Variety-specific transcriptional and alternative splicing regulations modulate salt tolerance in rice from early stage of stress

Guihua Jian, Yujian Mo, Yan Hu, Yongxiang Huang, Lei Ren, Yueqin Zhang, Hanqiao Hu, Shuangxi Zhou, Gang Liu, Jianfu Guo*, Yu Ling*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    6 Citations (Scopus)
    27 Downloads (Pure)


    Salt stress poses physiological drought, ionic toxicity and oxidative stress to plants, which causes premature senescence and death of the leaves if the stress sustained. Salt tolerance varied between different rice varieties, but how different rice varieties respond at the early stage of salt stress has been seldom studied comprehensively. By employing third generation sequencing technology, we compared gene expressional changes in leaves of three rice varieties that varied in their level of tolerance after salt stress treatment for 6 h. Commonly up-regulated genes in all rice varieties were related to water shortage response and carbon and amino acids metabolism at the early stage of salt stress, while reactive oxygen species cleavage genes were induced more in salt-tolerant rice. Unexpectedly, genes involved in chloroplast development and photosynthesis were more significantly down-regulated in the two salt tolerant rice varieties ‘C34’ and ‘Nona Bokra’. At the same time, genes coding ribosomal protein were suppressed to a more severe extent in the salt-sensitive rice variety ‘IR29’. Interestingly, not only variety-specific gene transcriptional regulation, but also variety-specific mRNA alternative splicing, on both coding and long-noncoding genes, were found at the early stage of salt stress. In summary, differential regulation in gene expression at both transcriptional and post-transcriptional levels, determine and fine-tune the observed response in level of damage in leaves of specific rice genotypes at early stage of salt stress.

    Original languageEnglish
    Article number56
    Pages (from-to)1-21
    Number of pages21
    Issue number1
    Publication statusPublished - 3 Nov 2022

    Bibliographical note

    Copyright the Author(s) 2022. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.


    • Chloroplast
    • Gene expression
    • mRNA alternative splicing
    • Rice
    • ROS
    • Salt stress


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