Dataset Information

Profile of the Spleen Transcriptome in Beef Steers with Variation in Gain and Feed Intake.

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 influencing individual 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 1216 genes were identified as differentially expressed. Genes were over-represented in Kyoto encyclopedia of genes and genomes (KEGG) pathways including biological regulation, protein folding, cell communication, immune systems process, response to stress, and RNA metabolic process. 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. 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.

SUBMITTER: Lindholm-Perry AK

PROVIDER: S-EPMC4958634 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Profile of the Spleen Transcriptome in Beef Steers with Variation in Gain and Feed Intake.

Lindholm-Perry Amanda K AK Kern Rebecca J RJ Keel Brittney N BN Snelling Warren M WM Kuehn Larry A LA Freetly Harvey C HC

Frontiers in genetics 20160725

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 influencing individual 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 tot ...[more]

PMID: 27504120

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Project description:Average daily gain (ADG) and daily dry matter intake (DMI) are key determinants of beef industry profitability. These traits together with metabolic body weight (MWT) are combined as component traits to calculate residual feed intake (RFI), a common measure of feed efficiency in beef cattle. Recently, there have been significant efforts towards molecular genetic characterization of RFI through transcriptomic studies in different breeds and tissues. However, molecular mechanisms of RFI component traits still remain predominately unexplored. Therefore, in the current study, we investigated the hepatic transcriptomic profiles and their associations with ADG, DMI, and MWT in Angus, Charolais, and Kinsella Composite (KC) populations through global RNAseq analyses. In each population and for each trait, 12 steers with extreme phenotypes (n = 6 low and n = 6 high) were analyzed for differential gene expression. These animals were from 20 beef steers of each Angus, Charolais, and KC breed population that were initially selected for a transcriptome study of RFI. At a false discovery rate <0.05 and fold change >1.5, we identified 123, 102, and 78 differentially expressed (DE) genes between high- and low-ADG animals of Angus, Charolais, and KC populations, respectively. For DMI, 108, 180, and 156 DE genes were identified between high- and low-DMI from Angus, Charolais, and KC populations, respectively, while for MWT, 80, 82, and 84 genes were differentially expressed between high- and low-MWT animals in Angus, Charolais, and KC populations, respectively. The identified DE genes were largely breed specific (81.7% for ADG, 82.7% for DMI, and 83% for MWT), but were largely involved in the same biological functions across the breeds. Among the most enriched biological functions included metabolism of major nutrients (lipids, carbohydrates, amino acids, vitamins, and minerals), small molecule biochemistry, cellular movement, cell morphology, and cell-to-cell signaling and interaction. Notably, we identified multiple DE genes that are involved in cholesterol biosynthesis, and immune response pathways for the 3 studied traits. Thus, our findings present potential molecular genetic mechanisms and candidate genes that influence feed intake, growth, and MWT of beef cattle.

Project description:BackgroundFeed efficient cattle consume less feed and produce less environmental waste than inefficient cattle. Many factors are known to contribute to differences in feed efficiency, however the underlying molecular mechanisms are largely unknown. Our study aimed to understand how host gene expression in the rumen epithelium contributes to differences in residual feed intake (RFI), a measure of feed efficiency, using a transcriptome profiling based approach.ResultsThe rumen epithelial transcriptome from highly efficient (low (L-) RFI, n = 9) and inefficient (high (H-) RFI, n = 9) Hereford x Angus steers was obtained using RNA-sequencing. There were 122 genes differentially expressed between the rumen epithelial tissues of L- and H- RFI steers (p < 0.05) with 85 up-regulated and 37 down-regulated in L-RFI steers. Functional analysis of up-regulated genes revealed their involvement in acetylation, remodeling of adherens junctions, cytoskeletal dynamics, cell migration, and cell turnover. Additionally, a weighted gene co-expression network analysis (WGCNA) identified a significant gene module containing 764 genes that was negatively correlated with RFI (r = -0.5, p = 0.03). Functional analysis revealed significant enrichment of genes involved in modulation of intercellular adhesion through adherens junctions, protein and cell turnover, and cytoskeletal organization that suggest possible increased tissue morphogenesis in the L-RFI steers. Additionally, the L-RFI epithelium had increased expression of genes involved with the mitochondrion, acetylation, and energy generating pathways such as glycolysis, tricarboxylic acid cycle, and oxidative phosphorylation. Further qPCR analysis of steers with different RFI (L-RFI, n = 35; M-RFI, n = 34; H-RFI, n = 35) revealed that the relative mitochondrial genome copy number per cell of the epithelium was positively correlated with RFI (r = 0.21, p = 0.03).ConclusionsOur results suggest that the rumen epithelium of L-RFI (efficient) steers may have increased tissue morphogenesis that possibly increases paracellular permeability for the absorption of nutrients and increased energy production to support the energetic demands of increased tissue morphogenesis compared to those of H-RFI (inefficient) animals. Greater expression of mitochondrial genes and lower relative mitochondrial genome copy numbers suggest a greater rate of transcription in the rumen epithelial mitochondria of L-RFI steers. Understanding how host gene expression profiles are associated with RFI could potentially lead to identification of mechanisms behind this trait, which are vital to develop strategies for the improvement of cattle feed efficiency.

Dataset Information

Profile of the Spleen Transcriptome in Beef Steers with Variation in Gain and Feed Intake.

Publications

Profile of the Spleen Transcriptome in Beef Steers with Variation in Gain and Feed Intake.

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