Weighted gene coexpression network analysis-based identification of key modules and hub genes associated with drought sensitivity in rice

Abstract

Background: Drought stress is an adverse factor with deleterious effects on several aspects of rice growth. However, the mechanism underlying drought resistance in rice remains unclear. To understand the molecular mechanism of the drought response in rice, drought-sensitive CSSL (Chromosome Single-substitution Segment Line) PY6 was used to map QTLs of sensitive phenotypes and to reveal the impact of the QTLs on transcriptional profiling.Results: The QTL dss-1 was mapped onto the short arm of chromosome 1 of rice. According to transcriptomic analysis, the identified differentially expressed genes (DEGs) exhibited a downregulated pattern and were mainly enriched in photosynthesis-related GO terms, indicating that photosynthesis was greatly inhibited under drought. Further, according to weighted gene coexpression network analysis (WGCNA), specific gene modules (designating a group of genes with a similar expression pattern) were strongly correlated with H2O2 (4 modules) and MDA (3 modules), respectively. Likewise, GO analysis revealed that the photosynthesis-related GO terms were consistently overrepresented in H2O2-correlated modules. Functional annotation of the differentially expressed hub genes (DEHGs) in the H2O2 and MDA-correlated modules revealed cross-talk between abiotic and biotic stress responses for these genes, which were annotated as encoding WRKYs and PR family proteins, were notably differentially expressed between PY6 and PR403.Conclusions: We speculated that drought-induced photosynthetic inhibition leads to H2O2 and MDA accumulation, which can then trigger the reprogramming of the rice transcriptome, including the hub genes involved in ROS scavenging, to prevent oxidative stress damage. Our results shed light on and provide deep insight into the drought resistance mechanism in rice.

Comparative transcriptomic analyses of two sugarcane Saccharum L. cultivars differing in drought tolerance

“…(2018) reported that drought inhibits photosynthesis; further, MAPK cascades modulate plant tolerance to drought ( Bashir et al., 2019 ). Drought can also affect the levels of secondary plant metabolites such as calcium, anthocyanins, flavonoids, phenolic acids, chlorophyll and saponins ( Yu et al., 2020 ; Contiliani et al., 2022 ; Yang et al., 2022 ). Wan et al.…”

“…Weighted correlation network analysis has been an important method used in previous studies on plant drought resistance ( Yu et al., 2020 ; Cao et al., 2021 ). In Arabidopsis thaliana , both blue and salmon modules responded to drought ( Sharma et al., 2018 ).…”

“…Many other physiological and metabolic processes in plants are involved in the drought stress response; Takahashi et al (2018) reported that drought inhibits photosynthesis; further, MAPK cascades modulate plant tolerance to drought (Bashir et al, 2019). Drought can also affect the levels of secondary plant metabolites such as calcium, anthocyanins, flavonoids, phenolic acids, chlorophyll and saponins (Yu et al, 2020;Contiliani et al, 2022;. Wan et al (2021) found that changes in the cyanoamino acid metabolism pathway might be a key factor causing the difference in drought resistance between two cherry rootstocks.…”