Genetics Selection Evolution最新文献

{"title":"Meta-analysis of six dairy cattle breeds reveals biologically relevant candidate genes for mastitis resistance","authors":"Zexi Cai, Terhi Iso-Touru, Marie-Pierre Sanchez, Naveen Kadri, Aniek C. Bouwman, Praveen Krishna Chitneedi, Iona M. MacLeod, Christy J. Vander Jagt, Amanda J. Chamberlain, Birgit Gredler-Grandl, Mirjam Spengeler, Mogens Sandø Lund, Didier Boichard, Christa Kühn, Hubert Pausch, Johanna Vilkki, Goutam Sahana","doi":"10.1186/s12711-024-00920-8","DOIUrl":"https://doi.org/10.1186/s12711-024-00920-8","url":null,"abstract":"Mastitis is a disease that incurs significant costs in the dairy industry. A promising approach to mitigate its negative effects is to genetically improve the resistance of dairy cattle to mastitis. A meta-analysis of genome-wide association studies (GWAS) across multiple breeds for clinical mastitis (CM) and its indicator trait, somatic cell score (SCS), is a powerful method to identify functional genetic variants that impact mastitis resistance. We conducted meta-analyses of eight and fourteen GWAS on CM and SCS, respectively, using 30,689 and 119,438 animals from six dairy cattle breeds. Methods for the meta-analyses were selected to properly account for the multi-breed structure of the GWAS data. Our study revealed 58 lead markers that were associated with mastitis incidence, including 16 loci that did not overlap with previously identified quantitative trait loci (QTL), as curated at the Animal QTLdb. Post-GWAS analysis techniques such as gene-based analysis and genomic feature enrichment analysis enabled prioritization of 31 candidate genes and 14 credible candidate causal variants that affect mastitis. Our list of candidate genes can help to elucidate the genetic architecture underlying mastitis resistance and provide better tools for the prevention or treatment of mastitis, ultimately contributing to more sustainable animal production.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"74 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141618321","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 high-density SNP data to unravel the origin of the Franches-Montagnes horse breed","authors":"Annik Imogen Gmel, Sofia Mikko, Anne Ricard, Brandon D. Velie, Vinzenz Gerber, Natasha Anne Hamilton, Markus Neuditschko","doi":"10.1186/s12711-024-00922-6","DOIUrl":"https://doi.org/10.1186/s12711-024-00922-6","url":null,"abstract":"The Franches-Montagnes (FM) is the last native horse breed of Switzerland, established at the end of the 19th century by cross-breeding local mares with Anglo-Norman stallions. We collected high-density SNP genotype data (Axiom™ 670 K Equine genotyping array) from 522 FM horses, including 44 old-type horses (OF), 514 European Warmblood horses (WB) from Sweden and Switzerland (including a stallion used for cross-breeding in 1990), 136 purebred Arabians (AR), 32 Shagya Arabians (SA), and 64 Thoroughbred (TB) horses, as introgressed WB stallions showed TB origin in their pedigrees. The aim of the study was to ascertain fine-scale population structures of the FM breed, including estimation of individual admixture levels and genomic inbreeding (FROH) by means of Runs of Homozygosity. To assess fine-scale population structures within the FM breed, we applied a three-step approach, which combined admixture, genetic contribution, and FROH of individuals into a high-resolution network visualization. Based on this approach, we were able to demonstrate that population substructures, as detected by model-based clustering, can be either associated with a different genetic origin or with the progeny of most influential sires. Within the FM breed, admixed horses explained most of the genetic variance of the current breeding population, while OF horses only accounted for a small proportion of the variance. Furthermore, we illustrated that FM horses showed high TB admixture levels and we identified inconsistencies in the origin of FM horses descending from the Arabian stallion Doktryner. With the exception of WB, FM horses were less inbred compared to the other breeds. However, the relatively few but long ROH segments suggested diversity loss in both FM subpopulations. Genes located in FM- and OF-specific ROH islands had known functions involved in conformation and behaviour, two traits that are highly valued by breeders. The FM remains the last native Swiss breed, clearly distinguishable from other historically introgressed breeds, but it suffered bottlenecks due to intensive selection of stallions, restrictive mating choices based on arbitrary definitions of pure breeding, and selection of rare coat colours. To preserve the genetic diversity of FM horses, future conservation managements strategies should involve a well-balanced selection of stallions (e.g., by integrating OF stallions in the FM breeding population) and avoid selection for rare coat colours.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"24 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141566248","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 and genomic analysis of Belgian Blue's susceptibility for psoroptic mange.","authors":"Roel Meyermans, Steven Janssens, Annelies Coussé, Susanne Tinel, Wim Gorssen, Fabrice Lepot, Xavier Hubin, Patrick Mayeres, Wim Veulemans, Nathalie De Wilde, Tom Druet, Michel Georges, Carole Charlier, Edwin Claerebout, Nadine Buys","doi":"10.1186/s12711-024-00921-7","DOIUrl":"10.1186/s12711-024-00921-7","url":null,"abstract":"<p><strong>Background: </strong>Psoroptic mange, caused by Psoroptes ovis mites, is affecting Belgian Blue cattle's welfare and production potential. The Belgian Blue cattle-known for its high degree of muscling, low feed conversion ratio and high beef quality-is highly susceptible for this disease.</p><p><strong>Results: </strong>In this study, we phenotyped 1975 Belgian Blue cattle from more than 100 different groups on commercial beef farms for their psoroptic mange susceptibility. Substantial individual differences were observed within these management groups, with lesion extent differences up to ± 15%. Animal models showed that estimated heritabilities were low for lesion extent and severe lesion extent (0.07 and 0.09, respectively) and 0.12 for the number of mites. A genome wide association study for mange susceptibility revealed signals on BTA6, BTA11, BTA15 and BTA24. In these regions, candidate genes GBA3, RAG2, and TRAF6 were identified.</p><p><strong>Conclusions: </strong>Despite the challenges in phenotyping for psoroptic mange due to the timing of screening, the continuous evolution of lesions and different management conditions, we successfully conducted a study on the genetic susceptibility to psoroptic mange in Belgian Blue cattle. Our results clearly indicate that psoroptic mange is under polygenic control and the underlying candidate genes should be studied more thoroughly. This is the first study providing candidate genes for this complex disease. These results are already valuable for Belgian Blue breeding, however, further research is needed to unravel the architecture of this disease and to identify causal mutations.</p>","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"56 1","pages":"52"},"PeriodicalIF":3.6,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11227209/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141538969","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":"The black honey bee genome: insights on specific structural elements and a first step towards pangenomes","authors":"Sonia E. Eynard, Christophe Klopp, Kamila Canale-Tabet, William Marande, Céline Vandecasteele, Céline Roques, Cécile Donnadieu, Quentin Boone, Bertrand Servin, Alain Vignal","doi":"10.1186/s12711-024-00917-3","DOIUrl":"https://doi.org/10.1186/s12711-024-00917-3","url":null,"abstract":"The honey bee reference genome, HAv3.1, was produced from a commercial line sample that was thought to have a largely dominant Apis mellifera ligustica genetic background. Apis mellifera mellifera, often referred to as the black bee, has a separate evolutionary history and is the original type in western and northern Europe. Growing interest in this subspecies for conservation and non-professional apicultural practices, together with the necessity of deciphering genome backgrounds in hybrids, triggered the necessity for a specific genome assembly. Moreover, having several high-quality genomes is becoming key for taking structural variations into account in pangenome analyses. Pacific Bioscience technology long reads were produced from a single haploid black bee drone. Scaffolding contigs into chromosomes was done using a high-density genetic map. This allowed for re-estimation of the recombination rate, which was over-estimated in some previous studies due to mis-assemblies, which resulted in spurious inversions in the older reference genomes. The sequence continuity obtained was very high and the only limit towards continuous chromosome-wide sequences seemed to be due to tandem repeat arrays that were usually longer than 10 kb and that belonged to two main families, the 371 and 91 bp repeats, causing problems in the assembly process due to high internal sequence similarity. Our assembly was used together with the reference genome to genotype two structural variants by a pangenome graph approach with Graphtyper2. Genotypes obtained were either correct or missing, when compared to an approach based on sequencing depth analysis, and genotyping rates were 89 and 76% for the two variants. Our new assembly for the Apis mellifera mellifera honey bee subspecies demonstrates the utility of multiple high-quality genomes for the genotyping of structural variants, with a test case on two insertions and deletions. It will therefore be an invaluable resource for future studies, for instance by including structural variants in GWAS. Having used a single haploid drone for sequencing allowed a refined analysis of very large tandem repeat arrays, raising the question of their function in the genome. High quality genome assemblies for multiple subspecies such as presented here, are crucial for emerging projects using pangenomes.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"59 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141462511","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":"Allele-specific binding variants causing ChIP-seq peak height of histone modification are not enriched in expression QTL annotations","authors":"Mohammad Ghoreishifar, Amanda J. Chamberlain, Ruidong Xiang, Claire P. Prowse-Wilkins, Thomas J. Lopdell, Mathew D. Littlejohn, Jennie E. Pryce, Michael E. Goddard","doi":"10.1186/s12711-024-00916-4","DOIUrl":"https://doi.org/10.1186/s12711-024-00916-4","url":null,"abstract":"Genome sequence variants affecting complex traits (quantitative trait loci, QTL) are enriched in functional regions of the genome, such as those marked by certain histone modifications. These variants are believed to influence gene expression. However, due to the linkage disequilibrium among nearby variants, pinpointing the precise location of QTL is challenging. We aimed to identify allele-specific binding (ASB) QTL (asbQTL) that cause variation in the level of histone modification, as measured by the height of peaks assayed by ChIP-seq (chromatin immunoprecipitation sequencing). We identified DNA sequences that predict the difference between alleles in ChIP-seq peak height in H3K4me3 and H3K27ac histone modifications in the mammary glands of cows. We used a gapped k-mer support vector machine, a novel best linear unbiased prediction model, and a multiple linear regression model that combines the other two approaches to predict variant impacts on peak height. For each method, a subset of 1000 sites with the highest magnitude of predicted ASB was considered as candidate asbQTL. The accuracy of this prediction was measured by the proportion where the predicted direction matched the observed direction. Prediction accuracy ranged between 0.59 and 0.74, suggesting that these 1000 sites are enriched for asbQTL. Using independent data, we investigated functional enrichment in the candidate asbQTL set and three control groups, including non-causal ASB sites, non-ASB variants under a peak, and SNPs (single nucleotide polymorphisms) not under a peak. For H3K4me3, a higher proportion of the candidate asbQTL were confirmed as ASB when compared to the non-causal ASB sites (P < 0.01). However, these candidate asbQTL did not enrich for the other annotations, including expression QTL (eQTL), allele-specific expression QTL (aseQTL) and sites conserved across mammals (P > 0.05). We identified putatively causal sites for asbQTL using the DNA sequence surrounding these sites. Our results suggest that many sites influencing histone modifications may not directly affect gene expression. However, it is important to acknowledge that distinguishing between putative causal ASB sites and other non-causal ASB sites in high linkage disequilibrium with the causal sites regarding their impact on gene expression may be challenging due to limitations in statistical power.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"312 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141462486","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":"Predictive ability of multi-population genomic prediction methods of phenotypes for reproduction traits in Chinese and Austrian pigs","authors":"Xue Wang, Zipeng Zhang, Hehe Du, Christina Pfeiffer, Gábor Mészáros, Xiangdong Ding","doi":"10.1186/s12711-024-00915-5","DOIUrl":"https://doi.org/10.1186/s12711-024-00915-5","url":null,"abstract":"Multi-population genomic prediction can rapidly expand the size of the reference population and improve genomic prediction ability. Machine learning (ML) algorithms have shown advantages in single-population genomic prediction of phenotypes. However, few studies have explored the effectiveness of ML methods for multi-population genomic prediction. In this study, 3720 Yorkshire pigs from Austria and four breeding farms in China were used, and single-trait genomic best linear unbiased prediction (ST-GBLUP), multitrait GBLUP (MT-GBLUP), Bayesian Horseshoe (BayesHE), and three ML methods (support vector regression (SVR), kernel ridge regression (KRR) and AdaBoost.R2) were compared to explore the optimal method for joint genomic prediction of phenotypes of Chinese and Austrian pigs through 10 replicates of fivefold cross-validation. In this study, we tested the performance of different methods in two scenarios: (i) including only one Austrian population and one Chinese pig population that were genetically linked based on principal component analysis (PCA) (designated as the “two-population scenario”) and (ii) adding reference populations that are unrelated based on PCA to the above two populations (designated as the “multi-population scenario”). Our results show that, the use of MT-GBLUP in the two-population scenario resulted in an improvement of 7.1% in predictive ability compared to ST-GBLUP, while the use of SVR and KKR yielded improvements in predictive ability of 4.5 and 5.3%, respectively, compared to MT-GBLUP. SVR and KRR also yielded lower mean square errors (MSE) in most population and trait combinations. In the multi-population scenario, improvements in predictive ability of 29.7, 24.4 and 11.1% were obtained compared to ST-GBLUP when using, respectively, SVR, KRR, and AdaBoost.R2. However, compared to MT-GBLUP, the potential of ML methods to improve predictive ability was not demonstrated. Our study demonstrates that ML algorithms can achieve better prediction performance than multitrait GBLUP models in multi-population genomic prediction of phenotypes when the populations have similar genetic backgrounds; however, when reference populations that are unrelated based on PCA are added, the ML methods did not show a benefit. When the number of populations increased, only MT-GBLUP improved predictive ability in both validation populations, while the other methods showed improvement in only one population.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"29 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141452815","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":"Breeding for resilience in finishing pigs can decrease tail biting, lameness and mortality","authors":"Wim Gorssen, Carmen Winters, Roel Meyermans, Léa Chapard, Katrijn Hooyberghs, Jürgen Depuydt, Steven Janssens, Han Mulder, Nadine Buys","doi":"10.1186/s12711-024-00919-1","DOIUrl":"https://doi.org/10.1186/s12711-024-00919-1","url":null,"abstract":"Previous research showed that deviations in longitudinal data are heritable and can be used as a proxy for pigs’ general resilience. However, only a few studies investigated the relationship between these resilience traits and other traits related to resilience and welfare. Therefore, this study investigated the relationship between resilience traits derived from deviations in longitudinal data and traits related to animal resilience, health and welfare, such as tail and ear biting wounds, lameness and mortality. In our experiment, 1919 finishing pigs with known pedigree (133 Piétrain sires and 266 crossbred dams) were weighed every 2 weeks and scored for physical abnormalities, such as lameness and ear and tail biting wounds (17,066 records). Resilience was assessed via deviations in body weight, deviations in weighing order and deviations in observed activity during weighing. The association between these resilience traits and physical abnormality traits was investigated and genetic parameters were estimated. Deviations in body weight had moderate heritability estimates (h2 = 25.2 to 36.3%), whereas deviations in weighing order (h2 = 4.2%) and deviations in activity during weighing (h2 = 12.0%) had low heritability estimates. Moreover, deviations in body weight were positively associated and genetically correlated with tail biting wounds (rg = 0.22 to 0.30), lameness (rg = 0.15 to 0.31) and mortality (rg = 0.19 to 0.33). These results indicate that events of tail biting, lameness and mortality are associated with deviations in pigs’ body weight evolution. This relationship was not found for deviations in weighing order and activity during weighing. Furthermore, individual body weight deviations were positively correlated with uniformity at the pen level, providing evidence that breeding for these resilience traits might increase both pigs’ resilience and within-family uniformity. In summary, our findings show that breeding for resilience traits based on deviations in longitudinal weight data can decrease pigs’ tail biting wounds, lameness and mortality while improving uniformity at the pen level. These findings are valuable for pig breeders, as they offer evidence that these resilience traits are an indication of animals’ general health, welfare and resilience. Moreover, these results will stimulate the quantification of resilience via longitudinal body weights in other species.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"31 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141430342","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 RHCE gene encodes the chicken blood system I","authors":"Janet E. Fulton, Amy M. McCarron, Ashlee R. Lund, Wioleta Drobik-Czwarno, Abigail Mullen, Anna Wolc, Joanna Szadkowska, Carl J. Schmidt, Robert L. Taylor","doi":"10.1186/s12711-024-00911-9","DOIUrl":"https://doi.org/10.1186/s12711-024-00911-9","url":null,"abstract":"There are 13 known chicken blood systems, which were originally detected by agglutination of red blood cells by specific alloantisera. The genomic region or specific gene responsible has been identified for four of these systems (A, B, D and E). We determined the identity of the gene responsible for the chicken blood system I, using DNA from multiple birds with known chicken I blood system serology, 600K and 54K single nucleotide polymorphism (SNP) data, and lowpass sequence information. The gene responsible for the chicken I blood system was identified as RHCE, which is also one of the genes responsible for the highly polymorphic human Rh blood group locus, for which maternal/fetal antigenic differences can result in fetal hemolytic anemia with fetal mortality. We identified 17 unique RHCE haplotypes in the chicken, with six haplotypes corresponding to known I system serological alleles. We also detected deletions in the RHCE gene that encompass more than 6000 bp and that are predicted to remove its last seven exons. RHCE is the gene responsible for the chicken I blood system. This is the fifth chicken blood system for which the responsible gene and gene variants are known. With rapid DNA-based testing now available, the impact of I blood system variation on response against disease, general immune function, and animal production can be investigated in greater detail.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"1 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141425471","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 impact of paternal age, paternal heat stress, and estimation of non-genetic paternal variance on dairy cow phenotype","authors":"Corentin Fouéré, Chris Hozé, Florian Besnard, Mekki Boussaha, Didier Boichard, Marie-Pierre Sanchez","doi":"10.1186/s12711-024-00918-2","DOIUrl":"https://doi.org/10.1186/s12711-024-00918-2","url":null,"abstract":"Linear models that are commonly used to predict breeding values in livestock species consider paternal influence solely as a genetic effect. However, emerging evidence in several species suggests the potential effect of non-genetic semen-mediated paternal effects on offspring phenotype. This study contributes to such research by analyzing the extent of non-genetic paternal effects on the performance of Holstein, Montbéliarde, and Normande dairy cows. Insemination data, including semen Batch Identifier (BI, a combination of bull identification and collection date), was associated with various traits measured in cows born from the insemination. These traits encompassed stature, milk production (milk, fat, and protein yields), udder health (somatic cell score and clinical mastitis), and female fertility (conception rates of heifers and cows). We estimated (1) the effects of age at collection and heat stress during spermatogenesis, and (2) the variance components associated with BI or Weekly aggregated BI (WBI). Overall, the non-genetic paternal effect estimates were small and of limited biological importance. However, while heat stress during spermatogenesis did not show significant associations with any of the traits studied in daughters, we observed significant effects of bull age at semen collection on the udder health of daughters. Indeed, cows born from bulls collected after 1500 days of age had higher somatic cell scores compared to those born from bulls collected at a younger age (less than 400 days old) in both Holstein and Normande breeds (+ 3% and + 5% of the phenotypic mean, respectively). In addition, across all breeds and traits analyzed, the estimates of non-genetic paternal variance were consistently low, representing on average 0.13% and 0.09% of the phenotypic variance for BI and WBI, respectively (ranging from 0 to 0.7%). These estimates did not significantly differ from zero, except for milk production traits (milk, fat, and protein yields) in the Holstein breed and protein yield in the Montbéliarde breed when WBI was considered. Our findings indicate that non-genetic paternal information transmitted through semen does not substantially influence the offspring phenotype in dairy cattle breeds for routinely measured traits. This lack of substantial impact may be attributed to limited transmission or minimal exposure of elite bulls to adverse conditions.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"46 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141334153","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":"Genomic analyses of withers height and linear conformation traits in German Warmblood horses using imputed sequence-level genotypes","authors":"Paula Reich, Sandra Möller, Kathrin F. Stock, Wietje Nolte, Mario von Depka Prondzinski, Reinhard Reents, Ernst Kalm, Christa Kühn, Georg Thaller, Clemens Falker-Gieske, Jens Tetens","doi":"10.1186/s12711-024-00914-6","DOIUrl":"https://doi.org/10.1186/s12711-024-00914-6","url":null,"abstract":"Body conformation, including withers height, is a major selection criterion in horse breeding and is associated with other important traits, such as health and performance. However, little is known about the genomic background of equine conformation. Therefore, the aim of this study was to use imputed sequence-level genotypes from up to 4891 German Warmblood horses to identify genomic regions associated with withers height and linear conformation traits. Furthermore, the traits were genetically characterised and putative causal variants for withers height were detected. A genome-wide association study (GWAS) for withers height confirmed the presence of a previously known quantitative trait locus (QTL) on Equus caballus (ECA) chromosome 3 close to the LCORL/NCAPG locus, which explained 16% of the phenotypic variance for withers height. An additional significant association signal was detected on ECA1. Further investigations of the region on ECA3 identified a few promising candidate causal variants for withers height, including a nonsense mutation in the coding sequence of the LCORL gene. The estimated heritability for withers height was 0.53 and ranged from 0 to 0.34 for the conformation traits. GWAS identified significantly associated variants for more than half of the investigated conformation traits, among which 13 showed a peak on ECA3 in the same region as withers height. Genetic parameter estimation revealed high genetic correlations between these traits and withers height for the QTL on ECA3. The use of imputed sequence-level genotypes from a large study cohort led to the discovery of novel QTL associated with conformation traits in German Warmblood horses. The results indicate the high relevance of the QTL on ECA3 for various conformation traits, including withers height, and contribute to deciphering causal mutations for body size in horses.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"111 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141315582","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}