Genome wide association studies for body conformation traits in the Chinese Holstein cattle population

Xiaoping Wu,Guosheng Su,Dongxiao Sun,Yuan Zhang,Mogens Sandø Lund,Xiangdong Ding,Lv Qiao,Qin Zhang,Sheng Wang,Shengli Zhang,Lin Liu,Ming Fang,Jianfeng Liu

doi:10.1186/1471-2164-14-897

Abstract

BackgroundGenome-wide association study (GWAS) is a powerful tool for revealing the genetic basis of quantitative traits. However, studies using GWAS for conformation traits of cattle is comparatively less. This study aims to use GWAS to find the candidates genes for body conformation traits.ResultsThe Illumina BovineSNP50 BeadChip was used to identify single nucleotide polymorphisms (SNPs) that are associated with body conformation traits. A least absolute shrinkage and selection operator (LASSO) was applied to detect multiple SNPs simultaneously for 29 body conformation traits with 1,314 Chinese Holstein cattle and 52,166 SNPs. Totally, 59 genome-wide significant SNPs associated with 26 conformation traits were detected by genome-wide association analysis; five SNPs were within previously reported QTL regions (Animal Quantitative Trait Loci (QTL) database) and 11 were very close to the reported SNPs. Twenty-two SNPs were located within annotated gene regions, while the remainder were 0.6–826 kb away from known genes. Some of the genes had clear biological functions related to conformation traits. By combining information about the previously reported QTL regions and the biological functions of the genes, we identified DARC, GAS1, MTPN, HTR2A, ZNF521, PDIA6, and TMEM130 as the most promising candidate genes for capacity and body depth, chest width, foot angle, angularity, rear leg side view, teat length, and animal size traits, respectively. We also found four SNPs that affected four pairs of traits, and the genetic correlation between each pair of traits ranged from 0.35 to 0.86, suggesting that these SNPs may have a pleiotropic effect on each pair of traits.ConclusionsA total of 59 significant SNPs associated with 26 conformation traits were identified in the Chinese Holstein population. Six promising candidate genes were suggested, and four SNPs showed genetic correlation for four pairs of traits.

Highlights

Genome-wide association study (GWAS) is a powerful tool for revealing the genetic basis of quantitative traits
The Single-nucleotide polymorphism (SNP) on BTA24 associated with rear leg side view is near ZNF521 and is within a Quantitative trait locus (QTL) region that has been reported to have a significant effect on dairy cattle rear leg set [22]
The SNP on BTA10 associated with teat length is near PDIA6 and is located within a QTL region that has been shown to have a significant effect on teat length [36]

Summary

Introduction

Genome-wide association study (GWAS) is a powerful tool for revealing the genetic basis of quantitative traits. With the availability of a high-density chip with single nucleotide polymorphisms (SNPs) for bovine, genomewide association study (GWAS) has become a useful tool for fine-scale QTL mapping. This approach has been widely applied to causative mutation detection in human [5,6], mouse [7] and cattle [8,9]. By using very large numbers of SNPs researcher can detect statistical associations between SNPs and phenotypes, and biologically meaningful candidate genes close to the significant SNPs are identified for further study This procedure greatly narrows down the regions of the genome that contain the causative mutations. The associations can provide direct and necessary evidence for the function of a gene

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