title: Genome wide association studies for body conformation traits in the Chinese Holstein cattle population.
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 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.
  
  
  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.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Wu
authors.forename: Ming
authors.initials: M
authors.lastname: Fang
authors.forename: Lin
authors.initials: L
authors.lastname: Liu
authors.forename: Sheng
authors.initials: S
authors.lastname: Wang
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Liu
authors.forename: Xiangdong
authors.initials: X
authors.lastname: Ding
authors.forename: Shengli
authors.initials: S
authors.lastname: Zhang
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhang
authors.forename: Yuan
authors.initials: Y
authors.lastname: Zhang
authors.forename: Lv
authors.initials: L
authors.lastname: Qiao
authors.forename: Mogens Sandø
authors.initials: MS
authors.lastname: Lund
authors.forename: Guosheng
authors.initials: G
authors.lastname: Su
authors.affiliation: 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, Beijing 100193, China. sundx@cau.edu.cn.
authors.forename: Dongxiao
authors.initials: D
authors.lastname: Sun
mesh_terms: D000818:Animals; D049628:Body Size / Q000235:genetics*; D002417:Cattle / Q000145:classification / Q000235:genetics*; D002681:China; D005260:Female; D055106:Genome-Wide Association Study; D016014:Linear Models; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci