Rice GROWTH UNDER DROUGHT KINASE is required for drought tolerance and grain yield under normal and drought stress conditions

An AP2/ERF transcription factor confers chilling tolerance in rice

Cold stress, a prominent adverse environmental factor, severely hinders rice growth and productivity. Unraveling the complex mechanisms governing chilling tolerance in rice is crucial for molecular breeding of cold-tolerant varieties. Here, we identify an APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factor, OsERF52, as a positive modulator in response to low temperatures. OsERF52 directly regulates the expression of C-Repeat Binding Factor (CBF) genes in rice. In addition, Osmotic Stress/ABA-Activated Protein Kinase 9-mediated phosphorylation of OsERF52 at S261 enhances its stability and interaction with Ideal Plant Architecture 1 and OsbHLH002/OsICE1. This collaborative activation leads to the expression of OsCBFs, thereby initiating the chilling response in rice. Notably, plants with base-edited OsERF52S261D-3HA exhibit enhanced chilling resistance without yield penalty. Our findings unveil the mechanism orchestrated by a regulatory framework involving a protein kinase and transcription factors from diverse families, offering potential genetic resources for developing chilling-tolerant rice varieties.

Overexpression of FERONIA receptor kinase MdMRLK2 regulates lignin accumulation and enhances water use efficiency in apple under long-term water deficit condition

Water use efficiency (WUE) is crucial for apple tree fitness and survival, especially in response to climatic changes. The receptor-like kinase FERONIA is reportedly an essential regulator of plant stress responses, but its role in regulating WUE under water deficit conditions is unclear. Here, we found that overexpressing the apple FERONIA receptor kinase gene, MdMRLK2, enhanced apple WUE under long-term water deficit conditions. Under drought treatment, 35S::MdMRLK2 apple plants exhibited higher photosynthetic capacity and antioxidant enzyme activities than wild-type (WT) plants. 35S::MdMRLK2 apple plants also showed increased biomass accumulation, root activity, and water potential compared to WT plants. Moreover, MdMRLK2 physically interacts with and phosphorylates cinnamoyl-CoA reductase 1, MdCCR1, an enzyme essential for lignin synthesis, at position Ser260. This interaction likely contributed to increased vessel density, vascular cylinder area, and lignin content in 35S::MdMRLK2 apple plants under drought conditions. Therefore, our findings reveal a novel function of MdMRLK2 in regulating apple WUE under water deficit conditions.

Receptor-like cytoplasmic kinases: orchestrating plant cellular communication

The receptor-like kinase (RLK) family of receptors and the associated receptor-like cytoplasmic kinases (RLCKs) have expanded in plants because of selective pressure from environmental stress and evolving pathogens. RLCKs link pathogen perception to activation of coping mechanisms. RLK-RLCK modules regulate hormone synthesis and responses, reactive oxygen species (ROS) production, Ca2+ signaling, activation of mitogen-activated protein kinase (MAPK), and immune gene expression, all of which contribute to immunity. Some RLCKs integrate responses from multiple receptors recognizing distinct ligands. RLKs/RLCKs and nucleotide-binding domain, leucine-rich repeats (NLRs) were found to synergize, demonstrating the intertwined genetic network in plant immunity. Studies in arabidopsis (Arabidopsis thaliana) have provided paradigms about RLCK functions, but a lack of understanding of crop RLCKs undermines their application. In this review, we summarize current understanding of the diverse functions of RLCKs, based on model systems and observations in crop species, and the emerging role of RLCKs in pathogen and abiotic stress response signaling.

Overexpression of OsNAR2.1 by OsNAR2.1 promoter increases drought resistance by increasing the expression of OsPLDα1 in rice

BACKGROUND

pOsNAR2.1:OsNAR2.1 expression could significantly increase nitrogen uptake efficiency and grain yield of rice.

RESULT

This study reported the effects of overexpression of OsNAR2.1 by OsNAR2.1 promoter on physiological and agronomic traits associated with drought tolerance. In comparison to the wild-type (WT), the pOsNAR2.1:OsNAR2.1 transgenic lines exhibited a significant improvement in survival rate when subjected to drought stress and then irrigation. Under limited water supply conditions, compared with WT, the photosynthesis and water use efficiency (WUE) of transgenic lines were increased by 39.2% and 28.8%, respectively. Finally, the transgenic lines had 25.5% and 66.4% higher grain yield than the WT under full watering and limited water supply conditions, respectively. Compared with the WT, the agronomic nitrogen use efficiency (NUE) of transgenic lines increased by 25.5% and 66.4% under full watering and limited water supply conditions, and the N recovery efficiency of transgenic lines increased by 29.3% and 50.2%, respectively. The interaction between OsNAR2.1 protein and OsPLDα1 protein was verified by yeast hybrids. After drought treatment, PLDα activity on the plasma membrane of the transgenic line increased 85.0% compared with WT.

CONCLUSION

These results indicated that pOsNAR2.1:OsNAR2.1 expression could improve the drought resistance of rice by increasing nitrogen uptake and regulating the expression of OsPLDα1.

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.

Understanding AP2/ERF Transcription Factor Responses and Tolerance to Various Abiotic Stresses in Plants: A Comprehensive Review

Abiotic stress is an adverse environmental factor that severely affects plant growth and development, and plants have developed complex regulatory mechanisms to adapt to these unfavourable conditions through long-term evolution. In recent years, many transcription factor families of genes have been identified to regulate the ability of plants to respond to abiotic stresses. Among them, the AP2/ERF (APETALA2/ethylene responsive factor) family is a large class of plant-specific proteins that regulate plant response to abiotic stresses and can also play a role in regulating plant growth and development. This paper reviews the structural features and classification of AP2/ERF transcription factors that are involved in transcriptional regulation, reciprocal proteins, downstream genes, and hormone-dependent signalling and hormone-independent signalling pathways in response to abiotic stress. The AP2/ERF transcription factors can synergise with hormone signalling to form cross-regulatory networks in response to and tolerance of abiotic stresses. Many of the AP2/ERF transcription factors activate the expression of abiotic stress-responsive genes that are dependent or independent of abscisic acid and ethylene in response to abscisic acid and ethylene. In addition, the AP2/ERF transcription factors are involved in gibberellin, auxin, brassinosteroid, and cytokinin-mediated abiotic stress responses. The study of AP2/ERF transcription factors and interacting proteins, as well as the identification of their downstream target genes, can provide us with a more comprehensive understanding of the mechanism of plant action in response to abiotic stress, which can improve plants' ability to tolerate abiotic stress and provide a more theoretical basis for increasing plant yield under abiotic stress.

QTLs and Candidate Loci Associated with Drought Tolerance Traits of Kaybonnet x ZHE733 Recombinant Inbred Lines Rice Population

Rice is the most important staple crop for the sustenance of the world's population, and drought is a major factor limiting rice production. Quantitative trait locus (QTL) analysis of drought-resistance-related traits was conducted on a recombinant inbred line (RIL) population derived from the self-fed progeny of a cross between the drought-resistant tropical japonica U.S. adapted cultivar Kaybonnet and the drought-sensitive indica cultivar ZHE733. K/Z RIL population of 198 lines was screened in the field at Fayetteville (AR) for three consecutive years under controlled drought stress (DS) and well-watered (WW) treatment during the reproductive stage. The effects of DS were quantified by measuring morphological traits, grain yield components, and root architectural traits. A QTL analysis using a set of 4133 single nucleotide polymorphism (SNP) markers and the QTL IciMapping identified 41 QTLs and 184 candidate genes for drought-related traits within the DR-QTL regions. RT-qPCR in parental lines was used to confirm the putative candidate genes. The comparison between the drought-resistant parent (Kaybonnet) and the drought-sensitive parent (ZHE733) under DS conditions revealed that the gene expression of 15 candidate DR genes with known annotations and two candidate DR genes with unknown annotations within the DR-QTL regions was up-regulated in the drought-resistant parent (Kaybonnet). The outcomes of this research provide essential information that can be utilized in developing drought-resistant rice cultivars that have higher productivity when DS conditions are prevalent.

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.

Genome-Wide Identification and Expression Analysis of RLCK-VII Subfamily Genes Reveal Their Roles in Stress Responses of Upland Cotton

Receptor-like cytoplasmic kinase VII (RLCK-VII) subfamily members are vital players in plant innate immunity and are also involved in plant development and abiotic stress tolerance. As a widely cultivated textile crop, upland cotton (Gossypium hirsutum) attaches great importance to the cotton industry worldwide. To obtain details of the composition, phylogeny, and putative function of RLCK-VII genes in upland cotton, genome-wide identification, evolutionary event analysis, and expression pattern examination of RLCK-VII subfamily genes in G. hirsutum were performed. There are 129 RLCK-VII members in upland cotton (GhRLCKs) and they were divided into nine groups based on their phylogenetic relationships. The gene structure and sequence features are relatively conserved within each group, which were divided based on their phylogenetic relationships, and consistent with those in Arabidopsis. The phylogenetic analysis results showed that RLCK-VII subfamily genes evolved in plants before the speciation of Arabidopsis and cotton, and segmental duplication was the major factor that caused the expansion of GhRLCKs. The diverse expression patterns of GhRLCKs in response to abiotic stresses (temperature, salt, and drought) and V. dahliae infection were observed. The candidates that may be involved in cotton's response to these stresses are highlighted. GhRLCK7 (GhRLCK7A and D), which is notably induced by V. dahliae infection, was demonstrated to positively regulate cotton defense against V. dahliae by the loss-of-function assay in cotton. These findings shed light on the details of the RLCK-VII subfamily in cotton and provide a scaffold for the further function elucidation and application of GhRLCKs for the germplasm innovation of cotton.

OsGSTU17, a Tau Class Glutathione S-Transferase Gene, Positively Regulates Drought Stress Tolerance in Oryza sativa

As a great threat to the normal growth of rice, drought not only restricts the growth of rice, but also affects its yield. Glutathione S-transferases (GSTs) have antioxidant and detoxification functions. In rice, GSTs can not only effectively cope with biological stress, but also play a defense role against abiotic stress. In this study, we selected OsGSTU17, a member gene that was induced by drought, to explore the role of GSTs and analyze their physiological mechanisms that are involved in rice drought tolerance. With the CRISPR/Cas9 knockout system techniques, we obtained two independent mutant lines of osgstu17. After 14 days of drought stress treatment, and then re-supply of the water for 10 days, the survival rate of the osgstu17 mutant lines was significantly reduced compared to the wild-type (WT). Similarly, with the 10% (w/v) PEG6000 hydroponics experiment at the seedling stage, we also found that compared with the WT, the shoot and root biomass of osgstu17 mutant lines decreased significantly. In addition, both the content of the MDA and H2O2, which are toxic to plants, increased in the osgtu17 mutant lines. On the other hand, chlorophyll and proline decreased by about 20%. The activity of catalase and superoxide dismutase, which react with peroxides, also decreased by about 20%. Under drought conditions, compared with the WT, the expressions of the drought stress-related genes OsNAC10, OsDREB2A, OsAP37, OsP5CS1, OsRAB16C, OsPOX1, OsCATA, and OsCATB in the osgtu17 mutant lines were significantly decreased. Finally, we concluded that knocking out OsGSTU17 significantly reduced the drought tolerance of rice; OsGSTU17 could be used as a candidate gene for rice drought-tolerant cultivation. However, the molecular mechanism of OsGSTU17 involved in rice drought resistance needs to be further studied.

Genome-wide identification of Apetala2 gene family in Hypericum perforatum L and expression profiles in response to different abiotic and hormonal treatments

The Apetala2 (AP2) gene family of transcription factors (TFs) play important functions in plant development, hormonal response, and abiotic stress. To reveal the biological functions and the expression profiles of AP2 genes in Hypericum perforatum, genome-wide identification of HpAP2 family members was conducted.

Methods

We identified 21 AP2 TFs in H. perforatum using bioinformatic methods; their physical and chemical properties, gene structures, conserved motifs, evolutionary relationships, cis-acting elements, and expression patterns were investigated.

Results

We found that based on the structural characteristics and evolutionary relationships, the HpAP2 gene family can be divided into three subclasses: euANT, baselANT, and euAP2. A canonical HpAP2 TF shared a conserved protein structure, while a unique motif 6 was found in HpAP2_1, HpAP2_4, and HpAP2_5 from the euANT subgroup, indicating potential biological and regulatory functions of these genes. Furthermore, a total of 59 cis-acting elements were identified, most of which were associated with growth, development, and resistance to stress in plants. Transcriptomics data showed that 57.14% of the genes in the AP2 family were differentially expressed in four organs. For example, HpAP2_18 was specifically expressed in roots and stems, whereas HpAP2_17 and HpAP2_11 were specifically expressed in leaves and flowers, respectively. HpAP2_5, HpAP2_11, and HpAP2_18 showed tissue-specific expression patterns and responded positively to hormones and abiotic stresses.

Conclusion

These results demonstrated that the HpAP2 family genes are involved in diverse developmental processes and generate responses to abiotic stress conditions in H. perforatum. This article, for the first time, reports the identification and expression profiles of the AP2 family genes in H. perforatum, laying the foundation for future functional studies with these genes.

Receptor-like cytoplasmic kinase ScRIPK in sugarcane regulates disease resistance and drought tolerance in Arabidopsis

Introduction

Receptor-like cytoplastic kinases (RLCKs) are known in many plants to be involved in various processes of plant growth and development and regulate plant immunity to pathogen infection. Environmental stimuli such as pathogen infection and drought restrict the crop yield and interfere with plant growth. However, the function of RLCKs in sugarcane remains unclear.

Methods and results

In this study, a member of the RLCK VII subfamily, ScRIPK, was identified in sugarcane based on sequence similarity to the rice and Arabidopsis RLCKs. ScRIPK was localized to the plasma membrane, as predicted, and the expression of ScRIPK was responsive to polyethylene glycol treatment and Fusarium sacchari infection. Overexpression of ScRIPK in Arabidopsis enhanced drought tolerance and disease susceptibility of seedlings. Moreover, the crystal structure of the ScRIPK kinase domain (ScRIPK KD) and the mutant proteins (ScRIPK-KD K124R and ScRIPK-KD S253A|T254A) were characterized in order to determine the activation mechanism. We also identified ScRIN4 as the interacting protein of ScRIPK.

Discussion

Our work identified a RLCK in sugarcane, providing a potential target for sugarcane responses to disease infection and drought, and a structural basis for kinase activation mechanisms.

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.

Knockout Mutants of OsPUB7 Generated Using CRISPR/Cas9 Revealed Abiotic Stress Tolerance in Rice

Plants produce and accumulate stress-resistant substances when exposed to abiotic stress, which involves a protein conversion mechanism that breaks down stress-damaged proteins and supplies usable amino acids. Eukaryotic protein turnover is mostly driven by the ubiquitination pathway. Among the three enzymes required for protein degradation, E3 ubiquitin ligase plays a pivotal role in most cells, as it determines the specificity of ubiquitination and selects target proteins for degradation. In this study, to investigate the function of OsPUB7 (Plant U-box gene in Oryza sativa), we constructed a CRISPR/Cas9 vector, generated OsPUB7 gene-edited individuals, and evaluated resistance to abiotic stress using gene-edited lines. A stress-tolerant phenotype was observed as a result of drought and salinity stress treatment in the T2 OsPUB7 gene-edited null lines (PUB7-GE) lacking the T-DNA. In addition, although PUB7-GE did not show any significant change in mRNA expression analysis, it showed lower ion leakage and higher proline content than the wild type (WT). Protein–protein interaction analysis revealed that the expression of the genes (OsPUB23, OsPUB24, OsPUB66, and OsPUB67) known to be involved in stress increased in PUB7-GE and this, by forming a 1-node network with OsPUB66 and OsPUB7, acted as a negative regulator of drought and salinity stress. This result provides evidence that OsPUB7 will be a useful target for both breeding and future research on drought tolerance/abiotic stress in rice.

Enhancement of Heat and Drought Stress Tolerance in Rice by Genetic Manipulation: A Systematic Review

As a result of global warming, plants are subjected to ever-increasing abiotic stresses including heat and drought. Drought stress frequently co-occurs with heat stress as a result of water evaporation. These stressors have adverse effects on crop production, which in turn affects human food security. Rice is a major food resource grown widely in crop-producing regions throughout the world. However, increasingly common heat and drought stresses in growth regions can have negative impacts on seedling morphogenesis, reproductive organ establishment, overall yield, and quality. This review centers on responses to heat and drought stress in rice. Current knowledge of molecular regulation mechanisms is summarized. We focus on approaches to cope with heat and drought stress, both at the genetic level and from an agricultural practice perspective. This review establishes a basis for improving rice stress tolerance, grain quality, and yield for human benefit.

Molecular Events of Rice AP2/ERF Transcription Factors

APETALA2/ethylene response factor (AP2/ERF) is widely found in the plant kingdom and plays crucial roles in transcriptional regulation and defense response of plant growth and development. Based on the research progress related to AP2/ERF genes, this paper focuses on the classification and structural features of AP2/ERF transcription factors, reviews the roles of rice AP2/ERF genes in the regulation of growth, development and stress responses, and discusses rice breeding potential and challenges. Taken together; studies of rice AP2/ERF genes may help to elucidate and enrich the multiple molecular mechanisms of how AP2/ERF genes regulate spikelet determinacy and floral organ development, flowering time, grain size and quality, embryogenesis, root development, hormone balance, nutrient use efficiency, and biotic and abiotic response processes. This will contribute to breeding excellent rice varieties with high yield and high resistance in a green, organic manner.

CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice

In cereals, the root system is mainly composed of post-embryonic shoot-borne roots, named crown roots. The CROWN ROOTLESS1 (CRL1) transcription factor, belonging to the ASYMMETRIC LEAVES2-LIKE/LATERAL ORGAN BOUNDARIES DOMAIN (ASL/LBD) family, is a key regulator of crown root initiation in rice (Oryza sativa). Here, we show that CRL1 can bind, both in vitro and in vivo, not only the LBD-box, a DNA sequence recognized by several ASL/LBD transcription factors, but also another not previously identified DNA motif that was named CRL1-box. Using rice protoplast transient transactivation assays and a set of previously identified CRL1-regulated genes, we confirm that CRL1 transactivates these genes if they possess at least a CRL1-box or an LBD-box in their promoters. In planta, ChIP-qPCR experiments targeting two of these genes that include both a CRL1- and an LBD-box in their promoter show that CRL1 binds preferentially to the LBD-box in these promoter contexts. CRISPR/Cas9-targeted mutation of these two CRL1-regulated genes, which encode a plant Rho GTPase (OsROP) and a basic helix-loop-helix transcription factor (OsbHLH044), show that both promote crown root development. Finally, we show that OsbHLH044 represses a regulatory module, uncovering how CRL1 regulates specific processes during crown root formation.

Differential Microbial Communities in Paddy Soils Between Guiyang Plateaus and Chengdu Basins Drive the Incidence of Rice Bacterial Diseases

Southwest China has the most complex rice-growing regions in China. With great differences in topography, consisting mainly of basins and plateaus, ecological factors differ greatly between regions. In this study, bulk paddy soils collected from long-term rice fields in Chengdu (basins) and Guiyang (plateaus) were used to study the correlation between microbial diversity and the incidence of rice bacterial diseases. Results showed that the microbial community composition in paddy soils and the microbial functional categories differed significantly between basins and plateaus. They shared >70% of the dominant genera (abundance >1%), but the abundance of the dominant genera differed significantly. Functional analysis found that bulk paddy soils from Chengdu were significantly enriched in virulence factor-related genes; soils from Guiyang were enriched in biosynthesis of secondary metabolites, especially antibiotics. Correspondingly, Chengdu was significantly enriched in leaf bacterial pathogens Acidovorax, Xanthomonas, and Pseudomonas. Greenhouse experiments and correlation analysis showed that soil chemical properties had a greater effect on microbial community composition and positively correlated with the higher incidence of rice bacterial foot rot in Guiyang, whereas temperature had a greater effect on soil microbial functions and positively correlated with the higher severity index of leaf bacterial diseases in Chengdu. Our results provide a new perspective on how differences in microbial communities in paddy soils can influence the incidence of rice bacterial diseases in areas with different topographies.

Regulation of plant responses to biotic and abiotic stress by receptor-like cytoplasmic kinases

As sessile organisms, plants have to cope with environmental change and numerous biotic and abiotic stress. Upon perceiving environmental cues and stress signals using different types of receptors, plant cells initiate immediate and complicated signaling to regulate cellular processes and respond to stress. Receptor-like cytoplasmic kinases (RLCKs) transduce signals from receptors to cellular components and play roles in diverse biological processes. Recent studies have revealed the hubbing roles of RLCKs in plant responses to biotic stress. Emerging evidence indicates the important regulatory roles of RLCKs in plant responses to abiotic stress, growth, and development. As a pivot of cellular signaling, the activity and stability of RLCKs are dynamically and tightly controlled. Here, we summarize the current understanding of how RLCKs regulate plant responses to biotic and abiotic stress.

Overexpression of Arabidopsis nucleolar GTP-binding 1 (NOG1) proteins confers drought tolerance in rice

As a major adverse environmental factor in most parts of the world, drought causes substantial crop yield losses. Rice (Oryza sativa) is one of the staple foods for more than one-half of the world's population. Rice plants are sensitive to even mild drought stress and need almost twice the amount of water compared to wheat (Triticum aestivum) or maize (Zea mays). Arabidopsis (Arabidopsis thaliana) small GTPase Nucleolar GTP-binding protein 1 (AtNOG1) plays a role in biotic stress tolerance. Here, we created transgenic rice lines constitutively overexpressing AtNOG1-1 or AtNOG1-2. We also developed rice RNA interference (RNAi) lines that show downregulation of OsNOG1. AtNOG1-1 and AtNOG1-2 overexpressors showed enhanced drought tolerance without compromising grain yield, whereas OsNOG1-RNAi was more susceptible to drought when compared to wild-type plants. Analysis of physiological parameters showed increased cell sap osmolality, relative water content, and abscisic acid (ABA) level, but decreased leaf water loss in AtNOG1-1 or AtNOG1-2 overexpressor lines compared to the control. We found upregulation of several genes involved in ABA and jasmonic acid (JA) signaling, stomata regulation, osmotic potential maintenance, stress protection, and disease resistance in AtNOG1-1 and AtNOG1-2 overexpressor lines compared to the control. We elucidated the role of NOG1-2 and NOG1-1 in regulation of silica body formation around stomata to prevent transpirational water loss. These results provide an avenue to confer drought tolerance in rice.

Transcript profiling of stress-responsive genes and metabolic changes during salinity in indica and japonica rice exhibit distinct varietal difference

In the present study, we carried out comprehensive transcript profiling of diverse genes under salinity (200 mM NaCl) at different time points, accompanied by certain biochemical alterations of the indica (IR-64 and Pokkali) and japonica (Nipponbare and M-202) rice. The higher susceptibility of Nipponbare and IR-64 was reflected by lower relative water content, chlorophyll loss, higher malondialdehyde content, and accumulation of H₂ O₂ , and reduced nitrate reductase activity, compared to M-202 and Pokkali, where such changes were less pronounced. Enhanced levels of anthocyanins and reduced glutathione, together with elevated phenylalanine ammonia lyase activity, mainly conferred protection to Nipponbare and IR-64, while metabolites like phenolics, flavonoids, proline, and polyamines were more induced in M-202 and Pokkali. Varietal differences in the expression pattern of diverse groups of genes during different durations (6, 24, and 48 h) of stress were striking. A gene showing early induction for a particular variety exhibited a delayed induction in another variety or a gradually decreased expression with treatment time. Pokkali was clearly identified as the salt-tolerant genotype among the examined varieties based on increased antioxidant potential and enhanced expression of genes encoding for PAL, CHS, and membrane transporters like SOS3, NHX-1, and HKT-1. The results presented in this work provide insight into the complex varying regulation patterns for different genes across the investigated rice varieties in providing salt tolerance and highlights distinct differences in expression patterns between susceptible and tolerant indica and japonica rice.

Large-scale integration of meta-QTL and genome-wide association study discovers the genomic regions and candidate genes for yield and yield-related traits in bread wheat

Based on the large-scale integration of meta-QTL and Genome-Wide  Association Study, 76 high-confidence MQTL regions and 237 candidate genes that affected wheat yield and yield-related traits were discovered. Improving yield and yield-related traits are key goals in wheat breeding program. The integration of accumulated wheat genetic resources provides an opportunity to uncover important genomic regions and candidate genes that affect wheat yield. Here, a comprehensive meta-QTL analysis was conducted on 2230 QTL of yield-related traits obtained from 119 QTL studies. These QTL were refined into 145 meta-QTL (MQTL), and 89 MQTL were verified by GWAS with different natural populations. The average confidence interval (CI) of these MQTL was 2.92 times less than that of the initial QTL. Furthermore, 76 core MQTL regions with a physical distance less than 25 Mb were detected. Based on the homology analysis and expression patterns, 237 candidate genes in the MQTL involved in photoperiod response, grain development, multiple plant growth regulator pathways, carbon and nitrogen metabolism and spike and flower organ development were determined. A novel candidate gene TaKAO-4A was confirmed to be significantly associated with grain size, and a CAPS marker was developed based on its dominant haplotype. In summary, this study clarified a method based on the integration of meta-QTL, GWAS and homology comparison to reveal the genomic regions and candidate genes that affect important yield-related traits in wheat. This work will help to lay a foundation for the identification, transfer and aggregation of these important QTL or candidate genes in wheat high-yield breeding.

Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance

Gene regulatory networks underpin stress response pathways in plants. However, parsing these networks to prioritize key genes underlying a particular trait is challenging. Here, we have built the Gene Regulation and Association Network (GRAiN) of rice (Oryza sativa). GRAiN is an interactive query-based web-platform that allows users to study functional relationships between transcription factors (TFs) and genetic modules underlying abiotic-stress responses. We built GRAiN by applying a combination of different network inference algorithms to publicly available gene expression data. We propose a supervised machine learning framework that complements GRAiN in prioritizing genes that regulate stress signal transduction and modulate gene expression under drought conditions. Our framework converts intricate network connectivity patterns of 2160 TFs into a single drought score. We observed that TFs with the highest drought scores define the functional, structural, and evolutionary characteristics of drought resistance in rice. Our approach accurately predicted the function of OsbHLH148 TF, which we validated using in vitro protein-DNA binding assays and mRNA sequencing loss-of-function mutants grown under control and drought stress conditions. Our network and the complementary machine learning strategy lends itself to predicting key regulatory genes underlying other agricultural traits and will assist in the genetic engineering of desirable rice varieties.

Combined application of ascorbic acid and endophytic N-fixing Azotobacter chroococcum Avi2 modulates photosynthetic efficacy, antioxidants and growth-promotion in rice under moisture deficit stress

This group has previously reported the role of ascorbic acid (AA) as an antioxidant for survivability and ability to enhancing diazotrophic efficacy in Azotobacter chroococcum Avi2 under hydrogen peroxide (H₂O₂) stress. However, the present study showed the combined application of AA and Avi2 in drought-susceptible (IR64 and Naveen) and drought-tolerant (Ankit and Satyabhama) rice cultivars to determine their photosynthetic efficacy (chlorophyll fluorescence-imaging), antioxidants, and plant growth-promotion (PGP) under moisture deficit stress (MS, -60 kPa). The results indicated that combined application of AA and Avi2 significantly (p < 0.05) increased the total chlorophyll, relative water content, electrolytic leakage, super oxide dismutase, and catalase activities in all rice cultivars as compared to other MS treatments, whereas stress indicators like proline and H₂O₂ contents were proportionally increased under MS and their concentration were normalized under combined application of AA and Avi2. Photochemical quenching, non-photochemical quenching, photosynthetic electron transport rate, and the effective quantum efficiency were found to be increased significantly (p < 0.05) in Avi2 + AA as compared to other MS treatments. Moreover, rice roots harbored significantly (p < 0.05) higher copy number of nifH gene in Avi2 + AA treatment followed by Avi2 compared to flooded control and other MS treatments. Combined application of AA and Avi2 also increased the grain yield significantly (p < 0.05) by 7.09 % and 3.92 % in drought-tolerant (Ankit and Satyabhama, respectively) and 31.70 % and 34.19 % in drought-susceptible (IR64 and Naveen, respectively) rice cultivars compared to MS treatment. Overall, the present study indicated that AA along with Avi2 could be an effective formulation to alleviate MS vis à vis enhances PGP traits in rice.

Wild soybean SNARE proteins BET1s mediate the subcellular localization of the cytoplasmic receptor-like kinases CRCK1s to modulate salt stress responses

Plants have evolved numerous receptor-like kinases (RLKs) that modulate environmental stress responses. However, little is known regarding soybean (Glycine max) RLKs. We have previously identified that Glycine soja Ca2+ /CAM-binding RLK (GsCBRLK) is involved in salt tolerance. Here, we report that soluble NSF attachment protein receptor proteins BET1s mediate subcellular localization of calmodulin-binding receptor-like cytoplasmic kinases CRCK1s to modulate salt stress responses. Direct interaction between GsCBRLK and GsBET11a was initially identified via yeast two-hybrid and bimolecular fluorescence complementation assays. Further analysis demonstrated conserved interaction between BET1s and CRCK1s. GsCBRLK interacted with all BET1 proteins in wild soybean (Glycine soja) and Arabidopsis, and GsBET11a strongly associated with GsCRCK1a-1d, but slightly with AtCRCK1. In addition, GsBET11a interacted with GsCBRLK via its C-terminal transmembrane domain (TMD), where the entire TMD, not the sequence, was critical for the interaction. Moreover, the N-terminal variable domain (VD) of GsCBRLK was responsible for interacting with GsBET11a, and the intensity of interaction between GsCBRLK/AtCRCK1 and GsBET11a was dependent on VD. Furthermore, GsBET11a was able to mediate the GsCBRLK subcellular localization via direct interaction with VD. Additionally, knockout of AtBET11 or AtBET12 individually did not alter GsCBRLK localization, while GsBET11a expression caused partial internalization of GsCBRLK from the plasma membrane (PM). We further suggest the necessity of GsCBRLK VD for its PM localization via N-terminal truncation assays. Finally, GsBET11a was shown to confer enhanced salt stress tolerance when overexpressed in Arabidopsis and soybean. These results revealed the conserved and direct interaction between BET1s and CRCK1s, and suggested their involvement in salt stress responses.

Phosphoproteomic Profiling Reveals Early Salt-Responsive Mechanisms in Two Foxtail Millet Cultivars

Excess soluble salts in saline soils are harmful to most plants. Understanding the biochemical responses to salts in plants and studying the salt tolerance-associated genetic resources in nature will contribute to the improvement of salt tolerance in crops. As an emerging model crop, foxtail millet (Setaria italica L.) has been regarded as a novel species for stress resistance investigation. Here, the dynamic proteomic and phosphoproteomic profiling of two foxtail millet varieties of An04 and Yugu2 with contrasting salt tolerance characteristics were investigated under salt stress. In total, 10,366 sites representing to 2,862 proteins were detected and quantified. There were 759 and 990 sites corresponding to 484 and 633 proteins identified under salinity in An04 and Yugu2, respectively, and 1,264 and 1,131 phosphorylation sites corresponding to 789 and 731 proteins were identified between these two varieties before and after salt stress, respectively. The differentially-regulated phosphoproteins (DRPPs) were mainly involved in signal transduction, regulation of gene expression, translation, ion transport, and metabolism processes. Yugu2 possessed signal perception and transduction capabilities more rapidly and had a more intense response compared with An04 upon salinity. The sucrose metabolism pathway, in particularly, might play a vital role in salt response in foxtail millet, which not only provides UDP-glucose for the cellulose synthesis and energy production, but also promotes flavonoid related synthesis to enhance the salt tolerance ability. Over-expressing the phospho-mimic sucrose synthase (SuS) (SuS ^S10D ) in soybean roots enhanced salt tolerance compared with over-expressing SuS lines. The knowledge of this research will shed light on elucidating the mechanisms of salt response, and pave the way for crop varieties innovation and cultivation under salinity and stresses.

Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance

Gene regulatory networks underpin stress response pathways in plants. However, parsing these networks to prioritize key genes underlying a particular trait is challenging. Here, we have built the Gene Regulation and Association Network (GRAiN) of rice (Oryza sativa). GRAiN is an interactive query-based web-platform that allows users to study functional relationships between transcription factors (TFs) and genetic modules underlying abiotic-stress responses. We built GRAiN by applying a combination of different network inference algorithms to publicly available gene expression data. We propose a supervised machine learning framework that complements GRAiN in prioritizing genes that regulate stress signal transduction and modulate gene expression under drought conditions. Our framework converts intricate network connectivity patterns of 2160 TFs into a single drought score. We observed that TFs with the highest drought scores define the functional, structural, and evolutionary characteristics of drought resistance in rice. Our approach accurately predicted the function of OsbHLH148 TF, which we validated using in vitro protein-DNA binding assays and mRNA sequencing loss-of-function mutants grown under control and drought stress conditions. Our network and the complementary machine learning strategy lends itself to predicting key regulatory genes underlying other agricultural traits and will assist in the genetic engineering of desirable rice varieties.

Overexpression of OsRLCK241 confers enhanced salt and drought tolerance in transgenic rice (Oryza sativa L.)

Receptor-like cytoplasmic kinases (RLCKs) have been demonstrated to be involved in the regulation of growth, development, and pathogen responses in plants. However, the identity of RLCKs involved in abiotic tolerance remains elusive. In this study, we present data on OsRLCK241, a receptor-like cytoplasmic kinase that is induced by salt and drought stresses. Subcellular localization revealed the presence of an OsRLCK241-GFP fusion protein at the plasma membrane. Under normal conditions, we did not observe any measurable discrepancies between the development and growth of WT and OsRLCK241 transgenic plants. In OsRLCK241 transgenic plants, the overexpression of OsRLCK241 conferred improved tolerance to salt and drought stresses. OsRLCK241 expression improved ROS detoxification by enhancing the activities of ROS scavengers as well as the accumulation of compatible osmolytes to alleviate the osmotic stress evoked by salt and drought stresses. Additionally, several stress-responsive genes showed higher expression levels in OsRLCK241 transgenic plants upon exposure to salt and drought conditions. Collectively, our observations suggest that OsRLCK241 improved salt and drought tolerance in rice is mainly due to improved ROS detoxification, increased accumulation of osmolytes, and altered expression of stress-responsive genes.

Whole-genome mining of abiotic stress gene loci in rice

We projected meta-QTL (MQTL) for drought, salinity, cold state, and high metal ion tolerance in rice using a meta-analysis based on high-density consensus maps. In addition, a genome-wide association analysis was used to validate the results of the meta-analysis, and four new chromosome intervals for mining abiotic stress candidate genes were obtained. Drought, severe cold, high salinity, and high metallic ion concentrations severely restrict rice production. Consequently, the breeding of abiotic stress-tolerant variety is being paid increasingly more attention. This study aimed to identify meta-quantitative trait loci (MQTL) for abiotic stress tolerance in rice, as well as the molecular markers and potential candidate genes of the MQTL regions. We summarized 2785 rice QTL and conducted a meta-analysis of 159 studies. We found 82 drought tolerance (DT), 70 cold tolerance (CT), 70 salt tolerance (ST), and 51 heavy metal ion tolerance (IT) meta-QTL, as well as 20 DT, 11 CT, 22 ST, and 5 IT candidate genes in the MQTL interval. Thirty-one multiple-tolerance related MQTL regions, which were highly enriched, were also detected, and 13 candidate genes related to multiple-tolerance were obtained. In addition, the correlation between DT, CT, and ST was significant in the rice genome. Four candidate genes and four MM-QTL regions were detected simultaneously by GWAS and meta-analysis. The four candidate genes showed distinct genetic differentiation and substantial genetic distance between indica and japonica rice, and the four MM-QTL are potential intervals for mining abiotic stress-related candidate genes. The candidate genes identified in this study will not only be useful for marker-assisted selection and pyramiding but will also accelerate the fine mapping and cloning of the candidate genes associated with abiotic stress-tolerance mechanisms in rice.

An efficient multi-locus mixed model framework for the detection of small and linked QTLs in F2

In the genetic system that regulates complex traits, metabolites, gene expression levels, RNA editing levels and DNA methylation, a series of small and linked genes exist. To date, however, little is known about how to design an efficient framework for the detection of these kinds of genes. In this article, we propose a genome-wide composite interval mapping (GCIM) in F₂. First, controlling polygenic background via selecting markers in the genome scanning of linkage analysis was replaced by estimating polygenic variance in a genome-wide association study. This can control large, middle and minor polygenic backgrounds in genome scanning. Then, additive and dominant effects for each putative quantitative trait locus (QTL) were separately scanned so that a negative logarithm P-value curve against genome position could be separately obtained for each kind of effect. In each curve, all the peaks were identified as potential QTLs. Thus, almost all the small-effect and linked QTLs are included in a multi-locus model. Finally, adaptive least absolute shrinkage and selection operator (adaptive lasso) was used to estimate all the effects in the multi-locus model, and all the nonzero effects were further identified by likelihood ratio test for true QTL identification. This method was used to reanalyze four rice traits. Among 25 known genes detected in this study, 16 small-effect genes were identified only by GCIM. To further demonstrate GCIM, a series of Monte Carlo simulation experiments was performed. As a result, GCIM is demonstrated to be more powerful than the widely used methods for the detection of closely linked and small-effect QTLs.

Chloride and amino acids are associated with K+-alleviated drought stress in tea (Camellia sinesis)

Drought is one of the main limiting factors affecting tea plant yield and quality. Previous studies have reported that K+ (potassium) application significantly alleviated drought-induced damage in tea plants. However, the intrinsic mechanisms underlying K+-alleviated drought stress are still obscure. In our study, two contrasting varieties, Taicha12 (drought tolerant) and Fuyun6 (drought sensitive), were used to investigate the intrinsic mechanisms behind K+-alleviated drought stress in tea plants. In the present study, we compared with the case of tea plants under drought: higher water and chlorophyll contents were found in drought-stressed tea plants with an external K+ supply, confirming the role of externally supplied K+ in mitigating drought stress. We also found that an adequate K+ supply promoted Cl- accumulation in the mesophyll of Taicha12 (drought tolerant) over that of in Fuyun6 (drought sensitive). Moreover, Gly, Cys, Lys and Arg were not detected in Fuyun6 under 'Drought' or 'Drought + K+' conditions. Results showed that an exogenous supply of Arg and Val significantly alleviated drought-induced damage in Fuyun6, suggesting their role in K+-alleviated drought stress in tea plants. Collectively, our results show that chloride and amino acids are important components associated with K+-alleviated drought stress in tea plants.

Rice SnRK protein kinase OsSAPK8 acts as a positive regulator in abiotic stress responses

SnRK2 (sucrose non-fermenting 1-related protein kinases 2) protein kinase family involves in several abiotic stress response in plants. Although the regulatory mechanism of SnRK2 have been well demonstrated in Arabidopsis thaliana, their functions in rice are still largely unknown. Here, we report a SnRK2 family gene, OsSAPK8, can be strongly induced by abiotic stresses, including low-temperature, drought and high salt stress. The ossapk8 mutants showed lower tolerance to low-temperature, high salinity and drought stresses at the vegetative stages. Moreover, the expressions of marker genes for those abiotic stresses, e.g. OsDREB1, OsDREB2, OsNCED and OsRAB21, were downregulated in the ossapk8 mutants. We further confirmed that the yield was reduced in ossapk8 mutant lines compared with the wild type. Our results provide evidence for OsSAPK8 acting as a positive regulator in cold, drought, and salt stress responses.

Integrating the dynamics of yield traits in rice in response to environmental changes

Reductions in crop yields as a consequence of global climate change threaten worldwide food security. It is therefore imperative to develop high-yielding crop plants that show sustainable production under stress conditions. In order to achieve this aim through breeding or genetic engineering, it is crucial to have a complete and comprehensive understanding of the molecular basis of plant architecture and the regulation of its sub-components that contribute to yield under stress. Rice is one of the most widely consumed crops and is adversely affected by abiotic stresses such as drought and salinity. Using it as a model system, in this review we present a summary of our current knowledge of the physiological and molecular mechanisms that determine yield traits in rice under optimal growth conditions and under conditions of environmental stress. Based on physiological functioning, we also consider the best possible combination of genes that may improve grain yield under optimal as well as environmentally stressed conditions. The principles that we present here for rice will also be useful for similar studies in other grain crops.

The Effect of Drought on Transcriptome and Hormonal Profiles in Barley Genotypes With Contrasting Drought Tolerance

Like many cereal crops, barley is also negatively affected by drought stress. However, due to its simple genome as well as enhanced stress resilient nature compared to rice and wheat, barley has been considered as a model to decipher drought tolerance in cereals. In the present study, transcriptomic and hormonal profiles along with several biochemical features were compared between drought-tolerant (Otis) and drought-sensitive (Baronesse) barley genotypes subjected to drought to identify molecular and biochemical differences between the genotypes. The drought-induced decrease in the leaf relative water content, net photosynthesis, and biomass accumulation was relatively low in Otis compared to Baronesse. The hormonal profiles did not reveal significant differences for majority of the compounds other than the GA20 and the cis-zeatin-o-glucoside (c-ZOG), whose levels were greatly increased in Otis compared to Baronesse under drought. The major differences that emerged from the transcriptome analysis are; (1), the overall number of differentially expressed genes was relatively low in drought-tolerant Otis compared to drought-sensitive Baronesse; (2), a wax biosynthesis gene (CER1), and NAC transcription factors were specifically induced in Otis but not in Baronesse; (3), the degree of upregulation of betaine aldehyde dehydrogenase and a homeobox transcription factor (genes with proven roles in imparting drought tolerance), was greater in Otis compared to Baronesse; (4) the extent of downregulation of gene expression profiles for proteins of the reaction center photosystem II (PSII) (D1 and D2) was low in Otis compared to Baronesse; and, (5), alternative splicing (AS) was also found to differ between the genotypes under drought. Taken together, the overall transcriptional responses were low in drought-tolerant Otis but the genes that could confer drought tolerance were either specifically induced or greatly upregulated in the tolerant genotype and these differences could be important for drought tolerance in barley.

An S-domain receptor-like kinase, OsESG1, regulates early crown root development and drought resistance in rice

Plant receptor-like kinase (RLKs) are serine/threonine protein kinases that play fundamental roles in development, innate immunity, and abiotic stress response. Here, we identified an S-domain receptor-like kinase OsESG1 from rice (Oryza sativa), and identified its involvement in early crown root (CR) development and drought response. The OsESG1 kinase domain possessed auto-phosphorylation activity and was able to phosphorylate MBP and His proteins. OsESG1 was expressed ubiquitously in all tissues that were examined, with relatively higher expression in the embryo. And it could be induced to express by treating with PEG, NaCl and ABA. Transgenic plants carrying anti-sense (AS) OsESG1 were generated by knockdown of OsESG1 expression. At the early seedling stage, AS lines had fewer CRs and shorter shoot compared with wild type (WT) plants. IAA flux and the genes' expressions of the auxin responsive and efflux carrier were infected in the AS lines. These results indicated that auxin signaling and polar auxin transport (PAT) were disrupted. The AS lines were more sensitive to osmotic stress compared to WT, and showed excessive accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA), lower activities of antioxidant enzymes, and impaired expressions of stress-related genes under PEG treatment. Results above suggested that OsESG1 may regulate CR initiation and development by controlling auxin response and distribution, and participate in stress response by regulating the activities of antioxidants and expressions of stress-regulated genes.

The Salix psammophila SpRLCK1 involved in drought and salt tolerance

Receptor-like cytoplasmic kinases (RLCKs) play critical roles in biotic and abiotic stress responses in plants. However, the functions of RLCKs from the desert shrub willow Salix psammophila have not been characterized. Here, we focused on the biological function of SpRLCK1, which was previously identified as a potential drought-related gene. Phylogenetic analysis and subcellular localization revealed that SpRLCK1 was a cytoplasmic-localized protein with a protein kinase domain and belonged to the RLCK VIIa subclass. Gene expression profile revealed that SpRLCK1 was predominantly expressed in the root, being consistent with the GUS staining of pSpRLCK1:GUS transgenic plants. Additionally, the expression of SpRLCK1 was significantly induced by drought and salt stresses. To verify the function of SpRLCK1, we generated its overexpressing transgenic lines in Arabidopsis thaliana. The SpRLCK1-overexpressing plants exhibited higher tolerance to drought and salt stresses, as evidenced by the higher survival rate, relative water content and antioxidant enzyme activity than those of wild-type plants. The SpRLCK1-overexpressing plants enhanced drought and salt tolerance by improving ROS-scavenging activities. A co-expression network for SpRLCK1 was constructed, and the expression analysis indicated that SpRLCK1 regulated the expression of a series of stress-related genes. Taken together, our results demonstrate that SpRLCK1 confers plant drought and salt tolerance through enhancing the activity of antioxidant enzymes and cooperating with stress-related genes.

Cold tolerance response mechanisms revealed through comparative analysis of gene and protein expression in multiple rice genotypes

Due to its tropical origin and adaptation, rice is significantly impacted by cold stress, and consequently sustains large losses in growth and productivity. Currently, rice is the second most consumed cereal in the world and production losses caused by extreme temperature events in the context of "major climatic changes" can have major impacts on the world economy. We report here an analysis of rice genotypes in response to low-temperature stress, studied through physiological gas-exchange parameters, biochemical changes in photosynthetic pigments and antioxidants, and at the level of gene and protein expression, towards an understanding and identification of multiple low-temperature tolerance mechanisms. The first effects of cold stress were observed on photosynthesis among all genotypes. However, the tropical japonica genotypes Secano do Brazil and Cypress had a greater reduction in gas exchange parameters like photosynthesis and water use efficiency in comparison to the temperate japonica Nipponbare and M202 genotypes. The analysis of biochemical profiles showed that despite the impacts of low temperature on tolerant plants, they quickly adjusted to maintain their cellular homeostasis by an accumulation of antioxidants and osmolytes like phenolic compounds and proline. The cold tolerant and sensitive genotypes showed a clear difference in gene expression at the transcript level for OsGH3-2, OsSRO1a, OsZFP245, and OsTPP1, as well as for expression at the protein level for LRR-RLKs, bHLH, GLYI, and LTP1 proteins. This study exemplifies the cold tolerant features of the temperate japonica Nipponbare and M202 genotypes, as observed through the analysis of physiological and biochemical responses and the associated changes in gene and protein expression patterns. The genes and proteins showing differential expression response are notable candidates towards understanding the biological pathways affected in rice and for engineering cold tolerance, to generate cultivars capable of maintaining growth, development, and reproduction under cold stress. We also propose that the mechanisms of action of the genes analyzed are associated with the tolerance response.

A late embryogenesis abundant protein GsPM30 interacts with a receptor like cytoplasmic kinase GsCBRLK and regulates environmental stress responses

A Glycine soja receptor like cytoplasmic kinase GsCBRLK was previously characterized as a positive regulator of salt tolerance. However, how GsCBRLK regulates stress responses remains obscure. Here, we report the interaction between GsCBRLK and a group 3 late embryogenesis abundant protein GsPM30, and suggest its role in stress responses. GsPM30 was found to physically associate with GsCBRLK through yeast two hybrid assays, which was verified by bimolecular fluorescence complementation analysis. Deletion analyses showed that the N-terminal variable domain of GsCBRLK was sufficient for GsPM30 interaction. Besides GsPM30, GsCBRLK could associate with several group 3 LEAs, of which the N-terminus sequences show high identity with GsPM30. Lower binding affinity or even no interaction was observed between GsCBRLK and other group 3 LEAs, which are less closely related to GsPM30. Furthermore, we observed that GsPM30 could localize surrounding the internal circumference of plant cells, as well as in cytoplasm and nucleus. In addition, GUS staining and quantitative real-time PCR results suggested the ubiquitous expression in different tissues and induced expression by NaCl and mannitol treatments for GsPM30. Consistently, GsPM30 overexpression in Arabidopsis caused increased tolerance to high salinity and dehydration/water deficit at both the young and adult seedling stages. Our results demonstrated the interaction between GsCBRLK and LEAs, and revealed the positive role of GsPM30 in stress responses.

Identification and characterization of the first cytokinin glycosyltransferase from rice

BACKGROUND

Cytokinins are one of the five major hormones families in plants and are important for their normal growth and environmental adaptability. In plants, cytokinins are mostly present as glycosides in plants, and their glycosylation modifications are catalyzed by family 1 glycosyltransferases. Current research on cytokinin glycosylation has focused on the biochemical identification of enzymes and the analysis of metabolites in Arabidopsis. There are few studies that examine how cytokinin glycosylation affects its synthesis and accumulation in plants. It is particularly important to understand these processes in food crops such as rice (Oryza sativa); however, to date, cytokinin glycosyltransferase genes in rice have not been reported.

RESULTS

In this study, we identified eight rice genes that were functionally homologous to an Arabidopsis cytokinin glycosyltransferase gene. These genes were cloned and expressed in a prokaryotic system to obtain their purified proteins. Through enzymatic analysis and liquid chromatography-mass spectrometry, a single rice glycosyltransferase, Os6, was identified that glycosylated cytokinin in vitro. Os6 was overexpressed in Arabidopsis, and the extraction of cytokinin glycosides showed that Os6 is functionally active in planta.

CONCLUSIONS

The identification and characterization of the first cytokinin glycosyltransferase from rice is important for future studies on the cytokinin metabolic pathway in rice. An improved understanding of rice cytokinin glycosyltransferases may facilitate genetic improvements in rice quality.

Physiological and transcriptional responses to low-temperature stress in rice genotypes at the reproductive stage

Rice growth and productivity is adversely affected by low-temperature stress. From a previous screen of diverse rice genotypes for cold tolerance parameters at the vegetative stage, we selected the tolerant Nipponbare and M202 genotypes and sensitive Cypress and Secano do Brazil genotypes for further analysis at the reproductive stage for physiological and yield parameters. Cold stress severely affected grain yield as estimated by the number of grain per panicle, panicle length, and 100 seed weight. Analysis of gene expression of 21 genes involved in physiological responses to low temperature tested, in the flag leaf and inflorescence tissue of these genotypes, showed an increased expression of the Lipid Transfer Protein genes LTP7 and LTP10 in flag leaf tissue of the tolerant Nipponbare and M202, along with a significant increase in the relative expression of stress-responsive transcription factors (TFs) and cold-inducible genes. In flag leaf tissue OsNAC9, OsNAC10 and OsNAP genes showed high correlation with photosynthesis, stomatal conductance, transpiration and Quantum Efficiency of PSII. In consequence of the foregoing results, we conclude that Nipponbare and M202 are cold tolerant genotypes and that LTP7, LTP10, OsNAC9, OsNAC10 and OsNAP genes can be used as markers in screening for cold tolerance at the reproductive stage. Furthermore based on the results we propose a model of low-temperature tolerance mechanism of how stress is perceived, and how the signal cascade acts to promote tolerance at below-ideal temperatures.

OsNAR2.1 Positively Regulates Drought Tolerance and Grain Yield Under Drought Stress Conditions in Rice

Drought is an important environmental factor that severely restricts crop production. The high-affinity nitrate transporter partner protein OsNAR2.1 plays an essential role in nitrate absorption and translocation in rice. Our results suggest that OsNAR2.1 expression is markedly induced by water deficit. After drought stress conditions and irrigation, compared with wild-type (WT), the survival rate was significantly improved in OsNAR2.1 over-expression lines and decreased in OsNAR2.1 RNAi lines. The survival rate of Wuyunjing7 (WYJ), OsNRT2.1 over-expression lines and OsNRT2.3a over-expression lines was not significantly different. Compared with WT, overexpression of OsNAR2.1 could significantly increase nitrogen uptake in rice, and OsNAR2.1 RNAi could significantly reduce nitrogen uptake. Under drought conditions, the expression of OsNAC10, OsSNAC1, OsDREB2a, and OsAP37 was significantly reduced in OsNAR2.1 RNAi lines and increased substantially in OsNAR2.1 over-expression lines. Also, the chlorophyll content, relative water content, photosynthetic rate and water use efficiency were decreased considerably in OsNAR2.1 RNAi lines and increased significantly in OsNAR2.1 over-expression lines under drought conditions. Finally, compared to WT, grain yield increased by about 9.1 and 26.6%, in OsNAR2.1 over-expression lines under full and limited irrigation conditions, respectively. These results indicate that OsNAR2.1 regulates the response to drought stress in rice and increases drought tolerance.

Drought Induced Signaling in Rice: Delineating Canonical and Non-canonical Pathways

Drought induced stress is often a bottleneck of agricultural crop production. Invariably, field crops across all agro-ecological regions succumb to it with an yield penalty. Drought massively affects the growth and harvestable yield in crops and has become an imminent problem necessitating breeding of tolerant crops. It induces myriad changes of biochemical, molecular, and physiological nature that manifest into aberrant plant morphology. The response to drought in plants incites a signaling cascade that involves perception and translation of drought signal leading to concomitant modulation of gene expression and de novo osmolyte synthesis. The intricate patterns of expression of these genes vary from early induction to late responsive genes. While one class of genes codes for products imparting osmotolerance and protection to plants, the second class predominantly modulates target gene expression by an intricate signal transduction mechanism. This review summarizes both canonical and non-canonical cascades of drought stress response in plants, delineating the mechanism in rice (Oryza sativa) and emphasizes hydropenia induced lipid signaling.

Roles of a maize phytochrome-interacting factors protein ZmPIF3 in regulation of drought stress responses by controlling stomatal closure in transgenic rice without yield penalty

ZmPIF3 plays an important role in ABA-mediated regulation of stomatal closure in the control of water loss, and can improve both drought tolerance and did not affect the grain yield in the transgenic rice. Phytochrome-interacting factors (PIFs) are a subfamily of basic helix-loop-helix (bHLH) transcription factors and play important roles in regulating plant growth and development. In our previous study, overexpression of a maize PIFs family gene, ZmPIF3, improved drought tolerance in transgenic rice. In this study, measurement of water loss rate, transpiration rate, stomatal conductance, guard cell aperture, density and length of ZmPIF3 transgenic plants showed that ZmPIF3 can enhance water-saving and drought-resistance by decreasing stomatal aperture and reducing transpiration in both transgenic rice and transgenic Arabidopsis. Scrutiny of sensitivity to ABA showed that ZmPIF3 transgenic rice was hypersensitive to ABA, while the endogenous ABA level was not significantly changed. These results indicate that ZmPIF3 plays a major role in the ABA signaling pathway. In addition, DGE results further suggest that ZmPIF3 participates in the ABA signaling pathway and regulates stomatal aperture in rice. Comparison analysis of the phenotype, physiology, and transcriptome of ZmPIF3 transgenic rice compared to control plants further suggests that ZmPIF3 is a positive regulator of ABA signaling and enhances water-saving and drought-resistance traits by reducing stomatal openings to control water loss. Moreover, investigation of the agronomic traits of ZmPIF3 transgenic rice from four cultivating seasons showed that ZmPIF3 expression increased the tiller and panicle number and did not affect the grain yield in the transgenic rice. These results demonstrate that ZmPIF3 is a promising candidate gene in the transgenic breeding of water-saving and drought-resistant rice plants and crop improvement.

The Receptor-Like Cytoplasmic Kinase STRK1 Phosphorylates and Activates CatC, Thereby Regulating H2O2 Homeostasis and Improving Salt Tolerance in Rice

Salt stress can significantly affect plant growth and agricultural productivity. Receptor-like kinases (RLKs) are believed to play essential roles in plant growth, development, and responses to abiotic stresses. Here, we identify a receptor-like cytoplasmic kinase, salt tolerance receptor-like cytoplasmic kinase 1 (STRK1), from rice (Oryza sativa) that positively regulates salt and oxidative stress tolerance. Our results show that STRK1 anchors and interacts with CatC at the plasma membrane via palmitoylation. CatC is phosphorylated mainly at Tyr-210 and is activated by STRK1. The phosphorylation mimic form CatC^Y210D exhibits higher catalase activity both in vitro and in planta, and salt stress enhances STRK1-mediated tyrosine phosphorylation on CatC. Compared with wild-type plants, STRK1-overexpressing plants exhibited higher catalase activity and lower accumulation of H₂O₂ as well as higher tolerance to salt and oxidative stress. Our findings demonstrate that STRK1 improves salt and oxidative tolerance by phosphorylating and activating CatC and thereby regulating H₂O₂ homeostasis. Moreover, overexpression of STRK1 in rice not only improved growth at the seedling stage but also markedly limited the grain yield loss under salt stress conditions. Together, these results offer an opportunity to improve rice grain yield under salt stress.

Receptor-Like Cytoplasmic Kinases: Central Players in Plant Receptor Kinase-Mediated Signaling

Receptor kinases (RKs) are of paramount importance in transmembrane signaling that governs plant reproduction, growth, development, and adaptation to diverse environmental conditions. Receptor-like cytoplasmic kinases (RLCKs), which lack extracellular ligand-binding domains, have emerged as a major class of signaling proteins that regulate plant cellular activities in response to biotic/abiotic stresses and endogenous extracellular signaling molecules. By associating with immune RKs, RLCKs regulate multiple downstream signaling nodes to orchestrate a complex array of defense responses against microbial pathogens. RLCKs also associate with RKs that perceive brassinosteroids and signaling peptides to coordinate growth, pollen tube guidance, embryonic and stomatal patterning, floral organ abscission, and abiotic stress responses. The activity and stability of RLCKs are dynamically regulated not only by RKs but also by other RLCK-associated proteins. Analyses of RLCK-associated components and substrates have suggested phosphorylation relays as a major mechanism underlying RK-mediated signaling.

Effect of Drought on Agronomic Traits of Rice and Wheat: A Meta-Analysis

Drought has been one of the most important limiting factors for crop production, which deleteriously affects food security worldwide. The main objective of the present study was to quantitatively assess the effect of drought on the agronomic traits (e.g., plant height, biomass, yield, and yield components) of rice and wheat in combination with several moderators (e.g., drought stress intensity, rooting environment, and growth stage) using a meta-analysis study. The database was created from 55 published studies on rice and 60 published studies on wheat. The results demonstrated that drought decreased the agronomic traits differently between rice and wheat among varying growth stages. Wheat and rice yields decreased by 27.5% and 25.4%, respectively. Wheat grown in pots showed greater decreases in agronomic traits than those grown in the field. Rice showed opposite growing patterns when compared to wheat in rooting environments. The effect of drought on rice increased with plant growth and drought had larger detrimental influences during the reproductive phase (e.g., blooming stage, filling stage, and maturity). However, an exception was found in wheat, which had similar decreased performance during the complete growth cycle. Based on these results, future droughts could produce lower yields of rice and wheat when compared to the current drought.

Regulatory Role of Silicon in Mediating Differential Stress Tolerance Responses in Two Contrasting Tomato Genotypes Under Osmotic Stress

Previous studies have shown the role of silicon (Si) in mitigating the adverse effect of drought stress in different crop species. However, data are lacking on a comparison of drought tolerant and drought sensitive crop cultivars in response to Si nutrition. Therefore, the aim of this study was to elucidate the mechanism (s) by which two contrasting tomato genotypes respond to Si nutrition under osmotic stress condition. Two tomato lines contrasting in their response to drought stress were hydroponically grown under polyethylene glycol (PEG, 6000) and two regimes of Si (0 and 1.5 mM). Metabolite profiling was performed in two lines. Growth and relevant physiological parameters, and expression levels of selected genes were also measured. Si application resulted in improved osmotic stress tolerance in both drought tolerant line LA0147 and drought sensitive line FERUM. In the drought tolerant line, Si enhanced uptake of sulfur (S) and ammonium ( NH 4 + ) which led to a significantly higher production of amino acids arginine, methionine, serine, and glycine. While in the drought sensitive line, Si significantly increased production of amino acids proline and GABA which further lowered the level of GSSG to GSH ratio and thus balanced the redox homeostasis under osmotic stress. The higher significant production of amino acids arginine, methionine, GABA, and proline enhanced production of free polyamines putrescine and spermidine and improved osmotic stress tolerance. Therefore, we conclude that Si distinctively regulated osmotic stress tolerance in two contrasting tomato genotypes by differential accumulation of relevant amino acids which eventually led to enhanced polyamine metabolism.

GBF3 transcription factor imparts drought tolerance in Arabidopsis thaliana

Drought transcriptome analysis of finger millet (Eleusine coracana) by cDNA subtraction identified drought responsive genes that have a potential role in drought tolerance. Through virus-induced gene silencing (VIGS) in a related crop species, maize (Zea mays), several genes, including a G-BOX BINDING FACTOR 3 (GBF3) were identified as candidate drought stress response genes and the role of GBF3 in drought tolerance was studied in Arabidopsis thaliana. Overexpression of both EcGBF3 and AtGBF3 in A. thaliana resulted in improved tolerance to osmotic stress, salinity and drought stress in addition to conferring insensitivity to ABA. Conversely, loss of function of this gene increased the sensitivity of A. thaliana plants to drought stress. EcGBF3 transgenic A. thaliana results also suggest that drought tolerance of sensitive plants can be improved by transferring genes from far related crops like finger millet. Our results demonstrate the role of GBF3 in imparting drought tolerance in A. thaliana and indicate the conserved role of this gene in drought and other abiotic stress tolerance in several plant species.

Is RAF1 protein from Synechocystis sp. PCC 6803 really needed in the cyanobacterial Rubisco assembly process?

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is responsible for carbon dioxide conversion during photosynthesis and, therefore, is the most important protein in biomass generation. Modifications of this biocatalyst toward improvements in its properties are hindered by the complicated and not yet fully understood assembly process required for the formation of active holoenzymes. An entire set of auxiliary factors, including chaperonin GroEL/GroES and assembly chaperones RbcX or Rubisco accumulation factor 1 (RAF1), is involved in the folding and subsequent assembly of Rubisco subunits. Recently, it has been shown that cyanobacterial RAF1 acts during the formation of the large Rubisco subunit (RbcL) dimer. However, both its physiological function and its necessity in the prokaryotic Rubisco formation process remain elusive. Here, we demonstrate that the Synechocystis sp. PCC 6803 strain with raf1 gene disruption shows the same growth rate as wild-type cells under standard conditions. Moreover, the Rubisco biosynthesis process seems to be unperturbed in mutant cells despite the absence of RbcL-RAF1 complexes. However, in the tested environmental conditions, sulfur starvation triggers the degradation of RbcL and subsequent proteolysis of other polypeptides in wild-type but not Δraf1 strains. Pull-down experiments also indicate that, apart from Rubisco, RAF1 co-purifies with phycocyanins. We postulate that RAF1 is not an obligatory factor in cyanobacterial Rubisco assembly, but rather participates in environmentally regulated Rubisco homeostasis.