Detection of differentially expressed genes in broiler pectoralis major muscle affected by White Striping – Wooden Breast myopathies

The interleukin-1 (IL-1), IL-18, and IL-33 families of cytokines are related by mechanism of origin, receptor structure, and signal transduction pathways utilized. All three cytokines are synthesized as precursor molecules and cleaved by the enzyme caspase-1 before or during release from the cell. The NALP-3 inflammasome is of crucial importance in generating active caspase-1. The IL-1 family contains two agonists, IL-1alpha and IL-1beta, a specific inhibitor, IL-1 receptor antagonist (IL-1Ra), and two receptors, the biologically active type IL-1R and inactive type II IL-1R. Both IL-1RI and IL-33R utilize the same interacting accessory protein (IL-1RAcP). The balance between IL-1 and IL-1Ra is important in preventing disease in various organs, and excess production of IL-1 has been implicated in many human diseases. The IL-18 family also contains a specific inhibitor, the IL-18-binding protein (IL-18BP), which binds IL-18 in the fluid phase. The IL-18 receptor is similar to the IL-1 receptor complex, including a single ligand-binding chain and a different interacting accessory protein. IL-18 provides an important link between the innate and adaptive immune responses. Newly described IL-33 binds to the orphan IL-1 family receptor T1/ST2 and stimulates T-helper 2 responses as well as mast cells.

For a number of years, poultry selection has concentrated on growth velocity in meat lines, producing improvements in growth that have not been without consequence for muscle structure, metabolism, and meat quality. Higher growth rates may induce morphological abnormalities, induce larger fiber diameters and a higher proportion of glycolytic fibers, and a lower proteolytic potential in the muscles. After death, the faster development of rigor mortis increases the likelihood of paler color and reduced water holding capacity and poorer quality of further processed products. Reduced proteolytic potential is likely to increase toughness of poultry meats.

Background Improvements in poultry production within the past 50 years have led to increased muscle yield and growth rate, which may be contributing to an increased rate and development of new muscle disorders in chickens. Previously reported muscle disorders and conditions are generally associated with poor meat quality traits and have a significant negative economic impact on the poultry industry. Recently, a novel myopathy phenotype has emerged 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 colloquially referred to as “Wooden Breast”, through the use of RNA-sequencing technology. Methods We constructed cDNA libraries from five affected and six unaffected breast muscle samples from a line of commercial broiler chickens. After paired-end sequencing of samples using the Illumina Hiseq platform, we used Tophat to align the resulting sequence reads to the chicken reference genome and then used Cufflinks to find significant changes in gene transcript expression between each group. By comparing our gene list to previously published histology findings on this disorder and using Ingenuity Pathways Analysis (IPA®), we aim to develop a characteristic gene expression profile for this novel disorder through analyzing genes, gene families, and predicted biological pathways. Results Over 1500 genes were differentially expressed between affected and unaffected birds. There was an average of approximately 98 million reads per sample, across all samples. Results from the IPA analysis suggested “Diseases and Disorders” such as connective tissue disorders, “Molecular and Cellular Functions” such as cellular assembly and organization, cellular function and maintenance, and cellular movement, “Physiological System Development and Function” such as tissue development, and embryonic development, and “Top Canonical Pathways” such as, coagulation system, axonal guidance signaling, and acute phase response signaling, are associated with the Wooden Breast disease. Conclusions There is convincing evidence by RNA-seq analysis to support localized hypoxia, oxidative stress, increased intracellular calcium, as well as the possible presence of muscle fiber-type switching, as key features of Wooden Breast Disease, which are supported by reported microscopic lesions of the disease. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1623-0) contains supplementary material, which is available to authorized users.