title: Genome-wide association study for pigmentation traits in Chinese Holstein population.
abstract: With the Illumina BovineSNP50K BeadChip, we performed a genome-wide association study (GWAS) for two pigmentation traits in a Chinese Holstein population: proportion of black (PB) and teat colour (TC). A case-control design was used. Cases were the cows with PB <0.30 (n = 129) and TC <2 points (n = 140); controls were those with PB >0.90 (n = 58) and TC >4 points (n = 281). The RM test of roadtrips (version 1.2) was applied to detect SNPs for the two traits with 42 883 and 42 741 SNPs respectively. A total of nine and 12 genome-wide significant (P < 0.05) SNPs associated with PB and TC respectively were identified. Of these, two SNPs for PB were located within the KIT and IGFBP7 genes, and the other four SNPs were 23~212 kb away from the PDGFRA gene on BTA6; nine SNPs associated with TC were located within or 21~78.8 kb away from known genes on chromosomes 4, 11, 22, 23 and 24. By combing through our GWAS results and the biological functions of the genes, we suggest that the KIT, IGFBP7, PDGFRA, MITF, ING3 and WNT16 genes are promising candidates for PB and TC in Holstein cattle, providing a basis for further investigation on the genetic mechanism of pigmentation formation.
authors.affiliation: College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing, 100193, China.
authors.forename: Yipeng
authors.initials: Y
authors.lastname: Fan
authors.forename: Peng
authors.initials: P
authors.lastname: Wang
authors.forename: Weixuan
authors.initials: W
authors.lastname: Fu
authors.forename: Tian
authors.initials: T
authors.lastname: Dong
authors.forename: Chao
authors.initials: C
authors.lastname: Qi
authors.forename: Lin
authors.initials: L
authors.lastname: Liu
authors.forename: Gang
authors.initials: G
authors.lastname: Guo
authors.forename: Cong
authors.initials: C
authors.lastname: Li
authors.forename: Xiaogang
authors.initials: X
authors.lastname: Cui
authors.forename: Shengli
authors.initials: S
authors.lastname: Zhang
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhang
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhang
authors.forename: Dongxiao
authors.initials: D
authors.lastname: Sun
mesh_terms: D000818:Animals; D002417:Cattle; D005260:Female; D056726:Genetic Association Studies; D005838:Genotype; D010641:Phenotype; D010858:Pigmentation / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable
keywords: coat colour; dairy cattle; genome-wide association study; single nucleotide polymorphism; teat colour