Genes in Skeletal Muscle Associated with Gain and Intake Identified in a Multi-Season Study of Crossbred Beef Steers

The purpose of this study was to identify genes differentially expressed in the muscle of beef cattle associated with gain and intake regardless of breed of origin and season or year of study. Crossbred animals of 19 different breeds with variation in body weight gain and feed intake were selected from fall and spring seasons over three years to reduce the influence of gene expression that was either breed-specific or related to environment or cohort. RNA sequencing was performed on longissimus dorsi muscle from 80 steers selected (5 cohorts, each with 16 animals). Each cohort displayed a clear segregation of phenotypes, thus, a meta-analysis for the main effects of gain, intake and their interaction was chosen to identify differentially expressed genes across the five RNA-seq data sets. A total of 148 genes were differentially expressed for the main effect of gain, 1,738 genes for intake, and 59 genes for the gain x intake interaction. There were nine genes associated with gain and 12 genes associated with intake that shared the same gene expression directionality across all five groups of steers. The nine genes with common directionality associated with gain were LDHB, PITHD1, PDLIM1, MYHB7, GSTM2, MYL12A, NFKBIA and two LOC genes. These genes have been associated with functions including protein oxidation, oxidative metabolism, oxidative stress and cytokine inhibition. The 12 genes identified for feed intake were of ART5, ALDH5A1, ARHGEF25, BGN, C15H11orf31, CC2D1B, CLSTN2, CAMK1D, LOC101902407, PON1, SOCS3, and UBE2B involved in ion binding, G-coupled receptor signaling, signal transducer activity, and striated muscle contraction. Pathway analysis of the complete list of 1738 genes for feed intake identified genes over-represented in oxidative phosphylation, mTOR, and EIF2 signaling pathways; however, many of these genes displayed different effects by season. The variation among the lists of genes identified as differentially expressed by cohort in this study underscores the importance of including animals from more than one cohort of livestock to obtain biologically relevant data for complex traits. USDA is an equal opportunity provider and employer.