Acta Veterinaria et Zootechnica Sinica ›› 2024, Vol. 55 ›› Issue (9): 3833-3842.doi: 10.11843/j.issn.0366-6964.2024.09.009

• Animal Genetics and Breeding • Previous Articles     Next Articles

Analysis of the Whole Genome Run of Homozygosity (ROH) and Selection Signal in Beijing Black Pigs

Jingjing TIAN(), Xiaoqing WANG, Mianyan LI, Hailing WANG, Qitian WU, Lixian WANG, Longchao ZHANG*(), Fuping ZHAO*()   

  1. Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
  • Received:2024-03-06 Online:2024-09-23 Published:2024-09-27
  • Contact: Longchao ZHANG, Fuping ZHAO E-mail:tianjingjing9321@163.com;zhlchias@163.com; zhanglongchao@caas.cn;zhaofuping@caas.cn

Abstract:

This study aimed to investigate the genetic structure of the Beijing black pigs based on runs of homozygosity (ROH) and selection signals|iHS|analysis and to identify candidate genes related to economic traits. The subjects of this study were Beijing black pigs, with an average age of 210 days. After quality control and imputation of the illumina Porcine 50K chip data from 729 Beijing black pigs, the ROH and|iHS|were analyzed. In this study, the threshold for ROH islands was set at the SNPs that constituted the top 1% of ROHs, and regions exceeding this threshold were termed ROH islands. All SNPs in the top 1% of standardized |iHS| values were retained, and the areas extending 200 kb upstream and downstream of these SNPs were considered as the strong selection regions obtained by the iHS. The overlapping areas between the strong selection regions of the selection signals and the ROH islands were defined as the candidate regions for this study. In this study, 724 individuals and 45 585 SNPs were retained, and a total of 10 ROH islands containing 449 SNPs were identified by ROH analysis, and the results of|iHS|analysis showed that a total of 376 strongly selected SNPs were retained after the top 1% SNPs with the highest score were retained. In the end, a total of 18 genes in the overlapping regions of the 5 strongly selected regions of |iHS| and ROH islands were annotated, including some genes known to affect pork quality and growth and development. This study analyzed the distribution of ROH in the Beijing black pigs and revealed potential selected SNPs and candidate genes combined with selection signals. The results provide an important reference for further exploring the population characteristics and genetic mechanisms of economic traits of Beijing black pigs.

Key words: Beijing black pig, chip data, ROH, iHS

CLC Number: