Receptor-like kinase OsSIK1 improves drought and salt stress tolerance in rice (Oryza sativa) plants

TaRLK2.4, a transgressive expression receptor like kinase, improves powdery mildew resistance in wheat

Plants form two immune systems, pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI), to combat Blumeria graminis f. sp. tritici (Bgt) infection during the evolutionary process. In PTI, receptor-like kinases (RLKs) play important roles during pathogen infections. Based on our previous reports, there were 280 TaRLKs identified in early response to powdery mildew infection, which were divided into 34 subfamilies in this study. Differences in gene structures, cis-acting elements, and expression levels implied the function diversity of TaRLKs. TaRLK2.4, a member of LRK10L-RLKs subfamily, contained 665 amino acids, and located on the cell membrane. The main objective of this study was to investigate the role of the receptor-like kinase gene TaRLK2.4 in conferring powdery mildew resistance in wheat. Real-time quantitative PCR results indicated that TaRLK2.4 expressed during Bgt infection process, and exhibited a transgressive expression characteristic in disease resistance NILs (BJ-1). To elucidate the function of TaRLK2.4 during Bgt infection, the comprehensive analysis of virus induced gene silence and over-expression demonstrated that TaRLK2.4 promoted powdery mildew resistance positively. In summary, these results contribute to a deeper understanding of the complex and diverse biological functions of RLKs, and provide new genetic resources for wheat molecular breeding.

Identification of DEMETER-like DNA demethylase gene family in citrus and their role in drought stress-adaptive responses

DEMETER-Like DNA demethylases (DMLs) are epigenetic regulators of many developmental and biological processes in plants. No comprehensive information about the DML gene family in citrus is available to date. Here, a total of three DML genes in the genomes of Citrus sinensis (named CsDML1-3) and C. clementina (named CcDML1-3) were identified and analyzed. They encode hydrophilic and relatively large proteins, with prediction of nuclear localization, containing the conserved domains and motifs typical of plant DMLs. Protein interaction network analysis suggested that they interact primarily with proteins related to the maintenance of DNA methylation and remodeling of chromatin. Analysis of their promoter regions led to the identification of several cis-acting regulatory elements involved in stress response, including drought, heat and cold stresses. The presence of several miRNA targets and potential phosphorylation sites suggest that their expression is also regulated at post-transcriptional and post-translational levels. RNA-Seq data and quantitative real-time PCR analysis showed a low and drought-regulated gene expression of the citrus DMLs in different plant tissues. CsDML1 and CsDML3 were also differentially regulated by deficit irrigation in fruits at different developmental stages, with a positive and significant correlation found between CsDML1 and PHYTOENE SYNTHASE (PSY) and between CsDML3 and ATP CITRATE LYASEs (ACLs) and ZETA-CAROTENE DESATURASE (ZDS) gene expression. These results indicate that the citrus DMLs are potentially functional enzymes involved in developmental processes and drought stress-adaptive responses, providing a useful reference for further investigation of their functions and applications on the citrus improvement.

Overexpression of rice lectin receptor-like kinase, OsLec-RLK, confers salinity stress tolerance and increases seed yield in pigeon pea (Cajanus cajan (L.) Millsp.)

KEY MESSAGE

OsLec-RLK overexpression enhances cell signalling and salt stress tolerance in pigeon pea, enhancing seed yield and harvest index and thus, enabling marginal lands to increase food and nutritional security. Lectin Receptor-like kinases (Lec-RLKs) are highly effective cell signaling molecules that counteract various stresses, including salt stress. We engineered pigeon pea by overexpressing OsLec-RLK gene for enhancing salt tolerance. The OsLec-RLK overexpression lines demonstrated superior performance under salt stress, from vegetative to reproductive phase, compared to wild types (WT). The overexpression lines had significantly higher K+/Na+ ratio than WT exposed to 100 mM NaCl. Under salt stress, transgenic lines showed higher levels of chlorophyll, proline, total soluble sugars, relative water content, and peroxidase and catalase activity than WT plants. Membrane injury index and lipid peroxidation were significantly reduced in transgenic lines. Analysis of phenological and yield attributes confirmed that the OsLec-RLK pigeon pea lines maintain plant vigor, with 10.34-fold increase in seed yield (per plant) and 4-5-fold increase in harvest index of overexpression lines, compared to wild type. Meanwhile, the overexpression of OsLec-RLK up-regulated the expression levels of histone deacetylase1, acyl CoA, ascorbate peroxidase, peroxidase, glutathione reductase and catalase, which were involved in the K+/Na+ homeostasis pathway. This study showed the potential of OsLec-RLK gene for increasing crop productivity and yields under salt stress and enabling the crops to be grown on marginal lands for increasing food and nutritional security.

An Accurate Representation of the Number of bZIP Transcription Factors in the Triticum aestivum (Wheat) Genome and the Regulation of Functional Genes during Salt Stress

Climate change is dramatically increasing the overall area of saline soils around the world, which is increasing by approximately two million hectares each year. Soil salinity decreases crop yields and, thereby, makes farming less profitable, potentially causing increased poverty and hunger in many areas. A solution to this problem is increasing the salt tolerance of crop plants. Transcription factors (TFs) within crop plants represent a key to understanding salt tolerance, as these proteins play important roles in the regulation of functional genes linked to salt stress. The basic leucine zipper (bZIP) TF has a well-documented role in the regulation of salt tolerance. To better understand how bZIP TFs are linked to salt tolerance, we performed a genome-wide analysis in wheat using the Chinese spring wheat genome, which has been assembled by the International Wheat Genome Sequencing Consortium. We identified 89 additional bZIP gene sequences, which brings the total of bZIP gene sequences in wheat to 237. The majority of these 237 sequences included a single bZIP protein domain; however, different combinations of five other domains also exist. The bZIP proteins are divided into ten subfamily groups. Using an in silico analysis, we identified five bZIP genes (ABF2, ABF4, ABI5, EMBP1, and VIP1) that were involved in regulating salt stress. By scrutinizing the binding properties to the 2000 bp upstream region, we identified putative functional genes under the regulation of these TFs. Expression analyses of plant tissue that had been treated with or without 100 mM NaCl revealed variable patterns between the TFs and functional genes. For example, an increased expression of ABF4 was correlated with an increased expression of the corresponding functional genes in both root and shoot tissues, whereas VIP1 downregulation in root tissues strongly decreased the expression of two functional genes. Identifying strategies to sustain the expression of the functional genes described in this study could enhance wheat's salt tolerance.

Genome-Wide Association Study of Rice Diversity Panel Reveals New QTLs for Tolerance to Water Deficit Under the Egyptian Conditions

Drought has a significant impact on rice yield by restricting the crop's ability to grow and develop. Producing rice cultivars adapted to water deficit conditions is still the main interest of rice breeders and geneticists. To address this challenge, a set of 413 highly diverse rice populations were evaluated under normal and water deficit conditions for two growing seasons of 2021 and 2022. High genetic variation was found among genotypes for all studied traits. The heritability estimates ranged from 0.82 (panicle length) to 0.95 (plant height). Sterility percentage (SET%) was the most trait affected by water deficit in two growing seasons. 22 Rice genotypes were classified as drought tolerant in both years. Genome-wide association mapping was performed for all traits in the two growing seasons under both conditions using a total of 700,000 SNPs. The GWAS results revealed important and major SNPs associated with all traits. 26 Significant SNPs with stable allele effects were found to be associated with yield traits under water deficit conditions in both years. The results of this study provided rice genotypes that can be adapted under water deficit conditions and important stable SNP markers that can be used for marker-assisted selection after validation in different genetic backgrounds.

The zinc finger protein DHHC09 S-acylates the kinase STRK1 to regulate H2O2 homeostasis and promote salt tolerance in rice

Soil salinity results in oxidative stress and heavy losses to crop production. The S-acylated protein SALT TOLERANCE RECEPTOR-LIKE CYTOPLASMIC KINASE 1 (STRK1) phosphorylates and activates CATALASE C (CatC) to improve rice (Oryza sativa L.) salt tolerance, but the molecular mechanism underlying its S-acylation involved in salt signal transduction awaits elucidation. Here, we show that the DHHC-type zinc finger protein DHHC09 S-acylates STRK1 at Cys5, Cys10, and Cys14 and promotes salt and oxidative stress tolerance by enhancing rice H2O2-scavenging capacity. This modification determines STRK1 targeting to the plasma membrane or lipid nanodomains and is required for its function. DHHC09 promotes salt signaling from STRK1 to CatC via transphosphorylation, and its deficiency impairs salt signal transduction. Our findings demonstrate that DHHC09 S-acylates and anchors STRK1 to the plasma membrane to promote salt signaling from STRK1 to CatC, thereby regulating H2O2 homeostasis and improving salt stress tolerance in rice. Moreover, overexpression of DHHC09 in rice mitigates grain yield loss under salt stress. Together, these results shed light on the mechanism underlying the role of S-acylation in RLK/RLCK-mediated salt signal transduction and provide a strategy for breeding highly salt-tolerant rice.

The Receptor Kinases DRUS1 and DRUS2 Behave Distinctly in Osmotic Stress Tolerance by Modulating the Root System Architecture via Auxin Signaling

Receptor kinases DRUS1 (Dwarf and Runtish Spikelet1) and DRUS2 are orthologues of the renowned Arabidopsis thaliana gene FERONIA, which play redundant roles in rice growth and development. Whether the two duplicated genes perform distinct functions in response to environmental stress is largely unknown. Here, we found that osmotic stress (OS) and ABA increased DRUS1 expression while decreasing DRUS2. When subjected to osmotic stress, the increased DRUS1 in drus2 mutants suppresses the OsIAA repressors, resulting in a robust root system with an increased number of adventitious and lateral roots as well as elongated primary, adventitious, and lateral roots, conferring OS tolerance. In contrast, the decreased DRUS2 in drus1-1 mutants are not sufficient to suppress OsIAA repressors, leading to a feeble root system with fewer adventitious and lateral roots and hindering seminal root growth, rendering OS intolerance. All these findings offer valuable insights into the biological significance of the duplication of two homologous genes in rice, wherein, if one is impaired, the other one is able to continue auxin-signaling-mediated root growth and development to favor resilience to environmental stress, such as water shortage.

De novo transcriptomic analysis of Doum Palm (Hyphaene compressa) revealed an insight into its potential drought tolerance

BACKGROUND

Doum palms (Hyphaene compressa) perform a crucial starring role in the lives of Kenya's arid and semi-arid people for empowerment and sustenance. Despite the crop's potential for economic gain, there is a lack of genetic resources and detailed information about its domestication at the molecular level. Given the doum palm's vast potential as a widely distributed plant in semi-arid and arid climates and a source of many applications, coupled with the current changing climate scenario, it is essential to understand the molecular processes that provide drought resistance to this plant.

RESULTS

Assembly of the first transcriptome of doum palms subjected to water stress generated about 39.97 Gb of RNA-Seq data. The assembled transcriptome revealed 193,167 unigenes with an average length of 1655 bp, with 128,708 (66.63%) successfully annotated in seven public databases. Unigenes exhibited significant differentially expressed genes (DEGs) in well-watered and stressed-treated plants, with 45071 and 42457 accounting for up-regulated and down-regulated DEGs, respectively. GO term, KEGG, and KOG analysis showed that DEGs were functionally enriched cellular processes, metabolic processes, cellular and catalytic activity, metabolism, genetic information processing, signal transduction mechanisms, and posttranslational modification pathways. Transcription factors (TF), such as the MYB, WRKY, NAC family, FAR1, B3, bHLH, and bZIP, were the prominent TF families identified as doum palm DEGs encoding drought stress tolerance.

CONCLUSIONS

This study provides a complete understanding of DEGs involved in drought stress at the transcriptome level in doum palms. This research is, therefore, the foundation for the characterization of potential genes, leading to a clear understanding of its drought stress responses and providing resources for improved genetic modification.

How plants sense and respond to osmotic stress

Drought is one of the most serious abiotic stresses to land plants. Plants sense and respond to drought stress to survive under water deficiency. Scientists have studied how plants sense drought stress, or osmotic stress caused by drought, ever since Charles Darwin, and gradually obtained clues about osmotic stress sensing and signaling in plants. Osmotic stress is a physical stimulus that triggers many physiological changes at the cellular level, including changes in turgor, cell wall stiffness and integrity, membrane tension, and cell fluid volume, and plants may sense some of these stimuli and trigger downstream responses. In this review, we emphasized water potential and movements in organisms, compared putative signal inputs in cell wall-containing and cell wall-free organisms, prospected how plants sense changes in turgor, membrane tension, and cell fluid volume under osmotic stress according to advances in plants, animals, yeasts, and bacteria, summarized multilevel biochemical and physiological signal outputs, such as plasma membrane nanodomain formation, membrane water permeability, root hydrotropism, root halotropism, Casparian strip and suberin lamellae, and finally proposed a hypothesis that osmotic stress responses are likely to be a cocktail of signaling mediated by multiple osmosensors. We also discussed the core scientific questions, provided perspective about the future directions in this field, and highlighted the importance of robust and smart root systems and efficient source-sink allocations for generating future high-yield stress-resistant crops and plants.

Pectin demethylation-mediated cell wall Na+ retention positively regulates salt stress tolerance in oilseed rape

KEY MESSAGE

Integrated phenomics, ionomics, genomics, transcriptomics, and functional analyses present novel insights into the role of pectin demethylation-mediated cell wall Na+ retention in positively regulating salt tolerance in oilseed rape. Genetic variations in salt stress tolerance identified in rapeseed genotypes highlight the complicated regulatory mechanisms. Westar is ubiquitously used as a transgenic receptor cultivar, while ZS11 is widely grown as a high-production and good-quality cultivar. In this study, Westar was found to outperform ZS11 under salt stress. Through cell component isolation, non-invasive micro-test, X-ray energy spectrum analysis, and ionomic profile characterization, pectin demethylation-mediated cell wall Na+ retention was proposed to be a major regulator responsible for differential salt tolerance between Westar and ZS11. Integrated analyses of genome-wide DNA variations, differential expression profiling, and gene co-expression networks identified BnaC9.PME47, encoding a pectin methylesterase, as a positive regulator conferring salt tolerance in rapeseed. BnaC9.PME47, located in two reported QTL regions for salt tolerance, was strongly induced by salt stress and localized on the cell wall. Natural variation of the promoter regions conferred higher expression of BnaC9.PME47 in Westar than in several salt-sensitive rapeseed genotypes. Loss of function of AtPME47 resulted in the hypersensitivity of Arabidopsis plants to salt stress. The integrated multiomics analyses revealed novel insights into pectin demethylation-mediated cell wall Na+ retention in regulating differential salt tolerance in allotetraploid rapeseed genotypes. Furthermore, these analyses have provided key information regarding the rapid dissection of quantitative trait genes responsible for nutrient stress tolerance in plant species with complex genomes.

Genomic investigation of duplication, functional conservation, and divergence in the LRR-RLK Family of Saccharum

BACKGROUND

Sugarcane (Saccharum spp.) holds exceptional global significance as a vital crop, serving as a primary source of sucrose, bioenergy, and various by-products. The optimization of sugarcane breeding by fine-tuning essential traits has become crucial for enhancing crop productivity and stress resilience. Leucine-rich repeat receptor-like kinases (LRR-RLK) genes present promising targets for this purpose, as they are involved in various aspects of plant development and defense processes.

RESULTS

Here, we present a detailed overview of phylogeny and expression of 288 (495 alleles) and 312 (1365 alleles) LRR-RLK genes from two founding Saccharum species, respectively. Phylogenetic analysis categorized these genes into 15 subfamilies, revealing considerable expansion or reduction in certain LRR-type subfamilies. Compared to other plant species, both Saccharum species had more significant LRR-RLK genes. Examination of cis-acting elements demonstrated that SsLRR-RLK and SoLRR-RLK genes exhibited no significant difference in the types of elements included, primarily involved in four physiological processes. This suggests a broad conservation of LRR-RLK gene function during Saccharum evolution. Synteny analysis indicated that all LRR-RLK genes in both Saccharum species underwent gene duplication, primarily through whole-genome duplication (WGD) or segmental duplication. We identified 28 LRR-RLK genes exhibiting novel expression patterns in response to different tissues, gradient development leaves, and circadian rhythm in the two Saccharum species. Additionally, SoLRR-RLK104, SoLRR-RLK7, SoLRR-RLK113, and SsLRR-RLK134 were identified as candidate genes for sugarcane disease defense response regulators through transcriptome data analysis of two disease stresses. This suggests LRR-RLK genes of sugarcane involvement in regulating various biological processes, including leaf development, plant morphology, photosynthesis, maintenance of circadian rhythm stability, and defense against sugarcane diseases.

CONCLUSIONS

This investigation into gene duplication, functional conservation, and divergence of LRR-RLK genes in two founding Saccharum species lays the groundwork for a comprehensive genomic analysis of the entire LRR-RLK gene family in Saccharum. The results reveal LRR-RLK gene played a critical role in Saccharum adaptation to diverse conditions, offering valuable insights for targeted breeding and precise phenotypic adjustments.

Molecular Mechanisms and Regulatory Pathways Underlying Drought Stress Response in Rice

Rice is a staple food for 350 million people globally. Its yield thus affects global food security. Drought is a serious environmental factor affecting rice growth. Alleviating the inhibition of drought stress is thus an urgent challenge that should be solved to enhance rice growth and yield. This review details the effects of drought on rice morphology, physiology, biochemistry, and the genes associated with drought stress response, their biological functions, and molecular regulatory pathways. The review further highlights the main future research directions to collectively provide theoretical support and reference for improving drought stress adaptation mechanisms and breeding new drought-resistant rice varieties.

Beyond skin-deep: targeting the plant surface for crop improvement

The above-ground plant surface is a well-adapted tissue layer that acts as an interface between the plant and its surrounding environment. As such, its primary role is to protect against desiccation and maintain the gaseous exchange required for photosynthesis. Further, this surface layer provides a barrier against pathogens and herbivory, while attracting pollinators and agents of seed dispersal. In the context of agriculture, the plant surface is strongly linked to post-harvest crop quality and yield. The epidermal layer contains several unique cell types adapted for these functions, while the non-lignified above-ground plant organs are covered by a hydrophobic cuticular membrane. This review aims to provide an overview of the latest understanding of the molecular mechanisms underlying crop cuticle and epidermal cell formation, with focus placed on genetic elements contributing towards quality, yield, drought tolerance, herbivory defence, pathogen resistance, pollinator attraction, and sterility, while highlighting the inter-relatedness of plant surface development and traits. Potential crop improvement strategies utilizing this knowledge are outlined in the context of the recent development of new breeding techniques.

Meta-QTL analysis in wheat: progress, challenges and opportunities

Wheat, an important cereal crop globally, faces major challenges due to increasing global population and changing climates. The production and productivity are challenged by several biotic and abiotic stresses. There is also a pressing demand to enhance grain yield and quality/nutrition to ensure global food and nutritional security. To address these multifaceted concerns, researchers have conducted numerous meta-QTL (MQTL) studies in wheat, resulting in the identification of candidate genes that govern these complex quantitative traits. MQTL analysis has successfully unraveled the complex genetic architecture of polygenic quantitative traits in wheat. Candidate genes associated with stress adaptation have been pinpointed for abiotic and biotic traits, facilitating targeted breeding efforts to enhance stress tolerance. Furthermore, high-confidence candidate genes (CGs) and flanking markers to MQTLs will help in marker-assisted breeding programs aimed at enhancing stress tolerance, yield, quality and nutrition. Functional analysis of these CGs can enhance our understanding of intricate trait-related genetics. The discovery of orthologous MQTLs shared between wheat and other crops sheds light on common evolutionary pathways governing these traits. Breeders can leverage the most promising MQTLs and CGs associated with multiple traits to develop superior next-generation wheat cultivars with improved trait performance. This review provides a comprehensive overview of MQTL analysis in wheat, highlighting progress, challenges, validation methods and future opportunities in wheat genetics and breeding, contributing to global food security and sustainable agriculture.

Natural variation in OsSEC13 HOMOLOG 1 modulates redox homeostasis to confer cold tolerance in rice

Rice (Oryza sativa L.) is a cold-sensitive species that often faces cold stress, which adversely affects yield productivity and quality. However, the genetic basis for low-temperature adaptation in rice remains unclear. Here, we demonstrate that 2 functional polymorphisms in O. sativa SEC13 Homolog 1 (OsSEH1), encoding a WD40-repeat nucleoporin, between the 2 subspecies O. sativa japonica and O. sativa indica rice, may have facilitated cold adaptation in japonica rice. We show that OsSEH1 of the japonica variety expressed in OsSEH1MSD plants (transgenic line overexpressing the OsSEH1 allele from Mangshuidao [MSD], cold-tolerant landrace) has a higher affinity for O. sativa metallothionein 2b (OsMT2b) than that of OsSEH1 of indica. This high affinity of OsSEH1MSD for OsMT2b results in inhibition of OsMT2b degradation, with decreased accumulation of reactive oxygen species and increased cold tolerance. Transcriptome analysis indicates that OsSEH1 positively regulates the expression of the genes encoding dehydration-responsive element-binding transcription factors, i.e. OsDREB1 genes, and induces the expression of multiple cold-regulated genes to enhance cold tolerance. Our findings highlight a breeding resource for improving cold tolerance in rice.

Emerging Roles of Receptor-like Protein Kinases in Plant Response to Abiotic Stresses

The productivity of plants is hindered by unfavorable conditions. To perceive stress signals and to transduce these signals to intracellular responses, plants rely on membrane-bound receptor-like kinases (RLKs). These play a pivotal role in signaling events governing growth, reproduction, hormone perception, and defense responses against biotic stresses; however, their involvement in abiotic stress responses is poorly documented. Plant RLKs harbor an N-terminal extracellular domain, a transmembrane domain, and a C-terminal intracellular kinase domain. The ectodomains of these RLKs are quite diverse, aiding their responses to various stimuli. We summarize here the sub-classes of RLKs based on their domain structure and discuss the available information on their specific role in abiotic stress adaptation. Furthermore, the current state of knowledge on RLKs and their significance in abiotic stress responses is highlighted in this review, shedding light on their role in influencing plant-environment interactions and opening up possibilities for novel approaches to engineer stress-tolerant crop varieties.

Knocking Out OsRLK7-1 Impairs Rice Growth and Development but Enhances Its Resistance to Planthoppers

Leucine-rich repeat receptor-like kinases (LRR-RLKs) are an important subfamily of receptor-like kinases (RLKs) in plants that play key roles in sensing different biotic and abiotic stress. However, the role of LRR-RLKs in herbivore-induced plant defense remains largely elusive. Here, we found that the expression of a rice gene, OsRLK7-1, was induced by mechanical wounding, but was slightly suppressed by the infestation of gravid females of brown planthopper (BPH, Nilaparvata lugens) or white-backed planthopper (WBPH, Sogatella furcifera). Through targeted disruption of OsRLK7-1 (resulting in the ko-rlk lines), we observed an augmentation in transcript levels of BPH-induced OsMPK3, OsWRKY30, OsWRKY33, and OsWRKY45, alongside heightened levels of planthopper-induced jasmonic acid, JA-isoleucine, and abscisic acid in plant tissues. These dynamic changes further facilitated the biosynthesis of multiple phenolamides within the rice plants, culminating in an enhanced resistance to planthopper infestations under both lab and field conditions. In addition, knocking out OsRLK7-1 impaired plant growth and reproduction. These results suggest that OsRLK7-1 plays an important role in regulating rice growth, development, and rice-planthopper interactions.

The protein phosphatase PC1 dephosphorylates and deactivates CatC to negatively regulate H2O2 homeostasis and salt tolerance in rice

Catalase (CAT) is often phosphorylated and activated by protein kinases to maintain hydrogen peroxide (H2O2) homeostasis and protect cells against stresses, but whether and how CAT is switched off by protein phosphatases remains inconclusive. Here, we identified a manganese (Mn2+)-dependent protein phosphatase, which we named PHOSPHATASE OF CATALASE 1 (PC1), from rice (Oryza sativa L.) that negatively regulates salt and oxidative stress tolerance. PC1 specifically dephosphorylates CatC at Ser-9 to inhibit its tetramerization and thus activity in the peroxisome. PC1 overexpressing lines exhibited hypersensitivity to salt and oxidative stresses with a lower phospho-serine level of CATs. Phosphatase activity and seminal root growth assays indicated that PC1 promotes growth and plays a vital role during the transition from salt stress to normal growth conditions. Our findings demonstrate that PC1 acts as a molecular switch to dephosphorylate and deactivate CatC and negatively regulate H2O2 homeostasis and salt tolerance in rice. Moreover, knockout of PC1 not only improved H2O2-scavenging capacity and salt tolerance but also limited rice grain yield loss under salt stress conditions. Together, these results shed light on the mechanisms that switch off CAT and provide a strategy for breeding highly salt-tolerant rice.

OsOLP1 contributes to drought tolerance in rice by regulating ABA biosynthesis and lignin accumulation

Rice, as a major staple crop, employs multiple strategies to enhance drought tolerance and subsequently increase yield. Osmotin-like proteins have been shown to promote plant resistance to biotic and abiotic stress. However, the drought resistance mechanism of osmotin-like proteins in rice remains unclear. This study identified a novel osmotin-like protein, OsOLP1, that conforms to the structure and characteristics of the osmotin family and is induced by drought and NaCl stress. CRISPR/Cas9-mediated gene editing and overexpression lines were used to investigate the impact of OsOLP1 on drought tolerance in rice. Compared to wild-type plants, transgenic rice plants overexpressing OsOLP1 showed high drought tolerance with leaf water content of up to 65%, and a survival rate of 53.1% by regulating 96% stomatal closure and more than 2.5-fold proline content promotion through the accumulation of 1.5-fold endogenous ABA, and enhancing about 50% lignin synthesis. However, OsOLP1 knockout lines showed severely reduced ABA content, decreased lignin deposition, and weakened drought tolerance. In conclusion, the finding confirmed that OsOLP1 drought-stress modulation relies on ABA accumulation, stomatal regulation, proline, and lignin accumulation. These results provide new insights into our perspective on rice drought tolerance.

NtLTPI.38, a plasma membrane-localized protein, mediates lipid metabolism and salt tolerance in Nicotiana tabacum

Non-specific lipid transfer proteins (nsLTPs) typically have conserved structural resemblance, low sequence identity, and broad biological functions in plant growth and stress resistance. Here, a plasma membrane-localized nsLTP, NtLTPI.38, was identified in tobacco plants. Multi-omics integrated analysis revealed that NtLTPI.38 overexpression or knock out significantly changed glycerophospholipid and glycerolipid metabolism pathways. NtLTPI.38 overexpression remarkably increased phosphatidylcholine, phosphatidylethanolamine, triacylglycerol, and flavonoid levels, but decreased ceramides compared to wild type and mutant lines. Differentially expressed genes were associated with lipid metabolite and flavonoid synthesis. Many genes related to Ca²⁺ channels, abscisic acid (ABA) signal transduction, and ion transport pathways were upregulated in overexpressing plants. NtLTPI.38 overexpression in salt-stressed tobacco triggered a Ca²⁺ and K⁺ influx in leaves, increased the contents of chlorophyll, proline, flavonoids, and osmotic tolerance, and raised enzymatic antioxidant activities as well as the expression level of related genes. However, mutants accumulated more O₂^- and H₂O_2, exhibited ionic imbalance, gathered excess Na⁺, Cl^-, and malondialdehyde, with more severe ion leakage. Therefore, NtLTPI.38 enhanced salt tolerance in tobacco by regulating lipid and flavonoid synthesis, antioxidant activity, ion homeostasis, and ABA signaling pathways.

Phylogeny of the plant receptor-like kinase (RLK) gene family and expression analysis of wheat RLK genes in response to biotic and abiotic stresses

BACKGROUND

The receptor-like kinase (RLK) gene families in plants contains a large number of members. They are membrane proteins with an extracellular receptor domain and participate in biotic and abiotic stress responses.

RESULTS

In this study, we identified RLKs in 15 representative plant genomes, including wheat, and classified them into 64 subfamilies by using four types of phylogenetic trees and HMM models. Conserved exon‒intron structures with conserved exon phases in the kinase domain were found in many RLK subfamilies from Physcomitrella patens to Triticum aestivum. Domain distributions of RLKs were also diagrammed. Collinearity events and tandem gene clusters suggested that polyploidization and tandem duplication events contributed to the member expansions of T. aestivum RLKs. Global expression pattern analysis was performed by using public transcriptome data. These analyses were involved in T. aestivum, Aegilops tauschii and Brachypodium distachyon RLKs under biotic and abiotic stresses. We also selected 9 RLKs to validate the transcriptome prediction by using qRT‒PCR under drought treatment and with Fusarium graminearum infection. The expression trends of these 9 wheat RLKs from public transcriptome data were consistent with the results of qRT‒PCR, indicating that they might be stress response genes under drought or F. graminearum treatments.

CONCLUSION

In this study, we identified, classified, evolved, and expressed RLKs in wheat and related plants. Thus, our results will provide insights into the evolutionary history and molecular mechanisms of wheat RLKs.

Receptor-Like Cytoplasmic Kinase STK Confers Salt Tolerance in Rice

BACKGROUND

Soil salinization is a major abiotic environmental stress factor threatening crop production throughout the world. Salt stress drastically affects the growth, development, and grain yield of rice (Oryza sativa L.), and the improvement of rice tolerance to salt stress is a desirable approach for meeting increasing food demand. Receptor-like cytoplasmic kinases (RLCKs) play essential roles in plant growth, development and responses to environmental stresses. However, little is known about their functions in salt stress. Previous reports have demonstrated that overexpression of an RLCK gene SALT TOLERANCE KINASE (STK) enhances salt tolerance in rice, and that STK may regulate the expression of GST (Glutathione S-transferase) genes.

RESULTS

The expression of STK was rapidly induced by ABA. STK was highest expressed in the stem at the heading stage. STK was localized at the plasma membrane. Overexpression of STK in rice increased tolerance to salt stress and oxidative stress by increasing ROS scavenging ability and ABA sensitivity. In contrast, CRISPR/Cas9-mediated knockout of STK increased the sensitivity of rice to salt stress and oxidative stress. Transcriptome sequencing analysis suggested that STK increased the expression of GST genes (LOC_Os03g17480, LOC_Os10g38140 and LOC_Os10g38710) under salt stress. Reverse transcription quantitative PCR (RT-qPCR) suggested that four stress-related genes may be regulated by STK including OsABAR1, Os3BGlu6, OSBZ8 and OsSIK1.

CONCLUSIONS

These findings suggest that STK plays a positive regulatory role in salt stress tolerance by inducing antioxidant defense and associated with the ABA signaling pathway in rice.

The suppressed expression of a stress responsive gene 'OsDSR2' enhances rice tolerance in drought and salt stress

Rice is a crucial staple food crop in many countries, yet, abiotic factors like salt and drought impact its growth. The Domain of Unknown Function 966 (DUF966) gene family may be crucial in how rice plants respond to abiotic stress. Our earlier research showed that overexpression of OsDSR2 (DUF966-stress repressive gene 2 in Oryza sativa) decreased resistance to salt and drought stress. To further understand how OsDSR2 negatively affects rice tolerance to salt and drought stress, transgenic rice plants with decreased OsDSR2 expression levels were created employing the RNAi technique. We investigated alterations in rice phenotype, physiology, and differentially expressed genes (DEGs) using a combination of physio-biochemical measurement and RNA-seq analysis. The results of the study demonstrated that rice seedling lines with OsDSR2 knockdown exhibited improved salt and drought stress tolerance. Statistical analysis revealed that the transgenic plants' survival rate (56-68%) was higher than the control plants (30%), in addition to a roughly 3 fold, 3.5 fold, 20% and 10.5% reduction in cell membrane permeability, malondialdehyde (MDA), superoxide anion radical (O₂^-) and hydrogen peroxide (H₂O₂) contents, respectively. However, the proline content and antioxidant enzymes (superoxide dismutase (SOD) and peroxidase (POD)) activities were considerably increased by about 5.5 fold, 3.5 fold, and 4.5 fold, respectively, at physiological levels. There were 115 up-regulated and 173 down-regulated DEGs in the leaves of the transgenic lines on the transcriptional regulation under the combined salt-drought stress. Among these, both up-regulation DEGs (e.g., OsHAK5, OsIAA25) and the down-regulation DEGs (e.g., OsbZIP23, OsERF48, OsAP2-39, etc.) may be related to the enhanced tolerance of the transgenic lines under combined salt-drought stress. This possibly depended on the involvement of abscisic acid (ABA) and indoleacetic acid (IAA) signaling pathways. These findings further confirmed that OsDSR2 negatively affected rice's ability to withstand salt and drought, suggesting that it could be a helpful gene for CRISPR-Cas9 technology-based genetic modification of rice's ability to withstand abiotic stress.

MicroRNA156ab regulates apple plant growth and drought tolerance by targeting transcription factor MsSPL13

Drought stress substantially reduces the productivity of apple plants and severely restricts the development of the apple industry. Malus sieversii, a wild apple with excellent drought resistance, is a valuable wild resource for rootstock improvement of cultivated apple (Malus domestica). miRNAs and their targets play essential roles in plant growth and stress responses, but their roles in drought stress responses in apple are unknown. Here, we demonstrate that microRNA156ab is upregulated in M. sieversii in response to drought stress. Overexpressing msi-miR156ab promoted auxin accumulation, maintained the growth of apple plants, and increased plant resistance to osmotic stress. Antioxidant enzyme activities and proline contents were also increased in miR156ab-OE transgenic apple lines, which improved drought resistance. The SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor MsSPL13 is the target of msi-miR156ab, as demonstrated by 5-RACE and dual luciferase assays. Heterologous expression of MsSPL13 decreased auxin contents and inhibited growth in Arabidopsis (Arabidopsis thaliana) under normal and stress conditions. The activities of antioxidant enzymes were also suppressed in MsSPL13-OE transgenic Arabidopsis, reducing drought resistance. We showed that MsSPL13 regulates the expression of the auxin-related genes MsYUCCA5, PIN-FORMED7 (MsPIN7), and Gretchen Hagen3-5 (MsGH3-5) by binding to the GTAC cis-elements in their promoters, thereby regulating auxin metabolism. Finally, we demonstrated that the miR156ab-SPL13 module is involved in mediating the difference in auxin metabolism and stress responses between the M. sieversii and M26 (M. domestica) rootstocks. Overall, these findings reveal that the miR156ab-SPL13 module enhances drought stress tolerance in apples by regulating auxin metabolism and antioxidant enzyme activities.

Membrane Proteins in Plant Salinity Stress Perception, Sensing, and Response

Plants have several mechanisms to endure salinity stress. The degree of salt tolerance varies significantly among different terrestrial crops. Proteins at the plant's cell wall and membrane mediate different physiological roles owing to their critical positioning between two distinct environments. A specific membrane protein is responsible for a single type of activity, such as a specific group of ion transport or a similar group of small molecule binding to exert multiple cellular effects. During salinity stress in plants, membrane protein functions: ion homeostasis, signal transduction, redox homeostasis, and solute transport are essential for stress perception, signaling, and recovery. Therefore, comprehensive knowledge about plant membrane proteins is essential to modulate crop salinity tolerance. This review gives a detailed overview of the membrane proteins involved in plant salinity stress highlighting the recent findings. Also, it discusses the role of solute transporters, accessory polypeptides, and proteins in salinity tolerance. Finally, some aspects of membrane proteins are discussed with potential applications to developing salt tolerance in crops.

Orchard Management and Incorporation of Biochemical and Molecular Strategies for Improving Drought Tolerance in Fruit Tree Crops

Water scarcity is one of the greatest concerns for agronomy worldwide. In recent years, many water resources have been depleted due to multiple factors, especially mismanagement. Water resource shortages lead to cropland expansion, which likely influences climate change and affects global agriculture, especially horticultural crops. Fruit yield is the final aim in commercial orchards; however, drought can slow tree growth and/or decrease fruit yield and quality. It is therefore necessary to find approaches to solve this problem. The main objective of this review is to discuss the most recent horticultural, biochemical, and molecular strategies adopted to improve the response of temperate fruit crops to water stress. We also address the viability of cultivating fruit trees in dry areas and provide precise protection methods for planting fruit trees in arid lands. We review the main factors involved in planting fruit trees in dry areas, including plant material selection, regulated deficit irrigation (DI) strategies, rainwater harvesting (RWH), and anti-water stress materials. We also provide a detailed analysis of the molecular strategies developed to combat drought, such as Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) through gene overexpression or gene silencing. Finally, we look at the molecular mechanisms associated with the contribution of the microbiome to improving plant responses to drought.

Genome-Wide Association Study of Agronomic and Physiological Traits Related to Drought Tolerance in Potato

Potato (Solanum tuberosum L.) is often considered a water-sensitive crop and its production can be threatened by drought events, making water stress tolerance a trait of increasing interest. In this study, a panel of 144 tetraploid potato genotypes was evaluated for two consecutive years (2019 and 2020) to observe the variation of several physiological traits such as chlorophyll content and fluorescence, stomatal conductance, NDVI, and leaf area and circumference. In addition, agronomic parameters such as yield, tuber fresh weight, tuber number, starch content, dry matter and reducing sugars were determined. GGP V3 Potato array was used to genotype the population, obtaining a total of 18,259 high-quality SNP markers. Marker-trait association was performed using GWASpoly package in R software and Q + K linear mixed models were considered. This approach allowed us to identify eighteen SNP markers significantly associated with the studied traits in both treatments and years, which were related to genes with known functions. Markers related to chlorophyll content and number of tubers under control and stress conditions, and related to stomatal conductance, NDVI, yield and reducing sugar content under water stress, were identified. Although these markers were distributed throughout the genome, the SNPs associated with the traits under control conditions were found mainly on chromosome 11, while under stress conditions they were detected on chromosome 4. These results contribute to the knowledge of the mechanisms of potato tolerance to water stress and are useful for future marker-assisted selection programs.

Molecular characterization reveals that OsSAPK3 improves drought tolerance and grain yield in rice

BACKGROUND

Many data suggest that the sucrose non-fermenting 1-related kinases 2 (SnRK2s) are very important to abiotic stress for plants. In rice, these kinases are known as osmotic stress/ABA-activated protein kinases (SAPKs). Osmotic stress/ABA-activated protein kinase 3 (OsSAPK3) is a member of SnRK2II in rice, but its function is still unclear.

RESULTS

The expression of OsSAPK3 was up regulated by drought, NaCl, PEG and ABA. OsSAPK3 mutated seedings (sapk3-1 and sapk3-2) showed reduced hypersensitivity to exogenous ABA. In addition, under drought conditions, sapk3-1 and sapk3-2 showed more intolerance to drought, including decreased survival rate, increased water loss rate, increased stomatal conductance and significantly decreased expression levels of SLAC1 and SLAC7. Physiological and metabolic analyses showed that OsSAPK3 might play an important role in drought stress signaling pathway by affecting osmotic adjustment and osmolytes, ROS detoxification and expression of ABA dependent and independent dehydration-responsive genes. All gronomic traits analyses demonstrated that OsSAPK3 could improve rice yield by affecting the regulation of tiller numbers and grain size.

CONCLUSION

OsSAPK3 plays an important role in both ABA-dependent and ABA-independent drought stress responses. More interestingly, OsSAPK3 could improve rice yield by indirectly regulating tiller number and grain size. These findings provide new insight for the development of drought-resistant rice.

Variety-Specific Transcriptional and Alternative Splicing Regulations Modulate Salt Tolerance in Rice from Early Stage of Stress

Salt stress poses physiological drought, ionic toxicity and oxidative stress to plants, which causes premature senescence and death of the leaves if the stress sustained. Salt tolerance varied between different rice varieties, but how different rice varieties respond at the early stage of salt stress has been seldom studied comprehensively. By employing third generation sequencing technology, we compared gene expressional changes in leaves of three rice varieties that varied in their level of tolerance after salt stress treatment for 6 h. Commonly up-regulated genes in all rice varieties were related to water shortage response and carbon and amino acids metabolism at the early stage of salt stress, while reactive oxygen species cleavage genes were induced more in salt-tolerant rice. Unexpectedly, genes involved in chloroplast development and photosynthesis were more significantly down-regulated in the two salt tolerant rice varieties 'C34' and 'Nona Bokra'. At the same time, genes coding ribosomal protein were suppressed to a more severe extent in the salt-sensitive rice variety 'IR29'. Interestingly, not only variety-specific gene transcriptional regulation, but also variety-specific mRNA alternative splicing, on both coding and long-noncoding genes, were found at the early stage of salt stress. In summary, differential regulation in gene expression at both transcriptional and post-transcriptional levels, determine and fine-tune the observed response in level of damage in leaves of specific rice genotypes at early stage of salt stress.

Whole-Genome Sequencing of KMR3 and Oryza rufipogon-Derived Introgression Line IL50-13 (Chinsurah Nona 2/Gosaba 6) Identifies Candidate Genes for High Yield and Salinity Tolerance in Rice

The genomes of an elite rice restorer line KMR3 (salinity-sensitive) and its salinity-tolerant introgression line IL50-13, a popular variety of coastal West Bengal, India, were sequenced. High-quality paired-end reads were obtained for KMR3 (147.6 million) and IL50-13 (131.4 million) with a sequencing coverage of 30X-39X. Scaffolds generated from the pre-assembled contigs of each sequenced genome were mapped separately onto the reference genome of Oryza sativa ssp. japonica cultivar Nipponbare to identify genomic variants in terms of SNPs and InDels. The SNPs and InDels identified for KMR3 and IL50-13 were then compared with each other to identify polymorphic SNPs and InDels unique and common to both the genomes. Functional enrichment analysis of the protein-coding genes with unique InDels identified GO terms involved in protein modification, ubiquitination, deubiquitination, peroxidase activity, and antioxidant activity in IL50-13. Linoleic acid metabolism, circadian rhythm, and alpha-linolenic acid metabolism pathways were enriched in IL50-13. These GO terms and pathways are involved in reducing oxidative damage, thus suggesting their role in stress responses. Sequence analysis of QTL markers or genes known to be associated with grain yield and salinity tolerance showed polymorphism in 20 genes, out of which nine were not previously reported. These candidate genes encoded Nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC) domain-containing protein, cyclase, receptor-like kinase, topoisomerase II-associated protein PAT1 domain-containing protein, ion channel regulatory protein, UNC-93 domain-containing protein, subunit A of the heteromeric ATP-citrate lyase, and three conserved hypothetical genes. Polymorphism was observed in the coding, intron, and untranslated regions of the genes on chromosomes 1, 2, 4, 7, 11, and 12. Genes showing polymorphism between the two genomes were considered as sequence-based new candidates derived from Oryza rufipogon for conferring high yield and salinity tolerance in IL50-13 for further functional studies.

WATER-SOAKED SPOT1 Controls Chloroplast Development and Leaf Senescence via Regulating Reactive Oxygen Species Homeostasis in Rice

Transmembrane kinases (TMKs) play important roles in plant growth and signaling cascades of phytohormones. However, its function in the regulation of early leaf senescence (ELS) of plants remains unknown. Here, we report the molecular cloning and functional characterization of the WATER-SOAKED SPOT1 gene which encodes a protein belongs to the TMK family and controls chloroplast development and leaf senescence in rice (Oryza sativa L.). The water-soaked spot1 (oswss1) mutant displays water-soaked spots which subsequently developed into necrotic symptoms at the tillering stage. Moreover, oswss1 exhibits slightly rolled leaves with irregular epidermal cells, decreased chlorophyll contents, and defective stomata and chloroplasts as compared with the wild type. Map-based cloning revealed that OsWSS1 encodes transmembrane kinase TMK1. Genetic complementary experiments verified that a Leu396Pro amino acid substitution, residing in the highly conserved region of leucine-rich repeat (LRR) domain, was responsible for the phenotypes of oswss1. OsWSS1 was constitutively expressed in all tissues and its encoded protein is localized to the plasma membrane. Mutation of OsWSS1 led to hyper-accumulation of reactive oxygen species (ROS), more severe DNA fragmentation, and cell death than that of the wild-type control. In addition, we found that the expression of senescence-associated genes (SAGs) was significantly higher, while the expression of genes associated with chloroplast development and photosynthesis was significantly downregulated in oswss1 as compared with the wild type. Taken together, our results demonstrated that OsWSS1, a member of TMKs, plays a vital role in the regulation of ROS homeostasis, chloroplast development, and leaf senescence in rice.

OsSCL30 overexpression reduces the tolerance of rice seedlings to low temperature, drought and salt

Rice is one of the main food crops for the world population. Various abiotic stresses, such as low temperature, drought, and high salinity, affect rice during the entire growth period, determining its yield and quality, and even leading to plant death. In this study, by constructing overexpression vectors D-163 + 1300:OsSCL30 and D-163 + 1300-AcGFP:OsSCL30-GFP, the mechanism of action of OsSCL30 in various abiotic stresses was explored. Bioinformatics analysis showed that OsSCL30 was located on the chromosome 12 of rice Nipponbare, belonging to the plant-specific SCL subfamily of the SR protein family. The 1500 bp section upstream of the open reading frame start site contains stress-related cis-acting elements such as ABRE, MYC, and MYB. Under normal conditions, the expression of OsSCL30 was higher in leaves and leaf sheaths. The results of reverse transcription polymerase chain reaction showed that the expression of OsSCL30 decreased after low temperature, drought and salt treatment. In root cells OsSCL30 was localized in the nuclei. The results of the rice seedling tolerance and recovery tests showed that overexpression of OsSCL30 diminished the resistance to low temperature, drought and salt stresses in transgenic rice and resulted in larger accumulation of reactive oxygen species. This study is of great significance for exploring the response mechanisms of SR proteins under abiotic stresses.

Combined GWAS and Transcriptome Analyses Provide New Insights Into the Response Mechanisms of Sunflower Against Drought Stress

Sunflower is one of the most important oil crops in the world, and drought stress can severely limit its production and quality. To understand the underlying mechanism of drought tolerance, and identify candidate genes for drought tolerance breeding, we conducted a combined genome-wide association studies (GWAS) and RNA-seq analysis. A total of 226 sunflower inbred lines were collected from different regions of China and other countries. Eight phenotypic traits were evaluated under control and drought stress conditions. Genotyping was performed using a Specific-Locus Amplified Fragment Sequencing (SLAF-seq) approach. A total of 934.08 M paired-end reads were generated, with an average Q30 of 91.97%. Based on the 243,291 polymorphic SLAF tags, a total of 94,162 high-quality SNPs were identified. Subsequent analysis of linkage disequilibrium (LD) and population structure in the 226 accessions was carried out based on the 94,162 high-quality SNPs. The average LD decay across the genome was 20 kb. Admixture analysis indicated that the entire population most likely originated from 11 ancestors. GWAS was performed using three methods (MLM, FarmCPU, and BLINK) simultaneously. A total of 80 SNPs showed significant associations with the 8 traits (p < 1.062 × 10-6). Next, a total of 118 candidate genes were found. To obtain more reliable candidate genes, RNA-seq analysis was subsequently performed. An inbred line with the highest drought tolerance was selected according to phenotypic traits. RNA was extracted from leaves at 0, 7, and 14 days of drought treatment. A total of 18,922 differentially expressed genes were obtained. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis showed up-regulated genes were mainly enriched in the branched-chain amino acid catabolic process, while the down-regulated genes were mainly enriched in the photosynthesis-related process. Six DEGs were randomly selected from all DEGs for validation; these genes showed similar patterns in RNA-seq and RT-qPCR analysis, with a correlation coefficient of 0.8167. Through the integration of the genome-wide association study and the RNA-sequencing, 14 candidate genes were identified. Four of them (LOC110885273, LOC110872899, LOC110891369, LOC110920644) were abscisic acid related protein kinases and transcription factors. These genes may play an important role in sunflower drought response and will be used for further study. Our findings provide new insights into the response mechanisms of sunflowers against drought stress and contribute to further genetic breeding.

Mining Beneficial Genes for Salt Tolerance From a Core Collection of Rice Landraces at the Seedling Stage Through Genome-Wide Association Mapping

Rice is a salt-sensitive plant. High concentration of salt will hinder the absorption of water and nutrients and ultimately affect the yield. In this study, eight seedling-stage salt-related traits within a core collection of rice landraces were evaluated under salinity stress (100 mM NaCl) and normal conditions in a growth chamber. Genome-wide association study (GWAS) was performed with the genotypic data including 2,487,353 single-nucleotide polymorphisms (SNPs) detected in the core collection. A total of 65 QTLs significantly associated with salt tolerance (ST) were identified by GWAS. Among them, a co-localization QTL qTL4 associated with the SKC, RN/K, and SNC on chromosome 6, which explained 14.38-17.94% of phenotypic variation, was selected for further analysis. According to haplotype analysis, qRT-PCR analysis, and sequence alignment, it was finally determined that 4 candidate genes (LOC_Os06g47720, LOC_Os06g47820, LOC_Os06g47850, LOC_Os06g47970) were related to ST. The results provide useful candidate genes for marker assisted selection for ST in the rice molecular breeding programs.

Time-course transcriptome and WGCNA analysis revealed the drought response mechanism of two sunflower inbred lines

Drought is one of the most serious abiotic stress factors limiting crop yields. Although sunflower is considered a moderate drought-tolerant plant, drought stress still has a negative impact on sunflower yield as cultivation expands into arid regions. The extent of drought stress is varieties and time-dependent, however, the molecular response mechanisms of drought tolerance in sunflower with different varieties are still unclear. Here, we performed comparative physiological and transcriptome analyses on two sunflower inbred lines with different drought tolerance at the seedling stage. The analysis of nine physiological and biochemical indicators showed that the leaf surface area, leaf relative water content, and cell membrane integrity of drought tolerance inbred line were higher than those of drought-sensitive inbred line under drought stress, indicating that DT had stronger drought resistance. Transcriptome analyses identified 24,234 differentially expressed genes (DEGs). Gene ontology (GO) analysis showed the up-regulated genes were mainly enriched in gibberellin metabolism and rRNA processing, while the down-regulated genes were mainly enriched in cell-wall, photosynthesis, and terpene metabolism. Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis showed genes related to GABAergic synapse, ribosome biogenesis were up-regulated, while genes related with amino sugar and nucleotide sugar metabolism, starch and sucrose metabolism, photosynthesis were down-regulated. Mapman analysis revealed differences in plant hormone-signaling genes over time and between samples. A total of 1,311 unique putative transcription factors (TFs) were identified from all DEGs by iTAK, among which the high abundance of transcription factor families include bHLH, AP2/ERF, MYB, C2H2, etc. Weighted gene co-expression network analysis (WGCNA) revealed a total of 2,251 genes belonging to two modules(blue 4, lightslateblue), respectively, which were significantly associated with six traits. GO and KEGG enrichment analysis of these genes was performed, followed by visualization with Cytoscape software, and the top 20 Hub genes were screened using the CytoHubba plugin.

Impact of Pre-Anthesis Drought Stress on Physiology, Yield-Related Traits, and Drought-Responsive Genes in Green Super Rice

Optimum soil water availability is vital for maximum yield production in rice which is challenged by increasing spells of drought. The reproductive stage drought is among the main limiting factors leading to the drastic reduction in grain yield. The objective of this study was to investigate the molecular and morphophysiological responses of pre-anthesis stage drought stress in green super rice. The study assessed the performance of 26 rice lines under irrigated and drought conditions. Irrigated treatment was allowed to grow normally, while drought stress was imposed for 30 days at the pre-anthesis stage. Three important physiological traits including pollen fertility percentage (PFP), cell membrane stability (CMS), and normalized difference vegetative index (NDVI) were recorded at anthesis stage during the last week of drought stress. Agronomic traits of economic importance including grain yield were recorded at maturity stage. The analysis of variance demonstrated significant variation among the genotypes for most of the studied traits. Correlation and principal component analyses demonstrated highly significant associations of particular agronomic traits with grain yield, and genetic diversity among genotypes, respectively. Our study demonstrated a higher drought tolerance potential of GSR lines compared with local cultivars, mainly by higher pollen viability, plant biomass, CMS, and harvest index under drought. In addition, the molecular basis of drought tolerance in GSR lines was related to upregulation of certain drought-responsive genes including OsSADRI, OsDSM1, OsDT11, but not the DREB genes. Our study identified novel drought-responsive genes (LOC_Os11g36190, LOC_Os12g04500, LOC_Os12g26290, and LOC_Os02g11960) that could be further characterized using reverse genetics to be utilized in molecular breeding for drought tolerance.

Global gene expression profiling under nitrogen stress identifies key genes involved in nitrogen stress adaptation in maize (Zea mays L.)

Maize is a heavy consumer of fertilizer nitrogen (N) which not only results in the high cost of cultivation but may also lead to environmental pollution. Therefore, there is a need to develop N-use efficient genotypes, a prerequisite for which is a greater understanding of N-deficiency stress adaptation. In this study, comparative transcriptome analysis was performed using leaf and root tissues from contrasting inbred lines, viz., DMI 56 (tolerant to N stress) and DMI 81 (susceptible to N stress) to delineate the differentially expressed genes (DEGs) under low-N stress. The contrasting lines were grown hydroponically in modified Hoagland solution having either sufficient- or deficient-N, followed by high-throughput RNA-sequencing. A total of 8 sequencing libraries were prepared and 88–97% of the sequenced raw reads were mapped to the reference B73 maize genome. Genes with a p value ≤ 0.05 and fold change of ≥ 2.0 or ≤ − 2 were considered as DEGs in various combinations performed between susceptible and tolerant genotypes. DEGs were further classified into different functional categories and pathways according to their putative functions. Gene Ontology based annotation of these DEGs identified three different functional categories: biological processes, molecular function, and cellular component. The KEGG and Mapman based analysis revealed that most of the DEGs fall into various metabolic pathways, biosynthesis of secondary metabolites, signal transduction, amino acid metabolism, N-assimilation and metabolism, and starch metabolism. Some of the key genes involved in N uptake (high-affinity nitrate transporter 2.2 and 2.5), N assimilation and metabolism (glutamine synthetase, asparagine synthetase), redox homeostasis (SOD, POX), and transcription factors (MYB36, AP2-EREBP) were found to be highly expressed in the tolerant genotype compared to susceptible one. The candidate genes identified in the present study might be playing a pivotal role in low-N stress adaptation in maize and hence could be useful in augmenting further research on N metabolism and development of N-deficiency tolerant maize cultivars.

Physiological Adaptation of Three Wild Halophytic Suaeda Species: Salt Tolerance Strategies and Metal Accumulation Capacity

Understanding salt tolerance mechanisms in halophytes is critical for improving the world's agriculture under climate change scenarios. Herein, the physiological and metabolic responses of Suaeda monoica, Suaeda vermiculata, and Suaeda schimperi against abiotic stress in their natural saline environment on the east coast of the Red Sea were investigated. The tested species are exposed to different levels of salinity along with elemental disorders, including deficiency in essential nutrients (N&P in particular) and/or elevated levels of potentially toxic elements. The tested species employed common and species-specific tolerance mechanisms that are driven by the level of salinity and the genetic constitution of Suaeda species. These mechanisms include: (i) utilization of inorganic elements as cheap osmotica (Na+ in particular), (ii) lowering C/N ratio (S. monoica and S. schimperi) that benefits growth priority, (iii) efficient utilization of low soil N (S. vermiculata) that ensures survival priority, (v) biosynthesis of betacyanin (S. schimperi and S. vermiculata) and (vi) downregulation of overall metabolism (S. vermiculata) to avoid oxidative stress. Based on their cellular metal accumulation, S. monoica is an efficient phytoextractor of Cr, Co, Cu, Ni, and Zn, whereas S. vermiculata is a hyper-accumulator of Hg and Pb. S. schimperi is an effective phytoextractor of Fe, Hg, and Cr. These results highlight the significance of Suaeda species as a promising model halophyte and as phytoremediators of their hostile environments.

Global N6-Methyladenosine Profiling Revealed the Tissue-Specific Epitranscriptomic Regulation of Rice Responses to Salt Stress

N6-methyladenosine (m6A) methylation represents a new layer of the epitranscriptomic regulation of plant development and growth. However, the effects of m6A on rice responses to environmental stimuli remain unclear. In this study, we performed a methylated-RNA immunoprecipitation sequencing analysis and compared the changes in m6A methylation and gene expression in rice under salt stress conditions. Salt stress significantly increased the m6A methylation in the shoots (p value < 0.05). Additionally, 2537 and 2304 differential m6A sites within 2134 and 1997 genes were identified in the shoots and roots, respectively, under salt stress and control conditions. These differential m6A sites were largely regulated in a tissue-specific manner. A unique set of genes encoding transcription factors, antioxidants, and auxin-responsive proteins had increased or decreased m6A methylation levels only in the shoots or roots under salt stress, implying m6A may mediate salt tolerance by regulating transcription, ROS homeostasis, and auxin signaling in a tissue-specific manner. Integrating analyses of m6A modifications and gene expression changes revealed that m6A changes regulate the expression of genes controlling plant growth, stress responses, and ion transport under saline conditions. These findings may help clarify the regulatory effects of m6A modifications on rice salt tolerance.

How to Cope with the Challenges of Environmental Stresses in the Era of Global Climate Change: An Update on ROS Stave off in Plants

With the advent of human civilization and anthropogenic activities in the shade of urbanization and global climate change, plants are exposed to a complex set of abiotic stresses. These stresses affect plants’ growth, development, and yield and cause enormous crop losses worldwide. In this alarming scenario of global climate conditions, plants respond to such stresses through a highly balanced and finely tuned interaction between signaling molecules. The abiotic stresses initiate the quick release of reactive oxygen species (ROS) as toxic by-products of altered aerobic metabolism during different stress conditions at the cellular level. ROS includes both free oxygen radicals {superoxide (O₂^•−) and hydroxyl (OH⁻)} as well as non-radicals [hydrogen peroxide (H₂O₂) and singlet oxygen (¹O₂)]. ROS can be generated and scavenged in different cell organelles and cytoplasm depending on the type of stimulus. At high concentrations, ROS cause lipid peroxidation, DNA damage, protein oxidation, and necrosis, but at low to moderate concentrations, they play a crucial role as secondary messengers in intracellular signaling cascades. Because of their concentration-dependent dual role, a huge number of molecules tightly control the level of ROS in cells. The plants have evolved antioxidants and scavenging machinery equipped with different enzymes to maintain the equilibrium between the production and detoxification of ROS generated during stress. In this present article, we have focused on current insights on generation and scavenging of ROS during abiotic stresses. Moreover, the article will act as a knowledge base for new and pivotal studies on ROS generation and scavenging.

BnA.JAZ5 Attenuates Drought Tolerance in Rapeseed through Mediation of ABA–JA Crosstalk

Drought stress reduces water availability in plant cells and influences rapeseed yield. Currently, key genetic regulators that contribute to rapeseed response to drought remain largely unexplored, which limits breeding of drought-resistant rapeseed. In this study, we found that Brassica napus JASMONATE ZIM-DOMAIN 5 (BnA.JAZ5), one of the transcriptional repressors functioning in the jasmonate (JA) signaling pathway, was triggered by drought treatment in rapeseed, and drought-susceptibility increased in BnA.JAZ5-overexpressing rapeseed plants as compared to wild-type plants, resulting in a lower survival rate after recovery from dehydration. After recovery for 3 days, 22–40% of p35S::BnA.JAZ5 transgenic plants survived, while approximately 61% of wild-type plants survived. Additionally, seed germination of BnA.JAZ5-overexpressing rapeseed was hyposensitive to abscisic acid (ABA). The germination rate of five transgenic lines was 32~42% under 9 µM ABA treatment, while the germination rate of wild-type plants was 14%. We also found that the average stomatal density of five overexpressing lines was 371~446/mm2, which is higher than that of wild-type (232/mm2) plants under normal conditions. These results indicate that BnA.JAZ5 regulated drought response in an ABA-dependent manner, possibly by affecting stomatal density. Interestingly, methyl jasmonate (MeJA) treatment rescued the ABA-hyposensitive seed germination, revealing crosstalk between JAZ5-meidated JA and the ABA signaling pathway. Taken together, our results suggest that BnA.JAZ5 attenuated drought resistance through the ABA-dependent pathway, which could represent important genetic loci for drought-resistant rapeseed breeding.

OsRLCK160 contributes to flavonoid accumulation and UV-B tolerance by regulating OsbZIP48 in rice

Plants produce specialized metabolites to adapt to the ever-changing environments. Flavonoids are antioxidants essential for growth, development, and breeding with increased stress resistance in crops. However, the mechanism of the involvement of flavonoids in ultraviolet-B (UV-B) stress in rice (Oryza sativa) is largely unknown. In this study, we cloned and functionally identified a receptor-like kinase (OsRLCK160) and a bZIP transcription factor (OsbZIP48) positively regulating flavonoid accumulation through metabolite-based genome-wide association study of the flavonoid content in rice. Meanwhile, OsRLCK160 interacted with and phosphorylated OsbZIP48 to regulate the flavonoid accumulation and participate in UV-B tolerance in rice. Our study indicates the importance of applying OsRLCK160 and OsbZIP48 to advance the fundamental understanding of stable rice production and breed UV-B-tolerant rice varieties, which may contribute to breeding high-yield rice varieties.

Plant Salinity Sensors: Current Understanding and Future Directions

Salt stress is a major limiting factor for plant growth and crop yield. High salinity causes osmotic stress followed by ionic stress, both of which disturb plant growth and metabolism. Understanding how plants perceive salt stress will help efforts to improve salt tolerance and ameliorate the effect of salt stress on crop growth. Various sensors and receptors in plants recognize osmotic and ionic stresses and initiate signal transduction and adaptation responses. In the past decade, much progress has been made in identifying the sensors involved in salt stress. Here, we review current knowledge of osmotic sensors and Na⁺ sensors and their signal transduction pathways, focusing on plant roots under salt stress. Based on bioinformatic analyses, we also discuss possible structures and mechanisms of the candidate sensors. With the rapid decline of arable land, studies on salt-stress sensors and receptors in plants are critical for the future of sustainable agriculture in saline soils. These studies also broadly inform our overall understanding of stress signaling in plants.

OsPSKR15, a phytosulfokine receptor from rice enhances abscisic acid response and drought stress tolerance

Abscisic acid (ABA) is a major phytohormone that acts as stimuli and plays an important role in plant growth, development, and environmental stress responses. Membrane-localized receptor-like kinases (RLKs) help to detect extracellular stimuli and activate downstream signaling responses to modulate a variety of biological processes. Phytosulfokine receptor (PSKR), a Leu-rich repeat (LRR)-RLK, has been characterized for its role in growth, development and biotic stress. Here, we observed that OsPSKR15, a rice PSKR, was upregulated by ABA in Oryza sativa. We demonstrated OsPSKR15 is a positive regulator in plant response to ABA. Ectopic expression of OsPSKR15 in Arabidopsis thaliana increased the sensitivity to ABA during germination, growth and stomatal closure. Consistently, the expression of ABA-inducible genes was significantly upregulated in these plants. OsPSKR15 also regulated reactive oxygen species (ROS)-mediated ABA signaling in guard cells, thereby governing stomatal closure. Furthermore, the constitutive expression of OsPSKR15 enhanced drought tolerance by reducing the transpirational water loss in Arabidopsis. We also reported that OsPSKR15 directly interacts with AtPYL9 and its orthologue OsPYL11 of rice through its kinase domain in the plasma membrane and nucleus. Altogether, these results reveal an important role of OsPSKR15 in plant response toward abiotic stress in an ABA-dependent manner.

Revealing plant growth-promoting mechanisms of Bacillus strains in elevating rice growth and its interaction with salt stress

Soil salinity is a major environmental stress that has been negatively affecting the growth and productivity of rice. However, various salt-resistant plant growth-promoting rhizobacteria (PGPR) have been known to promote plant growth and alleviate the damaging effects of salt stress via mitigating physio-biochemical and molecular characteristics. This study was conducted to examine the salt stress potential of Bacillus strains identified from harsh environments of the Qinghai-Tibetan plateau region of China. The Bacillus strains NMTD17, GBSW22, and FZB42 were screened for their response under different salt stress conditions (1, 4, 7, 9, 11, 13, and 16%). The screening analysis revealed strains NMTD17, GBSW22, and FZB42 to be high-salt tolerant, moderate-salt tolerant, and salt-sensitive, respectively. The NMTD17 strain produced a strong biofilm, followed by GBSW22 and FZB42. The expression of salt stress-related genes in selected strains was also analyzed through qPCR in various salt concentrations. Further, the Bacillus strains were used in pot experiments to study their growth-promoting ability and antioxidant activities at various concentrations (0, 100, 150, and 200 mmol). The analysis of growth-promoting traits in rice exhibited that NMTD17 had a highly significant effect and GSBW22 had a moderately significant effect in comparison with FZB42. The highly resistant strain NMTD17 that stably promoted rice plant growth was further examined for its function in the composition of rhizobacterial communities. The inoculation of NMTD17 increased the relative abundance and richness of rhizobacterial species. These outcomes propose that NMTD17 possesses the potential of PGPR traits, antioxidants enzyme activities, and reshaping the rhizobacterial community that together mitigate the harmful effects of salinity in rice plants.

Joint GWAS and WGCNA uncover the genetic control of calcium accumulation under salt treatment in maize seedlings

Soil salinization is an important factor threatening the yield and quality of maize. Ca²⁺ plays a considerable role in regulating plant growth under salt stress. Herein, we examined the shoot Ca²⁺ concentrations, root Ca²⁺ concentrations, and transport coefficients of seedlings in an association panel composed of 305 maize inbred lines under normal and salt conditions. A genome-wide association study was conducted by using the investigated phenotypes and 46,408 single-nucleotide polymorphisms of the panel. As a result, 53 significant SNPs were specifically detected under salt treatment, and 544 genes were identified in the linkage disequilibrium regions of these SNPs. According to the expression data of the 544 genes, we carried out a weighted coexpression network analysis. Combining the enrichment analyses and functional annotations, four hub genes (GRMZM2G051032, GRMZM2G004314, GRMZM2G421669, and GRMZM2G123314) were finally determined, which were then used to evaluate the genetic variation effects by gene-based association analysis. Only GRMZM2G123314, which encodes a pentatricopeptide repeat protein, was significantly associated with Ca²⁺ transport and the haplotype G-CT was identified as the superior haplotype. Our study brings novel insights into the genetic and molecular mechanisms of salt stress response and contributes to the development of salt-tolerant varieties in maize.

Rice functional genomics: decades' efforts and roads ahead

Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.

A novel LRR-RLK (CTLK) confers cold tolerance through regulation on the C-repeat-binding factor pathway, antioxidants, and proline accumulation

Leucine-rich repeat-receptor-like kinase (LRR-RLK) is a large subfamily of plant RLKs; however, its role in cold tolerance is still unknown. A novel cold tolerance LRR-RLK gene (MtCTLK1) in Medicago truncatula was identified using the transgenic lines overexpressing MtCTLK1 (MtCTLK1-OE) and mtctlk1 lines with Tnt1 retrotransposon insertion. Compared with the wild-type, MtCTLK1-OE lines had increased cold tolerance and mtctlk1 showed decreased cold tolerance. The impaired cold tolerance in mtctlk1 could be complemented by the transgenic expression of MtCTLK1 or its homolog MfCTLK1 from Medicago falcata. Antioxidant enzyme activities and proline accumulation as well as transcript levels of the associated genes were increased in response to cold, with higher levels in MtCTLK1-OE or lower levels in mtctlk1 lines as compared with wild type. C-Repeat-Binding Factors (CBFs) and CBF-dependent cold-responsive genes were also induced in response to cold, and higher transcript levels of CBFs and CBF-dependent cold-responsive genes were observed in MtCTLK1-OE lines whereas lower levels in mtctlk1 mutants. The results validate the role of MtCTLK1 or MfCTLK1 in the regulation of cold tolerance through the CBF pathway, antioxidant defense system and proline accumulation. It also provides a valuable gene for the molecular breeding program to improve cold tolerance in crops.

Meta-QTLs, ortho-MQTLs and candidate genes for the traits contributing to salinity stress tolerance in common wheat (Triticum aestivum L.)

A meta-analysis of QTLs associated with the traits contributing to salinity tolerance was undertaken in wheat to detect consensus and robust meta-QTLs (MQTLs) using 844 known QTLs retrieved from 26 earlier studies. A consensus map with a total length of 4621.56 cM including 7710 markers was constructed using 21 individual linkage maps and three previously published integrated genetic maps. Out of 844 QTLs, 571 QTLs were projected on the consensus map which gave origin to 100 MQTLs. Interestingly, 49 MQTLs were co-located with marker-trait associations reported in wheat genome-wide association studies for the traits contributing to salinity stress tolerance. Five potential MQTLs associated with the major salinity-responsive traits were also identified to be utilized in the breeding programme. In the resulted MQTLs, the average confidence interval (CI, 3.58 cM) was reduced up to 4.16 folds compared to the mean CI of the initial QTLs. Furthermore, as many as 617 gene models including 81 most likely candidate genes (CGs) were identified in the high confidence MQTL regions. These most likely CGs encoded proteins mainly belonging to the following families: B-box-type zinc finger, cytochrome P450 protein, pentatricopeptide repeat, phospholipid/glycerol acyltransferase, F-box protein, small auxin-up RNA, UDP-glucosyltransferase, glutathione S-transferase protein, etc. In addition, ortho-MQTL analysis based on synteny among wheat, rice and barley was also performed which permitted the identification of six ortho-MQTLs among these three cereals. This meta-analysis defines a genome-wide landscape on the most stable and consistent loci associated with reliable molecular markers and candidate genes for salinity tolerance in wheat.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01112-0.