Xu Zhong, Mei Shuqi, Zhou Jiawei, Zhang Yu, Qiao Mu, Sun Hua, Li Zipeng, Li Lianghua, Dong Binke, Oyelami Favour Oluwapelumi, Wu Junjing, Peng Xianwen
Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China.
Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
Front Genet. 2021 Sep 1;12:720081. doi: 10.3389/fgene.2021.720081. eCollection 2021.
The primary purpose of the current study was to assess the genetic diversity, runs of homozygosity (ROH) and ROH islands in a Chinese composite pig and explore hotspot regions for traces of selection. First, we estimated the length, number, and frequency of ROH in 262 Xidu black pigs using the Porcine SNP50 BeadChip and compared the estimates of inbreeding coefficients, which were calculated based on ROHs (F) and homozygosity (F). Our result shows that a total of 7,248 ROH exceeding 1Mb were detected in 262 pigs. In addition, chromosome (SSC) 8 and SSC10, respectively, has the highest and lowest chromosome coverage by ROH. These results suggest that inbreeding estimation based on total ROH may be a useful method, especially for crossbreed or composite populations. We also calculated an inbreeding coefficient of 0.077 from the total ROH. Eight ROH islands were found in this study. These ROH islands harbored genes associated with fat deposition, muscular development, reproduction, ear shape, and adaptation, such as , , , , , and . These findings may help to understand the effects of environmental and artificial selection on the genome structure of composite pigs. Our results provide a basis for subsequent genomic selection (GS), and provides a reference for the hybrid utilization of other pig breeds.
本研究的主要目的是评估中国杂交猪的遗传多样性、纯合子连续片段（ROH）和ROH岛，并探索选择痕迹的热点区域。首先，我们使用猪SNP50芯片估计了262头西杜黑猪中ROH的长度、数量和频率，并比较了基于ROH计算的近交系数估计值（F）和纯合度（F）。我们的结果显示，在262头猪中总共检测到7248个超过1Mb的ROH。此外，第8号染色体（SSC8）和第10号染色体（SSC10）分别具有最高和最低的ROH染色体覆盖率。这些结果表明，基于总ROH的近交估计可能是一种有用的方法，特别是对于杂交或复合群体。我们还从总ROH中计算出近交系数为0.077。本研究发现了8个ROH岛。这些ROH岛含有与脂肪沉积、肌肉发育、繁殖、耳形和适应性相关的基因，如 、 、 、 、 和 。这些发现可能有助于理解环境和人工选择对杂交猪基因组结构的影响。我们的结果为后续的基因组选择（GS）提供了依据，并为其他猪种的杂交利用提供了参考。
