Ruan Donglin, Yang Jie, Zhuang Zhanwei, Ding Rongrong, Huang Jinyan, Quan Jianping, Gu Ting, Hong Linjun, Zheng Enqin, Li Zicong, Cai Gengyuan, Wang Xiaopeng, Wu Zhenfang
College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China.
Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China.
Front Genet. 2022 Jan 27;12:812456. doi: 10.3389/fgene.2021.812456. eCollection 2021.
Heterozygosity can effectively reflect the diverse models of population structure and demographic history. However, the genomic distribution of heterozygotes and the correlation between regions of heterozygosity (runs of heterozygosity, ROHet) and phenotypes are largely understudied in livestock. The objective of this study was to identify ROHet in the Duroc pig genome, and investigate the relationships between ROHet and eight important economic traits. Here, we genotyped 3,770 American Duroc (S21) and 2,096 Canadian Duroc (S22) pigs using 50 K single nucleotide polymorphism array to analyze heterozygosity. A total of 145,010 and 84,396 ROHets were characterized for S21 and S22 populations, respectively. ROHet segments were mostly enriched in 1-2 Mb length classification (75.48% in S21 and 72.25% in S22). The average genome length covered by ROHet was 66.53 ± 12.20 Mb in S21 and 73.32 ± 13.77 Mb in S22 pigs. Additionally, we detected 20 and 13 ROHet islands in S21 and S22 pigs. Genes in these genomic regions were mainly involved in the biological processes of immunity and reproduction. Finally, the genome-wide ROHet-phenotypes association analysis revealed that 130 ROHets of S21 and 84 ROHets of S22 were significantly associated with eight economic traits. Among the candidate genes in the significant ROHet regions, 16 genes related to growth, metabolism, and meat quality were considered as candidate genes for important economic traits of pigs. This work preliminarily explores the effect of heterozygosity-rich regions in the pig genome on production performance and provides new insights for subsequent research on pig genetic improvement.
杂合性能够有效反映种群结构和种群历史的多样模式。然而，家畜中杂合子的基因组分布以及杂合性区域（杂合性片段，ROHet）与表型之间的相关性在很大程度上尚未得到充分研究。本研究的目的是在杜洛克猪基因组中鉴定ROHet，并研究ROHet与八个重要经济性状之间的关系。在此，我们使用50K单核苷酸多态性芯片对3770头美国杜洛克猪（S21）和2096头加拿大杜洛克猪（S22）进行基因分型，以分析杂合性。S21和S22群体分别鉴定出总共145,010个和84,396个ROHet。ROHet片段大多富集在长度分类为1 - 2 Mb的区域（S21中为75.48%，S22中为72.25%）。S21猪中ROHet覆盖的平均基因组长度为66.53 ± 12.20 Mb，S22猪中为73.32 ± 13.77 Mb。此外，我们在S21和S22猪中分别检测到20个和13个ROHet岛。这些基因组区域中的基因主要参与免疫和繁殖的生物学过程。最后，全基因组ROHet - 表型关联分析表明，S21的130个ROHet和S22的84个ROHet与八个经济性状显著相关。在显著ROHet区域的候选基因中，16个与生长、代谢和肉质相关的基因被认为是猪重要经济性状的候选基因。本研究初步探索了猪基因组中富含杂合性的区域对生产性能的影响，为后续猪遗传改良研究提供了新的见解。
