Gedam Pranjali A, Khandagale Kiran, Shirsat Dhananjay, Thangasamy A, Kulkarni Onkar, Kulkarni Abhijeet, Patil Swaranjali S, Barvkar Vitthal T, Mahajan Vijay, Gupta Amar Jeet, Bhagat Kiran P, Khade Yogesh P, Singh Major, Gawande Suresh
Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India.
Bioinformatics Centre, Savitribai Phule Pune University, Pune, India.
Front Plant Sci. 2023 Aug 8;14:1150909. doi: 10.3389/fpls.2023.1150909. eCollection 2023.
Waterlogging is a major stress that severely affects onion cultivation worldwide, and developing stress-tolerant varieties could be a valuable measure for overcoming its adverse effects. Gathering information regarding the molecular mechanisms and gene expression patterns of waterlogging-tolerant and sensitive genotypes is an effective method for improving stress tolerance in onions. To date, the waterlogging tolerance-governing molecular mechanism in onions is unknown.
This study identified the differentially expressed genes (DEGs) through transcriptome analysis in leaf tissue of two onion genotypes (Acc. 1666; tolerant and W-344; sensitive) presenting contrasting responses to waterlogging stress.
Differential gene expression analysis revealed that in Acc. 1666, 1629 and 3271 genes were upregulated and downregulated, respectively. In W-344, 2134 and 1909 genes were upregulated and downregulated, respectively, under waterlogging stress. The proteins coded by these DEGs regulate several key biological processes to overcome waterlogging stress such as phytohormone production, antioxidant enzymes, programmed cell death, and energy production. The clusters of orthologous group pathway analysis revealed that DEGs contributed to the post-translational modification, energy production, and carbohydrate metabolism-related pathways under waterlogging stress. The enzyme assay demonstrated higher activity of antioxidant enzymes in Acc. 1666 than in W-344. The differential expression of waterlogging tolerance related genes, such as those related to antioxidant enzymes, phytohormone biosynthesis, carbohydrate metabolism, and transcriptional factors, suggested that significant fine reprogramming of gene expression occurs in response to waterlogging stress in onion. A few genes such as ADH, PDC, PEP carboxylase, WRKY22, and Respiratory burst oxidase D were exclusively upregulated in Acc. 1666.
The molecular information about DEGs identified in the present study would be valuable for improving stress tolerance and for developing waterlogging tolerant onion varieties.
涝害是一种严重影响全球洋葱种植的主要胁迫，培育耐胁迫品种可能是克服其不利影响的一项重要措施。收集耐涝和敏感基因型的分子机制及基因表达模式的信息是提高洋葱胁迫耐受性的有效方法。迄今为止，洋葱中耐涝性的分子调控机制尚不清楚。
本研究通过转录组分析，在两种对涝害胁迫表现出不同反应的洋葱基因型（Acc. 1666，耐涝；W-344，敏感）的叶片组织中鉴定差异表达基因（DEGs）。
差异基因表达分析显示，在Acc. 1666中，分别有1629个和3271个基因上调和下调。在W-344中，涝害胁迫下分别有2134个和1909个基因上调和下调。这些DEGs编码的蛋白质调节多个关键生物学过程以克服涝害胁迫，如植物激素产生、抗氧化酶、程序性细胞死亡和能量产生。直系同源簇途径分析表明，DEGs在涝害胁迫下参与翻译后修饰、能量产生和碳水化合物代谢相关途径。酶活性测定表明，Acc. 1666中的抗氧化酶活性高于W-344。与耐涝相关基因的差异表达，如与抗氧化酶、植物激素生物合成、碳水化合物代谢和转录因子相关的基因，表明洋葱在响应涝害胁迫时发生了显著的基因表达精细重编程。一些基因如乙醇脱氢酶（ADH）、丙酮酸脱羧酶（PDC）、磷酸烯醇式丙酮酸羧化酶（PEP羧化酶）、WRKY22和呼吸爆发氧化酶D仅在Acc. 1666中上调。
本研究中鉴定的DEGs的分子信息对于提高胁迫耐受性和培育耐涝洋葱品种具有重要价值。
