Kong Rebecca S G, Liang Guanxiang, Chen Yanhong, Stothard Paul, Guan Le Luo
Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, 416F, Edmonton, AB, T6G 2P5, Canada.
BMC Genomics. 2016 Aug 9;17:592. doi: 10.1186/s12864-016-2935-4.
Feed efficient cattle consume less feed and produce less environmental waste than inefficient cattle. Many factors are known to contribute to differences in feed efficiency, however the underlying molecular mechanisms are largely unknown. Our study aimed to understand how host gene expression in the rumen epithelium contributes to differences in residual feed intake (RFI), a measure of feed efficiency, using a transcriptome profiling based approach.
The rumen epithelial transcriptome from highly efficient (low (L-) RFI, n = 9) and inefficient (high (H-) RFI, n = 9) Hereford x Angus steers was obtained using RNA-sequencing. There were 122 genes differentially expressed between the rumen epithelial tissues of L- and H- RFI steers (p < 0.05) with 85 up-regulated and 37 down-regulated in L-RFI steers. Functional analysis of up-regulated genes revealed their involvement in acetylation, remodeling of adherens junctions, cytoskeletal dynamics, cell migration, and cell turnover. Additionally, a weighted gene co-expression network analysis (WGCNA) identified a significant gene module containing 764 genes that was negatively correlated with RFI (r = -0.5, p = 0.03). Functional analysis revealed significant enrichment of genes involved in modulation of intercellular adhesion through adherens junctions, protein and cell turnover, and cytoskeletal organization that suggest possible increased tissue morphogenesis in the L-RFI steers. Additionally, the L-RFI epithelium had increased expression of genes involved with the mitochondrion, acetylation, and energy generating pathways such as glycolysis, tricarboxylic acid cycle, and oxidative phosphorylation. Further qPCR analysis of steers with different RFI (L-RFI, n = 35; M-RFI, n = 34; H-RFI, n = 35) revealed that the relative mitochondrial genome copy number per cell of the epithelium was positively correlated with RFI (r = 0.21, p = 0.03).
Our results suggest that the rumen epithelium of L-RFI (efficient) steers may have increased tissue morphogenesis that possibly increases paracellular permeability for the absorption of nutrients and increased energy production to support the energetic demands of increased tissue morphogenesis compared to those of H-RFI (inefficient) animals. Greater expression of mitochondrial genes and lower relative mitochondrial genome copy numbers suggest a greater rate of transcription in the rumen epithelial mitochondria of L-RFI steers. Understanding how host gene expression profiles are associated with RFI could potentially lead to identification of mechanisms behind this trait, which are vital to develop strategies for the improvement of cattle feed efficiency.
饲料效率高的牛比效率低的牛消耗更少的饲料，产生的环境废弃物也更少。已知许多因素会导致饲料效率的差异，然而其潜在的分子机制在很大程度上尚不清楚。我们的研究旨在通过基于转录组分析的方法，了解瘤胃上皮中的宿主基因表达如何导致剩余采食量（RFI，一种饲料效率的衡量指标）的差异。
使用RNA测序获得了高效（低（L-）RFI，n = 9）和低效（高（H-）RFI，n = 9）的赫里福德×安格斯阉牛的瘤胃上皮转录组。L-和H-RFI阉牛的瘤胃上皮组织之间有122个基因差异表达（p < 0.05），其中85个在L-RFI阉牛中上调，37个下调。对上调基因的功能分析表明它们参与乙酰化、黏附连接的重塑、细胞骨架动力学、细胞迁移和细胞更新。此外，加权基因共表达网络分析（WGCNA）确定了一个包含764个基因的显著基因模块，该模块与RFI呈负相关（r = -0.5，p = 0.03）。功能分析显示，参与通过黏附连接调节细胞间黏附、蛋白质和细胞更新以及细胞骨架组织的基因显著富集，这表明L-RFI阉牛可能有更高的组织形态发生。此外，L-RFI上皮中与线粒体、乙酰化以及糖酵解、三羧酸循环和氧化磷酸化等能量产生途径相关的基因表达增加。对不同RFI的阉牛（L-RFI，n = 35；中RFI，n = 34；H-RFI，n = 35）进行进一步的qPCR分析发现，上皮细胞每个细胞的相对线粒体基因组拷贝数与RFI呈正相关（r = 0.21，p = 0.03）。
我们的结果表明，与H-RFI（低效）动物相比，L-RFI（高效）阉牛的瘤胃上皮可能具有更高的组织形态发生，这可能增加细胞旁通透性以促进营养物质吸收，并增加能量产生以支持更高组织形态发生的能量需求。线粒体基因的更高表达和更低的相对线粒体基因组拷贝数表明L-RFI阉牛瘤胃上皮线粒体中的转录速率更高。了解宿主基因表达谱如何与RFI相关，可能有助于识别该性状背后的机制，这对于制定提高牛饲料效率的策略至关重要。
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