Comparative Tiller-Bud Transcriptomics Analyses Reveal OsNAC4-Associated Regulation of Salt Tolerance and Tillering...

Salt-induced inhibition of tillering constrains rice plant architecture and yield potential. To clarify the molecular links between salt tolerance and tiller development, we compared physiological responses and tiller-bud transcriptomes of the salt-tolerant japonica cultivar Nipponbare (NIP) and the salt-susceptible cultivar Kongyu 131 (KY131) under salt stress. Time-resolved RNA sequencing revealed cultivar-specific transcriptional dynamics, suggesting that rapid acclimation and transcriptome stabilisation in tiller buds contribute to salt tolerance. Functional enrichment highlighted redox regulation, phenylpropanoid metabolism, chlorophyll biosynthesis, nitrogen metabolism, and phytohormone signalling as key processes coordinating salt adaptation and tiller-bud development. Co-expression analysis identified the NAC transcription factor OsNAC4 as a central regulatory hub. Functional analyses showed that OsNAC4 negatively regulates rice salt tolerance and tillering. Loss-of-function Osnac4 mutants exhibited enhanced salt tolerance, reduced ROS accumulation and membrane damage, increased antioxidant enzyme activities, and higher tiller number. Further analysis indicated that OsNAC4 functions as a transcriptional activator of stress-, redox-, metabolic-, and ABA-associated pathways, with OsNCED5 implicated as a downstream target mediating salt-induced ABA accumulation. Through integrated transcriptomic, physiological, and genetic evidence from comparative analyses, this study establishes a molecular connection between salt adaptation and rice tiller development and identifies candidate targets for breeding salt-tolerant rice with improved architecture.