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Multi-Omics Reveals Divergent Gut Microbiome–Metabolome Associations Between High-Altitude Snowcock and Low-Altitude Pheasant 多组学揭示高海拔雪公鸡和低海拔野鸡肠道微生物代谢组学差异
IF 2.2 3区 生物学
Animal genetics Pub Date : 2026-11-06 DOI: 10.1002/age.70231
Xueting Chai, Wenjun Yan, Lanting Wei, Lihong Ning, Chenxin Gao, Yong Zhang, Ping Cuo, Runjin Wang, Manjun Yang, Hui Wang
{"title":"Multi-Omics Reveals Divergent Gut Microbiome–Metabolome Associations Between High-Altitude Snowcock and Low-Altitude Pheasant","authors":"Xueting Chai,&nbsp;Wenjun Yan,&nbsp;Lanting Wei,&nbsp;Lihong Ning,&nbsp;Chenxin Gao,&nbsp;Yong Zhang,&nbsp;Ping Cuo,&nbsp;Runjin Wang,&nbsp;Manjun Yang,&nbsp;Hui Wang","doi":"10.1002/age.70231","DOIUrl":"10.1002/age.70231","url":null,"abstract":"<div>\u0000 \u0000 <p>The gut microecological differences associated with high-altitude habitats remain poorly understood. The Snowcock (<i>Tetraogallus tibetanus</i>), a high-altitude bird endemic to the Qinghai-Xizang Plateau, and the low-altitude Pheasant (<i>Phasianus colchicus</i>) differ strikingly in habitat elevation and diet, providing an ideal comparative model. Fecal samples from six Snowcocks and six Pheasants were analyzed using 16S rRNA gene sequencing and UPLC-MS/MS untargeted metabolomics. Multi-omics integration was performed via Procrustes analysis, correlation networks, and random forest classification. Snowcocks displayed significantly lower alpha diversity and distinct beta diversity clustering compared with Pheasants. The Snowcock microbiota was dominated by Actinobacteriota and enriched in cold-tolerant genera such as <i>Psychrobacillus</i>. In contrast, the Pheasant microbiota showed higher diversity and was dominated by Firmicutes and Bacteroidota. Metabolomics revealed that differential metabolites enriched in Pheasants were predominantly mapped to amino acid metabolism and terpenoid biosynthesis pathways, while those enriched in Snowcocks were linked to glycerophospholipid and sphingolipid metabolism. Multi-omics integration demonstrated a significantly correlated microbiome–metabolome association, and the random forest model discriminated the two species in this dataset. The Snowcock microbiota was simplified and enriched with psychrophilic genera, and its fecal metabolome showed specific glycerophospholipid signatures. These features may reflect microecological divergence associated with the harsh plateau environment. Our findings provide multi-omics insights into high-altitude divergence in wild birds.</p>\u0000 </div>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 6","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149340386","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
Genome-Wide Analysis of Resistance to Gastrointestinal Parasites in Portuguese Merino and Merino-Related Sheep 葡萄牙美利奴及美利奴亲缘羊对胃肠道寄生虫耐药性的全基因组分析。
IF 2.2 3区 生物学
Animal genetics Pub Date : 2026-11-04 DOI: 10.1002/age.70218
Daniel Gaspar, Catarina Ginja, Nuno Carolino, Célia Leão, Helena Monteiro, Lino Tábuas, Sandra Branco, Pedro Caetano, Ricardo Romão, Claudino Matos, Elisa Bettencourt, António Marcos Ramos, Ana Usié, Ludovina Padre
{"title":"Genome-Wide Analysis of Resistance to Gastrointestinal Parasites in Portuguese Merino and Merino-Related Sheep","authors":"Daniel Gaspar,&nbsp;Catarina Ginja,&nbsp;Nuno Carolino,&nbsp;Célia Leão,&nbsp;Helena Monteiro,&nbsp;Lino Tábuas,&nbsp;Sandra Branco,&nbsp;Pedro Caetano,&nbsp;Ricardo Romão,&nbsp;Claudino Matos,&nbsp;Elisa Bettencourt,&nbsp;António Marcos Ramos,&nbsp;Ana Usié,&nbsp;Ludovina Padre","doi":"10.1002/age.70218","DOIUrl":"10.1002/age.70218","url":null,"abstract":"<p>Gastrointestinal nematodes (GIN) are one of the main constraints affecting sheep production worldwide. For decades, control methods based on anthelmintics have been extensively used, which ended up in multiple drug-resistant helminth strains. Selective breeding for disease resistance is a long-term and sustainable strategy to improve animal health, welfare and productivity. Therefore, we performed a genome-wide association study using a customized SNP panel to identify genomic regions and molecular mechanisms associated with GIN resistance/susceptibility among Portuguese Merino and Merino-related sheep. Two SNPs located within <i>centromere protein K</i> (chr 16; 14 439 999 bp) and <i>NADH: ubiquinone oxidoreductase complex assembly factor 2</i> (chr 16; 19 366 442 bp) genic regions reached genome-wide Bonferroni significance (<i>p</i> = 2.08 × 10<sup>−6</sup>). Additionally, five genome-wide suggestive SNPs were detected within genic regions of <i>adenomatous polyposis coli regulator of WNT signaling pathway</i> (chr 7; 1 050 994 bp), <i>regulator of G protein signaling 8</i> (chr 12; 68 278 650 bp) and <i>hypoxia inducible factor 3 subunit alpha</i> (chr 14; 57 059 428 bp), as well as in intergenic regions near <i>calcium binding and coiled-coil domain 1</i> and <i>ATP synthase membrane subunit C locus 2</i> (chr 3 142 391 546 bp) and <i>semaphorin-6D</i> (chr 7; 65 321 727 bp). Candidate genes located in these regions are involved in intestinal homeostasis, epithelial barrier reinforcement, and regulatory mechanisms of immune response. These results provide new and useful information about the genetic architecture underlying GIN infection in Portuguese Merino sheep. Further analyses are needed to validate these SNPs and assess their contribution to selection strategies focused on breeding animals with enhanced GIN resistance.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 6","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13732543/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149317253","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
Generative Adversarial Networks for Omics Data: An Overview and Future Directions for Livestock Applications 组学数据的生成对抗网络:畜牧业应用的概述和未来方向。
IF 2.2 3区 生物学
Animal genetics Pub Date : 2026-10-27 DOI: 10.1002/age.70226
Edgar Caballero Vargas, Tiago Bresolin
{"title":"Generative Adversarial Networks for Omics Data: An Overview and Future Directions for Livestock Applications","authors":"Edgar Caballero Vargas,&nbsp;Tiago Bresolin","doi":"10.1002/age.70226","DOIUrl":"10.1002/age.70226","url":null,"abstract":"<p>Generative adversarial networks (GANs) are artificial intelligence models designed to generate novel data that is indistinguishable from real data. Originally developed to generate images to complement existing datasets and create more diverse samples, GAN-based data can enhance downstream analysis for machine learning and deep learning applications. GAN-based approaches are also versatile and suitable for augmenting omics data, improving downstream analyses such as genotype prediction, biomarker detection, and protein de novo design. In addition, GANs can preserve and reconstruct genomic regions under selective pressure, increase sample sizes from underrepresented groups, and mitigate class imbalance effects in genomic analyses, transcriptomics, and single-cell omics. Recent work also demonstrates that GAN-generated data can support privacy-preserving data sharing and the design of novel biological sequences and proteins. This literature review presents the foundational concepts of GANs, explores diverse applications across omics fields, and highlights novel opportunities for applying GAN approaches in livestock genomics.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 6","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13713198/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149284863","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
Functional Effects of IGF2BP2 Genetic Variants on Growth Traits in Sheep IGF2BP2遗传变异对绵羊生长性状的功能影响
IF 2.2 3区 生物学
Animal genetics Pub Date : 2026-10-26 DOI: 10.1002/age.70228
Tingting Li, Enzhao Dong, Haitao Wang, Na Zhang, Jianning He, Qiuyue Liu
{"title":"Functional Effects of IGF2BP2 Genetic Variants on Growth Traits in Sheep","authors":"Tingting Li,&nbsp;Enzhao Dong,&nbsp;Haitao Wang,&nbsp;Na Zhang,&nbsp;Jianning He,&nbsp;Qiuyue Liu","doi":"10.1002/age.70228","DOIUrl":"https://doi.org/10.1002/age.70228","url":null,"abstract":"<div>\u0000 \u0000 <p>Growth traits are economically important in sheep, but the regulatory variants contributing to body-weight variation remain incompletely characterized. A selective-sweep analysis identified a candidate region on chromosome 1 containing <i>IGF2BP2</i>. Sequence comparison indicated that <i>IGF2BP2</i> is highly conserved across mammals. Genotyping of Hu sheep, Hulunbuir sheep, and Tan sheep identified Chr1 g.202274996G&gt;A was significantly associated with sheep body weight at 6 months of age. Epigenomic data indicated that the region containing this variant has features of an active cis-regulatory element, and dual-luciferase assays showed that the A allele reduced enhancer activity relative to the G allele. In isogenic sheep fetal fibroblast clones generated by cytosine base editing, the AA genotype was associated with lower <i>IGF2BP2</i> and <i>CCAR1</i> expression than the GG genotype. MeRIP-qPCR further indicated genotype-dependent differences in m<sup>6</sup>A-enriched <i>CCAR1</i> RNA. Together, these findings support Chr1 g.202274996G&gt;A as a candidate regulatory variant affecting <i>IGF2BP2</i> expression and body weight in Hu sheep, and provide a potential molecular marker for the genetic improvement of growth traits in sheep.</p>\u0000 </div>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 6","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149259460","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
Resequencing-Based GWAS Highlights SNP and Indel Loci and lncRNA Candidates for Carcass Yield and Meat Quality in Yellow-Feathered Broilers 基于重测序的GWAS揭示了黄羽肉鸡胴体产量和肉品质的SNP、Indel位点和lncRNA候选位点
IF 2.2 3区 生物学
Animal genetics Pub Date : 2026-10-22 DOI: 10.1002/age.70224
Ziqing Li, Hanxue Sun, Jun Xu, Rahmani Mohammad Malyar, Li Chen, Tao Zeng, Wei Ding, Xingwang Lu, Lizhi Lu, Fangxiong Shi
{"title":"Resequencing-Based GWAS Highlights SNP and Indel Loci and lncRNA Candidates for Carcass Yield and Meat Quality in Yellow-Feathered Broilers","authors":"Ziqing Li,&nbsp;Hanxue Sun,&nbsp;Jun Xu,&nbsp;Rahmani Mohammad Malyar,&nbsp;Li Chen,&nbsp;Tao Zeng,&nbsp;Wei Ding,&nbsp;Xingwang Lu,&nbsp;Lizhi Lu,&nbsp;Fangxiong Shi","doi":"10.1002/age.70224","DOIUrl":"https://doi.org/10.1002/age.70224","url":null,"abstract":"<div>\u0000 \u0000 <p>Carcass and meat quality traits are economically important in poultry breeding. To investigate their genetic architecture and identify potential candidate regulators, we performed whole-genome resequencing (WGS) and an integrative genome-wide association study (GWAS) on 315 breast muscle samples from yellow-feathered broilers, jointly analyzing SNP and Indels across 14 carcass and meat quality traits. We identified about 13.5 million SNPs and 1.24 million Indels. Across 14 carcass and meat quality traits, 364 significant SNPs (<i>p</i> &lt; 1.0 × 10<sup>6</sup>) and 52 significant Indels (<i>p</i> &lt; 1.0 × 10<sup>−6</sup>) were detected, clustering into nine genomic regions. Key candidate genes included <i>CNTN5</i> for leg muscle percentage, <i>SORCS1</i> for crude fat (CF), <i>CNN3</i> for shear force, and <i>APOB</i> and <i>SQLE</i> for total cholesterol. We further used tissue-specific transcriptome-derived lncRNA annotations to identify candidate lncRNAs located within ±100 kb of significant GWAS loci. These lncRNAs were prioritized as genomic-proximity-based candidates for future functional validation. Functional enrichment analysis indicated involvement of PI3K-Akt and Wnt signaling pathways, lipid metabolism, and cytoskeletal regulation. These findings provide new insights into the genetic basis of carcass yield and meat quality traits in yellow-feathered chickens and offer molecular markers and regulatory candidates for future molecular breeding strategies.</p>\u0000 </div>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 6","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149235339","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
Genome-Wide Characterization of Heterozygosity-Rich Regions in Kazakh Native Sheep Breeds. 哈萨克地方绵羊品种杂合性丰富区域的全基因组特征
IF 2.2 3区 生物学
Animal genetics Pub Date : 2026-10-01 DOI: 10.1002/age.70219
Sholpan Bakhtybekkyzy, Zarina Orazymbetova, Aizhan Mussayeva, Aidana Bekitayeva, Ajoy Mandal, Hasan Baneh
{"title":"Genome-Wide Characterization of Heterozygosity-Rich Regions in Kazakh Native Sheep Breeds.","authors":"Sholpan Bakhtybekkyzy, Zarina Orazymbetova, Aizhan Mussayeva, Aidana Bekitayeva, Ajoy Mandal, Hasan Baneh","doi":"10.1002/age.70219","DOIUrl":"10.1002/age.70219","url":null,"abstract":"<p><p>Heterozygosity-rich regions (HRR) are genomic segments characterized by high heterozygosity that may arise from admixture, introgression, or balancing selection and may harbor loci associated with adaptation and fitness-related traits. This study aimed to characterize HRR patterns in five Kazakh sheep breeds using a publicly available OvineSNP50 genotyping dataset. After quality control, ~25 000 SNPs were retained for 1634 Akzhaiyk, 1089 Edilbay, 532 Kazakh Fine-Wool, 932 Kazakh Semi-Coarse, and 282 Saryarka sheep. HRR were detected separately in each breed using the sliding-window approach in detectRUNS R package, with a minimum segment length of 250 kb, at least 10 SNPs per window and segment, and a maximum of two opposing homozygous and one missing SNP per window. The average number of HRR per individual ranged from 40.75 ± 6.38 in Saryarka to 54.75 ± 7.34 in Kazakh Fine-Wool sheep. HRR lengths ranged from 259.07 kb to 3.26 Mb, with an average of 0.7 Mb across breeds. Seventeen HRR islands, defined as regions shared by HRR in at least 25% of individuals within a breed, were identified, including regions on chromosomes 8 and 17 shared across all breeds. Genes overlapping these islands were associated with cellular homeostasis, immunity, metabolism, growth, and stress response, while the HRR islands overlapped with QTL associated with health, wool characteristics, and reproduction. These findings highlight the potential of HRR analysis to identify candidate genomic regions relevant to adaptation and economically important traits, providing insights for the conservation and genetic improvement of Kazakh sheep populations.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 5","pages":"e70219"},"PeriodicalIF":2.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13669415/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149178996","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
Implementation of Metafounders in the Genomic Prediction for the Polled Trait in Brahman Cattle Using a Multi-Breed Population. 利用多品种群体实现元创始人对婆罗门牛轮询性状的基因组预测。
IF 2.2 3区 生物学
Animal genetics Pub Date : 2026-10-01 DOI: 10.1002/age.70211
Lanna Maryana Costa Pereira, Fernando Baldi, Ludmilla Costa Brunes, Luís Camaripano, Cláudio Ulhôa Magnabosco
{"title":"Implementation of Metafounders in the Genomic Prediction for the Polled Trait in Brahman Cattle Using a Multi-Breed Population.","authors":"Lanna Maryana Costa Pereira, Fernando Baldi, Ludmilla Costa Brunes, Luís Camaripano, Cláudio Ulhôa Magnabosco","doi":"10.1002/age.70211","DOIUrl":"10.1002/age.70211","url":null,"abstract":"<p><p>The absence of horns (polled trait) in cattle is associated with better animal welfare by reducing the need for dehorning. In Brahman cattle, population size and the scarcity of phenotypic records challenge the accuracy of genomic predictions for this trait. This study aimed to evaluate the genetic architecture of this trait in Brahman cattle using single-breed and multi-breed genomic prediction models, including metafounders, and to assess the influence of phenotypic classifications on heritability, prediction accuracy, bias, and dispersion. Phenotypic and genotypic data from 14 333 Nelore and Brahman animals were analyzed using threshold and linear models implemented in the BLUPF90+ software suite. Single-breed models (n = 12) were considered phenotypes (polled, scab, scur, horned), while multi-breed models (n = 10) incorporated metafounders and breed effects. Variance components were estimated via threshold models with Gibbs sampling, and predictive ability was assessed using the LR method with datasets. Single-breed models showed heritability estimates (h<sup>2</sup>) ranging from 0.56 to 0.72, but with predictive ability reflecting the Brahman population size. Multi-breed models improved predictive performance. Results were obtained with Model 20, which included alternative phenotypes, metafounders, and breed effects, yielding accuracy (0.79), reduced bias (0.36), and dispersion close to 1. These findings demonstrate that the polled trait in Brahman cattle exhibits additive genetic variability amenable to selection. The use of multi-breed analyses and metafounders enhances predictive accuracy, providing a strategy for populations and traits, and enables the inclusion of traits as genomic selection criterion to increase allele frequency in Brahman cattle and improve animal welfare.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 5","pages":"e70211"},"PeriodicalIF":2.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13621921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149073375","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
FLCN Multi-Exon Deletion in a Chihuahua With Renal Cysts and Nodular Dermatofibrosis. 患有肾囊肿和结节性皮肤纤维化的吉娃娃FLCN多外显子缺失。
IF 2.2 3区 生物学
Animal genetics Pub Date : 2026-10-01 DOI: 10.1002/age.70215
Melvin Schneiter, Julie Selz, Jacky Jonker, Martina Dettwiler, Vidhya Jagannathan, Tosso Leeb, Elisa Maina
{"title":"FLCN Multi-Exon Deletion in a Chihuahua With Renal Cysts and Nodular Dermatofibrosis.","authors":"Melvin Schneiter, Julie Selz, Jacky Jonker, Martina Dettwiler, Vidhya Jagannathan, Tosso Leeb, Elisa Maina","doi":"10.1002/age.70215","DOIUrl":"10.1002/age.70215","url":null,"abstract":"","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 5","pages":"e70215"},"PeriodicalIF":2.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13621923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149073400","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
Weighted Single-Step GWAS Reveals Genetic Mechanisms Underlying Pregnancy Loss in Early Nellore Heifers. 加权单步GWAS揭示了早期母牛妊娠丢失的遗传机制。
IF 2.2 3区 生物学
Animal genetics Pub Date : 2026-10-01 DOI: 10.1002/age.70212
Flávia C Bis, Nedenia Bonvino Stafuzza, Elisângela Chicaroni de Mattos, Angélica Simone Cravo Pereira, José Bento Sterman Ferraz, Fernando Baldi, Sabrina T Amorim
{"title":"Weighted Single-Step GWAS Reveals Genetic Mechanisms Underlying Pregnancy Loss in Early Nellore Heifers.","authors":"Flávia C Bis, Nedenia Bonvino Stafuzza, Elisângela Chicaroni de Mattos, Angélica Simone Cravo Pereira, José Bento Sterman Ferraz, Fernando Baldi, Sabrina T Amorim","doi":"10.1002/age.70212","DOIUrl":"10.1002/age.70212","url":null,"abstract":"<p><p>Pregnancy loss (PL) affects reproductive efficiency in beef cattle, yet its genetic architecture remains poorly understood in Bos indicus populations. Here, PL was defined as failure from pregnancy diagnosis to calving, capturing a window approximately 60 days after the breeding season. This study aimed to identify genomic regions and biological pathways associated with PL in early Nellore heifers using weighted single-step genome-wide association study (WssGWAS). Phenotypic records from 23 507 Nellore heifers were analyzed, including 17 052 genotyped animals (GGP Indicus panel, Neogen) and 44 233 SNPs. Genomic regions explaining more than 0.5% of additive genetic variance were used to identify putative candidate genes and perform functional enrichment analysis. The estimated heritability for PL was low (0.033), indicating strong environmental influence. WssGWAS identified 25 genomic regions across 16 chromosomes, explaining 31.16% of additive genetic variance for PL. The most relevant region was located on BTA16, explaining 6.51% of the variance, although no annotated protein-coding genes were found. Additional regions occurred on BTA6, BTA14, BTA22, BTA25, and BTA29. Putative candidate genes included IL4R, IL21R, LRRC4C, RBMS3, ZFPM2, PRSS23, and NDST4, involved in immune regulation, cell adhesion, extracellular matrix remodeling, and transcriptional regulation. Functional enrichment identified Gene Ontology terms and REACTOME pathways related to nucleosome assembly, epigenetic regulation, transmembrane transport, focal adhesion, calcium signaling, immune response, and WNT signaling. These findings inform the genetic architecture of PL in Nellore cattle and suggest roles for embryo-maternal communication, immune regulation, chromatin organization, and placental development in pregnancy maintenance, supporting future functional validation and genomic selection strategies.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 5","pages":"e70212"},"PeriodicalIF":2.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13624523/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149079497","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
Breed Composition and Heterozygosity in Brangus and Braford Composite Cattle Breeds. Brangus和brford复合牛品种组成及杂合度。
IF 2.2 3区 生物学
Animal genetics Pub Date : 2026-10-01 DOI: 10.1002/age.70217
Danny Julio Cruz, Sebastián Munilla, Pamela Villalba, Hugo Toledo-Alvarado, Andrés Rogberg-Muñoz
{"title":"Breed Composition and Heterozygosity in Brangus and Braford Composite Cattle Breeds.","authors":"Danny Julio Cruz, Sebastián Munilla, Pamela Villalba, Hugo Toledo-Alvarado, Andrés Rogberg-Muñoz","doi":"10.1002/age.70217","DOIUrl":"https://doi.org/10.1002/age.70217","url":null,"abstract":"<p><p>Composite cattle breeds are developed to combine favorable traits from parental populations and to exploit heterosis across diverse production environments. However, their genomic structure becomes progressively more complex across generations, and it remains unclear to what extent patterns of local ancestry and heterozygosity are conserved across breeds. The objective of this study was to characterize genomic breed composition in Argentine Brangus and Braford at both global and local levels, and to identify shared genomic segments with extreme values of indicine ancestry and heterozygosity. A total of 783 animals from six breeds were analyzed using SNP data. Global ancestry proportions were estimated using STRUCTURE, whereas local ancestry was inferred through haplotype phasing (Shapeit5) and local ancestry inference using LOTER. Deviations between observed and expected breed composition and heterozygosity were evaluated at the SNP level using chi-square tests with multiple testing correction. Shared genomic segments were defined as contiguous genomic intervals composed of SNPs showing significant deviations in both breeds. Brangus and Braford showed lower indicine proportions than the expected 37.5%, with reductions of 1.2% and 7.1%, respectively. Local ancestry analysis revealed heterogeneous genomic patterns, with shared segments enriched for indicine ancestry on chromosomes 3, 6, 20, and 28. In contrast, segments with reduced indicine ancestry were more broadly distributed. No SNP exceeded the expected heterozygosity; however, multiple regions showed significant reductions, particularly on chromosome 18. These results demonstrate that Brangus and Braford exhibit complex and heterogeneous genomic architectures, with shared genomic regions showing extreme patterns of ancestry and heterozygosity.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 5","pages":"e70217"},"PeriodicalIF":2.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149126522","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
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