Genome-wide association studies identified multiple genetic loci for body size at four growth stages in Chinese Holstein cattle

Xu Zhang; Qin Chu; Gang Guo; Ganghui Dong; Xizhi Li; Qin Zhang; Shengli Zhang; Zhiwu Zhang; Yachun Wang

doi:10.1371/journal.pone.0175971

Genome-wide association studies identified multiple genetic loci for body size at four growth stages in Chinese Holstein cattle

PLoS One. 2017 Apr 20;12(4):e0175971. doi: 10.1371/journal.pone.0175971. eCollection 2017.

Authors

Xu Zhang^{1

2}, Qin Chu³, Gang Guo⁴, Ganghui Dong⁴, Xizhi Li⁴, Qin Zhang¹, Shengli Zhang¹, Zhiwu Zhang², Yachun Wang¹

Affiliations

¹ Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China.
² Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America.
³ Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, P.R. China.
⁴ Beijing Sunlon Livestock Development Co. Ltd, Beijing, P.R. China.

Abstract

The growth and maturity of cattle body size affect not only feed efficiency, but also productivity and longevity. Dissecting the genetic architecture of body size is critical for cattle breeding to improve both efficiency and productivity. The volume and weight of body size are indicated by several measurements. Among them, Heart Girth (HG) and Hip Height (HH) are the most important traits. They are widely used as predictors of body weight (BW). Few association studies have been conducted for HG and HH in cattle focusing on single growth stage. In this study, we extended the Genome-wide association studies to a full spectrum of four growth stages (6-, 12-, 18-, and 24-months after birth) in Chinese Holstein heifers. The whole genomic single nucleotide polymorphisms (SNPs) were obtained from the Illumina BovineSNP50 v2 BeadChip genotyped on 3,325 individuals. Estimated breeding values (EBVs) were derived for both HG and HH at the four different ages and analyzed separately for GWAS by using the Fixed and random model Circuitous Probability Unification (FarmCPU) method. In total, 27 SNPs were identified to be significantly associated with HG and HH at different growth stages. We found 66 candidate genes located nearby the associated SNPs, including nine genes that were known as highly related to development and skeletal and muscular growth. In addition, biological function analysis was performed by Ingenuity Pathway Analysis and an interaction network related to development was obtained, which contained 16 genes out of the 66 candidates. The set of putative genes provided valuable resources and can help elucidate the genomic architecture and mechanisms underlying growth traits in dairy cattle.

MeSH terms

Animals
Cattle / genetics*
Cattle / growth & development
Genome-Wide Association Study*
Growth / genetics*
Polymorphism, Single Nucleotide

Grants and funding

This work was financially supported by the earmarked fund for Modern Agro-industry Technology Research System (CARS-37), the Agricultural Research Center at Washington State University, College of Agricultural, Human, and Natural Resource Sciences (17A-3019-8663), Washington Grain Commission (126593), China Scholarship Council (201406350114), and the Program for Changjiang Scholar and Innovation Research Team in University (IRT1191). Beijing Sunlon Livestock Development Co. Ltd. provided support in the form of salaries for authors GG, GD, and XL and assisted in measurement and data collection for this study. The funder had no additional role in study design, decision to publish, or preparation of the manuscript.