Transcriptome differences in the rumen of beef steers with variation in feed intake and gain

Authors: KERN, REBECCA - University Of Wyoming; Lindholm-Perry, Amanda; Freetly, Harvey; Snelling, Warren; KERN, JOHN - Kern Statistical Services; Keele, John; Miles, Jeremy; Foote, Andrew; Oliver, William; Kuehn, Larry; LUDDEN, PAUL - University Of Wyoming

Submitted to: Gene
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/18/2016
Publication Date: 3/29/2016
Publication URL: http://handle.nal.usda.gov/10113/62352
Citation: Kern, R.J., Lindholm-Perry, A.K., Freetly, H.C., Snelling, W.M., Kern, J.W., Keele, J.W., Miles, J.R., Foote, A.P., Oliver, W.T., Kuehn, L.A., Ludden, P.A. 2016. Transcriptome differences in the rumen of beef steers with variation in feed intake and gain. Gene. 586:12-26.

Interpretive Summary: The ability of a beef steer to convert feed to muscle mass or meat (feed efficiency) can affect the profitability of beef production. The lining of the first compartment of a steer’s stomach (rumen wall) is involved in the digestion and absorption of key nutrients indicating it may play a critical role in feed efficiency. One way to improve the feed efficiency of beef steers is through genetic selection. The first step to accomplish this goal is to identify genes that have the potential to be used to select for animals with an improved feed efficiency (candidate genes). Steers were evaluated for feed efficiency traits and divided into four groups: high intake high gain, high intake low gain, low intake high gain, and low intake low gain. Four steers from each group were chosen for this study. Samples of the rumen wall were taken from each steer. Gene expression was evaluated using RNA-Sequencing. Three statistical methods (Negative Binomial, Kruskall-Wallis, and an analysis performed by Cofactor Genomics) were used to identify candidate genes. Genes identified as candidate genes were tested to determine the accuracy of the analysis using real-time polymerase chain reaction. Several genes identified in this study were also identified in other studies as being candidate genes for the selection of cattle based on feed efficiency (CYP1A2, KLK10, KLK12, MYL1, PDE1A, and IRX3). From the genes identified as candidate genes, the top interaction networks among these genes were identified. Cell death and survival, immunological diseases, and metabolic diseases were the top networks associated with the feed efficiency traits of gain, intake, and efficiency, respectively. Our findings suggest that genes involved in immune function may be important to the feed efficiency of beef steers.

Technical Abstract: Feed efficiency is an economically important trait in beef production. The rumen wall interacts with feed, microbial populations and volatile fatty acids important to ruminant nutrition indicating it may play a critical role in the beef steer’s ability to utilize feedstuffs efficiently. To identify candidate genes associated with steer feed efficiency traits, and to gain an understanding of molecules and pathways involved in feed intake and utilization, RNA-Seq was performed on rumen papillae from 16 steers with extreme feed efficiency phenotypes (i.e., high vs. low intake and high vs. low BW gain). Four steers were chosen from each of the four Cartesian quadrants for gain × feed intake and used to generate individual RNA-Seq libraries. Three statistical methods (Negative Binomial, Kruskall Wallis, and a separate analysis conducted by Cofactor Genomics) were used to identify genes differentially expressed by feed efficiency phenotype from the RNA-Seq libraries. The top 27 genes were selected from the Negative Binomial Analysis based on their false discovery rate (FDR < 0.05). The top 19 genes were selected from the Kruskall Wallis Analysis based on P-value (P < 0.05). The top 120 genes were identified by Cofactor Genomics based on P-value (P < 0.05) and fold change (FC > 2). All genes identified in the Negative Binomial and Kruskall Wallis analyses and a subset of genes (n=20) identified by Cofactor Genomics were tested for validation using real-time PCR. Five genes were identified by more than one analysis; however, the majority was identified by a single analysis. Several genes identified in this study were previously identified as candidate genes for feed efficiency (CYP1A2, KLK10, KLK12, MYL1, PDE1A, and IRX3). The top gene networks identified were cell death and survival, immunological diseases, and metabolic diseases associated with gain, intake, and efficiency, respectively, suggesting that genes involved with apoptosis, immune function and response and metabolic pathways may be important predictors of feed efficiency in beef cattle.