Several variants on chromosome 10 are associated with coarse hair diameter in Dazu black goats (Capra hircus)

Goats typically have double coats, with the outermost coarse hairs providing protection against mechanical and radiation damage. While much attention has been paid to cashmere due to its status as a high-end textile material, there is limited information available on coarse hair. This study aimed to identify genomic variants, such as single nucleotide polymorphisms (SNPs) and insertion/deletions (indels), associated with coarse hair diameter using a genome-wide association study (GWAS). Coarse hairs and blood samples were collected from 263 adult female goats. The diameter of coarse hairs was measured using an inverted microscope, and whole genome sequencing was conducted on the blood samples. After reads mapping, variants calling, and quality control, totals of 11 322 006 SNPs and 863 734 indels were included for SNP-GWAS and indel-GWAS analyses. Eight significant SNPs (p < 8.98e-8) and three significant indels (p < 1.16e-6) were identified. Among those, one SNP was located on Chromosome 4 and near the genes COL28A1 and C1GALT1. Seven significant SNPs were found in the region chr10_96664101-96670958, with the genes CDO1 and TMED7 located upstream and downstream, respectively. Haplotype analysis revealed that the diverse haplotypes of these seven SNPs presented varying values for coarse hair diameter. Notably, the only consistently significant insertion (chr10_96665085, GTA>G) was also located within the region chr10_96664101-96670958, further highlighting the importance of this genomic region in influencing coarse hair diameter. These significant variants and genomic regions provide valuable insights for investigating the genetic mechanisms underlying the variation in fiber diameter.