Small intestine mass and cellularity were previously associated with cattle feed efficiency. The small intestine is responsible for the digestion of nutrients and absorption of fatty acids, amino acids and carbohydrates, and it contributes to the overall feed efficiency of cattle. The objective of this study was to evaluate transcriptome differences among the small intestine from cattle with divergent gain and feed intake. Animals most divergent from the bivariate mean in each of the four phenotypic Cartesian quadrants for gain × intake were selected, and the transcriptomes of duodenum, jejunum and ileum were evaluated. Gene expression analyses were performed comparing high gain vs. low gain animals, high intake vs. low intake animals and each of the phenotypic quadrants to all other groups. Genes differentially expressed within the high gain-low intake and low gain-high intake groups of animals included those involved in immune function and inflammation in all small intestine sections. The high gain-high intake group differed from the high gain-low intake group by immune response genes in all sections of the small intestine. In all sections of small intestine, animals with low gain-low intake displayed greater abundance of heat-shock genes compared to other groups. Several over-represented pathways were identified. These include the antigen-processing/presentation pathway in high gain animals and PPAR signaling, starch/sucrose metabolism, retinol metabolism and melatonin degradation pathways in the high intake animals. Genes with functions in immune response, inflammation, stress response, influenza pathogenesis and melatonin degradation pathways may have a relationship with gain and intake in beef steers.

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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.

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Feed costs are the most expensive input in beef production. Improvement in the ability of beef cattle to convert feed into meat would lower feed inputs and reduce the cost of production. The rumen epithelium is responsible for absorption and metabolism of nutrients and microbial by-products, and may play a significant role in gain or feed intake. Our objective was to determine the relationships among rumen papillae morphology, gene expression, volatile fatty acid concentrations, and gain and feed intake. Average daily gain (ADG) and average daily feed intake (ADFI) were collected on a crossbred population of beef steers over three feeding trials. Based on feed intake and weight gain differences, 48 steers were selected for the project (16 from each feeding study). At harvest, rumen epithelial samples were taken from three locations in the rumen of each animal. The number of papillae on 1 cm 2 of epithelium was counted to determine density. Papillae (n = 30) from each sample were measured for length and width. The density, length, and width were combined to determine surface enlargement factor (SEF). None of the morphological characteristics of the papillae (length, width, density or SEF) were associated with feed intake or gain (P > 0.10). Ruminal fluid was collected from steers (n = 15) in the third trial for volatile fatty acid (VFA) analysis to determine if a relationship between VFA and ADG or ADFI existed. No differences in volatile fatty acid (VFA) concentrations were associated (P > 0.17) with ADFI or ADG. VFA variation was also evaluated for a relationship with kallikrein (KLK) genes since ruminal butyrate concentrations have previously been associated with the transcript abundance KLK genes. Additionally, qRT-PCR data showed that variation in the transcript abundance of KLK6,8-10, and 13 associated with feed intake in our first trial of steers. Thus, we evaluated the transcript abundance of eight KLK genes in rumen 3 papillae from steers in the third trial (n = 16). Expression levels of KLK5 correlated with valerate concentrations in the rumen (P < 0.05), KLK10 correlated with acetate concentrations in the rumen (P < 0.05), KLK12 correlated with acetate and butyrate concentrations in the rumen (P < 0.05), and the expression levels of KLK9 and KLK10 were associated with gain. While rumen papillae morphology was not associated with beef steer gain or intake, our data suggests members of the kallikrein gene family have a relationship with the VFA environment in the rumen, and also appear to play a role in the highly correlated traits of ADG and ADFI.

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Ruminal genes differentially expressed in crossbred beef steers from USMARC with variation in gain and feed intake were identified in a previous study. Several of the genes identified with expression patterns differing between animals with high gain-low feed intake and low gain-high feed intake were evaluated in a separate, unrelated population of Angus × Hereford beef steers from the University of Wyoming that was classified to differ in residual feed intake (RFI). Of the 17 genes tested, two were differentially expressed by RFI class in the Angus × Hereford animals. These genes included NAD(P)H dehydrogenase, quinone 1 (NQO1; P = 0.0009) and regulator of G-protein signaling 5 (RGS5; P = 0.01). A third gene, acetyl-CoA acetyltransferase 1 (ACAT1; P = 0.06), displayed a trend toward association with RFI. These data suggest that some of the genes identified in a previous rumen transcriptome discovery study may have utility for identifying or selecting for animals with superior feed efficiency phenotypes across cattle breeds and populations.

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