Animal genetics最新文献

{"title":"Integrated Genome-Wide Association Studies and Selection Signature Analysis Reveal the Genetic Architecture of the Wattle Trait in Goats","authors":"Siyi Hu,&nbsp;Chen Wei,&nbsp;Da Feng,&nbsp;Shangquan Gan","doi":"10.1002/age.70198","DOIUrl":"10.1002/age.70198","url":null,"abstract":"<p>Wattles are finger-like appendages on the ventral neck of goats, serving as a distinctive morphological marker for breed identification that serves potential implications for production performance. However, their genetic basis remains incompletely characterized. Here, we integrated a genome-wide association study (GWAS) and selection signature analysis to identify candidate genes and genomic regions associated with the wattle trait in goats. Using a linear mixed model, GWAS on 463 goats (23 wattled and 440 non-wattled) identified 385 quantitative trait loci (QTLs) at a 5% false discovery rate, yielding 346 candidate genes. The most significant association signal was observed on chromosome 10 (72.61–73.48 Mb), where the lead SNP (rs636481767) is located within a region containing <i>GJD2</i>, <i>GREM1</i>, and <i>FMN1</i>, showing strong linkage disequilibrium (<i>r</i>² &gt; 0.6) with surrounding loci. Subsequent selection signature analysis (23 wattled and 23 non-wattled) identified 83 genomic regions harboring 119 candidate genes. The strongest signals were detected at <i>MFSD14B</i> on chromosome 8 (<i>F</i>_ST = 0.154, log₂π-ratio = 2.611) and <i>PDLIM7</i> on chromosome 7 (<i>F</i>_ST = 0.144, log₂π-ratio = 0.806). KEGG pathway enrichment analysis revealed that GWAS-associated genes were involved in glycosylation and immune responses, whereas selection-signature genes were enriched in DNA repair and the Hippo, Notch, and Wnt pathways. Furthermore, cross-species PheWAS revealed that human <i>FMN1</i> is associated with dermatological, skeletal, and metabolic phenotypes, while porcine <i>FMN1</i> is associated with backfat thickness and loin muscle depth. Overall, this study provides molecular markers of potential value for goat breeding and pinpoints key candidate genes for future functional validation of wattle development.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 5","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13551058/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148904940","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":"Genome Wide Analysis Reveals Divergence and Ancestral Origins of Min Pigs","authors":"Long Jin,&nbsp;Fengyi Dong,&nbsp;Chengyue Feng,&nbsp;Jiayi Ning,&nbsp;Xiaoran Zhang,&nbsp;Wuyang Liu,&nbsp;Changyi Chen,&nbsp;Dali Wang,&nbsp;Luyao Bie,&nbsp;Chunyan Bai,&nbsp;Hao Sun,&nbsp;Boxing Sun","doi":"10.1002/age.70204","DOIUrl":"10.1002/age.70204","url":null,"abstract":"<div>\u0000 \u0000 <p>The Min pig, a representative northern Chinese indigenous breed, carries a unique ancestral background shaped by the historical phylogeography of Northeast Asia. This study aimed to dissect the population structure, temporal genetic divergence, and ancestral composition of Min pigs, trace their evolutionary origin, and identify trait-linked functional genes, providing information regarding their evolutionary history and conservation. We analyzed 61 Min pigs sampled across nearly 20 years and 701 reference pigs comprising other Chinese indigenous breeds, Western commercial lines, and Chinese wild boars, using PCA, NJ phylogenetic analysis, Admixture, TreeMix, D-statistic, f4-ratio, and combined selection signature scans (sliding-window F_ST, XP-EHH, and π-ratio). Clear genetic stratification was observed among Min pig subpopulations, reflecting long-term divergence under natural and artificial selection. PCA and Admixture (<i>K</i> = 2–4) separated East Asian indigenous and Western ancestral components, verifying an admixed Northeast Asian origin with a dominant ancient East Asian component and a Western component. Compared with early-2000s Min pigs, contemporary individuals are genetically closer to Western breeds and exhibit a more scattered structure due to shifted ancestral component proportions, further confirmed by D-statistic and f4-ratio values. We identified 321 differentiated SNP loci based on the Animal QTL database, corresponding to core candidate genes (<i>AKT3</i>, <i>ACACA</i>, <i>MAP3K5</i>, <i>FGFR4</i>, <i>C3</i>, and <i>SERPINC1</i>) enriched for meat quality, growth, reproduction, immunity, energy metabolism, and MAPK/PI3K-Akt/AMPK pathways. This study reveals Min pigs' admixed origin and temporal divergence, clarifying their Northeast Asian evolution and providing molecular markers for genetic monitoring and conservation.</p>\u0000 </div>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 5","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148904994","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":"The Animal Variant Classification Guidelines v2: An Update With New Criteria and Improved Clarifications","authors":"Lore Desmet,&nbsp;Carlotta Ferrari,&nbsp;Marie Abitbol,&nbsp;Heidi Anderson,&nbsp;Danika Bannasch,&nbsp;Hubert Bauer,&nbsp;Jerold Bell,&nbsp;Nüket Bilgen,&nbsp;Lucie Chevallier,&nbsp;Caroline Dufaure de Citres,&nbsp;Jonas Donner,&nbsp;Carrie J. Finno,&nbsp;Guillermo Giovambattista,&nbsp;Steven M. Harrison,&nbsp;Jessica J. Hayward,&nbsp;Jens Häggström,&nbsp;Jason T. Huff,&nbsp;Tosso Leeb,&nbsp;Ingrid Ljungvall,&nbsp;Maria Longeri,&nbsp;Leslie A. Lyons,&nbsp;Marcela Martinez,&nbsp;Cathryn Mellersh,&nbsp;Frank W. Nicholas,&nbsp;Åsa Ohlsson,&nbsp;Jessica L. Petersen,&nbsp;Pascale Smets,&nbsp;Maria G. Strillacci,&nbsp;Imke Tammen,&nbsp;Samantha Van Buren,&nbsp;Frank G. van Steenbeek,&nbsp;Bart J. G. Broeckx","doi":"10.1002/age.70197","DOIUrl":"10.1002/age.70197","url":null,"abstract":"<div>\u0000 \u0000 <p>The Animal Variant Classification Guidelines (AVCG) were developed to standardize and objectify the classification of putative disease-causing variants. These guidelines are sufficiently reproducible and are used to classify previously published and new disease-causing variants across species. Here, the guidelines are updated (AVCG.v2), based on a three-phase decision process. Overall, four new criteria and seven clarifying comments were added. The number of criteria has increased from 23 to 27, with three new criteria supporting pathogenicity and one new criterion supporting benign classification. Pharmacogenomic variants were determined to fall within the scope of the guidelines. These updated guidelines are being used by the Variant Pathogenicity Working Group (VPWG), part of the Animal Genetic Testing Standardization standing committee, which is a committee of elected members of the International Society for Animal Genetics (ISAG). Under the auspices of ISAG, the VPWG retrospectively classifies published putative disease-causing variants. The pathogenicity label for a variant will be presented in the variant tables of Online Mendelian Inheritance in Animals (OMIA; https://omia.org/). The AVCGv.2 criteria and recommendations were developed by the expertise of the animal genetics community and the ISAG Executive Committee through the Animal Genetics Testing Standardization Committee endorses and strongly encourages their use to evaluate the evidence supporting pathogenicity of putative disease-causing variants.</p>\u0000 </div>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 5","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890724","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 Monitoring of Tibial Hemimelia in Galloway Cattle","authors":"Bertram Brenig","doi":"10.1002/age.70196","DOIUrl":"10.1002/age.70196","url":null,"abstract":"&lt;p&gt;Tibial hemimelia is a recessive developmental defect reported in various cattle breeds. The first reports of the defect date back to 1951 (Young &lt;span&gt;1951&lt;/span&gt;). Subsequent case reports appeared for Galloway cattle in 1974, 1977, 1978 and 1979 (Leipold et al. &lt;span&gt;1977&lt;/span&gt;, &lt;span&gt;1978&lt;/span&gt;; Ojo et al. &lt;span&gt;1974&lt;/span&gt;; Pollock et al. &lt;span&gt;1979&lt;/span&gt;). While the underlying genetic defect in Shorthorns was identified in 2012, the causative genetic variant in Galloway cattle was not elucidated until 2015 (Beever and Marron &lt;span&gt;2012&lt;/span&gt;; Brenig et al. &lt;span&gt;2015&lt;/span&gt;, &lt;span&gt;2024&lt;/span&gt;; Buitkamp et al. &lt;span&gt;2023&lt;/span&gt;). In Galloway cattle, tibial hemimelia is caused by a 20 bp duplication in exon 2 of the Aristaless-like Homeobox 4 gene (&lt;i&gt;ALX4&lt;/i&gt;) (Brenig et al. &lt;span&gt;2015&lt;/span&gt;). As this is a lethal factor in Galloway cattle, all breeding animals have since been screened for this genetic defect prior to breeding. Only animals that are not carriers (= THF) of the variant allele are approved for breeding. To verify the current genotype and allele frequencies in the German Galloway population, we tested a total of 1586 animals of Galloway (&lt;i&gt;n&lt;/i&gt; = 906), Belted Galloway (&lt;i&gt;n&lt;/i&gt; = 279) and White Galloway (&lt;i&gt;n&lt;/i&gt; = 401) for the variant in the &lt;i&gt;ALX4&lt;/i&gt; gene. Genotyping was performed using the same PCR assay and scoring criteria as in 2015, supporting comparability of genotype calls across years (Brenig et al. &lt;span&gt;2015&lt;/span&gt;). Cohort comparability with respect to herd/region composition and familial clustering was not evaluated and could influence temporal comparisons, particularly in subpopulations with small effective sizes. A total of 1342 DNA samples were successfully genotyped. For 244 animals, the genotype could not be determined due to poor DNA quality. Of the 1342 cattle, 1220 were THF and 122 were carriers of the variant (= THC). The genotypes of the individual breeds are shown in Figure 1. The average allele frequency of the variant allele within the 1342 DNA samples was 0.046. However, within the three Galloway breeds allele frequencies differed markedly, at 0.019 (Galloway = GAL), 0.009 (Belted Galloway = BGA), and 0.119 (White Galloway = WGA).&lt;/p&gt;&lt;p&gt;Compared with the earlier study (Brenig et al. &lt;span&gt;2015&lt;/span&gt;), the current allele frequency of the causative allele differs. The allele frequency for WGA in 2015 was 0.064, whereas in the current survey an allele frequency of 0.119 was determined. The 2015 study did not distinguish between the other Galloway breeds (GAL, BGA), but calculated an allele frequency of 0.014 for this group. If the data for GAL and BGA are combined in this study, the allele frequency is 0.017.&lt;/p&gt;&lt;p&gt;To examine changes in genotype frequencies from the time the genetic defect was first described (Brenig et al. &lt;span&gt;2015&lt;/span&gt;) to the present day, the number of genotypes from 2015 was compared with the current data in a 2 × 2 contingency table, and the &lt;i&gt;Χ&lt;/i&gt;&lt;sup&gt;2&lt;/sup&gt;-value","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 5","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13537897/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148878974","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":"Genetic Diversity Analysis of Red Fox Populations (Vulpes vulpes L., 1758) in Natural and Anthropogenic Isolation","authors":"A. E. Hrebianchuk,&nbsp;V. M. Lukashkova,&nbsp;N. S. Parfionava,&nbsp;R. Ogden,&nbsp;I. S. Tsybovsky","doi":"10.1002/age.70189","DOIUrl":"10.1002/age.70189","url":null,"abstract":"<div>\u0000 \u0000 <p>This study presents a comparative analysis of the genetic structure and diversity of three red fox (<i>Vulpes vulpes</i> L.) populations representing different microevolutionary scenarios: panmixia (free-ranging Belarusian foxes), geographic isolation (free-ranging Scottish foxes), and anthropogenic selection (farm-bred foxes). Using a validated set of STR markers, multivariate statistical analysis was conducted to assess the genetic structure and the degree of genetic erosion across the studied groups. The wild red fox population in Belarus has been shown to maintain a state close to panmixia (<i>P</i>_HWE = 0.090), characterized by a high effective population size (<i>N</i>_e = 694) and high allelic diversity. The island population from Scotland exhibits moderate gene pool depletion (<i>N</i>_e = 75.9) and a pronounced heterozygote deficiency (<i>F</i>_IS = 0.18). Critical genetic erosion, which was characterized by a minimal effective population size (<i>N</i>_e = 60.2) and allelic fixation, was detected in the farm-bred group. The genetic distance between farm-bred and wild foxes (<i>F</i>_ST = 0.279; <i>p</i> = 0.001) reflects both the phylogeographic divergence between the Nearctic ancestors of farmed lineages and Palearctic wild populations, and the consequences of prolonged anthropogenic isolation, genetic drift, and selective breeding. These data indicate that artificial isolation and the impacts of genetic drift and targeted selection lead to a substantial depletion of the species' adaptive potential.</p>\u0000 </div>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 5","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148863166","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":"Safe and Stable Germline Transmission of MSTN Mutations in Cattle","authors":"Gyeong-Min Gim,&nbsp;Bae Young Choi,&nbsp;Jeongbin Yi,&nbsp;Kyeong-Hyeon Eom,&nbsp;Soo-Young Yum,&nbsp;Dae-Jin Jung,&nbsp;Do-Yoon Kim,&nbsp;Bokyoung Yang,&nbsp;Jong-Seo Kim,&nbsp;Donghwan Shim,&nbsp;Goo Jang","doi":"10.1002/age.70192","DOIUrl":"10.1002/age.70192","url":null,"abstract":"<p>With the global population expected to reach 10 billion by 2050, sustainable livestock production is critical. Gene editing of the myostatin (MSTN) gene represents a promising strategy to enhance muscle growth in cattle. In this study, MSTN-mutated founder (F0) cows were used to generate F1 offspring via ovum pick-up, in vitro fertilization, and embryo transfer. Four F1 calves were born, all confirmed to be heterozygous for the MSTN mutation. Long-term monitoring showed normal growth and no visible health abnormalities. Whole-genome sequencing identified SNPs, INDELs, and structural variants, most with minimal predicted functional effects. Proteomic profiling of Longissimus dorsi muscle quantified 2947 proteins, revealing only subtle expression differences between MSTN-mutated and wild-type cattle. These results demonstrate stable inheritance and confirm that MSTN editing does not disrupt genome integrity or protein expression. Overall, our findings support the safety and utility of MSTN gene editing to improve livestock productivity for future food security.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 5","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13527548/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148863269","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":"Transcriptome and Functional Analysis Uncover the Role of ADCY5 in Bovine Adipogenesis","authors":"Xuefeng Wei,&nbsp;Xinyue Shan,&nbsp;Lize Yang,&nbsp;Xue Zhao,&nbsp;Yun Ma,&nbsp;Pengpeng Zhang,&nbsp;Yongjie Xu,&nbsp;Ruijie Hao","doi":"10.1002/age.70191","DOIUrl":"10.1002/age.70191","url":null,"abstract":"<div>\u0000 \u0000 <p>Adipose deposition is genetically regulated and acts as a core determinant of meat quality in livestock. Therefore, exploring the gene regulatory mechanisms underlying adipose deposition is essential to advance the research on adipose tissue development and molecular breeding in livestock. To clarify the molecular basis of the superior meat quality of Pinan (PN) cattle, high-throughput RNA sequencing was performed to screen the key genes regulating adipose deposition in PN, with Nanyang (NY) cattle serving as the control (<i>n</i> = 3 per breed). A total of 265 differentially expressed genes (DEGs) were identified in the adipose tissue of PN cattle relative to NY cattle, comprising 135 upregulated and 130 downregulated genes. GO and KEGG enrichment analysis revealed that these DEGs were primarily enriched in lipid binding-related functional categories, particularly lipid antigen binding and exogenous lipid antigen binding, as well as enzymatic functions such as protein xylosyltransferase activity. Meanwhile, RT-qPCR confirmed significant differential expression of <i>WNT16, IGFBP2</i>, <i>PEMT</i>, <i>ADCY5</i>, and <i>IDH3B</i> in adipose tissue between PN and NY cattle, consistent with the RNA-seq data. Moreover, functional validation experiments, including RT-qPCR, CCK-8, EdU, and Oil Red O staining, revealed that RNA interference (RNAi)-mediated <i>ADCY5</i> knockdown markedly promoted adipocyte proliferation, while significantly inhibiting adipocyte differentiation and lipid droplet formation. Collectively, the present study indicates that the identified DEGs are potentially involved in the regulation of bovine adipose tissue development. Notably, <i>ADCY5</i> exhibits a crucial regulatory effect on cattle adipose deposition; however, the precise molecular mechanism remains to be further elucidated in future studies.</p>\u0000 </div>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 5","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148811794","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":"SINE Insertion in LAMA3 in Dogs With Junctional Epidermolysis Bullosa","authors":"Sarah Kiener,&nbsp;Ronnie Kaufmann,&nbsp;Ori Brenner,&nbsp;Vidhya Jagannathan,&nbsp;Tosso Leeb","doi":"10.1002/age.70190","DOIUrl":"10.1002/age.70190","url":null,"abstract":"<p>Junctional epidermolysis bullosa (JEB) is a hereditary skin disorder caused by defects in proteins responsible for dermal-epidermal adhesion. We investigated the genetic cause of JEB in three related mixed-breed puppies presenting with congenital skin blistering and ulceration. Whole-genome sequencing of one affected dog followed by comparison with 1538 control genomes identified a private candidate variant, XM_038543644.1:c.5690_5691ins240, in <i>LAMA3</i>, a known JEB-associated gene. Visual inspection of the short-read alignments and Sanger sequencing revealed a homozygous 240-bp SINE insertion in exon 45 that had initially been miscalled as a heterozygous short insertion. Fragment length analysis confirmed complete co-segregation of the variant with the disease phenotype within the available family. The SINE insertion is flanked by a 16-bp target site duplication, contains a 45-nt poly(A) tail, and is predicted to remain in-frame, introducing an additional 80 amino acids into the laminin α3 coiled-coil domain without introducing a premature stop codon. Although the molecular consequences were not functionally investigated, the insertion is expected to disrupt normal laminin-332 heterotrimer assembly and secretion. This study expands the spectrum of pathogenic <i>LAMA3</i> variants associated with canine JEB and highlights the importance of visual inspection of short-read sequencing data for the detection and correct interpretation of structurally complex variants such as transposable element insertions.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 5","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13500218/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148808040","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":"Whole-Genome Resequencing Reveals Selection Signatures Associated With Lambskin Patterns in Hu Sheep","authors":"Kebede Habtegiorgis Beshah,&nbsp;Jing Xie,&nbsp;Muhammad Tariq,&nbsp;Abdul Quddus,&nbsp;Daxiang Wang,&nbsp;Bingru Zhao,&nbsp;Dagan Mao","doi":"10.1002/age.70186","DOIUrl":"10.1002/age.70186","url":null,"abstract":"<div>\u0000 \u0000 <p>In China, Hu sheep lambskin quality is largely determined by wool curvature, with wavy-wool lambs producing higher-quality pelts than straight-wool lambs. However, the genetic mechanisms underlying wool curvature formation remain poorly understood. To address this knowledge gap, we conducted whole-genome resequencing and transcriptomic analyses to identify candidate genes associated with wool curvature in Hu sheep. Phenotypic records from 3047 Hu lambs identified significant differences between wavy- and straight-wool groups. Twenty representative animals (10 per group) were selected for whole-genome resequencing. Selective sweep analyses based on the fixation index (FST), absolute log₂-transformed nucleotide diversity ratio [|log₂(<i>π</i> ratio)|], and Tajima's D (Taj<i>D</i>) identified 157 genomic windows under positive selection. Four major genomic regions showing strong selective signatures were located on chromosomes 4, 7, 13, and 18. Several biologically relevant candidate genes were identified within these regions, including <i>KRTDAP</i>, <i>FGF2</i>, <i>FGF7</i>, <i>OCLN</i>, <i>MAPK1</i>, <i>SHC4</i>, <i>LAMA2</i>, and <i>COL9A3</i>. Functional enrichment analysis indicated that these genes are primarily associated with extracellular matrix (ECM) organization, focal adhesion, PI3K–Akt, MAPK, and Ras signaling pathways. In addition, RNA sequencing (RNA-seq) data from an independent cohort of eight lambs were integrated with genomic selection signals. This integrative analysis identified 61 overlapping genes, from which 12 high-confidence candidate genes were prioritized, including <i>LUM, COL6A1, SPARC, ITGA11,</i> and <i>DCLK1</i>. These findings highlight genomic regions and candidate genes potentially associated with ECM remodeling and other biological processes relevant to lambskin pattern formation, providing valuable genomic resources for future functional studies and marker-assisted selection in Hu sheep.</p>\u0000 </div>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 5","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148808117","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":"Evaluation of Multi-Breed Genomic Prediction Models for Carcass and Reproductive Traits in Zebu Beef Cattle","authors":"Gabriel Gubiani,&nbsp;Larissa Temp,&nbsp;Marisol Londoño-Gil,&nbsp;Miller Teodoro,&nbsp;Eduarda Oliveira,&nbsp;Ignacio Aguilar,&nbsp;Matias Bermann,&nbsp;Daniela Lourenco,&nbsp;Angelica S. C. Pereira,&nbsp;Fernando Baldi","doi":"10.1002/age.70188","DOIUrl":"https://doi.org/10.1002/age.70188","url":null,"abstract":"<p>Genomic prediction in beef cattle is particularly challenging in breeds with limited phenotypic and genotypic data. In this context, multi-breed methodologies that integrate information from genetically related populations have emerged as a promising strategy to improve prediction accuracy and calibration under data-scarce conditions. This study evaluated different genomic prediction approaches in a multi-breed population of Zebu cattle, including Nellore, Guzerat, Brahman, and Tabapua, using 653 785 phenotypic records, 190 865 genotypic records, and 3 681 158 pedigree records. The traits analyzed were rib eye area (REA), rump fat thickness (RFT), age at first calving (AFC), and accumulated productivity (ACP). Genomic estimated breeding values were obtained using the single-step GBLUP method under four models: single-breed (G_SB), standard multi-breed (G₀), metafounders (MF), and an adjusted genomic relationship matrix (AGR). Model performance was assessed using the linear regression method, which compares predictions from complete and partial datasets to estimate accuracy, bias, and dispersion. Multi-breed models, particularly MF and AGR, produced higher accuracy than the single-breed approach in several analyses for underrepresented breeds such as Guzerat, Brahman, and Tabapua, especially for carcass and reproductive-related traits. For example, in Guzerat, REA accuracy increased from 0.44 with G_SB to 0.62 with AGR, while in Tabapua, ACP accuracy improved substantially from 0.23 with G_SB to 0.51 with AGR. These results highlight the importance of leveraging genetically related breeds and well-structured reference populations to improve the reliability of genomic predictions in Zebu cattle under limited data conditions.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 5","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/age.70188","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148784408","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}