Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
Int J Mol Sci. 2024 Oct 16;25(20):11086. doi: 10.3390/ijms252011086.
RNA-sequencing enables the comprehensive detection of gene expression levels at specific time points and facilitates the identification of stress-related genes through co-expression network analysis. Understanding the molecular mechanisms and identifying key genes associated with salt tolerance is crucial for developing rice varieties that can thrive in saline environments, particularly in regions affected by soil salinization. In this study, we conducted an RNA-sequencing-based time-course transcriptome analysis of 'Jao Khao', a salt-tolerant Thai rice variety, grown under normal or saline (160 mM NaCl) soil conditions. Leaf samples were collected at 0, 3, 6, 12, 24, and 48 h. In total, 36 RNA libraries were sequenced. 'Jao Khao' was found to be highly salt-tolerant, as indicated by the non-significant differences in relative water content, cell membrane stability, leaf greenness, and chlorophyll fluorescence over a 9-day period under saline conditions. Plant growth was slightly retarded during days 3-6 but recovered by day 9. Based on time-series transcriptome data, we conducted differential gene expression and weighted gene co-expression network analyses. Through centrality change from normal to salinity network, 111 key hub genes were identified among 1,950 highly variable genes. Enriched genes were involved in ATP-driven transport, light reactions and response to light, ATP synthesis and carbon fixation, disease resistance and proteinase inhibitor activity. These genes were upregulated early during salt stress and RT-qPCR showed that 'Jao Khao' exhibited an early upregulation trend of two important genes in energy metabolism: RuBisCo () and ATP synthase (). Our findings highlight the importance of managing energy requirements in the initial phase of the plant salt-stress response. Therefore, manipulation of the energy metabolism should be the focus in plant resistance breeding and the genes identified in this work can serve as potentially effective candidates.
RNA 测序能够全面检测特定时间点的基因表达水平，并通过共表达网络分析鉴定与应激相关的基因。了解与盐度耐受性相关的分子机制和关键基因对于开发能够在盐环境中茁壮成长的水稻品种至关重要，特别是在受土壤盐化影响的地区。在这项研究中，我们对耐盐泰国水稻品种“Jao Khao”进行了基于 RNA 测序的时间过程转录组分析，该品种在正常或盐（160mM NaCl）土壤条件下生长。在 0、3、6、12、24 和 48 小时采集叶片样本。总共测序了 36 个 RNA 文库。在盐胁迫条件下，“Jao Khao”在 9 天内相对水含量、细胞膜稳定性、叶片绿色度和叶绿素荧光没有显著差异，表明其具有高度的耐盐性。在第 3-6 天，植物生长略有滞后，但在第 9 天恢复。基于时间序列转录组数据，我们进行了差异基因表达和加权基因共表达网络分析。通过从正常到盐网络的中心性变化，在 1950 个高变基因中鉴定出 111 个关键枢纽基因。富集基因参与 ATP 驱动的运输、光反应和对光的反应、ATP 合成和碳固定、疾病抗性和蛋白酶抑制剂活性。这些基因在盐胁迫早期上调，RT-qPCR 显示“Jao Khao”在能量代谢的两个重要基因中表现出早期上调趋势：RuBisCo（）和 ATP 合酶（）。我们的研究结果强调了在植物盐胁迫反应的初始阶段管理能量需求的重要性。因此，能量代谢的调控应该是植物抗性育种的重点，本研究中鉴定的基因可以作为潜在有效的候选基因。
