Genetics Selection Evolution最新文献

{"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}

{"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}

{"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}

{"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}

{"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}

{"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}

{"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}

{"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":"21 1","pages":""},"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":"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}

{"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":"4 1","pages":""},"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}