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Differential gene expression and molecular mechanisms associated with development of pale, soft and exudative (PSE) turkey meat.

机译：与苍白，柔软和渗出（PSE）火鸡肉发育相关的差异基因表达和分子机制。

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摘要

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) 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.
机译：火鸡育种的成功与被称为淡，软和渗出（PSE）肉的肉品质缺陷的发生率增加相吻合。已经提出了将基于分子的方法（例如遗传标记）用于动物选择或防止这种肉缺陷发展的途径干预的建议，这是潜在的长期解决方案。然而，与这种改变有关的分子机制仍不清楚。这项研究的总体目标是要更好地了解PSE火鸡发展的分子机制。该研究包括两个具体目标：1）评估正常和PSE火鸡之间的整体差异基因表达；和2）在从目标1选出的候选基因的蛋白质水平上确认正常和PSE肉样品之间的差异。从22wk随机对照品系（RBC2）和16wk商业（COMM）火鸡中收集土耳其胸肌样品。根据腌泡汁摄取情况，将乳房样品分为正常或PSE（高=正常，低= PSE）。从肌肉样品中腌制液摄入量最高（正常，n = 6）和最低（PSE，n = 6）的肌肉样品中分离出总RNA。使用两个平台进行转录组分析：火鸡骨骼肌长寡核苷酸微阵列，以及使用Illumina Genome Analyzer IIX（RNA-Seq）进行深度转录组测序。 RBC2样品的微阵列研究显示了49个差异表达的转录本（错误发现率，FDR <0.1）。使用两种标准确定用于途径分析的基因：倍数变化排名（FC 1.66）和FDR <0.35。钙信号传导途径被强调为最典型的途径。另外，肌动蛋白细胞骨架信号通路中基因表达的变化表明肌动蛋白丝的结构发生改变，可能影响肌肉细胞的强度和柔韧性。在RNA-Seq分析中，对来自RBC2品系的每个极端正常和PSE特征的四个RNA样品进行了测序（n = 4）。通过RNA-Seq鉴定的494个差异表达的转录本（FDR <0.05）的途径分析已证实先前表明钙稳态和肌动蛋白细胞骨架组织的变化。调节葡萄糖氧化的丙酮酸脱氢酶激酶同工酶4（PDK4）在微阵列（FC = -25.9）和RNA-Seq（FC = -14.1）中均表现出明显降低的表达；因此，该基因被选作进一步评估的候选基因。在RBC2系的PSE样本（n = 6）中，PDK4的蛋白质丰度显着降低（FC = -3.4，P <0.001）。在COMM系的PSE土耳其（n = 6）中也观察到PDK4在转录水平（FC = -12.8，P <0.05）和翻译水平（FC = -2.8，P <0.001）上的表达降低，支持生物学相关性在PSE火鸡的发展中抑制PDK4的研究，也表明导致RBC2火鸡亚群中PDK4减少的机制已经在商业化生产中得到了维持。通过鉴定包括PDK4在内的几种候选基因，本研究为旨在确定PSE火鸡发育机理的未来研究奠定了基础。

著录项

  • 作者

    Malila, Yuwares.;

  • 作者单位

    Michigan State University.;

  • 授予单位 Michigan State University.;
  • 学科 Biology Molecular.;Agriculture Food Science and Technology.
  • 学位 Ph.D.
  • 年度 2013
  • 页码 144 p.
  • 总页数 144
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

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