Drought-sensitive Rice Research Articles

Morphological, physiological, and biochemical responses of rice (Oryza sativa L.) varieties to drought stress via regulating respiration and ROS metabolism during germination

Germination marks a pivotal and sensitive phase in the life cycle of crops, with drought stress, precipitated by water scarcity, posing a significant impediment to the germination process in rice. Despite this, the regulation mechanism of respiratory and reactive oxygen species (ROS) metabolism during rice germination under drought stress remains to be fully elucidated. This manuscript presents an integrative analysis encompassing morphological, physiological, biochemical, and molecular attributes of germinated seeds from a cultivated drought-sensitive rice variety (JN10) and a drought-resistant rice variety (NG36). Our findings revealed that drought stress adversely affected the germination of both rice varieties, with NG36 exhibiting a more rapid germination rate compared to JN10 under such stress conditions. This differential response was attributed to the heightened activity of key enzymes, elevated levels of metabolic intermediates, and upregulated expression of genes encoding enzymes involved in ROS and respiratory metabolic pathways in NG36. To further dissect the interplay between these metabolic pathways, we selected specific enzyme activities for detailed examination. Notably, a robust positive linear correlation was established among phosphofructokinase (PFK), α-ketoglutarate dehydrogenase (KGDH), citrate synthase (CS), and isocitrate dehydrogenase (ICDH) in NG36. This correlation underscores the pivotal role of glycolytic pathways, particularly the tricarboxylic acid (TCA) cycle, in conferring drought resistance to NG36 during the germination phase under drought stress. To encapsulate our findings, the results of this investigation suggest that the rice cultivar NG36 manifests a heightened degree of drought tolerance relative to JN10. This is primarily achieved through the adept modulation of its respiratory metabolic pathways and the stringent preservation of ROS homeostasis during the germination phase under conditions of water deficit. These revelations provide unprecedented insights into the intricate regulatory mechanisms that subserve rice's drought resistance, potentially paving the way for the development of novel strategies in the breeding of rice cultivars with improved drought resilience.

Influence of polyethylene glycol, sodium nitroprusside, and carbon sources on in vitro callus induction and regeneration in drought-tolerant and drought-sensitive rice (Oryza sativa L.)

Influence of polyethylene glycol, sodium nitroprusside, and carbon sources on in vitro callus induction and regeneration in drought-tolerant and drought-sensitive rice (Oryza sativa L.)

Moderate alternate wetting and drying irrigation enhances drought-resistance abilities by improving structural mesophyll conductance of water-saving and drought-resistant rice under severe drought.

Water-saving and drought-resistant rice (WDR) coupled with alternate wetting and drying irrigation (AWDI) possesses a high photosynthetic potential due to higher mesophyll conductance (gm) under drought conditions. However, the physiological and structural contributions to the gm of leaves and their mechanisms in WDR under AWDI are still unclear. In this study, WDR (Hanyou 73) and drought-sensitive rice (Huiliangyou 898) were selected as materials. Three irrigation patterns were established from transplanting to the heading stage, including conventional flooding irrigation (W1), moderate AWDI (W2), and severe AWDI (W3). A severe drought with a soil water potential of -50 kPa was applied for a week at the heading stage across all treatments and cultivars. The results revealed that severe drought reduced gas exchange parameters and gm but enhanced antioxidant enzyme activities and malondialdehyde content in the three treatments and both cultivars. The maximal photosynthetic rate (Amax) of HY73 in the W2 treatment was greater than that in the other combinations of cultivars and irrigation patterns. The contribution of leaf structure (54%) to gm (gm-S, structural gm) was higher than that of leaf physiology (46%) to gm (gm-P, physiological gm) in the W2 treatment of Hanyou 73. Additionally, gm-S was significantly and linearly positively correlated with gm under severe drought. Moreover, both the initial and apparent quantum efficiencies were significantly and positively with gm in rice plants (p < 0.05). These results suggest that the improvements in photosynthesis and yield in the WDR combined with moderate AWDI can mainly be attributed to the enhancement of gm-S under severe drought conditions. Quantum efficiency may be a potential factor in regulating photosynthesis by cooperating with the gm of rice plants under severe drought conditions.

A detailed study on genetic diversity, antioxidant machinery, and expression profile of drought-responsive genes in rice genotypes exposed to artificial osmotic stress

Seasonal variations in rainfall patterns, particularly during sowing, early growing season, and flowering, drastically affect rice production in northeastern India. However, sensitivity to drought stress is genotype-specific. Since 80% of the land in this region is used for rice production, it is crucial to understand how they have adapted to water stress. This study evaluated 112 rice genotypes grown in NE India for seed germination percentage and seedling development under PEG-mediated drought stress. Among the rice genotype, Sahbhagi dhan, RCPL-1-82, Bhalum-3 and RCPL-1-128 showed drought-tolerant traits, while Ketaki Joha, Chakhao, Chandan, RCPL-1-185 and IR-64 were the most drought-sensitive rice genotypes. Drought-tolerant rice also showed significantly higher seed germination potential, proline content, antioxidant activity and expression of drought-responsive genes than drought-sensitive rice genotypes. A similar expression pattern of genes was also observed in the rice genotype treated with a 50% water deficit in pot culture. In addition, drought stress reduced the pollen fertility and yield per plant in sensitive rice genotypes. Molecular markers associated with drought stress were also used to characterize genetic diversity among the rice genotypes studied.

Integrated transcriptome, proteome and metabolome analyses revealed secondary metabolites and auxiliary carbohydrate metabolism augmenting drought tolerance in rice

Drought is one of the major consequences of climate change and a serious threat to rice production. Drought stress activates interactions among genes, proteins and metabolites at the molecular level. A comparative multi-omics analysis of drought-tolerant and drought-sensitive rice cultivars can decipher the molecular mechanisms involved in drought tolerance/response. Here, we characterized the global-level transcriptome, proteome, and metabolome profiles, and performed integrated analyses thereof in a drought-sensitive (IR64) and a drought-tolerant (Nagina 22) rice cultivar under control and drought-stress conditions. The transcriptional dynamics and its integration with proteome analysis revealed the role of transporters in regulation of drought stress. The proteome response illustrated the contribution of translational machinery to drought tolerance in N22. The metabolite profiling revealed that aromatic amino acids and soluble sugars contribute majorly to drought tolerance in rice. The integrated transcriptome, proteome and metabolome analysis performed using statistical and knowledge-based methods revealed the preference for auxiliary carbohydrate metabolism through glycolysis and pentose phosphate pathway contributed to drought tolerance in N22. In addition, L-phenylalanine and the genes/proteins responsible for its biosynthesis were also found to contribute to drought tolerance in N22. In conclusion, our study provided mechanistic insights into the drought response/adaptation mechanism and is expected to facilitate engineering of drought tolerance in rice.

Delineating the tissue-mediated drought stress governed tuning of conserved miR408 and its targets in rice.

Engineering drought tolerance in rice needs to focus on regulators that enhance tolerance while boosting plant growth and vigor. The present study delineated the concealed function and tissue-mediated interplay of the miR408/target module in imparting drought stress tolerance in rice. The plant miR408 family comprises three dominant mature forms (21 nt), including a distinct monocot variant (F-7 with 5' C) and is divided into six groups. miR408 majorly cleaves genes belonging to the blue copper protein in addition to several other species-specific targets in plants. Comparative sequence analysis in 4726 rice accessions identified 22 sequence variants (SNP and InDELs) in its promoter (15) and pre-miR408 region. Haplotype analysis of the sequence variants indicated eight haplotypes (three: Japonica-specific and five: Indica-specific) of the miR408 promoter. In drought-tolerant Nagina 22, miR408 follows flag leaf preferential expression. Under drought conditions, its levels are upregulated in flag leaf and roots which seems to be regulated by a differential fraction of methylated cytosines (mCs) in the precursor region. The active pool of miR408 regulated targets under control and drought conditions is impacted by the tissue type. Comparative expression analysis of the miR408/target module under different sets of conditions features 83 targets exhibiting antagonistic expression in rice, out of which 12 genes, including four PLANTACYANINS (OsUCL6, 7, 9 and 30), PIRIN, OsLPR1, OsCHUP1, OsDOF12, OsBGLU1, glycine-rich cell wall gene, OsDUT, and OsERF7, are among the high confidence targets. Further, overexpression of MIR408 in drought-sensitive rice cultivar (PB1) leads to the massive enhancement of vegetative growth in rice with improved ETR and Y(II) and enhanced dehydration stress tolerance. The above results suggest that miR408 is likely to act as a positive regulator of growth and vigor, as well as dehydration stress, making it a potential candidate for engineering drought tolerance in rice.

Phosphoprotein Profile of Rice (Oryza sativa L.) Seedlings under Osmotic Stress after Pretreatment with Chitosan.

This study aims to identify novel chitosan (CTS)-responsive phosphoproteins in Leung Pratew 123 (LPT123) and Khao Dawk Mali 105 (KDML105) as drought-sensitive rice cultivars and differences in the CTS response. Rice seeds were soaked in CTS solution before germination, and 2- and 4-week-old rice seedlings sprayed with CTS before osmotic stress comprised the following four groups: (1) seedlings treated with distilled water; (2) seedlings treated with CTS; (3) seedlings pretreated with distilled water and subjected to osmotic stress; and (4) seedlings pretreated with CTS and subjected to osmotic stress. Phosphoproteins of leaf tissues were enriched using immobilized metal affinity chromatography (IMAC) before tryptic digestion and analysis via LC-MS. Phosphoprotein profiling analyses led to the identification of 4721 phosphoproteins representing 1052 and 1040 unique phosphoproteins in the LPT123 and KDML105 seedlings, respectively. In response to CTS pretreatment before osmotic stress, 22 differently expressed proteins were discovered, of which 10 and 12 were identified in the LPT123 and KDML105, respectively. These proteins are typically involved in signaling, transport, protein folding, protein degradation, and metabolism. This study provides fruitful data to understand the signal transduction mechanisms of rice seedlings pretreated with CTS before exposure to osmotic stress.

Halo- and UV-B priming-mediated drought tolerance and recovery in rice seedlings

Drought stress is a major stress constraint for the growth and establishment of rice seedlings. The objective of this study was to investigate the effects of UV-B and halo priming induced physiochemical changes in the seedling stage of drought-sensitive rice variety exposed to drought stress and recovery. The seedlings of Oryza sativa L. var. Neeraja were UV-B and halo primed and was further subjected to drought stress and recovery. Drought stress induced reactive oxygen species leads to the accumulation of carbonyl content indicating the impairment of photosynthetic machinery and various cellular activities. However, the seed priming resulted in the enhanced production of various metabolites such as proline, amino acids, soluble protein, total phenolics and total soluble sugar. Moreover, it increased the activities of antioxidant enzymes such as superoxide dismutase, catalase and ascorbate peroxidase in rice seedlings exposed to drought stress. After re-watering, all the increased physiochemical parameters of primed and non-primed rice seedlings returned to the levels as in control. The retention of priming memory in seedlings emerged from primed seeds make them more tolerant towards drought and rapid recovery occurs in response to re-watering. Thus, these results suggest that halo and UV-B priming of Oryza sativa seeds is an effective means for reducing drought stress impacts and enhancing the recovery rate from drought at the seedling stage .

Effects of drought stress on pigment and protein contents and antioxidant enzyme activities in five varieties of rice (Oryza sativa L.)

Drought stress caused the decrease of pigment contents - chlorophyll a, chlorophyll b, chlorophyll a/b ratio, total chlorophyll content and carotenoids content of leaves of five rice varieties (var. BRRI Dhan-30, BRRI Dhan-32, BRRI Dhan-34, BRRI Dhan-38 and BRRI Dhan-56). Among five rice varieties, BRRI Dhan- 56 showed the least decrease of pigment content under stress. It caused the decrease of protein content of leaves of five rice varieties whereas BRRI Dhan-56 showed the least decrease (3.64%) of protein content under stress. On the other hand, drought stress increased CAT and SOD activities in the leaf of five varieties of rice and BRRI Dhan-56 showed the highest increase of CAT (37.67%) and SOD (94.17%) activity under stress. It may be assumed that higher antioxidant enzymes activities (CAT and SOD) and less reduction of protein content were related to the mechanisms of drought tolerance in rice. It is indicated that BRRI Dhan- 56 may be drought tolerant while BRRI Dhan-30, BRRI Dhan-32, BRRI Dhan-34 and BRRI Dhan-38 were drought sensitive rice varieties. Drought tolerant rice variety is selected based on pigment content, protein content and antioxidant enzymes activities (CAT and SOD).

Novel Digital Features Discriminate Between Drought Resistant and Drought Sensitive Rice Under Controlled and Field Conditions.

Dynamic quantification of drought response is a key issue both for variety selection and for functional genetic study of rice drought resistance. Traditional assessment of drought resistance traits, such as stay-green and leaf-rolling, has utilized manual measurements, that are often subjective, error-prone, poorly quantified and time consuming. To relieve this phenotyping bottleneck, we demonstrate a feasible, robust and non-destructive method that dynamically quantifies response to drought, under both controlled and field conditions. Firstly, RGB images of individual rice plants at different growth points were analyzed to derive 4 features that were influenced by imposition of drought. These include a feature related to the ability to stay green, which we termed greenness plant area ratio (GPAR) and 3 shape descriptors [total plant area/bounding rectangle area ratio (TBR), perimeter area ratio (PAR) and total plant area/convex hull area ratio (TCR)]. Experiments showed that these 4 features were capable of discriminating reliably between drought resistant and drought sensitive accessions, and dynamically quantifying the drought response under controlled conditions across time (at either daily or half hourly time intervals). We compared the 3 shape descriptors and concluded that PAR was more robust and sensitive to leaf-rolling than the other shape descriptors. In addition, PAR and GPAR proved to be effective in quantification of drought response in the field. Moreover, the values obtained in field experiments using the collection of rice varieties were correlated with those derived from pot-based experiments. The general applicability of the algorithms is demonstrated by their ability to probe archival Miscanthus data previously collected on an independent platform. In conclusion, this image-based technology is robust providing a platform-independent tool for quantifying drought response that should be of general utility for breeding and functional genomics in future.

Unraveling the molecular basis of oxidative stress management in a drought tolerant rice genotype Nagina 22.

BackgroundDrought stress tolerance for crop improvement is an important goal worldwide. Drought is a complex trait, and it is vital to understand the complex physiological, biochemical, and molecular mechanisms of drought tolerance to tackle it effectively. Osmotic adjustment, oxidative stress management (OSM), and cell membrane stability (CMS) are major components of cellular tolerance under drought stress. In the current study, we explored the molecular basis of OSM in the drought tolerant rice variety, Nagina 22 and compared it with the popular drought sensitive rice variety, IR 64, under drought imposed at the reproductive stage, to understand how the parental polymorphisms correlate with the superiority of Nagina 22 and tolerant bulk populations under drought.ResultsWe generated recombinant inbred lines (RIL) from contrasting parents Nagina 22 and IR 64 and focussed on spikelet fertility (SF), in terms of its correlation with OSM, which is an important component of drought tolerance in Nagina 22. Based on SF under drought stress and its correlations with other yield related traits, we used superoxide dismutase (SOD), glutathione reductase (GR), and ascorbate peroxidase (APX) activity assays to establish the relationship between SF and OSM genes in the tolerant and sensitive lines. Among the OSM enzymes studied, GR had a significant and positive correlation with single plant yield (SPY) under drought stress. GR was also positively correlated with APX but negatively so with SOD. Interestingly, none of the enzyme-morphology correlations were significant under irrigated control (IC). Through genome-wide SNP analysis of the 21 genes encoding for OSM enzymes, we identified the functional polymorphisms between the parents and identified superior alleles. By using network analysis of OSM genes in rice, we identified the genes that are central to the OSM network.ConclusionsFrom the biochemical and morphological data and the SNP analysis, the superiority of Nagina 22 in spikelet fertility under drought stress is because of its superior alleles for SOD (SOD2, SODCC1, SODA) and GR (GRCP2) rather than for APX, for which IR 64 had the superior allele (APX8). Nagina 22 can bypass APX8 by directly interacting with SODA. For nine of the 11 genes present in the central network, Nagina 22 had the superior alleles. We propose that Nagina 22 tolerance could mainly be because of SODA which is a reactive oxygen scavenger in mitochondria which is directly associated with spikelet fertility.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3131-2) contains supplementary material, which is available to authorized users.

Enhanced Gene Expression Rather than Natural Polymorphism in Coding Sequence of the OsbZIP23 Determines Drought Tolerance and Yield Improvement in Rice Genotypes.

Drought is one of the major limiting factors for productivity of crops including rice (Oryza sativa L.). Understanding the role of allelic variations of key regulatory genes involved in stress-tolerance is essential for developing an effective strategy to combat drought. The bZIP transcription factors play a crucial role in abiotic-stress adaptation in plants via abscisic acid (ABA) signaling pathway. The present study aimed to search for allelic polymorphism in the OsbZIP23 gene across selected drought-tolerant and drought-sensitive rice genotypes, and to characterize the new allele through overexpression (OE) and gene-silencing (RNAi). Analyses of the coding DNA sequence (CDS) of the cloned OsbZIP23 gene revealed single nucleotide polymorphism at four places and a 15-nucleotide deletion at one place. The single-copy OsbZIP23 gene is expressed at relatively higher level in leaf tissues of drought-tolerant genotypes, and its abundance is more in reproductive stage. Cloning and sequence analyses of the OsbZIP23-promoter from drought-tolerant O. rufipogon and drought-sensitive IR20 cultivar showed variation in the number of stress-responsive cis-elements and a 35-nucleotide deletion at 5’-UTR in IR20. Analysis of the GFP reporter gene function revealed that the promoter activity of O. rufipogon is comparatively higher than that of IR20. The overexpression of any of the two polymorphic forms (1083 bp and 1068 bp CDS) of OsbZIP23 improved drought tolerance and yield-related traits significantly by retaining higher content of cellular water, soluble sugar and proline; and exhibited decrease in membrane lipid peroxidation in comparison to RNAi lines and non-transgenic plants. The OE lines showed higher expression of target genes-OsRab16B, OsRab21 and OsLEA3-1 and increased ABA sensitivity; indicating that OsbZIP23 is a positive transcriptional-regulator of the ABA-signaling pathway. Taken together, the present study concludes that the enhanced gene expression rather than natural polymorphism in coding sequence of OsbZIP23 is accountable for improved drought tolerance and yield performance in rice genotypes.

English

Drought stress has now become a severe threat to ensure food security in the developing world as well as in Malaysia. To dertermine physiological and molecular determinants of drought stress and screeneng of drought tollarent rice varieties, an experiment was conducted in a greenhouse at Universiti Putra Malaysia using eleven rice varieties and two irrigation regimes (well irrigated and water stressed). The present study indicated that traditional rice variety Puteh Perak and Siam is superior drought tolerant while IRRI 2011- IRLON Plot no: 064, MR 220 and BRRI Dhan 56 are moderately drought tolerant and IRRI 2011- IRLON Plot no: 050 and MR 84 are drought sensitive rice variety. Drought tolerance of those varieties were measured based on rate of tiller reduction, leaf rolling score and drought score during water stress condition. Leaf rolling score was positively correlated to drought score, chlorophyll content and proline accumulation. Significant increase in the proline accumulation and antioxidant enzyme activities (peroxidase and catalase) were also observed under drought stress in all the rice varieties except Siam and Puteh Perak. All the rice varieties including drought tolerant and sensitive variety showed the existence of OsLEA 30 genes.

Genetic analysis of yield traits in rice under irrigated and water stress environments

Experiments were conducted to study the genetics and combining ability for yield and its components under irrigated (E I) and water stress environments (E II) using F1 hybrids derived from a full diallel mating involving four drought tolerant and four drought sensitive rice genotypes. Significant differences were observed for all the traits studied in both EI and EII environments, except harvest index in E II. Additive and non-additive gene actions for days to flowering, biomass and harvest index and nonadditive gene action for grain yield in both the environments were observed. Importance of additive gene action in E I and non-additive gene action in E II was observed for grains panicle–1, whereas shift in non-additive to additive from E I to E II was observed for productive tillers plant−1. The significance of gca and gca x environment interaction indicated the differential contribution of parents for days to flowering, biomass and harvest index. Based on the mean values and gca effects, landraces Nootripathu and Norungan were adjudged as the potential parents to improve grain yield under stress, where as CO43 and IR62266 were identified as good general combiners to improve grain yield and its component traits under irrigated environment. The hybrids viz., PMK2/CO43, CO43/Nootripathu, Nootripathu/Kallurundaikar, Norungan/IR64, Kallurundaikar x PMK2 and IR20 x IR62266 were identified as superior ones for improving yield under water stress.

Reactive oxygen species, ascorbate–glutathione pool, and enzymes of their metabolism in drought-sensitive and tolerant indica rice (Oryza sativa L.) seedlings subjected to progressing levels of water deficit

Water deficit for rice is a worldwide concern, and to produce drought-tolerant varieties, it is essential to elucidate molecular mechanisms associated with water deficit tolerance. In the present study, we investigated the differential responses of nonenzymatic antioxidants ascorbate (AsA), glutathione (GSH), and their redox pool as well as activity levels of enzymes of ascorbate-glutathione cycle in seedlings of drought-sensitive rice (Oryza sativa L.) cv. Malviya-36 and drought-tolerant cv. Brown Gora subjected to water deficit treatment of -1.0 and -2.1MPa for 24-72h using PEG-6000 in sand cultures. Water deficit caused increased production of reactive oxygen species such as O2[Symbol: see text](-), H2O2, and HO[Symbol: see text] in the tissues, and the level of production was higher in the sensitive than the tolerant cultivar. Water deficit caused reduction in AsA and GSH and decline in their redox ratios (AsA/DHA and GSH/GSSG) with lesser decline in tolerant than the sensitive seedlings. With progressive level of water deficit, the activities of monodehydroascorbate reductase, dehydroascorbate reductase, ascorbate peroxidase (APX), and glutathione transferase increased in the seedlings of both rice cultivars, but the increased activity levels were higher in the seedlings of drought-tolerant cv. Brown Gora compared to the sensitive cv. Malviya-36. Greater accumulation of proline was observed in stressed seedlings of tolerant than the sensitive cultivar. In-gel activity staining of APX revealed varying numbers of their isoforms and their differential expression in sensitive and tolerant seedlings under water deficit. Results suggest that an enhanced oxidative stress tolerance by a well-coordinated cellular redox state of ascorbate and glutathione in reduced forms and induction of antioxidant defense system by elevated activity levels of enzymes of ascorbate-glutathione cycle is associated with water deficit tolerance in rice.

Identification of Gene Modules Associated with Drought Response in Rice by Network-Based Analysis

Understanding the molecular mechanisms that underlie plant responses to drought stress is challenging due to the complex interplay of numerous different genes. Here, we used network-based gene clustering to uncover the relationships between drought-responsive genes from large microarray datasets. We identified 2,607 rice genes that showed significant changes in gene expression under drought stress; 1,392 genes were highly intercorrelated to form 15 gene modules. These drought-responsive gene modules are biologically plausible, with enrichments for genes in common functional categories, stress response changes, tissue-specific expression and transcription factor binding sites. We observed that a gene module (referred to as module 4) consisting of 134 genes was significantly associated with drought response in both drought-tolerant and drought-sensitive rice varieties. This module is enriched for genes involved in controlling the response of the plant to water and embryonic development, including a heat shock transcription factor as the key regulator in the expression of ABRE-containing genes. These results suggest that module 4 is highly conserved in the ABA-mediated drought response pathway in different rice varieties. Moreover, our study showed that many hub genes clustered in rice chromosomes had significant associations with QTLs for drought stress tolerance. The relationship between hub gene clusters and drought tolerance QTLs may provide a key to understand the genetic basis of drought tolerance in rice.