RNA-Seq Analysis of Abdominal Fat from Modern Commercial Broiler Chickens with High and Low Feed Efficiency

In the modern broiler industry, birds with high feed efficiency are preferred for economic and environmental reasons. High feed efficiency chickens typically have reduced abdominal fat, the major adipose tissue in chickens. In mammals, adipose tissue is a crucial organ involved not only in fat deposition, but also in energy metabolism, endocrine function and immune regulation. However, the role of adipose tissue in avian species is not well characterized. Through gene expression profiling of abdominal fat from broiler chickens, the present study aims to (i) provide insights into the functions of the adipose tissue in chickens; (ii) identify relationships between feed efficiency and gene expression in abdominal fat. Total RNA was extracted from abdominal fat of 22 commercial broilers with extreme residual feed consumption, i.e. high and low feed efficiency. After constructing a uniquely barcoded cDNA library for each RNA sample, the cDNA libraries were pooled and sequenced on Illumina HiSeq 2000 system, and the resulting sequence reads were aligned to the chicken reference genome (Ensembl Galgal4) with a mapping rate of 85%. We detected 11,565 genes that were expressed in abdominal fat tissue with at least 5 reads per gene. Using Cuffdiff, we identified 286 differentially expressed (DE) genes between high and low feed efficiency chickens. The DE genes are significantly (P<0.01) enriched for genes in the lipid metabolism, coagulation, and immune response pathways. Compared with high feed efficiency chickens, the low feed efficiency chickens had higher expression of lipid synthesis genes and lower expression of lipid oxidation genes.