Genome-wide association study for pigmentation traits in Chinese Holstein population. 2014

Yipeng Fan, and Peng Wang, and Weixuan Fu, and Tian Dong, and Chao Qi, and Lin Liu, and Gang Guo, and Cong Li, and Xiaogang Cui, and Shengli Zhang, and Qin Zhang, and Yi Zhang, and Dongxiao Sun
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.

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.

UI MeSH Term Description Entries
D010641 Phenotype The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment. Phenotypes
D010858 Pigmentation Coloration or discoloration of a part by a pigment. Pigmentations
D002417 Cattle Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor. Beef Cow,Bos grunniens,Bos indicus,Bos indicus Cattle,Bos taurus,Cow,Cow, Domestic,Dairy Cow,Holstein Cow,Indicine Cattle,Taurine Cattle,Taurus Cattle,Yak,Zebu,Beef Cows,Bos indicus Cattles,Cattle, Bos indicus,Cattle, Indicine,Cattle, Taurine,Cattle, Taurus,Cattles, Bos indicus,Cattles, Indicine,Cattles, Taurine,Cattles, Taurus,Cow, Beef,Cow, Dairy,Cow, Holstein,Cows,Dairy Cows,Domestic Cow,Domestic Cows,Indicine Cattles,Taurine Cattles,Taurus Cattles,Yaks,Zebus
D005260 Female Females
D005838 Genotype The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS. Genogroup,Genogroups,Genotypes
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D056726 Genetic Association Studies The analysis of a sequence such as a region of a chromosome, a haplotype, a gene, or an allele for its involvement in controlling the phenotype of a specific trait, metabolic pathway, or disease. Candidate Gene Identification,Candidate Gene Analysis,Candidate Gene Association Studies,Candidate Gene Association Study,Gene Discovery,Genotype-Phenotype Association,Genotype-Phenotype Associations,Genotype-Phenotype Correlation,Genotype-Phenotype Correlations,Analyses, Candidate Gene,Analysis, Candidate Gene,Association Studies, Genetic,Association Study, Genetic,Association, Genotype-Phenotype,Associations, Genotype-Phenotype,Candidate Gene Analyses,Correlation, Genotype-Phenotype,Correlations, Genotype-Phenotype,Discovery, Gene,Gene Analyses, Candidate,Gene Analysis, Candidate,Gene Identification, Candidate,Genetic Association Study,Genotype Phenotype Association,Genotype Phenotype Associations,Genotype Phenotype Correlation,Genotype Phenotype Correlations,Identification, Candidate Gene,Studies, Genetic Association,Study, Genetic Association
D019655 Quantitative Trait, Heritable A characteristic showing quantitative inheritance such as SKIN PIGMENTATION in humans. (From A Dictionary of Genetics, 4th ed) Heritable Quantitative Trait,Heritable Quantitative Traits,Quantitative Traits, Heritable,Trait, Heritable Quantitative,Traits, Heritable Quantitative
D020641 Polymorphism, Single Nucleotide A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population. SNPs,Single Nucleotide Polymorphism,Nucleotide Polymorphism, Single,Nucleotide Polymorphisms, Single,Polymorphisms, Single Nucleotide,Single Nucleotide Polymorphisms

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