Animal Bioscience

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
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Genome-wide association study dissection of candidate genes for fleece traits in Inner Mongolia cashmere goats based on whole-genome resequencing data

  • Huanfeng Yao (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Silang Zhu (Inner Mongolia Yiwei White Cashmere Goat Co., Ltd.) ;
  • Rigan Xu (Inner Mongolia Yiwei White Cashmere Goat Co., Ltd.) ;
  • E'erke Ale'de (Inner Mongolia Yiwei White Cashmere Goat Co., Ltd.) ;
  • Yongbin Liu (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Jinquan Li (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Qi Lv (Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction) ;
  • Ruijun Wang (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Yanjun Zhang (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Rui Su (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Zhiying Wang (College of Animal Science, Inner Mongolia Agricultural University)
  • Received : 2025.09.01
  • Accepted : 2025.12.13
  • Published : 2026.05.01
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Abstract

Objective: Genome-wide association study (GWAS) and haplotype analysis were employed to identify molecular markers and candidate genes associated with fleece traits in Inner Mongolia cashmere goats (IMCGs). Methods: GWASs using whole-genome resequencing data together with phenotypic data from 2,299 IMCGs, applying four models: mixed linear model, multiple locus mixed linear model, fixed and random model circulating probability unification, and Bayesian-information and linkage-disequilibrium iteratively nested keyway. We focused on the GWAS signals to conduct gene annotation and performed functional enrichment analyses to explore the biological processes underlying these signals. Additionally, haplotypes were constructed for the significant loci, and haplotype-phenotype association analyses were performed to identify molecular markers and candidate genes associated with these fleece traits in IMCGs. Results: We identified 542 SNPs and 179 candidate genes linked to fleece traits through GWAS and gene annotation. Genes such as LAMA3, KCTD1, PTK7, FGFR3, LEF1, TAPT1, PTCH1, ELOVL6, and EVC have emerged as important candidates that may influence fleece traits. Furthermore, 11 haplotype blocks related to fleece traits were constructed, among which A1A1, C1C1, E2E2, F1F1, G1G1, H1H1 and K1K1 were identified as the superior haplotype combinations for fleece traits. These could serve as important molecular markers to improve the accuracy of early selection and the economic efficiency of breeding programs for fleece traits in IMCGs. Conclusion: This study successfully employed GWAS to identify key genetic loci significantly associated with the fleece traits of IMCGs. The genetic basis of these traits was revealed through additional gene annotation and haplotype analysis. The findings provide important theoretical and practical foundations for molecular breeding in IMCGs.

Keywords

Acknowledgement

We would like to thank Professor Wang for their excellent technical assistance in preparing experimental data and constructing models. We also greatly appreciate the assistance with sample collection and phenotype determination provided by the herdsmen and workers in Inner Mongolia Yiwei White Cashmere Goats Company. The authors also sincerely thank the editors and anonymous reviewers for their constructive criticism and helpful comments, which greatly improved the manuscript.

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