Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran.
Animal Science Improvement Research Department, Agricultural and Natural Resources Research and Education Center, Safiabad AREEO, Dezful, Iran.
Sci Rep. 2022 Feb 15;12(1):2558. doi: 10.1038/s41598-022-06528-6.
Feed efficiency is an important economic trait and reduces the production costs per unit of animal product. Up to now, few studies have conducted transcriptome profiling of liver tissue in feed efficiency-divergent chickens (Ross vs native breeds). Also, molecular mechanisms contributing to differences in feed efficiency are not fully understood, especially in terms of long non-coding RNAs (lncRNAs). Hence, transcriptome profiles of liver tissue in commercial and native chicken breeds were analyzed. RNA-Seq data along with bioinformatics approaches were applied and a series of lncRNAs and target genes were identified. Furthermore, protein-protein interaction network construction, co-expression analysis, co-localization analysis of QTLs and functional enrichment analysis were used to functionally annotate the identified lncRNAs. In total, 2,290 lncRNAs were found (including 1,110 annotated, 593 known and 587 novel), of which 53 (including 39 known and 14 novel), were identified as differentially expressed genes between two breeds. The expression profile of lncRNAs was validated by RT-qPCR. The identified novel lncRNAs showed a number of characteristics similar to those of known lncRNAs. Target prediction analysis showed that these lncRNAs have the potential to act in cis or trans mode. Functional enrichment analysis of the predicted target genes revealed that they might affect the differences in feed efficiency of chicken by modulating genes associated with lipid metabolism, carbohydrate metabolism, growth, energy homeostasis and glucose metabolism. Some gene members of significant modules in the constructed co-expression networks were reported as important genes related to feed efficiency. Co-localization analysis of QTLs related to feed efficiency and the identified lncRNAs suggested several candidates to be involved in residual feed intake. The findings of this study provided valuable resources to further clarify the genetic basis of regulation of feed efficiency in chicken from the perspective of lncRNAs.
饲料效率是一个重要的经济性状，可以降低单位动物产品的生产成本。到目前为止，很少有研究对饲料效率差异的鸡（罗斯与本地品种）的肝脏组织进行转录组分析。此外，对于导致饲料效率差异的分子机制还不完全了解，特别是在长非编码 RNA（lncRNA）方面。因此，对商业鸡和本地鸡品种的肝脏组织进行了转录组分析。应用 RNA-Seq 数据和生物信息学方法，鉴定了一系列 lncRNA 和靶基因。此外，还进行了蛋白质-蛋白质相互作用网络构建、共表达分析、QTL 的共定位分析和功能富集分析，以对鉴定的 lncRNA 进行功能注释。总共发现了 2290 个 lncRNA（包括 1110 个注释、593 个已知和 587 个新的），其中 53 个（包括 39 个已知和 14 个新的）被鉴定为两个品种之间差异表达的基因。通过 RT-qPCR 验证了 lncRNA 的表达谱。鉴定的新 lncRNA 表现出与已知 lncRNA 相似的许多特征。靶基因预测分析表明，这些 lncRNA 可能通过调节与脂质代谢、碳水化合物代谢、生长、能量平衡和葡萄糖代谢相关的基因，以顺式或反式模式发挥作用。预测靶基因的功能富集分析表明，它们可能通过调节与脂质代谢、碳水化合物代谢、生长、能量平衡和葡萄糖代谢相关的基因，影响鸡的饲料效率差异。构建的共表达网络中的一些显著模块的基因成员被报道为与饲料效率相关的重要基因。与饲料效率相关的 QTL 与鉴定的 lncRNA 的共定位分析表明，有几个候选基因可能参与剩余饲料摄入量。本研究的结果从 lncRNA 的角度为进一步阐明鸡饲料效率调控的遗传基础提供了有价值的资源。
