Higgins Marc G, Kenny David A, Fitzsimons Claire, Blackshields Gordon, Coyle Séan, McKenna Clare, McGee Mark, Morris Derek W, Waters Sinéad M
Discipline of Biochemistry, National University of Ireland, Galway, Ireland.
Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre Teagasc, Grange, Dunsany, Co. Meath, Ireland.
BMC Genomics. 2019 Jun 26;20(1):525. doi: 10.1186/s12864-019-5906-8.
Feed efficiency is an important economic and environmental trait in beef production, which can be measured in terms of residual feed intake (RFI). Cattle selected for low-RFI (feed efficient) have similar production levels but decreased feed intake, while also emitting less methane. RFI is difficult and expensive to measure and is not widely adopted in beef production systems. However, development of DNA-based biomarkers for RFI may facilitate its adoption in genomic-assisted breeding programmes. Cattle have been shown to re-rank in terms of RFI across diets and age, while also RFI varies by breed. Therefore, we used RNA-Seq technology to investigate the hepatic transcriptome of RFI-divergent Charolais (CH) and Holstein-Friesian (HF) steers across three dietary phases to identify genes and biological pathways associated with RFI regardless of diet or breed.
Residual feed intake was measured during a high-concentrate phase, a zero-grazed grass phase and a final high-concentrate phase. In total, 322 and 33 differentially expressed genes (DEGs) were identified across all diets for CH and HF steers, respectively. Three genes, GADD45G, HP and MID1IP1, were differentially expressed in CH when both the high-concentrate zero-grazed grass diet were offered. Two canonical pathways were enriched across all diets for CH steers. These canonical pathways were related to immune function.
The absence of common differentially expressed genes across all dietary phases and breeds in this study supports previous reports of the re-ranking of animals in terms of RFI when offered differing diets over their lifetime. However, we have identified biological processes such as the immune response and lipid metabolism as potentially associated with RFI divergence emphasising the previously reported roles of these biological processes with respect to RFI.
饲料效率是肉牛生产中一项重要的经济和环境性状，可通过剩余采食量（RFI）来衡量。选择低RFI（饲料高效）的牛具有相似的生产水平，但采食量减少，同时甲烷排放量也较低。RFI的测定困难且成本高昂，在肉牛生产系统中未得到广泛应用。然而，开发基于DNA的RFI生物标志物可能有助于其在基因组辅助育种计划中的应用。研究表明，牛在不同日粮和年龄阶段的RFI排名会发生变化，而且RFI也因品种而异。因此，我们使用RNA测序技术研究了夏洛莱（CH）和荷斯坦-弗里生（HF）这两个RFI差异较大的肉牛品种在三个日粮阶段的肝脏转录组，以确定与RFI相关的基因和生物学途径，而不考虑日粮或品种因素。
在高能量日粮阶段、零放牧青草日粮阶段和最后的高能量日粮阶段测定了剩余采食量。在所有日粮中，CH肉牛和HF肉牛分别总共鉴定出322个和33个差异表达基因（DEG）。当提供高能量和零放牧青草日粮时，CH肉牛中有三个基因（GADD45G、HP和MID1IP1）差异表达。CH肉牛在所有日粮中富集了两条典型通路。这些典型通路与免疫功能有关。
本研究中所有日粮阶段和品种均未发现共同的差异表达基因，这支持了之前的报道，即动物在其一生中采食不同日粮时，其RFI排名会发生变化。然而，我们已经确定免疫反应和脂质代谢等生物学过程可能与RFI差异有关，这强调了这些生物学过程在RFI方面先前报道的作用。
