School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia, 3083; Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia, 3083.
Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia, 3083.
J Dairy Sci. 2021 Jan;104(1):575-587. doi: 10.3168/jds.2020-18503. Epub 2020 Nov 6.
Feed efficiency and energy balance are important traits underpinning profitability and environmental sustainability in animal production. They are complex traits, and our understanding of their underlying biology is currently limited. One measure of feed efficiency is residual feed intake (RFI), which is the difference between actual and predicted intake. Variation in RFI among individuals is attributable to the metabolic efficiency of energy utilization. High RFI (H_RFI) animals require more energy per unit of weight gain or milk produced compared with low RFI (L_RFI) animals. Energy balance (EB) is a closely related trait calculated very similarly to RFI. Cellular energy metabolism in mitochondria involves mitochondrial protein (MiP) encoded by both nuclear (NuMiP) and mitochondrial (MtMiP) genomes. We hypothesized that MiP genes are differentially expressed (DE) between H_RFI and L_RFI animal groups and similarly between negative and positive EB groups. Our study aimed to characterize MiP gene expression in white blood cells of H_RFI and L_RFI cows using RNA sequencing to identify genes and biological pathways associated with feed efficiency in dairy cattle. We used the top and bottom 14 cows ranked for RFI and EB out of 109 animals as H_RFI and L_RFI, and positive and negative EB groups, respectively. The gene expression counts across all nuclear and mitochondrial genes for animals in each group were used for differential gene expression analyses, weighted gene correlation network analysis, functional enrichment, and identification of hub genes. Out of 244 DE genes between RFI groups, 38 were MiP genes. The DE genes were enriched for the oxidative phosphorylation (OXPHOS) and ribosome pathways. The DE MiP genes were underexpressed in L_RFI (and negative EB) compared with the H_RFI (and positive EB) groups, suggestive of reduced mitochondrial activity in the L_RFI group. None of the MtMiP genes were among the DE MiP genes between the groups, which suggests a non-rate limiting role of MtMiP genes in feed efficiency and warrants further investigation. The role of MiP, particularly the NuMiP and OXPHOS pathways in RFI, was also supported by our gene correlation network analysis and the hub gene identification. We validated the findings in an independent data set. Overall, our study suggested that differences in feed efficiency in dairy cows may be linked to differences in cellular energy demand. This study broadens our knowledge of the biology of feed efficiency in dairy cattle.
饲料效率和能量平衡是动物生产中盈利能力和环境可持续性的重要特征。它们是复杂的特征，我们对其基础生物学的理解目前还很有限。饲料效率的一个衡量标准是剩余饲料摄入量（RFI），即实际摄入量与预测摄入量之间的差异。个体之间 RFI 的差异归因于能量利用的代谢效率。与低 RFI（L_RFI）动物相比，高 RFI（H_RFI）动物每单位体重增加或产奶所需的能量更多。能量平衡（EB）是一个密切相关的特征，其计算方法与 RFI 非常相似。线粒体中的细胞能量代谢涉及由核（NuMiP）和线粒体（MtMiP）基因组共同编码的线粒体蛋白（MiP）。我们假设 MiP 基因在 H_RFI 和 L_RFI 动物群体之间以及在负 EB 和正 EB 群体之间存在差异表达（DE）。我们的研究旨在使用 RNA 测序来表征 H_RFI 和 L_RFI 奶牛的白细胞中 MiP 基因的表达，以鉴定与奶牛饲料效率相关的基因和生物学途径。我们使用排名前 14 的高 RFI 和低 RFI 奶牛和排名前 14 的正 EB 和负 EB 奶牛分别作为 RFI 和 EB 组的 H_RFI 和 L_RFI 以及正 EB 和负 EB 组。每个组中所有核和线粒体基因的基因表达计数用于差异基因表达分析、加权基因相关网络分析、功能富集和枢纽基因鉴定。在 RFI 组之间的 244 个 DE 基因中，有 38 个是 MiP 基因。DE 基因富集了氧化磷酸化（OXPHOS）和核糖体途径。与 H_RFI（和正 EB）组相比，L_RFI（和负 EB）组中的 DE MiP 基因表达下调，表明 L_RFI 组中的线粒体活性降低。在两组之间的 DE MiP 基因中没有 MtMiP 基因，这表明 MtMiP 基因在饲料效率中不起限速作用，值得进一步研究。MiP 特别是 NuMiP 和 OXPHOS 途径在 RFI 中的作用也得到了我们的基因相关网络分析和枢纽基因鉴定的支持。我们在一个独立的数据集上验证了这些发现。总的来说，我们的研究表明，奶牛饲料效率的差异可能与细胞能量需求的差异有关。这项研究拓宽了我们对奶牛饲料效率生物学的认识。
