GWAS dissection of candidate genes for fleece traits in Inner Mongolia cashmere goats based on whole-genome resequencing data

¹College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
²Inner Mongolia Yiwei White Cashmere Goat Co., Ltd., Ordos, China
³Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, Hohhot, China
⁴Key Laboratory Of Mutton Sheep & Goat Genetics And Breeding, Ministry of Agriculture And Rural Affairs, Hohhot, China

Correspondence: Zhiying Wang, Tel: +86-13474737060, Email: wzhy0321@126.com

Received: 1 September 2025 • Revised: 4 November 2025 • Accepted: 13 December 2025

Abstract

Objective
Genome-wide association study and haplotype analysis to identified molecular markers and candidate genes associated with these fleece traits in Inner Mongolia cashmere goats.
Methods
Whole-genome resequencing and phenotypic data from 2,299 Inner Mongolia cashmere goats (IMCGs) were used to conduct Genome-wide association studies (GWAS) using multiple models. Significant SNPs were subsequently annotated and analyzed through functional enrichment. Additionally, Haplotypes were constructed for the significant sites, and association analysis was conducted between the haplotypes and phenotypes to identified molecular markers and candidate genes associated with these fleece traits.
Results
Nine key genes were detected to be associated with fleece traits using candidate gene-based association analysis. Including LAMA3, KCTD1, and PTK7 for cashmere yield (CY); FGFR3, LEF1, and TAPT1 for fiber length (FL); PTCH1 for cashmere length (CL); EVC and ELOVL6 for cashmere diameter (CD). Furthermore, Haplotype analysis identified that the A1A1, C1C1, E2E2, F1F1, G1G1, H1H1, and K1K1 haplotype combinations represent 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.
Conclusion
In conclusion, this study revealed the genetic architecture of fleece traits through GWAS, gene annotation, and haplotype analysis, offering valuable theoretical and marker resources for molecular breeding in IMCGs.

Keywords: Inner Mongolia Cashmere Goats; Fleece traits; GWAS; Genetic markers