Pub Date : 2025-02-17DOI: 10.1186/s12711-025-00953-7
Jean-Michel Elsen, Jérôme Raoul, Hélène Gilbert
Gametic variances can be predicted from the outcomes of a genomic prediction for any genotyped individual. This is widely used in plant breeding, applying the utility criterion (UC). This paper aims to examine the conditions to use UC for recurrent selection in livestock. Here, the UC for a selection candidate is the linear combination of the expected value of the future progeny (half of the candidate’s breeding value) and its predicted gametic variance weighted by a coefficient $$theta$$ to be optimized. First, generalizing previous results, we derived analytically the ratio of the variance of the candidate’s gametic variance and that of half of the candidate’s breeding value. This ratio depends strongly on the number of quantitative trait loci (QTL) affecting the trait and, to a lesser extent, on the distribution of QTL allele frequencies: highly unbalanced frequencies and a limited number of QTL (< 10) favor higher values of the ratio. Then, changes in average breeding values and genetic variances when recurrent selection in a population of infinite size is applied were analytically derived and analyzed for selection up to 15 generations: in this ideal situation, after 5 to 10 generations (depending on $$theta$$ ), the expected breeding values were higher with selection on UC and the genetic variance was always higher than with selection on estimated breeding values. To describe the potential of the UC in more general situations, simulations were applied to a population of 1000 males and 1000 females, with various selection rates, numbers and allele frequencies of QTL, and $$theta$$ . These simulations were performed assuming independent QTL with known positions and effects. The best values for $$theta$$ (i.e. providing the best genetic progress) were generally lower than 1, limiting the weight on the gametic variance. As expected from the analytical derivations, the gain in genetic progress from using UC was greatest when there were few QTL and allele frequencies were unbalanced, but they barely exceeded 5%. We conclude that the key factor to choose selection on UC rather than on estimated breeding values is the ratio between the variance of the gametic standard deviations and the variance of the breeding values (GEBV), which should be carefully evaluated.
{"title":"Is there an advantage of using genomic information to estimate gametic variances and improve recurrent selection in animal populations?","authors":"Jean-Michel Elsen, Jérôme Raoul, Hélène Gilbert","doi":"10.1186/s12711-025-00953-7","DOIUrl":"https://doi.org/10.1186/s12711-025-00953-7","url":null,"abstract":"Gametic variances can be predicted from the outcomes of a genomic prediction for any genotyped individual. This is widely used in plant breeding, applying the utility criterion (UC). This paper aims to examine the conditions to use UC for recurrent selection in livestock. Here, the UC for a selection candidate is the linear combination of the expected value of the future progeny (half of the candidate’s breeding value) and its predicted gametic variance weighted by a coefficient $$theta$$ to be optimized. First, generalizing previous results, we derived analytically the ratio of the variance of the candidate’s gametic variance and that of half of the candidate’s breeding value. This ratio depends strongly on the number of quantitative trait loci (QTL) affecting the trait and, to a lesser extent, on the distribution of QTL allele frequencies: highly unbalanced frequencies and a limited number of QTL (< 10) favor higher values of the ratio. Then, changes in average breeding values and genetic variances when recurrent selection in a population of infinite size is applied were analytically derived and analyzed for selection up to 15 generations: in this ideal situation, after 5 to 10 generations (depending on $$theta$$ ), the expected breeding values were higher with selection on UC and the genetic variance was always higher than with selection on estimated breeding values. To describe the potential of the UC in more general situations, simulations were applied to a population of 1000 males and 1000 females, with various selection rates, numbers and allele frequencies of QTL, and $$theta$$ . These simulations were performed assuming independent QTL with known positions and effects. The best values for $$theta$$ (i.e. providing the best genetic progress) were generally lower than 1, limiting the weight on the gametic variance. As expected from the analytical derivations, the gain in genetic progress from using UC was greatest when there were few QTL and allele frequencies were unbalanced, but they barely exceeded 5%. We conclude that the key factor to choose selection on UC rather than on estimated breeding values is the ratio between the variance of the gametic standard deviations and the variance of the breeding values (GEBV), which should be carefully evaluated.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"1 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143427027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-06DOI: 10.1186/s12711-025-00954-6
Pedro Sá, Rodrigo M. Godinho, Marta Gòdia, Claudia A. Sevillano, Barbara Harlizius, Ole Madsen, Henk Bovenhuis
The objectives of this study were to estimate genetic parameters and studying the influence of early-life and parental factors on the semen traits of boars. The dataset included measurements on 449,966 ejaculates evaluated using a Computer-Assisted Sperm Analysis (CASA) system from 5692 artificial insemination (AI) boars. In total, we considered 16 semen traits measured on fresh semen and 6 sperm motility traits measured on semen after storage. Early-life effects included the dam’s parity, ages of the dam and sire, gestation length, litter size, litter sex ratio, number of piglets born alive, number of litter mates at weaning, rearing length, and weight gain. A repeatability model accounting for effects at collection was used to (1) estimate heritabilities and repeatabilities for semen traits and genetic and phenotypic correlations between traits, (2) test the significance of early-life effects, (3) quantify the contribution of exclusive dam and sire inheritances to the phenotypic variation, i.e., mitochondrial DNA and the Y chromosome, identified using a pedigree-based approach, and (4) quantify the contribution of maternal and paternal environment effects to the phenotypic variation of semen traits. We reported heritabilities between 0.11 and 0.27 and repeatabilities between 0.20 and 0.65 for semen traits. Semen quality traits showed a skewed distribution, and their transformation significantly reduced their repeatability estimates. Motility traits measured after storage were genetically different from motility traits measured on fresh semen. Early-life had suggestive effects on a limited number of semen traits. Mitochondrial DNA and the Y chromosome did not explain a discerning proportion of the phenotypic variance and the effect of the paternal environment was also negligible. We estimated a significant maternal environment effect predominantly on sperm motility traits, explaining between 2.3 and 4.6% of the phenotypic variance. Including maternal environmental effects in the model reduced heritability estimates for sperm motility traits and total morphological abnormalities. Our findings indicate that trait transformation has a large effect on repeatability estimates of semen traits. Sperm motility traits measured on fresh semen are genetically different from sperm motility traits measured after storage. Early-life conditions can have an effect on later semen quantity and quality traits. Mitochondrial DNA and Y chromosome inheritances showed no effect on semen traits. Finally, we emphasize the importance of considering maternal effects when analysing semen traits, which results in lower heritability estimates.
本研究的目的是估算遗传参数，并研究早期生活和父母因素对公猪精液性状的影响。数据集包括使用计算机辅助精子分析（CASA）系统对5692头人工授精（AI）公猪的449 966次射精进行的测量。我们总共考虑了对新鲜精液测量的 16 个精液性状和对储存后精液测量的 6 个精子活力性状。早期生活的影响包括母猪的奇偶性、母猪和公猪的年龄、妊娠期长短、窝产仔数、窝产仔性别比、活产仔数、断奶时窝产仔数、饲养期长短和增重。采用重复性模型（考虑采集时的影响）：（1）估计精液性状的遗传力和重复性，以及性状之间的遗传和表型相关性；（2）检验早期生活影响的显著性；（3）量化母系和父系遗传对表型变异的贡献，即线粒体 DNA 和基因突变、(4) 量化母系和父系环境对精液性状表型变异的影响。我们发现精液性状的遗传率介于 0.11 和 0.27 之间，重复率介于 0.20 和 0.65 之间。精液质量性状呈偏斜分布，其转化显著降低了重复性估计值。贮藏后测定的精子活力性状与新鲜精液测定的精子活力性状存在遗传差异。早期生活对少数精液性状有提示性影响。线粒体 DNA 和 Y 染色体无法解释表型变异的明显比例，父系环境的影响也可以忽略不计。我们估计母源环境对精子活力性状的影响很大，可解释表型变异的 2.3% 到 4.6%。在模型中加入母源环境效应会降低精子活力性状和总形态异常的遗传率估计值。我们的研究结果表明，性状转化对精液性状的可重复性估计值有很大影响。在新鲜精液中测定的精子活力性状与贮存后测定的精子活力性状在遗传学上是不同的。早期生活条件会对后期精液数量和质量性状产生影响。线粒体 DNA 和 Y 染色体遗传对精液性状没有影响。最后，我们强调在分析精液性状时考虑母本效应的重要性，这将导致较低的遗传率估计值。
{"title":"Genetic parameters and parental and early-life effects of boar semen traits","authors":"Pedro Sá, Rodrigo M. Godinho, Marta Gòdia, Claudia A. Sevillano, Barbara Harlizius, Ole Madsen, Henk Bovenhuis","doi":"10.1186/s12711-025-00954-6","DOIUrl":"https://doi.org/10.1186/s12711-025-00954-6","url":null,"abstract":"The objectives of this study were to estimate genetic parameters and studying the influence of early-life and parental factors on the semen traits of boars. The dataset included measurements on 449,966 ejaculates evaluated using a Computer-Assisted Sperm Analysis (CASA) system from 5692 artificial insemination (AI) boars. In total, we considered 16 semen traits measured on fresh semen and 6 sperm motility traits measured on semen after storage. Early-life effects included the dam’s parity, ages of the dam and sire, gestation length, litter size, litter sex ratio, number of piglets born alive, number of litter mates at weaning, rearing length, and weight gain. A repeatability model accounting for effects at collection was used to (1) estimate heritabilities and repeatabilities for semen traits and genetic and phenotypic correlations between traits, (2) test the significance of early-life effects, (3) quantify the contribution of exclusive dam and sire inheritances to the phenotypic variation, i.e., mitochondrial DNA and the Y chromosome, identified using a pedigree-based approach, and (4) quantify the contribution of maternal and paternal environment effects to the phenotypic variation of semen traits. We reported heritabilities between 0.11 and 0.27 and repeatabilities between 0.20 and 0.65 for semen traits. Semen quality traits showed a skewed distribution, and their transformation significantly reduced their repeatability estimates. Motility traits measured after storage were genetically different from motility traits measured on fresh semen. Early-life had suggestive effects on a limited number of semen traits. Mitochondrial DNA and the Y chromosome did not explain a discerning proportion of the phenotypic variance and the effect of the paternal environment was also negligible. We estimated a significant maternal environment effect predominantly on sperm motility traits, explaining between 2.3 and 4.6% of the phenotypic variance. Including maternal environmental effects in the model reduced heritability estimates for sperm motility traits and total morphological abnormalities. Our findings indicate that trait transformation has a large effect on repeatability estimates of semen traits. Sperm motility traits measured on fresh semen are genetically different from sperm motility traits measured after storage. Early-life conditions can have an effect on later semen quantity and quality traits. Mitochondrial DNA and Y chromosome inheritances showed no effect on semen traits. Finally, we emphasize the importance of considering maternal effects when analysing semen traits, which results in lower heritability estimates.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"9 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143191737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-04DOI: 10.1186/s12711-025-00951-9
Ana-Marija Križanac, Christian Reimer, Johannes Heise, Zengting Liu, Jennie E. Pryce, Jörn Bennewitz, Georg Thaller, Clemens Falker-Gieske, Jens Tetens
Milk production traits are complex and influenced by many genetic and environmental factors. Although extensive research has been performed for these traits, with many associations unveiled thus far, due to their crucial economic importance, complex genetic architecture, and the fact that causal variants in cattle are still scarce, there is a need for a better understanding of their genetic background. In this study, we aimed to identify new candidate loci associated with milk production traits in German Holstein cattle, the most important dairy breed in Germany and worldwide. For that purpose, 180,217 cattle were imputed to the sequence level and large-scale genome-wide association study (GWAS) followed by fine-mapping and evolutionary and functional annotation were carried out to identify and prioritize new association signals. Using the imputed sequence data of a large cattle dataset, we identified 50,876 significant variants, confirming many known and identifying previously unreported candidate variants for milk (MY), fat (FY), and protein yield (PY). Genome-wide significant signals were fine-mapped with the Bayesian approach that determines the credible variant sets and generates the probability of causality for each signal. The variants with the highest probabilities of being causal were further classified using external information about the function and evolution, making the prioritization for subsequent validation experiments easier. The top potential causal variants determined with fine-mapping explained a large percentage of genetic variance compared to random ones; 178 variants explained 11.5%, 104 explained 7.7%, and 68 variants explained 3.9% of the variance for MY, FY, and PY, respectively, demonstrating the potential for causality. Our findings proved the power of large samples and sequence-based GWAS in detecting new association signals. In order to fully exploit the power of GWAS, one should aim at very large samples combined with whole-genome sequence data. These can also come with both computational and time burdens, as presented in our study. Although milk production traits in cattle are comprehensively investigated, the genetic background of these traits is still not fully understood, with the potential for many new associations to be revealed, as shown. With constantly growing sample sizes, we expect more insights into the genetic architecture of milk production traits in the future.
{"title":"Sequence-based GWAS in 180,000 German Holstein cattle reveals new candidate variants for milk production traits","authors":"Ana-Marija Križanac, Christian Reimer, Johannes Heise, Zengting Liu, Jennie E. Pryce, Jörn Bennewitz, Georg Thaller, Clemens Falker-Gieske, Jens Tetens","doi":"10.1186/s12711-025-00951-9","DOIUrl":"https://doi.org/10.1186/s12711-025-00951-9","url":null,"abstract":"Milk production traits are complex and influenced by many genetic and environmental factors. Although extensive research has been performed for these traits, with many associations unveiled thus far, due to their crucial economic importance, complex genetic architecture, and the fact that causal variants in cattle are still scarce, there is a need for a better understanding of their genetic background. In this study, we aimed to identify new candidate loci associated with milk production traits in German Holstein cattle, the most important dairy breed in Germany and worldwide. For that purpose, 180,217 cattle were imputed to the sequence level and large-scale genome-wide association study (GWAS) followed by fine-mapping and evolutionary and functional annotation were carried out to identify and prioritize new association signals. Using the imputed sequence data of a large cattle dataset, we identified 50,876 significant variants, confirming many known and identifying previously unreported candidate variants for milk (MY), fat (FY), and protein yield (PY). Genome-wide significant signals were fine-mapped with the Bayesian approach that determines the credible variant sets and generates the probability of causality for each signal. The variants with the highest probabilities of being causal were further classified using external information about the function and evolution, making the prioritization for subsequent validation experiments easier. The top potential causal variants determined with fine-mapping explained a large percentage of genetic variance compared to random ones; 178 variants explained 11.5%, 104 explained 7.7%, and 68 variants explained 3.9% of the variance for MY, FY, and PY, respectively, demonstrating the potential for causality. Our findings proved the power of large samples and sequence-based GWAS in detecting new association signals. In order to fully exploit the power of GWAS, one should aim at very large samples combined with whole-genome sequence data. These can also come with both computational and time burdens, as presented in our study. Although milk production traits in cattle are comprehensively investigated, the genetic background of these traits is still not fully understood, with the potential for many new associations to be revealed, as shown. With constantly growing sample sizes, we expect more insights into the genetic architecture of milk production traits in the future.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"25 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143125318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-22DOI: 10.1186/s12711-025-00949-3
Ziyi Kang, Jie Kong, Qi Li, Juan Sui, Ping Dai, Kun Luo, Xianhong Meng, Baolong Chen, Jiawang Cao, Jian Tan, Qiang Fu, Qun Xing, Sheng Luan
Family-based selective breeding programs typically employ both between-family and within-family selection in aquaculture. However, these programs may exhibit a reduced genetic gain in the presence of a genotype by environment interactions (G × E) when employing biosecurity-based breeding schemes (BS), compared to non-biosecurity-based breeding schemes (NBS). Fortunately, genomic selection shows promise in improving genetic gain by taking within-family variance into account. Stochastic simulation was employed to evaluate genetic gain and G × E trends in BS for improving the body weight of L. vannamei, considering selective genotyping strategies for test group (TG) at a commercial farm environment (CE), the number individuals of the selection group (SG) genotyped at nucleus breeding center (NE), and varying levels of G × E. The loss of genetic gain in BS ranged from 9.4 to 38.9% in pedigree-based selection and was more pronounced when G × E was stronger, as quantified by a lower genetic correlation for body weight between NE and CE. Genomic selection, particularly with selective genotyping of TG individuals with extreme performance, effectively offset the loss of genetic gain. With a genetic correlation of 0.8, genotyping 20 SG individuals in each candidate family achieved 93.2% of the genetic gain observed for NBS. However, when the genetic correlation fell below 0.5, the number of genotyped SG individuals per family had to be increased to 50 or more. Genetic gain improved by on average 9.4% when the number of genotyped SG individuals rose from 20 to 50, but the increase in genetic gain averaged only 2.4% when expanding from 50 to 80 individuals genotyped. In addition, the genetic correlation decreased by on average 0.13 over 30 generations of selection when performing BS and the genetic correlation fluctuated across generations. Genomic selection can effectively compensate for the loss of genetic gain in BS due to G × E. However, the number of genotyped SG individuals and the level of G × E significantly affected the extra genetic gain from genomic selection. A family-based BS selective breeding program should monitor the level of G × E and genotyping 50 SG individuals per candidate family to minimize the loss of genetic gain due to G × E, unless the level of G × E is confirmed to be low.
{"title":"Genomic selection strategies to overcome genotype by environment interactions in biosecurity-based aquaculture breeding programs","authors":"Ziyi Kang, Jie Kong, Qi Li, Juan Sui, Ping Dai, Kun Luo, Xianhong Meng, Baolong Chen, Jiawang Cao, Jian Tan, Qiang Fu, Qun Xing, Sheng Luan","doi":"10.1186/s12711-025-00949-3","DOIUrl":"https://doi.org/10.1186/s12711-025-00949-3","url":null,"abstract":"Family-based selective breeding programs typically employ both between-family and within-family selection in aquaculture. However, these programs may exhibit a reduced genetic gain in the presence of a genotype by environment interactions (G × E) when employing biosecurity-based breeding schemes (BS), compared to non-biosecurity-based breeding schemes (NBS). Fortunately, genomic selection shows promise in improving genetic gain by taking within-family variance into account. Stochastic simulation was employed to evaluate genetic gain and G × E trends in BS for improving the body weight of L. vannamei, considering selective genotyping strategies for test group (TG) at a commercial farm environment (CE), the number individuals of the selection group (SG) genotyped at nucleus breeding center (NE), and varying levels of G × E. The loss of genetic gain in BS ranged from 9.4 to 38.9% in pedigree-based selection and was more pronounced when G × E was stronger, as quantified by a lower genetic correlation for body weight between NE and CE. Genomic selection, particularly with selective genotyping of TG individuals with extreme performance, effectively offset the loss of genetic gain. With a genetic correlation of 0.8, genotyping 20 SG individuals in each candidate family achieved 93.2% of the genetic gain observed for NBS. However, when the genetic correlation fell below 0.5, the number of genotyped SG individuals per family had to be increased to 50 or more. Genetic gain improved by on average 9.4% when the number of genotyped SG individuals rose from 20 to 50, but the increase in genetic gain averaged only 2.4% when expanding from 50 to 80 individuals genotyped. In addition, the genetic correlation decreased by on average 0.13 over 30 generations of selection when performing BS and the genetic correlation fluctuated across generations. Genomic selection can effectively compensate for the loss of genetic gain in BS due to G × E. However, the number of genotyped SG individuals and the level of G × E significantly affected the extra genetic gain from genomic selection. A family-based BS selective breeding program should monitor the level of G × E and genotyping 50 SG individuals per candidate family to minimize the loss of genetic gain due to G × E, unless the level of G × E is confirmed to be low.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"17 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143020654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-13DOI: 10.1186/s12711-024-00945-z
Simona Antonios, Silvia T. Rodríguez-Ramilo, Andres Legarra, Jean-Michel Astruc, Luis Varona, Zulma G. Vitezica
The magnitude of inbreeding depression depends on the recessive burden of the individual, which can be traced back to the hidden (recessive) inbreeding load among ancestors. However, these ancestors carry different alleles at potentially deleterious loci and therefore there is individual variability of this inbreeding load. Estimation of the additive genetic value for inbreeding load is possible using a decomposition of inbreeding in partial inbreeding components due to ancestors. Both the magnitude of variation in partial inbreeding components and the additive genetic variance of inbreeding loads are largely unknown. Our study had three objectives. First, based on substitution effect under non-random matings, we showed analytically that inbreeding load of an ancestor can be expressed as an additive genetic effect. Second, we analysed the structure of individual inbreeding by examining the contributions of specific ancestors/founders using the concept of partial inbreeding coefficients in three French dairy sheep populations (Basco-Béarnaise, Manech Tête Noire and Manech Tête Rousse). Third, we included these coefficients in a mixed model as random regression covariates, to predict genetic variance and breeding values of the inbreeding load for milk yield in the same breeds. Pedigrees included 190,276, 166,028 and 633,655 animals of Basco-Béarnaise, Manech Tête Noire and Manech Tête Rousse, respectively, born between 1985 and 2021. A fraction of 99.1% of the partial inbreeding coefficients were lower than 0.01 in all breeds, meaning that in practice inbreeding occurs in pedigree loops that span several generations backwards. Less than 5% ancestors generate inbreeding, because mating is essentially between unrelated individuals. Inbreeding load estimations involved 658,731, 541,180 and 2,168,454 records of yearly milk yield from 178,123, 151,863 and 596,586 females in Basco-Béarnaise, Manech Tête Noire and Manech Tête Rousse, respectively. Adding the inbreeding load effect to the model improved the fitting (values of the statistic Likelihood Ratio Test between 132 and 383) for milk yield in the three breeds. The inbreeding load variances were equal to 11,804 and 9435 L squared of milk yield for a fully inbred (100%) descendant in Manech Tête Noire and Manech Tête Rousse. In Basco-Béarnaise, the estimate of the inbreeding load variance (11,804) was not significantly different from zero. The correlations between (direct effect) additive genetic and inbreeding load effects were − 0.09, − 0.08 and − 0.12 in Basco-Béarnaise, Manech Tête Noire and Manech Tête Rousse. The decomposition of inbreeding in partial coefficients in these populations shows that inbreeding is mostly due to several small contributions of ancestors (lower than 0.001) going back several generations (5 to 7 generations), which is according to the policy of avoiding close matings. There is variation of inbreeding load among animals, although its magnitude does not seem enough to warr
近交抑制的程度取决于个体的隐性负担，这可以追溯到祖先之间的隐性近交负荷。然而，这些祖先在潜在的有害位点上携带不同的等位基因，因此这种近交负荷存在个体差异。通过对由于祖先的部分近交成分的近交进行分解，可以估计近交负荷的加性遗传值。部分近交成分的变异幅度和近交负荷的加性遗传变异在很大程度上都是未知的。我们的研究有三个目标。首先，基于非随机交配下的替代效应，分析表明祖先近交负荷可以表达为加性遗传效应。其次，我们利用部分近交系数的概念，通过考察特定祖先/建立者对三个法国乳羊群体（basco - b arnaise， Manech Tête Noire和Manech Tête Rousse）的贡献，分析了个体近交的结构。第三，将这些系数作为随机回归协变量纳入混合模型，预测同一品种近交负荷对产奶量的遗传方差和育种值。在1985年至2021年间出生的basco - b阿纳斯，Manech Tête Noire和Manech Tête Rousse的血统分别为190,276,166,028和633,655只动物。99.1%的部分近交系数在所有品种中都低于0.01，这意味着在实践中近交发生在跨越几代的谱系循环中。只有不到5%的祖先会近亲交配，因为交配基本上是在没有血缘关系的个体之间进行的。近交负荷估计分别涉及basco - bassarnaise、Manech Tête Noire和Manech Tête Rousse地区178,123、151,863和596,586头雌性奶牛的年产奶量658,731、541,180和2168,454条记录。在模型中加入近交系负荷效应，提高了3个品种产奶量的拟合（统计似然比检验值在132 ~ 383之间）。全自交系（100%）后代产奶量的近交系负荷方差分别为11,804和9435 L平方。在basco - bsamarnaise中，近交负荷方差（11,804）的估计值与零没有显著差异。basco - bassarnaise、Manech Tête Noire和Manech Tête Rousse的加性遗传负荷效应（直接效应）与近交负荷效应的相关系数分别为- 0.09、- 0.08和- 0.12。近交的部分系数分解表明，近交主要是由于几代（5 ~ 7代）祖先的少量贡献（小于0.001），这符合避免近交的策略。动物之间的近亲繁殖负荷是有差异的，尽管其大小似乎不足以保证根据这一标准进行选择。
{"title":"Genetic inbreeding load and its individual prediction for milk yield in French dairy sheep","authors":"Simona Antonios, Silvia T. Rodríguez-Ramilo, Andres Legarra, Jean-Michel Astruc, Luis Varona, Zulma G. Vitezica","doi":"10.1186/s12711-024-00945-z","DOIUrl":"https://doi.org/10.1186/s12711-024-00945-z","url":null,"abstract":"The magnitude of inbreeding depression depends on the recessive burden of the individual, which can be traced back to the hidden (recessive) inbreeding load among ancestors. However, these ancestors carry different alleles at potentially deleterious loci and therefore there is individual variability of this inbreeding load. Estimation of the additive genetic value for inbreeding load is possible using a decomposition of inbreeding in partial inbreeding components due to ancestors. Both the magnitude of variation in partial inbreeding components and the additive genetic variance of inbreeding loads are largely unknown. Our study had three objectives. First, based on substitution effect under non-random matings, we showed analytically that inbreeding load of an ancestor can be expressed as an additive genetic effect. Second, we analysed the structure of individual inbreeding by examining the contributions of specific ancestors/founders using the concept of partial inbreeding coefficients in three French dairy sheep populations (Basco-Béarnaise, Manech Tête Noire and Manech Tête Rousse). Third, we included these coefficients in a mixed model as random regression covariates, to predict genetic variance and breeding values of the inbreeding load for milk yield in the same breeds. Pedigrees included 190,276, 166,028 and 633,655 animals of Basco-Béarnaise, Manech Tête Noire and Manech Tête Rousse, respectively, born between 1985 and 2021. A fraction of 99.1% of the partial inbreeding coefficients were lower than 0.01 in all breeds, meaning that in practice inbreeding occurs in pedigree loops that span several generations backwards. Less than 5% ancestors generate inbreeding, because mating is essentially between unrelated individuals. Inbreeding load estimations involved 658,731, 541,180 and 2,168,454 records of yearly milk yield from 178,123, 151,863 and 596,586 females in Basco-Béarnaise, Manech Tête Noire and Manech Tête Rousse, respectively. Adding the inbreeding load effect to the model improved the fitting (values of the statistic Likelihood Ratio Test between 132 and 383) for milk yield in the three breeds. The inbreeding load variances were equal to 11,804 and 9435 L squared of milk yield for a fully inbred (100%) descendant in Manech Tête Noire and Manech Tête Rousse. In Basco-Béarnaise, the estimate of the inbreeding load variance (11,804) was not significantly different from zero. The correlations between (direct effect) additive genetic and inbreeding load effects were − 0.09, − 0.08 and − 0.12 in Basco-Béarnaise, Manech Tête Noire and Manech Tête Rousse. The decomposition of inbreeding in partial coefficients in these populations shows that inbreeding is mostly due to several small contributions of ancestors (lower than 0.001) going back several generations (5 to 7 generations), which is according to the policy of avoiding close matings. There is variation of inbreeding load among animals, although its magnitude does not seem enough to warr","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"50 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142968270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-30DOI: 10.1186/s12711-024-00944-0
Andrei A. Kudinov, Antti Kause
Sex identification in farmed fish is important for the management of fish stocks and breeding programs, but identification based on visual characteristics is typically difficult or impossible in juvenile or premature fish. The amount of genomic data obtained from farmed fish is rapidly growing with the implementation of genomic selection in aquaculture. In comparison to mammals and birds, ray-finned fishes exhibit a greater diversity of sex determination systems, with an absence of conserved genomic regions. A group of genomic markers located on a standard genotyping array has been reported to potentially be linked with sex determination in rainbow trout. However, the set of markers suitable for sex identification may vary between populations. Sex identification from genomic data is usually performed using probabilistic methods, where suitable markers are known beforehand. In our study, we demonstrated the use of the Extreme Gradient Boosting approach from the supervised machine learning gradient boost framework to predict sex from unimputed genomic data, when the suitability of the markers was unknown a priori. The accuracy of the method was assessed using four simulated datasets with different genotyping error rates and one real dataset from the Finnish Rainbow Trout Breeding Program. The method showed high prediction quality on both simulated and real datasets. For simulated datasets with low (5%) and high (50%) genotyping error rates, the accuracies were 1.0 and 0.60, respectively. In the real data, the method achieved a prediction accuracy of 98%, which is suitable for routine use.
{"title":"Sex identification in rainbow trout using genomic information and machine learning","authors":"Andrei A. Kudinov, Antti Kause","doi":"10.1186/s12711-024-00944-0","DOIUrl":"https://doi.org/10.1186/s12711-024-00944-0","url":null,"abstract":"Sex identification in farmed fish is important for the management of fish stocks and breeding programs, but identification based on visual characteristics is typically difficult or impossible in juvenile or premature fish. The amount of genomic data obtained from farmed fish is rapidly growing with the implementation of genomic selection in aquaculture. In comparison to mammals and birds, ray-finned fishes exhibit a greater diversity of sex determination systems, with an absence of conserved genomic regions. A group of genomic markers located on a standard genotyping array has been reported to potentially be linked with sex determination in rainbow trout. However, the set of markers suitable for sex identification may vary between populations. Sex identification from genomic data is usually performed using probabilistic methods, where suitable markers are known beforehand. In our study, we demonstrated the use of the Extreme Gradient Boosting approach from the supervised machine learning gradient boost framework to predict sex from unimputed genomic data, when the suitability of the markers was unknown a priori. The accuracy of the method was assessed using four simulated datasets with different genotyping error rates and one real dataset from the Finnish Rainbow Trout Breeding Program. The method showed high prediction quality on both simulated and real datasets. For simulated datasets with low (5%) and high (50%) genotyping error rates, the accuracies were 1.0 and 0.60, respectively. In the real data, the method achieved a prediction accuracy of 98%, which is suitable for routine use.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"4 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142901813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The genome-wide association study (GWAS) is a powerful method for mapping quantitative trait loci (QTL). However, standard GWAS can detect only QTL that segregate in the mapping population. Crossing populations with different characteristics increases genetic variability but F2 or back-crosses lack mapping resolution due to the limited number of recombination events. This drawback can be overcome with advanced intercross line (AIL) populations, which increase the number recombination events and provide a more accurate mapping resolution. Recent studies in humans have revealed ancestry-dependent genetic architecture and shown the effectiveness of admixture mapping in admixed populations. Through the incorporation of line-of-origin effects and GWAS on an F9 AIL population, we identified genes that affect body weight at eight weeks of age (BW8) in chickens. The proposed ancestral-haplotype-based GWAS (testing only the origin regardless of the alleles) revealed three new QTLs on GGA12, GGA15, and GGA20. By using the concepts of ancestral homozygotes (individuals that carry two haplotypes of the same origin) and ancestral heterozygotes (carrying one haplotype of each origin), we identified 632 loci that exhibited high-parent (the heterozygote is better than both parents) and mid-parent (the heterozygote is better than the median of the parents) dominance across 12 chromosomes. Out of the 199 genes associated with BW8, EYA1, PDE1C, and MYC were identified as the best candidate genes for further validation. In addition to the candidate genes reported in this study, our research demonstrates the effectiveness of incorporating ancestral information in population genetic analyses, which can be broadly applicable for genetic mapping in populations generated by ancestors with distinct phenotypes and genetic backgrounds. Our methods can benefit both geneticists and biologists interested in the genetic determinism of complex traits.
{"title":"Haplotype analysis incorporating ancestral origins identified novel genetic loci associated with chicken body weight using an advanced intercross line","authors":"Lina Bu, Yuzhe Wang, Lizhi Tan, Zilong Wen, Xiaoxiang Hu, Zhiwu Zhang, Yiqiang Zhao","doi":"10.1186/s12711-024-00946-y","DOIUrl":"https://doi.org/10.1186/s12711-024-00946-y","url":null,"abstract":"The genome-wide association study (GWAS) is a powerful method for mapping quantitative trait loci (QTL). However, standard GWAS can detect only QTL that segregate in the mapping population. Crossing populations with different characteristics increases genetic variability but F2 or back-crosses lack mapping resolution due to the limited number of recombination events. This drawback can be overcome with advanced intercross line (AIL) populations, which increase the number recombination events and provide a more accurate mapping resolution. Recent studies in humans have revealed ancestry-dependent genetic architecture and shown the effectiveness of admixture mapping in admixed populations. Through the incorporation of line-of-origin effects and GWAS on an F9 AIL population, we identified genes that affect body weight at eight weeks of age (BW8) in chickens. The proposed ancestral-haplotype-based GWAS (testing only the origin regardless of the alleles) revealed three new QTLs on GGA12, GGA15, and GGA20. By using the concepts of ancestral homozygotes (individuals that carry two haplotypes of the same origin) and ancestral heterozygotes (carrying one haplotype of each origin), we identified 632 loci that exhibited high-parent (the heterozygote is better than both parents) and mid-parent (the heterozygote is better than the median of the parents) dominance across 12 chromosomes. Out of the 199 genes associated with BW8, EYA1, PDE1C, and MYC were identified as the best candidate genes for further validation. In addition to the candidate genes reported in this study, our research demonstrates the effectiveness of incorporating ancestral information in population genetic analyses, which can be broadly applicable for genetic mapping in populations generated by ancestors with distinct phenotypes and genetic backgrounds. Our methods can benefit both geneticists and biologists interested in the genetic determinism of complex traits.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"64 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142858434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-18DOI: 10.1186/s12711-024-00947-x
Jón H. Eiríksson, Þórdís Þórarinsdóttir, Egill Gautason
Scrapie is an infectious prion disease in sheep. Selective breeding for resistant genotypes of the prion protein gene (PRNP) is an effective way to prevent scrapie outbreaks. Genotyping all selection candidates in a population is expensive but existing pedigree records can help infer the probabilities of genotypes in relatives of genotyped animals. We used linear models to predict allele content for the various PRNP alleles found in Icelandic sheep and compiled the available estimates of relative scrapie susceptibility (RSS) associated with PRNP genotypes from the literature. Using the predicted allele content and the genotypic RSS we calculated estimated breeding values (EBV) for RSS. We tested the predictions on simulated data under different scenarios that varied in the proportion of genotyped sheep, genotyping strategy, pedigree recording accuracy, genotyping error rates and assumed heritability of allele content. Prediction of allele content for rare alleles was less successful than for alleles with moderate frequencies. The accuracy of allele content and RSS EBV predictions was not affected by the assumed heritability, but the dispersion of prediction was affected. In a scenario where 40% of rams were genotyped and no errors in genotyping or recorded pedigree, the accuracy of RSS EBV for ungenotyped selection candidates was 0.49. If only 20% of rams were genotyped, or rams and ewes were genotyped randomly, or there were 10% pedigree errors, or there were 2% genotyping errors, the accuracy decreased by 0.07, 0.08, 0.03 and 0.04, respectively. With empirical data, the accuracy of RSS EBV for ungenotyped sheep was 0.46–0.65. A linear model for predicting allele content for the PRNP gene, combined with estimates of relative susceptibility associated with PRNP genotypes, can provide RSS EBV for scrapie resistance for ungenotyped selection candidates with accuracy up to 0.65. These RSS EBV can complement selection strategies based on PRNP genotypes, especially in populations where resistant genotypes are rare.
{"title":"Predicted breeding values for relative scrapie susceptibility for genotyped and ungenotyped sheep","authors":"Jón H. Eiríksson, Þórdís Þórarinsdóttir, Egill Gautason","doi":"10.1186/s12711-024-00947-x","DOIUrl":"https://doi.org/10.1186/s12711-024-00947-x","url":null,"abstract":"Scrapie is an infectious prion disease in sheep. Selective breeding for resistant genotypes of the prion protein gene (PRNP) is an effective way to prevent scrapie outbreaks. Genotyping all selection candidates in a population is expensive but existing pedigree records can help infer the probabilities of genotypes in relatives of genotyped animals. We used linear models to predict allele content for the various PRNP alleles found in Icelandic sheep and compiled the available estimates of relative scrapie susceptibility (RSS) associated with PRNP genotypes from the literature. Using the predicted allele content and the genotypic RSS we calculated estimated breeding values (EBV) for RSS. We tested the predictions on simulated data under different scenarios that varied in the proportion of genotyped sheep, genotyping strategy, pedigree recording accuracy, genotyping error rates and assumed heritability of allele content. Prediction of allele content for rare alleles was less successful than for alleles with moderate frequencies. The accuracy of allele content and RSS EBV predictions was not affected by the assumed heritability, but the dispersion of prediction was affected. In a scenario where 40% of rams were genotyped and no errors in genotyping or recorded pedigree, the accuracy of RSS EBV for ungenotyped selection candidates was 0.49. If only 20% of rams were genotyped, or rams and ewes were genotyped randomly, or there were 10% pedigree errors, or there were 2% genotyping errors, the accuracy decreased by 0.07, 0.08, 0.03 and 0.04, respectively. With empirical data, the accuracy of RSS EBV for ungenotyped sheep was 0.46–0.65. A linear model for predicting allele content for the PRNP gene, combined with estimates of relative susceptibility associated with PRNP genotypes, can provide RSS EBV for scrapie resistance for ungenotyped selection candidates with accuracy up to 0.65. These RSS EBV can complement selection strategies based on PRNP genotypes, especially in populations where resistant genotypes are rare.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"54 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142849415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-17DOI: 10.1186/s12711-024-00941-3
Yvonne C. J. Wientjes, Katrijn Peeters, Piter Bijma, Abe E. Huisman, Mario P. L. Calus
Genetic selection improves a population by increasing the frequency of favorable alleles. Understanding and monitoring allele frequency changes is, therefore, important to obtain more insight into the long-term effects of selection. This study aimed to investigate changes in allele frequencies and in results of genome-wide association studies (GWAS), and how those two are related to each other. This was studied in two maternal pig lines where selection was based on a broad selection index. Genotypes and phenotypes were available from 2015 to 2021. Several large changes in allele frequencies over the years were observed in both lines. The largest allele frequency changes were not larger than expected under drift based on gene dropping simulations, but the average allele frequency change was larger with selection. Moreover, several significant regions were found in the GWAS for the traits under selection, but those regions did not overlap with regions with larger allele frequency changes. No significant GWAS regions were found for the selection index in both lines, which included multiple traits, indicating that the index is affected by many loci of small effect. Additionally, many significant regions showed pleiotropic, and often antagonistic, associations with other traits under selection. This reduces the selection pressure on those regions, which can explain why those regions are still segregating, although the traits have been under selection for several generations. Across the years, only small changes in Manhattan plots were found, indicating that the genetic architecture was reasonably constant. No significant GWAS regions were found for any of the traits under selection among the regions with the largest changes in allele frequency, and the correlation between significance level of marker associations and changes in allele frequency over one generation was close to zero for all traits. Moreover, the largest changes in allele frequency could be explained by drift and were not necessarily a result of selection. This is probably because selection acted on a broad index for which no significant GWAS regions were found. Our results show that selecting on a broad index spreads the selection pressure across the genome, thereby limiting allele frequency changes.
{"title":"Changes in allele frequencies and genetic architecture due to selection in two pig populations","authors":"Yvonne C. J. Wientjes, Katrijn Peeters, Piter Bijma, Abe E. Huisman, Mario P. L. Calus","doi":"10.1186/s12711-024-00941-3","DOIUrl":"https://doi.org/10.1186/s12711-024-00941-3","url":null,"abstract":"Genetic selection improves a population by increasing the frequency of favorable alleles. Understanding and monitoring allele frequency changes is, therefore, important to obtain more insight into the long-term effects of selection. This study aimed to investigate changes in allele frequencies and in results of genome-wide association studies (GWAS), and how those two are related to each other. This was studied in two maternal pig lines where selection was based on a broad selection index. Genotypes and phenotypes were available from 2015 to 2021. Several large changes in allele frequencies over the years were observed in both lines. The largest allele frequency changes were not larger than expected under drift based on gene dropping simulations, but the average allele frequency change was larger with selection. Moreover, several significant regions were found in the GWAS for the traits under selection, but those regions did not overlap with regions with larger allele frequency changes. No significant GWAS regions were found for the selection index in both lines, which included multiple traits, indicating that the index is affected by many loci of small effect. Additionally, many significant regions showed pleiotropic, and often antagonistic, associations with other traits under selection. This reduces the selection pressure on those regions, which can explain why those regions are still segregating, although the traits have been under selection for several generations. Across the years, only small changes in Manhattan plots were found, indicating that the genetic architecture was reasonably constant. No significant GWAS regions were found for any of the traits under selection among the regions with the largest changes in allele frequency, and the correlation between significance level of marker associations and changes in allele frequency over one generation was close to zero for all traits. Moreover, the largest changes in allele frequency could be explained by drift and were not necessarily a result of selection. This is probably because selection acted on a broad index for which no significant GWAS regions were found. Our results show that selecting on a broad index spreads the selection pressure across the genome, thereby limiting allele frequency changes.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"26 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142832236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-13DOI: 10.1186/s12711-024-00940-4
Christian Stricker, Rohan L. Fernando, Albrecht Melchinger, Hans-Juergen Auinger, Chris-Carolin Schoen
Accuracy of genomic prediction depends on the heritability of the trait, the size of the training set, the relationship of the candidates to the training set, and the $$text {Min}(N_{text {QTL}},M_e)$$ , where $$N_{text {QTL}}$$ is the number of QTL and $$M_e$$ is the number of independently segregating chromosomal segments. Due to LD, the number $$Q_e$$ of independently segregating QTL (effective QTL) can be lower than $$text {Min}(N_{text {QTL}},M_e)$$ . In this paper, we show that $$Q_e$$ is inversely associated with the trait-specific genomic relationship of a candidate to the training set. This provides an explanation for the inverse association between $$Q_e$$ and the accuracy of prediction. To quantify the genomic relationship of a candidate to all members of the training set, we considered the $$k^2$$ statistic that has been previously used for this purpose. It quantifies how well the marker covariate vector of a candidate can be represented as a linear combination of the rows of the marker covariate matrix of the training set. In this paper, we used Bayesian regression to make this statistic trait specific and argue that the trait-specific genomic relationship of a candidate to the training set is inversely associated with $$Q_e$$ . Simulation was used to demonstrate the dependence of the trait-specific $$k^2$$ statistic on $$Q_e$$ , which is related to $$N_{text {QTL}}$$ . The posterior distributions of the trait-specific $$k^2$$ statistic showed that the trait-specific genomic relationship between a candidate and the training set is inversely associated to $$Q_e$$ and $$N_{text {QTL}}$$ . Further, we show that trait-specific genomic relationship between a candidate and the training set is directly related to the size of the training set.
{"title":"On the inverse association between the number of QTL and the trait-specific genomic relationship of a candidate to the training set.","authors":"Christian Stricker, Rohan L. Fernando, Albrecht Melchinger, Hans-Juergen Auinger, Chris-Carolin Schoen","doi":"10.1186/s12711-024-00940-4","DOIUrl":"https://doi.org/10.1186/s12711-024-00940-4","url":null,"abstract":"Accuracy of genomic prediction depends on the heritability of the trait, the size of the training set, the relationship of the candidates to the training set, and the $$text {Min}(N_{text {QTL}},M_e)$$ , where $$N_{text {QTL}}$$ is the number of QTL and $$M_e$$ is the number of independently segregating chromosomal segments. Due to LD, the number $$Q_e$$ of independently segregating QTL (effective QTL) can be lower than $$text {Min}(N_{text {QTL}},M_e)$$ . In this paper, we show that $$Q_e$$ is inversely associated with the trait-specific genomic relationship of a candidate to the training set. This provides an explanation for the inverse association between $$Q_e$$ and the accuracy of prediction. To quantify the genomic relationship of a candidate to all members of the training set, we considered the $$k^2$$ statistic that has been previously used for this purpose. It quantifies how well the marker covariate vector of a candidate can be represented as a linear combination of the rows of the marker covariate matrix of the training set. In this paper, we used Bayesian regression to make this statistic trait specific and argue that the trait-specific genomic relationship of a candidate to the training set is inversely associated with $$Q_e$$ . Simulation was used to demonstrate the dependence of the trait-specific $$k^2$$ statistic on $$Q_e$$ , which is related to $$N_{text {QTL}}$$ . The posterior distributions of the trait-specific $$k^2$$ statistic showed that the trait-specific genomic relationship between a candidate and the training set is inversely associated to $$Q_e$$ and $$N_{text {QTL}}$$ . Further, we show that trait-specific genomic relationship between a candidate and the training set is directly related to the size of the training set.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"73 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142815891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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