Journal of Animal Breeding and Genetics最新文献

{"title":"Derivation of Economic Values for Breeding Objective Traits of Chinese Holstein Dairy Cows Using a Bio-Economic Model.","authors":"R Shi, A van der Linden, S Oosting, Y Wang, B Ducro","doi":"10.1111/jbg.12922","DOIUrl":"https://doi.org/10.1111/jbg.12922","url":null,"abstract":"<p><p>Holstein cattle account for the largest proportion of dairy cattle in China. The current China Performance Index (CPI) consists mainly of production traits. To derive economic values (EV) of additional traits for balanced breeding programs, a bio-economic model is necessary. Landless and intensive dairy farms are dominant in China, wherein all feed is purchased, and in-farm technicians and veterinarians are employed. Therefore, in the present study, a tailored bio-economic model was developed using the parameters of a typical dairy farm in North China. The typical farm had 1500 cows and 1400 youngstock, with a replacement rate of 33.5% per year and a productive life of 1090 days. The bio-economic model was on a per cow per year basis and described the revenues and costs from different animal categories. The EVs of 17 traits, including production, calving, fertility, longevity, and health traits, were derived and used to develop a more balanced selection index. Results showed that the bio-economic model can represent the typical dairy farm system in North China. The EVs of production traits were 2.39 Chinese Yuan (CNY), 32.85 CNY, and 89.60 CNY per kg milk yield, fat yield and protein yield, respectively. The EVs of production traits were two to three times higher than those in some European countries, due to the higher prices on milk volume and milk solids in China. The EVs of health traits ranged from -0.45 CNY to -11.95 CNY and were nearly half of those in other countries, due to the lower in-farm veterinarian labour costs. The EVs of most other functional traits were in line with the published values of other countries with similar economic assumptions in the model. Using the calculated EVs, a more balanced selection index was derived by including functional traits. This index had higher relative weight (46.8%) on functional traits than the current CPI (12.5%). With the high milk prices, it is still most profitable to allow for a decline in functional traits, although the decline is considerably smaller with the developed balanced index than with the CPI. Collectively, the bio-economic model and EVs provided the foundations for implementing balanced breeding programs in the Chinese Holstein population.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-Step Genome-Wide Association Study of Factors for Evaluated and Linearly Scored Traits in Swedish Warmblood Horses.","authors":"Anahit Nazari-Ghadikolaei, W Freddy Fikse, Åsa Gelinder Viklund, Sofia Mikko, Susanne Eriksson","doi":"10.1111/jbg.12923","DOIUrl":"https://doi.org/10.1111/jbg.12923","url":null,"abstract":"<p><p>Swedish Warmblood horses (SWB) are bred for show jumping and/or dressage with young horse test scores as indicator traits. This study aimed to investigate possible candidate genes and regions of importance for evaluated and linearly scored young horse test traits. A single-step genome-wide association study (ssGWAS) was done using the BLUPF90 suite of programs for factors scores from factor analysis of traits assessed at young horse tests together with height at withers. The ssGWAS included 20,814 SWB with factors scores for four factors for evaluated traits. A total of 6436 of these horses also had factor scores for 13 factors for linearly scored traits. Genotypes from a 670K SNP array were available for 380 of the horses in this study. All genotyped horses had factor scores for evaluated traits, and 379 also had factors scores for linearly scored traits. Significant SNPs associated with three factors related to size were located on ECA3 within or nearby a well-known region, including the genes ligand dependent nuclear receptor corepressor like (LCORL), non-SMC condensin I complex subunit G (NCAPG), DDB1 and CUL4 Associated Factor 16 (DCAF16), and the Family with Sequence Similarity 184 Member B (FAM184B). Significant SNPs were also detected for two factors for evaluated traits representing conformation and jumping, and four factors for linearly scored traits related to body length, neck conformation, walk and trot (hindleg position and activity), respectively. Among nearby genes, calcium/calmodulin-dependent protein kinase type 1D (CAMK1D) for the factor for linearly scored traits related to neck conformation and GLI Family Zinc Finger 2 (GLI2) for the factor for evaluated jumping traits, were most promising. For these, top associated SNPs were detected within the genes, and the known gene functions seems to be related to the phenotypes. In conclusion, ssGWAS is beneficial to detect plausible candidate genes/regions for desired traits in warmblood horses.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142928734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Estimation of Genetic Parameters and GWAS on Water Efficiency Traits in the Senepol Cattle.","authors":"Christhian B Souza, Gilberto R O Menezes, Andrea Gondo, Andrea A Egito, Pedro V B Ramos, Rodrigo C Gomes, Marcelo N Ribas, José Antônio Fernandes Júnior, Simone E F Guimarães","doi":"10.1111/jbg.12920","DOIUrl":"https://doi.org/10.1111/jbg.12920","url":null,"abstract":"<p><p>The need for producing in environmentally resilient system drives new research to achieve sustainable beef production. Water footprint of the beef supply chain is a concern that must be addressed, aiming to improve water use within the production chain. One approach is genetic selection of beef cattle for water efficiency. However, it is essential to understand the genetic architecture and mechanisms involved in the expression of this phenotype to choose the best selection criteria. Thus, our study aimed to estimate genetic parameters for water efficiency traits, conduct a genome-wide association study (GWAS) and identify the genetic networks and biological processes involved. A population of 1762 purebred Senepol cattle was phenotyped for the following water efficiency traits: water intake (WI), gross water efficiency (GWE), water conversion ratio (WCR), residual water intake based on average daily gain (RWI_ADG) and residual water intake based on dry matter intake (RWI_DMI). A subset of 1342 animals was genotyped using GGP Bovine 50 K SNP Chip with (734 animals) or 100 K (508 animals), and imputation from 50 K to 100 K was performed with Beagle software. The heritability estimates were 0.36 ± 0.06, 0.26 ± 0.05, 0.22 ± 0.05, 0.24 ± 0.05 and 0.20 ± 0.05 for WI, GWE, WCR, RWI_ADG and RWI_DMI, respectively. Unlike the raw measures of WI, the phenotypic correlations between average daily gain (ADG) and the residuals (RWI_DMI and RWI_ADG) were zero. All water efficiency traits were moderately to highly correlated with each other. GWAS were used to estimate the effect of 79,860 single nucleotide polymorphisms (SNPs), and significant SNPs were only observed for WCR. Enrichment analysis of genes in the significant regions revealed the involvement of different biological processes, such as saliva production, water transport, renal system and immune system. Genetic selection of Senepol cattle for water efficiency traits is feasible and can reduce water requirements for meat production. Water efficiency measures are polygenic traits, and different biological processes act simultaneously on the expression of related phenotypes.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using Weighted Goal Programming Model to Achieve Genetic Gain in a Beluga Sturgeon Breeding Program.","authors":"Mina Rahbar, Roghieh Safari, Carlos I Perez-Rostro","doi":"10.1111/jbg.12916","DOIUrl":"https://doi.org/10.1111/jbg.12916","url":null,"abstract":"<p><p>We estimated the desired genetic gains for important traits in Beluga sturgeon (Huso huso) using an analytic hierarchy process (AHP) and weighted goal programming (WGP). Two questionnaires were distributed to 122 private Beluga sturgeon farmers in Iran in two stages. The initial stage involved the first questionnaire, which aimed to gather information on the environmental and management aspects of the farms. Additionally, farmers were requested to rate 4 important traits from a list of 12 traits for genetic improvement in the Beluga breeding program. Based on the results, four traits, that is, ovarian fat lobe weight (OFW), total caviar weight (CW), body weight of broodstock (BW) and larval body area at hatching (LBA) were rated highest. In the second stage, the second questionnaire asked farmers to make six pairwise comparisons between the above traits to determine preferences of these traits. The analytical hierarchy process was used to estimate individual preference (Ind-P) values using Super Decisions software. The medians of the Ind-P values were OFW and CW (0.30), BW (0.27) and LBA (0.10). Social group preference (Soc-P) values were estimated for five categories, with 13 social groups using the WGP model in LINGO software. Most disagreements in Soc-P values were found between the commercial products and water temperature categories. Consensus preference values (Con-P) for the above two categories were obtained by the extended WGP model with the range of λ between 0 and 1 in LINGO software. The average best Con-P values were OFW = BW (0.29), LBA (0.21) and CW (0.19). Desired genetic gains (%) were calculated using the percentage genetic improvement (G%) multiplied by the mean of Con-P, yielding values of 2.09, 1.88, 1.44 and 0.62 for BW, CW, LBA and OFW, respectively. The most important achievements of this research are the determination of the economic traits importance and multi-traits selection in the Beluga breeding program.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bayesian Recursive and Structural Equation Models to Infer Causal Links Among Gait Visual Scores on Campolina Horses.","authors":"Fernando Bussiman, Jennifer Richter, Jorge Hidalgo, Fabyano Fonseca E Silva, Ricardo Vieira Ventura, Rachel Santos Bueno Carvalho, Elisângela Chicaroni Mattos, José Bento Sterman Ferraz, Joanir Pereira Eler, Júlio Cesar de Carvalho Balieiro","doi":"10.1111/jbg.12919","DOIUrl":"https://doi.org/10.1111/jbg.12919","url":null,"abstract":"<p><p>Gait visual scores are widely applied to horse breeding because they are a fast and easy phenotyping strategy, allowing the numeric interpretation of a complex biological process such as gait quality. However, they may suffer from subjectivity or high environmental influence. We aimed to investigate potential causal relationships among six visual gait scores in Campolina horses. The data included 5475 horses with records for at least one of the following traits: Dissociation (Di), Comfort (C), Style (S), Regularity (R), Development (De), and Gait total Scores (GtS). The pedigree comprised three generations with 14,079 horses in the additive relationship matrix. Under a Bayesian framework, (co)variance components were estimated through a multitrait animal model (MTM). Then, the inductive causation algorithm (IC) was applied to the residual (co)variance matrix samples. The resulting undirected graph from IC was directed in 6 possible causal structures, each fitted by a structural equation model. The final causal structure was chosen based on deviance information criteria (DIC). It was found that S significantly impacts the causal network of gait, directly and indirectly affecting C. The indirect causal effect of S on C was through the direct effect of S on De, then the direct effect of De on R, and finally, the direct effect of R on C. Di was caused by S, which is the reason for the genetic correlation between Di and GtS, due to causal effects being added to the model, they absorb the genetic correlation between Di and GtS. Those paths have biological meaning to horse movements and can help breeders and researchers better understand horses' complex causal network of gait.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142857033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple Trait Bayesian Analysis of Partitioned Genetic Trends Accounting for Uncertainty in Genetic Parameters. An Example With the Pirenaica and Rubia Gallega Beef Cattle Breeds.","authors":"David López-Carbonell, Andrés Legarra, Juan Altarriba, Carlos Hervás-Rivero, Manuel Sánchez-Díaz, Luis Varona","doi":"10.1111/jbg.12918","DOIUrl":"https://doi.org/10.1111/jbg.12918","url":null,"abstract":"<p><p>Genetic trends are a valuable tool for analysing the efficiency of breeding programs. They are calculated by averaging the predicted breeding values for all individuals born within a specific time period. Moreover, partitioned genetic trends allow dissecting the contributions of several selection paths to overall genetic progress. These trends are based on the linear relationship between breeding values and the Mendelian sampling terms of ancestors, enabling genetic trends to be split into contributions from different categories of individuals. However, (1) the use of predicted breeding values in calculating partitioned genetic trends depends on the variance components used and (2) a multiple trait analysis allows accounting for selection on correlated traits. These points are often not considered. To overcome these limitations, we present a software called \"TM_TRENDS.\" This software performs a Bayesian analysis of partitioned genetic trends in a multiple trait model, accounting for uncertainty in the variance components. To illustrate the capabilities of this tool, we analysed the partitioned genetic trends for five traits (Birth Weight, Weight at 210 days, Cold Carcass Weight, Carcass Conformation, and Fatness Conformation) in two Spanish beef cattle breeds, Pirenaica and Rubia Gallega. The global genetic trends showed an increase in Carcass Conformation and a decrease in Birth Weight, Weight at 210 days, Cold Carcass Weight, and Fatness Conformation. These trends were partitioned into six categories: non-reproductive individuals, dams of females and non-reproductive individuals, dams of sires, sires with fewer than 20 progeny, sires between 20 and 50 progeny, and sires with more than 50 progeny. The results showed that the main source of genetic progress comes from sires with more than 50 progenies, followed by dams of males. Additionally, two additional features of the Bayesian analysis are presented: the calculation of the posterior probability of the global and partitioned genetic response between two time points, and the calculation of the posterior probability of positive (or negative) genetic progress.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142857035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimal Combination of Different Selection and Mating Strategies on Exploiting Genetic Diversity and Genetic Gain in Small Pig Conservation Populations.","authors":"Qingbo Zhao, Huiming Liu, Qian Zhang, Qamar Raza Qadri, Yuchun Pan, Guosheng Su, Pinghua Li, Ruihua Huang","doi":"10.1111/jbg.12917","DOIUrl":"https://doi.org/10.1111/jbg.12917","url":null,"abstract":"<p><p>Both selection and mating systems are essential tools for breeders to conserve the genetic variance and improve the performance of livestock animals. How to effectively balance the genetic gain and inbreeding has always been an important issue in quantitative genetics research. In this study, a total of 11 selection methods, including random and truncation selection, six conventional selection methods, three different optimal contribution selection (OCS) methods and three mating strategies including random mating, minimum-coancestry mating based on pedigree (MCPed) and genomic information (MCmarker), were performed using stochastic simulations. The long-term effects of different combinations of selection and mating strategies on the genetic gain, the rate of inbreeding and genetic diversity in the small-scale pig conservation populations were investigated. The results showed that different strategies of selection and mating methods had different effects on genetic gain and inbreeding rate. For maintaining additive genetic variance, the optimal strategy was random selection with random mating, followed by SIREhalf-DAMfullRandom selection (which means selecting dams randomly from each full-sib family) and random mating. For mainting the number of common ancestors, the optimal strategy was SIREhalf-DAMfull selection (which means selecting dams with the highest estimated breeding value within each full-sib family) and random mating, followed by SIREhalf-DAMfullRandom selection and random mating, OCS and MCPed mating. For genetic diversity metrics, taking He and Ho as an example, the optimal strategy was GOCS (optimal contribution selection based on genomic information) with MCmarker mating. For genetic gain, the optimal strategy was truncation selection and MCmarker mating, followed by POCS (optimal contribution selection based on pedigree information) and MCmarker mating, truncation selection and MCPed mating. For the rate of inbreeding, the optimal strategy was SIREhalf-DAMfull selection and MCPed mating. Our findings can help breeding managers and farmers choose a more suitable and sustainable strategy for maintaining the genetic diversity and improving the genetic gain of local pig breeds.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Direct Heritability Estimates for Growth, Carcass and Precocity in Snails Cornu aspersum maximum (Synonym Helix aspersa maxima).","authors":"Thamires Aparecida Leôncio, Natalia Costa da Silva, José Teodoro de Paiva, Eula Regina Carrara, Claudiana de Fátima Miranda, Felipe André Oliveira Freitas, Kelvin Rodrigues Kelles, Matheus Aparecido Salviano Lourenço, Fernanda Larissa Cesar Santos, Graziela Tarôco, Aricia Chaves Zanetti Reis, Patrícia Lombardi de Souza, Leila de Genova Gaya","doi":"10.1111/jbg.12915","DOIUrl":"https://doi.org/10.1111/jbg.12915","url":null,"abstract":"<p><p>The aim was to estimate the heritabilities for accumulated weight gain between 60 and 90 days (WG1), 90 and 120 days (WG2) and 120 and 150 days of age (WG3), pre-slaughter body weight (PRE), meat-to-shell ratio (MS), carcass yield (CY) and age at first oviposition (AFO) in a population of snails Cornu aspersum maximum. Single (for heritabilities) and bi-trait (for genetic correlations) analyses were performed using Bayesian inference. The animal model included the random effect of animal and systematic effects of contemporary groups and covariates. The heritability estimates for WG1, WG2 and WG3 were 0.59, 0.60 and 0.32, respectively. Heritabilities for PRE, MS, CY and AFO ranged from 0.22 to 0.51. Environmental factors mostly influenced PRE among the studied traits. However, for carcass traits and age at first oviposition, the 95% HPD intervals of estimates were large. Only the genetic correlations between weight gains reached chain convergence. The correlation between WG1 and WG2 was 0.74, between WG2 and WG3 was 0.57, and between WG1 and WG3 was 0.22 (not statistically significant). In this sense, WG1 appears to be the optimal period for evaluating the body performance of snails. Genetic improvement in WG2 may be obtained by direct selection for WG1 in this population of Cornu aspersum maximum.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142774755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Practical Considerations When Using Mendelian Sampling Variances for Selection Decisions in Genomic Selection Programs.","authors":"Tobias A M Niehoff, Jan Ten Napel, Mario P L Calus","doi":"10.1111/jbg.12913","DOIUrl":"https://doi.org/10.1111/jbg.12913","url":null,"abstract":"<p><p>The purpose of this work was to test the application of selection criteria that consider the genetic variances of future generations. This has not been done previously in numerically large livestock breeding programs based on estimated rather than assumed known marker effects. A generic pure-line pig breeding program was simulated in which 40 males and 400 females were selected every generation. Daily gain was used as an example trait. Three variance-considering criteria as well as different reference population sizes were compared to investigate the effect of differences in genomic prediction accuracy on selection decisions. All variance-considering criteria retained more genetic variance than if selection was based on estimated breeding values (max. 20%). This effect was more pronounced for higher prediction accuracies and criteria assessing the variance more generations ahead. After 20 generations, the criterion with the longest planning horizon combined with the largest reference population resulted in a 2% higher genetic level of boars selected to produce finisher pigs. While the advantage of accounting for future generations diminished with lower accuracy or shorter planning horizons, the variance-considering criteria never performed worse than selection based on genomic estimated breeding values (GEBV) with respect to commercial genetic gain. We are reporting various accuracy metrics to help judge the effectiveness of using one of our tested criteria in real breeding programs. While we did not find large benefits for genetic gain when considering future variances in selection decisions, we also did not find negative side effects, while considerably more genetic variance was maintained. This means that using variance-considering criteria results in either equally good or better performance than truncation selection based on estimated breeding values. Our criteria can be applied to any genomic breeding program as long as phased genotypes, estimated marker effects and a genetic map are available.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142774889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic Diversity of U.S. Katahdin Hair Sheep.","authors":"Sara M Nilson, Joan M Burke, Gabrielle M Becker, Brenda M Murdoch, Jessica L Petersen, Ronald M Lewis","doi":"10.1111/jbg.12914","DOIUrl":"https://doi.org/10.1111/jbg.12914","url":null,"abstract":"<p><p>In the late 1950s, Katahdin hair sheep were developed as a composite breed of medium size and moderate prolificacy, with potential to express resistance to gastrointestinal nematodes. With increasing popularity and the recent adoption of genomic prediction in their genetic evaluation, there is a risk of decreasing variation with selection based on genomically enhanced estimated breeding values. While Katahdin pedigrees are readily available for monitoring diversity, they may not capture the entirety of genetic relationships. We aimed to characterise the genomic population structure and diversity present in the breed, and how these impact the size of a reference population necessary to achieve accurate genomic predictions. Genotypes of Katahdin sheep from 81 member flocks in the National Sheep Improvement Program (NSIP) were used. After quality control, there were 9704 animals and 31,984 autosomal single nucleotide polymorphisms analysed. Population structure was minimal as a single ancestral population explained 99.9% of the genetic variation among animals. The current N_e was estimated to be 150, and despite differences in trait heritabilities, the effect of N_e on the accuracy of genomic predictions suggested the breed should aim for a reference population size of 15,000 individuals. The average degree of inbreeding estimated from runs of homozygosity (ROH) was 16.6% ± 4.7. Four genomic regions of interest, previously associated with production traits, contained ROH shared among > 50% of the breed. Based on four additional methods, average genomic inbreeding coefficients ranged from 0.011 to 0.012. The current population structure and diversity of the breed reflects genetic connectedness across flocks due to the sharing of animals. Shared regions of ROH should be further explored for incorporation of functional effects into genomic predictions to increase selection gains. Negative impacts on genetic diversity due to genomic selection are not of immediate concern for Katahdin sheep engaged in NSIP.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142734822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}