Increased Drought Resistance 1 Mutation Increases Drought Tolerance of Upland Rice by Altering Physiological and Morphological Traits and Limiting ROS Levels

Deciphering molecular regulation of reactive oxygen species (ROS) and reactive nitrogen species (RNS) signalling networks in Oryza genus amid environmental stress

The Oryza genus, containing Oryza sativa L., is quintessential to sustain global food security. This genus has a lot of sophisticated molecular mechanisms to cope with environmental stress, particularly during vulnerable stages like flowering. Recent studies have found key involvements and genetic modifications that increase resilience to stress, including exogenous application of melatonin, allantoin, and trehalose as well as OsSAPK3 and OsAAI1 in the genetic realm. Due to climate change and anthropogenic reasons, there is a rise in sea level which raises a concern of salinity stress. It is tackled through osmotic adjustment and ion homeostasis, mediated by genes like P5CS, P5CR, GSH1, GSH2, and SPS, and ion transporters like NHX, NKT, and SKC, respectively. Oxidative damage is reduced by a complex action of antioxidants, scavenging RONS. A complex action of genes mediates cold stress with studies highlighting the roles of OsWRKY71, microRNA2871b, OsDOF1, and OsICE1. There is a need to research the mechanism of action of proteins like OsRbohA in ROS control and the action of regulatory genes in stress response. This is highly relevant due to the changing climate which will raise a lot of environmental changes that will adversely affect production and global food security if certain countermeasures are not taken. Overall, this study aims to unravel the molecular intricacies of ROS and RNS signaling networks in Oryza plants under stress conditions, with the ultimate goal of informing strategies for enhancing stress tolerance and crop performance in this important agricultural genus.

Analysis of drought and heat stress response genes in rice using co-expression network and differentially expressed gene analyses

Studies on Oryza sativa (rice) are crucial for improving agricultural productivity and ensuring global sustenance security, especially considering the increasing drought and heat stress caused by extreme climate change. Currently, the genes and mechanisms underlying drought and heat resistance in rice are not fully understood, and the scope for enhancing the development of new strains remains considerable. To accurately identify the key genes related to drought and heat stress responses in rice, multiple datasets from the Gene Expression Omnibus (GEO) database were integrated in this study. A co-expression network was constructed using a Weighted Correlation Network Analysis (WGCNA) algorithm. We further distinguished the core network and intersected it with differentially expressed genes and multiple expression datasets for screening. Differences in gene expression levels were verified using quantitative real-time polymerase chain reaction (PCR). OsDjC53, MBF1C, BAG6, HSP23.2, and HSP21.9 were found to be associated with the heat stress response, and it is also possible that UGT83A1 and OsCPn60a1, although not directly related, are affected by drought stress. This study offers significant insights into the molecular mechanisms underlying stress responses in rice, which could promote the development of stress-tolerant rice breeds.

Extra-large G proteins have extra-large effects on agronomic traits and stress tolerance in maize and rice

Heterotrimeric G proteins - comprising Gα, Gβ, and Gγ subunits - are ubiquitous elements in eukaryotic cell signaling. Plant genomes contain both canonical Gα subunit genes and a family of plant-specific extra-large G protein genes (XLGs) that encode proteins consisting of a domain with Gα-like features downstream of a long N-terminal domain. In this review we summarize phenotypes modulated by the canonical Gα and XLG proteins of arabidopsis and highlight recent studies in maize and rice that reveal dramatic phenotypic consequences of XLG clustered regularly interspaced short palindromic repeats (CRISPR) mutagenesis in these important crop species. XLGs have both redundant and specific roles in the control of agronomically relevant plant architecture and resistance to both abiotic and biotic stresses. We also point out areas of current controversy, suggest future research directions, and propose a revised, phylogenetically-based nomenclature for XLG protein genes.

The Mechanism of Manganese Ferrite Nanomaterials Promoting Drought Resistance in Rice

Strategies to reduce the risk of drought damage are urgently needed as intensified climate change threatens agricultural production. One potential strategy was using nanomaterials (NMs) to enhance plant resistance by regulating various physiological and biochemical processes. In the present study, 10 mg kg^-1 manganese ferrite (MnFe₂O₄) NMs had the optimal enhancement to elevate the levels of biomass, photosynthesis, nutrient elements, and polysaccharide in rice by 10.9-525.0%, respectively, under drought stress. The MnFe₂O₄ NMs were internalized by rice plants, which provided the possibility for rice to better cope with drought. Furthermore, as compared with drought control and equivalent ion control, the introduction of MnFe₂O₄ NMs into the roots significantly upregulated the drought-sensing gene CLE25 (29.4%) and the receptor gene NCED3 (59.9%). This activation stimulated downstream abscisic acid, proline, malondialdehyde, and wax biosynthesis by 23.3%, 38.9%, 7.2%, and 26.2%, respectively. In addition, 10 mg·kg^-1 MnFe₂O₄ NMs significantly upregulated the relative expressions of OR1, AUX2, AUX3, PIN1a, and PIN2, and increased IAA content significantly, resulting in an enlarged root angle and a deeper and denser root to help the plant withstand drought stresses. The nutritional quality of rice grains was also improved. Our study provides crucial insight for developing nano-enabled strategies to improve crop productivity and resilience to climate change.

Genome-wide discovery of genetic variations between rice cultivars with contrasting drought stress response and their potential functional relevance

Drought stress is a serious threat to rice productivity. Investigating genetic variations between drought-tolerant (DT) and drought-sensitive (DS) rice cultivars may decipher the candidate genes/regulatory regions involved in drought stress tolerance/response. In this study, whole-genome resequencing data of four DS and five DT rice cultivars were analyzed. We identified a total of approximately 4.8 million single nucleotide polymorphisms (SNPs) and 0.54 million insertions/deletions (InDels). The genetic variations (162,638 SNPs and 17,217 InDels) differentiating DS and DT rice cultivars were found to be unevenly distributed throughout the rice genome; however, they were more frequent near the transcription start and stop sites than in the genic regions. The cis-regulatory motifs representing the binding sites of stress-related transcription factors (MYB, HB, bZIP, ERF, ARR, and AREB) harboring the SNPs/InDels in the promoter regions of a few differentially expressed genes (DEGs) were identified. Importantly, many of these DEGs were located within the drought-associated quantitative trait loci. Overall, this study provides a valuable large-scale genotyping resource and facilitates the discovery of candidate genes associated with drought stress tolerance in rice.

Pseudouridylation of chloroplast ribosomal RNA contributes to low temperature acclimation in rice

Ribosomal RNAs (rRNAs) undergo many modifications during transcription and maturation; homeostasis of rRNA modifications is essential for chloroplast biogenesis in plants. The chloroplast acts as a hub to sense environmental signals, such as cold temperature. However, how RNA modifications contribute to low temperature responses remains unknown. Here we reveal that pseudouridine (Ψ) modification of rice chloroplast rRNAs mediated by the pseudouridine synthase (OsPUS1) contributes to cold tolerance at seedling stage. Loss-function of OsPUS1 leads to abnormal chloroplast development and albino seedling phenotype at low temperature. We find that OsPUS1 is accumulated upon cold and binds to chloroplast precursor rRNAs (pre-rRNAs) to catalyse the pseudouridylation on rRNA. These modifications on chloroplast rRNAs could be required for their processing, as the reduction of mature chloroplast rRNAs and accumulation of pre-rRNAs are observed in ospus1-1 at low temperature. Therefore, the ribosome activity and translation in chloroplasts is disturbed in ospus1-1. Furthermore, transcriptome and translatome analysis reveals that OsPUS1 balances growth and stress-responsive state, preventing excess reactive oxygen species accumulation. Taken together, our findings unveil a crucial function of Ψ in chloroplast ribosome biogenesis and cold tolerance in rice, with potential applications in crop improvement.

Gene Co-Expression Analysis Reveals Transcriptome Divergence between Wild and Cultivated Sugarcane under Drought Stress

Drought is the main abiotic stress that constrains sugarcane growth and production. To understand the molecular mechanisms that govern drought stress, we performed a comprehensive comparative analysis of physiological changes and transcriptome dynamics related to drought stress of highly drought-resistant (ROC22, cultivated genotype) and weakly drought-resistant (Badila, wild genotype) sugarcane, in a time-course experiment (0 h, 4 h, 8 h, 16 h and 32 h). Physiological examination reviewed that ROC22, which shows superior drought tolerance relative to Badila, has high performance photosynthesis and better anti-oxidation defenses under drought conditions. The time series dataset enabled the identification of important hubs and connections of gene expression networks. We identified 36,956 differentially expressed genes (DEGs) in response to drought stress. Of these, 15,871 DEGs were shared by the two genotypes, and 16,662 and 4423 DEGs were unique to ROC22 and Badila, respectively. Abscisic acid (ABA)-activated signaling pathway, response to water deprivation, response to salt stress and photosynthesis-related processes showed significant enrichment in the two genotypes under drought stress. At 4 h of drought stress, ROC22 had earlier stress signal transduction and specific up-regulation of the processes response to ABA, L-proline biosynthesis and MAPK signaling pathway–plant than Badila. WGCNA analysis used to compile a gene regulatory network for ROC22 and Badila leaves exposed to drought stress revealed important candidate genes, including several classical transcription factors: NAC87, JAMYB, bHLH84, NAC21/22, HOX24 and MYB102, which are related to some antioxidants and trehalose, and other genes. These results provide new insights and resources for future research and cultivation of drought-tolerant sugarcane varieties.