Genome-wide analysis reveals the effects of artificial selection on production and meat quality traits in Qinchuan cattle

Chugang Mei; Hongcheng Wang; Qijun Liao; Rajwali Khan; Sayed Haidar Abbas Raza; Chunping Zhao; Hongbao Wang; Gong Cheng; Wanqiang Tian; Yaokun Li; Linsen Zan

doi:10.1016/j.ygeno.2018.09.021

Genome-wide analysis reveals the effects of artificial selection on production and meat quality traits in Qinchuan cattle

Genomics. 2019 Dec;111(6):1201-1208. doi: 10.1016/j.ygeno.2018.09.021. Epub 2018 Oct 6.

Authors

Affiliations

¹ College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
² College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; College of Life Science, Guizhou Normal University, Guiyang 550001, China.
³ BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China.
⁴ Yangling Vocational & Technical College, Yangling 712100, China.
⁵ College of Animal Science and Technology, South China Agricultural University, Guangzhou 510642, China.
⁶ College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; National Beef Cattle Improvement Center, Yangling 712100, China. Electronic address: zanlinsen@163.com.

PMID: 30300672
DOI: 10.1016/j.ygeno.2018.09.021

Abstract

A new strain of Qinchuan cattle (QNS) has been obtained after more than forty years of selective breeding, and it shows good performance and production traits. To characterize the genetic changes that have resulted from breeding, we sequenced 10 QNS and 10 of the original breed Qinchuan cattle (QCC) for the first time, with average of 12.5-fold depth. A total of 31,242,284 and 29,612,517 SNPs were identified in the QCC and QNS genomes, 47.81% and 44.36% of which were found to be novel, respectively. Furthermore, population structure analysis revealed the selection that these cattle had experienced. Then, 332 and 571 potential selected genes were obtained, associated with enhanced immunity and acclimatization in QCC (CD5, SMARCA2, CATHL2, etc.) and production or meat quality traits in QNS (PLCD3, MB, PPARGC1A, etc.). These results revealed the efforts of selective breeding for Chinese Qinchuan cattle, and will be helpful for future cattle breeding.

Keywords: Breeding; Genome sequencing; Qinchuan cattle; Selection.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Breeding
Cattle / genetics*
Genetic Variation
INDEL Mutation
Meat*
Molecular Sequence Annotation
Phenotype
Polymorphism, Single Nucleotide
Whole Genome Sequencing