Liu Jiaxin, Shi Liangyu, Li Yang, Chen Liang, Garrick Dorian, Wang Lixian, Zhao Fuping
Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
The Affiliated High School of Peking University, Beijing, 100192, China.
J Anim Sci Biotechnol. 2021 Aug 5;12(1):95. doi: 10.1186/s40104-021-00608-9.
A run of homozygosity (ROH) is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents. Genomic inbreeding can be quantified based on ROH. Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands. We carried out ROH analyses in five Chinese indigenous sheep breeds; Altay sheep (n = 50 individuals), Large-tailed Han sheep (n = 50), Hulun Buir sheep (n = 150), Short-tailed grassland sheep (n = 150), and Tibetan sheep (n = 50), using genotypes from an Ovine Infinium HD SNP BeadChip.
A total of 18,288 ROH were identified. The average number of ROH per individual across the five sheep breeds ranged from 39 (Hulun Buir sheep) to 78 (Large-tailed Han sheep) and the average length of ROH ranged from 0.929 Mb (Hulun Buir sheep) to 2.544 Mb (Large-tailed Han sheep). The effective population size (Ne) of Altay sheep, Large-tailed Han sheep, Hulun Buir sheep, Short-tailed grassland sheep and Tibetan sheep were estimated to be 81, 78, 253, 238 and 70 five generations ago. The highest ROH-based inbreeding estimate (F) was 0.0808 in Large-tailed Han sheep, whereas the lowest F was 0.0148 in Hulun Buir sheep. Furthermore, the highest proportion of long ROH fragments (> 5 Mb) was observed in the Large-tailed Han sheep breed which indicated recent inbreeding. In total, 49 ROH islands (the top 0.1% of the SNPs most commonly observed in ROH) were identified in the five sheep breeds. Three ROH islands were common to all the five sheep breeds, and were located on OAR2: 12.2-12.3 Mb, OAR12: 78.4-79.1 Mb and OAR13: 53.0-53.6 Mb. Three breed-specific ROH islands were observed in Altay sheep (OAR15: 3.4-3.8 Mb), Large-tailed Han sheep (ORA17: 53.5-53.8 Mb) and Tibetan sheep (ORA5:19.8-20.2 Mb). Collectively, the ROH islands harbored 78 unique genes, including 19 genes that have been documented as having associations with tail types, adaptation, growth, body size, reproduction or immune response.
Different ROH patterns were observed in five Chinese indigenous sheep breeds, which reflected their different population histories. Large-tailed Han sheep had the highest genomic inbreeding coefficients and the highest proportion of long ROH fragments indicating recent inbreeding. Candidate genes in ROH islands could be used to illustrate the genetic characteristics of these five sheep breeds. Our findings contribute to the understanding of genetic diversity and population demography, and help design and implement breeding and conservation strategies for Chinese sheep.
纯合片段（ROH）是个体中一段连续的纯合基因型，表明其从双亲继承了相同的祖先单倍型。基因组近亲繁殖可基于ROH进行量化。富含ROH的基因组区域可能指示选择清除，被称为ROH岛。我们利用绵羊Infinium HD SNP基因分型芯片的基因型，对五个中国本土绵羊品种进行了ROH分析，包括阿勒泰羊（n = 50只）、大尾寒羊（n = 50只）、呼伦贝尔羊（n = 150只）、短尾草地羊（n = 150只）和藏羊（n = 50只）。
共鉴定出18288个ROH。五个绵羊品种中每个个体的ROH平均数量从39个（呼伦贝尔羊）到78个（大尾寒羊）不等，ROH的平均长度从0.929 Mb（呼伦贝尔羊）到2.544 Mb（大尾寒羊）。估计阿勒泰羊、大尾寒羊、呼伦贝尔羊、短尾草地羊和藏羊五代前的有效种群大小（Ne）分别为81、78、253、238和70。基于ROH的最高近亲繁殖估计值（F）在大尾寒羊中为0.0808，而在呼伦贝尔羊中最低，为0.0148。此外，在大尾寒羊品种中观察到长ROH片段（>5 Mb）的比例最高，表明近期存在近亲繁殖。在这五个绵羊品种中共鉴定出49个ROH岛（ROH中最常观察到的前0.1%的SNP）。所有五个绵羊品种共有三个ROH岛，分别位于OAR2：12.2 - 12.3 Mb、OAR12：78.4 - 79.1 Mb和OAR13：53.0 - 53.6 Mb。在阿勒泰羊（OAR15：3.4 - 3.8 Mb）、大尾寒羊（ORA17：53.5 - 53.8 Mb）和藏羊（ORA5：19.8 - 20.2 Mb）中观察到三个品种特异性的ROH岛。总体而言，ROH岛包含78个独特基因，其中19个基因已被证明与尾型、适应性、生长、体型、繁殖或免疫反应有关。
在五个中国本土绵羊品种中观察到不同的ROH模式，这反映了它们不同的种群历史。大尾寒羊的基因组近亲繁殖系数最高，长ROH片段的比例也最高，表明近期存在近亲繁殖。ROH岛中的候选基因可用于阐明这五个绵羊品种的遗传特征。我们的研究结果有助于理解遗传多样性和种群人口统计学，并有助于设计和实施中国绵羊的育种和保护策略。
