Genes associated with body weight gain and feed intake identified by meta-analysis of the mesenteric fat from crossbred beef steers

Authors: Lindholm-Perry, Amanda; Freetly, Harvey; Oliver, William; Rempel, Lea; Keel, Brittney

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/11/2019
Publication Date: 1/7/2020
Citation: Lindholm-Perry, A.K., Freetly, H.C., Oliver, W.T., Rempel, L.A., Keel, B.N. 2020. Genes associated with body weight gain and feed intake identified by meta-analysis of the mesenteric fat from crossbred beef steers. PLoS One. 15(1):e0227154. https://doi.org/10.1371/journal.pone.0227154.
DOI: https://doi.org/10.1371/journal.pone.0227154

Interpretive Summary: Mesenteric fat is a visceral fat depot that increases with cattle maturity and can be influenced by diet. There may be a relationship between the accumulation of mesenteric fat and feed efficiency in beef cattle. The purpose of this study was to identify genes that may be differentially expressed in steers with high and low body weight gain and feed intake. Mesenteric fat tissue from 78 animals collected over 5 seasons were evaluated for gene expression. An analysis method that allows for the inclusion of multiple groups of animals was used to determine which genes were differentially expressed for gain and intake was used. For gain, a total of 87 differentially expressed genes (DEG) were identified (PADJ<0.05), and 24 were identified in the analysis for feed intake. Genes identified for gain were involved in functions and pathways including lipid metabolism, stress response/protein folding, cell proliferation/growth, axon guidance and inflammation. The genes for feed intake did not cluster into pathways, but some of the DEG for intake had functions related to inflammation, immunity, and/or signal transduction. Only 4 genes were identified as differentially expressed in two or more cohorts, highlighting the importance of evaluating the transcriptome of more than one group of animals.

Technical Abstract: Mesenteric fat is a visceral fat depot that increases with cattle maturity and can be influenced by diet. There may be a relationship between the accumulation of mesenteric fat and feed efficiency in beef cattle. The purpose of this study was to identify genes that may be differentially expressed in steers with high and low BW gain and feed intake. RNA-Seq was used to evaluate the transcript abundance of genes in the mesenteric fat from a total of 78 steers collected over 5 different cohorts. A meta-analysis was used to identify genes involved with gain, feed intake or the interaction of both phenotypes. The interaction analysis identified 11 genes as differentially expressed. For the main effect of gain, a total of 87 differentially expressed genes (DEG) were identified (PADJ<0.05), and 24 were identified in the analysis for feed intake. Genes identified for gain were involved in functions and pathways including lipid metabolism, stress response/protein folding, cell proliferation/growth, axon guidance and inflammation. The genes for feed intake did not cluster into pathways, but some of the DEG for intake had functions related to inflammation, immunity, and/or signal transduction (JCHAIN, RIPK1, LY86, SPP1, LYZ, CD5, CD53, SRPX, and NF2). At PADJ<0.1, only 4 genes (OLFML3, LOC100300716, MRPL15, and PUS10) were identified as differentially expressed in two or more cohorts, highlighting the importance of evaluating the transcriptome of more than one group of animals and incorporating a meta-analysis. This meta-analysis has produced many mesenteric fat DEG that may be contributing to gain and feed intake in cattle.