Differential Gene Expression in the Hen Liver in Response to Different Feeding Conditions

Intense selection pressure for postnatal growth has led to great improvements in the broiler industry. In parent flocks, however, broiler breeder hens develop excessive follicles resulting in decreased egg production. Intensive feed restriction decreases these reproductive inefficiencies, but the hormonal mechanisms underlying the differential effect of feeding level on follicle development and whole animal metabolism are unknown. We used high-throughput RNA sequencing technology (Illumina HiSeq) to investigate the gene expression pattern in the liver of broiler breeders maintained on a feed-restricted diet (RF) or fed an ad libitum (FF) diet. Cobb 700 broiler breeder hens were reared using a (RF) feeding program according to breeder guidelines. During peak production, birds were randomly divided into two groups. One pen of hens was given FF and one pen remained on RF for six weeks. Liver ssRNA-seq libraries were prepared and run on Illumina HiSeq, generating 22-33 million reads per sample (n=3; each group). Reads were aligned to UCSC galGal4 using Tophat (v2.0.13) and transcripts were counted using cuffdiff (v.2.2.1). A MDS plot was generated to evaluate the variance among biological replicates, and identify sample outliers. Differentially expressed (DE) genes were determined using EdgeR’s generalized linear models (glm), which identified 176 differentially expressed genes in RF and FF hens (p<0.01; FDR<0.1). Sequencing results were validated by qRT-PCR and results indicated that FF broiler breeders had significantly higher levels of IGF1 mRNA (p<0.05) than RF hens. Further functional annotation and pathway analysis is ongoing.