Feed efficiency (FE) is an economically important trait. Thus, reliable predictors would help to reduce the production cost and provide sustainability to the pig industry. We carried out metabolome-transcriptome integration analysis on 40 purebred Duroc and Landrace uncastrated male pigs to identify potential gene-metabolite interactions and explore the molecular mechanisms underlying FE. To this end, we applied untargeted metabolomics and RNA-seq approaches to the same animals. After data quality control, we used a linear model approach to integrate the data and find significant differently correlated gene-metabolite pairs separately for the breeds (Duroc and Landrace) and FE groups (low and high FE) followed by a pathway over-representation analysis. We identified 21 and 12 significant gene-metabolite pairs for each group. The valine-leucine-isoleucine biosynthesis/degradation and arginine-proline metabolism pathways were associated with unique metabolites. The unique genes obtained from significant metabolite-gene pairs were associated with sphingolipid catabolism, multicellular organismal process, cGMP, and purine metabolic processes. While some of the genes and metabolites identified were known for their association with FE, others are novel and provide new avenues for further research. Further validation of genes, metabolites, and gene-metabolite interactions in larger cohorts will elucidate the regulatory mechanisms and pathways underlying FE.

中文翻译：

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代谢组学和转录组学谱的综合分析揭示了猪饲料效率的生物途径。


饲料效率（FE）是一个重要的经济特性。因此，可靠的预测将有助于降低生产成本并为养猪业提供可持续性。我们对 40 头纯种杜洛克和长白未去势公猪进行了代谢组-转录组整合分析，以确定潜在的基因-代谢物相互作用，并探索 FE 背后的分子机制。为此，我们对相同的动物应用了非靶向代谢组学和 RNA-seq 方法。数据质量控制后，我们使用线性模型方法整合数据，并分别为品种（杜洛克和长白）和 FE 组（低和高 FE）找到显着不同相关的基因代谢物对，然后进行途径过度代表性分析。我们为每组确定了 21 和 12 个重要的基因代谢物对。缬氨酸-亮氨酸-异亮氨酸生物合成/降解和精氨酸-脯氨酸代谢途径与独特的代谢物相关。从重要的代谢物-基因对中获得的独特基因与鞘脂分解代谢、多细胞生物过程、cGMP 和嘌呤代谢过程相关。虽然一些已确定的基因和代谢物因与 FE 相关而闻名，但其他基因和代谢物是新颖的，为进一步研究提供了新途径。在更大的队列中进一步验证基因、代谢物和基因-代谢物相互作用将阐明 FE 的调控机制和途径。