RNA-Seq Gene Expression Study of Breast Muscle from Broiler Chickens with High and Low Feed Efficiencies

Feed efficiency (FE) is an important trait for commercial poultry production.  Improving FE of broiler chickens not only can have economic impact to the poultry industry, but also can decrease nitrogenous waste and consequently benefit environment near intense poultry production. However, the biological basis of variation in FE in chickens is not well understood. Through RNA-seq analysis of the breast muscle samples from high and low FE chickens (measured as residual feed consumption), our research aims to identify genes and biological pathways associated with feed efficiency in broiler chickens. Total RNA was isolated from breast muscle samples from 10 high and 13 low FE chickens. Using Illumina Truseq Stranded RNA Prep kits, each sample was converted to a uniquely indexed cDNA library, and the resulting libraries were pooled and paired-end (PE) sequenced on an Illumina HiSeq 2000 sequencer. On average about 34 million PE sequence reads (2 x 75 nucleotides) were produced for each sample. Via Tophat alignment and Cufflinks differential expression analysis, we detected 1059 genes differentially expressed between high and low FE chickens.  Ingenuity Pathway Analysis (IPA) revealed that genes upregulated in the high FE chickens are enriched for genes in anabolic pathways, e.g. growth hormone signaling and insulin receptor signaling pathways. Conversely, genes upregulated in the low FE chickens are enriched for genes in catabolic pathways, e.g. PPARα/RXRα activation and amino acid degradation pathways. We also found that genes involved in the metabolism of reactive oxygen species are enriched in the high FE phenotypes.