RNA-Seq Analysis of Wooden Breast Disease: Characterizing a Novel Myopathy in Commercial Chickens through Differential Gene Expression

Breast meat yield of commercial broiler chickens has increased in recent decades. This improvement, mainly achieved through selective breeding for increased growth rate of the breast muscle, may inadvertently be contributing to the development of new muscle disorders in commercial chickens. Recently, a myopathy phenotype colloquially referred to as “Wooden Breast” has emerged in broilers, which is characterized by palpably “hard” or tough breast muscle. The objective of this study is to identify the underlying biological mechanisms that contribute to this emerging muscle disorder, through the use of RNA-sequencing technology. Complementary DNA (cDNA) libraries were constructed for 4 affected and 4 unaffected breast muscle samples from a line of commercial broiler chickens. After paired-end sequencing of samples using an Illumina HiSeq 2000, we used TopHat to align the resulting sequence reads to the chicken reference genome. Using Cufflink to determine significant changes in gene transcript expression between each group, our results indicate over 1000 genes differentially expressed between affected and unaffected birds. Furthermore, a characteristic gene expression profile emerged for the disorder through the use of Ingenuity Pathways Analysis (IPA®). By comparing the resultant gene list to previously reported histologic lesions for the myopathy, we have found convincing evidence to support the existence of fiber-type switching, localized hypoxia, oxidative stress, and increased intracellular calcium as characteristic features of Wooden Breast Disease in commercial broilers.