Zhang Jipan, Fang Jiabei, Zhang Siyuan, Xu Jiele, Zhao Yongju
College of Animal Science and Technology, Southwest University, Chongqing, China.
Chongqing Key Laboratory of Herbivore Science, Chongqing, China.
Anim Genet. 2025 Feb;56(1):e13509. doi: 10.1111/age.13509.
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.
山羊通常有双层被毛，最外层的粗毛可抵御机械损伤和辐射损伤。由于羊绒作为高端纺织材料的地位，人们对其给予了大量关注，但关于粗毛的信息却有限。本研究旨在通过全基因组关联研究（GWAS）鉴定与粗毛直径相关的基因组变异，如单核苷酸多态性（SNP）和插入/缺失（indel）。从263只成年雌性山羊采集了粗毛和血样。使用倒置显微镜测量粗毛直径，并对血样进行全基因组测序。在进行 reads 映射、变异位点检测和质量控制后，共纳入11322006个SNP和863734个indel用于SNP-GWAS和indel-GWAS分析。鉴定出8个显著的SNP（p < 8.98e-8）和3个显著的indel（p < 1.16e-6）。其中，一个SNP位于4号染色体上，靠近COL28A1和C1GALT1基因。在chr10_96664101-96670958区域发现了7个显著的SNP，CDO1和TMED7基因分别位于其上游和下游。单倍型分析表明，这7个SNP的不同单倍型呈现出不同的粗毛直径值。值得注意的是，唯一持续显著的插入（chr10_96665085，GTA>G）也位于chr10_96664101-96670958区域内，进一步突出了该基因组区域在影响粗毛直径方面的重要性。这些显著变异和基因组区域为研究纤维直径变异的遗传机制提供了有价值的见解。
