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《耐盐水稻品种 Pokkali 的长链非编码 RNA 组分析》

Pokkali: A Naturally Evolved Salt-Tolerant Rice Shows a Distinguished Set of lncRNAs Possibly Contributing to the Tolerant Phenotype.

机构信息

Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.

School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.

出版信息

Int J Mol Sci. 2023 Jul 20;24(14):11677. doi: 10.3390/ijms241411677.

DOI:10.3390/ijms241411677
PMID:37511436
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10380863/
Abstract

Pokkali is a strong representation of how stress-tolerant genotypes have evolved due to natural selection pressure. Numerous omics-based investigations have indicated different categories of stress-related genes and proteins, possibly contributing to salinity tolerance in this wild rice. However, a comprehensive study towards understanding the role of long-noncoding RNAs (lncRNAs) in the salinity response of Pokkali has not been done to date. We have identified salt-responsive lncRNAs from contrasting rice genotypes IR64 and Pokkali. A total of 63 and 81 salinity-responsive lncRNAs were differentially expressed in IR64 and Pokkali, respectively. Molecular characterization of lncRNAs and lncRNA-miRNA-mRNA interaction networks helps to explore the role of lncRNAs in the stress response. Functional annotation revealed that identified lncRNAs modulate various cellular processes, including transcriptional regulation, ion homeostasis, and secondary metabolite production. Additionally, lncRNAs were predicted to bind stress-responsive transcription factors, namely ERF, DOF, and WRKY. In addition to salinity, expression profiling was also performed under other abiotic stresses and phytohormone treatments. A positive modulation in TCONS_00035411, TCONS_00059828, and TCONS_00096512 under both abiotic stress and phytohormone treatments could be considered as being of potential interest for the further functional characterization of IncRNA. Thus, extensive analysis of lncRNAs under various treatments helps to delineate stress tolerance mechanisms and possible cross-talk.

摘要

波卡利是一个强有力的代表，说明耐受压力的基因型是如何在自然选择压力下进化而来的。大量基于组学的研究表明了不同类别与应激相关的基因和蛋白质，这些可能有助于这种野生稻的耐盐性。然而，迄今为止，还没有针对了解长非编码 RNA（lncRNA）在波卡利盐度响应中的作用进行全面的研究。我们已经从对照水稻基因型 IR64 和波卡利中鉴定出了盐响应 lncRNA。IR64 和波卡利中分别有 63 个和 81 个盐响应 lncRNA 差异表达。lncRNA 和 lncRNA-miRNA-mRNA 互作网络的分子特征有助于探索 lncRNA 在应激响应中的作用。功能注释表明，鉴定出的 lncRNA 调节各种细胞过程，包括转录调控、离子稳态和次生代谢产物的产生。此外，lncRNA 被预测与应激响应转录因子 ERF、DOF 和 WRKY 结合。除了盐度之外，还在其他非生物胁迫和植物激素处理下进行了表达谱分析。在两种非生物胁迫和植物激素处理下，TCONS_00035411、TCONS_00059828 和 TCONS_00096512 的表达呈正调控，可被认为是进一步对 lncRNA 进行功能表征的潜在兴趣点。因此，在各种处理下对 lncRNA 进行广泛分析有助于描绘出耐受机制和可能的交叉对话。

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