Section of Animal Genetics, Bioinformatics and Breeding, Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen Frederiksberg, Denmark.
Section of Animal Genetics, Bioinformatics and Breeding, Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen Frederiksberg, Denmark ; Pig Research Centre, Danish Agriculture and Food Council Copenhagen, Denmark.
Front Genet. 2014 Sep 9;5:307. doi: 10.3389/fgene.2014.00307. eCollection 2014.
Residual feed intake (RFI) is a complex trait that is economically important for livestock production; however, the genetic and biological mechanisms regulating RFI are largely unknown in pigs. Therefore, the study aimed to identify single nucleotide polymorphisms (SNPs), candidate genes and biological pathways involved in regulating RFI using Genome-wide association (GWA) and pathway analyses. A total of 596 Yorkshire boars with phenotypes for two different measures of RFI (RFI1 and 2) and 60k genotypic data was used. GWA analysis was performed using a univariate mixed model and 12 and 7 SNPs were found to be significantly associated with RFI1 and RFI2, respectively. Several genes such as xin actin-binding repeat-containing protein 2 (XIRP2),tetratricopeptide repeat domain 29 (TTC29),suppressor of glucose, autophagy associated 1 (SOGA1),MAS1,G-protein-coupled receptor (GPCR) kinase 5 (GRK5),prospero-homeobox protein 1 (PROX1),GPCR 155 (GPR155), and FYVE domain containing the 26 (ZFYVE26) were identified as putative candidates for RFI based on their genomic location in the vicinity of these SNPs. Genes located within 50 kbp of SNPs significantly associated with RFI and RFI2 (q-value ≤ 0.2) were subsequently used for pathway analyses. These analyses were performed by assigning genes to biological pathways and then testing the association of individual pathways with RFI using a Fisher's exact test. Metabolic pathway was significantly associated with both RFIs. Other biological pathways regulating phagosome, tight junctions, olfactory transduction, and insulin secretion were significantly associated with both RFI traits when relaxed threshold for cut-off p-value was used (p ≤ 0.05). These results implied porcine RFI is regulated by multiple biological mechanisms, although the metabolic processes might be the most important. Olfactory transduction pathway controlling the perception of feed via smell, insulin pathway controlling food intake might be important pathways for RFI. Furthermore, our study revealed key genes and genetic variants that control feed efficiency that could potentially be useful for genetic selection of more feed efficient pigs.
剩余采食量（RFI）是一个复杂的性状，对畜牧业生产具有重要的经济意义；然而，调控 RFI 的遗传和生物学机制在猪中还很大程度上未知。因此，本研究旨在使用全基因组关联（GWA）和途径分析来鉴定调控 RFI 的单核苷酸多态性（SNP）、候选基因和生物学途径。使用了具有两种不同 RFI 测量值（RFI1 和 RFI2）的 596 头约克夏公猪的表型和 60k 基因型数据。使用单变量混合模型进行 GWA 分析，发现了 12 个和 7 个 SNP 与 RFI1 和 RFI2 分别显著相关。几个基因，如 xin 肌动蛋白结合重复蛋白 2（XIRP2）、四肽重复结构域 29（TTC29）、葡萄糖抑制物、自噬相关蛋白 1（SOGA1）、MAS1、G 蛋白偶联受体（GPCR）激酶 5（GRK5）、prospero 同源盒蛋白 1（PROX1）、GPCR155（GPR155）和 FYVE 结构域包含 26（ZFYVE26），根据它们在这些 SNP 附近的基因组位置，被确定为 RFI 的候选基因。位于与 RFI 和 RFI2 显著相关的 SNP （q 值≤0.2）附近的 50 kbp 内的基因随后用于途径分析。通过将基因分配到生物途径中，然后使用 Fisher 精确检验测试单个途径与 RFI 的关联，进行这些分析。代谢途径与两个 RFI 均显著相关。当放宽截止 p 值时（p≤0.05），调节吞噬体、紧密连接、嗅觉转导和胰岛素分泌的其他生物学途径与两个 RFI 性状显著相关。这些结果表明，猪的 RFI 受多种生物学机制调控，尽管代谢过程可能是最重要的。通过嗅觉控制对饲料的感知的嗅觉转导途径、控制食物摄入的胰岛素途径可能是 RFI 的重要途径。此外，我们的研究揭示了控制饲料效率的关键基因和遗传变异，这可能对选择更高效饲料的猪具有潜在的应用价值。
