Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada; Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil.
Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
J Dairy Sci. 2019 Sep;102(9):8159-8174. doi: 10.3168/jds.2019-16451. Epub 2019 Jul 10.
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.
我们针对加拿大亚士厘牛、荷斯坦牛和娟姗牛的头三胎泌乳期的前三个阶段，进行了全基因组关联分析，以研究产奶量、乳脂量、乳蛋白量和体细胞评分。针对每个性状和胎次，我们考虑了三个不同的泌乳阶段，进行了全基因组关联分析：产奶期 5 到 95 天、96 到 215 天和 216 到 305 天。通过后解利用基因组最佳线性无偏预测和单性状随机回归测试日模型估计的直接育种值，对每个泌乳阶段、性状、胎次和品种的单核苷酸多态性（SNP）效应进行了估计，这些模型仅包含固定群体平均值曲线和随机基因组曲线。为了确定与分析的泌乳阶段、性状、胎次和品种相关的重要基因组区域，我们选择了 20 个相邻 SNP 的移动窗口（SNP-by-SNP），这些 SNP 解释了超过 0.30%的总遗传方差，以便进一步分析候选基因。与亚士厘牛和娟姗牛品种相比，荷斯坦牛品种中发现的具有相对较高遗传方差解释比例的基因组窗口数量较少。与分析性状相关的基因组区域分别位于亚士厘牛、荷斯坦牛和娟姗牛的 12、8 和 15 号染色体上。特别是对于荷斯坦牛品种，许多已确定的候选基因支持文献中的先前报道。然而，对产奶量性状有重大影响的知名基因（如二酰基甘油 O-酰基转移酶 1）在不同品种的泌乳阶段、性状和胎次中表现出相反的结果。因此，我们的研究结果表明，在不同品种、胎次和泌乳阶段，与分析性状的表型表达相关的候选基因存在不同的集合。需要进一步的功能研究来验证我们在独立群体中的发现。
