Animal genetics最新文献

{"title":"TG Nonsense Variant in Dwarf Rottweiler Dogs.","authors":"Marie Abitbol, Michaela Drögemüller, Cleo Schwarz, Etienne Furthner, Eva Dervas, Felicitas S Boretti, Nadja S Sieber-Ruckstuhl, Caroline Dufaure de Citres, Chloé Pauchard, Vidhya Jagannathan, Tosso Leeb","doi":"10.1002/age.70127","DOIUrl":"10.1002/age.70127","url":null,"abstract":"<p><p>We identified a dwarfism syndrome in six Rottweiler dogs characterized by reduced height and body weight; limb deformities, shortening of the tail and abnormally thick skin in puppies; developmental delays, pain and non-goitrous hypothyroidism. Histological examination of the thyroid gland revealed severe chronic diffuse bilateral atrophy with loss of thyroid follicles and lack of colloid. Pedigree analysis suggested an autosomal recessive transmission. Whole genome sequencing of an affected dog and filtering for private variants against 1539 control genomes identified a homozygous nonsense variant in the TG gene encoding thyroglobulin, NM_001048104.1:c.3694C>T. The variant was predicted to introduce a premature stop codon truncating 55% of the wild-type open reading frame, NP_001041569.1:p.(Arg1232*). The TG glycoprotein is the precursor to the thyroid hormones triiodothyronine (T3) and tetraiodothyronine (T4). TG deficiency leads to comparable phenotypes in human patients, cattle and goats. Genotyping six affected and 87 control Rottweiler dogs confirmed the expected genotype-phenotype association, with all affected dogs being homozygous for the mutant allele and control dogs being either heterozygous or homozygous wild-type. All four obligate carriers were heterozygous and among the 74 unrelated control dogs without known relationships to cases we found a 5.4% carrier frequency. Correct co-segregation in the available families was also observed. Taken together, this study provides an initial clinical and pathological characterization of an inherited dwarfism syndrome in Rottweilers and identifies a TG variant as a causal genetic defect. The results enable genetic testing to avoid unintentional risk matings.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70127"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148004024","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":"Integrated Transcriptomic and Metabolomic Analysis Reveals Gut Microbiota-Mediated Regulation of Muscle Fiber Composition and Metabolism in Germ-Free Pigs.","authors":"Yaxin Peng, Yapeng Yang, Chunpeng He, Hao Zuo, Zhifeng Wu, Panpan Yang, Jun Ma, Shuaifei Feng, Xiang Tan, Zaiyan Xu, Hong Wei, Bo Zuo","doi":"10.1002/age.70124","DOIUrl":"10.1002/age.70124","url":null,"abstract":"<p><p>The gut microbiota is a key regulator of host metabolism and skeletal muscle physiology, yet its role in muscle fiber-type transformation in pigs remains unclear. Here, we used germ-free (GF) and specific pathogen-free (SPF) Rongcheng piglets to explore how microbial absence influences muscle development. GF piglets showed significantly reduced body weight and an increased proportion of fast-twitch fibers compared with SPF controls. Transcriptome sequencing identified 1332 differentially expressed genes (DEGs), notably those involved in cGMP-PKG, Thyroid hormone, HIF-1, VEGF, and Butanoate metabolism signaling pathways, which are essential for myofiber specification. Non-targeted metabolomic profiling revealed 320 differentially expressed metabolites (DEMs), with major alterations in Bile secretion. Integrated transcriptomic and metabolomic uncovered 10 KEGG pathways co-enriched with DEGs and metabolites, including Bile secretion, Ferroptosis, Inflammatory mediator regulation of TRP channels, and HIF-1 signaling pathway. Correlation analysis revealed that strong positive correlations were observed between fast-twitch fiber genes (e.g., PRKCA, MYOZ3, NFATC1) and fatty acid-related metabolites (e.g., Dodecanoic acid, Valproic Acid, and Decanoic acid), whereas negative correlations were detected between these genes and bile acid-related metabolites (e.g., Cholic acid and 7-Ketolithocholic acid), suggesting microbial metabolites is associated with muscle fiber phenotype via metabolic and signaling crosstalk. Collectively, our findings demonstrate that gut microbial absence in pigs disrupts bile acid metabolism and fatty acid metabolism, which in turn drives the shift of skeletal muscle fiber composition toward fast-twitch glycolytic fibers. These metabolites are identified as key microbial mediators linking the gut microbiota to the transcriptional regulatory function of porcine muscle fiber type specialization, providing new insights into the gut-muscle axis and highlighting the important role of microbiota-derived metabolites in maintaining porcine muscle fiber composition and metabolic balance.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70124"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147970085","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":"Reproducibility of the Evaluation of Genetic Variant Pathogenicity Based on the Animal Variant Classification Guidelines.","authors":"Iris Casselman, Carlotta Ferrari, Marie Abitbol, Danika Bannasch, Jerold Bell, Caroline Dufaure de Citres, Carrie J Finno, Jessica J Hayward, Jens Häggström, Jason T Huff, Tosso Leeb, Ingrid Ljungvall, Maria Longeri, Leslie A Lyons, Marcela Martinez, Cathryn Mellersh, Frank W Nicholas, Åsa Ohlsson, Pascale Smets, Maria G Strillacci, Imke Tammen, Frank G van Steenbeek, Bart J G Broeckx","doi":"10.1002/age.70145","DOIUrl":"https://doi.org/10.1002/age.70145","url":null,"abstract":"<p><p>Until recently, due to the absence of standardized guidelines tailored for veterinary use, the evaluation of genetic variant pathogenicity for single-gene diseases was based on a personal interpretation of the presented evidence, which has led to inconsistencies. With the publication of the animal variant classification guidelines (AVCG), a more objective approach became available. Variants are evaluated by the International Society of Animal Genetics (ISAG)-endorsed Variant Pathogenicity Working Group (VPWG) based on 23 criteria and are subsequently labeled as pathogenic, likely pathogenic, variant of uncertain significance, likely benign or benign. While the accuracy was thoroughly tested in the original publication, the reproducibility of the various steps involved was only briefly checked, which is why the current analysis was performed. Each variant from a set of 150 published likely causal variants for single-gene diseases from three species (dog, cat, horse) was independently and blindly assessed by three different VPWG reviewers, each applying the same AVCG. An overall agreement of 93% for decisions on the scope, that is, whether they fit the inclusion criteria to allow evaluation with AVCG, was found. More importantly, the reproducibility of pathogenicity label assignment was 65% and the reproducibility of clinical relevance was 83%. The reproducibility of AVCG-pathogenicity classification is in line with reports using the human American College for Medical Genetics and Genomics and Association for Molecular Pathology guidelines for human variants. Overall, the reproducibility of the AVCG classifications as used by the ISAG-endorsed VPWG supports the utility of these classifications in veterinary species.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70145"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148275687","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":"Fecal DNA Identifies a Disjunct Population of an Endemic Deer (Mazama jucunda) From the Atlantic Forest, Brazil.","authors":"Jeferson L S Freitas, Pedro H F Peres, Francisco Grotta-Neto, Márcio L Oliveira, José M B Duarte","doi":"10.1002/age.70134","DOIUrl":"10.1002/age.70134","url":null,"abstract":"<p><p>Limited knowledge of brocket deer distribution persists due to their elusive behavior and the morphological similarities among species. A population of red brocket deer (genus Mazama) was recently discovered in the Rio Doce State Park (PERD), a protected area within the Brazilian Atlantic Forest; however, species-level identification was lacking. Given that two endemic and threatened red brocket species inhabit this biome, we aimed to identify the species present in PERD using fecal DNA analyses. We sequenced six mitochondrial DNA regions (1450 bp) from fecal samples collected in PERD and other Atlantic Forest sites, analyzing them against reference specimens. We conducted phylogenetic analyses and employed coalescent-based molecular species delimitation methods (GMYC and bPTP) to define molecular operational taxonomic units (MOTUs). Additionally, we constructed a haplotype network and a genetic distance matrix. Our analyses linked the PERD samples to Mazama jucunda (small red brocket) but revealed a reciprocally monophyletic topology, identifying two distinct MOTUs. PERD harbors unique haplotypes, and its genetic distance to M. jucunda is comparable to that between M. jucunda and M. nana (Brazilian dwarf brocket). We propose that PERD hosts an evolutionarily significant unit (ESU) of M. jucunda, located 700 km from its known range. The observed genetic structure and PERD's isolation support the hypothesis of a potentially new red brocket species, warranting further cytogenetic investigation. This study represents a significant advancement in understanding the distribution and genetic structure of a threatened Neotropical forest deer and has immediate conservation implications in one of the world's most degraded biodiversity hotspots.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70134"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13241587/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148175274","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":"Association of the Disheveled 2 (DVL2) Gene c.2044delC Variant with Increased Risk of Canine Cleft Palate.","authors":"Jonas Donner, Marjo Hytönen, Jamie Freyer, Hannes Lohi, Rebecca Chodroff Foran, Oliver P Forman","doi":"10.1002/age.70101","DOIUrl":"10.1002/age.70101","url":null,"abstract":"<p><p>Canine congenital cleft palate is one of the most common craniofacial anomalies in dogs, characterized by a failure of the palatal shelves to fuse properly during fetal development, leading to abnormal communication between the oral and nasopharyngeal cavities. Patients with cleft palate can experience significant challenges including feeding difficulties, aspiration pneumonia, and respiratory distress, all of which can profoundly impact quality of life and, in severe cases, survival. The clinical management of cleft palate in dogs involves a combination of medical and surgical interventions. The aim of this study was to identify common genomic variants associated with cleft palate. A GWAS with 266 cases ascertained from a general population of more than 1 million dogs attending primary care veterinary clinics in the United States was used to identify an association in the region of the disheveled 2 (DVL2) gene variant c.2044delC, previously linked to Robinow-like syndrome and the screw tail phenotype in Bulldogs and related breeds. The association was confirmed through genotyping of the DVL2 variant. In summary, this study identifies the DVL2 variant that is fixed and breed defining in several breeds as a risk factor for cleft palate in dogs.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70101"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13112132/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147760171","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":"Correction to \"Identifying Candidate Genes for Late-Feathering Subtypes of the Shouguang Chicken by Genome-Wide Association Study and Differential Expression Analysis\".","authors":"","doi":"10.1002/age.70138","DOIUrl":"10.1002/age.70138","url":null,"abstract":"","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70138"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148148006","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":"Genetic Basis of Growth and Carcass Traits in Sansui Duck Identified Through Genome-Wide Association Analysis.","authors":"Yulong Feng, Mengru Xu, Ziheng Cai, Xu Han, Jingjing Qi, Zhao Yang, Yang Xi, Meijuan Li, Chengcheng Tian, Yuxi Lu, Guotao Dai, Yu Zhao, Hehe Liu","doi":"10.1002/age.70151","DOIUrl":"https://doi.org/10.1002/age.70151","url":null,"abstract":"<p><p>The Sansui duck is a valuable Chinese genetic resource. However, incomplete exploration of its genetic resources has limited the full utilization of its genetic potential. This study systematically evaluated the growth and carcass performance in 305 Sansui ducks and explored their genetic basis through genome-wide association studies (GWAS). Body weight (recorded biweekly from 0 to 20 weeks), body measurement traits, and carcass yield traits (measured at 20 weeks) were collected. Growth curve analysis revealed a relatively slow growth rate, with early growth occurring from 0 to 14 weeks and a critical period for weight gain observed at 8-10 weeks. Sansui ducks exhibited small body size with favorable meat production traits: half-eviscerated yield percentage (HEYP) and eviscerated yield percentage (EYP) both above 70%, while breast muscle percentage (BMP) and leg muscle percentage (LMP) reached 11.99% and 11.01%, respectively. SNP-based heritability estimates indicated moderate to high heritability for growth and slaughter traits. GWAS identified 222 SNPs associated with growth and slaughter traits, which were annotated to 53 candidate genes, including EFEMP1, SKAP1, and MYO19. Linkage disequilibrium (LD) analysis further pinpointed two key genomic regions on chromosome 28 (1-200 kb and 250-320 kb) influencing multiple traits. These regions harbor critical candidate genes, including the HOXB family and IGF2BP1, which play important roles in regulating skeletal development, energy allocation, and growth rhythm in poultry. These findings enrich the genetic resource database of the Sansui duck and provide an important theoretical basis for further elucidating the genetic foundation of its growth and carcass performance.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70151"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148293200","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":"Heritability Patterns of Protein-Coding Genes Expression: Insights From the Pig Genotype-Tissue Expression Project.","authors":"Chao Su, Wenjing Zhang, Wenzhe Ning, Jinyan Teng, Yahui Gao, Zhe Zhang","doi":"10.1002/age.70131","DOIUrl":"10.1002/age.70131","url":null,"abstract":"<p><p>Understanding the genetic basis of gene expression is crucial for elucidating the mechanisms underlying complex traits, especially for protein-coding genes (PCGs) whose expression levels directly affect protein abundance and functionality. Recent studies have improved our understanding of local (cis-) and distal (trans-) regulatory mechanisms that control gene expression levels. However, a comprehensive understanding of the heritability patterns of PCG expression in pigs, which are valuable models for human biology, remains lacking. In this study, we used genomic and transcriptomic data from 4760 pigs across 13 tissues from the Pig Genotype-Tissue Expression (PigGTEx) project and applied linear mixed models (LMMs) to estimate cis-, trans-, and global- heritability of PCG expression. Our findings indicate the average cis-heritability of gene expression across all tissues is 0.13, whereas the trans- and global-heritability are significantly higher, at 0.64 and 0.67, respectively. While variants in cis-regulatory regions explain only a minor proportion of expression variance, a single variant with stronger effects is predominantly located near transcription start sites (TSS). In addition, the heritability of gene expression captures information about both expression levels and independent cis-expression quantitative trait loci (cis-eQTL). Comparing housekeeping genes (HKGs) and tissue-specific genes (TSGs), we found that HKGs are influenced by genetic variants across the genome, whereas TSGs are mainly affected by variants near their cis-regions in most tissues. This study is a comprehensive analysis of gene expression heritability across multiple pig tissues, enhancing our understanding of genetic regulation in pigs.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70131"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148249008","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":"A Longitudinal Genome-Wide Association Study Identifies New Candidate Genes for Abdominal Fat Thickness in White Feather Broilers.","authors":"Penghao Li, Na Luo, Fan Ying, Dan Zhu, Dawei Liu, Xianyi Song, Jie Wen, Guiping Zhao, Bingxing An","doi":"10.1002/age.70108","DOIUrl":"10.1002/age.70108","url":null,"abstract":"<p><p>Abdominal fat thickness (AFT) is a crucial indicator for assessing fat deposition in White Feather broilers. Previous genome-wide association studies (GWAS) have primarily focused on single-point measurements of abdominal fat, with limited attention given to longitudinal phenotype records. Compared to traditional GWAS models, the longitudinal data-based GWAS (LONG-GWAS) model accounts for temporal phase effects, thereby more effectively controlling the false positive rate. This study conducted a genome-wide association analysis on 1654 White Feather broilers at four distinct ages during the laying period of broiler breeders (25, 27, 35, and 43 weeks). Three SNP loci associated with fat were identified (rs16341267, rs740644432, and rs15049519), which were annotated to three candidate genes: FDFT1, HTR2C, and ALDH3A2. These genes are involved in regulating lipid metabolism, energy balance, and fat deposition. This study provides new insights into the genetic basis of abdominal fat thickness in White Feather broilers and offers stage-specific marker information that can accelerate precision breeding for abdominal fat control in white feathered broilers.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70108"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147760234","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":"A New TYR Splice Donor Variant Causing Oculocutaneous Albinism Type I in Angus Cattle.","authors":"Katie L M Eager, Phillip D Carter, Lillian Brancalion, Cali E Willet, Brendon A O'Rourke, Imke Tammen","doi":"10.1002/age.70119","DOIUrl":"10.1002/age.70119","url":null,"abstract":"","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 3","pages":"e70119"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13155181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147832487","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}