bHLH57 confers chilling tolerance and grain yield improvement in rice

Genome-wide analysis of the bHLH gene family in Spatholobus suberectus identifies SsbHLH112 as a regulator of flavonoid biosynthesis

Spatholobus suberectus Dunn (S. suberectus), a medicinal herb from the Leguminosae family, is widely utilized in traditional medicine. The dried stem of S. suberectus demonstrates a variety of pharmacological effects, primarily attributed to its rich content of flavonoid compounds, such as catechin. The bHLH gene family serves diverse functions in plants, including regulating flavonoid biosynthesis, yet its specific function in S. suberectus remains uncertain. To address this, the sequenced genome of S. suberectus was leveraged for an extensive genome-wide analysis of the bHLH gene family. This analysis identified 156 SsbHLH genes, which were phylogenetically classified into 19 distinct subgroups. Of these, 153 genes were mapped across 9 chromosomes, while 3 remained unlocalized. Furthermore, genes within the identical subgroups displayed preserved exon-intron arrangements and motif patterns. Ka/Ks analysis further revealed that most duplicated genes have undergone purifying selection. A subset of 12 SsbHLH genes was found to be markedly associated with flavonoid content, including catechin, isoliquiritigenin, formononetin, and genistein. Among these, SsbHLH112, which strongly correlates with catechin levels, was shown to markedly elevate flavonoids and catechin accumulation when overexpressed in Nicotiana benthamiana. This overexpression also notably upregulated NbDFR and NbLAR, consistent with increased catechin production. These results elucidate the role of SsbHLH transcription factors in flavonoid biosynthesis, providing a basis for additional exploration of SsbHLH gene functions in S. suberectus.

The molecular mechanism of transcription factor regulation of grain size in rice

Rice is a crucial food crop in China, and the continuous and stable improvement of rice yield is of great significance for ensuring national food security. Grain size in rice is closely related to thousand-grain weight, making it a key factor influencing yield. Identifying genes associated with grain size and elucidating their molecular mechanisms are essential for breeding high-yield, high-quality rice varieties. Transcription factors play a vital role in regulating plant growth and development, and many transcription factor families are crucial in controlling grain size in rice. Here, we review the mechanisms by which transcription factors regulate rice grain size, summarize and evaluate the regulatory mechanisms of transcription factors that have been discovered in recent decades to regulate rice grain size, construct two possible super networks composed of transcription factors as links to regulate rice grain size, and points out the application of transcription factors regulating grain size in rice breeding. This review will provide a roadmap for understanding the regulatory mechanisms of rice grain size and applying these genes to rice breeding using molecular breeding techniques.

The OsbHLH166-OsABCB4 module regulates grain length and weight via altering auxin efflux

Grain size is one of the key factors determining grain weight and yield. However, it remains largely unknown how the auxin signal regulates grain size in rice. Here, a quantitative trait locus qGL1 for grain length was identified with recombinant inbred lines 9311 and Nipponbare (NIP), and fine-mapped to the OsABCB4 gene, which encodes a member of the ATP Binding Cassette B (ABCB) subfamily. Compared to NIP, loss of OsABCB4 function leads to longer and heavier grains, while over-expression of OsABCB4 causes shorter and lighter grains, demonstrating a negative control of grain length and weight in rice. Haplotype analyses using 3024 rice-sequenced genomes indicated that SNP25 and SNP55 in OsABCB4 are correlated with grain length in rice. OsbHLH166, a basic helix-loop-helix transcription factor, was screened from a yeast one-hybrid library and confirmed to directly bind the promoter of OsABCB4 by electrophoretic mobility shift assay and yeast one hybridization validation and to activate the expression of OsABCB4 by dual-luciferase reporter assay. And OsbHLH166 expressions matching OsABCB4 were all higher expressed in stems and glumes. OsABCB4 was subcellularly localized on the plasma membrane, which was verified as an auxin efflux transporter. Histological analysis, IAA content measurement and DR5:GUS activity analyses demonstrated that OsbHLH166 and OsABCB4 control grain length by regulating cell expansion and auxin contents in glume cells and altering the expression of GL7, GS2, TGW3 and GS3 genes during rice grain development. This newly identified OsbHLH166-OsABCB4 module sheds light on our understanding of molecular mechanisms underlying the regulation of grain size and weight via auxin and provides a new gene resource for molecular design breeding of grain type.

Candidate Gene for Kernel-Related Traits in Maize Revealed by a Combination of GWAS and Meta-QTL Analyses

Maize kernel traits represent crucial agronomic characteristics that significantly determine yield potential. Analyzing the genetic basis of these traits is essential for yield improvement. In this study, we utilized 1283 maize inbred lines to investigate three kernel-related characteristics: kernel length (KL), kernel width (KW), and 100-kernel weight (HKW). We conducted a genome-wide association study (GWAS) on three kernel-related traits, resulting in the identification of 29 significantly associated SNPs and six candidate genes. Additionally, we compiled quantitative trait loci (QTL) information for 765 maize kernel-related traits from 56 studies, conducted a meta-analysis of QTL, and identified 65 meta-QTLs (MQTLs). Among the 23 MQTLs, we found 25 functional genes and reported candidate genes related to kernel traits. We identified 26 maize homologs across 19 MQTLs by utilizing 25 genes that affect rice grain traits. We compared the 29 significant SNPs detected with the physical locations of 65 MQTLs and found that 3 significant SNPs were located within these MQTL intervals, and another 10 significant SNPs were in proximity to these intervals, being less than 2 Mb away, although they were not included within the MQTL intervals. The results of this study provide a theoretical foundation for elucidating the genetic basis of maize kernel-related traits and advancing molecular marker-assisted breeding selection.

OsNCED5 confers cold stress tolerance through regulating ROS homeostasis in rice

Cold stress is one of the most serious abiotic stresses that affects the growth and yield in rice. However, the molecular mechanism by which abscisic acid (ABA) regulates plant cold stress tolerance is not yet clear. In this study, we identified a member of the OsNCED (9-cis-epoxycarotenoid dioxygenase) gene family, OsNCED5, which confers cold stress tolerance in rice. OsNCED5 encodes a chloroplast-localized ABA biosynthetic enzyme and its expression is strongly induced by cold stress. Disruption of OsNCED5 by CRISPR/Cas9-mediated mutagenesis led to a significant decrease in ABA content and exhibited significant reduced cold stress tolerance at the seedling stage. Exogenous ABA restored the cold stress tolerance of the osnced5 mutants. Overexpression of OsNCED5 gene significantly improved the cold stress tolerance of rice seedlings. Moreover, OsNCED5 mainly regulates cold stress tolerance through regulating reactive oxygen species (ROS) homeostasis. Taken together, we identified a new OsNCED regulator involved in cold stress tolerance, and provided a potential target gene for enhancing cold stress tolerance in rice.

Amur Grape VaMYB4a-VaERF054-Like Module Regulates Cold Tolerance Through a Regulatory Feedback Loop

Cold stress can limit the growth and development of grapevines, which can ultimately reduce productivity. However, the mechanisms by which grapevines respond to cold stress are not yet fully understood. Here, we characterized an APETALA2/ethylene response factor (AP2/ERF) which was shown to be a target gene of our previously identified VaMYB4a from Amur grape. We further investigated the molecular interactions between VaMYB4a and VaERF054-like transcription factors in grapes and their role in cold stress tolerance. Our results demonstrated that VaMYB4a directly binds to and activates the VaERF054-like gene promoter, leading to its enhanced expression. Moreover, we also explored the influence of ethylene precursors and inhibitors on VaERF054-like expression and grape cold tolerance. Our findings indicate that VaERF054-like contribute to cold tolerance in grapes through modulation of the ethylene pathway and the CBF signal pathway. Overexpression of VaERF054-like in Vitis vinifera 'Chardonnay' calli and transgenic grape lines resulted in increased freezing stress tolerance, confirming its role in the cold stress response. We further confirmed the interaction between VaMYB4a and VaERF054-like in vivo and in vitro. The co-transformation of VaMYB4a and VaERF054-like in grape calli demonstrates a synergistic interaction, enhancing the cold tolerance through a regulatory feedback mechanism. Our finding provides new insights into grape cold tolerance mechanisms, potentially contributing to the development of cold-resistant grape varieties.

Genome-wide identification of the bHLH gene family in Scutellaria baicalensis and their relationship with baicalin biosynthesis under drought stress

The bHLH gene family plays a critical role in regulating internal responses in plants. Although the pharmacological properties of Scutellaria baicalensis have been extensively studied, its bHLH gene family remains poorly investigated. In this study, 142 SbbHLH genes were identified using the complete genome data of S. baicalensis. Phylogenetic and conserved motif analyses were performed. Gene duplication events were analyzed, and cis-element analysis was conducted to explore regulatory factors. The expression patterns of these genes in different tissues and under drought stress were investigated using transcriptome data and qRT-PCR analysis. Phylogenetic and conserved motif analyses revealed that the gene structures within each SbbHLH clade are relatively conserved. Gene duplication analysis identified 29 duplication events in the SbbHLH gene family, most of which involved gene pairs under purifying selection. Cis-element analysis revealed that these genes are regulated by various environmental and hormonal factors. Transcriptomic data and qRT-PCR results demonstrated tissue-specific expression patterns for the 142 SbbHLH genes. Additionally, bHLH genes potentially involved in baicalin biosynthesis were identified under drought stress. The findings suggest that under drought stress, SbbHLH74, SbbHLH98, and SbbHLH142 are regulated by a network centered on SbbHLH53, which enhances baicalin biosynthesis. In conclusion, this study provides a comprehensive analysis of the bHLH gene family in S. baicalensis and identifies 4 potential SbbHLH genes involved in regulating baicalin biosynthesis under drought stress.

Comprehensive Genome-Wide Identification and Expression Profiling of bHLH Transcription Factors in Areca catechu Under Abiotic Stress

The basic helix-loop-helix (bHLH) transcription factor (TF) family, the second-largest among eukaryotes, is known for its evolutionary and functional diversity across plant species. However, bHLH genes have not yet been characterized in Areca catechu. In this study, we identified 76 AcbHLH genes, which exhibit a variety of physicochemical properties. Phylogenetic analysis revealed evolutionary relationships between Arabidopsis thaliana bHLH genes (AtbHLH) and their counterparts in A. catechu (AcbHLH). These analyses also highlighted conserved amino acid motifs (S, R, K, P, L, A, G, and D), conserved domains, and evolutionary changes, such as insertions, deletions, and exon gains or losses. Promoter analysis of AcbHLH genes revealed 76 cis-elements related to growth, phytohormones, light, and stress. Gene duplication analysis revealed four tandem duplications and twenty-three segmental duplications, while AcbHLH63 in the Areca genome exhibited significant synteny with bHLH genes from A. thaliana, Vitis vinifera, Solanum lycopersicum, Brachypodium distachyon, Oryza sativa, and Zea mays. Furthermore, relative expression analysis showed that under drought stress (DS), AcbHLH22, AcbHLH39, AcbHLH45, and AcbHLH58 showed distinct upregulation in leaves at specific time points, while all nine AcbHLH genes were upregulated in roots. Under salt stress (SS), AcbHLH22, AcbHLH39, AcbHLH45, and AcbHLH58 were upregulated in leaves, and AcbHLH22, AcbHLH34, and AcbHLH39 exhibited differential expression in roots at various time points. This study provides valuable insights into the bHLH superfamily in A. catechu, offering a solid foundation for further investigation into its role in responding to abiotic stresses.

An ABA biosynthesis enzyme gene OsNCED4 regulates NaCl and cold stress tolerance in rice

Rice (Oryza sativa L.) is susceptible to various abiotic stresses, such as salt, cold, and drought. Therefore, there is an urgent need to explore the relevant genes that enhance tolerance to these stresses. In this study, we identified a gene, OsNCED4 (9-cis-epoxycarotenoid dioxygenase 4), which regulates tolerance to multiple abiotic stresses. OsNCED4 encodes a chloroplast-localized abscisic acid (ABA) biosynthetic enzyme. The expression of OsNCED4 gene was significantly induced by 150 mM NaCl and cold stress. Disruption of OsNCED4 by CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9-mediated mutagenesis resulted in significant sensitivity to NaCl and cold stress. The salt and cold sensitivity of osnced4 mutant was due to the reduction of ABA content and the excessive accumulation of reactive oxygen species (ROS) under stress. Moreover, OsNCED4 also regulates drought stress tolerance of rice seedlings. Taken together, these results indicate that OsNCED4 is a new regulator for multiple abiotic stress tolerance in rice, and provided a potential target gene for enhancing multiple stress tolerance in the future.

A novel strategy of artificially regulating plant rhizosphere microbial community to promote plant tolerance to cold stress

Artificial regulation of plant rhizosphere microbial communities through the synthesis of microbial communities is one of the effective ways to improve plant stress resistance. However, the process of synthesizing stress resistant microbial communities with excellent performance is complex, time-consuming, and costly. To address this issue, we proposed a novel strategy for preparing functional microbial communities. We isolated a cultivable cold tolerant bacterial community (PRCBC) from the rhizosphere of peas, and studied its effectiveness in assisting rice to resist stress. The results indicate that PRCBC can not only improve the ability of rice to resist cold stress, but also promote the increase of rice yield after cold stress relieved. This is partly because PRCBC increases the nitrogen content in the rhizosphere soil, and promotes rice's absorption of nitrogen elements, thereby promoting rice growth and enhancing its ability to resist osmotic stress. More importantly, the application of PRCBC drives the succession of rice rhizosphere microbial communities, and promotes the succession of rice rhizosphere microbial communities towards stress resistance. Surprisingly, PRCBC drives the succession of rice rhizosphere microbial communities towards a composition similar to PRCBC. This provides a feasible novel method for artificially and directionally driving microbial succession. In summary, we not only proposed a novel and efficient strategy for preparing stress resistant microbial communities to promote plant stress resistance, but also unexpectedly discovered a possible directionally driving method for soil microbial community succession.

Recent advances of CRISPR-based genome editing for enhancing staple crops

An increasing population, climate change, and diminishing natural resources present severe threats to global food security, with traditional breeding and genetic engineering methods often falling short in addressing these rapidly evolving challenges. CRISPR/Cas systems have emerged as revolutionary tools for precise genetic modifications in crops, offering significant advancements in resilience, yield, and nutritional value, particularly in staple crops like rice and maize. This review highlights the transformative potential of CRISPR/Cas technology, emphasizing recent innovations such as prime and base editing, and the development of novel CRISPR-associated proteins, which have significantly improved the specificity, efficiency, and scope of genome editing in agriculture. These advancements enable targeted genetic modifications that enhance tolerance to abiotic stresses as well as biotic stresses. Additionally, CRISPR/Cas plays a crucial role in improving crop yield and quality by enhancing photosynthetic efficiency, nutrient uptake, and resistance to lodging, while also improving taste, texture, shelf life, and nutritional content through biofortification. Despite challenges such as off-target effects, the need for more efficient delivery methods, and ethical and regulatory concerns, the review underscores the importance of CRISPR/Cas in addressing global food security and sustainability challenges. It calls for continued research and integration of CRISPR with other emerging technologies like nanotechnology, synthetic biology, and machine learning to fully realize its potential in developing resilient, productive, and sustainable agricultural systems.

The MdHSC70-MdWRKY75 module mediates basal apple thermotolerance by regulating the expression of heat shock factor genes

Heat stress severely restricts the growth and fruit development of apple (Malus domestica). Little is known about the involvement of WRKY proteins in the heat tolerance mechanism in apple. In this study, we found that the apple transcription factor (TF) MdWRKY75 responds to heat and positively regulates basal thermotolerance. Apple plants that overexpressed MdWRKY75 were more tolerant to heat stress while silencing MdWRKY75 caused the opposite phenotype. RNA-seq and reverse transcription quantitative PCR showed that heat shock factor genes (MdHsfs) could be the potential targets of MdWRKY75. Electrophoretic mobility shift, yeast one-hybrid, β-glucuronidase, and dual-luciferase assays showed that MdWRKY75 can bind to the promoters of MdHsf4, MdHsfB2a, and MdHsfA1d and activate their expression. Apple plants that overexpressed MdHsf4, MdHsfB2a, and MdHsfA1d exhibited heat tolerance and rescued the heat-sensitive phenotype of MdWRKY75-Ri3. In addition, apple heat shock cognate 70 (MdHSC70) interacts with MdWRKY75, as shown by yeast two-hybrid, split luciferase, bimolecular fluorescence complementation, and pull-down assays. MdHSC70 acts as a negative regulator of the heat stress response. Apple plants that overexpressed MdHSC70 were sensitive to heat, while virus-induced gene silencing of MdHSC70 enhanced heat tolerance. Additional research showed that MdHSC70 exhibits heat sensitivity by interacting with MdWRKY75 and inhibiting MdHsfs expression. In summary, we proposed a mechanism for the response of apple to heat that is mediated by the "MdHSC70/MdWRKY75-MdHsfs" molecular module, which enhances our understanding of apple thermotolerance regulated by WRKY TFs.

Transcription factor OsbZIP10 modulates rice grain quality by regulating OsGIF1

Understanding and optimizing the process of grain filling helps the quest to maximize rice (Oryza sativa L.) seed yield and quality, yet the intricate mechanisms at play remain fragmented. Transcription factors (TFs) are major players in the gene networks underlying the grain filling process. Here, we employed grain incomplete filling (OsGIF1)/cell wall invertase 2, a key gene involved in grain filling, to explore its upstream TFs and identified a bZIP family TF, OsbZIP10, to be a transcriptional activator of OsGIF1. Rice grains of the knockouts of OsbZIP10 showed increased white-core rates but lower amylose content (AC), leading to better eating and cooking qualities in all genetic backgrounds investigated, though the impact of mutations in OsbZIP10 on grain weight depended on genetic background. Multi-omics analyses suggested that, in addition to OsGIF1, multiple genes involved in different biological processes contributing to grain filling were targeted by OsbZIP10, including OsAGPS1, a gene encoding the ADP-Glc pyrophosphorylase (AGPase) small subunit, and genes contributing to homeostasis of reactive oxygen species. Distinct genetic make-up was observed in OsbZIP10 between japonica and indica rice varieties, with the majority varieties of each subspecies belonging to two different haplotypes that were closely associated with AC. Overexpressing the haplotype linked to high-AC in the low-AC genetic background increased AC. Overall, this study sheds crucial light on the significance of the OsbZIP10-OsGIF1 module in the determination of rice grain quality, offering a potential avenue for genetic engineering of rice to produce seeds with tailored attributes.

Transcriptomic and Physiological Analyses for the Role of Hormones and Sugar in Axillary Bud Development of Wild Strawberry Stolon

Strawberries are mainly propagated by stolons, which can be divided into monopodial and sympodial types. Monopodial stolons consistently produce ramets at each node following the initial single dormant bud, whereas sympodial stolons develop a dormant bud before each ramet. Sympodial stolon encompasses both dormant buds and ramet buds, making it suitable for studying the formation mechanism of different stolon types. In this study, we utilized sympodial stolons from Fragaria nilgerrensis as materials and explored the mechanisms underlying sympodial stolon development through transcriptomic and phytohormonal analyses. The transcriptome results unveiled that auxin, cytokinin, and sugars likely act as main regulators. Endogenous hormone analysis revealed that the inactivation of auxin could influence bud dormancy. Exogenous cytokinin application primarily induced dormant buds to develop into secondary stolons, with the proportion of ramet formation being very low, less than 10%. Furthermore, weighted gene co-expression network analysis identified key genes involved in ramet formation, including auxin transport and response genes, the cytokinin activation gene LOG1, and glucose transport genes SWEET1 and SFP2. Consistently, in vitro cultivation experiments confirmed that glucose enhances the transition of dormant buds into ramets within two days. Collectively, cytokinin and glucose act as dormant breakers, with cytokinin mainly driving secondary stolon formation and glucose promoting ramet generation. This study improved our understanding of stolon patterning and bud development in the sympodial stolon of strawberries.

The Molecular Mechanism of Cold-Stress Tolerance: Cold Responsive Genes and Their Mechanisms in Rice (Oryza sativa L.)

Rice (Oryza sativa L.) production is highly susceptible to temperature fluctuations, which can significantly reduce plant growth and development at different developmental stages, resulting in a dramatic loss of grain yield. Over the past century, substantial efforts have been undertaken to investigate the physiological, biochemical, and molecular mechanisms of cold stress tolerance in rice. This review aims to provide a comprehensive overview of the recent developments and trends in this field. We summarized the previous advancements and methodologies used for identifying cold-responsive genes and the molecular mechanisms of cold tolerance in rice. Integration of new technologies has significantly improved studies in this era, facilitating the identification of essential genes, QTLs, and molecular modules in rice. These findings have accelerated the molecular breeding of cold-resistant rice varieties. In addition, functional genomics, including the investigation of natural variations in alleles and artificially developed mutants, is emerging as an exciting new approach to investigating cold tolerance. Looking ahead, it is imperative for scientists to evaluate the collective impacts of these novel genes to develop rice cultivars resilient to global climate change.

Functions of Basic Helix-Loop-Helix (bHLH) Proteins in the Regulation of Plant Responses to Cold, Drought, Salt, and Iron Deficiency: A Comprehensive Review

Abiotic stresses including cold, drought, salt, and iron deficiency severely impair plant development, crop productivity, and geographic distribution. Several bodies of research have shed light on the pleiotropic functions of BASIC HELIX-LOOP-HELIX (bHLH) proteins in plant responses to these abiotic stresses. In this review, we mention the regulatory roles of bHLH TFs in response to stresses such as cold, drought, salt resistance, and iron deficiency, as well as in enhancing grain yield in plants, especially crops. The bHLH proteins bind to E/G-box motifs in the target promoter and interact with various other factors to form a complex regulatory network. Through this network, they cooperatively activate or repress the transcription of downstream genes, thereby regulating various stress responses. Finally, we present some perspectives for future research focusing on the molecular mechanisms that integrate and coordinate these abiotic stresses. Understanding these molecular mechanisms is crucial for the development of stress-tolerant crops.

Genome-wide characterization of the bHLH gene family in Gynostemma pentaphyllum reveals its potential role in the regulation of gypenoside biosynthesis

BACKGROUND

Gynostemma pentaphyllum, an ancient Chinese herbal medicine, serves as a natural source of gypenosides with significant medicinal properties. Basic helix-loop-helix (bHLH) transcription factors play pivotal roles in numerous biological processes, especially in the regulation of secondary metabolism in plants. However, the characteristics and functions of the bHLH genes in G. pentaphyllum remain unexplored, and their regulatory role in gypenoside biosynthesis remains poorly elucidated.

RESULTS

This study identified a total of 111 bHLH members in G. pentaphyllum (GpbHLHs), categorizing them into 26 subgroups based on shared conserved motif compositions and gene structures. Collinearity analysis illustrated that segmental duplications predominately lead to the evolution of GpbHLHs, with most duplicated GpbHLH gene pairs undergoing purifying selection. Among the nine gypenoside-related GpbHLH genes, two GpbHLHs (GpbHLH15 and GpbHLH58) were selected for further investigation based on co-expression analysis and functional prediction. The expression of these two selected GpbHLHs was dramatically induced by methyl jasmonate, and their nuclear localization was confirmed. Furthermore, yeast one-hybrid and dual-luciferase assays demonstrated that GpbHLH15 and GpbHLH58 could bind to the promoters of the gypenoside biosynthesis pathway genes, such as GpFPS1, GpSS1, and GpOSC1, and activate their promoter activity to varying degrees.

CONCLUSIONS

In conclusion, our findings provide a detailed analysis of the bHLH family and valuable insights into the potential use of GpbHLHs to enhance the accumulation of gypenosides in G. pentaphyllum.

OsACA9, an Autoinhibited Ca2+-ATPase, Synergically Regulates Disease Resistance and Leaf Senescence in Rice

Calcium (Ca2+) is a versatile intracellular second messenger that regulates several signaling pathways involved in growth, development, stress tolerance, and immune response in plants. Autoinhibited Ca2+-ATPases (ACAs) play an important role in the regulation of cellular Ca2+ homeostasis. Here, we systematically analyzed the putative OsACA family members in rice, and according to the phylogenetic tree of OsACAs, OsACA9 was clustered into a separated branch in which its homologous gene in Arabidopsis thaliana was reported to be involved in defense response. When the OsACA9 gene was knocked out by CRISPR/Cas9, significant accumulation of reactive oxygen species (ROS) was detected in the mutant lines. Meanwhile, the OsACA9 knock out lines showed enhanced disease resistance to both rice bacterial blight (BB) and bacterial leaf streak (BLS). In addition, compared to the wild-type (WT), the mutant lines displayed an early leaf senescence phenotype, and the agronomy traits of their plant height, panicle length, and grain yield were significantly decreased. Transcriptome analysis by RNA-Seq showed that the differentially expressed genes (DEGs) between WT and the Osaca9 mutant were mainly enriched in basal immune pathways and antibacterial metabolite synthesis pathways. Among them, multiple genes related to rice disease resistance, receptor-like cytoplasmic kinases (RLCKs) and cell wall-associated kinases (WAKs) genes were upregulated. Our results suggest that the Ca2+-ATPase OsACA9 may trigger oxidative burst in response to various pathogens and synergically regulate disease resistance and leaf senescence in rice.

OsVPE2, a Member of Vacuolar Processing Enzyme Family, Decreases Chilling Tolerance of Rice

Chilling is a major abiotic stress affecting rice growth, development and geographical distribution. Plant vacuolar processing enzymes (VPEs) contribute to the seed storage protein processing and mediate the programmed cell death by abiotic and biotic stresses. However, little is known about the roles of plant VPEs in cold stress responses and tolerance regulation. Here, we found that OsVPE2 was a chilling-responsive gene. The early-indica rice variety Xiangzaoxian31 overexpressing OsVPE2 was more sensitive to chilling stress, whereas the OsVPE2-knockout mutants generated by the CRISPR-Cas9 technology exhibited significantly enhanced chilling tolerance at the seedling stage without causing yield loss. Deficiency of OsVPE2 reduces relative electrolyte leakage, accumulation of toxic compounds such as reactive oxygen species and malondialdehyde, and promotes antioxidant enzyme activities under chilling stress conditions. It was indicated that OsVPE2 mediated the disintegration of vacuoles under chilling stress, accompanied by the entry of swollen mitochondria into vacuoles. OsVPE2 suppressed the expression of genes that have a positive regulatory role in antioxidant process. Moreover, haplotype analysis suggested that the natural variation in the OsVPE2 non-coding region may endow OsVPE2 with different expression levels, thereby probably conferring differences in cold tolerance between japonica and indica sub-population. Our results thus reveal a new biological function of the VPE family in regulating cold resistance, and suggest that the gene editing or natural variations of OsVPE2 can be used to create cold tolerant rice varieties with stable yield.

Prospects for rice in 2050

A key to achieve the goals put forward in the UN's 2030 Agenda for Sustainable Development, it will need transformative change to our agrifood systems. We must mount to the global challenge to achieve food security in a sustainable manner in the context of climate change, population growth, urbanization, and depletion of natural resources. Rice is one of the major staple cereal crops that has contributed, is contributing, and will still contribute to the global food security. To date, rice yield has held pace with increasing demands, due to advances in both fundamental and biological studies, as well as genomic and molecular breeding practices. However, future rice production depends largely on the planting of resilient cultivars that can acclimate and adapt to changing environmental conditions. This Special Issue highlight with reviews and original research articles the exciting and growing field of rice-environment interactions that could benefit future rice breeding. We also outline open questions and propose future directions of 2050 rice research, calling for more attentions to develop environment-resilient rice especially hybrid rice, upland rice and perennial rice.