RNA-seq meta-analysis identifies genes in skeletal muscle associated with gain and intake across a multi-season study of crossbred beef steers

Authors: Keel, Brittney; Zarek, Christina; Keele, John; Kuehn, Larry; Snelling, Warren; Oliver, William; Freetly, Harvey; Lindholm-Perry, Amanda

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/9/2018
Publication Date: 6/4/2018
Citation: Keel, B.N., Zarek, C.M., Keele, J.W., Kuehn, L.A., Snelling, W.M., Oliver, W.T., Freetly, H.C., Lindholm-Perry, A.K. 2018. RNA-seq meta-analysis identifies genes in skeletal muscle associated with gain and intake across a multi-season study of crossbred beef steers. BMC Genomics. 19:430. https://doi.org/10.1186/s12864-018-4769-8.
DOI: https://doi.org/10.1186/s12864-018-4769-8

Interpretive Summary: Feed costs are the major component of production costs in the beef cattle industry, accounting for 55-75% of the total production costs. To reduce feed costs and increase productivity, biomarkers could be used to select for cattle that gain acceptable body weights while consuming less feed. In order to understand which genes may impact these traits, ARS scientists conducted a study across 5 seasons with crossbred steers that measured body weight gain and feed intake over a period of approximately 80 days. At the end of each of the 5 feed trials, sixteen steers with the greatest and lowest body weight gain and feed intake were selected to be used in the study, resulting in a total of 80 steers. Skeletal muscle samples were collected and analyzed in order to identify differences in gene expression between animals with high and low body weight gain and feed intake. A total of 9 genes were found to be associated with differences in body weight gain across all 5 seasons, while 12 genes were found to be associated with differences in feed intake across the seasons. These genes were analyzed to determine their primary functions and locations in known biological pathways. Many of these genes were identified to be involved in protein oxidation, oxidative metabolism, and oxidative stress. Data from this study suggests that oxidative stress within the skeletal muscle may be contributing to cattle feed intake and gain phenotypes. This is the first multi-season transcriptome analyses of cattle feed efficiency to be reported in the literature. It is the first step in identifying feed efficiency biomarkers that will be robust across the industry (across breeds and seasons). Continued examination of these biomarkers is expected to lead to the development of assays that will allow cattle producers and breeders to be able to make more rapid genetic progress by including them into their selection decisions.

Technical Abstract: Background: Feed intake and body weight gain are economically important inputs and outputs of beef production systems. The purpose of this study was to discover differentially expressed genes that will be robust for feed intake and gain across a large segment of the cattle industry. Transcriptomic studies often suffer from issues with reproducibility and cross-validation. One way to improve reproducibility is by integrating multiple datasets via meta-analysis. RNA sequencing (RNA-Seq) was performed on longissimus dorsi muscle from 80 steers (5 cohorts, each with 16 animals) selected from the outside fringe of a bivariate gain and feed intake distribution to understand the genes and pathways involved in feed efficiency. In each cohort, 16 steers were selected from one of four gain and feed intake phenotypes (n = 4 per phenotype) in a 2 × 2 factorial arrangement with gain and feed intake as main effect variables. Each cohort was analyzed as a single experiment using a generalized linear model and results from the 5 cohort analyses were combined in a meta-analysis to identify differentially expressed genes (DEG) across the cohorts. Results: A total of 51 genes were differentially expressed for the main effect of gain, 109 genes for the intake main effect, and 11 genes for the gain x intake interaction (Pcorrected < 0.05). A jackknife sensitivity analysis showed that, in general, the meta-analysis produced robust DEGs for the two main effects and their interaction. Pathways identified from over-represented genes included mitochondrial energy production and oxidative stress pathways for the main effect of gain due to DEG including GPD1, NDUFA6, UQCRQ, ACTC1, and MGST3. For intake, metabolic pathways including amino acid biosynthesis and degradation were identified, and for the interaction analysis the pathways identified included GADD45, pyridoxal 5’phosphate salvage, and caveolar mediated endocytosis signaling. Conclusions: Variation among DEG identified by cohort suggests that environment and breed may play large roles in the expression of genes associated with feed efficiency in the muscle of beef cattle. Meta-analyses of transcriptome data from groups of animals over multiple cohorts may be necessary to elucidate the genetics contributing these types of biological phenotypes.