Transcriptomic responses under combined bacterial blight and drought stress in rice reveal potential genes to improve multi-stress tolerance

Abstract

Background The unprecedented drought and frequent occurrence of pathogen infection in rice is becoming more due to climate change. Simultaneous occurrence of stresses lead to more crop loss. To cope up multiple stresses, the durable resistant cultivars needs to be developed, by identifying relevant genes from combined biotic and abiotic stress exposed plants. Results We studied the effect of drought stress, bacterial leaf blight disease causing Xanthomonas oryzae pv. oryzae (Xoo) pathogen infection and combined stress in contrasting BPT5204 and TN1 rice genotypes. Mild drought stress increased Xoo infection irrespective of the genotype. To identify relevant genes that could be used to develop multi-stress tolerant rice, RNA sequencing from individual drought, pathogen and combined stresses in contrasting genotypes has been developed. Many important genes are identified from resistant genotype and diverse group of genes are differentially expressed in contrasting genotypes under combined stress. Further, a meta-analysis from individual drought and Xoo pathogen stress from public domain data sets narrowed- down candidate differentially expressed genes. Many translation associated genes are differentially expressed suggesting their extra-ribosomal function in multi-stress adaptation. Overexpression of many of these genes showed their relevance in improving stress tolerance in rice by different scientific groups. In combined stress, many downregulated genes also showed their relevance in stress adaptation when they were over-expressed. Conclusions Our study identifies many important genes, which can be used as molecular markers and targets for genetic manipulation to develop durable resistant rice cultivars. Strategies should be developed to activate downregulated genes, to improve multi-stress tolerance in plants.

Exogenous application of nanocarrier‐mediated double‐stranded RNA manipulates physiological traits and defence response against bacterial diseases

“…The predicted off‐target DEK domain‐containing chromatin‐associated protein‐encoding transcripts were unaltered in all plants (Figure 6c). Expression of another off‐target gene, RPS12 , involved in the pathogen defence response (Pal et al., 2022), was not changed in dsRNA‐CPP6‐treated plants (Figure 6d). We anticipated that silencing of SDIR1 in rice through dsRNA should also provide resistance against BLB caused by Xoo.…”

“…Plant‐pathogenic bacteria can destroy whole crops if not controlled, they secrete effectors to hijack plant mechanisms to cause virulence (Ramu, Oh, et al., 2021). Many negative regulators are upregulated during pathogen infections along with effector‐hijacked genes (Pal et al., 2022). Much evidence has been reported on possible target genes for virus, insect and fungal resistance (Rank & Koch, 2021); however, no study has reported targeting plant genes to improve bacterial disease resistance.…”

“…Expression of another off-target gene, RPS12, involved in the pathogen defence response (Pal et al, 2022), was not changed in dsRNA-CPP6-treated plants (Figure 6d). We anticipated that silencing of SDIR1 in rice through dsRNA should also provide resistance against BLB caused by Xoo.…”

“…Therefore, there is a demand for alternative ways to control pathogenicity and to improve agronomic traits. Several genes may be targeted to manipulate plant growth and improve resistance against Xoo (Bakade et al., 2021; Pal et al., 2022; Vemanna et al., 2019). Overexpression of transcription factor OsWRKY62 compromised the basal defence and Xa21 ‐mediated resistance to Xoo (Peng et al., 2008).…”

Deciphering acclimation strategies to combined abiotic stresses in Arabidopsis thaliana

“…Accordingly, the stress magnitude, order and duration play crucial roles in determining the morpho-physiological outcomes of combinatorial stresses (Mittler, 2006a;Anwar et al, 2021a;Nadeem et al, 2022). Stress magnitude refers to the relative or absolute intensity of individual stressors, such as the absolute temperature during heat or cold stress (Praat et al, 2021;Zhu et al, 2022a), the soil water content during drought stress (Ma et al, 2014), light availability during submergence (Mohanty, 2003;Vashisht et al, 2011;Sasidharan et al, 2018), or the days post infection (dpi) during pathogenesis (Pal et al, 2022). Additionally, the number of co-existing stressors during a combinatorial stress scenario is also an important factor in determining the outcome for the plant.…”