Genome-wide association for milk production traits and somatic cell score in different lactation stages of Ayrshire, Holstein, and Jersey dairy cattle
Genome-wide association for milk production traits and somatic cell score in different lactation stages of Ayrshire, Holstein, and Jersey dairy cattle
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DOI：
10.3168/jds.2019-16451
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发表时间：
2019-09-01
影响因子：
3.5
通讯作者：
Schenkel, F. S.
中科院分区：
文献类型：
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作者：
Oliveira, H. R.;Cant, J. P.;Schenkel, F. S.
我们对加拿大艾尔郡牛、荷尔斯坦牛和泽西牛的前3胎哺乳阶段的产奶量、脂肪和蛋白质产量以及体细胞评分进行了全基因组关联分析。全基因组关联分析考虑了每个性状和胎次的3个不同的哺乳阶段：5至95天，96至215天，216至305天。单核苷酸多态性（SNP）对每个哺乳期、性状、胎次和品种的影响，通过反向求解使用基因组最佳线性无偏预测器和单性状随机回归测试日模型估计的直接育种值，仅包含固定群体平均曲线和随机基因组曲线。为了确定与所分析的哺乳阶段、性状、胎次和品种相关的重要基因组区域，选择了20个相邻SNP的移动窗口（SNP-by-SNP），这些SNP解释了总遗传变异的0.30%以上，用于进一步分析候选基因。与艾尔郡和泽西品种相比，在荷尔斯坦品种中发现了较少数量的基因组窗口和相对较高比例的可解释遗传变异。与所分析性状相关的基因组区域分别位于艾尔郡、荷尔斯坦和泽西品种的12、8和15条染色体上。特别是对于荷斯坦品种，许多已确定的候选基因支持先前文献中的报道。然而，众所周知的对产奶量性状有主要影响的基因（如二酰基甘油o -酰基转移酶1）在不同品种的泌乳期、性状和胎次之间显示出截然不同的结果。因此，我们的研究结果表明，在所分析的性状在不同品种、胎次和哺乳期的表型表达中存在不同的候选基因集。需要进一步的功能研究来验证我们在独立人群中的发现。
We performed genome-wide association analyses for milk, fat, and protein yields and somatic cell score based on lactation stages in the first 3 parities of Canadian Ayrshire, Holstein, and Jersey cattle. The genome-wide association analyses were performed considering 3 different lactation stages for each trait and parity: from 5 to 95, from 96 to 215, and from 216 to 305 d in milk. Effects of single nucleotide polymorphisms (SNP) for each lactation stage, trait, parity, and breed were estimated by back-solving the direct breeding values estimated using the genomic best linear unbiased predictor and single-trait random regression test-day models containing only the fixed population average curve and the random genomic curves. To identify important genomic regions related to the analyzed lactation stages, traits, parities and breeds, moving windows (SNP-by-SNP) of 20 adjacent SNP explaining more than 0.30% of total genetic variance were selected for further analyses of candidate genes. A lower number of genomic windows with a relatively higher proportion of the explained genetic variance was found in the Holstein breed compared with the Ayrshire and Jersey breeds. Genomic regions associated with the analyzed traits were located on 12, 8, and 15 chromosomes for the Ayrshire, Holstein, and Jersey breeds, respectively. Especially for the Holstein breed, many of the identified candidate genes supported previous reports in the literature. However, well-known genes with major effects on milk production traits (e.g., diacylglycerol O-acyltransferase 1) showed contrasting results among lactation stages, traits, and parities of different breeds. Therefore, our results suggest evidence of differential sets of candidate genes underlying the phenotypic expression of the analyzed traits across breeds, parities, and lactation stages. Further functional studies are needed to validate our findings in independent populations.