandry practices and scientific management for sustainable captive population. Copyright © 2014 Elsevier Inc. All rights reserved.

A deterministic, dynamic systems model of cow-calf production: The effects of breeding replacement heifers before mature cows over a 10-year horizon.

PubMed

Shane, D D; Larson, R L; Sanderson, M W; Miesner, M; White, B J

2017-10-01

Some cattle production experts believe that cow-calf producers should breed replacement heifers (nulliparous cows) before cows (primiparous and multiparous cows), sometimes referred to as providing a heifer lead time (tHL). Our objective was to model the effects different durations of tHL may have on measures of herd productivity, including the percent of the herd cycling before the end of the first 21 d of the breeding season (%C21), the percent of the herd pregnant at pregnancy diagnosis (%PPD), the distribution of pregnancy by 21-d breeding intervals, the kilograms of calf weaned per cow exposed (KPC), and the replacement percentage (%RH), using a deterministic, dynamic systems model of cow-calf production over a 10-yr horizon. We also wished to examine differences in the effect of tHL related to the primiparous duration of postpartum anestrus (dPPA). The study model examined 6 different dPPA for primiparous cows (60, 70, 80, 90, 100, or 110 d). The multiparous cow duration of postpartum anestrus was set to 60 d. The breeding season length for nulliparous cows was 63 d, as was the breeding season length for primiparous and multiparous cows. Nulliparous cows were modeled with a tHL of 0, 7, 14, 21, 28, 35, or 42 d. Results are reported for the final breeding season of the 10-yr horizon. Increasing tHL resulted in a greater %C21 for the herd and for primiparous cows. Length of tHL had minimal impact on the %PPD unless the dPPA was 80 d or greater. For a dPPA of 110 d, a 0 d tHL resulted in the herd having 88.1 %PPD. When tHL was 21 d, the %PPD increased to 93.0%. The KPC was 161.2 kg when the dPPA was 110 d and tHL was 0 d and improved to 183.2 kg when tHL was increased to 42 d. The %RH did not vary much unless the dPPA was 90 d or greater, but increasing tHL resulted in decreased %RH. Based on the model results, increasing tHL improves the production outcomes included in the analysis, but herds with dPPA of 90 d or greater had the greatest degree of improvement. For these herds, approximately two-thirds of the improvement in outcomes by increasing tHL from 0 d to 42 d was realized when tHL was 21 d. Costs are likely incurred when implementing tHL in a breeding management program, and an ideal tHL likely depends on the dPPA of the herd, the expected improvement in productivity, and the costs associated with increasing tHL. Determining the dPPA of a herd could help veterinarians and producers develop optimal herd management strategies.

9 CFR 145.15 - Diagnostic surveillance program for low pathogenic avian influenza.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 9 Animals and Animal Products 1 2011-01-01 2011-01-01 false Diagnostic surveillance program for low pathogenic avian influenza. 145.15 Section 145.15 Animals and Animal Products ANIMAL AND PLANT... PLAN FOR BREEDING POULTRY General Provisions § 145.15 Diagnostic surveillance program for low...

9 CFR 145.15 - Diagnostic surveillance program for low pathogenic avian influenza.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Diagnostic surveillance program for low pathogenic avian influenza. 145.15 Section 145.15 Animals and Animal Products ANIMAL AND PLANT... PLAN FOR BREEDING POULTRY General Provisions § 145.15 Diagnostic surveillance program for low...

An Ideal Remedial Reading Program.

ERIC Educational Resources Information Center

Boettcher, Judith A.

An ideal secondary level remedial reading program would be based on the philosophy that both freedom and structure are required, that learning demands involvement and feedback, and that success breeds success. Such programs should be structured (i.e., based on clearly defined content and a clearly designated mode of presentation). There are many…

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.

Do the Metrics Make the Mission?

DTIC Science & Technology

2008-09-01

view that, “multidimensional peacekeeping missions are complex with many unknown variables and fall victim to mission creep once a peacekeeping...techniques for breeding and vaccinating cattle . Since the vaccination program was implemented, over “nine million heads of livestock have received...Procurement of equipment, fish feed and brood stock is in progress, while 1,500 fish pond owners have been supplied with fish fingerlings. As a result

Friends and family: A software program for identification of unrelated individuals from molecular marker data.

PubMed

de Jager, Deon; Swarts, Petrus; Harper, Cindy; Bloomer, Paulette

2017-11-01

The identification of related and unrelated individuals from molecular marker data is often difficult, particularly when no pedigree information is available and the data set is large. High levels of relatedness or inbreeding can influence genotype frequencies and thus genetic marker evaluation, as well as the accurate inference of hidden genetic structure. Identification of related and unrelated individuals is also important in breeding programmes, to inform decisions about breeding pairs and translocations. We present Friends and Family, a Windows executable program with a graphical user interface that identifies unrelated individuals from a pairwise relatedness matrix or table generated in programs such as coancestry and genalex. Friends and Family outputs a list of samples that are all unrelated to each other, based on a user-defined relatedness cut-off value. This unrelated data set can be used in downstream analyses, such as marker evaluation or inference of genetic structure. The results can be compared to that of the full data set to determine the effect related individuals have on the analyses. We demonstrate one of the applications of the program: how the removal of related individuals altered the Hardy-Weinberg equilibrium test outcome for microsatellite markers in an empirical data set. Friends and Family can be obtained from https://github.com/DeondeJager/Friends-and-Family. © 2017 John Wiley & Sons Ltd.

A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate.

PubMed

Takai, Toshiyuki; Adachi, Shunsuke; Taguchi-Shiobara, Fumio; Sanoh-Arai, Yumiko; Iwasawa, Norio; Yoshinaga, Satoshi; Hirose, Sakiko; Taniguchi, Yojiro; Yamanouchi, Utako; Wu, Jianzhong; Matsumoto, Takashi; Sugimoto, Kazuhiko; Kondo, Katsuhiko; Ikka, Takashi; Ando, Tsuyu; Kono, Izumi; Ito, Sachie; Shomura, Ayahiko; Ookawa, Taiichiro; Hirasawa, Tadashi; Yano, Masahiro; Kondo, Motohiko; Yamamoto, Toshio

2013-01-01

Improvement of leaf photosynthesis is an important strategy for greater crop productivity. Here we show that the quantitative trait locus GPS (GREEN FOR PHOTOSYNTHESIS) in rice (Oryza sativa L.) controls photosynthesis rate by regulating carboxylation efficiency. Map-based cloning revealed that GPS is identical to NAL1 (NARROW LEAF1), a gene previously reported to control lateral leaf growth. The high-photosynthesis allele of GPS was found to be a partial loss-of-function allele of NAL1. This allele increased mesophyll cell number between vascular bundles, which led to thickened leaves, and it pleiotropically enhanced photosynthesis rate without the detrimental side effects observed in previously identified nal1 mutants, such as dwarf plant stature. Furthermore, pedigree analysis suggested that rice breeders have repeatedly selected the high-photosynthesis allele in high-yield breeding programs. The identification and utilization of NAL1 (GPS) can enhance future high-yield breeding and provides a new strategy for increasing rice productivity.

A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate

PubMed Central

Takai, Toshiyuki; Adachi, Shunsuke; Taguchi-Shiobara, Fumio; Sanoh-Arai, Yumiko; Iwasawa, Norio; Yoshinaga, Satoshi; Hirose, Sakiko; Taniguchi, Yojiro; Yamanouchi, Utako; Wu, Jianzhong; Matsumoto, Takashi; Sugimoto, Kazuhiko; Kondo, Katsuhiko; Ikka, Takashi; Ando, Tsuyu; Kono, Izumi; Ito, Sachie; Shomura, Ayahiko; Ookawa, Taiichiro; Hirasawa, Tadashi; Yano, Masahiro; Kondo, Motohiko; Yamamoto, Toshio

2013-01-01

Improvement of leaf photosynthesis is an important strategy for greater crop productivity. Here we show that the quantitative trait locus GPS (GREEN FOR PHOTOSYNTHESIS) in rice (Oryza sativa L.) controls photosynthesis rate by regulating carboxylation efficiency. Map-based cloning revealed that GPS is identical to NAL1 (NARROW LEAF1), a gene previously reported to control lateral leaf growth. The high-photosynthesis allele of GPS was found to be a partial loss-of-function allele of NAL1. This allele increased mesophyll cell number between vascular bundles, which led to thickened leaves, and it pleiotropically enhanced photosynthesis rate without the detrimental side effects observed in previously identified nal1 mutants, such as dwarf plant stature. Furthermore, pedigree analysis suggested that rice breeders have repeatedly selected the high-photosynthesis allele in high-yield breeding programs. The identification and utilization of NAL1 (GPS) can enhance future high-yield breeding and provides a new strategy for increasing rice productivity. PMID:23985993

Genetic Factors Involved in Fumonisin Accumulation in Maize Kernels and Their Implications in Maize Agronomic Management and Breeding

PubMed Central

Santiago, Rogelio; Cao, Ana; Butrón, Ana

2015-01-01

Contamination of maize with fumonisins depends on the environmental conditions; the maize resistance to contamination and the interaction between both factors. Although the effect of environmental factors is a determinant for establishing the risk of kernel contamination in a region, there is sufficient genetic variability among maize to develop resistance to fumonisin contamination and to breed varieties with contamination at safe levels. In addition, ascertaining which environmental factors are the most important in a region will allow the implementation of risk monitoring programs and suitable cultural practices to reduce the impact of such environmental variables. The current paper reviews all works done to address the influence of environmental variables on fumonisin accumulation, the genetics of maize resistance to fumonisin accumulation, and the search for the biochemical and/or structural mechanisms of the maize plant that could be involved in resistance to fumonisin contamination. We also explore the outcomes of breeding programs and risk monitoring of undertaken projects. PMID:26308050

Genetic Factors Involved in Fumonisin Accumulation in Maize Kernels and Their Implications in Maize Agronomic Management and Breeding.

PubMed

Santiago, Rogelio; Cao, Ana; Butrón, Ana

2015-08-20

Contamination of maize with fumonisins depends on the environmental conditions; the maize resistance to contamination and the interaction between both factors. Although the effect of environmental factors is a determinant for establishing the risk of kernel contamination in a region, there is sufficient genetic variability among maize to develop resistance to fumonisin contamination and to breed varieties with contamination at safe levels. In addition, ascertaining which environmental factors are the most important in a region will allow the implementation of risk monitoring programs and suitable cultural practices to reduce the impact of such environmental variables. The current paper reviews all works done to address the influence of environmental variables on fumonisin accumulation, the genetics of maize resistance to fumonisin accumulation, and the search for the biochemical and/or structural mechanisms of the maize plant that could be involved in resistance to fumonisin contamination. We also explore the outcomes of breeding programs and risk monitoring of undertaken projects.

Seasonal changes in testosterone and corticosterone levels in four social classes of a desert dwelling sociable rodent.

PubMed

Schradin, Carsten

2008-04-01

Animals have to adjust their physiology to seasonal changes, in response to variation in food availability, social tactics and reproduction. I compared basal corticosterone and testosterone levels in free ranging striped mouse from a desert habitat, comparing between the sexes, breeding and philopatric non-breeding individuals, and between the breeding and the non-breeding season. I expected differences between breeders and non-breeders and between seasons with high and low food availability. Basal serum corticosterone was measured from 132 different individuals and serum testosterone from 176 different individuals of free living striped mice. Corticosterone and testosterone levels were independent of age, body weight and not influenced by carrying a transmitter. The levels of corticosterone and testosterone declined by approximately 50% from the breeding to the non-breeding season in breeding females as well as non-breeding males and females. In contrast, breeding males showed much lower corticosterone levels during the breeding season than all other classes, and were the only class that showed an increase of corticosterone from the breeding to the non-breeding season. As a result, breeding males had similar corticosterone levels as other social classes during the non-breeding season. During the breeding season, breeding males had much higher testosterone levels than other classes, which decreased significantly from the breeding to the non-breeding season. My results support the prediction that corticosterone decreases during periods of low food abundance. Variation in the pattern of hormonal secretion in striped mice might assist them to cope with seasonal changes in energy demand in a desert habitat.

Breeding biology of the blue-gray noddy

USGS Publications Warehouse

Rauson, M.J.; Harrison, C.S.; Clapp, R.B.

1984-01-01

Blue-gray Noddies, the smallest marine terns, are similar in many respects to all tropical terns in Hawaii: single-egg clutches are laid, growth and development take about 7 weeks, breeding is colonial. Its small size results in eggs that comprise over 27% of adult body weight, compared to 15-20% for most marine terns (Langham 1983). Blue-gray Noddies are widespread in the tropical Pacific, but populations are generally small. This may be the result of its inshore feeding habits and the fact that it is a resident species (Diamond 1978). However, populations in the Hawaiian Archipelago are probably limited by the availability of suitable nest sites in cliffs or rocky outcrops, not food supplies..... Food habits in Hawaii confirm the unique dependence of this species on sea-striders but consumption may be seasonal Blue-gray Noddies take the smallest prey of any seabird in Hawaii and may feed on a lower trophic level..... The Hawaiian population is apparently heavier and produces larger eggs than Blue-gray Noddies elsewhere in the Pacific. This conforms with the general proposition that Hawaiian seabirds are larger than those in the central Pacific (Harrison et al. 1983). The Hawaiian population also has a more predictable breeding season than those farther south.This may be due to a greater seasonality of food supply, but the factors that control the timing of breeding are not clear. There does not appear to be any competition for nest sites with other seabirds.....Our information on growth and development will enable future investigators to estimate the ages of chicks during brief visits to Blue-gray Noddy colonies. This will facilitate programs that are designed to monitor the basic health of seabird populations and to detect changes from baseline that may result from human activities or oceanographic conditions.

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

PubMed

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

2010-01-01

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

Association Study Reveals Novel Genes Related to Yield and Quality of Fruit in Cape Gooseberry (Physalis peruviana L.).

PubMed

García-Arias, Francy L; Osorio-Guarín, Jaime A; Núñez Zarantes, Victor M

2018-01-01

Association mapping has been proposed as an efficient approach to assist plant breeding programs to investigate the genetic basis of agronomic traits. In this study, we evaluated 18 traits related to yield, (FWP, NF, FWI, and FWII), fruit size-shape (FP, FA, MW, WMH, MH, HMW, DI, FSI, FSII, OVO, OBO), and fruit quality (FIR, CF, and SST), in a diverse collection of 100 accessions of Physalis peruviana including wild, landraces, and anther culture derived lines. We identified seven accessions with suitable traits: fruit weight per plant (FWP) > 7,000 g/plant and cracked fruits (CF) < 4%, to be used as parents in cape gooseberry breeding program. In addition, the accessions were also characterized using Genotyping By Sequencing (GBS). We discovered 27,982 and 36,142 informative SNP markers based on the alignment against the two cape gooseberry references transcriptomes. Besides, 30,344 SNPs were identified based on alignment to the tomato reference genome. Genetic structure analysis showed that the population could be divided into two or three sub-groups, corresponding to landraces-anther culture and wild accessions for K = 2 and wild, landraces, and anther culture plants for K = 3. Association analysis was carried out using a Mixed Linear Model (MLM) and 34 SNP markers were significantly associated. These results reveal the basis of the genetic control of important agronomic traits and may facilitate marker-based breeding in P. peruviana .

Association Study Reveals Novel Genes Related to Yield and Quality of Fruit in Cape Gooseberry (Physalis peruviana L.)

PubMed Central

García-Arias, Francy L.; Osorio-Guarín, Jaime A.; Núñez Zarantes, Victor M.

2018-01-01

Association mapping has been proposed as an efficient approach to assist plant breeding programs to investigate the genetic basis of agronomic traits. In this study, we evaluated 18 traits related to yield, (FWP, NF, FWI, and FWII), fruit size-shape (FP, FA, MW, WMH, MH, HMW, DI, FSI, FSII, OVO, OBO), and fruit quality (FIR, CF, and SST), in a diverse collection of 100 accessions of Physalis peruviana including wild, landraces, and anther culture derived lines. We identified seven accessions with suitable traits: fruit weight per plant (FWP) > 7,000 g/plant and cracked fruits (CF) < 4%, to be used as parents in cape gooseberry breeding program. In addition, the accessions were also characterized using Genotyping By Sequencing (GBS). We discovered 27,982 and 36,142 informative SNP markers based on the alignment against the two cape gooseberry references transcriptomes. Besides, 30,344 SNPs were identified based on alignment to the tomato reference genome. Genetic structure analysis showed that the population could be divided into two or three sub-groups, corresponding to landraces-anther culture and wild accessions for K = 2 and wild, landraces, and anther culture plants for K = 3. Association analysis was carried out using a Mixed Linear Model (MLM) and 34 SNP markers were significantly associated. These results reveal the basis of the genetic control of important agronomic traits and may facilitate marker-based breeding in P. peruviana. PMID:29616069

Influence of cow breed type, age and previous lactation status on cow height, calf growth, and patterns of body weight, condition, and blood metabolites for cows grazing bahiagrass pastures

USDA-ARS?s Scientific Manuscript database

Economic analysis has revealed that in most parts of the country, the largest economic costs for cattle production are for winter feed. This study was initiated to evaluate the effect of two winter nutrition programs on three breeds of cows grazing bahiagrass pastures in central Florida. Data on 4...

Genotype disclosure in the genomics era: roles and responsibilities.

PubMed

Denholm, L

2017-09-01

Disclosure of affected breed without disclosure of major progenitors has been the usual practice in scientific papers reporting recessive heritable disorders of cattle. Before molecular genetics, carrier identity could not be used by breeders to control causal mutations because phenotypically normal heterozygotes among genetically related animals could not be detected other than by test mating. Accurate, low-cost DNA tests fundamentally changed this situation. Genomics can provide relief from the old problem of emerging recessive disorders in cattle breeding, but greater transparency of genotype data between breeders is necessary to fully exploit the opportunities for cost-efficient genetic disease control. Effective control of several recessive disorders has been demonstrated in Angus cattle, based entirely on voluntary DNA testing by breeders but mandatory public disclosure of test results and genotype probabilities for all registered animals. When a DNA test is available, major progenitors (particularly bulls from which semen has been distributed) should be identified and disclosed concurrently with the affected breed. As a minimum, whenever possible the closest common ancestors in the pedigrees of the parents of homozygous mutants should be disclosed after confirmation of carrier status. Progenitor disclosure in scientific publications should occur in cooperation with breed societies, which should have the opportunity to advise breeders and initiate management programs before scientific publication. Unless properly managed, genomic enhancement of animal selection using SNP markers may increase inbreeding, co-ancestry and emergence of recessive disorders. The information systems and genotype disclosure policies of some breed societies will be increasingly challenged, particularly with accelerating mutation discovery using next-generation sequencing. © 2017 State of New South Wales.

Breeding-assisted genomics.

PubMed

Poland, Jesse

2015-04-01

The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition. Copyright © 2015 Elsevier Ltd. All rights reserved.

Advocating a need for suitable breeding approaches to boost integrated pest management: a European perspective.

PubMed

Lamichhane, Jay Ram; Arseniuk, Edward; Boonekamp, Piet; Czembor, Jerzy; Decroocq, Veronique; Enjalbert, Jérome; Finckh, Maria R; Korbin, Małgorzata; Koppel, Mati; Kudsk, Per; Mesterhazy, Akos; Sosnowska, Danuta; Zimnoch-Guzowska, Ewa; Messéan, Antoine

2018-06-01

Currently, European farmers do not have access to sufficient numbers and diversity of crop species/varieties. This prevents them from designing cropping systems more resilient to abiotic and biotic stresses. Crop diversification is a key lever to reduce pest (pathogens, animal pests and weeds) pressures at all spatial levels from fields to landscapes. In this context, plant breeding should consist of: (1) increased efforts in the development of new or minor crop varieties to foster diversity in cropping systems, and (2) focus on more resilient varieties showing local adaptation. This new breeding paradigm, called here 'breeding for integrated pest management (IPM)', may boost IPM through the development of cultivars with tolerance or resistance to key pests, with the goal of reducing reliance on conventional pesticides. At the same time, this paradigm has legal and practical implications for future breeding programs, including those targeting sustainable agricultural systems. By putting these issues into the context, this article presents the key outcomes of a questionnaire survey and experts' views expressed during an EU workshop entitled 'Breeding for IPM in sustainable agricultural systems'. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Exploitation of induced 2n-gametes for plant breeding.

PubMed

Younis, Adnan; Hwang, Yoon-Jung; Lim, Ki-Byung

2014-02-01

Unreduced gamete formation derived via abnormal meiotic cell division is an important approach to polyploidy breeding. This process is considered the main driving force in spontaneous polyploids formation in nature, but the potential application of these gametes to plant breeding has not been fully exploited. An effective mechanism for their artificial induction is needed to attain greater genetic variation and enable efficient use of unreduced gametes in breeding programs. Different approaches have been employed for 2n-pollen production including interspecific hybridization, manipulation of environmental factors and treatment with nitrous oxide, trifluralin, colchicine, oryzalin and other chemicals. These chemicals can act as a stimulus to produce viable 2n pollen; however, their exact mode of action, optimum concentration and developmental stages are still not known. Identification of efficient methods of inducing 2n-gamete formation will help increase pollen germination of sterile interspecific hybrids for inter-genomic recombination and introgression breeding to develop new polyploid cultivars and increase heterozygosity among plant populations. Additionally, the application of genomic tools and identification and isolation of genes and mechanisms involved in the induction of 2n-gamete will enable increased exploitation in different plant species, which will open new avenues for plant breeding.

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

PubMed

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

2017-02-01

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

Identification and genetic effect of haplotype in the bovine BMP7 gene.

PubMed

Huang, Yong-Zhen; Wang, Xin-Lei; He, Hua; Lan, Xian-Yong; Lei, Chu-Zhao; Zhang, Chun-Lei; Chen, Hong

2013-12-15

Bone morphogenetic proteins (BMPs) are peptide growth factors belonging to the transforming growth factor-beta (TGF-β) superfamily, and some members of the BMP family support white adipocyte differentiation. In this study, we focused on the BMP7 which singularly promotes the differentiation of brown preadipocytes. Haplotypes involving 5 single nucleotide polymorphism (SNP) sites in the bovine BMP7 gene were identified and their effect on body weight was analyzed. 16 haplotypes and 18 combined haplotypes were revealed and the linkage disequilibrium was assessed in the cattle population with 602 individuals representing three main cattle breeds from China. The results showed that haplotypes 3, 10 and 14 were predominant and accounted for 75.64%, 69.85%, and 83.36% in Nanyang, Qinchuan and Jiaxian cattle breeds, respectively. The statistical analyses indicated that the SNP 1, 4, and 5 are associated with the body weight, body length, and heart girth at 12 and 24 months in Nanyang cattle population (P<0.05), whereas there is no significant association between their 16 haplotypes and 18 combined haplotypes. Our results provide evidence that some SNPs and haplotypes in BMP7 are associated with growth traits, and may be utilized as a genetic marker in marker-assisted selection for beef cattle breeding programs. Copyright © 2013. Published by Elsevier B.V.

Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.

PubMed

Yang, Huaan; Tao, Ye; Zheng, Zequn; Li, Chengdao; Sweetingham, Mark W; Howieson, John G

2012-07-17

In the last 30 years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting task to identify highly polymorphic and closely linked molecular markers for a target trait for molecular marker-assisted selection. The next-generation sequencing (NGS) technology is far more powerful than any existing generic DNA fingerprinting methods in generating DNA markers. In this study, we employed a grain legume crop Lupinus angustifolius (lupin) as a test case, and examined the utility of an NGS-based method of RAD (restriction-site associated DNA) sequencing as DNA fingerprinting for rapid, cost-effective marker development tagging a disease resistance gene for molecular breeding. Twenty informative plants from a cross of RxS (disease resistant x susceptible) in lupin were subjected to RAD single-end sequencing by multiplex identifiers. The entire RAD sequencing products were resolved in two lanes of the 16-lanes per run sequencing platform Solexa HiSeq2000. A total of 185 million raw reads, approximately 17 Gb of sequencing data, were collected. Sequence comparison among the 20 test plants discovered 8207 SNP markers. Filtration of DNA sequencing data with marker identification parameters resulted in the discovery of 38 molecular markers linked to the disease resistance gene Lanr1. Five randomly selected markers were converted into cost-effective, simple PCR-based markers. Linkage analysis using marker genotyping data and disease resistance phenotyping data on a F8 population consisting of 186 individual plants confirmed that all these five markers were linked to the R gene. Two of these newly developed sequence-specific PCR markers, AnSeq3 and AnSeq4, flanked the target R gene at a genetic distance of 0.9 centiMorgan (cM), and are now replacing the markers previously developed by a traditional DNA fingerprinting method for marker-assisted selection in the Australian national lupin breeding program. We demonstrated that more than 30 molecular markers linked to a target gene of agronomic trait of interest can be identified from a small portion (1/8) of one sequencing run on HiSeq2000 by applying NGS based RAD sequencing in marker development. The markers developed by the strategy described in this study are all co-dominant SNP markers, which can readily be converted into high throughput multiplex format or low-cost, simple PCR-based markers desirable for large scale marker implementation in plant breeding programs. The high density and closely linked molecular markers associated with a target trait help to overcome a major bottleneck for implementation of molecular markers on a wide range of germplasm in breeding programs. We conclude that application of NGS based RAD sequencing as DNA fingerprinting is a very rapid and cost-effective strategy for marker development in molecular plant breeding. The strategy does not require any prior genome knowledge or molecular information for the species under investigation, and it is applicable to other plant species.

Nest-site competition between invasive and native cavity nesting birds and its implication for conservation.

PubMed

Charter, Motti; Izhaki, Ido; Ben Mocha, Yitzchak; Kark, Salit

2016-10-01

Nesting cavities are often a limited resource that multiple species use. There is an ongoing discussion on whether invasive cavity nesting birds restrict the availability of this key limited resource. While the answer to this question has important conservation implications, little experimental work has been done to examine it. Here, we aimed to experimentally test whether alien cavity nesting birds affect the occupancy of cavities and the resulting breeding success of native cavity breeders in a large urban park located in Tel Aviv, Israel. Over three breeding seasons, we manipulated the entry size of nest boxes and compared the occupancy and breeding success of birds in nest boxes of two treatments. These included nest boxes with large-entrance and small-entrance holes. The large-entrance holes allowed access for both the native and invasive birds (the two main aliens in the park are the common mynas and rose-ringed parakeets). The smaller-entrance boxes, on the other hand, allowed only the smaller sized native cavity breeders (great tits and house sparrows) to enter the boxes but prevented the alien species from entering. We found that the large-entrance nest boxes were occupied by five different bird species, comprising three natives (great tit, house sparrow, Scops owl) and two invasive species (common myna, rose-ringed parakeet) while the small-entrance boxes were only occupied by the two native species. The alien common mynas and rose-ringed parakeets occupied 77.5% of the large-entrance nest boxes whereas native species, mainly great tits, occupied less than 9% of the large-entrance boxes and 36.5% of the small-entrance boxes. When examining the occupancy of those cavities that were not occupied by the aliens, natives occupied both the small and large-entrance nest boxes equally. Three quarters (78%) of the great tits breeding in the large-entrance boxes were usurped by common mynas during the breeding season and as a result breeding success was significantly lower for great tits breeding in the large-entrance boxes compared with the small-entrance boxes. The results of this study suggests that the invasive alien species can reduce the breeding potential of native cavity breeders both by exploiting the limited breeding resource (nest cavities) and by directly usurping cavities already occupied by the native species. Since the majority of large-entrance nest boxes were occupied by the larger alien birds, less native species bred in the limited number of unoccupied large-entrance nest boxes because of exploitation competition. We propose that for management purposes, nest-box programs that alter the entrance size of available natural cavities may be a practical approach, reducing the competition between native cavity breeders and alien invasive birds, and especially benefiting the smaller native cavity breeders. Copyright © 2016 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.

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

PubMed

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

2011-01-01

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

Genetic evaluation of the Association of Zoos and Aquariums Matschie's tree kangaroo (Dendrolagus matschiei) captive breeding program.

PubMed

McGreevy, Thomas J; Dabek, Lisa; Husband, Thomas P

2011-01-01

Matschie's tree kangaroo (Dendrolagus matschiei) is an endangered species that has been bred in captivity since the 1970s. In 1992, the Tree Kangaroo Species Survival Plan(®) (TKSSP) was established to coordinate the captive management of Association of Zoos and Aquariums (AZA) D. matschiei. The TKSSP makes annual breeding recommendations primarily based on the mean kinship (MK) strategy. Captive breeding programs often use the MK strategy to preserve genetic diversity in small populations-to avoid the negative consequences of inbreeding and retain their adaptive potential. The ability of a captive breeding program to retain the population's genetic diversity over time can be evaluated by comparing the genetic diversity of the captive population to wild populations. We analyzed DNA extracted from blood and fecal samples from AZA (n = 71), captive (n = 28), and wild (n = 22) D. matschiei using eight microsatellite markers and sequenced the partial mitochondrial DNA control region gene. AZA D. matschiei had a similar expected heterozygosity (H(e) = 0.595 ± 0.184) compared with wild D. matschiei (H(e) = 0.628 ± 0.143), but they had different allelic frequencies (F(ST) = 0.126; P < 0.001). AZA D. matschiei haplotype diversity was almost two times lower than wild D. matschiei Ĥ = 0.740 ± 0.063. These data will assist management of AZA D. matschiei and serve as a baseline for AZA and wild D. matschiei genetic diversity values that could be used to monitor future changes in their genetic diversity. © 2010 Wiley Periodicals, Inc.

Assortative mating and fragmentation within dog breeds

PubMed Central

2008-01-01

Background There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds. Results Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds. Conclusion The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored. In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic population structure. The same processes which have historically created dog breeds are still ongoing, and create further subdivision within current dog breeds. PMID:18226210

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

PubMed

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

2009-08-01

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

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.

Interspecific Potato Breeding Lines Display Differential Colonization Patterns and Induced Defense Responses after Ralstonia solanacearum Infection

PubMed Central

Ferreira, Virginia; Pianzzola, María J.; Vilaró, Francisco L.; Galván, Guillermo A.; Tondo, María L.; Rodriguez, María V.; Orellano, Elena G.; Valls, Marc; Siri, María I.

2017-01-01

Potato (Solanum tuberosum L.) is one of the main hosts of Ralstonia solanacearum, the causative agent of bacterial wilt. This plant pathogen bacteria produce asymptomatic latent infections that promote its global spread, hindering disease control. A potato breeding program is conducted in Uruguay based on the introgression of resistance from the wild native species S. commersonii Dun. Currently, several backcrosses were generated exploiting the high genetic variability of this wild species resulting in advanced interspecific breeding lines with different levels of bacterial wilt resistance. The overall aim of this work was to characterize the interaction of the improved potato germplasm with R. solanacearum. Potato clones with different responses to R. solanacearum were selected, and colonization, dissemination and multiplication patterns after infection were evaluated. A R. solanacearum strain belonging to the phylotype IIB-sequevar 1, with high aggressiveness on potato was genetically modified to constitutively generate fluorescence and luminescence from either the green fluorescence protein gene or lux operon. These reporter strains were used to allow a direct and precise visualization of fluorescent and luminescent cells in plant tissues by confocal microscopy and luminometry. Based on wilting scoring and detection of latent infections, the selected clones were classified as susceptible or tolerant, while no immune-like resistance response was identified. Typical wilting symptoms in susceptible plants were correlated with high concentrations of bacteria in roots and along the stems. Tolerant clones showed a colonization pattern restricted to roots and a limited number of xylem vessels only in the stem base. Results indicate that resistance in potato is achieved through restriction of bacterial invasion and multiplication inside plant tissues, particularly in stems. Tolerant plants were also characterized by induction of anatomical and biochemical changes after R. solanacearum infection, including hyperplasic activity of conductor tissue, tylose production, callose and lignin deposition, and accumulation of reactive oxygen species. This study highlights the potential of the identified tolerant interspecific potato clones as valuable genetic resources for potato-breeding programs and leads to a better understanding of resistance against R. solanacearum in potato. PMID:28894453

QTL mapping of soybean oil content for marker-assisted selection in plant breeding program.

PubMed

Leite, D C; Pinheiro, J B; Campos, J B; Di Mauro, A O; Unêda-Trevisoli, S H

2016-03-18

The present study was undertaken to detect and map the quantitative trait loci (QTL) related to soybean oil content. We used 244 progenies derived from a bi-parental cross of the Lineage 69 (from Universidade Estadual Paulista "Júlio de Mesquita Filho"/Faculdade de Ciências Agrárias e Veterinárias - Breeding Program) and Tucunaré cultivar. A total of 358 simple sequence repeat (SSR; microsatellite) markers were used to investigate the polymorphism between the parental lines, and for the polymorphic lines all the F2 individuals were tested. Evaluation of the oil content and phenotype was performed with the aid of a Tango equipment by near infra-red reflectance spectroscopy, using single F2 seeds and F2:3 progenies, in triplicate. The data were analyzed by QTL Cartographer program for 56 SSR polymorphic markers. Two oil-content related QTLs were detected on K and H linkage groups. The total phenotypic variation explained by QTLs ranged from 7.8 to 46.75% for oil content. New QTLs were identified for the oil content in addition to those previously identified in other studies. The results reported in this study show that regions different from those already known could be involved in the genetic control of soybean oil content.

Characterization of recombination features and the genetic basis in multiple cattle breeds.

PubMed

Shen, Botong; Jiang, Jicai; Seroussi, Eyal; Liu, George E; Ma, Li

2018-04-27

Crossover generated by meiotic recombination is a fundamental event that facilitates meiosis and sexual reproduction. Comparative studies have shown wide variation in recombination rate among species, but the characterization of recombination features between cattle breeds has not yet been performed. Cattle populations in North America count millions, and the dairy industry has genotyped millions of individuals with pedigree information that provide a unique opportunity to study breed-level variations in recombination. Based on large pedigrees of Jersey, Ayrshire and Brown Swiss cattle with genotype data, we identified over 3.4 million maternal and paternal crossover events from 161,309 three-generation families. We constructed six breed- and sex-specific genome-wide recombination maps using 58,982 autosomal SNPs for two sexes in the three dairy cattle breeds. A comparative analysis of the six recombination maps revealed similar global recombination patterns between cattle breeds but with significant differences between sexes. We confirmed that male recombination map is 10% longer than the female map in all three cattle breeds, consistent with previously reported results in Holstein cattle. When comparing recombination hotspot regions between cattle breeds, we found that 30% and 10% of the hotspots were shared between breeds in males and females, respectively, with each breed exhibiting some breed-specific hotspots. Finally, our multiple-breed GWAS found that SNPs in eight loci affected recombination rate and that the PRDM9 gene associated with hotspot usage in multiple cattle breeds, indicating a shared genetic basis for recombination across dairy cattle breeds. Collectively, our results generated breed- and sex-specific recombination maps for multiple cattle breeds, provided a comprehensive characterization and comparison of recombination patterns between breeds, and expanded our understanding of the breed-level variations in recombination features within an important livestock species.

Future animal improvement programs applied to global populations

USDA-ARS?s Scientific Manuscript database

Breeding programs evolved gradually from within-herd phenotypic selection to local and regional cooperatives to national evaluations and now international evaluations. In the future, breeders may adapt reproductive, computational, and genomic methods to global populations as easily as with national ...

Mating programs including genomic relationships and dominance effects

USDA-ARS?s Scientific Manuscript database

Breed associations, artificial-insemination organizations, and on-farm software providers need new computerized mating programs for genomic selection so that genomic inbreeding could be minimized by comparing genotypes of potential mates. Efficient methods for transferring elements of the genomic re...

Urban transmission of schistosomiasis: new epidemiological situation in the forest area of Pernambuco.

PubMed

Gomes, Elainne Christine de Souza; Mesquita, Millena Carla da Silva; Rehn, Vitorina Nerivânia Covello; Nascimento, Wheverton Ricardo Correia do; Loyo, Rodrigo; Barbosa, Constança Simões

2016-01-01

Schistosomiasis is considered an endemic disease in Vitória de Santo Antão, Pernambuco, a district which has presented both high incidence and prevalence of it for decades. Poor environmental conditions lead to contamination of water sources in rural areas, which are used by the population during daily activities, resulting in typical transmission. Recently, there has been evidence of vector snails in urban areas, which could set a new model for schistosomiasis transmission in this district. To identify the new epidemiological situation for the urban transmission of schistosomiasis in Vitória de Santo Antão, Pernambuco. A malacological survey was conducted in all water sources in the city limits to investigate schistosomiasis vector snails (Biomphalaria spp.). The collected snails were examined for taxonomic identification and Schistosoma mansoni infection. All breeding sites were georeferenced to build risk maps through the TrackMaker PRO program and ArcGIS software. We identified 22 Biomphalaria straminea breeding sites and collected 1,704 snails. One of these breeding sites was identified as a source of transmission and seven as potential sources of transmission. The designed maps identified two risk areas of urban transmission of schistosomiasis and expansion areas for breeding sites, establishing an increased risk of transmission to the population. This study verified the existence of a new epidemiological situation in which the possibility of the urban transmission of the disease was confirmed.

Aggression in pigtailed macaque (Macaca nemestrina) breeding groups affects pregnancy outcome

PubMed Central

Ha, James; Alloway, Hayley; Sussman, Adrienne

2011-01-01

Past research has shown that aggressive behaviors can affect female reproductive outcome in non-human primate captive breeding programs. In this study, aggressive behaviors were recorded in a colony of pigtailed macaque monkeys (Macaca nemestrina) and related to pregnancy outcome. For twenty-two weeks, behavioral data were collected from nine breeding groups, consisting of zero to one male (some males were removed after a cycle of conceptions for husbandry reasons) and four to eight females. Observations included all occurrences of eleven aggressive behaviors during 15-minute observation sessions, one to three times a week. Mean weekly aggression levels during the study period were determined for each group, as well as for each pregnancy. Aggression data were summarized with Principal Components Analyses (PCA). Results indicate that pigtailed macaque aggression falls into five distinctive categories: warn, engage, threaten, pursue, and attack. Breeding groups differed in their levels of aggression, even after controlling for group size, presence of a sire, and group stability. Levels of the five aggression categories were found to affect the probability that a pregnancy ended in either a natural birth of a live infant, a clinical intervention producing a live infant, or a nonviable outcome. The predictive value of aggression was significant when clinical interventions were included as possible reproductive outcomes, Behavioral observation of captive groups could identify “risk” conditions affecting pregnancy outcome and the requirement for clinical intervention. PMID:21898511

Albatross Long-Distance Navigation: Comparing Adults And Juveniles

NASA Astrophysics Data System (ADS)

Åkesson, Susanne; Weimerskirch, Henri

2005-09-01

Albatrosses are known for their extreme navigation performance enabling them to locate isolated breeding islands after long-distance migrations across open seas. Little is known about the migration of young albatrosses and how they reach the adults' navigation and foraging skills during the period of immaturity lasting several years and spent permanently flying across the open ocean. We tracked by satellite telemetry the dispersal and migration of 13 juvenile wandering albatrosses from the Crozet Islands during their first year at sea. The young albatrosses covered an average distance of 184,000 km during the first year, restricting their dispersal movement to the unproductive and low wind subtropical Indian Ocean and Tasman Sea. The juveniles initiated the migration by an innate phase of rapid dispersal encoded as a fixed flight direction assisted by southerly winds towards north and northeast. Thereafter each individual restricted its movement to a particular zone of the ocean that will possibly be used until they start breeding 7 10 years later and return in contact with breeding adults. This dispersal in young birds corresponds well with movements observed for adult non-breeding wandering albatrosses. The results show clearly an inherited ability to navigate back to already visited areas in young wandering albatrosses. The juvenile dispersal behaviour and migration at sea suggest a genetically based migration program, encoding navigation to a destination area used throughout the life.

Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects

PubMed Central

Pandey, Manish K.; Roorkiwal, Manish; Singh, Vikas K.; Ramalingam, Abirami; Kudapa, Himabindu; Thudi, Mahendar; Chitikineni, Anu; Rathore, Abhishek; Varshney, Rajeev K.

2016-01-01

Legumes play a vital role in ensuring global nutritional food security and improving soil quality through nitrogen fixation. Accelerated higher genetic gains is required to meet the demand of ever increasing global population. In recent years, speedy developments have been witnessed in legume genomics due to advancements in next-generation sequencing (NGS) and high-throughput genotyping technologies. Reference genome sequences for many legume crops have been reported in the last 5 years. The availability of the draft genome sequences and re-sequencing of elite genotypes for several important legume crops have made it possible to identify structural variations at large scale. Availability of large-scale genomic resources and low-cost and high-throughput genotyping technologies are enhancing the efficiency and resolution of genetic mapping and marker-trait association studies. Most importantly, deployment of molecular breeding approaches has resulted in development of improved lines in some legume crops such as chickpea and groundnut. In order to support genomics-driven crop improvement at a fast pace, the deployment of breeder-friendly genomics and decision support tools seems appear to be critical in breeding programs in developing countries. This review provides an overview of emerging genomics and informatics tools/approaches that will be the key driving force for accelerating genomics-assisted breeding and ultimately ensuring nutritional and food security in developing countries. PMID:27199998

50 CFR 15.26 - Approval of cooperative breeding programs.

Code of Federal Regulations, 2010 CFR

2010-10-01

...-sustaining population in captivity of the exotic bird species; (iii) Details on the system of recordkeeping... the exotic bird species in the world; (v) Details on the funding of this program; and (vi) Plans for... program intended to enhance the survival of the population from which the exotic bird species was or would...

Production objectives and trait preferences of village poultry producers of Ethiopia: implications for designing breeding schemes utilizing indigenous chicken genetic resources

PubMed Central

van der Waaij, Liesbeth H.; Dessie, Tadelle; van Arendonk, Johan A. M.

2010-01-01

To generate information essential for the implementation of breeding schemes suitable for village poultry producers in Ethiopia, a survey was conducted aimed at defining the socioeconomic characteristics of the production environments in different geographic regions, understanding the important functions of chickens, identifying farmers’ choice of chicken breeds and the underlying factors that determine the choice of genetic stock used. The survey included both questionnaire survey and a participatory group discussion. A total of 225 households (45 households from each of five Woredas) were interviewed. The questionnaire was designed to collect data covering general information on village poultry production such as socio-management characteristics, production objectives, population structure, breed choice and trait preferences, market preferences of specific traits, and farmers’ selection practices. The participatory farmers’ discussions were designed to involve stakeholders in defining the breeding objective “traits” and deriving their relative importance in the production environment based on the different functions of chickens and “traits” identified in the interviews. The results showed that production of eggs for consumption is the principal function of chickens in most regions followed by the use as source of income and meat for home consumption. The production system in all geographic regions studied revealed similar features generally characterized by extensive scavenging management, absence of immunization programs, increased risk of exposure of birds to disease and predators, and reproduction entirely based on uncontrolled natural mating and hatching of eggs using broody hens. Farmers’ ratings of indigenous chickens with respect to modern breeds showed the highest significance of the adaptive traits in general, and the superior merits of indigenous chickens to high yielding exotic breeds in particular. Adaptation to the production environment was the most important attribute of chickens in all the study areas. The high significance attributed to reproduction traits indicates the need for maintaining broody behavior and high level of hatchability while breeding for improved productivity of indigenous chickens for village conditions. The market price of chickens is primarily dictated by weight, but farmers rated growth (males) and number of eggs followed by growth (females) as the production traits they would like the most to be improved. Therefore, the ultimate breeding goal should be to develop a dual-purpose breed based on indigenous chicken genetic resources with any of the comb types other than single for all the regions studied having the most preferred white body plumage for farmers in the Amhara region and red body plumage for those in Oromia, Benshangul-Gumuz, and Southern regions. PMID:20512411

Production objectives and trait preferences of village poultry producers of Ethiopia: implications for designing breeding schemes utilizing indigenous chicken genetic resources.

PubMed

Dana, Nigussie; van der Waaij, Liesbeth H; Dessie, Tadelle; van Arendonk, Johan A M

2010-10-01

To generate information essential for the implementation of breeding schemes suitable for village poultry producers in Ethiopia, a survey was conducted aimed at defining the socioeconomic characteristics of the production environments in different geographic regions, understanding the important functions of chickens, identifying farmers' choice of chicken breeds and the underlying factors that determine the choice of genetic stock used. The survey included both questionnaire survey and a participatory group discussion. A total of 225 households (45 households from each of five Woredas) were interviewed. The questionnaire was designed to collect data covering general information on village poultry production such as socio-management characteristics, production objectives, population structure, breed choice and trait preferences, market preferences of specific traits, and farmers' selection practices. The participatory farmers' discussions were designed to involve stakeholders in defining the breeding objective "traits" and deriving their relative importance in the production environment based on the different functions of chickens and "traits" identified in the interviews. The results showed that production of eggs for consumption is the principal function of chickens in most regions followed by the use as source of income and meat for home consumption. The production system in all geographic regions studied revealed similar features generally characterized by extensive scavenging management, absence of immunization programs, increased risk of exposure of birds to disease and predators, and reproduction entirely based on uncontrolled natural mating and hatching of eggs using broody hens. Farmers' ratings of indigenous chickens with respect to modern breeds showed the highest significance of the adaptive traits in general, and the superior merits of indigenous chickens to high yielding exotic breeds in particular. Adaptation to the production environment was the most important attribute of chickens in all the study areas. The high significance attributed to reproduction traits indicates the need for maintaining broody behavior and high level of hatchability while breeding for improved productivity of indigenous chickens for village conditions. The market price of chickens is primarily dictated by weight, but farmers rated growth (males) and number of eggs followed by growth (females) as the production traits they would like the most to be improved. Therefore, the ultimate breeding goal should be to develop a dual-purpose breed based on indigenous chicken genetic resources with any of the comb types other than single for all the regions studied having the most preferred white body plumage for farmers in the Amhara region and red body plumage for those in Oromia, Benshangul-Gumuz, and Southern regions.

Perceptions of households on purpose of keeping, trait preference, and production constraints for selected goat types in Ethiopia.

PubMed

Tadesse, Dereje; Urge, Mengistu; Animut, Getachew; Mekasha, Yoseph

2014-02-01

A study was carried out to understand the needs and perception of goat keepers in selected areas of Ethiopia in order to identify the breeding objectives, traits of preference, and production constraints that may be required in designing improvement programs. The study was conducted in three districts (Bati, Meta, and Kebri-Beyah) representing the lowland crop-livestock (LLCL), highland cereal-livestock (HLCL), and pastoral/agropastoral (P/AP) systems, respectively. The study targeted the three goat types (Bati, Hararghe Highland, and Short-eared Somali) found in Ethiopia. Households in all systems considered meat production, milk production, and income generation as major purpose of keeping goats. However, those in the low rainfall and arid environments of P/AP systems gave high ranking to adaptability to harsh environments and also to building social and religious values. In LLCL and HLCL systems, goat skin and manure were more valued than in P/AP systems. Principally, in P/AP systems, the awareness of households to skin utilization and marketing was very low. Despite diverse multiple breeding objectives identified, household breeding practices were affected by constraints related to disease prevalence, feed shortage and water scarcity, and lack of awareness on skin management, utilization, and marketing. Thus, designing and implementing of sustainable goat improvement programs is an overriding priority and should take into account the breeding objectives and knowledge of goat keepers in all production systems. Along with the breed improvement, a strategy should also be devised to enhance the utilization and marketing of goat skin at all levels of production.

The relative role of captive breeding and of zoo-bred animals in North American conservation translocations.

PubMed

Brichieri-Colombi, Typhenn A; Lloyd, Natasha A; Mcpherson, Jana M; Moehrenschlager, Axel

2018-06-19

With the loss of biodiversity accelerating, conservation translocations such as reintroductions are becoming an increasingly common conservation tool. Conservation translocations must source individuals for release from either wild or captive-bred populations. We asked what proportion of North American conservation translocations rely on captive breeding, and to what extent zoos and aquaria (hereafter zoos) fulfill captive breeding needs. Our comprehensive literature review indicates that North American conservation translocations published before 2014 involved captive breeding for 162 (58%) of the 279 animal species translocated. Fifty-four zoos contributed animals for release; the fourty species of animals bred for release by zoos represents only 14% of all animal species for which conservation translocations were published, and only 25% of all animal species that were bred for releases occurring in North America. Zoo contributions varied by taxon, ranging from zoo-bred animals released in 42% of amphibian conservation translocations to zero contributions for marine invertebrates. Proportional involvement of zoos in captive breeding programs for release has increased over time as has the proportion of translocation-focused scientific papers co-authored by zoo professionals. While zoos also contribute to conservation translocations through education, funding, and professional expertise, increasing the contribution of animals for release in responsible conservation translocation programs presents a future conservation need and opportunity. We especially encourage increased dialogue and planning between the zoo community, academic institutions, and governments to optimize the direct contribution zoos can make to wildlife conservation through conservation translocations. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Population and habitat viability assessment for the Wyoming toad (Bufo baxteri): Final workshop report

USGS Publications Warehouse

2001-01-01

The Wyoming toad was listed as an endangered species under the Endangered Species Act on January 17, 1984, with a recovery plan approved in 1991. Currently the total population of the Wyoming toad includes approximately 200 animals in the captive breeding program and as few as 62 toads surviving at reintroduction sites in the Laramie Basin based upon fall 2000 survey data (after releases of more than 10,000 toads and tadpoles since 1995). Necessary conservation measures include improving reproduction and survival in the captive breeding program, improving survival at reintroduction sites, developing techniques to control the effects of the amphibian chytrid fungus, and eliminating threats and further habitat degradation in the wild.

Use of microsatellite markers to assign goats to their breeds.

PubMed

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

2015-08-07

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

Poplar breeding and testing strategies in the north-central U.S.: Demonstration of potential yield and consideration of future research needs1

Treesearch

Don E. Riemenschneider; William E. Berguson; Donald I. Dickmann; Richard B. Hall; J. G. Isebrands; Carl A. Mohn; Glen R. Stanosz; Gerald A. Tuskan

2001-01-01

We present results from a Populus Regional Testing Program that has been conducted in Minnesota, Iowa, Wisconsin, and Michigan over the past six years. Our objectives have been to: 1) identify highly productive, disease resistant intra- and inter-specific clonal selections and 2) understand patterns of genotype x environment interactions within the region that would,...

Accelerating plant breeding.

PubMed

De La Fuente, Gerald N; Frei, Ursula K; Lübberstedt, Thomas

2013-12-01

The growing demand for food with limited arable land available necessitates that the yield of major food crops continues to increase over time. Advances in marker technology, predictive statistics, and breeding methodology have allowed for continued increases in crop performance through genetic improvement. However, one major bottleneck is the generation time of plants, which is biologically limited and has not been improved since the introduction of doubled haploid technology. In this opinion article, we propose to implement in vitro nurseries, which could substantially shorten generation time through rapid cycles of meiosis and mitosis. This could prove a useful tool for speeding up future breeding programs with the aim of sustainable food production. Copyright © 2013 Elsevier Ltd. All rights reserved.

Review of major sweetpotato pests in Japan, with information on resistance breeding programs.

PubMed

Okada, Yoshihiro; Kobayashi, Akira; Tabuchi, Hiroaki; Kuranouchi, Toshikazu

2017-01-01

Sweetpotato ( Ipomoeae batatas (L.) Lam.) is an important food crop affected by several pests throughout the world, especially in tropical, subtropical, and temperate regions. Although Japan is relatively free from many serious sweetpotato pests, some pests, especially soil-borne pathogens, viruses, and insects such as plant-parasitic nematodes and weevils, cause severe damage in Japan. In this review, we describe the current status and management options for sweetpotato pests and diseases in Japan and review research related to sweetpotato breeding that can promote resistance to these problems. Furthermore, we describe methods to evaluate resistance to pests and disease used in sweetpotato breeding at the National Agriculture and Food Research Organization (NARO).

Resistance to Elsinoë Ampelina and Expression of Related Resistant Genes in Vitis Rotundifolia Michx. Grapes

PubMed Central

Louime, Clifford; Lu, Jiang; Onokpise, Oghenekome; Vasanthaiah, Hemanth K. N.; Kambiranda, Devaiah; Basha, Sheikh M.; Yun, Hae Keun

2011-01-01

Muscadine grapes (Vitis rotundifolia Michx) are considered as excellent genetic resources for grape breeding programs as they are known for their hardiness and resistance to pests and diseases. However, contrary to popular belief, our study indicated that not all muscadine cultivars are resistant to anthracnose disease. In order to identify a source of genetic tolerance towards anthracnose among muscadine cultivars, a series of in-situ and ex-situ experiments were conducted through strict and sensitive screening processes. Two consecutive years of field evaluation of 54 grape cultivars showed various levels of anthracnose incidence among the cultivars between a scale of 0 (tolerant) to 5 (highly-susceptible). Resistance bioassay by inoculation of different spore densities of Elsinoë ampelina on 40 cultivars presented similar results and was consistent with those obtained from the field test. A real-time PCR analysis was conducted to investigate differences of gene expression between susceptible and tolerant cultivars and to confirm results by phenotypic identification. Expression of genes encoding chalcone synthase, stilbene synthase, polygalacturonase-inhibiting protein, chitinase and lipid transfer-protein was only detected in tolerant cultivars. Resistant muscadine cultivars identified in this study could be excellent candidates for grape disease resistance breeding programs. PMID:21747689

Environmental enrichment affects adrenocortical stress responses in the endangered black-footed ferret

USGS Publications Warehouse

Poessel, S.A.; Biggins, D.E.; Santymire, R.M.; Livieri, T.M.; Crooks, K.R.; Angeloni, L.

2011-01-01

Potential stressors of wildlife living in captivity, such as artificial living conditions and frequent human contact, may lead to a higher occurrence of disease and reduced reproductive function. One successful method used by wildlife managers to improve general well-being is the provision of environmental enrichment, which is the practice of providing animals under managed care with environmental stimuli. The black-footed ferret (Mustela nigripes) is a highly-endangered carnivore species that was rescued from extinction by removal of the last remaining individuals from the wild to begin an ex situ breeding program. Our goal was to examine the effect of environmental enrichment on adrenocortical activity in ferrets by monitoring fecal glucocorticoid metabolites (FGM). Results demonstrated that enrichment lowered FGM in juvenile male ferrets, while increasing it in adult females; enrichment had no effect on FGM in juvenile females and adult males. These results correspond with our findings that juvenile males interacted more with the enrichment items than did adult females. However, we did not detect an impact of FGM on the incidence of disease or on the ability of ferrets to become reproductive during the following breeding season. We conclude that an environmental enrichment program could benefit captive juvenile male ferrets by reducing adrenocortical activity. ?? 2011 Elsevier Inc.

Environmental enrichment affects adrenocortical stress responses in the endangered black-footed ferret.

PubMed

Poessel, Sharon A; Biggins, Dean E; Santymire, Rachel M; Livieri, Travis M; Crooks, Kevin R; Angeloni, Lisa

2011-07-01

Potential stressors of wildlife living in captivity, such as artificial living conditions and frequent human contact, may lead to a higher occurrence of disease and reduced reproductive function. One successful method used by wildlife managers to improve general well-being is the provision of environmental enrichment, which is the practice of providing animals under managed care with environmental stimuli. The black-footed ferret (Mustela nigripes) is a highly-endangered carnivore species that was rescued from extinction by removal of the last remaining individuals from the wild to begin an ex situ breeding program. Our goal was to examine the effect of environmental enrichment on adrenocortical activity in ferrets by monitoring fecal glucocorticoid metabolites (FGM). Results demonstrated that enrichment lowered FGM in juvenile male ferrets, while increasing it in adult females; enrichment had no effect on FGM in juvenile females and adult males. These results correspond with our findings that juvenile males interacted more with the enrichment items than did adult females. However, we did not detect an impact of FGM on the incidence of disease or on the ability of ferrets to become reproductive during the following breeding season. We conclude that an environmental enrichment program could benefit captive juvenile male ferrets by reducing adrenocortical activity. Copyright © 2011 Elsevier Inc. All rights reserved.

Pedigree and herd characterization of a donkey breed vulnerable to extinction.

PubMed

Quaresma, M; Martins, A M F; Rodrigues, J B; Colaço, J; Payan-Carreira, R

2014-03-01

Most donkey and local horse breeds are vulnerable to extinction as mechanization of agriculture progress throughout the world. The present study analyzed the pedigree and herd records of the donkey Asinina de Miranda breed (RAM), identifying genealogical and human factors that may affect the breed genetic diversity in the future and suggesting suitable strategies to breed preservation, early on the conservation program. The breeding rate was very low, with a ratio of foaling/live animals of 0.23 (178/760). The estimated number of founders and ancestors contributing to the reference population was 128 and 121. The number of founder herds in the reference population was 64, with an effective number of founder herds for the reference population of 7.6. The mean age of herd owners was 65.50 ± 0.884 years, with a negative association among the herd size and owner's age (P<0.001). In contrast, the size of the herd and the ownership of a male were both positively associated (P<0.001) with the herd number of in-born foals. Both the owners' age and the herd location (RAM home region v. dispersal region) were negatively associated with the foaling number (P<0.001). The main identified risk factors were: low breeding rates; low number of males and their unequal contribution to the genetic pool; unequal contribution of the herds to genetic pool; and advanced age of herd owners.

[The importance of conservation of rare domestic animal breeds using the example of Arc Warder].

PubMed

Frölich, Kai; Jandowsky, Anabell

2017-02-09

The domestic animals descend from various wild ancestors. Thus, for example, of the wolf, the dog (15  000 BC), of the Bezoar goat the goat (10  000 BC), of the Asian mouflon the sheep (10  000 BC), of the wild boar the pig (8000 BC) and of the aurochs the cattle (7000 BC). Domestication has dramatically changed our culture and led to a great diversity of animal breeds. This is a unique cultural and historical treasure, which we have to preserve for future generations. The zoological park Arc Warder is Europe's largest center for rare and endangered domestic animal breeds. Arc Warder is more than a zoo; it is a landscape park, a conservation venture for genetic resources and furthermore a research project. Five principles guide the conservation efforts of Arc Warder: 1. Conservation through preservation. The breeding program will improve the quality of the genetic reservoir of breeds. 2. Conservation through the establishment of satellite stations. These pastures outside the park allow to increase the gene pool and ensure the protection of breeds against epidemics. 3. Conservation through high level education. 4. Protection by networking with national and international institutions. 5. Protection through research. Arc Warder is actively involved in close scientific cooperation with various universities and other research institutions on a number of scientific projects concerning the biological characteristics of old breeds.

Comparing power and precision of within-breed and multibreed genome-wide association studies of production traits using whole-genome sequence data for 5 French and Danish dairy cattle breeds.

PubMed

van den Berg, Irene; Boichard, Didier; Lund, Mogens Sandø

2016-11-01

The objective of this study was to compare mapping precision and power of within-breed and multibreed genome-wide association studies (GWAS) and to compare the results obtained by the multibreed GWAS with 3 meta-analysis methods. The multibreed GWAS was expected to improve mapping precision compared with a within-breed GWAS because linkage disequilibrium is conserved over shorter distances across breeds than within breeds. The multibreed GWAS was also expected to increase detection power for quantitative trait loci (QTL) segregating across breeds. GWAS were performed for production traits in dairy cattle, using imputed full genome sequences of 16,031 bulls, originating from 6 French and Danish dairy cattle populations. Our results show that a multibreed GWAS can be a valuable tool for the detection and fine mapping of quantitative trait loci. The number of QTL detected with the multibreed GWAS was larger than the number detected by the within-breed GWAS, indicating an increase in power, especially when the 2 Holstein populations were combined. The largest number of QTL was detected when all populations were combined. The analysis combining all breeds was, however, dominated by Holstein, and QTL segregating in other breeds but not in Holstein were sometimes overshadowed by larger QTL segregating in Holstein. Therefore, the GWAS combining all breeds except Holstein was useful to detect such peaks. Combining all breeds except Holstein resulted in smaller QTL intervals on average, but this outcome was not the case when the Holstein populations were included in the analysis. Although no decrease in the average QTL size was observed, mapping precision did improve for several QTL. Out of 3 different multibreed meta-analysis methods, the weighted z-scores model resulted in the most similar results to the full multibreed GWAS and can be useful as an alternative to a full multibreed GWAS. Differences between the multibreed GWAS and the meta-analyses were larger when different breeds were combined than when the 2 Holstein populations were combined. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Composition of fatty acids in virgin olive oils from cross breeding segregating populations by gas chromatography separation with flame ionization detection.

PubMed

Sánchez de Medina, Verónica; El Riachy, Milad; Priego-Capote, Feliciano; Luque de Castro, María Dolores

2015-11-01

Recent technological advances to improve the quality of virgin olive oil (VOO) have been focused on olive breeding programs by selecting outstanding cultivars and target progenies. Fatty acid (FA) composition, with special emphasis on oleic acid (C18:1) and palmitic acid (C16:0), is one of the most critical quality factors to be evaluated in VOO. For this reason, the profile of FAs is frequently used as a decision tool in olive breeding programs. A method based on gas chromatography with flame ionization detection (GC-FID) was used to study the influence of genotype on the concentration of ten of the most important FAs in VOOs from target crosses Arbequina × Arbosana, Picual × Koroneiki and Sikitita × Arbosana and their corresponding genitors Arbequina, Arbosana, Koroneiki, Picual and Sikitita. For this purpose, a targeted approach was selected for determination of esterified FAs (EFAs) and non-esterified FAs (NEFAs) in a dual analysis by the same chromatographic method. A Pearson analysis revealed correlations between pairs of FAs, which allowed detecting metabolic connections through desaturation and elongation enzymes. An ANOVA test (with P < 0.01) led to identification of C16:0 EFA, C16:1 EFA and C18:1 EFA and also C16:1 NEFA and C18:0 NEFA as the FAs more influenced by cross breeding. Statistical analysis was carried out by unsupervised analysis using principal component analysis (PCA) and cluster analysis (CA) to look for variability sources. Crosses with a common genitor (Arbequina × Arbosana and Sikitita × Arbosana) were partially overlapped in the PCAs using the profile of FAs. The CA results revealed clear differences between Sikitita × Arbosana and Picual × Koroneiki crosses in the composition of the most significant FAs, while Arbequina × Arbosana was not properly discriminated from the other crosses. © 2014 Society of Chemical Industry.

Romanian Maize (Zea mays) Inbred Lines as a Source of Genetic Diversity in SE Europe, and Their Potential in Future Breeding Efforts

PubMed Central

Haș, Voichița; Haș, Ioan; Miclăuș, Mihai

2013-01-01

Maize has always been under constant human selection ever since it had been domesticated. Intensive breeding programs that resulted in the massive use of hybrids nowadays have started in the 60s. That brought significant yield increases but reduced the genetic diversity at the same time. Consequently, breeders and researchers alike turned their attention to national germplasm collections established decades ago in many countries, as they may hold allelic variations that could prove useful for future improvements. These collections are mainly composed of inbred lines originating from well-adapted local open pollinated varieties. However, there is an overall lack of data in the literature about the genetic diversity of maize in SE Europe, and its potential for future breeding efforts. There are no data, whatsoever, on the nutritional quality of the grain, primarily dictated by the zein proteins. We therefore sought to use the Romanian maize germplasm as an entry point in understanding the molecular make-up of maize in this part of Europe. By using 80 SSR markers, evenly spread throughout the genome, on 82 inbred lines from various parts of the country, we were able to decipher population structure and the existing relationships between those and the eight international standards used, including the reference sequenced genome B73. Corroborating molecular data with a standardized morphological, physiological, and biochemical characterization of all 90 inbred lines, this is the first comprehensive such study on the existing SE European maize germplasm. The inbred lines we present here are an important addition to the ever-shrinking gene pool that the breeding programs are faced-with, because of the allelic richness they hold. They may serve as parental lines in crosses that will lead to new hybrids, characterized by a high level of heterosis, nationwide and beyond, due to their existing relationship with the international germplasm. PMID:24392016

Genetic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel

PubMed Central

Makina, Sithembile O.; Muchadeyi, Farai C.; van Marle-Köster, Este; MacNeil, Michael D.; Maiwashe, Azwihangwisi

2014-01-01

Information about genetic diversity and population structure among cattle breeds is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of cattle breeds. This study investigated genetic diversity and the population structure among six cattle breeds in South African (SA) including Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), Bonsmara (n = 44), Angus (n = 31), and Holstein (n = 29). Genetic diversity within cattle breeds was analyzed using three measures of genetic diversity namely allelic richness (AR), expected heterozygosity (He) and inbreeding coefficient (f). Genetic distances between breed pairs were evaluated using Nei's genetic distance. Population structure was assessed using model-based clustering (ADMIXTURE). Results of this study revealed that the allelic richness ranged from 1.88 (Afrikaner) to 1.73 (Nguni). Afrikaner cattle had the lowest level of genetic diversity (He = 0.24) and the Drakensberger cattle (He = 0.30) had the highest level of genetic variation among indigenous and locally-developed cattle breeds. The level of inbreeding was lower across the studied cattle breeds. As expected the average genetic distance was the greatest between indigenous cattle breeds and Bos taurus cattle breeds but the lowest among indigenous and locally-developed breeds. Model-based clustering revealed some level of admixture among indigenous and locally-developed breeds and supported the clustering of the breeds according to their history of origin. The results of this study provided useful insight regarding genetic structure of SA cattle breeds. PMID:25295053

Genetic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel.

PubMed

Makina, Sithembile O; Muchadeyi, Farai C; van Marle-Köster, Este; MacNeil, Michael D; Maiwashe, Azwihangwisi

2014-01-01

Information about genetic diversity and population structure among cattle breeds is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of cattle breeds. This study investigated genetic diversity and the population structure among six cattle breeds in South African (SA) including Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), Bonsmara (n = 44), Angus (n = 31), and Holstein (n = 29). Genetic diversity within cattle breeds was analyzed using three measures of genetic diversity namely allelic richness (AR), expected heterozygosity (He) and inbreeding coefficient (f). Genetic distances between breed pairs were evaluated using Nei's genetic distance. Population structure was assessed using model-based clustering (ADMIXTURE). Results of this study revealed that the allelic richness ranged from 1.88 (Afrikaner) to 1.73 (Nguni). Afrikaner cattle had the lowest level of genetic diversity (He = 0.24) and the Drakensberger cattle (He = 0.30) had the highest level of genetic variation among indigenous and locally-developed cattle breeds. The level of inbreeding was lower across the studied cattle breeds. As expected the average genetic distance was the greatest between indigenous cattle breeds and Bos taurus cattle breeds but the lowest among indigenous and locally-developed breeds. Model-based clustering revealed some level of admixture among indigenous and locally-developed breeds and supported the clustering of the breeds according to their history of origin. The results of this study provided useful insight regarding genetic structure of SA cattle breeds.

Biotechnology and apple breeding in Japan

PubMed Central

Igarashi, Megumi; Hatsuyama, Yoshimichi; Harada, Takeo; Fukasawa-Akada, Tomoko

2016-01-01

Apple is a fruit crop of significant economic importance, and breeders world wide continue to develop novel cultivars with improved characteristics. The lengthy juvenile period and the large field space required to grow apple populations have imposed major limitations on breeding. Various molecular biological techniques have been employed to make apple breeding easier. Transgenic technology has facilitated the development of apples with resistance to fungal or bacterial diseases, improved fruit quality, or root stocks with better rooting or dwarfing ability. DNA markers for disease resistance (scab, powdery mildew, fire-blight, Alternaria blotch) and fruit skin color have also been developed, and marker-assisted selection (MAS) has been employed in breeding programs. In the last decade, genomic sequences and chromosome maps of various cultivars have become available, allowing the development of large SNP arrays, enabling efficient QTL mapping and genomic selection (GS). In recent years, new technologies for genetic improvement, such as trans-grafting, virus vectors, and genome-editing, have emerged. Using these techniques, no foreign genes are present in the final product, and some of them show considerable promise for application to apple breeding. PMID:27069388

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

PubMed

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

2015-09-25

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

Biotechnology and apple breeding in Japan.

PubMed

Igarashi, Megumi; Hatsuyama, Yoshimichi; Harada, Takeo; Fukasawa-Akada, Tomoko

2016-01-01

Apple is a fruit crop of significant economic importance, and breeders world wide continue to develop novel cultivars with improved characteristics. The lengthy juvenile period and the large field space required to grow apple populations have imposed major limitations on breeding. Various molecular biological techniques have been employed to make apple breeding easier. Transgenic technology has facilitated the development of apples with resistance to fungal or bacterial diseases, improved fruit quality, or root stocks with better rooting or dwarfing ability. DNA markers for disease resistance (scab, powdery mildew, fire-blight, Alternaria blotch) and fruit skin color have also been developed, and marker-assisted selection (MAS) has been employed in breeding programs. In the last decade, genomic sequences and chromosome maps of various cultivars have become available, allowing the development of large SNP arrays, enabling efficient QTL mapping and genomic selection (GS). In recent years, new technologies for genetic improvement, such as trans-grafting, virus vectors, and genome-editing, have emerged. Using these techniques, no foreign genes are present in the final product, and some of them show considerable promise for application to apple breeding.

The importance of reproductive barriers and the effect of allopolyploidization on crop breeding

PubMed Central

Tonosaki, Kaoru; Osabe, Kenji; Kawanabe, Takahiro; Fujimoto, Ryo

2016-01-01

Inter-specific hybrids are a useful source for increasing genetic diversity. Some reproductive barriers before and/or after fertilization prevent production of hybrid plants by inter-specific crossing. Therefore, techniques to overcome the reproductive barrier have been developed, and have contributed to hybridization breeding. In recent studies, identification of molecules involved in plant reproduction has been studied to understand the mechanisms of reproductive barriers. Revealing the molecular mechanisms of reproductive barriers may allow us to overcome reproductive barriers in inter-specific crossing, and to efficiently produce inter-specific hybrids in cross-combinations that cannot be produced through artificial techniques. Inter-specific hybrid plants can potentially serve as an elite material for plant breeding, produced through the merging of genomes of parental species by allopolyploidization. Allopolyploidization provides some benefits, such as heterosis, increased genetic diversity and phenotypic variability, which are caused by dynamic changes of the genome and epigenome. Understanding of allopolyploidization mechanisms is important for practical utilization of inter-specific hybrids as a breeding material. This review discusses the importance of reproductive barriers and the effect of allopolyploidization in crop breeding programs. PMID:27436943

Statistical inference for classification of RRIM clone series using near IR reflectance properties

NASA Astrophysics Data System (ADS)

Ismail, Faridatul Aima; Madzhi, Nina Korlina; Hashim, Hadzli; Abdullah, Noor Ezan; Khairuzzaman, Noor Aishah; Azmi, Azrie Faris Mohd; Sampian, Ahmad Faiz Mohd; Harun, Muhammad Hafiz

2015-08-01

RRIM clone is a rubber breeding series produced by RRIM (Rubber Research Institute of Malaysia) through "rubber breeding program" to improve latex yield and producing clones attractive to farmers. The objective of this work is to analyse measurement of optical sensing device on latex of selected clone series. The device using transmitting NIR properties and its reflectance is converted in terms of voltage. The obtained reflectance index value via voltage was analyzed using statistical technique in order to find out the discrimination among the clones. From the statistical results using error plots and one-way ANOVA test, there is an overwhelming evidence showing discrimination of RRIM 2002, RRIM 2007 and RRIM 3001 clone series with p value = 0.000. RRIM 2008 cannot be discriminated with RRIM 2014; however both of these groups are distinct from the other clones.

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.

Review: Sustainability of crossbreeding in developing countries; definitely not like crossing a meadow….

PubMed

Leroy, G; Baumung, R; Boettcher, P; Scherf, B; Hoffmann, I

2016-02-01

Crossbreeding, considering either terminal or rotational crossing, synthetic breed creation or breed replacement, is often promoted as an efficient strategy to increase farmers' income through the improvement of productivity of local livestock in developing countries. Sustainability of crossbreeding is however frequently challenged by constraints such as poor adaptation to the local environment or lack of logistic support. In this review, we investigate factors that may influence the long-term success or the failure of crossbreeding programs, based on the scientific literature and country reports submitted for The Second Report on the State of the World's Animal Genetic Resources for Food and Agriculture. Crossbreeding activities vary widely across species and countries. Its sustainability is dependent on different prerequisites such as continual access to adequate breeding stock (especially after the end of externally funded crossbreeding projects), the opportunity of improved livestock to express their genetic potential (e.g. through providing proper inputs) and integration within a reliable market chain. As formal crossbreeding programs are often associated with adoption of other technologies, they can be a catalyst for innovation and development for smallholders. Given the increasing global demand for animal products, as well as the potential environmental consequences of climate change, there is a need for practical research to improve the implementation of long-term crossbreeding programs in developing countries.

Genomic Tools in Groundnut Breeding Program: Status and Perspectives

PubMed Central

Janila, P.; Variath, Murali T.; Pandey, Manish K.; Desmae, Haile; Motagi, Babu N.; Okori, Patrick; Manohar, Surendra S.; Rathnakumar, A. L.; Radhakrishnan, T.; Liao, Boshou; Varshney, Rajeev K.

2016-01-01

Groundnut, a nutrient-rich food legume, is cultivated world over. It is valued for its good quality cooking oil, energy and protein rich food, and nutrient-rich fodder. Globally, groundnut improvement programs have developed varieties to meet the preferences of farmers, traders, processors, and consumers. Enhanced yield, tolerance to biotic and abiotic stresses and quality parameters have been the target traits. Spurt in genetic information of groundnut was facilitated by development of molecular markers, genetic, and physical maps, generation of expressed sequence tags (EST), discovery of genes, and identification of quantitative trait loci (QTL) for some important biotic and abiotic stresses and quality traits. The first groundnut variety developed using marker assisted breeding (MAB) was registered in 2003. Since then, USA, China, Japan, and India have begun to use genomic tools in routine groundnut improvement programs. Introgression lines that combine foliar fungal disease resistance and early maturity were developed using MAB. Establishment of marker-trait associations (MTA) paved way to integrate genomic tools in groundnut breeding for accelerated genetic gain. Genomic Selection (GS) tools are employed to improve drought tolerance and pod yield, governed by several minor effect QTLs. Draft genome sequence and low cost genotyping tools such as genotyping by sequencing (GBS) are expected to accelerate use of genomic tools to enhance genetic gains for target traits in groundnut. PMID:27014312

Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples

PubMed Central

Cornille, Amandine; Feurtey, Alice; Gélin, Uriel; Ropars, Jeanne; Misvanderbrugge, Kristine; Gladieux, Pierre; Giraud, Tatiana

2015-01-01

Gene flow is an essential component of population adaptation and species evolution. Understanding of the natural and anthropogenic factors affecting gene flow is also critical for the development of appropriate management, breeding, and conservation programs. Here, we explored the natural and anthropogenic factors impacting crop-to-wild and within wild gene flow in apples in Europe using an unprecedented dense sampling of 1889 wild apple (Malus sylvestris) from European forests and 339 apple cultivars (Malus domestica). We made use of genetic, environmental, and ecological data (microsatellite markers, apple production across landscapes and records of apple flower visitors, respectively). We provide the first evidence that both human activities, through apple production, and human disturbance, through modifications of apple flower visitor diversity, have had a significant impact on crop-to-wild interspecific introgression rates. Our analysis also revealed the impact of previous natural climate change on historical gene flow in the nonintrogressed wild apple M. sylvestris, by identifying five distinct genetic groups in Europe and a north–south gradient of genetic diversity. These findings identify human activities and climate as key drivers of gene flow in a wild temperate fruit tree and provide a practical basis for conservation, agroforestry, and breeding programs for apples in Europe. PMID:25926882

Field techniques and methods of data collection used in studies of wood storks of the Birdsville Colony and swamps of the Savannah River Plant

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

Coulter, M.C.; Bryan, A.L. Jr.

1988-10-01

The United States population of Wood Storks (Mycteria americana) has been declining over the last 50 years, although there has been disagreement as to the magnitude of the decrease. In 1984, the US Fish and Wildlife Service listed the US breeding population as endangered. In that year the University of Georgia's Savannah River Ecology Laboratory began an extensive research program on the breeding biology and foraging ecology of Wood Storks of the Birdsville colony in Millen, Jenkins county, east-central Georgia, USA. The SREL Wood Stork program was designed to evaluate the importance of foraging habitat on the Savannah River Plantmore » to storks, and to design and develop management plans for artificial foraging ponds at the National Audubon Society's Silver Bluff Plantation Sanctuary. It was necessary to develop an understanding of the general foraging ecology of the birds, and to understand their forage needs during the breeding season. We have summarized the methods that we developed during this program as an aid to researchers studying storks or other wading birds. Although the methods described here were designed to answer questions important to our program, we hope that they are general enough to be helpful to others. Some of the methods were designed in 1983, during a preliminary part of the study. All the methods have evolved during the program, improving from our experience. Many people have been involved in the study and all have contributed to the methods and their improvement.« less

Utilization of farm animal genetic resources in a changing agro-ecological environment in the Nordic countries.

PubMed

Kantanen, Juha; Løvendahl, Peter; Strandberg, Erling; Eythorsdottir, Emma; Li, Meng-Hua; Kettunen-Præbel, Anne; Berg, Peer; Meuwissen, Theo

2015-01-01

Livestock production is the most important component of northern European agriculture and contributes to and will be affected by climate change. Nevertheless, the role of farm animal genetic resources in the adaptation to new agro-ecological conditions and mitigation of animal production's effects on climate change has been inadequately discussed despite there being several important associations between animal genetic resources and climate change issues. The sustainability of animal production systems and future food security require access to a wide diversity of animal genetic resources. There are several genetic questions that should be considered in strategies promoting adaptation to climate change and mitigation of environmental effects of livestock production. For example, it may become important to choose among breeds and even among farm animal species according to their suitability to a future with altered production systems. Some animals with useful phenotypes and genotypes may be more useful than others in the changing environment. Robust animal breeds with the potential to adapt to new agro-ecological conditions and tolerate new diseases will be needed. The key issue in mitigation of harmful greenhouse gas effects induced by livestock production is the reduction of methane (CH4) emissions from ruminants. There are differences in CH4 emissions among breeds and among individual animals within breeds that suggest a potential for improvement in the trait through genetic selection. Characterization of breeds and individuals with modern genomic tools should be applied to identify breeds that have genetically adapted to marginal conditions and to get critical information for breeding and conservation programs for farm animal genetic resources. We conclude that phenotyping and genomic technologies and adoption of new breeding approaches, such as genomic selection introgression, will promote breeding for useful characters in livestock species.

Utilization of farm animal genetic resources in a changing agro-ecological environment in the Nordic countries

PubMed Central

Kantanen, Juha; Løvendahl, Peter; Strandberg, Erling; Eythorsdottir, Emma; Li, Meng-Hua; Kettunen-Præbel, Anne; Berg, Peer; Meuwissen, Theo

2015-01-01

Livestock production is the most important component of northern European agriculture and contributes to and will be affected by climate change. Nevertheless, the role of farm animal genetic resources in the adaptation to new agro-ecological conditions and mitigation of animal production’s effects on climate change has been inadequately discussed despite there being several important associations between animal genetic resources and climate change issues. The sustainability of animal production systems and future food security require access to a wide diversity of animal genetic resources. There are several genetic questions that should be considered in strategies promoting adaptation to climate change and mitigation of environmental effects of livestock production. For example, it may become important to choose among breeds and even among farm animal species according to their suitability to a future with altered production systems. Some animals with useful phenotypes and genotypes may be more useful than others in the changing environment. Robust animal breeds with the potential to adapt to new agro-ecological conditions and tolerate new diseases will be needed. The key issue in mitigation of harmful greenhouse gas effects induced by livestock production is the reduction of methane (CH4) emissions from ruminants. There are differences in CH4 emissions among breeds and among individual animals within breeds that suggest a potential for improvement in the trait through genetic selection. Characterization of breeds and individuals with modern genomic tools should be applied to identify breeds that have genetically adapted to marginal conditions and to get critical information for breeding and conservation programs for farm animal genetic resources. We conclude that phenotyping and genomic technologies and adoption of new breeding approaches, such as genomic selection introgression, will promote breeding for useful characters in livestock species. PMID:25767477

Introduction - regional monitoring programs

Treesearch

Richard L. Hutto; C. John Ralph

2005-01-01

There is increasing interest in the initiation of regional or statewide monitoring programs that are less extensive than national efforts such as the Breeding Bird Survey. A number of regional programs have been in existence for a decade or more, so the papers in this section represented an effort to bring together the collective experience of the people who had...

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.

Development of Novel SSR Markers for Flax (Linum usitatissimum L.) Using Reduced-Representation Genome Sequencing.

PubMed

Wu, Jianzhong; Zhao, Qian; Wu, Guangwen; Zhang, Shuquan; Jiang, Tingbo

2016-01-01

Flax ( Linum usitatissimum L.) is a major fiber and oil yielding crop grown in northeastern China. Identification of flax molecular markers is a key step toward improving flax yield and quality via marker-assisted breeding. Simple sequence repeat (SSR) markers, which are based on genomic structural variation, are considered the most valuable type of genetic marker for this purpose. In this study, we screened 1574 microsatellites from Linum usitatissimum L. obtained using reduced representation genome sequencing (RRGS) to systematically identify SSR markers. The resulting set of microsatellites consisted mainly of trinucleotide (56.10%) and dinucleotide (35.23%) repeats, with each motif consisting of 5-8 repeats. We then evaluated marker sensitivity and specificity based on samples of 48 flax isolates obtained from northeastern China. Using the new SSR panel, the results demonstrated that fiber flax and oilseed flax varieties clustered into two well separated groups. The novel SSR markers developed in this study show potential value for selection of varieties for use in flax breeding programs.

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

PubMed Central

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

2018-01-01

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

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

PubMed

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

2018-02-01

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