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A genome‐wide association study suggests new candidate genes for milk production traits in Chinese Holstein cattle
Author(s) -
Yue S. J.,
Zhao Y. Q.,
Gu X. R.,
Yin B.,
Jiang Y. L.,
Wang Z. H.,
Shi K. R.
Publication year - 2017
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12593
Subject(s) - biology , genome wide association study , genetics , candidate gene , snp , genetic association , population , single nucleotide polymorphism , dairy cattle , genome , snp array , gene , genotype , medicine , environmental health
Summary A genome‐wide association study ( GWAS ) was conducted on 15 milk production traits in Chinese Holstein. The experimental population consisted of 445 cattle, each genotyped by the GGP (GeneSeek genomic profiling)‐Bovine LD V3 SNP chip, which had 26 151 public SNP s in its manifest file. After data cleaning, 20 326 SNP s were retained for the GWAS . The phenotypes were estimated breeding values of traits, provided by a public dairy herd improvement program center that had been collected once a month for 3 years. Two statistical models, a fixed‐effect linear regression model and a mixed‐effect linear model, were used to estimate the association effects of SNP s on each of the phenotypes. Genome‐wide significant and suggestive thresholds were set at 2.46E‐06 and 4.95E‐05 respectively. The two statistical models concurrently identified two genome‐wide significant ( P < 0.05) SNP s on milk production traits in this Chinese Holstein population. The positional candidate genes, which were the ones closest to these two identified SNP s, were EEF 2K ( eukaryotic elongation factor 2 kinase ) and KLHL 1 ( kelch like family member 1 ). These two genes could serve as new candidate genes for milk yield and lactation persistence, yet their roles need to be verified in further function studies.