Pub Date : 2024-06-10DOI: 10.1186/s12711-024-00908-4
Hui Wen, Jay S. Johnson, Leonardo S. Gloria, Andre C. Araujo, Jacob M. Maskal, Sharlene Olivette Hartman, Felipe E. de Carvalho, Artur Oliveira Rocha, Yijian Huang, Francesco Tiezzi, Christian Maltecca, Allan P. Schinckel, Luiz F. Brito
Longitudinal records of automatically-recorded vaginal temperature (TV) could be a key source of data for deriving novel indicators of climatic resilience (CR) for breeding more resilient pigs, especially during lactation when sows are at an increased risk of suffering from heat stress (HS). Therefore, we derived 15 CR indicators based on the variability in TV in lactating sows and estimated their genetic parameters. We also investigated their genetic relationship with sows’ key reproductive traits. The heritability estimates of the CR traits ranged from 0.000 ± 0.000 for slope for decreased rate of TV (SlopeDe) to 0.291 ± 0.047 for sum of TV values below the HS threshold (HSUB). Moderate to high genetic correlations (from 0.508 ± 0.056 to 0.998 ± 0.137) and Spearman rank correlations (from 0.431 to 1.000) between genomic estimated breeding values (GEBV) were observed for five CR indicators, i.e. HS duration (HSD), the normalized median multiplied by normalized variance (Nor_medvar), the highest TV value of each measurement day for each individual (MaxTv), and the sum of the TV values above (HSUA) and below (HSUB) the HS threshold. These five CR indicators were lowly to moderately genetically correlated with shoulder skin surface temperature (from 0.139 ± 0.008 to 0.478 ± 0.048) and respiration rate (from 0.079 ± 0.011 to 0.502 ± 0.098). The genetic correlations between these five selected CR indicators and sow reproductive performance traits ranged from − 0.733 to − 0.175 for total number of piglets born alive, from − 0.733 to − 0.175 for total number of piglets born, and from − 0.434 to − 0.169 for number of pigs weaned. The individuals with the highest GEBV (most climate-sensitive) had higher mean skin surface temperature, respiration rate (RR), panting score (PS), and hair density, but had lower mean body condition scores compared to those with the lowest GEBV (most climate-resilient). Most of the CR indicators evaluated are heritable with substantial additive genetic variance. Five of them, i.e. HSD, MaxTv, HSUA, HSUB, and Nor_medvar share similar underlying genetic mechanisms. In addition, individuals with higher CR indicators are more likely to exhibit better HS-related physiological responses, higher body condition scores, and improved reproductive performance under hot conditions. These findings highlight the potential benefits of genetically selecting more heat-tolerant individuals based on CR indicators.
{"title":"Genetic parameters for novel climatic resilience indicators derived from automatically-recorded vaginal temperature in lactating sows under heat stress conditions","authors":"Hui Wen, Jay S. Johnson, Leonardo S. Gloria, Andre C. Araujo, Jacob M. Maskal, Sharlene Olivette Hartman, Felipe E. de Carvalho, Artur Oliveira Rocha, Yijian Huang, Francesco Tiezzi, Christian Maltecca, Allan P. Schinckel, Luiz F. Brito","doi":"10.1186/s12711-024-00908-4","DOIUrl":"https://doi.org/10.1186/s12711-024-00908-4","url":null,"abstract":"Longitudinal records of automatically-recorded vaginal temperature (TV) could be a key source of data for deriving novel indicators of climatic resilience (CR) for breeding more resilient pigs, especially during lactation when sows are at an increased risk of suffering from heat stress (HS). Therefore, we derived 15 CR indicators based on the variability in TV in lactating sows and estimated their genetic parameters. We also investigated their genetic relationship with sows’ key reproductive traits. The heritability estimates of the CR traits ranged from 0.000 ± 0.000 for slope for decreased rate of TV (SlopeDe) to 0.291 ± 0.047 for sum of TV values below the HS threshold (HSUB). Moderate to high genetic correlations (from 0.508 ± 0.056 to 0.998 ± 0.137) and Spearman rank correlations (from 0.431 to 1.000) between genomic estimated breeding values (GEBV) were observed for five CR indicators, i.e. HS duration (HSD), the normalized median multiplied by normalized variance (Nor_medvar), the highest TV value of each measurement day for each individual (MaxTv), and the sum of the TV values above (HSUA) and below (HSUB) the HS threshold. These five CR indicators were lowly to moderately genetically correlated with shoulder skin surface temperature (from 0.139 ± 0.008 to 0.478 ± 0.048) and respiration rate (from 0.079 ± 0.011 to 0.502 ± 0.098). The genetic correlations between these five selected CR indicators and sow reproductive performance traits ranged from − 0.733 to − 0.175 for total number of piglets born alive, from − 0.733 to − 0.175 for total number of piglets born, and from − 0.434 to − 0.169 for number of pigs weaned. The individuals with the highest GEBV (most climate-sensitive) had higher mean skin surface temperature, respiration rate (RR), panting score (PS), and hair density, but had lower mean body condition scores compared to those with the lowest GEBV (most climate-resilient). Most of the CR indicators evaluated are heritable with substantial additive genetic variance. Five of them, i.e. HSD, MaxTv, HSUA, HSUB, and Nor_medvar share similar underlying genetic mechanisms. In addition, individuals with higher CR indicators are more likely to exhibit better HS-related physiological responses, higher body condition scores, and improved reproductive performance under hot conditions. These findings highlight the potential benefits of genetically selecting more heat-tolerant individuals based on CR indicators.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"7 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141299045","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 : 2024-06-06DOI: 10.1186/s12711-024-00912-8
Irene van den Berg, Amanda J. Chamberlain, Iona M. MacLeod, Tuan V. Nguyen, Mike E. Goddard, Ruidong Xiang, Brett Mason, Susanne Meier, Claire V. C. Phyn, Chris R. Burke, Jennie E. Pryce
Female fertility is an important trait in dairy cattle. Identifying putative causal variants associated with fertility may help to improve the accuracy of genomic prediction of fertility. Combining expression data (eQTL) of genes, exons, gene splicing and allele specific expression is a promising approach to fine map QTL to get closer to the causal mutations. Another approach is to identify genomic differences between cows selected for high and low fertility and a selection experiment in New Zealand has created exactly this resource. Our objective was to combine multiple types of expression data, fertility traits and allele frequency in high- (POS) and low-fertility (NEG) cows with a genome-wide association study (GWAS) on calving interval in Australian cows to fine-map QTL associated with fertility in both Australia and New Zealand dairy cattle populations. Variants that were significantly associated with calving interval (CI) were strongly enriched for variants associated with gene, exon, gene splicing and allele-specific expression, indicating that there is substantial overlap between QTL associated with CI and eQTL. We identified 671 genes with significant differential expression between POS and NEG cows, with the largest fold change detected for the CCDC196 gene on chromosome 10. Our results provide numerous candidate genes associated with female fertility in dairy cattle, including GYS2 and TIGAR on chromosome 5 and SYT3 and HSD17B14 on chromosome 18. Multiple QTL regions were located in regions with large numbers of copy number variants (CNV). To identify the causal mutations for these variants, long read sequencing may be useful. Variants that were significantly associated with CI were highly enriched for eQTL. We detected 671 genes that were differentially expressed between POS and NEG cows. Several QTL detected for CI overlapped with eQTL, providing candidate genes for fertility in dairy cattle.
{"title":"Using expression data to fine map QTL associated with fertility in dairy cattle","authors":"Irene van den Berg, Amanda J. Chamberlain, Iona M. MacLeod, Tuan V. Nguyen, Mike E. Goddard, Ruidong Xiang, Brett Mason, Susanne Meier, Claire V. C. Phyn, Chris R. Burke, Jennie E. Pryce","doi":"10.1186/s12711-024-00912-8","DOIUrl":"https://doi.org/10.1186/s12711-024-00912-8","url":null,"abstract":"Female fertility is an important trait in dairy cattle. Identifying putative causal variants associated with fertility may help to improve the accuracy of genomic prediction of fertility. Combining expression data (eQTL) of genes, exons, gene splicing and allele specific expression is a promising approach to fine map QTL to get closer to the causal mutations. Another approach is to identify genomic differences between cows selected for high and low fertility and a selection experiment in New Zealand has created exactly this resource. Our objective was to combine multiple types of expression data, fertility traits and allele frequency in high- (POS) and low-fertility (NEG) cows with a genome-wide association study (GWAS) on calving interval in Australian cows to fine-map QTL associated with fertility in both Australia and New Zealand dairy cattle populations. Variants that were significantly associated with calving interval (CI) were strongly enriched for variants associated with gene, exon, gene splicing and allele-specific expression, indicating that there is substantial overlap between QTL associated with CI and eQTL. We identified 671 genes with significant differential expression between POS and NEG cows, with the largest fold change detected for the CCDC196 gene on chromosome 10. Our results provide numerous candidate genes associated with female fertility in dairy cattle, including GYS2 and TIGAR on chromosome 5 and SYT3 and HSD17B14 on chromosome 18. Multiple QTL regions were located in regions with large numbers of copy number variants (CNV). To identify the causal mutations for these variants, long read sequencing may be useful. Variants that were significantly associated with CI were highly enriched for eQTL. We detected 671 genes that were differentially expressed between POS and NEG cows. Several QTL detected for CI overlapped with eQTL, providing candidate genes for fertility in dairy cattle.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"336 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141264867","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 : 2024-06-06DOI: 10.1186/s12711-024-00913-7
Christine Anglhuber, Christian Edel, Eduardo C. G. Pimentel, Reiner Emmerling, Kay-Uwe Götz, Georg Thaller
Limitations of the concept of identity by descent in the presence of stratification within a breeding population may lead to an incomplete formulation of the conventional numerator relationship matrix ( $$mathbf{A}$$ ). Combining $$mathbf{A}$$ with the genomic relationship matrix ( $$mathbf{G}$$ ) in a single-step approach for genetic evaluation may cause inconsistencies that can be a source of bias in the resulting predictions. The objective of this study was to identify stratification using genomic data and to transfer this information to matrix $$mathbf{A}$$ , to improve the compatibility of $$mathbf{A}$$ and $$mathbf{G}$$ . Using software to detect population stratification (ADMIXTURE), we developed an iterative approach. First, we identified 2 to 40 strata ( $$k$$ ) with ADMIXTURE, which we then introduced in a stepwise manner into matrix $$mathbf{A}$$ , to generate matrix $${mathbf{A}}^{{varvec{Gamma}}}$$ using the metafounder methodology. Improvements in consistency between matrix $$mathbf{G}$$ and $${mathbf{A}}^{{varvec{Gamma}}}$$ were evaluated by regression analysis and through the comparison of the overall mean and mean diagonal values of both matrices. The approach was tested on genotype and pedigree information of European and North American Brown Swiss animals (85,249). Analyses with ADMIXTURE were initially performed on the full set of genotypes (S1). In addition, we used an alternative dataset where we avoided sampling of closely related animals (S2). Results of the regression analyses of standard $$mathbf{A}$$ on $$mathbf{G}$$ were – 0.489, 0.780 and 0.647 for intercept, slope and fit of the regression. When analysing S1 data results of the regression for $${mathbf{A}}^{{varvec{Gamma}}}$$ on $$mathbf{G}$$ corresponding values were – 0.028, 1.087 and 0.807 for $$k$$ =7, while there was no clear optimum $$k$$ . Analyses of S2 gave a clear optimal $$k$$ =24, with − 0.020, 0.998 and 0.817 as results of the regression. For this $$k$$ differences in mean and mean diagonal values between both matrices were negligible. The derivation of hidden stratification information based on genotyped animals and its integration into $$mathbf{A}$$ improved compatibility of the resulting $${mathbf{A}}^{{varvec{Gamma}}}$$ and $$mathbf{G}$$ considerably compared to the initial situation. In dairy breeding populations with large half-sib families as sub-structures it is necessary to balance the data when applying population structure analysis to obtain meaningful results.
{"title":"Definition of metafounders based on population structure analysis","authors":"Christine Anglhuber, Christian Edel, Eduardo C. G. Pimentel, Reiner Emmerling, Kay-Uwe Götz, Georg Thaller","doi":"10.1186/s12711-024-00913-7","DOIUrl":"https://doi.org/10.1186/s12711-024-00913-7","url":null,"abstract":"Limitations of the concept of identity by descent in the presence of stratification within a breeding population may lead to an incomplete formulation of the conventional numerator relationship matrix ( $$mathbf{A}$$ ). Combining $$mathbf{A}$$ with the genomic relationship matrix ( $$mathbf{G}$$ ) in a single-step approach for genetic evaluation may cause inconsistencies that can be a source of bias in the resulting predictions. The objective of this study was to identify stratification using genomic data and to transfer this information to matrix $$mathbf{A}$$ , to improve the compatibility of $$mathbf{A}$$ and $$mathbf{G}$$ . Using software to detect population stratification (ADMIXTURE), we developed an iterative approach. First, we identified 2 to 40 strata ( $$k$$ ) with ADMIXTURE, which we then introduced in a stepwise manner into matrix $$mathbf{A}$$ , to generate matrix $${mathbf{A}}^{{varvec{Gamma}}}$$ using the metafounder methodology. Improvements in consistency between matrix $$mathbf{G}$$ and $${mathbf{A}}^{{varvec{Gamma}}}$$ were evaluated by regression analysis and through the comparison of the overall mean and mean diagonal values of both matrices. The approach was tested on genotype and pedigree information of European and North American Brown Swiss animals (85,249). Analyses with ADMIXTURE were initially performed on the full set of genotypes (S1). In addition, we used an alternative dataset where we avoided sampling of closely related animals (S2). Results of the regression analyses of standard $$mathbf{A}$$ on $$mathbf{G}$$ were – 0.489, 0.780 and 0.647 for intercept, slope and fit of the regression. When analysing S1 data results of the regression for $${mathbf{A}}^{{varvec{Gamma}}}$$ on $$mathbf{G}$$ corresponding values were – 0.028, 1.087 and 0.807 for $$k$$ =7, while there was no clear optimum $$k$$ . Analyses of S2 gave a clear optimal $$k$$ =24, with − 0.020, 0.998 and 0.817 as results of the regression. For this $$k$$ differences in mean and mean diagonal values between both matrices were negligible. The derivation of hidden stratification information based on genotyped animals and its integration into $$mathbf{A}$$ improved compatibility of the resulting $${mathbf{A}}^{{varvec{Gamma}}}$$ and $$mathbf{G}$$ considerably compared to the initial situation. In dairy breeding populations with large half-sib families as sub-structures it is necessary to balance the data when applying population structure analysis to obtain meaningful results.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"4 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141264874","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 : 2024-05-21DOI: 10.1186/s12711-024-00910-w
Pablo A. S. Fonseca, Aroa Suárez-Vega, Juan J. Arranz, Beatriz Gutiérrez-Gil
Livestock populations are under constant selective pressure for higher productivity levels for different selective purposes. This pressure results in the selection of animals with unique adaptive and production traits. The study of genomic regions associated with these unique characteristics has the potential to improve biological knowledge regarding the adaptive process and how it is connected to production levels and resilience, which is the ability of an animal to adapt to stress or an imbalance in homeostasis. Sheep is a species that has been subjected to several natural and artificial selective pressures during its history, resulting in a highly specialized species for production and adaptation to challenging environments. Here, the data from multiple studies that aim at mapping selective sweeps across the sheep genome associated with production and adaptation traits were integrated to identify confirmed selective sweeps (CSS). In total, 37 studies were used to identify 518 CSS across the sheep genome, which were classified as production (147 prodCSS) and adaptation (219 adapCSS) CSS based on the frequency of each type of associated study. The genes within the CSS were associated with relevant biological processes for adaptation and production. For example, for adapCSS, the associated genes were related to the control of seasonality, circadian rhythm, and thermoregulation. On the other hand, genes associated with prodCSS were related to the control of feeding behaviour, reproduction, and cellular differentiation. In addition, genes harbouring both prodCSS and adapCSS showed an interesting association with lipid metabolism, suggesting a potential role of this process in the regulation of pleiotropic effects between these classes of traits. The findings of this study contribute to a deeper understanding of the genetic link between productivity and adaptability in sheep breeds. This information may provide insights into the genetic mechanisms that underlie undesirable genetic correlations between these two groups of traits and pave the way for a better understanding of resilience as a positive ability to respond to environmental stressors, where the negative effects on production level are minimized.
{"title":"Integration of selective sweeps across the sheep genome: understanding the relationship between production and adaptation traits","authors":"Pablo A. S. Fonseca, Aroa Suárez-Vega, Juan J. Arranz, Beatriz Gutiérrez-Gil","doi":"10.1186/s12711-024-00910-w","DOIUrl":"https://doi.org/10.1186/s12711-024-00910-w","url":null,"abstract":"Livestock populations are under constant selective pressure for higher productivity levels for different selective purposes. This pressure results in the selection of animals with unique adaptive and production traits. The study of genomic regions associated with these unique characteristics has the potential to improve biological knowledge regarding the adaptive process and how it is connected to production levels and resilience, which is the ability of an animal to adapt to stress or an imbalance in homeostasis. Sheep is a species that has been subjected to several natural and artificial selective pressures during its history, resulting in a highly specialized species for production and adaptation to challenging environments. Here, the data from multiple studies that aim at mapping selective sweeps across the sheep genome associated with production and adaptation traits were integrated to identify confirmed selective sweeps (CSS). In total, 37 studies were used to identify 518 CSS across the sheep genome, which were classified as production (147 prodCSS) and adaptation (219 adapCSS) CSS based on the frequency of each type of associated study. The genes within the CSS were associated with relevant biological processes for adaptation and production. For example, for adapCSS, the associated genes were related to the control of seasonality, circadian rhythm, and thermoregulation. On the other hand, genes associated with prodCSS were related to the control of feeding behaviour, reproduction, and cellular differentiation. In addition, genes harbouring both prodCSS and adapCSS showed an interesting association with lipid metabolism, suggesting a potential role of this process in the regulation of pleiotropic effects between these classes of traits. The findings of this study contribute to a deeper understanding of the genetic link between productivity and adaptability in sheep breeds. This information may provide insights into the genetic mechanisms that underlie undesirable genetic correlations between these two groups of traits and pave the way for a better understanding of resilience as a positive ability to respond to environmental stressors, where the negative effects on production level are minimized.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"90 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141074293","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 : 2024-05-21DOI: 10.1186/s12711-024-00909-3
Julien Corbeau, Cécile Grohs, Jeanlin Jourdain, Mekki Boussaha, Florian Besnard, Anne Barbat, Vincent Plassard, Julie Rivière, Christophe Hamelin, Jeremy Mortier, Didier Boichard, Raphaël Guatteo, Aurélien Capitan
Nine male and eight female calves born to a Normande artificial insemination bull named “Ly” were referred to the French National Observatory of Bovine Abnormalities for multiple fractures, shortened gestation, and stillbirth or perinatal mortality. Using Illumina BovineSNP50 array genotypes from affected calves and 84 half-sib controls, the associated locus was mapped to a 6.5-Mb interval on chromosome 19, assuming autosomal inheritance with germline mosaicism. Subsequent comparison of the whole-genome sequences of one case and 5116 control genomes, followed by genotyping in the affected pedigree, identified a de novo missense substitution within the NC1 domain of the COL1A1 gene (Chr19 g.36,473,965G > A; p.D1412N) as unique candidate variant. Interestingly, the affected residue was completely conserved among 243 vertebrate orthologs, and the same substitution in humans has been reported to cause type II osteogenesis imperfecta (OI), a connective tissue disorder that is characterized primarily by bone deformity and fragility. Moreover, three COL1A1 mutations have been described to cause the same syndrome in cattle. Necropsy, computed tomography, radiology, and histology confirmed the diagnosis of type II OI, further supporting the causality of this variant. In addition, a detailed analysis of gestation length and perinatal mortality in 1387 offspring of Ly and more than 160,000 progeny of 63 control bulls allowed us to statistically confirm in a large pedigree the association between type II OI and preterm delivery, which is probably due to premature rupture of fetal membranes and has been reported in several isolated cases of type II OI in humans and cattle. Finally, analysis of perinatal mortality rates and segregation distortion supported a low level of germ cell mosaicism in Ly, with an estimate of 4.5% to 7.7% of mutant sperm and thus 63 to 107 affected calves born. These numbers contrast with the 17 cases reported and raise concerns about the underreporting of congenital defects to heredo-surveillance platforms, even for textbook genetic syndromes. In conclusion, we describe a large animal model for a recurrent substitution in COL1A1 that is responsible for type II OI in humans. More generally, this study highlights the utility of such datasets and large half-sib families available in livestock species to characterize sporadic genetic defects.
一头名为 "Ly "的诺曼底人工授精公牛所产的九头公牛犊和八头母牛犊因多发性骨折、妊娠期缩短、死胎或围产期死亡而被转诊至法国国家牛畸形观察站。利用 Illumina BovineSNP50 阵列对患病小牛和 84 个半同父异母对照的基因型分析，相关基因座被映射到 19 号染色体上的一个 6.5 兆字节区间，假定为常染色体遗传与种系镶嵌。随后对一个病例和 5116 个对照基因组的全基因组序列进行了比较，并对受影响的血统进行了基因分型，确定了 COL1A1 基因 NC1 结构域内的一个新的错义置换（Chr19 g.36,473,965G > A; p.D1412N）是唯一的候选变异。有趣的是，受影响的残基在 243 个脊椎动物直系同源物中完全保密，而且据报道，在人类中，相同的置换可导致 II 型成骨不全症（OI），这是一种结缔组织疾病，主要特征是骨骼畸形和脆弱。此外，有报道称三种 COL1A1 基因突变可导致牛患相同的综合征。尸检、计算机断层扫描、放射学和组织学证实了 II 型 OI 的诊断，进一步支持了这种变异的因果关系。此外，通过对 Ly 的 1387 头后代和 63 头对照组公牛的 16 万多头后代的妊娠期长度和围产期死亡率进行详细分析，我们在一个大型血统中统计证实了 II 型 OI 与早产之间的关联，早产可能是由于胎膜早破造成的，在人类和牛的几例 II 型 OI 孤例中均有报道。最后，对围产期死亡率和分离畸变的分析表明，Ly 的生殖细胞嵌合程度较低，估计突变精子的比例为 4.5% 至 7.7%，因此出生的受影响小牛为 63 至 107 头。这些数字与报告的 17 个病例形成鲜明对比，并引发了人们对先天性缺陷向遗传监测平台报告不足的担忧，即使是教科书上的遗传综合征也是如此。总之，我们描述了一个大型动物模型，该动物模型中的 COL1A1 发生了复发性置换，而这种置换是导致人类 II 型 OI 的原因。更广泛地说，这项研究强调了此类数据集和家畜物种中的大型半同父异母家系在描述零星遗传缺陷方面的实用性。
{"title":"A recurrent de novo missense mutation in COL1A1 causes osteogenesis imperfecta type II and preterm delivery in Normande cattle","authors":"Julien Corbeau, Cécile Grohs, Jeanlin Jourdain, Mekki Boussaha, Florian Besnard, Anne Barbat, Vincent Plassard, Julie Rivière, Christophe Hamelin, Jeremy Mortier, Didier Boichard, Raphaël Guatteo, Aurélien Capitan","doi":"10.1186/s12711-024-00909-3","DOIUrl":"https://doi.org/10.1186/s12711-024-00909-3","url":null,"abstract":"Nine male and eight female calves born to a Normande artificial insemination bull named “Ly” were referred to the French National Observatory of Bovine Abnormalities for multiple fractures, shortened gestation, and stillbirth or perinatal mortality. Using Illumina BovineSNP50 array genotypes from affected calves and 84 half-sib controls, the associated locus was mapped to a 6.5-Mb interval on chromosome 19, assuming autosomal inheritance with germline mosaicism. Subsequent comparison of the whole-genome sequences of one case and 5116 control genomes, followed by genotyping in the affected pedigree, identified a de novo missense substitution within the NC1 domain of the COL1A1 gene (Chr19 g.36,473,965G > A; p.D1412N) as unique candidate variant. Interestingly, the affected residue was completely conserved among 243 vertebrate orthologs, and the same substitution in humans has been reported to cause type II osteogenesis imperfecta (OI), a connective tissue disorder that is characterized primarily by bone deformity and fragility. Moreover, three COL1A1 mutations have been described to cause the same syndrome in cattle. Necropsy, computed tomography, radiology, and histology confirmed the diagnosis of type II OI, further supporting the causality of this variant. In addition, a detailed analysis of gestation length and perinatal mortality in 1387 offspring of Ly and more than 160,000 progeny of 63 control bulls allowed us to statistically confirm in a large pedigree the association between type II OI and preterm delivery, which is probably due to premature rupture of fetal membranes and has been reported in several isolated cases of type II OI in humans and cattle. Finally, analysis of perinatal mortality rates and segregation distortion supported a low level of germ cell mosaicism in Ly, with an estimate of 4.5% to 7.7% of mutant sperm and thus 63 to 107 affected calves born. These numbers contrast with the 17 cases reported and raise concerns about the underreporting of congenital defects to heredo-surveillance platforms, even for textbook genetic syndromes. In conclusion, we describe a large animal model for a recurrent substitution in COL1A1 that is responsible for type II OI in humans. More generally, this study highlights the utility of such datasets and large half-sib families available in livestock species to characterize sporadic genetic defects.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"21 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141074240","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 : 2024-05-21DOI: 10.1186/s12711-024-00899-2
Tobias A. M. Niehoff, Jan ten Napel, Piter Bijma, Torsten Pook, Yvonne C. J. Wientjes, Bernadett Hegedűs, Mario P. L. Calus
Breeding programs are judged by the genetic level of animals that are used to disseminate genetic progress. These animals are typically the best ones of the population. To maximise the genetic level of very good animals in the next generation, parents that are more likely to produce top performing offspring need to be selected. The ability of individuals to produce high-performing progeny differs because of differences in their breeding values and gametic variances. Differences in gametic variances among individuals are caused by differences in heterozygosity and linkage. The use of the gametic Mendelian sampling variance has been proposed before, for use in the usefulness criterion or Index5, and in this work, we extend existing approaches by not only considering the gametic Mendelian sampling variance of individuals, but also of their potential offspring. Thus, the criteria developed in this study plan one additional generation ahead. For simplicity, we assumed that the true quantitative trait loci (QTL) effects, genetic map and the haplotypes of all animals are known. In this study, we propose a new selection criterion, ExpBVSelGrOff, which describes the genetic level of selected grand-offspring that are produced by selected offspring of a particular mating. We compare our criterion with other published criteria in a stochastic simulation of an ongoing breeding program for 21 generations for proof of concept. ExpBVSelGrOff performed better than all other tested criteria, like the usefulness criterion or Index5 which have been proposed in the literature, without compromising short-term gains. After only five generations, when selection is strong (1%), selection based on ExpBVSelGrOff achieved 5.8% more commercial genetic gain and retained 25% more genetic variance without compromising inbreeding rate compared to selection based only on breeding values. Our proposed selection criterion offers a new tool to accelerate genetic progress for contemporary genomic breeding programs. It retains more genetic variance than previously published criteria that plan less far ahead. Considering future gametic Mendelian sampling variances in the selection process also seems promising for maintaining more genetic variance.
{"title":"Improving selection decisions with mating information by accounting for Mendelian sampling variances looking two generations ahead","authors":"Tobias A. M. Niehoff, Jan ten Napel, Piter Bijma, Torsten Pook, Yvonne C. J. Wientjes, Bernadett Hegedűs, Mario P. L. Calus","doi":"10.1186/s12711-024-00899-2","DOIUrl":"https://doi.org/10.1186/s12711-024-00899-2","url":null,"abstract":"Breeding programs are judged by the genetic level of animals that are used to disseminate genetic progress. These animals are typically the best ones of the population. To maximise the genetic level of very good animals in the next generation, parents that are more likely to produce top performing offspring need to be selected. The ability of individuals to produce high-performing progeny differs because of differences in their breeding values and gametic variances. Differences in gametic variances among individuals are caused by differences in heterozygosity and linkage. The use of the gametic Mendelian sampling variance has been proposed before, for use in the usefulness criterion or Index5, and in this work, we extend existing approaches by not only considering the gametic Mendelian sampling variance of individuals, but also of their potential offspring. Thus, the criteria developed in this study plan one additional generation ahead. For simplicity, we assumed that the true quantitative trait loci (QTL) effects, genetic map and the haplotypes of all animals are known. In this study, we propose a new selection criterion, ExpBVSelGrOff, which describes the genetic level of selected grand-offspring that are produced by selected offspring of a particular mating. We compare our criterion with other published criteria in a stochastic simulation of an ongoing breeding program for 21 generations for proof of concept. ExpBVSelGrOff performed better than all other tested criteria, like the usefulness criterion or Index5 which have been proposed in the literature, without compromising short-term gains. After only five generations, when selection is strong (1%), selection based on ExpBVSelGrOff achieved 5.8% more commercial genetic gain and retained 25% more genetic variance without compromising inbreeding rate compared to selection based only on breeding values. Our proposed selection criterion offers a new tool to accelerate genetic progress for contemporary genomic breeding programs. It retains more genetic variance than previously published criteria that plan less far ahead. Considering future gametic Mendelian sampling variances in the selection process also seems promising for maintaining more genetic variance.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"70 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141074275","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 : 2024-05-15DOI: 10.1186/s12711-024-00907-5
Afees A. Ajasa, Solomon A. Boison, Hans M. Gjøen, Marie Lillehammer
The accuracy of genomic prediction is partly determined by the size of the reference population. In Atlantic salmon breeding programs, four parallel populations often exist, thus offering the opportunity to increase the size of the reference set by combining these populations. By allowing a reduction in the number of records per population, multi-population prediction can potentially reduce cost and welfare issues related to the recording of traits, particularly for diseases. In this study, we evaluated the accuracy of multi- and across-population prediction of breeding values for resistance to amoebic gill disease (AGD) using all single nucleotide polymorphisms (SNPs) on a 55K chip or a selected subset of SNPs based on the signs of allele substitution effect estimates across populations, using both linear and nonlinear genomic prediction (GP) models in Atlantic salmon populations. In addition, we investigated genetic distance, genetic correlation estimated based on genomic relationships, and persistency of linkage disequilibrium (LD) phase across these populations. The genetic distance between populations ranged from 0.03 to 0.07, while the genetic correlation ranged from 0.19 to 0.99. Nonetheless, compared to within-population prediction, there was limited or no impact of combining populations for multi-population prediction across the various models used or when using the selected subset of SNPs. The estimates of across-population prediction accuracy were low and to some extent proportional to the genetic correlation estimates. The persistency of LD phase between adjacent markers across populations using all SNP data ranged from 0.51 to 0.65, indicating that LD is poorly conserved across the studied populations. Our results show that a high genetic correlation and a high genetic relationship between populations do not guarantee a higher prediction accuracy from multi-population genomic prediction in Atlantic salmon.
{"title":"Accuracy of genomic prediction using multiple Atlantic salmon populations","authors":"Afees A. Ajasa, Solomon A. Boison, Hans M. Gjøen, Marie Lillehammer","doi":"10.1186/s12711-024-00907-5","DOIUrl":"https://doi.org/10.1186/s12711-024-00907-5","url":null,"abstract":"The accuracy of genomic prediction is partly determined by the size of the reference population. In Atlantic salmon breeding programs, four parallel populations often exist, thus offering the opportunity to increase the size of the reference set by combining these populations. By allowing a reduction in the number of records per population, multi-population prediction can potentially reduce cost and welfare issues related to the recording of traits, particularly for diseases. In this study, we evaluated the accuracy of multi- and across-population prediction of breeding values for resistance to amoebic gill disease (AGD) using all single nucleotide polymorphisms (SNPs) on a 55K chip or a selected subset of SNPs based on the signs of allele substitution effect estimates across populations, using both linear and nonlinear genomic prediction (GP) models in Atlantic salmon populations. In addition, we investigated genetic distance, genetic correlation estimated based on genomic relationships, and persistency of linkage disequilibrium (LD) phase across these populations. The genetic distance between populations ranged from 0.03 to 0.07, while the genetic correlation ranged from 0.19 to 0.99. Nonetheless, compared to within-population prediction, there was limited or no impact of combining populations for multi-population prediction across the various models used or when using the selected subset of SNPs. The estimates of across-population prediction accuracy were low and to some extent proportional to the genetic correlation estimates. The persistency of LD phase between adjacent markers across populations using all SNP data ranged from 0.51 to 0.65, indicating that LD is poorly conserved across the studied populations. Our results show that a high genetic correlation and a high genetic relationship between populations do not guarantee a higher prediction accuracy from multi-population genomic prediction in Atlantic salmon.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"10 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140925174","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 : 2024-05-13DOI: 10.1186/s12711-024-00904-8
Zhou Zhang, Huashui Ai, Lusheng Huang
Anas, is a genus of dabbling ducks and encompasses a considerable number of species, among which some are the progenitors of domestic ducks. However, the taxonomic position of the Anas genus remains uncertain because several of its species, initially categorized as Anas based on morphological characteristics, were subsequently reclassified and grouped with the South American genus Tachyeres, primarily based on analysis of their mitochondrial gene sequences. Here, we constructed a phylogenetic tree using nine of our recently assembled Anas genomes, two Tachyeres genomes, and one Cairina genome that are publicly available. The results showed that the Northern shoveler (Anas clypeata) and Baikal teal (Anas formosa) clustered with the other Anas species at the whole-genome level rather than with the Steamer ducks (genus Tachyeres). Therefore, we propose to restore the original classification of the Anas genus, which includes the Northern shoveler and Baikal teal species, 47 species in total. Moreover, our study unveiled extensive incomplete lineage sorting and an ancient introgression event from Tachyeres to Anas, which has led to notable phylogenetic incongruence within the Anas genome. This ancient introgression event not only supports the theory that Anas originated in South America but also that it played a significant role in shaping the evolutionary trajectory of Anas, including the domestic duck.
鸭属（Anas）是鸭类的一个属，包括相当多的物种，其中一些物种是家鸭的祖先。然而，鸭属在分类学上的地位仍不确定，因为最初根据形态特征将其归类为鸭属的几个物种后来被重新分类，并与南美洲的Tachyeres属归为一类，主要依据是对其线粒体基因序列的分析。在此，我们利用最近组装的九个 Anas 基因组、两个 Tachyeres 基因组和一个 Cairina 基因组构建了系统发生树。结果表明，在全基因组水平上，北方锹形目（Anas clypeata）和贝加尔凫（Anas formosa）与其他雉科物种聚类，而不是与斯泰默鸭（Tachyeres属）聚类。因此，我们建议恢复安氏鸭属的原始分类，其中包括北方锹形目和贝加尔凫目，共 47 种。此外，我们的研究还揭示了广泛的不完全世系分类以及从 Tachyeres 到 Anas 的古老引入事件，这导致了 Anas 基因组内显著的系统发育不一致。这一古老的引入事件不仅支持了 Anas 起源于南美洲的理论，而且在塑造 Anas（包括家鸭）的进化轨迹方面发挥了重要作用。
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Pub Date : 2024-05-03DOI: 10.1186/s12711-024-00906-6
Liviu Radu Totir
<p>Rohan Fernando is known and celebrated for many outstanding technical contributions to Animal Breeding and Quantitative Genetics [1]. The intent of this Editorial is to provide a personal perspective on the impact of Rohan’s scientific and pedagogical excellence on global agriculture. In the animal breeding and genetics community, it is well known that Rohan has played key technical roles in multiple public/private partnerships that resulted in measurable improvements in animal agriculture. What is less known is that Rohan has also made important contributions towards the productivity and resilience of the seed industry and thus plant agriculture.</p><p>I am a former graduate and post-doctoral student of Rohan, working under his supervision from August 1995 to September 2004, first at the University of Illinois at Urbana Champaign (UIUC) and then at Iowa State University (ISU). I joined DuPont Pioneer—now Corteva Agriscience, one of the leading global Agriscience companies, in October 2004. Here, I have spent my entire career working with teams that develop and deploy methodology and software for optimized breeding analytics and decision systems to accelerate global crop improvement. Given this background, I will provide a personal perspective on Rohan’s contributions to the seed industry and thus plant agriculture.</p><p>The seed industry is a key component in building productive, resilient, and sustainable agricultural systems (Fig. 1).</p><figure><figcaption><b data-test="figure-caption-text">Fig. 1</b></figcaption><picture><source srcset="//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs12711-024-00906-6/MediaObjects/12711_2024_906_Fig1_HTML.png?as=webp" type="image/webp"/><img alt="figure 1" aria-describedby="Fig1" height="507" loading="lazy" src="//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs12711-024-00906-6/MediaObjects/12711_2024_906_Fig1_HTML.png" width="685"/></picture><p>Example of the outcome of continuous improvement in US corn (maize) yield, measured in terms of land mass kept out of production (left Y axis) because of the increased production (right Y axis) due to 6.5-fold increase in yield per hectare from 1921 to 2021 (data from https://quickstats.nass.usda.gov/)</p><span>Full size image</span><svg aria-hidden="true" focusable="false" height="16" role="img" width="16"><use xlink:href="#icon-eds-i-chevron-right-small" xmlns:xlink="http://www.w3.org/1999/xlink"></use></svg></figure><p>Increased yield output per unit area of land is critical given the societal constraint of restricted land use for agriculture [2]. To achieve this, modern plant agriculture makes use of scientific and technological expertise from a very wide range of domains, in an integrated and coordinated systems-based approach. The coordinated use of applied statistics, quantitative genetics, statistical computing, and decision science, focused on optimization of artificial selection within plant breeding progra
然而，罗汉认为这些只是实现对当前科学问题的全面理解、培养他的学生以及帮助推进与农业相关的科学知识的垫脚石。因此，除了路线图类型的出版物使他对所从事研究领域的关键技术方面有了清晰的认识和理解（例如，从 2006 年开始，他发表了大量关于全基因组分析和基因组选择的出版物），罗汉共同编写的软件包使社区能够将这些知识应用于大规模的实际使用案例中[20, 21]。罗汉的科学出版物记录包含了他对植物育种的许多贡献，例如[22, 23]，最近的一篇发表于 2023 年[24]。罗汉采用三步 "系统 "方法解决复杂而实用的遗传评估问题，种业是其受益者之一。例如，作为杜邦先锋与伊利诺伊大学合作的一部分，从 2005 年到 2011 年，我有机会每周与罗汉在伊利诺伊大学共事一天。这些每周一次的一对一工作会议主要侧重于讨论和理解与新兴的全基因组分析和基因组选择领域相关的方法论和软件开发策略的复杂性。罗汉一直热衷于确保这些新兴领域不仅仅是理论上的练习，还应该由植物育种人员来实施，以帮助全球种植者高效地创造新的改良作物品种。因此，我们的合作有助于杜邦先锋/科蒂娃农业科学公司更快地为全球客户提供更好的种子产品。这有助于提高单位面积土地的生产率。托马斯-杰斐逊（Thomas Jefferson）有一句名言："能为任何国家提供的最大服务就是为其文化增添一种有用的植物"[25]。通过与杜邦先锋/Corteva Agriscience 的合作，罗汉不仅为一个国家，而且为人类提供了这项伟大的服务。接下来，我将谈谈罗汉培养研究生和博士后的方式。回首我与他共度的岁月，从学生到合作者，我再一次认识到 "系统 "的培养方法。在我看来，罗汉培养学生时注重四种行为：(1) 和蔼可亲；(2) 技术卓越；(3) 无私协作；(4) 尊重探究。我第一次见到罗翰是在 1995 年 8 月，当时我从罗马尼亚来到 UIUC 开始攻读动物育种与遗传学研究生课程。罗翰知道我没有住处，便让我在他家暂住，尽管玛吉-费尔南多（罗翰的第三个孩子）在我抵达前一周出生。这是罗汉多次对我表示友好而不求回报的第一次。这不仅让我感受到了自己的价值，还让我认识到，善意是建立有凝聚力的技术团队的重要杠杆。虽然罗翰总是很亲切，但他从一开始就明确表示，要想在他的项目中取得成功，就必须在应用和理论统计、定量遗传学和科学编程方面达到卓越的技术水平。不知不觉中，通过努力在罗翰的项目中取得卓越的技术成就，我也奠定了从动物育种无缝过渡到植物育种的基础。难能可贵的是，为了帮助我达到预期的卓越技术水平，Rohan 花了无数个小时与我并肩作战，研究算法和理论，用 C + + 编程，并撰写科学文章的草稿。通过这些工作，我认识到善良和卓越的技术是相辅相成的，两者结合在一起会非常有效。无私合作的重要性是我从 Rohan 身上学到的下一课。在我与罗汉共事期间，他以一种非常无私的合作方式对待所有的科研工作。他总是把主要精力放在解决感兴趣的科学问题上，而不担心因自己的贡献而获得荣誉。这种无私的合作方式，再加上他卓越的技术水平和仁慈，使罗汉成为查尔斯-亨德森（Charles Henderson）、丹-贾诺拉（Dan Gianola）、丹尼尔-索伦森（Daniel Sorensen）、莫什-索勒（Moshe Soller）、比尔-希尔（Bill Hill）、罗伯特-埃尔斯顿（Robert Elston）、杰克-德克斯（Jack Dekkers）、多里安-加里克（Dorian Garrick）、阿尔布雷希特-梅尔辛格（Albrecht Melchinger）等许多杰出科学家争相聘请和尊敬的合作者。不过，罗汉对待学生和职业生涯初期的科学家也同样具有无私的合作精神，因此通过导师和指导帮助他们中的许多人在项目上取得进展。 0/）适用于本文提供的数据，除非在数据的信用行中另有说明。转载和授权引用本文Totir, L.R. Academic research and training to advance global agriculture through quantitative genetics: a personal perspective on the contributions of Rohan Fernando.Genet Sel Evol 56, 36 (2024). https://doi.org/10.1186/s12711-024-00906-6Download citationPublished: 03 May 2024DOI: https://doi.org/10.1186/s12711-024-00906-6Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard Provided by the Springer Nature SharedIt content-sharing initiative.
{"title":"Academic research and training to advance global agriculture through quantitative genetics: a personal perspective on the contributions of Rohan Fernando","authors":"Liviu Radu Totir","doi":"10.1186/s12711-024-00906-6","DOIUrl":"https://doi.org/10.1186/s12711-024-00906-6","url":null,"abstract":"<p>Rohan Fernando is known and celebrated for many outstanding technical contributions to Animal Breeding and Quantitative Genetics [1]. The intent of this Editorial is to provide a personal perspective on the impact of Rohan’s scientific and pedagogical excellence on global agriculture. In the animal breeding and genetics community, it is well known that Rohan has played key technical roles in multiple public/private partnerships that resulted in measurable improvements in animal agriculture. What is less known is that Rohan has also made important contributions towards the productivity and resilience of the seed industry and thus plant agriculture.</p><p>I am a former graduate and post-doctoral student of Rohan, working under his supervision from August 1995 to September 2004, first at the University of Illinois at Urbana Champaign (UIUC) and then at Iowa State University (ISU). I joined DuPont Pioneer—now Corteva Agriscience, one of the leading global Agriscience companies, in October 2004. Here, I have spent my entire career working with teams that develop and deploy methodology and software for optimized breeding analytics and decision systems to accelerate global crop improvement. Given this background, I will provide a personal perspective on Rohan’s contributions to the seed industry and thus plant agriculture.</p><p>The seed industry is a key component in building productive, resilient, and sustainable agricultural systems (Fig. 1).</p><figure><figcaption><b data-test=\"figure-caption-text\">Fig. 1</b></figcaption><picture><source srcset=\"//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs12711-024-00906-6/MediaObjects/12711_2024_906_Fig1_HTML.png?as=webp\" type=\"image/webp\"/><img alt=\"figure 1\" aria-describedby=\"Fig1\" height=\"507\" loading=\"lazy\" src=\"//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs12711-024-00906-6/MediaObjects/12711_2024_906_Fig1_HTML.png\" width=\"685\"/></picture><p>Example of the outcome of continuous improvement in US corn (maize) yield, measured in terms of land mass kept out of production (left Y axis) because of the increased production (right Y axis) due to 6.5-fold increase in yield per hectare from 1921 to 2021 (data from https://quickstats.nass.usda.gov/)</p><span>Full size image</span><svg aria-hidden=\"true\" focusable=\"false\" height=\"16\" role=\"img\" width=\"16\"><use xlink:href=\"#icon-eds-i-chevron-right-small\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"></use></svg></figure><p>Increased yield output per unit area of land is critical given the societal constraint of restricted land use for agriculture [2]. To achieve this, modern plant agriculture makes use of scientific and technological expertise from a very wide range of domains, in an integrated and coordinated systems-based approach. The coordinated use of applied statistics, quantitative genetics, statistical computing, and decision science, focused on optimization of artificial selection within plant breeding progra","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"79 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140821146","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 : 2024-05-02DOI: 10.1186/s12711-024-00891-w
Andres Legarra, Matias Bermann, Quanshun Mei, Ole F. Christensen
Metafounders are a useful concept to characterize relationships within and across populations, and to help genetic evaluations because they help modelling the means and variances of unknown base population animals. Current definitions of metafounder relationships are sensitive to the choice of reference alleles and have not been compared to their counterparts in population genetics—namely, heterozygosities, FST coefficients, and genetic distances. We redefine the relationships across populations with an arbitrary base of a maximum heterozygosity population in Hardy–Weinberg equilibrium. Then, the relationship between or within populations is a cross-product of the form $${Gamma }_{left(b,{b}^{prime}right)}=left(frac{2}{n}right)left(2{mathbf{p}}_{b}-mathbf{1}right)left(2{mathbf{p}}_{{b}^{prime}}-mathbf{1}right)^{prime}$$ with $$mathbf{p}$$ being vectors of allele frequencies at $$n$$ markers in populations $$b$$ and $$b^{prime}$$ . This is simply the genomic relationship of two pseudo-individuals whose genotypes are equal to twice the allele frequencies. We also show that this coding is invariant to the choice of reference alleles. In addition, standard population genetics metrics (inbreeding coefficients of various forms; FST differentiation coefficients; segregation variance; and Nei’s genetic distance) can be obtained from elements of matrix $${varvec{Gamma}}$$ .
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