Tolerant Rice Research Articles

A cystathionine beta-synthase domain containing protein, OsCBSCBS4, interacts with OsSnRK1A and OsPKG and functions in abiotic stress tolerance in rice.

The Cystathionine-β-Synthase (CBS) domain-containing proteins (CDCPs) constitute a functionally diverse protein superfamily, sharing an evolutionary conserved CBS domain either in pair or quad. Rice genome (Oryza sativa subsp. indica) encodes 42 CDCPs; their functions remain largely unexplored. This study examines OsCBSCBS4, a quadruple CBS domain containing protein towards its role in regulating the abiotic stress tolerance in rice. Gene expression analyses revealed upregulation of OsCBSCBS4 in response to diverse abiotic stresses. Further, the cytoplasm-localised OsCBSCBS4 showed interaction with two different kinases, a cytoplasmic localised cGMP-dependant protein kinase (OsPKG) and the nucleo-cytoplasmic catalytic subunit of sucrose-nonfermentation 1-related protein kinase 1 (OsSnRK1A). The interaction with the latter assisted in trafficking of OsCBSCBS4 to the nucleus as well. Overexpression of OsCBSCBS4 in rice resulted in enhanced tolerance to drought and salinity stress, via maintaining better physiological parameters and antioxidant activity. Additionally, OsCBSCBS4-overexpressing rice plants exhibited reduced yield penalty under stress conditions. The in silico docking and in vitro binding analyses of OsCBSCBS4 with ATP suggest its involvement in cellular energy balance. Overall, this study provides novel insight into the unexplored functions of OsCBSCBS4 and demonstrates it as a new promising target for augmenting crop resilience.

Identification and Characterization of miRNAs and lncRNAs Associated with Salinity Stress in Rice Panicles.

Salinity is a common abiotic stress that limits crop productivity. Although there is a wealth of evidence suggesting that miRNA and lncRNA play important roles in the response to salinity in rice seedlings and reproductive stages, the mechanism by which competing endogenous RNAs (ceRNAs) influence salt tolerance and yield in rice has been rarely reported. In this study, we conducted full whole-transcriptome sequencing of rice panicles during the reproductive period to clarify the role of ceRNAs in the salt stress response and yield. A total of 214 lncRNAs, 79 miRNAs, and 584 mRNAs were identified as differentially expressed RNAs under salt stress. Functional analysis indicates that they play important roles in GO terms such as response to stress, biosynthesis processes, abiotic stimuli, endogenous stimulus, and response to stimulus, as well as in KEGG pathways such as secondary metabolite biosynthesis, carotenoid biosynthesis, metabolic pathways, and phenylpropanoid biosynthesis. A ceRNA network comprising 95 lncRNA-miRNA-mRNA triplets was constructed. Two lncRNAs, MSTRG.51634.2 and MSTRG.48576.1, were predicted to bind to osa-miR172d-5p to regulate the expression of OsMYB2 and OsMADS63, which have been reported to affect salt tolerance and yield, respectively. Three lncRNAs, MSTRG.30876.1, MSTRG.44567.1, and MSTRG.49308.1, may bind to osa-miR5487 to further regulate the expression of a stress protein (LOC_Os07g48460) and an aquaporin protein (LOC_Os02g51110) to regulate the salt stress response. This study is helpful for understanding the underlying molecular mechanisms of ceRNA that drive the response of rice to salt stress and provide new genetic resources for salt-resistant rice breeding.

Screening and analysis of candidate genes conferring alkalinity tolerance in rice (Oryza sativa L.) at the bud burst stage based on QTL-seq and RNA-seq

BackgroundSoil salinization is one of the key factors restricting the production of cropland. Once rice is subjected to alkali stress at the bud burst stage, the yield will suffer irreparable serious loss. Compared with salt tolerance, studies on QTL mapping and candidate gene analysis of rice alkali tolerance are limited. ResultsIn this study, we used the F2:3 population derived from the alkali-tolerant cultivar LD21 and the alkali-sensitive cultivar WL138 to construct an alkali-tolerant DNA mixing pool, and the BSA (Bulked Segregation Analysis) method was used for re-sequencing. The main QTL qRSLB9 controlling the relative shoot length of rice under alkali stress was mapped by QTL-seq. The candidate interval was narrowed to 346.5 kb by regional linkage mapping, which containing 6 DEGs screened through transcriptome sequencing. The qRT-PCR and candidate gene sequencing showed that LOC_Os09g24260 was most likely to control relative shoot length (RSL) in rice as a major gene who encodes the WD domain, G-beta repeat domain-containing protein. ConclusionsBased on these results, LOC_Os09g24260 was the candidate gene of qRSLB9 conferring alkalinity tolerance to rice at the bud burst stage. Our study provides valuable genetic information and materials for breeding new rice varieties with alkalinity tolerance.How to cite: Wang J, Bian J, Liu L, et al. Screening and analysis of candidate genes conferring alkalinity tolerance in rice (Oryza sativa L.) at the bud burst stage based on QTL-seq and RNA-seq. Electron J Biotechnol 2024;71. https://doi.org/10.1016/j.ejbt.2024.07.002.

Both Short-term and Long-term Ozone Pollution Alters the Chemical Composition of rice Grain.

The increasing ground-level ozone (O3) is threatening food security, especially in Asian areas, where rice is one of the most important staple crops. O3 impacts on rice could be exacerbated by its spatiotemporal heterogeneity. To improve evaluation accuracy and develop effective adaptations, direct data is urgently needed. Studies on the short-term effects of O3 on rice grain, however, are lacking. Which may lead to an underestimation of the O3 impacts. Through a field experiment, we studied the responses of grain nitrogen, grain carbon, and grain protein in rice cultivars to elevated concentrations of O3 (40 ppb plus that in background air, eO3), especially examining the effects of short-term eO3 during different plant growth stages. We found that long-term eO3 increased grain nitrogen by 29.29% in a sensitive rice cultivar, and short-term eO3 at the tillering and jointing stages increased grain nitrogen by 19.31%, and the grain carbon to nitrogen ratio was decreased by 14.70%, and 21.14% by short-term and long-term eO3. Here we demonstrate that short-term eO3 may significantly affect the chemical composition of rice grains. Previous evaluations of the effects of eO3 may be underestimated. Moreover, changes in the grain nitrogen and grain protein were greater when the short-term eO3 was added to rice plants during the tillering and jointing stage, compared to heading and ripening stage. These results suggest that to improve the tolerance of rice to eO3 to achieve food security, studies on cultivar screening, as well as developing growth-stage-specific adaptations are needed in future.

The invertase gene PWIN1 confers chilling tolerance of rice at the booting stage via mediating pollen development.

Pollen fertility is a primary regulator of grain yield and is highly susceptible to cold and other environmental stress. We revealed the roles of rice cell wall invertase gene PWIN1 in pollen development and chilling tolerance. We uncovered its preferential expression in microspores and bicellular pollen and identified its knock-down and knock-out mutants. pwin1 mutants produced a higher proportion of abnormal pollen than wild-type plants. The contents of sucrose, glucose, and fructose were increased, while ATP content and primary metabolism activity were reduced in the mutant pollen. Furthermore, the loss of function of PWIN1 coincided with an increase in SnRK1 activity and a decrease in TOR activity. Under chilling conditions, pwin1 mutants displayed significantly reduced pollen viability and seed-setting rate, while overexpressing PWIN1 notably increased pollen viability and seed-setting rate as compared with the wild-type, indicating that PWIN1 is essential for rice pollen development and grain yield under cold stress. This study provides insights into the molecular mechanisms underlying rice pollen fertility during chilling stress, and a new module to improve chilling tolerance of rice at the booting stage by molecular design.

Transcriptome-wide m6A methylation and metabolomic analysis reveal regulatory networks in rice roots under manganese stress

Rice (Oryza sativa) has a higher tolerance to manganese (Mn) stress than other cereals. However, the regulatory mechanisms governing Mn tolerance in rice remain poorly understood. In this work, seedlings of the rice cultivar Nipponbare were treated with 1.0 mM MnCl2 for 10 days before root samples were collected for transcriptome-wide N6-methyladenosine (m6A) methylation and metabolome profiling. In the presence of extra Mn, we identified 2050 significantly modified m6A peaks and 2549 differentially expressed genes (DEGs). These DEGs were linked to key signaling pathways such as MAPK signaling, calcium signaling, and peroxides. Among these, 282 DEGs showed differential m6A methylation peaks, including 29 transcription factors, indicating they might be key upstream regulators of the Mn toxicity response. Furthermore, metabolomic research indicated considerable metabolic alterations in rice roots under Mn stress, notably in purine metabolism, amino acid biosynthesis, and glycerophospholipid metabolic pathways. Almost half of the metabolites were lipids or lipid-like compounds, indicating a potential function in signal transduction and membrane biogenesis. The findings lead to a better understanding of regulatory networks in rice roots that aid in Mn stress tolerance.

Transcriptome analysis of the molecular basis of 11‐eicosenoic acid‐mediated salt stress tolerance in rice

AbstractSalt stress is one of the major abiotic factors severely hampering rice production. Fatty acids play a crucial role in plants response to such stress. Previous studies have demonstrated the potential of unsaturated fatty acid (11‐eicosenoic acid [EA]) to enhance salt tolerance in rice, but the molecular mechanism remains unclear. Our study indicates that the exogenous application of EA could alleviate salt stress‐induced damage as well as improve the survival rate of rice seedlings. Transcriptome analysis was performed following treatment of rice seedlings with EA, NaCl, and NaCl + EA. The results showed that there were 4970, 11, 304, and 4735 differentially expressed genes (DEGs) in NaCl versus CK, EA versus CK, NaCl + EA versus NaCl, and NaCl + EA versus CK, respectively. Notably, pathways such as unsaturated fatty acid metabolism, diterpenoid phytoalexin biosynthesis, and phytohormone signal transduction were significantly enriched in NaCl + EA versus NaCl. Specifically, genes related to ethylene, abscisic acid, jasmonic acid, salicylic acid, gibberellin signaling, and fatty acid metabolism were implicated in the mitigation effect of EA on salt stress in rice. Furthermore, DEGs involved in rice diterpenoid biosynthesis were analyzed in detail, revealing that EA induced the biosynthesis of multiple diterpenoids. Metabolomic analysis showed that the levels of various fatty acids, phytohormones, and terpenes increased. The presented data may serve as a useful guide for further exploration of the various biological functions of EA in enhancing plant resilience to salt stress. Additionally, it offers a valuable list of genes for the development of crop plants with improved salt resistance.

Phytochrome interacting factor ZmPIF6 simultaneously enhances chilling tolerance and grain size in rice

Chilling is a prevalent type of abiotic stress that adversely affects agricultural productivity worldwide. Phytochrome interacting factors (PIFs) are a group of transcription factor that are crucial for plant abiotic stress response. Our research reveals that the maize PIF family gene ZmPIF6 is responsive to chilling stress, which mitigates the negative impacts of chilling through reducing reactive oxygen species content and enhancing cell membrane stability at the physiological and biochemical levels. We also found that the ZmPIF6 overexpression lines showed a significant increase in grain size, encompassing both length and width, which mainly due to the increase in cell size. In addition, digital gene expression results suggested that ZmPIF6 regulates the expression of cold-related and grain size-related genes in rice. In light of these findings, ZmPIF6 has a hopeful prospect as a candidate gene of chilling tolerance and crop productivity in the transgenic breeding.

Development of High Yielding Deep Water Rice Variety MTU 1184 Suitable for Semi-Deep Flooded Ecosystem of South Eastern Region of India

In recent years due to heavy and intense rainfall and cyclonic storms, paddy crop is experiencing damage due to flooding. If the flood water stagnation remains for more than a week the varieties are unable to sustain and there by the yield levels are drastically reduced. Hence, there is a need to develop submergence tolerant variety to minimize the yield losses. Acharya NG Ranga Agricultural University (ANGRAU), Regional Agricultural Research Station, Maruteru has developed flood tolerant variety MTU 1184 through conventional plant breeding using PLA 1100 and BM 71 as parents. The flood tolerant rice culture was extensively evaluated for yield in semi deep water ecosystem at RARS, Maruteru over the years of kharif, 2012 to kharif, 2016 in Station yield trials. The variety recorded superior grain yield (4370 kg/ha) against check PLA 1100 (3811 kg/ha) and yield advantage over check was 14.67%. The entry was tested in AICRIP trials from 2014 to 2017 at RARS, Maruteru and the results revealed that MTU 1184 registered 4650 kg/ha and found to be significantly superior over the national check, Sabitha (3703 kg/ha) and the per cent increase over check was 25.57. The variety recorded a mean grain yield of 4281 kg/ha and found to be significantly superior over the national check, Sabitha (3011 kg/ha) and yield advantage was 1270 kg/ha and per cent increase over national check was 42.17 and zonal check Poornendu in 8 locations of six states of south eastern region. Multi location testing of the variety from 2015 to 2017 revealed that the variety has out yielded (5370 kg/ha) and found superior over the best check PLA 1100 (4290 kg/ha) and the per cent increase over check was 25.18. Minikit testing in 890 locations for a period of three years from 2016 to 2018 revealed that the average mean yield of the variety over three years was 6039 kg/ha against local popular check PLA 1100 (5700 kg/ha) and per cent increase over check was 6.0 when tested in Andhra Pradesh.

Drought Stress Tolerance in Rice: Physiological and Biochemical Insights

Rice (Oryza sativa L.), an important food crop, necessitates more water to complete its life cycle than other crops. Therefore, there is a serious risk to rice output due to water-related stress. Drought stress results in morphological changes, including the inhibition of seed germination, reduced seeding growth, leaf area index, flag leaf area, increased leaf rolling, as well as the decrement of yield traits, such as plant height, plant biomass, number of tillers, and 1000-grain yield. Stress also causes the formation of reactive oxygen species (ROS) such as O2−, H2O2, and OH−, which promote oxidative stress in plants and cause oxidative damage. The process of oxidative degradation owing to water stress produces cell damage and a reduction in nutrient intake, photosynthetic rate, leaf area, RWC, WUE, and stomatal closure, which may be responsible for the decrement of the transpiration rate and plant dry matter under decreasing soil moisture. Plants have the ability to produce antioxidant species that can either be enzymatic (SOD, POD, CAT, GPX, APX) or non-enzymatic (AsA, GSH) in nature to overcome oxidative stress. During drought, several biochemical osmoprotectants, like proline, polyamines, and sugars, can be accumulated, which can enhance drought tolerance in rice. To meet the demands of an ever-growing population with diminishing water resources, it is necessary to have crop varieties that are highly adapted to dry environments, and it may also involve adopting some mitigation strategies. This study aims to assess the varying morphological, physiological, and biochemical responses of the rice plant to drought, and the various methods for alleviating drought stress.

Comparative transcriptome profiling to untie the drought tolerance molecular mechanism of backcross rice (Oryza sativa L.) inbred

AbstractRice production is severely hampered by drought stress, which causes enormous economic losses. The issue of global climate change is gaining importance, and hence development of rice genotypes tolerant to drought stress is becoming more critical. To address this issue, backcross inbred lines (BILs) developed were subjected to drought stress, and their molecular mechanism was studied. The drought‐tolerant parent Apo and drought‐susceptible, high‐yielding IR64 along with two BILs, namely, CB 229 (qDTY2.2 + qDTY3.1 + qDTY8.1) and CB 193‐3 (qDTY3.1 + qDTY8.1) were tested in a greenhouse for their response to drought. In this study, CB 229 showed better performance under water stress irrigated conditions; it was on par with IR64. Drought‐responsive transcriptome profiling was carried out in both the parents and the superior BIL CB 229 through the RNA‐Seq approach. About 3050 differentially expressed genes (DEGs) (2021 upregulated and 1029 downregulated) were detected in tolerant BIL CB 229 in drought stress. Most of the DEGs were involved in carbohydrate metabolism and the formation of cell walls, as well as genes associated with metabolite adaptability, ROS homeostasis and post‐transcriptional regulation. Genes such as chaperone protein, senescence‐induced receptor‐like serine, mannose‐6‐phosphate isomerase, aquaporin and heat shock proteins (LOC_Os02g26840, LOC_Os02g25720, LOC_Os07g35570, LOC_Os01g64970, etc.) were upregulated in the tolerant Apo and CB 229. It was observed that the BIL CB 229 yielded higher grains than both parents under moisture stress. Ninety‐four genes in the quantitative trait loci (QTLs) region were found to be differentially regulated in CB 229, Apo and IR64. Out of 94, nine genes co‐localized within the QTL qDTY2.2, 12 genes within qDTY3.1 and four genes within qDTY8.1 were differentially upregulated in CB 229 and downregulated in the susceptible genotype. The study revealed that the QTLs qDTY2.2, qDTY3.1 and qDTY8.1 are found to have complementary effects and offer enhanced levels of tolerance against drought due to complementation. Additionally, this analysis discovered new DEGs that may be involved in functions related to drought tolerance but lack function annotations. Future research can focus on a few of the significant DEGs found in this study. Taken together, our findings provide insight into drought tolerance mechanisms and could assist the development of novel strategies for improving drought tolerance in rice.

Occurrence of Abiotic and Biotic Stress Tolerance in Rice: A Multigene Approach

A sustainable food system ensures food security and nourishment for future generations. Rice (Oryza sativa L.) requires emergence stress tolerance for successful cultivation in germination and early establishment stages. According to the FAO (Food and Agriculture Organization) study, rice is one of the most important worldwide cereal crops and a staple food for more than half of the world’s population. Over the past few years, drastic climatic changes have been subjected to many abiotic and biotic stresses. Global estimates express that a total of 1000 million hectares of cultivated land is affected by abiotic and biotic stress. Besides this around 30% of the irrigated land area is also disturbed. This review discusses the mechanisms of stress-tolerant variants and understanding the recent developments of complex tolerance phenomena. Here, we have compiled the logical pieces as evidence of successful applications of potent molecular tools for boosting stress tolerance in rice, their prospects and limitation. This information would help researchers better understand the genetic enhancement of stress tolerance in rice.

Stress-induced nuclear translocation of ONAC023 improves drought and heat tolerance through multiple processes in rice

Drought and heat are major abiotic stresses frequently coinciding to threaten rice production. Despite hundreds of stress-related genes being identified, only a few have been confirmed to confer resistance to multiple stresses in crops. Here we report ONAC023, a hub stress regulator that integrates the regulations of both drought and heat tolerance in rice. ONAC023 positively regulates drought and heat tolerance at both seedling and reproductive stages. Notably, the functioning of ONAC023 is obliterated without stress treatment and can be triggered by drought and heat stresses at two layers. The expression of ONAC023 is induced in response to stress stimuli. We show that overexpressed ONAC23 is translocated to the nucleus under stress and evidence from protoplasts suggests that the dephosphorylation of the remorin protein OSREM1.5 can promote this translocation. Under drought or heat stress, the nuclear ONAC023 can target and promote the expression of diverse genes, such as OsPIP2;7, PGL3, OsFKBP20-1b, and OsSF3B1, which are involved in various processes including water transport, reactive oxygen species homeostasis, and alternative splicing. These results manifest that ONAC023 is fine-tuned to positively regulate drought and heat tolerance through the integration of multiple stress-responsive processes. Our findings provide not only an underlying connection between drought and heat responses, but also a promising candidate for engineering multi-stress-resilient rice.

Effect of exogenous abscisic acid on improving low-phosphorus (P) response in rice (Oryza sativa L.)

Phosphorus (P) deficiency is a major constraint to rice productivity worldwide. Exogenous application of abscisic acid (ABA) has not been reported to improve rice response toward P-deficiency. Present study analyzed the biochemical response in the shoots and roots of two rice cultivars, CSR10 (low-P tolerant) and Pusa44 (low-P susceptible) at 36, 72 and 216 h after normal P (NP) (10 ppm) (control), low P (LP) (1 ppm), and LP + ABA given to 12-d old seedlings. Results found that biomass and P-uptake reduced in Pusa44 compared to CSR10 under LP but improved significantly under LP + ABA. P-fractionation was utilized efficiently by CSR10 under LP while LP + ABA improved P-fractionation in both cultivars. LP + ABA improved acid phosphatases in both cultivars. Hexose and sucrose levels were depleted while starch hydrolyzed poorly in Pusa44 compared to CSR10 under LP while LP + ABA enhanced starch hydrolysis and levels of sugars in both cultivars. Starch increased at a late stage in the roots of CSR10 under LP while Pusa44 improved it under LP + ABA. Antioxidant capacity was low while H2O2 was high at early stage in Pusa44 compared to CSR10 under LP. LP + ABA improved antioxidant capacity and reduced H2O2 in both cultivars. Results concluded that ABA is a versatile regulator of not only P-acquisition/P-utilization but also carbohydrates and antioxidant activities under P-deficiency, and exogenous ABA improved low-P tolerance in rice.

Biotic Stress Tolerant Rice Variety with Enhanced Method of Gene Pyramiding

Rice, as a staple food crop, faces various difficulties from biotic burdens like sicknesses, bugs, and weeds. Customary raising strategies have shown a halfway outcome in creating rice arrangements with a thorough battle against numerous biotic burdens. The superbiotic elements that lessen rice efficiency are bacterial curse (BB) and organism-impact diseases. The potential for yield of the rice varieties must be developed by including genes for biotic stress resistance if yield improvements in rice are to be sustained. This research paper aims to explore innovative methods of gene pyramiding to upgrade biotic stress, and resilience in rice varieties. We examine the standards and headways in quality pyramiding procedures, including sub-atomic markers, and determination on marker-helped and genome-altering apparatuses, to stack numerous opposition qualities proficiently. By utilizing these methods, we propose a clever methodology for raising rice assortments with upgraded biotic pressure patience. In this review, two principal BB (Xa21 and xa13) and two critical impact obstruction qualities (Pi54 and Pi1) were all the while brought into Tellahamsa with the use of the marker-helped backcross rearing (MABB) system. The paper underlines the expected advantages, challenges, and moral contemplations related to quality pyramiding, and talks about future exploration bearings to speed up the organization of versatile rice assortments.

The UDP-glycosyltransferase gene OsUGT706E2 negatively regulates rice tolerance to blast disease and abiotic stresses

Despite the crucial role of UDP-glycosyltransferases (UGTs) in various stress responses in plants, their biological functions in rice (Oryza sativa L.) remain poorly understood. In this study, we introduce a novel gene, OsUGT706E2, which is expressed at significantly higher levels in wild rice compared to cultivated rice. OsUGT706E2 is active in multiple tissues and localizes to both the nucleus and cytoplasm. Its transcription is notably up-regulated in response to cold stress, blast disease, and several hormone treatments. Overexpression of OsUGT706E2 markedly reduces seedling tolerance to blast disease, cold, and osmotic stress, whereas knocking out OsUGT706E2 enhances seedling tolerance to blast disease and osmotic stress. The expression levels of stress-related genes in OsUGT706E2 overexpressing plants were significantly lower compared to wild-type plants following stress treatment. Conversely, OsUGT706E2 knockout plants exhibited markedly higher expression levels of these genes than the control plants after stress treatment. Metabolome analysis further indicated that OsUGT760E2 influences metabolite content in rice. Specifically, OsUGT760E2-overexpressing seedlings had higher amino acid content and lower lipid content compared to wild-type seedlings, while OsUGT760E2-knockout seedlings showed lower amino acid content and higher lipid content than control seedlings. These findings suggest that OsUGT760E2 negatively regulates resistance to blast disease as well as tolerance to cold and osmotic stress in rice. As a result, OsUGT760E2 represents a promising target for enhancing rice stress tolerance through gene editing approaches.

OsG6PGH1 affects various grain quality traits and participates in the salt stress response of rice.

Cytoplasmic 6-phosphogluconate dehydrogenase (G6PGH) is a key enzyme in the pentose phosphate pathway that is involved in regulating various biological processes such as material metabolism, and growth and development in plants. However, it was unclear if OsG6PGH1 affected rice grain quality traits. We perform yeast one-hybrid experiments and reveal that OsG6PGH1 may interact with OsAAP6. Subsequently, yeast in vivo point-to-point experiments and local surface plasmon resonance experiments verified that OsG6PGH1 can bind to OsAAP6. OsG6PGH1 in rice is a constitutive expressed gene that may be localized in the cytoplasm. OsAAP6 and protein-synthesis metabolism-related genes are significantly upregulated in OsG6PGH1 overexpressing transgenic positive endosperm, corresponding to a significant increase in the number of protein bodies II, promoting accumulation of related storage proteins, a significant increase in grain protein content (GPC), and improved rice nutritional quality. OsG6PGH1 positively regulates amylose content, negatively regulates chalkiness rate and taste value, significantly affects grain quality traits such as appearance, cooking, and eating qualities of rice, and is involved in regulating the expression of salt stress related genes, thereby enhancing the salt-stress tolerance of rice. Therefore, OsG6PGH1 represents an important genetic resource to assist in the design of high-quality and multi-resistant rice varieties.

Identification of candidate genes controlling cold tolerance at the early seedling stage from Dongxiang wild rice by QTL mapping, BSA-Seq and RNA-Seq

BackgroundThe cold tolerance of rice is closely related to its production and geographic distribution. The identification of cold tolerance-related genes is of important significance for developing cold-tolerant rice. Dongxiang wild rice (Oryza rufipogon Griff.) (DXWR) is well-adapted to the cold climate of northernmost-latitude habitats ever found in the world, and is one of the most valuable rice germplasms for cold tolerance improvement.ResultsTranscriptome analysis revealed genes differentially expressed between Xieqingzao B (XB; a cold sensitive variety) and 19H19 (derived from an interspecific cross between DXWR and XB) in the room temperature (RT), low temperature (LT), and recovery treatments. The results demonstrated that chloroplast genes might be involved in the regulation of cold tolerance in rice. A high-resolution SNP genetic map was constructed using 120 BC5F2 lines derived from a cross between 19H19 and XB based on the genotyping-by-sequencing (GBS) technique. Two quantitative trait loci (QTLs) for cold tolerance at the early seedling stage (CTS), qCTS12 and qCTS8, were detected. Moreover, a total of 112 candidate genes associated with cold tolerance were identified based on bulked segregant analysis sequencing (BSA-seq). These candidate genes were divided into eight functional categories, and the expression trend of candidate genes related to ‘oxidation-reduction process’ and ‘response to stress’ differed between XB and 19H19 in the RT, LT and recovery treatments. Among these candidate genes, the expression level of LOC_Os12g18729 in 19H19 (related to ‘response to stress’) decreased in the LT treatment but restored and enhanced during the recovery treatment whereas the expression level of LOC_Os12g18729 in XB declined during recovery treatment. Additionally, XB contained a 42-bp deletion in the third exon of LOC_Os12g18729, and the genotype of BC5F2 individuals with a survival percentage (SP) lower than 15% was consistent with that of XB. Weighted gene coexpression network analysis (WGCNA) and modular regulatory network learning with per gene information (MERLIN) algorithm revealed a gene interaction/coexpression network regulating cold tolerance in rice. In the network, differentially expressed genes (DEGs) related to ‘oxidation-reduction process’, ‘response to stress’ and ‘protein phosphorylation’ interacted with LOC_Os12g18729. Moreover, the knockout mutant of LOC_Os12g18729 decreased cold tolerance in early rice seedling stage signifcantly compared with that of wild type.ConclusionsIn general, study of the genetic basis of cold tolerance of rice is important for the development of cold-tolerant rice varieties. In the present study, QTL mapping, BSA-seq and RNA-seq were integrated to identify two CTS QTLs qCTS8 and qCTS12. Furthermore, qRT-PCR, genotype sequencing and knockout analysis indicated that LOC_Os12g18729 could be the candidate gene of qCTS12. These results are expected to further exploration of the genetic mechanism of CTS in rice and improve cold tolerance of cultivated rice by introducing the cold tolerant genes from DXWR through marker-assisted selection.

Comprehensive analyses show the enhancement effect of exogenous melatonin on fluroxypyr-meptyl multiple phase metabolisms in Oryza sativa for reducing environmental risks

The role of melatonin (MT), an essential phytohormone controlling the physiological and biochemical reactions of plants to biotic and abiotic stress, in alleviating pesticide phytotoxicity remains unclear. This study explores the effects of MT (0 and 200 mg/L) and six doses of fluroxypyr-meptyl (FLUME) (0–0.14 mg/L) on the physiological response of rice (Oryza sativa). FLUME exposure inhibited the growth of rice seedlings, with MT treatment ameliorating this effect. To determine the biochemical processes and catalytic events involved in FLUME breakdown in rice, six rice root and shoot libraries exposed to either FLUME or FLUME–MT were generated and then subjected to RNA-Seq–LC-Q-TOF-HRMS/MS analyses. The results showed that 1510 root genes and 139 shoot genes exhibited higher upregulation in plants treated with an ecologically realistic FLUME concentration and MT than in those treated with FLUME alone. Gene enrichment analysis revealed numerous FLUME-degradative enzymes operating in xenobiotic tolerance to environmental stress and molecular metabolism. Regarding the FLUME degradation process, certain differentially expressed genes were responsible for producing important enzymes, such as cytochrome P450, glycosyltransferases, and acetyltransferases. Four metabolites and ten conjugates in the pathways involving hydrolysis, malonylation, reduction, glycosylation, or acetylation were characterized using LC-Q-TOF-HRMS/MS to support FLUME-degradative metabolism. Overall, external application of MT can increase rice tolerance to FLUME-induced oxidative stress by reducing phytotoxicity and FLUME accumulation. This study provides insights into MT's role in facilitating FLUME degradation, with potential implications for engineering genotypes supporting FLUME degradation in paddy crops.

Zinc finger protein ZFP36 and pyruvate dehydrogenase kinase PDK1 function in ABA-mediated aluminum tolerance in rice

Aluminum (Al) toxicity poses a significant constraint on field crop yields in acid soils. Zinc finger protein 36 (ZFP36) is well-documented for its pivotal role in enhancing tolerance to both drought and oxidative stress in rice. This study unveils a novel function of ZFP36 modulated by abscisic acid (ABA)-dependent mechanisms, specifically aimed at alleviating Al toxicity in rice. Under Al stress, the expression of ZFP36 significantly increased through an ABA-dependent pathway. Knocking down ZFP36 heightened Al sensitivity, while overexpressing ZFP36 conferred increased resistance to Al stress. Additionally, our investigations revealed a physical interaction between ZFP36 and pyruvate dehydrogenase kinase 1 in rice (OsPDK1). Biochemical assays further elucidated that OsPDK1 phosphorylates ZFP36 at the amino acid site 73–161. Subsequent experiments demonstrated that ZFP36 positively regulates the expression of ascorbate peroxidases (OsAPX1) and OsALS1 by binding to specific elements in their upstream segments in rice. Through genetic and phenotypic analyses, we unveiled that OsPDK1 influences ABA-triggered antioxidant defense to alleviate Al toxicity by interacting with ZFP36. In summary, our study underscores that pyruvate dehydrogenase kinase 1 (OsPDK1) phosphorylates ZFP36 to modulate the activities of antioxidant enzymes via an ABA-dependent pathway, influencing tolerance of rice to soil Al toxicity.