Animal genetics最新文献_第3页

Ascertainment Bias in Cattle SNP Arrays and Implications for Multibreed Genomic Predictions 牛SNP序列的确定偏差及其对多品种基因组预测的影响。

IF 2.1 3区生物学

Animal genetics Pub Date : 2026-03-17 DOI: 10.1002/age.70081

Christie L. Warburton, Ben J. Hayes

引用次数: 0

Genome Sequencing and Genome-Wide Analysis Uncover Candidate Genes and Loci Linked to Key Production Traits in the Philippine Black Tiger Shrimp (Penaeus monodon) 基因组测序和全基因组分析揭示了菲律宾黑虎对虾（Penaeus monodon）关键生产性状的候选基因和位点。

IF 2.1 3区生物学

Animal genetics Pub Date : 2026-03-16 DOI: 10.1002/age.70082

Kreighton E. Cadorna, Zae-Zae A. Aguinaldo, Miguel Paolo E. de la Cruz, Hannah Mae E. Pasaquian, Valeriano L. Corre Jr, Fe Dolores P. Estepa, Edgar C. Amar, Mary Beth B. Maningas, Arturo O. Lluisma

{"title":"Genome Sequencing and Genome-Wide Analysis Uncover Candidate Genes and Loci Linked to Key Production Traits in the Philippine Black Tiger Shrimp (Penaeus monodon)","authors":"Kreighton E. Cadorna, Zae-Zae A. Aguinaldo, Miguel Paolo E. de la Cruz, Hannah Mae E. Pasaquian, Valeriano L. Corre Jr, Fe Dolores P. Estepa, Edgar C. Amar, Mary Beth B. Maningas, Arturo O. Lluisma","doi":"10.1002/age.70082","DOIUrl":"10.1002/age.70082","url":null,"abstract":"<div>\u0000 \u0000 Penaeus monodon (black tiger shrimp) is a key species in aquaculture globally and in the Philippines. The selection and development of stocks with desirable production traits, such as enhanced growth and disease resistance, are critical for improving production. In this study, we leveraged a newly assembled, high-quality genome sequence from a Philippine population to perform genome-wide scans for SNPs associated with key production traits. Using cohort-based extreme phenotype GWAS (XP-GWAS), we identified variants linked to resistance against white spot syndrome virus (WSSV), body weight, and carapace length-to-abdomen length (CL/AL) ratio. Candidate genes previously implicated in immune defense and growth regulation were located within 1-Mb regions surrounding these variants, reinforcing their likely functional involvement and providing biological support for the associations. These findings highlight genomic loci and gene candidates of direct relevance to selective breeding, offering molecular markers with potential utility in stock improvement programs for P. monodon. These genomic data, alongside the identified polymorphisms, constitute a valuable resource for enhancement of production and selective breeding strategies in the Penaeid species, contributing to the improvement of shrimp aquaculture.\u0000 </div>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147466648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evidence That GYPA (Glycophorin A) Encodes the K Blood Group System in Horses GYPA（糖蛋白A）编码马K血型系统的证据。

IF 2.1 3区生物学

Animal genetics Pub Date : 2026-03-16 DOI: 10.1002/age.70083

Mariusz Mackowski, Arkadiusz Kajdasz, Kaja Laskowska, Jakub Cieslak

{"title":"Evidence That GYPA (Glycophorin A) Encodes the K Blood Group System in Horses","authors":"Mariusz Mackowski, Arkadiusz Kajdasz, Kaja Laskowska, Jakub Cieslak","doi":"10.1002/age.70083","DOIUrl":"10.1002/age.70083","url":null,"abstract":"<div>\u0000 \u0000 Although serological and genetic studies of equine blood group systems have been conducted for many years, the molecular basis of erythrocyte antigens' variability has remained largely unexplored. In this study, we aimed to elucidate the genetic basis of serological variation within equine blood group K. Using mRNA extracted from peripheral blood samples (n = 100) collected from horses with known serological blood types (Ka or K-), we performed a transcriptome-wide association study (TWAS), which revealed a significantly associated region on equine chromosome 2 (ECA2). A detailed analysis of this region identified GYPA (glycophorin A) as the most promising candidate gene. Resequencing its entire coding sequence revealed the presence of a dinucleotide missense variant in exon 3 (ENSECAT00000026370.3:c.145_146delinsAT; p.Asp49Ile), which is predicted to potentially alter the function of the GYPA protein. Genotyping this variant in a large, breed-diverse cohort, which included family-based samples, confirmed perfect cosegregation between the identified GYPA missense substitution and serological K blood group typing results. Our findings demonstrate that blood transcriptome-based approaches, despite certain limitations, can effectively reveal the molecular basis of equine erythrocyte antigen variability.\u0000 </div>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147466646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring the Role of Rumen Microbiota and KLF15 Gene in the Performance of Growing Hu Sheep 瘤胃微生物群及KLF15基因对生长湖羊生产性能的影响

IF 2.1 3区生物学

Animal genetics Pub Date : 2026-03-13 DOI: 10.1002/age.70080

Xiaobin Yang, Jiangbo Cheng, Xiaoxue Zhang, Huibin Tian, Xiuxiu Weng, Yukun Zhang, Deyin Zhang, Dan Xu, Kai Huang, Xiaolong Li, Yuan Zhao, Liming Zhao, Quanzhong Xu, Zongwu Ma, Fadi Li, Weimin Wang

{"title":"Exploring the Role of Rumen Microbiota and KLF15 Gene in the Performance of Growing Hu Sheep","authors":"Xiaobin Yang, Jiangbo Cheng, Xiaoxue Zhang, Huibin Tian, Xiuxiu Weng, Yukun Zhang, Deyin Zhang, Dan Xu, Kai Huang, Xiaolong Li, Yuan Zhao, Liming Zhao, Quanzhong Xu, Zongwu Ma, Fadi Li, Weimin Wang","doi":"10.1002/age.70080","DOIUrl":"10.1002/age.70080","url":null,"abstract":"<div>\u0000 \u0000 Exon mutations and the rumen microbiome play crucial roles in influencing growth performance in meat animals, making them key factors for enhancing meat production efficiency. This study aimed to further investigate the effects of host genetics (KLF15 c.6256511 A>G) and rumen microorganisms on the growth performance of Hu sheep. This study selected 50 growing Hu sheep with extreme body weight and uniformly fed them a diet with a concentrateto-roughage ratio of approximately 1.5:1. Rumen content samples were collected for 16S rDNA sequencing. Growth traits and feed efficiency were measured at 80, 100, 120, 140, 160, and 180 days of age. The high body weight (H-BW) group exhibited better production performance, with significant differences found in growth traits, slaughter traits, and fat deposition traits between the H-BW and low weight (L-BW) group (P < 0.05). Among the 23 different bacterial genera identified, Rikenellaceae_RC9_gut_group was significantly correlated with 180-day body weight and muscle fat content of Hu sheep. The relative abundance of Rikenellaceae_RC9_gut_group was lowest in Hu sheep with the AA genotype (P < 0.05). No significant difference in rumen microbial diversity was observed between the H-BW and L-BW groups. Rikenellaceae_RC9_gut_group may activate the mTOR signaling pathway through the metabolic pathway of valeric acid, promote the growth of muscle cells, and thus regulate the body weight of Hu sheep. Utilizing the KLF15 c.6256511 A>G mutation site and the Rikenellaceae_RC9_gut_group provides a valuable approach to enhance the growth traits and overall production performance of Hu sheep.\u0000 </div>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147442251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrative analysis of quantitative trait loci of alternative polyadenylation and GWAS highlights key regulators of milk production and immune traits in Holstein 选择性聚腺苷酸化和GWAS数量性状位点的综合分析揭示了荷斯坦奶牛产奶量和免疫性状的关键调控因子。

IF 2.1 3区生物学

Animal genetics Pub Date : 2026-03-03 DOI: 10.1002/age.70071

Xinyue Tao, Yongjie Tang, Xueqin Liu, Miaozhuo Ni, Wanyi Lai, Siqian Chen, Ying Yu

{"title":"Integrative analysis of quantitative trait loci of alternative polyadenylation and GWAS highlights key regulators of milk production and immune traits in Holstein","authors":"Xinyue Tao, Yongjie Tang, Xueqin Liu, Miaozhuo Ni, Wanyi Lai, Siqian Chen, Ying Yu","doi":"10.1002/age.70071","DOIUrl":"10.1002/age.70071","url":null,"abstract":"Understanding the genetic regulation of complex traits like mastitis in Holstein dairy cows remains a challenge, despite significant advancements in breeding techniques. This study integrates 3′-untranslated region alternative polyadenylation (APA) quantitative trait loci (3′aQTL) mapping with genome-wide association studies (GWASs) to identify key genetic variants and regulatory genes influencing traits during early lactation. Heritability analysis showed that, on average, cis-acting SNPs explained 22% of percentage of distal polyA site usage index (PDUI) variance, supporting a genetic basis for APA regulation. Building on this, we identified 1143 significant cis-3′aQTL associated with PDUI variation across 215 genes (3′aGenes), with significant enrichment in immune system and disease-related pathways. Comparisons with expression quantitative trait loci (eQTL) revealed limited overlap, suggesting distinct regulatory mechanisms. SNP rs109421300 was found to co-localize with GWAS signals for milk protein, mastitis and ketosis traits. Further analysis linked rs109421300 to the regulation of GRINA via APA, with predicted transcription factor interactions involving NRF1 and RUNX. These findings enhance our understanding of the genetic basis of economically important traits in dairy cows and provide a foundation for precision breeding strategies.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12955697/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147343243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

FGF5 Allelic Heterogeneity in Long-Haired Belgian Shepherd Dogs 比利时长毛牧羊犬FGF5等位基因异质性研究

IF 2.1 3区生物学

Animal genetics Pub Date : 2026-03-03 DOI: 10.1002/age.70084

Marcela Bielikova, Evelina Hrckova Turnova, Viktoria Kostal, Zuzana Majchrakova, Jan Turna, Andrej Dudas

引用次数: 0

Correction to “GJB6 missense variant in a Labrador Retriever with paw pad hyperkeratosis” 更正“患爪垫角化过度的拉布拉多猎犬的GJB6错义变异”。

IF 2.1 3区生物学

Animal genetics Pub Date : 2026-02-18 DOI: 10.1002/age.70079

引用次数: 0

Longitudinal Genome-Wide Association Study for Female Fertility Traits in German Holstein Cattle 德国荷斯坦牛雌性生育性状的纵向全基因组关联研究。

IF 2.1 3区生物学

Animal genetics Pub Date : 2026-02-11 DOI: 10.1002/age.70078

S. Sakhaeifar, T. Yin, S. König

{"title":"Longitudinal Genome-Wide Association Study for Female Fertility Traits in German Holstein Cattle","authors":"S. Sakhaeifar, T. Yin, S. König","doi":"10.1002/age.70078","DOIUrl":"10.1002/age.70078","url":null,"abstract":"The aim of this genome-wide association study (GWAS) was to detect significant SNP effects influencing the dynamic process of female fertility in dairy cattle over lactations, to identify possible candidate genes and to study their role in pathway analyses. We considered records for the female fertility traits non-return rate after 56 days (NRR56), interval from calving to first service (CTFS) and days open (DO) up to parity six from 190 269 lactating Holstein cows and heifers. The longitudinal GWAS followed a 2-step approach. In step 1, we estimated (co)variance components by combining pedigree and genomic relationships in random regression models with additive-genetic and permanent environmental regressions on the time-dependent gradient ‘parity’. The matrix for estimated (co)variance components for random regression coefficients from step 1 was integrated into the longitudinal GWAS in step 2 to estimate SNP effects and significance for (a) the outer ‘layer’ representing baseline effects (intercept), (b) the middle ‘layer’ representing the slope and (c) the inner ‘layer’ indicating significant SNPs in all lactations, but with differing effects. For the ‘inner layer’, we detected the following five potential candidate genes: TMEM132C and IMPG1 for NRR56, DCHS2 for CTFS and CSMD1 and CSNK1A1 for DO. The identified genes also play a dominant role in biological pathways related to physiological fertility mechanisms. Overall, the longitudinal GWAS illustrated the dynamic genetic mechanisms of gene regulations on female fertility traits with progressing time.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 1","pages":""},"PeriodicalIF":2.1,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12893027/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146155891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development of a 21-plex STR typing system for the identification of individuals and parentage testing in pig 猪个体鉴定和亲子鉴定用21层STR分型系统的研制。

IF 2.1 3区生物学

Animal genetics Pub Date : 2026-02-04 DOI: 10.1002/age.70072

Xiao-cui Duan, Shang-tong Li, Ayoola Ebenezer Afe, Shao-jie Wang, Zhi-qiang Chen, Xu-dong Zhang, Kui Li, Gang Liu, Rong Zhou

{"title":"Development of a 21-plex STR typing system for the identification of individuals and parentage testing in pig","authors":"Xiao-cui Duan, Shang-tong Li, Ayoola Ebenezer Afe, Shao-jie Wang, Zhi-qiang Chen, Xu-dong Zhang, Kui Li, Gang Liu, Rong Zhou","doi":"10.1002/age.70072","DOIUrl":"10.1002/age.70072","url":null,"abstract":"Precise identification of individuals and accurate parentage verification is critical to livestock breeding programs, facilitating efficient genetic improvement and management practices. Short tandem repeat (STR)-based genotyping in pigs, current genotyping methods are often limited by inadequate resolution, suboptimal throughput and susceptibility to cross-species amplification. This study addresses these limitations by developing and validating a robust, species-specific 21-plex STR typing system. Integrating 13 core loci recommended by International Society for Animal Genetics/Food and Agriculture Organization with eight additional polymorphic markers identified from high-throughput sequencing, the multiplex assay was optimized for simultaneous amplification using fluorescence-labeled primers and capillary electrophoresis. Comprehensive primer optimization and thermal cycling adjustments established uniform amplification conditions, achieving balanced peak heights and distinct genotyping profiles with a sensitivity threshold of 0.5 ng DNA input per reaction. Species-specificity testing demonstrated no cross-reactivity with sheep, cattle and dogs and only weak amplification for the IGF1 locus in cats without compromising genotyping accuracy. Validation using diverse pig populations confirmed the assay's high discriminatory power and reproducibility. The resulting assay is technically rigorous, scalable and cost-effective, making it suitable for broad application in pig genetic improvement programs, pedigree verification, meat traceability and germplasm conservation.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 1","pages":""},"PeriodicalIF":2.1,"publicationDate":"2026-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146117724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Large deletions in the DNA primase large subunit PRIM2 are associated with NADP-malate dehydrogenase activity in a porcine F2 cross 在猪F2杂交中，DNA引物酶大亚基PRIM2的大缺失与nadp -苹果酸脱氢酶活性相关。

IF 2.1 3区生物学

Animal genetics Pub Date : 2026-02-02 DOI: 10.1002/age.70077

Clemens Falker-Gieske, Iulia Blaj, Ana-Marija Krizanac, Isabel Kilic, Paula Reich, Jörn Bennewitz, Jens Tetens

{"title":"Large deletions in the DNA primase large subunit PRIM2 are associated with NADP-malate dehydrogenase activity in a porcine F2 cross","authors":"Clemens Falker-Gieske, Iulia Blaj, Ana-Marija Krizanac, Isabel Kilic, Paula Reich, Jörn Bennewitz, Jens Tetens","doi":"10.1002/age.70077","DOIUrl":"10.1002/age.70077","url":null,"abstract":"Large porcine F2 crosses are a valuable resource for discovering QTL and genetic variants for relevant traits. Past studies have been largely limited to SNPs and short insertions and deletions. Structural variants (SVs) are becoming a major area of interest in this respect. Here we present results from a genome-wide association study with SVs imputed from medium-density SNP array to the whole genome sequence level that were used to investigate the genetic relationship between important production traits and metabolic enzyme activity in an F2 cross based on the breeds Meishan, Piétrain, and European wild boar. Genetic and phenotypic correlations between the two trait classes were high. We were able to pinpoint common genetic loci to a QTL on SSC7, encompassing numerous large intron deletions in the PRIM2 gene as well as in HMGCLL1, BMP5, TRERF1, COL21A1, LRRC1, and UBR2. The most pronounced genetic associations were observed for the content of NADP-malate dehydrogenase in the tissue. Hence, we propose that the content and activity of malate dehydrogenase is directly connected to important pig production traits, and we present a comprehensive list of large intronic deletions as promising candidates for causality. The variants were validated in independent pig populations, where the majority of the discovered SVs were present, indicating that they are not only relevant to the breeds investigated here.","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 1","pages":""},"PeriodicalIF":2.1,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12864183/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146103616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0