Network-based analysis of crucial genes for salt tolerance in rice

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ID: 317508
2026
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Ranked #247 of 501 articles by views in Plant physiology and biochemistry : PPB

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Abstract
Abstract Rice responds to salt stress by modulating a vast array of genes integrated into a sophisticated regulatory network. This complexity makes it challenging to identify the key genes and the specific alleles that confer tolerance. We used time-course expression analysis to profile gene and miRNA expression associated with salt tolerance in Pokkali, a salt-tolerant rice variety. We established a framework for studying transcription factor-target(mRNA/miRNA) interactions using gene co-expression and machine-learning models. Moreover, we developed a hypergeometric distribution-based method to elucidate the interactions of salt stress-related miRNA-targets. Using these approaches, we established co-expression (GCN) and gene regulatory networks (GRN) based on co-expression and TF/miRNA-target interactions. Hub genes with high connectivity in our networks were enriched for previously reported salt tolerance genes, a finding largely supported by subsequent haplotype analysis of 374 rice accessions. Finally, we functionally validated three crucial hub genes, OsCAF1B, OsADR3 and Ospdr9, by demonstrating their roles in salt tolerance using their knockout mutants. The crucial genes, haplotypes and networks for salt tolerance identified in this study (resource available at https://cbi.njau.edu.cn/RiceSALTnet) provide a foundation for breeding rice cultivars with enhanced salt tolerance.
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openalex_W7164911713 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Lulu Li, Yang Long, Yamin Nie, Xueai Zhu, Liu Y, Dan Ding, Jianbo Li, Xianglei Wei, Yiming Xia, Weihua Qiao, Ji Huang
Journal Plant physiology and biochemistry : PPB
Year 2026
DOI
10.1093/plphys/kiag383
URL
https://doi.org/10.1093/plphys/kiag383
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