RNA-Seq detection of differential gene expression in the rumen of beef steers associated with feed efficiency phenotypes

Abstract Text: The efficient utilization of feedstuffs is an economically important trait in beef production.  The rumen is important to the digestive process of steers interacting with feed, microbial populations, and volatile fatty acids indicating it may play a critical role in feed efficiency.  To gain an understanding of the molecules and pathways involved in gain, intake and utilization and identify candidate genes associated with steer feed efficiency, RNA-Seq was performed on rumen papillae from steers with extreme feed efficiency phenotypes (n=16).  The study population was divided into four Cartesian quadrants for intake × gain and steers (n=4) from each quadrant were sampled. Three statistical analyses were performed to identify differentially expressed genes among feed efficiency phenotype.  Two analyses were performed on total gene expression, the Negative Binomial and the Kruskall-Wallis.  A separate analysis was performed by Cofactor Genomics on exon cluster expression.  The Negative Binomial analysis identified 27 genes differentially expressed among feed efficiency phenotypes based on false discovery rate (FDR < 0.05).  The Kruskall-Wallis analysis identified 19 differentially expressed genes based on P-value (P < 0.05).  Cofactor Genomics identified 187 differentially expressed genes based on P-value (P < 0.05) and fold change (FC >2).  All genes identified by the Negative Binomial and Kruskall-Wallis analyses were tested for validation using real-time PCR and a subset of genes (n=23) identified by Cofactor Genomics were tested for validation.  Several genes (ACAT1, CYP1A2, KLK10, KLK12, MIF, PDEE1A, and MYL1) were identified by at least one analysis in this study and are supported by other studies.  Five genes were identified by more than one analysis in this study (KLK7, KLK10, KLK12, ARHGAP27, and RGS5).  Cell death and survival, immunological disease, and metabolic disease were the top gene networks identified in association with gain, intake, and efficiency respectively.  Genes expressed in rumen papillae of beef steers may play a role in the feed efficiency of the animal.  USDA is an equal opportunity provider and employer.

Keywords: RNA-Seq, Beef Cattle, Rumen Papillae