Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China.
Laboratory of Dairy Cattle Genetic Improvement and Milk Quality Research in Zhejiang Province, Wenzhou, 325000 China.
J Dairy Sci. 2024 Nov;107(11):9638-9655. doi: 10.1016/j.jods.2024.10.001.
Lifetime productivity is a trait of great importance to dairy cattle populations, as it combines information from production and longevity variables. Therefore, we investigated the genetic background of lifetime productivity in high-producing dairy cattle by integrating genomics and transcriptomics datasets. A total of 3,365,612 test-day milk yield records from 134,029 Chinese Holstein cows were used to define 6 lifetime productivity traits, including lifetime milk yield covering full lifespan and 5 cumulative milk yield traits covering partial lifespan. Genetic parameters were estimated based on univariate and bivariate linear animal models and the restricted maximum likelihood method. Genome-wide association studies and weighted gene co-expression network analyses (WGCNA) were performed to identify candidate genes associated with lifetime productivity based on genomic data from 3,424 cows and peripheral blood RNA-sequencing data from 23 cows, respectively. Lifetime milk yield averaged 24,800.8 ± 14,396.6 kg (mean ± SD) across an average of 2.4 parities in Chinese Holstein population. The heritability estimates for lifetime productivity traits ranged from 0.05 (±0.01 for SE) to 0.10 (±0.02 for SE). The estimate of genetic correlation between lifetime milk yield and productive life is 0.88 (±0.3 for SE), whereas the genetic correlation with 305-d milk yield in the first lactation was 0.49 (±0.08 for SE). Absolute values for most genetic correlation estimates between lifetime productivity and type traits were lower than 0.30. Moderate genetic correlations were found between udder related traits and lifetime productivity, such as with udder depth (0.33), rear udder attachment height (0.33), and udder system (0.34). Some single nucleotide polymorphisms and gene co-expression modules significantly associated with lifetime milk yield were identified based on GWAS and WGCNA analyses, respectively. Functional enrichment analyses of the candidate genes identified revealed important pathways related to immune system, longevity, energy utilization, and metabolism, and FoxO signaling. The genes NTMT1, FNBP1, and S1PR1 were considered to be the most important candidate genes influencing lifetime productivity in Holstein cows. Overall, our findings indicate that lifetime productivity is heritable in Chinese Holstein cattle, and important candidate genes were identified by integrating genomic and transcriptomic datasets.
终生生产力是奶牛群体非常重要的特征，因为它结合了生产和寿命变量的信息。因此，我们通过整合基因组学和转录组学数据集来研究高产奶牛的终生生产力的遗传背景。使用了来自 134029 头中国荷斯坦奶牛的 3365612 次测试日牛奶产量记录来定义 6 个终生生产力特征，包括涵盖整个寿命的终生牛奶产量和 5 个涵盖部分寿命的累积牛奶产量特征。基于单变量和双变量线性动物模型和限制最大似然法估计遗传参数。基于 3424 头牛的基因组数据和 23 头牛的外周血 RNA 测序数据，分别进行全基因组关联研究和加权基因共表达网络分析（WGCNA），以鉴定与终生生产力相关的候选基因。在中国荷斯坦牛群体中，终生牛奶产量的平均值为 24800.8 ± 14396.6kg（平均值±标准差），平均产次为 2.4 次。终生生产力特征的遗传力估计值范围为 0.05（±0.01 为 SE）至 0.10（±0.02 为 SE）。终生牛奶产量与生产寿命之间的遗传相关性估计值为 0.88（±0.3 为 SE），而与第一泌乳期 305 天牛奶产量的遗传相关性为 0.49（±0.08 为 SE）。终生生产力与类型特征之间的大多数遗传相关估计值的绝对值低于 0.30。在与乳房相关的性状与终生生产力之间发现了中等遗传相关性，例如乳房深度（0.33）、后乳房附着高度（0.33）和乳房系统（0.34）。基于全基因组关联分析和 WGCNA 分析，分别鉴定了与终生牛奶产量显著相关的一些单核苷酸多态性和基因共表达模块。候选基因的功能富集分析揭示了与免疫系统、长寿、能量利用和新陈代谢以及 FoxO 信号相关的重要途径。NTMT1、FNBP1 和 S1PR1 基因被认为是影响荷斯坦奶牛终生生产力的最重要候选基因。总的来说，我们的研究结果表明，中国荷斯坦奶牛的终生生产力是可遗传的，并通过整合基因组学和转录组学数据集鉴定了重要的候选基因。
