{"title":"Straightened Small Pinnae in TRPV4 c.1024G>T Heterozygous Cats.","authors":"Yuki Matsumoto, Ryuga Ishii, Hisashi Ukawa, Saaya Hiyoshi-Kanemoto, Hinako Hayashi, Haruka Onishi, Kai Ataka, Ryo Horie","doi":"10.1002/age.70114","DOIUrl":"10.1002/age.70114","url":null,"abstract":"<p><p>The folded-ear phenotype of Scottish Fold cats results from a dominant variant of the TRPV4 gene (c.1024G>T). Producing homozygous individuals is discouraged due to severe osteochondrodysplasia and identifying heterozygous carriers is critical for breeding. Although carriers are generally expected to have folded ears, straight-eared individuals have also been suspected among them. Here, we investigated the relationship between ear phenotype and TRPV4 genotype using longitudinal photographic data and TRPV4 genotyping in 114 cats. We identified seven individuals that transitioned from folded to straight ear phenotype during maturation. Genotyping confirmed all were heterozygous carriers, with 12.7% found among heterozygous cats. Morphometric analysis of 14 cats with high-quality photographs demonstrated these \"straightened\" cats had smaller pinnae than genetically wild-type straight-eared cats (p < 0.05), suggesting cartilage anomalies. These findings confirm \"cryptic folds\"-phenotypically straight but genetically heterozygous cats. Consequently, visual inspection for breeding selection is insufficient, highlighting the necessity of TRPV4 genotyping to prevent unintentional production of homozygous offspring with severe osteochondrodysplasia.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70114"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13147223/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147832501","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}
{"title":"Additional Evidence Fails to Associate Variation in KCNE4 With Equine Anhidrosis.","authors":"Jessica L Petersen, Carrie J Finno","doi":"10.1002/age.70109","DOIUrl":"10.1002/age.70109","url":null,"abstract":"<p><p>A prior genome-wide association (GWA; N = 200) including Thoroughbreds and stock horses implicated chromosome 6 (NC_009149.3) in owner-reported equine anhidrosis. A missense variant in KCNE4 (NC_009149.3:g.11813731A>G) was proposed as a risk allele, although its association with anhidrosis was not reported. Variant annotation and protein modelling in the original study suggested the G allele conferred risk. We reported no association of the G allele with anhidrosis in 50 horses phenotyped by an intradermal terbutaline sweat test (ITST); all horses produced sweat regardless of genotype. It later appeared the A allele was instead suggested to confer disease risk. To reassess this, we genotyped 20 ITST-tested Thoroughbreds including 9 with partial or complete anhidrosis. The KCNE4 A allele was not associated with phenotype when analyzed as a binary trait (p = 0.16) or when classifying affected horses as having either partial or complete anhidrosis (p = 0.21). The locus was also uninformative in four clinical cases (AA = 1, AG = 1, GG = 2). Reasoning that a true risk allele should be in linkage disequilibrium (LD) with the associated GWA SNV (AX-103822151; rs68656009), we evaluated whole-genome sequence (N = 2) from the initial publication. Both case and control were homozygous AA at the putative risk locus; the case was heterozygous at the GWA SNV. In public data (N = 897), LD between loci was low (r<sup>2</sup> = 0.19). In 369 Thoroughbreds, LD was 0.58. Restricting to Thoroughbreds in the original GWA (N = 85), we found no association of chromosome 6 with anhidrosis. Collectively, these data do not support a role of the KCNE4 variant or the GWA SNV in equine anhidrosis.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70109"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13110899/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147760168","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}
{"title":"Identifying Candidate Genes for Late-Feathering Subtypes of the Shouguang Chicken by Genome-Wide Association Study and Differential Expression Analysis.","authors":"Xiayi Liu, Junying Li, Haigang Bao","doi":"10.1002/age.70115","DOIUrl":"10.1002/age.70115","url":null,"abstract":"<p><p>Late-feathering phenotype can be classified into subtypes based on the difference in length between primary and primary-covert feathers of 1-day-old chicks. In this study, a chick with its primary feathers shorter than its primary-covert feathers is identified as Subtype 1 (T1), and a chick with its primary feathers as long as its primary-covert feathers is identified as Subtype 2 (T2). The objective of this study was to obtain candidate genes for late-feathering subtypes in Shouguang chickens. Fifty-three Shouguang chickens were genotyped using a 600 K SNP chip, and two genomic regions on Chromosome 3 and 10 were identified as being associated with late-feathering subtypes by Genome-wide association study (GWAS). Twelve hair follicle samples of flight feathers from 12 1-day-old Shouguang chicks, including 6 of each subtype, were collected. RNA sequencing analysis was performed, and no overlapping genes were found between differentially expressed genes (DEGs) identified by differential expression analysis and candidate genes by GWAS. In order to find the relationship between the two sets of genes, a protein-protein interaction (PPI) network was constructed using all protein-coding genes in the two sets, and the result showed that four genes (CDC40, EFL1, AK9, and ZBTB24) from GWAS and 21 DEGs were enriched in the largest subnetwork associated with muscle function. Considering the spatiotemporal characteristics of gene differential expression and the fact that the two most significant SNP loci in GWAS were located on EFL1 and CDC40, we propose that the two genes are more suitable as candidate genes for late-feathering subtypes.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70115"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147866357","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}
{"title":"ASIP Variants in Livestock: It's Not Black and White.","authors":"Isabella M Brown, Kylie A Munyard","doi":"10.1002/age.70139","DOIUrl":"10.1002/age.70139","url":null,"abstract":"<p><p>Fur and feather pigmentation play an important role in the survival and reproduction of many species, as well as in selective breeding and agriculture. The synthesis of pigment molecules, eumelanin and pheomelanin, is partially regulated by the agouti signalling protein (ASIP) encoded by the ASIP gene. Although ASIP has been widely studied, variants and associated phenotypes are often studied within individual species. This review synthesises current knowledge across mammalian and avian livestock, classifying ASIP variants by type and genomic location and linking them to characteristic pigmentation outcomes. Regulatory and structural variants primarily affect spatial and temporal expression, producing region-specific pigmentation or whole-body pheomelanic phenotypes, whereas coding variants are consistently associated with eumelanic phenotypes through loss of ASIP function. Comparative analysis highlights conserved relationships between variant classes and phenotypic outcomes across livestock species and emphasises the central role of regulatory architecture, including promoter usage, copy-number variation and fusion transcripts. This demonstrates the value of cross-species approaches for interpreting ASIP functional variants and provides a framework for understanding pigmentation diversity in livestock.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70139"},"PeriodicalIF":2.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148155031","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}
Li Rong, Xueying Wu, Md Ahsanul Kabir, Jiao Li, Yanping Feng, Shijun Li
{"title":"Unraveling the Genetic Basis of an Abnormal Gold Feather Phenotype in Auto-Sexing Chickens.","authors":"Li Rong, Xueying Wu, Md Ahsanul Kabir, Jiao Li, Yanping Feng, Shijun Li","doi":"10.1002/age.70132","DOIUrl":"10.1002/age.70132","url":null,"abstract":"<p><p>The silver-gold (S/s) sex-linked locus is critically employed in chicken breeding for the auto-sexing of day-old layer chicks. However, the emergence of an abnormal gold feather phenotype, where females lack the characteristic dorsal stripes, leads to frequent misidentification and substantial economic loss. The genetic basis of this abnormality was unknown. To address this, we conducted a genome-wide association study (GWAS) using 9 445 763 high-quality SNPs obtained from whole genome resequencing of 103 female chicks (53 abnormal, 50 normal). Our analysis identified a single sharp peak on chromosome 2 (-log<sub>10</sub>(P) = 34.7; 236 significant SNPs), which was refined to a 390-kb interval (102.62-103.01 Mb) by FST analysis. The top Absolute allele frequency difference (absAFD) variant, NC_006089.5:g.102638974T>C, located in intron 2 of the GATA6 gene, showed an allele frequency difference of 0.567 (p = 1.35 × 10<sup>-12</sup>). This study identifies chromosome 2 as the major genomic region responsible for the abnormal gold feather phenotype, with a noncoding variant in GATA6 as the primary candidate causal mutation. This is the first study of the abnormal gold feather phenotype, and it provides a molecular target for developing a diagnostic assay to preserve auto-sexing accuracy in commercial layer breeding.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70132"},"PeriodicalIF":2.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148148024","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}
Yang Shen, Qiuju Su, Jiao Yuan, Qinghua Yang, Ming Fu, Zuhong Liu, Jennifer J Michal, Zhihua Jiang, Bang Liu, Xiang Zhou
{"title":"Integrating GWAS and RNA-Seq Reveals QTLs and Candidate Genes for Fat Deposition in Large White × Tongcheng Crossbred Pigs.","authors":"Yang Shen, Qiuju Su, Jiao Yuan, Qinghua Yang, Ming Fu, Zuhong Liu, Jennifer J Michal, Zhihua Jiang, Bang Liu, Xiang Zhou","doi":"10.1002/age.70110","DOIUrl":"10.1002/age.70110","url":null,"abstract":"<p><p>Fat deposition traits are crucial economic characteristics that directly influence production efficiency in pigs. To better understand the genetic mechanisms underlying fat deposition, four traits including backfat thickness (BF), caul fat rate (CFR), leaf fat rate (LFR), and internal fat rate (IFR) were measured in 421 Large White × Tongcheng crossbred pigs. A GWAS analysis identified 666, 15, 22, and 61 SNPs significantly associated with BF, LFR, CFR, and IFR, respectively. Bayesian fine-mapping revealed a major QTL on SSC7 (29.62-30.62 Mb) that influences all four fatness traits and harbors the candidate gene HMGA1 and NUDT3. Additionally, a QTL on SSC5 (28.67-30.52 Mb) was associated with BF and contains the candidate gene TBK1, while a QTL on SSC18 (8.01-9.88 Mb) associated with CFR includes AGK and TBXAS1. Integration of transcriptome, 3D genomic, and epigenomic data identified rs703100168 on SSC7 as a candidate functional SNP to control HMGA1 expression and regulate fat deposition in pigs. These findings provide valuable candidate genes and genetic variants for improving fatness traits in pig breeding programs.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70110"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147760183","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}
{"title":"Unraveling Sexual Size Dimorphism in Growth Traits of Dairy Goats: A Genetic Evaluation That Accounts for Dominance Effects.","authors":"Jamshid Ehsaninia, Alireza Bagheripour","doi":"10.1002/age.70125","DOIUrl":"10.1002/age.70125","url":null,"abstract":"<p><p>Sexual size dimorphism (SSD) is a major determinant of growth and productivity in domestic animals, yet dominance genetic effects have rarely been incorporated into its evaluation in goats. This work presents an extensive analysis of SSD in Murciano-Granadina (MG) goats for pre-weaning growth traits, birth weight (BWT), weaning weight (WWT), average daily gain (ADG), Kleiber ratio (KR), and growth efficiency (GE) through genetic models including additive, dominance, and maternal components. Data from 17 404 kids of 337 sires and 3966 dams indicated pronounced SSD as males were 9% heavier at birth, 4% heavier at weaning, and 6%-11% higher for ADG, KR, and GE. Models including dominance effects provided better fit, with dominance heritabilities ( <math> <semantics> <mrow><msubsup><mi>h</mi> <mi>d</mi> <mn>2</mn></msubsup> </mrow> <annotation>$$ {h}_{mathrm{d}}^2 $$</annotation></semantics> </math> = 0.12-0.54) exceeding additive ones ( <math> <semantics> <mrow><msubsup><mi>h</mi> <mi>a</mi> <mn>2</mn></msubsup> </mrow> <annotation>$$ {h}_{mathrm{a}}^2 $$</annotation></semantics> </math> = 0.03-0.14), highlighting significance of nonadditive genetic variance. Maternal effects were trait- and sex-specific ( <math> <semantics> <mrow><msubsup><mi>h</mi> <mi>m</mi> <mn>2</mn></msubsup> </mrow> <annotation>$$ {h}_{mathrm{m}}^2 $$</annotation></semantics> </math> = 0.04-0.18). Cross-sex additive genetic correlations ( <math> <semantics> <mrow><msub><mi>r</mi> <mi>a</mi></msub> <mfenced><mrow><mi>m</mi> <mo>,</mo> <mi>f</mi></mrow> </mfenced> </mrow> <annotation>$$ {r}_{mathrm{a}}left(mathrm{m},mathrm{f}right) $$</annotation></semantics> </math> ) were usually high (0.73-1.00), whereas dominance correlations were moderate to high (0.44-0.92), indicating partial sex-specific nonadditive effect. Traits that were lower in <math> <semantics> <mrow><msub><mi>r</mi> <mi>a</mi></msub> <mfenced><mrow><mi>m</mi> <mo>,</mo> <mi>f</mi></mrow> </mfenced> </mrow> <annotation>$$ {r}_{mathrm{a}}left(mathrm{m},mathrm{f}right) $$</annotation></semantics> </math> like BWT and WWT revealed higher potential of divergence under sex-specific selection. Comparisons of sex-joint and sex-specific evaluations indicated substantial re-ranking of top sires for WWT and BWT, moderate re-ranking for ADG and minimal changes for KR and GE. Overall, while sex-joint models are suitable for standard evaluation work, integrating dominance effects and sex-specific models improves selection accuracy of SSD traits, offering a practical framework to refine genetic evaluations and optimize breeding programs in dairy goats.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70125"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148025849","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}
Mohammad Mehdi Akbarin, Zahra Farjami, Cecilia Rodríguez Murillo, Víctor David González-Fernández, Gabriel Eduardo Acevedo-Jiménez, Lucero de María Ávila-De la Vega, Hugo Ramírez Álvarez
{"title":"Stage-Dependent Transcriptional Reprogramming of B-Cell Receptor Signaling and Antigen Presentation During Bovine Leukemia Virus-Driven Lymphomagenesis.","authors":"Mohammad Mehdi Akbarin, Zahra Farjami, Cecilia Rodríguez Murillo, Víctor David González-Fernández, Gabriel Eduardo Acevedo-Jiménez, Lucero de María Ávila-De la Vega, Hugo Ramírez Álvarez","doi":"10.1002/age.70136","DOIUrl":"10.1002/age.70136","url":null,"abstract":"<p><p>Bovine leukemia virus (BLV), an oncogenic deltaretrovirus, establishes lifelong infection in cattle and induces enzootic bovine leukosis in a subset of animals following prolonged latency. Despite extensive evidence of immune dysregulation, stage-specific transcriptional reprogramming of B cells, the primary viral reservoir remains incompletely understood. In this study, we performed a targeted RNA-sequencing analysis to characterize B-cell-associated transcriptional profiles across three clinical stages: uninfected controls (CT), asymptomatic BLV-infected cattle (AC), and persistent lymphocytosis (PL). Differential gene expression analysis revealed a dynamic, stage-dependent remodeling of B-cell immune functions. Asymptomatic infection was characterized by significant upregulation of key B-cell receptor (BCR) signaling components, including CD79B and SYK, alongside increased expression of major histocompatibility complex class II genes (BoLA-DRA, BoLA-DRB3) and immunoglobulin assembly gene JCHAIN, indicating enhanced antigen responsiveness and partial activation of antibody-related pathways. However, transcriptional regulators of terminal plasma cell differentiation (PRDM1 and XBP1) remained unchanged, suggesting incomplete maturation. In contrast, progression to persistent lymphocytosis was associated with attenuation of canonical BCR signaling and reduced expression of antigen presentation and immunoglobulin assembly genes relative to the asymptomatic stage. Notably, germinal center-associated transcription factors (BCL6, AICDA, RGS13, MEF2B) remained largely unchanged across all comparisons, indicating that BLV-driven lymphomagenesis does not resemble a classical germinal center-derived process. Collectively, these findings support a biphasic model of BLV-induced B-cell modulation, characterized by early immune activation followed by functional reprogramming and immune attenuation during disease progression. This stage-dependent remodeling provides new mechanistic insights into BLV pathogenesis and B-cell transformation.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70136"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13240601/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148161578","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}
{"title":"Meta-Analysis of Transcriptomic Datasets Reveals Key Immune Gene Profiles and Signaling Pathways in Bos taurus.","authors":"Vennila Kanchana Devi Marimuthu, Kishore Matheswaran, Menaka Thambiraja, Suneel Kumar Onteru, Ragothaman M Yennamalli","doi":"10.1002/age.70117","DOIUrl":"10.1002/age.70117","url":null,"abstract":"<p><p>Improving disease resistance in cattle relies on informed breeding and vaccine development, both depend on our understanding of immune mechanisms in cattle. However, transcriptomic studies of bovine immune responses often show considerable variability due to differences in tissue type, pathogen, time point, and experimental design, limiting the generalizability. Meta-analysis integrates multiple transcriptomic studies to identify consistent gene expression patterns and enhance statistical power. We integrated bovine RNA-seq datasets using immune-response specific keywords, species constraints, and high-throughput sequencing filters to prioritize biologically comparable and meta-analysis-ready studies. Specifically, in this study, we performed a meta-analysis of four bovine transcriptomic datasets to identify immune-related differentially expressed genes (DEGs) in Bos taurus. These datasets showed consistent results across analyses and represent immune responses related to mycobacterial infections (Mycobacterium bovis and Mycobacterium avium subsp. paratuberculosis), making them suitable for combined analysis. Our pipeline included FastQC, Trimmomatic, Bowtie2, SAMtools, FeatureCounts, DESeq2, and MetaRNASeq, identifying 28 DEGs (12 upregulated and 16 downregulated). We identified key immune-related genes (IL1A, RGS2, RCAN1, ZBP1, TIMD4, PPARG, TLR10, and ACP5) with known regulatory roles in immunity. KEGG enrichment analysis revealed involvement in necroptosis, osteoclast differentiation, oxytocin signaling, and cGMP-PKG signaling pathways, associated with inflammatory cell death, cytokine signaling, and immune cell differentiation. Using reproducible transcriptomic signals across systematically selected bovine immune datasets rather than relying on single-experiment analyses, we provide a robust meta-analytic framework. This meta-analysis enhances our understanding of conserved immune signaling mechanisms in cattle for identifying conserved immune mechanisms with broader biological and translational relevance.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70117"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147866413","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}