Analysis of transcription factor regulatory networks in two-line male sterile rice seedling roots in response to salt stress

To comprehensively elucidate the transcription factor regulatory network underlying salt-stress responses in rice seedling roots, we used the rice male sterile line Huaxing 166S as material, treated seedling roots with three NaCl concentrations (0, 0.25%, and 0.50%) for one week and recorded phenotypic data. RNA-seq was then used to characterize gene expression patterns, detecting 30,378 genes, of which 26,315 were identified as significantly differentially expressed genes (DEGs). Pathway enrichment analysis showed that, across all three NaCl treatments, DEGs were significantly enriched in secondary metabolism-related pathways. Based on the DEG dataset, we further identified 326 differentially expressed transcription factors and constructed a core interaction network comprising 88 transcription factors. Functional enrichment analysis indicated that this core network was mainly involved in plant hormone signal transduction, the plant MAPK signaling pathway, and the plant circadian rhythm pathway. In addition, quantitative real-time PCR (qPCR) validation showed that, following salt stress, 10 WRKY family genes were specifically highly expressed in rice roots. Together, these transcriptome data across three NaCl concentrations define the gene expression landscape and a core transcription factor interaction network in rice seedling roots, providing a basis for dissecting the molecular regulatory mechanisms of rice root responses to salt stress.