Abstract
BackgroundFeed 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.ResultsA 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.ConclusionsVariation 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.
Highlights
Feed intake and body weight gain are economically important inputs and outputs of beef production systems
Dry matter intake (DMI), residual feed intake (RFI), average daily gain (ADG), and feed conversion ratio (FCR) have been shown to be under genetic control, with heritabilities estimated between 0.2 and 0.5 [3, 4], indicating that these traits could be improved through selection
Since our goal was to identify differentially expressed genes (DEG) that could explain the overall variation in gain and feed intake across all cohorts, we performed a meta-analysis of differential expression across the 5 cohorts
Summary
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. 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. One way to potentially reduce these costs is to improve efficiency of beef cattle. Feed intake and weight gain are two measureable component phenotypes that are often used to characterize the feed efficiency of an animal. Information is lacking for generation of predictions of total genetic merit for feed intake and efficiency in major cattle breeds. An improved understanding of the regulation of genes underlying efficiency could improve the effectiveness of selection for efficiency as well as significantly reduce the cost of doing so
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