Genetics Selection Evolution最新文献

{"title":"A computationally efficient algorithm to leverage average information REML for (co)variance component estimation in the genomic era","authors":"Ismo Strandén, Esa A. Mäntysaari, Martin H. Lidauer, Robin Thompson, Hongding Gao","doi":"10.1186/s12711-024-00939-x","DOIUrl":"https://doi.org/10.1186/s12711-024-00939-x","url":null,"abstract":"Methods for estimating variance components (VC) using restricted maximum likelihood (REML) typically require elements from the inverse of the coefficient matrix of the mixed model equations (MME). As genomic information becomes more prevalent, the coefficient matrix of the MME becomes denser, presenting a challenge for analyzing large datasets. Thus, computational algorithms based on iterative solving and Monte Carlo approximation of the inverse of the coefficient matrix become appealing. While the standard average information REML (AI-REML) is known for its rapid convergence, its computational intensity imposes limitations. In particular, the standard AI-REML requires solving the MME for each VC, which can be computationally demanding, especially when dealing with complex models with many VC. To bridge this gap, here we (1) present a computationally efficient and tractable algorithm, named the augmented AI-REML, which facilitates the AI-REML by solving an augmented MME only once within each REML iteration; and (2) implement this approach for VC estimation in a general framework of a multi-trait GBLUP model. VC estimation was investigated based on the number of VC in the model, including a two-trait, three-trait, four-trait, and five-trait GBLUP model. We compared the augmented AI-REML with the standard AI-REML in terms of computing time per REML iteration. Direct and iterative solving methods were used to assess the advances of the augmented AI-REML. When using the direct solving method, the augmented AI-REML and the standard AI-REML required similar computing times for models with a small number of VC (the two- and three-trait GBLUP model), while the augmented AI-REML demonstrated more notable reductions in computing time as the number of VC in the model increased. When using the iterative solving method, the augmented AI-REML demonstrated substantial improvements in computational efficiency compared to the standard AI-REML. The elapsed time of each REML iteration was reduced by 75%, 84%, and 86% for the two-, three-, and four-trait GBLUP models, respectively. The augmented AI-REML can considerably reduce the computing time within each REML iteration, particularly when using an iterative solver. Our results demonstrate the potential of the augmented AI-REML as an appealing approach for large-scale VC estimation in the genomic era.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"11 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142678314","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":"On the ability of the LR method to detect bias when there is pedigree misspecification and lack of connectedness","authors":"Alan M. Pardo, Andres Legarra, Zulma G. Vitezica, Natalia S. Forneris, Daniel O. Maizon, Sebastián Munilla","doi":"10.1186/s12711-024-00943-1","DOIUrl":"https://doi.org/10.1186/s12711-024-00943-1","url":null,"abstract":"Cross-validation techniques in genetic evaluations encounter limitations due to the unobservable nature of breeding values and the challenge of validating estimated breeding values (EBVs) against pre-corrected phenotypes, challenges which the Linear Regression (LR) method addresses as an alternative. Furthermore, beef cattle genetic evaluation programs confront challenges with connectedness among herds and pedigree errors. The objective of this work was to evaluate the LR method's performance under pedigree errors and weak connectedness typical in beef cattle genetic evaluations, through simulation. We simulated a beef cattle population resembling the Argentinean Brangus, including a quantitative trait selected over six pseudo-generations with a heritability of 0.4. This study considered various scenarios, including: 25% and 40% pedigree errors (PE-25 and PE-40), weak and strong connectedness among herds (WCO and SCO, respectively), and a benchmark scenario (BEN) with complete pedigree and optimal herd connections. Over six pseudo-generations of selection, genetic gain was simulated to be under- and over-estimated in PE-40 and WCO, respectively, contrary to the BEN scenario which was unbiased. In genetic evaluations with PE-25 and PE-40, true biases of − 0.13 and − 0.18 genetic standard deviations were simulated, respectively. In the BEN scenario, the LR method accurately estimated bias, however, in PE-25 and PE-40 scenarios, it overestimated biases by 0.17 and 0.25 genetic standard deviations, respectively. In herds facing WCO, significant true bias due to confounding environmental and genetic effects was simulated, and the corresponding LR statistic failed to accurately estimate the magnitude and direction of this bias. On average, true dispersion values were close to one for BEN, PE-40, SCO and WCO, showing no significant inflation or deflation, and the values were accurately estimated by LR. However, PE-25 exhibited inflation of EBVs and was slightly underestimated by LR. Accuracies and reliabilities showed good agreement between true and LR estimated values for the scenarios evaluated. The LR method demonstrated limitations in identifying biases induced by incomplete pedigrees, including scenarios with as much as 40% pedigree errors, or lack of connectedness, but it was effective in assessing dispersion, and population accuracies and reliabilities even in the challenging scenarios addressed.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"14 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142678315","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":"Empirical versus estimated accuracy of imputation: optimising filtering thresholds for sequence imputation","authors":"Tuan V. Nguyen, Sunduimijid Bolormaa, Coralie M. Reich, Amanda J. Chamberlain, Christy J. Vander Jagt, Hans D. Daetwyler, Iona M. MacLeod","doi":"10.1186/s12711-024-00942-2","DOIUrl":"https://doi.org/10.1186/s12711-024-00942-2","url":null,"abstract":"Genotype imputation is a cost-effective method for obtaining sequence genotypes for downstream analyses such as genome-wide association studies (GWAS). However, low imputation accuracy can increase the risk of false positives, so it is important to pre-filter data or at least assess the potential limitations due to imputation accuracy. In this study, we benchmarked three different imputation programs (Beagle 5.2, Minimac4 and IMPUTE5) and compared the empirical accuracy of imputation with the software estimated accuracy of imputation (Rsqsoft). We also tested the accuracy of imputation in cattle for autosomal and X chromosomes, SNP and INDEL, when imputing from either low-density or high-density genotypes. The accuracy of imputing sequence variants from real high-density genotypes was higher than from low-density genotypes. In our software benchmark, all programs performed well with only minor differences in accuracy. While there was a close relationship between empirical imputation accuracy and the imputation Rsqsoft, this differed considerably for Minimac4 compared to Beagle 5.2 and IMPUTE5. We found that the Rsqsoft threshold for removing poorly imputed variants must be customised according to the software and this should be accounted for when merging data from multiple studies, such as in meta-GWAS studies. We also found that imposing an Rsqsoft filter has a positive impact on genomic regions with poor imputation accuracy due to large segmental duplications that are susceptible to error-prone alignment. Overall, our results showed that on average the imputation accuracy for INDEL was approximately 6% lower than SNP for all software programs. Importantly, the imputation accuracy for the non-PAR (non-Pseudo-Autosomal Region) of the X chromosome was comparable to autosomal imputation accuracy, while for the PAR it was substantially lower, particularly when starting from low-density genotypes. This study provides an empirically derived approach to apply customised software-specific Rsqsoft thresholds for downstream analyses of imputed variants, such as needed for a meta-GWAS. The very poor empirical imputation accuracy for variants on the PAR when starting from low density genotypes demonstrates that this region should be imputed starting from a higher density of real genotypes.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"29 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142637636","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":"The effect of phenotyping, adult selection, and mating strategies on genetic gain and rate of inbreeding in black soldier fly breeding programs","authors":"Margot Slagboom, Hanne Marie Nielsen, Morten Kargo, Mark Henryon, Laura Skrubbeltrang Hansen","doi":"10.1186/s12711-024-00938-y","DOIUrl":"https://doi.org/10.1186/s12711-024-00938-y","url":null,"abstract":"The aim of this study was to compare genetic gain and rate of inbreeding for different mass selection breeding programs with the aim of increasing larval body weight (LBW) in black soldier flies. The breeding programs differed in: (1) sampling of individuals for phenotyping (either random over the whole population or a fixed number per full sib family), (2) selection of adult flies for breeding (based on an adult individual’s phenotype for LBW or random from larvae preselected based on LBW), and (3) mating strategy (mating in a group with unequal male contributions or controlled between two females and one male). In addition, the numbers of phenotyped and preselected larvae were varied. The sex of an individual was unknown during preselection and females had higher LBW, resulting in more females being preselected. Selecting adult flies based on their phenotype for LBW increased genetic gain by 0.06 genetic standard deviation units compared to randomly selecting from the preselected larvae. Fixing the number of phenotyped larvae per family increased the rate of inbreeding by 0.15 to 0.20% per generation. Controlled mating compared to group mating decreased the rate of inbreeding by 0.02 to 0.03% per generation. Phenotyping more than 4000 larvae resulted in a lack of preselected males due to the sexual dimorphism. Preselecting both too few and too many larvae could negatively impact genetic gain, depending on the breeding program. A mass selection breeding programs in which the adult fly is selected based on their larval phenotype, breeding animals mate in a group and sampling larvae for phenotyping at random over the whole population is recommended for black soldier flies, considering the positive effect on rates of genetic gain and inbreeding. The number of phenotyped and preselected larvae should be calculated based on the expected female weight deviation to ensure sufficient male and female candidates are selected.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"25 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142574491","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":"Investigating genotype by environment interaction for beef cattle fertility traits in commercial herds in northern Australia with multi-trait analysis","authors":"James P. Copley, Benjamin J. Hayes, Elizabeth M. Ross, Shannon Speight, Geoffry Fordyce, Benjamin J. Wood, Bailey N. Engle","doi":"10.1186/s12711-024-00936-0","DOIUrl":"https://doi.org/10.1186/s12711-024-00936-0","url":null,"abstract":"Genotype by environment interactions (GxE) affect a range of production traits in beef cattle. Quantifying the effect of GxE in commercial and multi-breed herds is challenging due to unknown genetic linkage between animals across environment levels. The primary aim of this study was to use multi-trait models to investigate GxE for three heifer fertility traits, corpus luteum (CL) presence, first pregnancy and second pregnancy, in a large tropical beef multibreed dataset (n = 21,037). Environmental levels were defined by two different descriptors, burden of heat load (temperature humidity index, THI) and nutritional availability (based on mean average daily gain for the herd, ADWG). To separate the effects of genetic linkage and real GxE across the environments, 1000 replicates of a simulated phenotype were generated by simulating QTL effects with no GxE onto real marker genotypes from the population, to determine the genetic correlations that could be expected across environments due to the existing genetic linkage only. Correlations from the real phenotypes were then compared to the empirical distribution under the null hypothesis from the simulated data. By adopting this approach, this study attempted to establish if low genetic correlations between environmental levels were due to GxE or insufficient genetic linkage between animals in each environmental level. The correlations (being less than <0.8) for the real phenotypes were indicative of GxE for CL presence between ADWG environmental levels and in pregnancy traits. However, none of the correlations for CL presence or first pregnancy between ADWG levels were below the 5th percentile value for the empirical distribution under the null hypothesis from the simulated data. Only one statistically significant (P < 0.05) indication of GxE for first pregnancy was found between THI environmental levels, where rg = 0.28 and 5th percentile value = 0.29, and this result was marginal. Only one case of statistically significant GxE for fertility traits was detected for first pregnancy between THI environmental levels 2 and 3. Other initial indications of GxE that were observed from the real phenotypes did not prove significant when compared to an empirical null distribution from simulated phenotypes. The lack of compelling evidence of GxE indicates that direct selection for fertility traits can be made accurately, using a single evaluation, regardless of environment.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"27 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142555824","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":"Combined genomic evaluation of Merino and Dohne Merino Australian sheep populations","authors":"Marine Wicki, Daniel J. Brown, Phillip M. Gurman, Jérôme Raoul, Andrés Legarra, Andrew A. Swan","doi":"10.1186/s12711-024-00934-2","DOIUrl":"https://doi.org/10.1186/s12711-024-00934-2","url":null,"abstract":"The Dohne Merino sheep was introduced to Australia from South Africa in the 1990s. It was primarily used in crosses with the Merino breed sheep to improve on attributes such as reproduction and carcass composition. Since then, this breed has continued to expand in Australia but the number of genotyped and phenotyped purebred individuals remains low, calling into question the accuracy of genomic selection. The Australian Merino, on the other hand, has a substantial reference population in a separate genomic evaluation (MERINOSELECT). Combining these resources could fast track the impact of genomic selection on the smaller breed, but the efficacy of this needs to be investigated. This study was based on a dataset of 53,663 genotypes and more than 2 million phenotypes. Its main objectives were (1) to characterize the genetic structure of Merino and Dohne Merino breeds, (2) to investigate the utility of combining their evaluations in terms of quality of predictions, and (3) to compare several methods of genetic grouping. We used the ‘LR-method’ (Linear Regression) for these assessments. We found very low Fst values (below 0.048) between the different Merino lines and Dohne breed considered in our study, indicating very low genetic differentiation. Principal component analysis revealed three distinct groups, identified as purebred Merino, purebred Dohne, and crossbred animals. Considering the whole population in the reference led to the best quality of predictions and the largest increase in accuracy (from ‘LR-method’) from pedigree to genomic-based evaluations: 0.18, 0.14 and 0.16 for yearling fibre diameter (YFD), yearling greasy fleece weight (YGFW) and yearling liveweight (YWT), respectively. Combined genomic evaluations showed higher accuracies than the evaluation based on the Dohne reference only (accuracies increased by 0.16, 0.06 and 0.07 for YFD, YGFW, and YWT, respectively). For the combined genomic evaluations, metafounder models were more accurate than Unknown Parent Groups models (accuracies increased by 0.04, 0.04 and 0.06 for YFD, YGFW and YWT, respectively). We found promising results for the future transition of the Dohne breed from pedigree to genomic selection. A combined genomic evaluation, with the MERINOSELECT evaluation in addition to using metafounders, is expected to enhance the quality of genomic predictions for the Dohne Merino breed.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"22 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142329889","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":"QTL analysis to identify genes involved in the trade-off between silk protein synthesis and larva-pupa transition in silkworms","authors":"Rui Gao, Chunlin Li, Ang Zhou, Xiachao Wang, Kupeng Lu, Weidong Zuo, Hai Hu, Minjin Han, Xiaoling Tong, Fangyin Dai","doi":"10.1186/s12711-024-00937-z","DOIUrl":"https://doi.org/10.1186/s12711-024-00937-z","url":null,"abstract":"Insect-based food and feed are increasingly attracting attention. As a domesticated insect, the silkworm (Bombyx mori) has a highly nutritious pupa that can be easily raised in large quantities through large-scale farming, making it a highly promising source of food. The ratio of pupa to cocoon (RPC) refers to the proportion of the weight of the cocoon that is attributed to pupae, and is of significant value for edible utilization, as a higher RPC means a higher ratio of conversion of mulberry leaves to pupa. In silkworm production, there is a trade-off between RPC and cocoon shell ratiao(CSR), which refers the ratio of silk protein to the entire cocoon, during metamorphosis process. Understanding the genetic basis of this balance is crucial for breeding edible strains with a high RPC and further advancing its use as feed. Using QTL-seq, we identified a quantitative trait locus (QTL) for the balance between RPC and CSR that is located on chromosome 11 and covers a 9,773,115-bp region. This locus is an artificial selection hot spot that contains ten non-overlapping genomic regions under selection that were involved in the domestication and genetic breeding processes. These regions include 17 genes, nine of which are highly expressed in the silk gland, which is a vital component in the trade-off between RPC and CSR. These genes are annotate with function related with epigenetic modifications and the regulation of DNA replication et al. We identified one and two single nucleotide polymorphisms (SNPs) in the exons of teh KWMTBOMO06541 and KWMTBOMO06485 genes that result in amino acid changes in the protein domains. These SNPs have been strongly selected for during the domestication process. The KWMTBOMO06485 gene encodes the Bombyx mori (Bm) tRNA methyltransferase (BmDnmt2) and its knockout results in a significant change in the trade-off between CSR and RPC in both sexes. Taken together, our results contribute to a better understanding of the genetic basis of RPC and CSR. The identified QTL and genes that affect RPC can be used for marker-assisted and genomic selection of silkworm strains with a high RPC. This will further enhance the production efficiency of silkworms and of closely-related insects for edible and feed purposes.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"77 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142329890","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":"Identification of genomic regions associated with fatty acid metabolism across blood, liver, backfat and muscle in pigs","authors":"Junhui Liu, Cristina Sebastià, Teodor Jové-Juncà, Raquel Quintanilla, Olga González-Rodríguez, Magí Passols, Anna Castelló, Armand Sánchez, Maria Ballester, Josep M. Folch","doi":"10.1186/s12711-024-00933-3","DOIUrl":"https://doi.org/10.1186/s12711-024-00933-3","url":null,"abstract":"The composition and distribution of fatty acids (FA) are important factors determining the quality, flavor, and nutrient value of meat. In addition, FAs synthesized in the body participate in energy metabolism and are involved in different regulatory pathways in the form of signaling molecules or by acting as agonist or antagonist ligands of different nuclear receptors. Finally, synthesis and catabolism of FAs affect adaptive immunity by regulating lymphocyte metabolism. The present study performed genome-wide association studies using FA profiles of blood, liver, backfat and muscle from 432 commercial Duroc pigs. Twenty-five genomic regions located on 15 Sus scrofa chromosomes (SSC) were detected. Annotation of the quantitative trait locus (QTL) regions identified 49 lipid metabolism-related candidate genes. Among these QTLs, four were identified in more than one tissue. The ratio of C20:4n-6/C20:3n-6 was associated with the region on SSC2 at 7.56–14.26 Mb for backfat, liver, and muscle. Members of the fatty acid desaturase gene cluster (FADS1, FADS2, and FADS3) are the most promising candidate genes in this region. Two QTL regions on SSC14 (103.81–115.64 Mb and 100.91–128.14 Mb) were identified for FA desaturation in backfat and muscle. In addition, two separate regions on SSC9 at 0 – 14.55 Mb and on SSC12 at 0–1.91 Mb were both associated with the same multiple FA traits for backfat, with candidate genes involved in de novo FA synthesis and triacylglycerol (TAG) metabolism, such as DGAT2 and FASN. The ratio C20:0/C18:0 was associated with the region on SSC5 at 64.84–78.32 Mb for backfat. Furthermore, the association of the C16:0 content with the region at 118.92–123.95 Mb on SSC4 was blood specific. Finally, candidate genes involved in de novo lipogenesis regulate T cell differentiation and promote the generation of palmitoleate, an adipokine that alleviates inflammation. Several SNPs and candidate genes were associated with lipid metabolism in blood, liver, backfat, and muscle. These results contribute to elucidating the molecular mechanisms implicated in the determination of the FA profile in different pig tissues and can be useful in selection programs that aim to improve health and energy metabolism in pigs.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"38 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142325403","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 million-cow genome-wide association study of productive life in U.S. Holstein cows","authors":"Zuoxiang Liang, Dzianis Prakapenka, Hafedh B. Zaabza, Paul M. VanRaden, Curtis P. Van Tassell, Yang Da","doi":"10.1186/s12711-024-00935-1","DOIUrl":"https://doi.org/10.1186/s12711-024-00935-1","url":null,"abstract":"Productive life (PL) of a cow is the time the cow remains in the milking herd from first calving to exit from the herd due to culling or death and is an important economic trait in U.S. Holstein cattle. The large samples of Holstein genomic evaluation data that have become available recently provided unprecedented statistical power to identify genetic factors affecting PL in Holstein cows using the approach of genome-wide association study (GWAS). The GWAS analysis used 1,103,641 Holstein cows with phenotypic observations on PL and genotypes of 75,282 single nucleotide polymorphism (SNP) markers. The statistical tests and estimation of SNP additive and dominance effects used the approximate generalized least squares method implemented by the EPISNPmpi computer program. The GWAS detected 5390 significant additive effects of PL distributed over all 29 autosomes and the X–Y nonrecombining region of the X chromosome (Chr31). Two chromosome regions had the most significant and largest cluster of additive effects, the SLC4A4-GC-NPFFR2 (SGN) region of Chr06 with pleiotropic effects for PL, fertility, somatic cell score and milk yield; and the 32–52 Mb region of Chr10 with peak effects for PL in or near RASGRP1 with many important immunity functions. The dominance tests detected 38 significant dominance effects including 12 dominance effects with sharply negative homozygous recessive genotypes on Chr18, Chr05, Chr23 and Chr24. The GWAS results showed that highly significant genetic effects for PL were in chromosome regions known to have highly significant effects for fertility and health and a chromosome region with multiple genes with reproductive and immunity functions. SNPs with rare but sharply negative homozygous recessive genotypes for PL existed and should be used for eliminating heifers carrying those homozygous recessive genotypes.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"24 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142325507","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":"Genotyping both live and dead animals to improve post-weaning survival of pigs in breeding programs","authors":"Md Sharif-Islam, Julius H. J. van der Werf, Mark Henryon, Thinh Tuan Chu, Benjamin J. Wood, Susanne Hermesch","doi":"10.1186/s12711-024-00932-4","DOIUrl":"https://doi.org/10.1186/s12711-024-00932-4","url":null,"abstract":"In this study, we tested whether genotyping both live and dead animals (GSD) realises more genetic gain for post-weaning survival (PWS) in pigs compared to genotyping only live animals (GOS). Stochastic simulation was used to estimate the rate of genetic gain realised by GSD and GOS at a 0.01 rate of pedigree-based inbreeding in three breeding schemes, which differed in PWS (95%, 90% and 50%) and litter size (6 and 10). Pedigree-based selection was conducted as a point of reference. Variance components were estimated and then estimated breeding values (EBV) were obtained in each breeding scheme using a linear or a threshold model. Selection was for a single trait, i.e. PWS with a heritability of 0.02 on the observed scale. The trait was simulated on the underlying scale and was recorded as binary (0/1). Selection candidates were genotyped and phenotyped before selection, with only live candidates eligible for selection. Genotyping strategies differed in the proportion of live and dead animals genotyped, but the phenotypes of all animals were used for predicting EBV of the selection candidates. Based on a 0.01 rate of pedigree-based inbreeding, GSD realised 14 to 33% more genetic gain than GOS for all breeding schemes depending on PWS and litter size. GSD increased the prediction accuracy of EBV for PWS by at least 14% compared to GOS. The use of a linear versus a threshold model did not have an impact on genetic gain for PWS regardless of the genotyping strategy and the bias of the EBV did not differ significantly among genotyping strategies. Genotyping both dead and live animals was more informative than genotyping only live animals to predict the EBV for PWS of selection candidates, but with marginal increases in genetic gain when the proportion of dead animals genotyped was 60% or greater. Therefore, it would be worthwhile to use genomic information on both live and more than 20% dead animals to compute EBV for the genetic improvement of PWS under the assumption that dead animals reflect increased liability on the underlying scale.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"63 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236385","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}