PEGASE, INRAE, Institut Agro, Saint-Gilles, F-35590, France.
University Rennes, Inria, CNRS, IRISA - UMR 6074, Rennes, F-35000, France.
BMC Genomics. 2023 Oct 27;24(1):647. doi: 10.1186/s12864-023-09751-1.
Feed efficiency is a research priority to support a sustainable meat production. It is recognized as a complex trait that integrates multiple biological pathways orchestrated in and by various tissues. This study aims to determine networks between biological entities to explain inter-individual variation of feed efficiency in growing pigs.
The feed conversion ratio (FCR), a measure of feed efficiency, and its two component traits, average daily gain and average daily feed intake, were obtained from 47 growing pigs from a divergent selection for residual feed intake and fed high-starch or high-fat high-fiber diets during 58 days. Datasets of transcriptomics (60 k porcine microarray) in the whole blood and metabolomics (1H-NMR analysis and target gas chromatography) in plasma were available for all pigs at the end of the trial. A weighted gene co-expression network was built from the transcriptomics dataset, resulting in 33 modules of co-expressed molecular probes. The eigengenes of eight of these modules were significantly ([Formula: see text]) or tended to be ([Formula: see text]) correlated to FCR. Great homogeneity in the enriched biological pathways was observed in these modules, suggesting co-expressed and co-regulated constitutive genes. They were mainly enriched in genes participating to immune and defense-related processes, and to a lesser extent, to translation, cell development or learning. They were also generally associated with growth rate and percentage of lean mass. In the whole network, only one module composed of genes participating to the response to substances, was significantly associated with daily feed intake and body adiposity. The plasma profiles in circulating metabolites and in fatty acids were summarized by weighted linear combinations using a dimensionality reduction method. Close association was thus found between a module composed of co-expressed genes participating to T cell receptor signaling and cell development process in the whole blood and related to FCR, and the circulating concentrations of polyunsaturated fatty acids in plasma.
These systemic approaches have highlighted networks of entities driving key biological processes involved in the phenotypic difference in feed efficiency between animals. Connecting transcriptomics and metabolic levels together had some additional benefits.
饲料效率是支持可持续肉类生产的研究重点。它被认为是一种复杂的特征，整合了各种组织中协调的多个生物学途径。本研究旨在确定生物实体之间的网络，以解释生长猪饲料效率的个体间差异。
饲料转化率（FCR），一种衡量饲料效率的指标，及其两个组成性状，平均日增重和平均日采食量，是从 47 头生长猪中获得的，这些猪进行了残留饲料摄入量的分歧选择，并在 58 天内饲喂高淀粉或高脂肪高纤维饮食。试验结束时，所有猪的全血转录组学（60 k 猪微阵列）和血浆代谢组学（1H-NMR 分析和靶向气相色谱）数据集均可获得。从转录组学数据集构建了加权基因共表达网络，得到 33 个共表达分子探针模块。这 8 个模块的特征基因与 FCR 显著（[公式：见文本]）或倾向于相关（[公式：见文本]）。这些模块中观察到丰富的生物学途径具有很大的同质性，表明共表达和共调控的组成基因。它们主要富集于参与免疫和防御相关过程的基因，在较小程度上，也富集于翻译、细胞发育或学习相关的基因。它们通常与生长速度和瘦肉百分比相关。在整个网络中，只有一个由参与物质反应的基因组成的模块与日采食量和体脂率显著相关。使用降维方法，通过加权线性组合总结了循环代谢物和脂肪酸中的血浆特征。因此，在全血中参与 T 细胞受体信号和细胞发育过程的共表达基因组成的模块与 FCR 密切相关，与血浆中多不饱和脂肪酸的循环浓度密切相关。
这些系统方法强调了驱动动物间饲料效率表型差异的关键生物学过程的实体网络。将转录组学和代谢水平联系起来具有一些额外的好处。
