Ropka-Molik Katarzyna, Zukowski Kacper, Eckert Robert, Gurgul Artur, Piórkowska Katarzyna, Oczkowicz Maria
Laboratory of Genomics, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
Anim Genet. 2014 Oct;45(5):674-84. doi: 10.1111/age.12184. Epub 2014 Jun 24.
Next-generation sequencing RNA-Seq technology is a powerful tool that creates new possibilities for whole-transcriptome analysis. In our study, the RNA-Seq method was applied to analyze global changes in transcriptome from muscle tissue (m. semimembranosus) in two pig breeds (Pietrain and Polish Landrace, PL). The breeds differ in terms of muscularity, growth rate and reproduction traits. Using three different approaches (deseq, cufflinks and edger) and taking into account the most restrictive criteria, 35 genes differentially expressed between Pietrain and PL pigs were identified. In both breeds, the most abundant were transcripts encoding ribosomal and cytoskeletal proteins (TPM3, TCAP, TMOD4, TPM2, TNNC1) and calcium-binding proteins involved in muscle contraction, calcium-mediated signaling or cation transport (CASQ1, MLC2V, SLC25A4, MYL3). In PL pigs, we identified up-regulation of several genes that play crucial roles in reproduction: female gamete generation (BDP1, PTPN21, USP9X), fertilization (EGFR) and embryonic development (CPEB4). In the Pietrain breed, only seven genes were over-expressed (CISH, SPP1, TUBA8, ATP6V1C2, IGKC, predicted LOC100510960 and LOC100626400), and they play important roles in, for example, negative regulation of apoptosis, immune response, cell-cell signaling, cell growth and migration as well as the metabolic process. The functions of the majority of selected genes were consistent with phenotypic variation in investigated breeds; thus, we proposed a new panel of candidate genes that can be associated with economically important pig traits.
下一代测序RNA-Seq技术是一种强大的工具，为全转录组分析创造了新的可能性。在我们的研究中，RNA-Seq方法被用于分析两个猪品种（皮特兰猪和波兰大白猪，PL）肌肉组织（半膜肌）转录组的全局变化。这两个品种在肌肉发达程度、生长速度和繁殖性状方面存在差异。使用三种不同的方法（deseq、cufflinks和edger）并考虑最严格的标准，鉴定出了皮特兰猪和PL猪之间差异表达的35个基因。在这两个品种中，最丰富的转录本是编码核糖体和细胞骨架蛋白（TPM3、TCAP、TMOD4、TPM2、TNNC1）以及参与肌肉收缩、钙介导信号传导或阳离子转运的钙结合蛋白（CASQ1、MLC2V、SLC25A4、MYL3）。在PL猪中，我们鉴定出几个在繁殖中起关键作用的基因上调：雌配子生成（BDP1、PTPN21、USP9X）、受精（EGFR）和胚胎发育（CPEB4）。在皮特兰品种中，只有七个基因过度表达（CISH、SPP1、TUBA8、ATP6V1C2、IGKC、预测的LOC100510960和LOC100626400），它们在例如细胞凋亡的负调控、免疫反应、细胞间信号传导、细胞生长和迁移以及代谢过程中发挥重要作用。大多数选定基因的功能与所研究品种的表型变异一致；因此，我们提出了一组新的候选基因，它们可能与猪的重要经济性状相关。
