Genetics Selection Evolution最新文献

{"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":null,"pages":null},"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}

{"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":null,"pages":null},"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}

{"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":null,"pages":null},"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}

{"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":null,"pages":null},"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}

{"title":"Whole-genome sequences restore the original classification of dabbling ducks (genus Anas)","authors":"Zhou Zhang, Huashui Ai, Lusheng Huang","doi":"10.1186/s12711-024-00904-8","DOIUrl":"https://doi.org/10.1186/s12711-024-00904-8","url":null,"abstract":"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.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140914930","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}

{"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":null,"pages":null},"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}

{"title":"Redefining and interpreting genomic relationships of metafounders","authors":"Andres Legarra, Matias Bermann, Quanshun Mei, Ole F. Christensen","doi":"10.1186/s12711-024-00891-w","DOIUrl":"https://doi.org/10.1186/s12711-024-00891-w","url":null,"abstract":"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 $${varvec{Gamma}}$$ .","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140819257","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}

{"title":"Estimating genomic relationships of metafounders across and within breeds using maximum likelihood, pseudo-expectation–maximization maximum likelihood and increase of relationships","authors":"Andres Legarra, Matias Bermann, Quanshun Mei, Ole F. Christensen","doi":"10.1186/s12711-024-00892-9","DOIUrl":"https://doi.org/10.1186/s12711-024-00892-9","url":null,"abstract":"The theory of “metafounders” proposes a unified framework for relationships across base populations within breeds (e.g. unknown parent groups), and base populations across breeds (crosses) together with a sensible compatibility with genomic relationships. Considering metafounders might be advantageous in pedigree best linear unbiased prediction (BLUP) or single-step genomic BLUP. Existing methods to estimate relationships across metafounders $${varvec{Gamma}}$$ are not well adapted to highly unbalanced data, genotyped individuals far from base populations, or many unknown parent groups (within breed per year of birth). We derive likelihood methods to estimate $${varvec{Gamma}}$$ . For a single metafounder, summary statistics of pedigree and genomic relationships allow deriving a cubic equation with the real root being the maximum likelihood (ML) estimate of $${varvec{Gamma}}$$ . This equation is tested with Lacaune sheep data. For several metafounders, we split the first derivative of the complete likelihood in a term related to $${varvec{Gamma}}$$ , and a second term related to Mendelian sampling variances. Approximating the first derivative by its first term results in a pseudo-EM algorithm that iteratively updates the estimate of $${varvec{Gamma}}$$ by the corresponding block of the H-matrix. The method extends to complex situations with groups defined by year of birth, modelling the increase of $${varvec{Gamma}}$$ using estimates of the rate of increase of inbreeding ( $$Delta F$$ ), resulting in an expanded $${varvec{Gamma}}$$ and in a pseudo-EM+ $$Delta F$$ algorithm. We compare these methods with the generalized least squares (GLS) method using simulated data: complex crosses of two breeds in equal or unsymmetrical proportions; and in two breeds, with 10 groups per year of birth within breed. We simulate genotyping in all generations or in the last ones. For a single metafounder, the ML estimates of the Lacaune data corresponded to the maximum. For simulated data, when genotypes were spread across all generations, both GLS and pseudo-EM(+ $$Delta F$$ ) methods were accurate. With genotypes only available in the most recent generations, the GLS method was biased, whereas the pseudo-EM(+ $$Delta F$$ ) approach yielded more accurate and unbiased estimates. We derived ML, pseudo-EM and pseudo-EM+ $$Delta F$$ methods to estimate $${varvec{Gamma}}$$ in many realistic settings. Estimates are accurate in real and simulated data and have a low computational cost.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140819149","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}

{"title":"Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics","authors":"Elisa Somenzi, Erika Partel, Mario Barbato, Ana María Chero Osorio, Licia Colli, Niccolò Franceschi, Roberto Mantovani, Fabio Pilla, Matteo Komjanc, Alessandro Achilli, Heidi Christine Hauffe, Paolo Ajmone Marsan","doi":"10.1186/s12711-024-00900-y","DOIUrl":"https://doi.org/10.1186/s12711-024-00900-y","url":null,"abstract":"Rendena is a dual-purpose cattle breed, which is primarily found in the Italian Alps and the eastern areas of the Po valley, and recognized for its longevity, fertility, disease resistance and adaptability to steep Alpine pastures. It is categorized as 'vulnerable to extinction' with only 6057 registered animals in 2022, yet no comprehensive analyses of its molecular diversity have been performed to date. The aim of this study was to analyse the origin, genetic diversity, and genomic signatures of selection in Rendena cattle using data from samples collected in 2000 and 2018, and shed light on the breed's evolution and conservation needs. Genetic analysis revealed that the Rendena breed shares genetic components with various Alpine and Po valley breeds, with a marked genetic proximity to the Original Braunvieh breed, reflecting historical restocking efforts across the region. The breed shows signatures of selection related to both milk and meat production, environmental adaptation and immune response, the latter being possibly the result of multiple rinderpest epidemics that swept across the Alps in the eighteenth century. An analysis of the Rendena cattle population spanning 18 years showed an increase in the mean level of inbreeding over time, which is confirmed by the mean number of runs of homozygosity per individual, which was larger in the 2018 sample. The Rendena breed, while sharing a common origin with Brown Swiss, has developed distinct traits that enable it to thrive in the Alpine environment and make it highly valued by local farmers. Preserving these adaptive features is essential, not only for maintaining genetic diversity and enhancing the ability of this traditional animal husbandry to adapt to changing environments, but also for guaranteeing the resilience and sustainability of both this livestock system and the livelihoods within the Rendena valley.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140819266","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}

{"title":"Equivalence of variance components between standard and recursive genetic models using LDL′ transformations","authors":"Luis Varona, David López-Carbonell, Houssemeddine Srihi, Carlos Hervás-Rivero, Óscar González-Recio, Juan Altarriba","doi":"10.1186/s12711-024-00901-x","DOIUrl":"https://doi.org/10.1186/s12711-024-00901-x","url":null,"abstract":"Recursive models are a category of structural equation models that propose a causal relationship between traits. These models are more parameterized than multiple trait models, and they require imposing restrictions on the parameter space to ensure statistical identification. Nevertheless, in certain situations, the likelihood of recursive models and multiple trait models are equivalent. Consequently, the estimates of variance components derived from the multiple trait mixed model can be converted into estimates under several recursive models through LDL′ or block-LDL′ transformations. The procedure was employed on a dataset comprising five traits (birth weight—BW, weight at 90 days—W90, weight at 210 days—W210, cold carcass weight—CCW and conformation—CON) from the Pirenaica beef cattle breed. These phenotypic records were unequally distributed among 149,029 individuals and had a high percentage of missing data. The pedigree used consisted of 343,753 individuals. A Bayesian approach involving a multiple-trait mixed model was applied using a Gibbs sampler. The variance components obtained at each iteration of the Gibbs sampler were subsequently used to estimate the variance components within three distinct recursive models. The LDL′ or block-LDL′ transformations applied to the variance component estimates achieved from a multiple trait mixed model enabled inference across multiple sets of recursive models, with the sole prerequisite of being likelihood equivalent. Furthermore, the aforementioned transformations simplify the handling of missing data when conducting inference within the realm of recursive models.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140819249","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}