Genetics Selection Evolution最新文献

{"title":"Across-breed analyses of genome-wide association studies for stature and mammary gland morphology in cattle reveal pleiotropic effects of the Friesian POLLED haplotype.","authors":"Natasha Watson, Qiongyu He, Naveen Kumar Kadri, Alexander S Leonard, Franz R Seefried, Hubert Pausch","doi":"10.1186/s12711-026-01042-z","DOIUrl":"10.1186/s12711-026-01042-z","url":null,"abstract":"","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12983537/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147437168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A comprehensive genome-wide scan for parent-of-origin expressed genes in the pig clarifies the conservation landscape of genomic imprinting.","authors":"Mathilde Perret, Nathalie Iannuccelli, Sophie Leroux, Katia Fève, Patrice Dehais, Eva Jacomet, Jean-Noël Hubert, Carole Iampietro, Céline Vandecasteele, Sarah Maman-Haddad, Thomas Faraut, Laurence Liaubet, Agnès Bonnet, Cécile Donnadieu, Juliette Riquet, Julie Demars","doi":"10.1186/s12711-026-01031-2","DOIUrl":"10.1186/s12711-026-01031-2","url":null,"abstract":"<p><strong>Background: </strong>Genomic imprinting, a mechanism resulting in parent-of-origin expression of genes through epigenetic regulation, intersects with a broad range of biological fields, including evolution, molecular genetics and epigenetics, and determinism of complex traits. Although next generation sequencing technologies nowadays enable imprinted genes to be detected in a genome-wide manner, a wide spectrum of this phenomena is evaluated only in humans and rodents.</p><p><strong>Results: </strong>Here, we propose to map genes showing a parental expression imbalance in hypothalamus, muscle and placenta in piglets around birth using an extensive strategy that minimized biases and relied on reciprocal crosses, reconstruction of parental phases after imputation, and statistical analyses discriminating parent-of-origin from allele-specific expression. We detected 141 genes with strong to exclusive parental expression imbalance (ratio > 25:75). A large proportion (80%) of these genes have never been shown to exhibit parent-of-origin expression and a small proportion (15%) are shared by at least two tissues, suggesting an overall weak conservation landscape of genomic imprinting. Interestingly, we identified novel parent-of-origin expressed genes involved in neurodevelopmental (PREPL, Prolyl Endopeptidase Like) and fetal growth (FAM20B, Glycosaminoglycan Xylosylkinase, and POU6F2, POU Class 6 Homeobox 2) functions. In-depth analyses of specific loci highlighted specific imprinted isoforms of COPG2 (COPI Coat Complex Subunit Gamma 2) and confirmed livestock-specific imprinted genes such as the Zinc Finger Protein 300-like gene.</p><p><strong>Conclusions: </strong>Altogether, our results provide an atlas of parent-of-origin expressed genes in the pig, making it the most documented species for genomic imprinting after humans and rodents. Our findings indicate weak conservation of this mechanism across species and tissues, suggesting a small number of core imprinted genes shared across eutherians and another imprinted genes that seem specific to species or tissues. These latter parent-of-origin expressed genes may have been subjected to evolutionary forces that have determine their imprinting status in either a livestock-specific or a tissue-specific manner.</p>","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"58 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12969872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147391788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic information increases prediction accuracy of behavior traits of Labrador Retrievers used as guide dogs.","authors":"Molly M Riser, Jane Russenberger, Madeline Zimmermann, Frances L Chen, Caroline Moeser, Eldin Leighton, Breno Fragomeni","doi":"10.1186/s12711-026-01033-0","DOIUrl":"10.1186/s12711-026-01033-0","url":null,"abstract":"<p><strong>Background: </strong>This study aimed to evaluate the accuracy of prediction of breeding values in a genomic selection program for behavior traits in a population of Labrador Retrievers used as guide dogs. Implementing genomic selection as a new tool in service dogs has the potential to increase genetic gain, improving the performance of populations. Additionally, genomic predictions may help service dog organizations in identifying training candidates with higher accuracy.</p><p><strong>Results: </strong>Phenotypes for 17 traits on 4,841 Labrador Retrievers collected from 2008 to 2019 from the International Working Dog Registry's (IWDR) behavior checklist were analyzed. The Behavior Checklist (BCL) standardizes a scoring system for a dog's reaction to a variety of environmental stimuli. Data are used to assess a dog's behavior and suitability for training as well as genetic selection using a selection index of prioritized traits with estimated breeding values. Genomic data were available for 1076 individuals from whole genome sequences and reduced to 94 K SNPs. Variance components were estimated using AIREML. Genomic information was included under a single-step GBLUP approach. Accuracies were evaluated among a sample of the higher accuracy animals using the linear regression method. Genomic estimates of heritability ranged from 0.08 to 0.21. Accuracies were calculated with the LR method and ranged from 0.30 to 0.58 for pedigree information, with an average of 0.46. Accuracies of genomic predictions ranged from 0.32 to 0.63, with an average of 0.50, and were higher than pedigree predictions for all traits.</p><p><strong>Conclusions: </strong>The gains in accuracy from inclusion of SNP genotype data show that genomic prediction using single-step GBLUP can improve selection by identifying the cohort of young dogs that have the highest genetic merit for the desired traits. Gains in validation accuracy were limited by the small number of genotyped animals and are expected to increase as more animals are genotyped.</p>","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12964705/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147328096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pangenome-based association testing between a structural variant located upstream of the KIT gene and head depigmentation across a diverse panel of cattle breeds.","authors":"V Sorin, M P Sanchez, L Drouilhet, G Tosser-Klopp, M M Naji, D Boichard, H Pausch, M Boussaha, A S Leonard","doi":"10.1186/s12711-026-01037-w","DOIUrl":"10.1186/s12711-026-01037-w","url":null,"abstract":"<p><p>Coat color variation is a key phenotypic trait in domestic animals. Among the genetic factors involved, the KIT gene has frequently been associated with pigmentation diversity across species. In cattle, spotting or piebald phenotypes have been linked to variation in the genomic region encompassing KIT, but the identification of causal variants was not always possible. This is largely due to the regulatory nature of the underlying variants and the structural complexity of this genomic region, which remains difficult to investigate with linear reference genome-based approaches. In the present study, we used a local pangenome strategy to investigate a genomic region on chromosome 6 encompassing KIT which was recently suggested to be associated with head depigmentation in white-headed cattle breeds. We constructed a 2 Mb pangenome graph encompassing the associated region using 79 assemblies from 20 cattle breeds. Through the evaluation of the coverage at the node level on this pangenome graph, we identified a ~ 7 kb structural variant which was supported by 21 assemblies only from breeds exhibiting a white-headed phenotype. To validate these findings, we aligned 564 short-read sequencing data to a local graph of 30 kb, spanning the structural variant identified, and computed normalized coverage across the region. White-headed cattle breeds consistently exhibited higher coverage values, while color-headed breeds displayed nearly zero coverage. Together, these results confirm the association between a structural variant upstream of KIT with the white-headed phenotype. More broadly, our study demonstrates how targeted local pangenome graphs can efficiently resolve complex structural variants (SVs) with phenotypic impact, offering an interesting and computationally feasible alternative to whole-genome graph approaches.</p>","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12964817/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147312172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic architecture of backfat thickness in laying hens: implications for extended egg production.","authors":"Nicolas Bédère, Frédéric Hérault, Lorry Bécot, Thierry Burlot, Christian Diot, Sandrine Lagarrigue, Pascale Le Roy","doi":"10.1186/s12711-026-01036-x","DOIUrl":"10.1186/s12711-026-01036-x","url":null,"abstract":"","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12964622/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147286376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A modified indirect method for computing inbreeding coefficients.","authors":"Che Hsuan Huang, Seijiro Hirama, Toshimi Baba, Junpei Kawakami, Takeshi Yamazaki, Koichi Hagiya","doi":"10.1186/s12711-026-01035-y","DOIUrl":"10.1186/s12711-026-01035-y","url":null,"abstract":"<p><p>The performance of existing methods for computing inbreeding coefficients-including tabular-based methods, Cholesky decomposition-based methods, and indirect methods-has been limited by either memory usage, pedigree depth, or average half-sib family size. In this note, we present a modified indirect method that efficiently identifies, computes, and stores the necessary elements for computing inbreeding coefficients. The algorithm was tested on pedigrees of 8.6 million Japanese Holsteins born from 1901 to 2023, with an average longest ancestral path number of 17 and 42,120 sires with progenies. Compared to a previous indirect method, the modifications reduced computation time from 103.4 to 7.2 s. When parallelized using 32 threads, the computation completed in 1.1 s. Simulation results suggested that the proposed method is less affected by pedigree depth or family size, making it practical for most livestock populations reproduced via artificial insemination.</p>","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12964822/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147272732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Strategies to improve on selection based on estimated breeding values.","authors":"Torsten Pook, Azadeh Hassanpour, Tobias A M Niehoff, Mario P L Calus","doi":"10.1186/s12711-026-01034-z","DOIUrl":"10.1186/s12711-026-01034-z","url":null,"abstract":"<p><strong>Background: </strong>Selection of individuals based on their estimated breeding values (EBV) aims to maximize response to selection in the next generation under an additive model. However, when the aim does not only include short-term population-wide genetic gain but also genetic gain over multiple generations, an optimal strategy is not as clear-cut, as maintenance of genetic diversity may become an important factor. This study provides an extended comparison of existing selection strategies in a unifying testing pipeline using the simulation software MoBPS.</p><p><strong>Results: </strong>Applying a weighting factor on estimated SNP effects based on the frequency of the beneficial allele resulted in an increase of the long-term genetic gain of 1.6% after 50 generations, while reducing inbreeding rates by 16.2% compared to truncation selection based on EBV. However, this also resulted in short-term losses in genetic gain of 1.2% with the break-even point reached after 25 generations. In contrast, inclusion of the average kinship of an individual with individuals that would be selected based on their EBVs as an additional trait in the selection index with a weight of 17.5% resulted in no short-term losses and increased long-term genetic gain by 4.3%, while reducing inbreeding by 15.8%. Combining multiple diversity management strategies, with weights for each strategy optimized using an evolutionary algorithm, resulted in a breeding scheme with 5.1% greater genetic gain and 37.3% lower inbreeding rates than selection based on EBVs. The proposed combined strategy included the use of optimum contribution selection, weighting of SNP effects based on allele frequency, average kinship as a trait in the selection index, avoiding matings between related individuals, and lowering the proportion of selected individuals.</p><p><strong>Conclusions: </strong>The combination of strategies for the management of genetic diversity in a breeding program was shown to be far superior to the use of any singular method tested in this study. As the use of strategies for management of genetic diversity and inbreeding does not necessarily lead to short-term losses in genetic gain and comes at no extra costs, it is critical for breeding companies to implement such strategies for long-term success.</p>","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":" ","pages":"13"},"PeriodicalIF":3.1,"publicationDate":"2026-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12922190/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146198219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic variation of hypoxia tolerance in farmed fish: a systematic review for selective breeding purposes.","authors":"Sergio P Barahona, Nicolás Salinas-Parra, Rodrigo Pulgar, José Gallardo-Matus","doi":"10.1186/s12711-026-01032-1","DOIUrl":"10.1186/s12711-026-01032-1","url":null,"abstract":"","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":" ","pages":"12"},"PeriodicalIF":3.1,"publicationDate":"2026-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12903247/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146133679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Blood lipidome profiling reveals potential biomarkers linked to health and carcass quality traits in pigs.","authors":"Carles Hernández-Banqué,Teodor Jové-Juncà,Manel Portero-Otin,Elia Obis,Olga González-Rodríguez,Maria Ballester,Raquel Quintanilla","doi":"10.1186/s12711-026-01030-3","DOIUrl":"https://doi.org/10.1186/s12711-026-01030-3","url":null,"abstract":"BACKGROUNDThe modulation, activation, and differentiation of several immune cells is highly dependent on lipid metabolism. The objective of this study was to analyse the genetic determinism of the porcine plasma lipidome and its association to the animal immune capacity and production performance. The analysis of the blood lipidome of 300 60-day-old Duroc pigs allowed semi-quantification of 982 circulating lipid molecules. We evaluated the genetic determinism of the lipidome abundances, as well as their phenotypic and genetic correlations with health, stress, and carcass phenotypes.RESULTSTriacylglycerols were the most abundant lipid class among the plasma lipid features, followed by glycerophosphocholines, glycerophosphoethanolamines, diacylglycerols, and fatty acids/esters. Lipidome abundances showed low to moderate phenotypic correlations with the health and production traits, which clustered in two groups with opposite phenotypic correlation patterns with the lipidome. Mean heritability estimates for the circulating lipids abundance was generally low, but 184 lipid molecules showed significant heritability ranging between 0.25 and 0.85. At the genetic level, the percentage and phagocytic capacity of lymphocytes, the proportion of γδ T lymphocytes, and the cortisol concentration in hair were especially correlated with the lipidome, showing more than 200 significant genetic correlations with different lipidic compounds. Putative identification of associated metabolites by mass similarity revealed a large presence of phospholipids and glycerolipids among lipid molecules genetically correlated with immunity traits. Regarding production traits, fatness and lean meat measures showed an opposite pattern of genetic correlations with the porcine lipidome. Lipids positively correlated with fatness were mainly composed of diacyl- and triacyl-glycerides, while potential ceramides and phospholipids were more abundant among the lipids positively correlated with lean meat content at the genetic level.CONCLUSIONSOur results demonstrate a genetic determinism of the porcine blood lipidomic profile and suggest genetic correlations of the lipidome abundances with health and production performance phenotypes. We identify potential lipid biomarkers for assessing animal health and productivity.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"43 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146088995","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 the genetic basis of susceptibility to amoebic gill disease and idiopathic gill lesions in Atlantic salmon populations using field data.","authors":"Afees A Ajasa,Solomon A Boison,Muhammad L Aslam,Marie Lillehammer,Hans M Gjøen","doi":"10.1186/s12711-025-01025-6","DOIUrl":"https://doi.org/10.1186/s12711-025-01025-6","url":null,"abstract":"BACKGROUNDGill-related morbidity and mortality have become a major concern to the Atlantic salmon industry worldwide. Understanding the genetic mechanisms underlying susceptibility to gill diseases or lesions can help guide mitigation efforts. Genome-wide association analysis was conducted on gill scores from two large cohorts of Atlantic salmon populations, reared in Norway and Canada, that were phenotyped during amoebic gill disease (AGD) outbreaks and at harvest (referred to as idiopathic gill lesions (IGL)), respectively.RESULTSWhereas one novel quantitative trait locus (QTL) region on chromosome 12 was associated with susceptibility to AGD, two QTL regions on chromosomes 2 and 12 were associated with IGL. There was an overlap between the QTL region on chromosome 12 for AGD and IGL. The lead variant(s) identified explained approximately 7% of the additive genetic variance for AGD, and 3 and 10% for IGL, for the QTL on chromosomes 2 and 12, respectively. Putative candidate genes identified within or close to the lead variants include tfeb, zscan12l, and ifi44l, with the majority of these genes playing roles relating to immune functions. Fine-mapping the identified QTL region associated with AGD using re-sequence data revealed a lead intergenic variant explaining 9% of the additive genetic variance.CONCLUSIONSOur results provide valuable insight into the genetic architecture of susceptibility to AGD and IGL, suggesting that both traits may be partly under the same genetic control. Future studies are warranted, especially on the genetic correlation between AGD and IGL.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"47 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146021640","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}