Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array
Author:
Hu Mingyue1, Jiang Hao1ORCID, Lai Weining1, Shi Lulu1, Yi Wenfeng1, Sun Hao1, Chen Chengzhen1, Yuan Bao1ORCID, Yan Shouqing1, Zhang Jiabao1ORCID
Affiliation:
1. College of Animal Science, Jilin University, Changchun 130062, China
Abstract
Chinese Red Steppe Cattle (CRS), a composite cattle breed, is well known for its milk production, high slaughter rate, carcass traits, and meat quality. Nowadays, it is widely bred in Jilin and Hebei Province and the Inner Mongolia Autonomous region. However, the population structure and the genetic basis of prominent characteristics of CRS are still unknown. In this study, we systematically describe their population structure, genetic diversity, and selection signature based on genotyping data from 61 CRS individuals with GGP Bovine 100 K chip. The results showed that CRS cattle had low inbreeding levels and had formed a unique genetic structure feature. Using two complementary methods (including comprehensive haplotype score and complex likelihood ratio), we identified 1291 and 1285 potentially selected genes, respectively. There were 141 genes annotated in common 106 overlapping genomic regions covered 5.62 Mb, including PLAG1, PRKG2, DGAT1, PARP10, TONSL, ADCK5, and BMP3, most of which were enriched in pathways related to muscle growth and differentiation, milk production, and lipid metabolism. This study will contribute to understanding the genetic mechanism behind artificial selection and give an extensive reference for subsequent breeding.
Funder
National Natural Science Foundation of China China Agriculture Research System of MOF and MARA
Subject
General Veterinary,Animal Science and Zoology
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