Transcriptome analysis of table grapes (Vitis vinifera L.) identified a gene network module associated with berry firmness

Berry firmness is one of the main selection criteria for table grape breeding. However, the underlying genetic determinants and mechanisms involved in gene expression during berry development are still poorly understood. In this study, eighteen libraries sampled from <i>Vitis vinifera</i> L. cv. ‘Red Globe’ and ‘Muscat Hamburg’ at three developmental stages (preveraison, veraison and maturation) were analyzed by RNA sequencing (RNA-Seq). The firmness of ‘Red Globe’ was significantly higher than that of ‘Muscat Hamburg’ at the three developmental stages. In total, a set of 4,559 differentially expressed genes (DEGs) was identified between ‘Red Globe’ and ‘Muscat Hamburg’ in the preveraison (2,259), veraison (2030) and maturation stages (2682), including 302 transcription factors (TFs). Weighted gene coexpression network analysis (WGCNA) showed that 23 TFs were predicted to be highly correlated with fruit firmness and propectin content. In addition, the differential expression of the PE, PL, PG, β-GAL, GATL, WAK, XTH and EXP genes might be the reason for the differences in firmness between ‘Red Globe’ and ‘Muscat Hamburg’. The results will provide new information for analysis of grape berry firmness and softening.浆果硬度是鲜食葡萄育种的核心选择指标之一。然而，葡萄浆果发育过程中基因表达调控的潜在遗传决定因素与分子机制仍未得到充分阐释。本研究针对葡萄（Vitis vinifera L.）品种‘红地球’（Red Globe）与‘玫瑰香’（Muscat Hamburg）的三个发育阶段——转色前期、转色期、成熟期——采集的18个样本文库进行了RNA测序（RNA-Seq）分析。三个发育阶段中，红地球的浆果硬度均显著高于玫瑰香。共计在两个品种的三个发育阶段中鉴定得到4559个差异表达基因（differentially expressed genes, DEGs）：转色前期2259个、转色期2030个、成熟期2682个，其中包含302个转录因子（transcription factors, TFs）。加权基因共表达网络分析（weighted gene coexpression network analysis, WGCNA）结果显示，共有23个转录因子被预测与果实硬度及原果胶含量呈显著相关。此外，PE、PL、PG、β-GAL、GATL、WAK、XTH与EXP基因的差异表达，可能是红地球与玫瑰香浆果硬度产生差异的关键原因。本研究结果可为葡萄浆果硬度调控与软化机制的解析提供全新的理论参考。