Genome‐wide association study for pigmentation traits in Chinese Holstein population

Summary With the Illumina Bovine SNP 50K 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 SNP s for the two traits with 42 883 and 42 741 SNP s respectively. A total of nine and 12 genome‐wide significant ( P  <   0.05) SNP s associated with PB and TC respectively were identified. Of these, two SNP s for PB were located within the KIT and IGFBP 7 genes, and the other four SNP s were 23~212 kb away from the PDGFRA gene on BTA 6; nine SNP s 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 , IGFBP 7 , PDGFRA , MITF , ING 3 and WNT 16 genes are promising candidates for PB and TC in Holstein cattle, providing a basis for further investigation on the genetic mechanism of pigmentation formation.