Using RNA-Sequencing to Characterize a Novel Muscle Disorder in Chickens through Differential Gene Expression and Pathway Analysis

Improvements in poultry production within the past 50 years have led to increased muscle yield and growth rate in the industry, which may be contributing to an increased rate and development of new muscle disorders in chickens. Many types of muscle disorders such as deep pectoral myopathy, nutritional myopathy, and white striping, and muscle conditions such as dark, firm, dry (DFD) and pale, soft, exudative (PSE) meats have been researched in recent years. These muscle disorders and conditions are generally associated with poor meat quality traits and have a significant economic impact on the poultry industry. In this project we aim to understand the biological mechanisms that impact a novel muscle disorder colloquially referred to as “wooden breast”, through the use of RNA-sequencing technology. This phenotype is characterized by abnormally hard or tough breast muscle. We first constructed uniquely indexed cDNA libraries from tissue samples harvested from two breeding lines and one commercial cross, containing four affected and four unaffected samples within each line/cross. After paired-end sequencing of samples using an Illumina HiSeq 2000, we used Tophat to align the resulting sequence reads (~100 million reads per sample) to the chicken reference genome (Ensembl Galgal4), and then used Cuffdiff to find significant changes in gene transcript expression between affected and unaffected samples. Our preliminary results indicate over 1000 genes differentially expressed between affected and unaffected birds. Using Ingenuity Pathway Analysis (IPA), further research will be conducted to determine biological pathways and upstream regulatory factors that are involved in this disorder.