Transcriptomic reprogramming of rice cultivars in response to herbicide, salt and their combined stresses

Abstract

With the frequent fluctuations in global climate, plants are increasingly exposed to co-occurring abiotic stresses, which have adverse effects on plant growth and productivity. In order to understand the transcriptional responses of contrasting rice cultivars to combined stresses, we conducted transcriptome sequencing of rice seedlings grown under herbicide (2,4-Dichlorophenoxyacetic acid) and salinity (NaCl) treatments, both individually and in combination. The results revealed that the individual herbicide treatment alone led to the differential expression of genes related to herbicide response (such as Cytochrome P450), hormones regulation (including auxin, ethylene and abscisic acid), and glutathione metabolism, with unique patterns observed in each cultivar. Under saline stress, the resistant cultivar exhibited fewer unique stress-regulated differentially expressed genes (DEGs), while the sensitive cultivar showed increased expression of cation transporters compared to the resistant cultivar. The sensitive cultivar demonstrated greater susceptibility under the combined stress treatment, which was attributed to the malfunctioning of herbicide detoxification genes and the upregulation of key cation transporters (i.e. OsCNGCs, OsHKTs), resulting in unregulated Na+ accumulation and oxidative toxicity in plants. Conversely, the resistant cultivar exhibited enrichment and activation of salt responsive DEGs associated with stress response, osmotic stress, and redox balance. Functional analysis of the DEGs also indicated an interconnected relationship between oxidative metabolism and cation transporters, which are dynamically coordinated to maintain optimal cellular redox and ion balance. This coordination enables the initiation of proper signaling mechanisms to induce plant acclimation to individual or combined salinity and herbicide stresses.