Weighted Single-Step Genome-Wide Association Study for Growth Traits in Chinese Simmental Beef Cattle.

Zhanwei Zhuang,Xue Gao,Lingyang Xu,Bo Zhu,Lupei Zhang,Huijiang Gao,Jie Yang,Junya Li

doi:10.3390/genes11020189

Abstract

Improving the genetic process of growth traits is one of the major goals in the beef cattle industry, as it can increase meat production and reduce the cost of raising animals. Although several quantitative trait loci affecting growth traits in beef cattle have been identified, the genetic architecture of these economically important traits remains elusive. This study aims to map single nucleotide polymorphisms (SNPs) and genes associated with birth weight (BW), yearling weight (YW), average daily gain from birth to yearling (BYADG), and body weight at the age of 18 months (18MW) in a Chinese Simmental beef cattle population using a weighted, single-step, genome-wide association study (wssGWAS). Phenotypic and pedigree data from 6022 animals and genotypes from 744 animals (596,297 SNPs) were used for an association analysis. The results showed that 66 genomic windows explained 1.01–20.15% of the genetic variance for the four examined traits, together with the genes near the top SNP within each window. Furthermore, the identified genomic windows (>1%) explained 50.56%, 57.71%, 61.78%, and 37.82% of the genetic variances for BW, YW, BYADG, and 18MW, respectively. Genes with potential functions in muscle development and regulation of cell growth were highlighted as candidates for growth traits in Simmental cattle (SQOR and TBCB for BW, MYH10 for YW, RLF for BYADG, and ARHGAP31 for 18MW). Moreover, we found 40 SNPs that had not previously been identified as being associated with growth traits in cattle. These findings will further advance our understanding of the genetic basis for growth traits and will be useful for the molecular breeding of BW, YW, BYADG, and 18MW in the context of genomic selection in beef cattle.

Highlights

IntroductionBeef cattle provide a large proportion of the meat consumed by humans throughout the world [1]
Beef cattle provide a large proportion of the meat consumed by humans throughout the world [1].Improving the genetic process of growth traits is one of the major goals in the beef cattle breeding industry, as it can increase meat production and reduce the cost of raising animals [2,3]
6022 animals were used in wssGWAS for birth weight (BW); 3996 individuals were used in wssGWAS for yearling weight (YW) and BYADG; 3137 animals were used in wssGWAS for 18MW

Summary

Introduction

Beef cattle provide a large proportion of the meat consumed by humans throughout the world [1]. Improving the genetic process of growth traits (e.g., body weight and average daily gain) is one of the major goals in the beef cattle breeding industry, as it can increase meat production and reduce the cost of raising animals [2,3]. The key to accelerating the progress towards this goal is to genetically select elite cattle and to mine major genes that affect growth traits. GWASs have recently been used to identify several quantitative trait loci (QTLs) and genes associated with growth traits in beef cattle [1,3,5]. Kim et al [6] used

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