Differential Gene Expression Detected via Transcriptome Sequencing in Angus Steers Differing for Feed Efficiency

The function and heritability of gene expression associated with economically important traits is being investigated in a population of Angus steers with extreme measures of residual feed intake (RFI).  RNA-Seq was performed using Illumina next generation sequencing technology and sequence reads were processed using NextGENe software (SoftGenetics, State College, PA).  Specifically, NextGENe was used for quality trimming and aligning the sequence reads to the UMD3.1 reference genome and generating counts of matched reads.  Differential expression analysis was performed using EdgeR software.  Genes found to be differentially expressed were then aligned with genome wide association analysis in order to determine if genomic regions that were found to be significantly associated with RFI harbor differentially expressed genes.