Integrative RNA-seq and ATAC-seq analysis unveils antioxidant defense mechanisms in salt-tolerant rice variety Pokkali.

IF 4.3 2区 生物学 Q1 PLANT SCIENCES
Qiaoyu Yang, Yutong Zheng, Xitao Li
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引用次数: 0

Abstract

Background: Salt stress is one of the most significant environmental challenges, severely impacting rice growth and yield. While different rice varieties exhibit varying levels of tolerance to salinity, Pokkali, a traditional salt-tolerant variety, stands out for its ability to thrive in saline conditions. Understanding the molecular and physiological mechanisms that underpin this tolerance is essential for breeding and developing rice varieties with enhanced resilience to salt stress.

Methods: In this study, we selected the salt-tolerant rice variety Pokkali and the salt-sensitive variety IR29 for a controlled saline stress experiment. Plants were subjected to a 150 mM NaCl treatment for 7 days, after which leaf samples were collected from both varieties. Antioxidant physiological parameters were measured, and RNA-seq and ATAC-seq analyses were conducted to explore gene expression and chromatin accessibility. Key genes identified through sequencing were validated using RT-qPCR.

Results: Under salt stress, Pokkali demonstrated strong tolerance and a higher antioxidant capacity compared to IR29, as evidenced by increased survival rates and fresh weight. Pokkali also showed elevated activity of antioxidant enzymes such as superoxide dismutase, peroxidase, and catalase, along with reduced accumulation of hydrogen peroxide. Transcriptomic and ATAC-seq analyses revealed that Pokkali's upregulated genes were significantly enriched in pathways related to redox homeostasis. These genes were also involved in metabolic processes such as glycan biosynthesis, amino acid metabolism, carbohydrate metabolism, and energy production. Furthermore, ATAC-seq analysis indicated increased chromatin accessibility in the promoter regions of key antioxidant genes under salt stress in Pokkali, reflecting enhanced transcriptional activity. Four key antioxidant-related genes-MnSOD1, OsAPx7, OsGR1, and Osppc3-were identified and validated by qPCR, showing significant upregulation in Pokkali. ATAC-seq data further supported that these genes had increased promoter accessibility under salt stress, aligning with the RNA-seq findings.

Conclusion: This study underscores the critical role of antioxidant defense mechanisms in conferring salt tolerance in Pokkali. The identification of key genes involved in redox regulation provides valuable insights into the molecular basis of salt tolerance, offering potential targets for the genetic improvement of salt-sensitive rice varieties through breeding programs.

RNA-seq和ATAC-seq整合分析揭示了耐盐水稻品种Pokkali的抗氧化防御机制。
背景:盐胁迫是最重要的环境挑战之一,严重影响水稻生长和产量。虽然不同的水稻品种表现出不同程度的耐盐性,但传统的耐盐品种Pokkali因其在盐水条件下茁壮成长的能力而脱颖而出。了解支撑这种耐受性的分子和生理机制,对于培育和开发抗盐胁迫能力增强的水稻品种至关重要。方法:选择耐盐水稻品种Pokkali和盐敏感水稻品种IR29进行对照盐胁迫试验。植株接受150 mM NaCl处理7 d,之后采集两个品种的叶片样品。测定抗氧化生理参数,并进行RNA-seq和ATAC-seq分析,探讨基因表达和染色质可及性。通过测序鉴定的关键基因采用RT-qPCR进行验证。结果:在盐胁迫下,与IR29相比,Pokkali表现出更强的耐受性和更高的抗氧化能力,这可以从存活率和鲜重的增加中得到证明。Pokkali还显示,抗氧化酶(如超氧化物歧化酶、过氧化物酶和过氧化氢酶)的活性升高,同时过氧化氢的积累减少。转录组学和ATAC-seq分析显示,Pokkali上调的基因在与氧化还原稳态相关的途径中显著富集。这些基因还参与代谢过程,如聚糖生物合成、氨基酸代谢、碳水化合物代谢和能量产生。此外,ATAC-seq分析表明,盐胁迫下Pokkali关键抗氧化基因启动子区域的染色质可及性增加,反映了转录活性的增强。通过qPCR鉴定并验证了四个关键抗氧化相关基因mnsod1、OsAPx7、OsGR1和osppc3,在Pokkali中表达显著上调。ATAC-seq数据进一步支持这些基因在盐胁迫下增加启动子可及性,与RNA-seq结果一致。结论:本研究强调了抗氧化防御机制在Pokkali耐盐性中的关键作用。参与氧化还原调控的关键基因的鉴定为耐盐性的分子基础提供了有价值的见解,为通过育种计划对盐敏感水稻品种进行遗传改良提供了潜在的目标。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
BMC Plant Biology
BMC Plant Biology 生物-植物科学
CiteScore
8.40
自引率
3.80%
发文量
539
审稿时长
3.8 months
期刊介绍: BMC Plant Biology is an open access, peer-reviewed journal that considers articles on all aspects of plant biology, including molecular, cellular, tissue, organ and whole organism research.
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