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Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal Publication Acceptance Date: 7/5/2016 Publication Date: 7/25/2016 Publication URL: https://handle.nal.usda.gov/10113/5661749 Citation: Lindholm-Perry, A.K., Kern, R.J., Keel, B.N., Snelling, W.M., Kuehn, L.A., Freetly, H.C. 2016. Profile of the spleen transcriptome in beef steers with variation in gain and feed intake. Frontiers in Genetics. 7:127. doi:10.3389/fgene.2016.00127. Interpretive Summary: The spleen is a major lymph organ that lies near the digestive tract. We had previously identified that beef steers with differences in gain and feed intake also had differences in levels of gene transcripts in digestive tract organs that were related to immune responses. The purpose of this study was to evaluate the transcript levels of over 24,000 genes in the spleen of 16 beef steers that were selected for variation in gain and intake to determine whether the spleen was also contributing to variation in immune response. A total of 1,216 genes were identified as differentially expressed. Of the genes differentially expressed, there were an over-abundance of genes that belong to pathways that included antigen processing and presentation, olfactory transduction, and nucleotide metabolism. Several stress response genes were also identified as a gene cluster identified by function. These genes were identified by increased expression in animals with low gain and low feed intake. An analysis of genes that were expressed and have addition numbers of gene copies in the spleen produced some of the same genes and gene families that were differentially expressed. Our data suggests the splenic contribution to some of the underlying variation among gain and intake within this group of animals may be a result of immune function and stress response. In addition, some of the differences in immune response functions may be related to the number of gene copies. Technical Abstract: We have previously identified components of the immune system contributing to feed intake and gain in both the rumen and small intestine of beef steers. In this study, we examined the spleen, a major lymphatic organ near the digestive tract, to determine whether it was also contributing to an animal’s feed efficiency status through immune responses. Animals (n=16) that were divergent for gain and intake were selected for tissue sampling. The spleen transcriptomes were evaluated by microarray. A total of 1,216 genes were identified as differentially expressed. Genes were over-represented in Kyoto encyclopedia of genes and genomes (KEGG) pathways including antigen processing and presentation, olfactory transduction, and nucleotide metabolism. Several stress response or heat shock genes including HSPH1, HSPA1A, HSPA4, DNAJB4, DNAJA4, etc., were identified as a stress response functional gene cluster in the low gain-low intake animals. These genes were up-regulated amongst the low gain-low intake animals compared to all other groups. Other functional gene clusters included olfactory receptor activity due to the expression of olfactory receptor and olfactory receptor-like genes. Canonical pathways associated with the differentially expressed genes included the coagulation system, extrinsic prothrombin activation, protein ubiquitination, unfolded protein response and aldosterone signaling in epithelial cells. An analysis of expressed copy number variable (CNV) genes in the spleen produced some of the same genes and gene families that were differentially expressed. Our data suggests the splenic contribution to some of the underlying variation among gain and intake within this group of animals may be a result of immune function and stress response. In addition, some of the differences in immune response functions may be related to gene copy number. |
