The transcriptome and physiological morphology of rumen epithelium in association with feed efficiency traits gain and intake in the beef steer

The global population is predicted to increase by 2 billion people by the year 2050, and along with this increase will come greater urbanization and incomes resulting in increased demand for beef. The cost of feed stuffs commonly used to produce beef is also rising. These factors combined make feed efficiency an economically important trait in beef cattle. The rumen is involved in the fermentation, absorption and metabolism of important nutrients and microbial byproducts indicating that it may play a role in the feed efficiency of beef cattle. The goals of this thesis are to gain a better understanding of factors affecting feed efficiency in the rumen of beef cattle and to identify candidate genes that could be valuable tools for the selection of beef cattle with superior feed efficiency phenotypes. Feed efficiency data were collected on 48 crossbred beef steers over three trial periods. At harvest rumen epithelial samples were taken from each animal. Papillae were clipped and flash frozen at harvest of the first and third trial for subsequent gene expression evaluations. Rumen fluid was also collected at harvest of the third trial. Rumen papillae were counted on one square centimeter of rumen epithelium as density. Papillae (n = 30/sample) were also measured for length and width. The three variables were then combined into an equation to give surface enlargement factor (SEF). Length, width, density and SEF were analyzed using the GLM procedure of SAS to determine if any of the variables were associated with feed intake or gain. These morphological characteristics of rumen papillae were not found to be associated with intake or gain (P > 0.10). Volatile fatty acids (VFAs) in rumen fluid samples (n=15) collected from steers in the third trial were measured using gas chromatography and analyzed using a one way ANOVA to determine if any of the VFAs were associated with intake or gain. Butyrate was found to be associated with gain (P= 0.03). RNA Sequencing (RNA-Seq) was performed on papillae from steers (n = 16) in the first trial. Three different statistical methods (Negative Binomial, Kruskal- Wallis, and a separate analysis conducted by Cofactor Genomics) were used to identify genes differentially expressed in association with feed intake, gain and efficiency. Genes were selected by the Negative Binomial Analysis based on their false discovery rate (FDR < 0.05). Genes were selected by the Kruskal-Wallis Analysis based on P-value ( P< 0.05). Genes were identified by Cofactor Genomics based on P-value (P 2). Real-time Polymerase Chain Reaction was used to validate genes identified by the analyses. Five genes were identified by more than one analysis and several genes had been previously been identified as candidate genes for feed efficiency in beef steers (CYP1A2, KLK10, KLK12, MIF, PDE1A, and MYL1). Ingenuity Pathway Analysis was employed to determine gene networks among genes identified as being differentially expressed. Cell death and survival, immunological diseases, and metabolic diseases were the top gene networks identified in association with gain, intake and efficiency respectively. Taking into account butyrate's association with gain as well as with residual feed intake (RFI) and kallikrein transcript abundance in the rumen, expression levels of KLK 5, 6, 7, 8, 9, 10, 12 and 13 were evaluated for association with butyrate concentration in rumen fluid. Increased transcript abundance for KLK8 and KLK13 were correlated with higher ruminal butyrate concentrations. Our results suggest that the morphology of the rumen does not play a role in feed efficiency of the beef steer, however the rumen's functions in metabolism and immunity may be responsible for differences in feed efficiency among individual beef steers.