Yue S J, Zhao Y Q, Gu X R, Yin B, Jiang Y L, Wang Z H, Shi K R
Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China.
State Key Laboratory for Agrobiotechnology, College of Biological Science, China Agricultural University, Beijing, 100193, China.
Anim Genet. 2017 Dec;48(6):677-681. doi: 10.1111/age.12593. Epub 2017 Aug 30.
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)-BovineLD V3 SNP chip, which had 26 151 public SNPs in its manifest file. After data cleaning, 20 326 SNPs 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 SNPs 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) SNPs on milk production traits in this Chinese Holstein population. The positional candidate genes, which were the ones closest to these two identified SNPs, were EEF2K (eukaryotic elongation factor 2 kinase) and KLHL1 (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.
对中国荷斯坦牛的15个产奶性状进行了全基因组关联研究（GWAS）。实验群体由445头牛组成，每头牛都通过GGP（GeneSeek基因组分析）-牛LD V3 SNP芯片进行基因分型，其清单文件中有26151个公共单核苷酸多态性（SNP）。经过数据清理后，保留了20326个SNP用于GWAS。表型为性状的估计育种值，由一个公共奶牛群改良计划中心提供，该中心已连续3年每月收集一次数据。使用固定效应线性回归模型和混合效应线性模型这两种统计模型来估计SNP对每个表型的关联效应。全基因组显著阈值和提示性阈值分别设定为2.46E-06和4.95E-05。这两种统计模型同时在该中国荷斯坦牛群体的产奶性状上鉴定出两个全基因组显著（P < 0.05）的SNP。位置候选基因是最接近这两个已鉴定SNP的基因，分别为EEF2K（真核延伸因子2激酶）和KLHL1（kelch样家族成员1）。这两个基因可作为产奶量和泌乳持续性的新候选基因，但其作用需要在进一步的功能研究中得到验证。
