Identification of single nucleotide polymorphisms (SNPs) potentially associated with residual feed intake in Qinchuan beef cattle by hypothalamus and duodenum RNA-Seq data

The regulation of residual feed intake (RFI) in beef cattle involves brain-gut mechanisms due to the interaction between neural signals in the brain and hunger or satiety in the gut. RNA-Seq data contain an extensive resource of untapped SNPs. Therefore, hypothalamic and duodenal tissues from ten extreme RFI individuals were collected, and transcriptome sequenced in this study. All the alignment data were combined according to RFI, and the SNPs in the same group were identified. A total of 270,410 SNPs were found in the high RFI group, and 255,120 SNPs were found in the low RFI group. Most SNPs were detected in the intronic region, followed by the intergenic region, and the exon region accounts for 1.11% and 1.38% in the high and low RFI groups, respectively. Prediction of high-impact SNPs and annotation of the genes in which they are located yielded 83 and 97 genes in the high-RFI and low-RFI groups, respectively. GO enrichment analysis of these genes revealed multiple NADH/NADPH-related pathways, with <i>ND4</i>, <i>ND5</i>, and <i>ND6</i> significantly enriched as core subunits of NADH dehydrogenase (complex I), and is closely related to mitochondrial function. KEGG enrichment analysis of <i>ND4</i>, <i>ND5</i>, and <i>ND6</i> genes was enriched in the thermogenic pathway. Multiple genes, such as <i>ATP1A2</i>, <i>SLC9A4</i>, and <i>PLA2G5</i>, were reported to be associated with RFI energy metabolism in the concurrent enrichment analysis. Protein-protein interaction analysis identified multiple potential candidate genes related to energy metabolism that were hypothesized to be potentially associated with the RFI phenotype. The results of this study will help to increase our understanding of identifying SNPs with significant genetic effects and their potential biological functions.