Sun Xueliang, Guo Jiazhong, Li Ran, Zhang Huanhuan, Zhang Yifei, Liu George E, Emu Quzhe, Zhang Hongping
Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
Animals (Basel). 2024 Jan 29;14(3):444. doi: 10.3390/ani14030444.
Understanding the genetic makeup of local sheep breeds is essential for their scientific conservation and sustainable utilization. The Liangshan semi-fine-wool sheep (LSS), a Chinese semi-fine-wool breed renowned for its soft wool, was analyzed using whole-genome sequencing data including 35 LSS, 84 sheep from other domestic breeds, and 20 Asiatic mouflons. We investigated the genetic composition of LSS by conducting analyses of the population structure, runs of homozygosity, genomic inbreeding coefficients, and selection signature. Our findings indicated that LSS shares greater genetic similarity with Border Leicester and Romney sheep than with Tibetan (TIB), Yunnan (YNS), and Chinese Merino sheep. Genomic analysis indicated low to moderate inbreeding coefficients, ranging from 0.014 to 0.154. In identifying selection signals across the LSS genome, we pinpointed 195 candidate regions housing 74 annotated genes (e.g., , , and ). We also found the overlaps between the candidate regions and several known quantitative trait loci related to wool traits, such as the wool staple length and wool fiber diameter. A selective sweep region, marked by the highest value of cross-population extended haplotype homozygosity, encompassed -an influential candidate gene affecting fleece fiber traits. Furthermore, notable differences in genotype frequency at a mutation site (c.1051 + 46T > C, Chr25: 6,784,190 bp) within were observed between LSS and TIB and YNS sheep (Fisher's exact test, < 2.2 × 10). Taken together, these findings offer insights crucial for the conservation and breeding enhancement of LSS.
了解当地绵羊品种的基因组成对于其科学保护和可持续利用至关重要。凉山半细毛羊（LSS）是一种以其柔软羊毛而闻名的中国半细毛品种，我们使用全基因组测序数据对其进行了分析，这些数据包括35只凉山半细毛羊、84只其他国内品种的绵羊以及20只亚洲摩弗伦羊。我们通过进行群体结构分析、纯合子连续片段分析、基因组近亲繁殖系数分析和选择信号分析，研究了凉山半细毛羊的基因组成。我们的研究结果表明，与藏羊（TIB）、云南羊（YNS）和中国美利奴羊相比，凉山半细毛羊与边区莱斯特羊和罗姆尼羊的遗传相似性更高。基因组分析表明近亲繁殖系数较低至中等，范围为0.014至0.154。在识别凉山半细毛羊基因组中的选择信号时，我们确定了195个候选区域，其中包含74个注释基因（例如， 、 和 ）。我们还发现了候选区域与几个已知的与羊毛性状相关的数量性状位点之间的重叠，如羊毛纤维长度和羊毛纤维直径。一个以跨群体扩展单倍型纯合度最高值为标志的选择清除区域，包含一个影响羊毛纤维性状的有影响力的候选基因。此外，在凉山半细毛羊与藏羊和云南羊之间，观察到 在一个突变位点（c.1051 + 46T > C，Chr25: 6,784,190 bp）处的基因型频率存在显著差异（Fisher精确检验， < 2.2 × 10）。综上所述，这些发现为凉山半细毛羊的保护和育种改良提供了至关重要的见解。
