Using RNA-seq to characterize the biological basis of variation in feed efficiency in broiler chickens

Zhou, Nan
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University of Delaware
Feed cost plays a key role in the total expenses of modern broiler chicken production. Especially with feed prices increasing constantly in recent years, improving feed efficiency has become a concern for poultry producers. Although huge progress has been made on the optimization of feed efficiency in broiler chickens over the past 50 years, a significant portion of feed energy and nutrients is still wasted because of poor efficiency of nutrient utilization. A further consequence is that an excess of manure is produced, causing environmental concerns in the regions with intense poultry production. Therefore, from both economical and environmental standpoints, efficient use of feed is vital for sustainable poultry production. Different selection criteria have been used for improving feed efficiency in broiler chickens. However, the biological basis of the variation in chicken feed efficiency is not well understood. As a result, some undesirable side effects would appear with the cumulative genetic selection for high feed efficiency. A more profound understanding of this highly complex trait is needed to develop more efficient selection strategies and to foresee potential long-term issues that may arise by selection for high feed efficiency. The objective of this project is to characterize the molecular basis of the variation in chicken feed efficiency, with a long-term goal of sustainably improving feed efficiency in poultry production. Using high-throughput RNA sequencing, we aimed to identify the gene expression differences in breast muscle tissues of broiler chickens with extremely high and low feed efficiencies. Total RNA was isolated from breast muscle samples harvested from 10 high and 13 low feed efficiency chickens at 7 weeks of age. Using Truseq Stranded RNA Prep kit (Illumina), each sample was converted to a uniquely indexed cDNA library, and the resulting cDNA libraries were pooled and sequenced on an Illumina Hiseq 2000 sequencer. An average of 34 million paired end reads (75 bp) were produced from each sample, 80% of which were properly mapped to the reference genome (Ensembl Galgal4). We analyzed the sequence data using bioinformatics tools Tophat and Cufflinks and detected 1059 genes differentially expressed (FDR < 0.05) in the breast muscle between the high and low feed efficiency chickens. Gene function analysis revealed that genes involved in muscle remodeling, inflammatory response and free radical scavenging were mostly up regulated in the high feed efficiency birds. Additionally, growth hormone and IGFs/PI3K/AKT signaling pathways were enriched in differentially expressed genes, which might contribute to the high breast muscle yield in high feed efficiency birds and partly explain the FE advantage of these chickens.