Comparison between skeletal transcriptomes of Korean native pig and Yorkshire

The pig could be a useful model to characterize molecular aspects determining several delicate phenotypes because they have been bred for those characteristics. The Korean native pig (KNP) is a regional breed in Korea that was characterized by relatively high intramuscular fat content and reddish meat color compared to other western breeds such as Yorkshire (YS). YS grew faster and contained more lean muscle than KNP. We compared the KNP to Yorksire to find molecular clues determining muscle characteristics. The comparison of skeletal gene expression profiles between these two breeds showed molecular differences in muscle. We found 82 differentially expressed genes (DEGs) defined by fold change (more than 1.5 fold difference) and statistical significance (within 5% of false discovery rate). Functional analyses of these DEGs indicated up-regulation of most genes involved in cell cycle arrest, down-regulation of most genes involved in cellular differentiation and its inhibition, down-regulation of most genes encoding component of muscular-structural system, and up-regulation of most genes involved in diverse metabolism in KNP. Especially, DEGs in above-mentioned categories included a large number of genes encoding proteins directly or indirectly involved in p53 pathway. Our results indicated a possible role of p53 to determine muscle characteristics between these two breeds. Comparing gene expression profiles to discover differentially expressed genes from skeletal muscles of two different pig breeds.

猪因针对特定表型特征选育，可作为解析调控多种精细表型的分子机制的理想模型。韩国本土猪（Korean native pig, KNP）是韩国本土猪种，与约克夏（Yorkshire, YS）等西方商业猪种相比，其肌内脂肪含量较高、肉色偏红；而约克夏猪生长速度更快，瘦肌肉含量也高于韩国本土猪。本研究通过对比韩国本土猪与约克夏猪，旨在挖掘调控肌肉特性的分子线索。对两个猪种的骨骼肌基因表达谱进行比较分析，发现二者肌肉组织存在分子层面的差异。本研究筛选得到82个差异表达基因（differentially expressed genes, DEGs），筛选标准为表达倍数变化差异≥1.5倍，且错误发现率（false discovery rate, FDR）小于5%的统计学显著性阈值。对上述DEGs的功能分析显示，韩国本土猪中，绝大多数参与细胞周期阻滞的基因呈上调表达；参与细胞分化及其抑制过程的基因、编码肌肉结构系统组分的基因则大多呈下调表达；此外，参与多种代谢过程的基因则呈现上调表达。尤为值得注意的是，上述功能类别中的DEGs包含大量编码直接或间接参与p53通路的蛋白质的基因。本研究结果提示，p53通路可能在调控两个猪种肌肉特性差异中发挥关键作用。本研究通过比较两个不同猪种的骨骼肌基因表达谱，以筛选差异表达基因。