Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China.
Chongqing Academy of Animal Sciences, Chongqing, China.
PLoS One. 2021 Sep 28;16(9):e0257974. doi: 10.1371/journal.pone.0257974. eCollection 2021.
Sichuan, China, has abundant genetic resources of sheep (Ovis aries). However, their genetic diversity and population structure have been less studied, especially at the genome-wide level. In the present study, we employed the specific-locus amplified fragment sequencing for identifying genome-wide single nucleotide polymorphisms (SNPs) among five breeds of sheep distributed in Sichuan, including three local pure breeds, one composite breed, and one exotic breed of White Suffolk. From 494 million clean paired-end reads, we obtained a total of 327,845 high-quality SNPs that were evenly distributed among all 27 chromosomes, with a transition/transversion ratio of 2.56. Based on this SNP panel, we found that the overall nucleotide diversity was 0.2284 for all five breeds, with the highest and lowest diversity observed in Mage sheep (0.2125) and Butuo Black (0.1963) sheep, respectively. Both Wright's fixation index and Identity-by-State distance revealed that all individuals of Liangshan Semifine-wool, White Suffolk, and Butuo Black sheep were respectively clustered together, and the breeds could be separated from each other, whereas Jialuo and Mage sheep had the closest genetic relationship and could not be distinguished from each other. In conclusion, we provide a reference panel of genome-wide and high-quality SNPs in five sheep breeds in Sichuan, by which their genetic diversity and population structures were investigated.
中国四川拥有丰富的绵羊（Ovis aries）遗传资源。然而，它们的遗传多样性和群体结构尚未得到充分研究，特别是在全基因组水平上。本研究采用特定基因座扩增片段测序技术，对分布于四川的五个绵羊品种（包括三个本地绵羊品种、一个杂交品种和一个外来的白萨福克品种）进行了全基因组单核苷酸多态性（SNP）的鉴定。从 4.94 亿条高质量的配对末端reads 中，我们共获得了 327845 个高质量的 SNPs，这些 SNPs 均匀分布在 27 条染色体上，转换/颠换比为 2.56。基于该 SNP 面板，我们发现五个绵羊品种的总体核苷酸多样性为 0.2284，其中马阁绵羊（0.2125）和布拖黑绵羊（0.1963）的多样性最高和最低。Wright 的固定指数和等位基因状态相似性距离均表明，凉山半细毛羊、白萨福克和布拖黑绵羊的所有个体分别聚在一起，并且可以将这些品种彼此区分开来，而嘉洛和马阁绵羊具有最密切的遗传关系，无法将它们区分开来。总之，我们为四川五个绵羊品种提供了一个全基因组范围的高质量 SNP 参考面板，通过该面板研究了它们的遗传多样性和群体结构。
