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

BMC Genomics

Research Article

Lv Qiao¹  Lin Liu¹  Mogens Sandø Lund²  Guosheng Su²  Sheng Wang³  Xiangdong Ding³  Qin Zhang³  Xiaoping Wu³  Dongxiao Sun³  Shengli Zhang³  Yuan Zhang³  Jianfeng Liu³  Ming Fang⁴ 

[1] Beijing Dairy Cattle Center, 100192, Beijing, China;Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark;Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 2 Yuanmingyuan West Road, 100193, Beijing, China;Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 2 Yuanmingyuan West Road, 100193, Beijing, China;Life Science College, Heilongjiang Bayi Agricultural University, 163319, Daqing, China;

关键词: Dairy cattle;    GWAS;    Body conformation traits;    SNP;    Holstein;    QTL;   

DOI  :  10.1186/1471-2164-14-897

 received in 2013-03-12, accepted in 2013-12-10,  发布年份 2013

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Wu et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.