The success of turkey breeding has coincided with an increased incidence of a meat quality defect known as pale, soft and exudative (PSE) meat. Application of molecular-based approaches such as genetic markers for animal selection or pathway intervention to prevent development of this meat defect have been suggested as a potential long-term solution. However, molecular mechanisms associated with this alteration remain unclear. The overall goal of this study was to obtain better understanding of molecular mechanisms underlying development of PSE turkey. The study comprised two specific aims: 1) to assess global differential gene expression between normal and PSE turkey; and 2) to confirm differences between normal and PSE meat samples at the protein level of a candidate gene selected from aim 1. Turkey breast muscle samples were collected from 22wk randombred control line (RBC2) and 16wk commercial (COMM) turkeys. Breast samples were classified as normal or PSE based on marinade uptake (high = normal, low = PSE). Total RNA was isolated from muscle samples with the highest (normal, n = 6) and the lowest (PSE, n = 6) marinade uptake. Transcriptome analyses were conducted using two platforms: the turkey skeletal muscle long oligonucleotide microarray, and deep transcriptome sequencing with an Illumina Genome Analyzer IIX (RNA-Seq). The microarray study of RBC2 samples revealed 49 differentially expressed transcripts (false discovery rate, FDR < 0.1). Genes selected for pathway analysis were determined using two criteria: fold change ranking (FC < -1.66, FC > 1.66) and FDR < 0.35. The calcium signaling pathway was highlighted as the top canonical pathway. In addition, changes in expression of genes in the actin cytoskeleton signaling pathway suggested altered structures of actin filaments that may affect strength and flexibility of muscle cells. In RNA-Seq analysis, four RNA samples for each of the extreme normal and PSE characteristics from the RBC2 line were sequenced (n = 4). Pathway analysis of 494 differentially expressed transcripts (FDR < 0.05) identified by RNA-Seq confirmed previously suggested changes in calcium homeostasis and organization of actin cytoskeleton. Pyruvate dehydrogenase kinase isozyme 4 (PDK4), which regulates glucose oxidation, showed substantial decreased expression with both microarray (FC = -25.9) and RNA-Seq (FC = -14.1); thus, this gene was chosen as a candidate gene for further evaluation. The protein abundance of PDK4 was significantly decreased (FC = -3.4, P < 0.001) in PSE samples (n = 6) of the RBC2 line. Reduced expression of PDK4 at both transcriptional (FC = -12.8, P < 0.05) and translational levels (FC = -2.8, P < 0.001) was also observed in PSE turkey of the COMM line (n = 6), supporting the biological relevance of PDK4 suppression in the development of PSE turkey, and also suggesting that the mechanism responsible for the decreased PDK4 in RBC2 turkey subpopulations has been maintained in a commercial line. By identifying several candidate genes including PDK4, this study lays the foundation for future studies aimed at defining the mechanisms of development of PSE turkey.
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