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- Title
Genome wide association studies for body conformation traits in the Chinese Holstein cattle population.
- Authors
Xiaoping Wu; Ming Fang; Lin Liu; Sheng Wang; Jianfeng Liu; Xiangdong Ding; Shengli Zhang; Qin Zhang; Yuan Zhang; Lv Qiao; Mogens Sandø Lund; Guosheng Su; Dongxiao Sun
- Abstract
Background Genome-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. Results The 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 genomewide 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. Conclusions A 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.
- Subjects
DAIRY cattle genetics; SINGLE nucleotide polymorphisms; DOMESTIC animal genome mapping; CHROMOSOME analysis; QUANTITATIVE research
- Publication
BMC Genomics, 2013, Vol 14, Issue 1, p1
- ISSN
1471-2164
- Publication type
Article
- DOI
10.1186/1471-2164-14-897