Genome wide association study identifies SNPs associated with fatty acid composition in Chinese Wagyu cattle

Zezhao Wang,Huijiang Gao,Yan Chen,Xue Gao,Bo Zhu,Lingyang Xu,Wengang Zhang,Lei Xu,Shengli Zhang,Junya Li,Ling Xu,Hong Niu,Lupei Zhang

doi:10.1186/s40104-019-0322-0

Abstract

BackgroundFatty acids are important traits that affect meat quality and nutritive values in beef cattle. Detection of genetic variants for fatty acid composition can help to elucidate the genetic mechanism underpinning these traits and promote the improvement of fatty acid profiles. In this study, we performed a genome-wide association study (GWAS) on fatty acid composition using high-density single nucleotide polymorphism (SNP) arrays in Chinese Wagyu cattle.ResultsIn total, we detected 15 and 8 significant genome-wide SNPs for individual fatty acids and fatty acid groups in Chinese Wagyu cattle, respectively. Also, we identified nine candidate genes based on 100 kb regions around associated SNPs. Four SNPs significantly associated with C14:1 cis-9 were embedded with stearoyl-CoA desaturase (SCD), while three SNPs in total were identified for C22:6 n-3 within Phospholipid scramblase family member 5 (PLSCR5), Cytoplasmic linker associated protein 1 (CLASP1), and Chymosin (CYM). Notably, we found the top candidate SNP within SCD can explain ~ 7.37% of phenotypic variance for C14:1 cis-9. Moreover, we detected several blocks with high LD in the 100 kb region around SCD. In addition, we found three significant SNPs within a 100 kb region showing pleiotropic effects related to multiple FA groups (PUFA, n-6, and PUFA/SFA), which contains BAI1 associated protein 2 like 2 (BAIAP2L2), MAF bZIP transcription factor F (MAFF), and transmembrane protein 184B (TMEM184B).ConclusionsOur study identified several significant SNPs and candidate genes for individual fatty acids and fatty acid groups in Chinese Wagyu cattle, and these findings will further assist the design of breeding programs for meat quality in cattle.

Highlights

Fatty acids are important traits that affect meat quality and nutritive values in beef cattle
Descriptive statistics and heritability estimations of fatty acid compositions Descriptive statistics and heritability estimate results were presented in Table 1 for 21 individual FAs and eight FA groups
We observed that the most abundant individual saturated FAs were C18:1 cis-9 (46.87%), and C16:0 (27.46%), while relatively high proportions of the total FAs were found for C18:0 (11.96%), C16:1 cis-9 (4.22%), and C18:2 n-6 (3.84%) among the 21 individual FAs

Summary

Introduction

Fatty acids are important traits that affect meat quality and nutritive values in beef cattle. We performed a genome-wide association study (GWAS) on fatty acid composition using high-density single nucleotide polymorphism (SNP) arrays in Chinese Wagyu cattle. Many studies have identified candidate markers associated with FA composition in different populations, such as Japanese Black cattle, Hereford, Angus, and Shorthorn [16, 20,21,22,23]. Most of these studies were carried out using low density SNP arrays. The genetic basis of FA composition may vary among populations, and the use of genomic technologies for improving fatty acid profiles in beef cattle have not been comprehensively addressed [8, 16, 21, 23,24,25,26,27,28,29]

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