Chilling tolerance in rice: Past and present

A C2H2 zinc finger protein, OsZOS2-19, modulates ABA sensitivity and cold response in rice

Cold stress is a major factor limiting rice (Oryza sativa L.) productivity, making it crucial to understand the molecular mechanisms underlying stress responses to develop resilient crops. In this study, we characterized OsZOS2-19, a cold- and abscisic acid (ABA)-responsive C2H2 zinc finger protein, which functions as a transcriptional repressor. Overexpression of OsZOS2-19 in rice lines increases sensitivity to both cold and ABA, reducing cold tolerance, disrupting osmotic balance, and impairing reactive oxygen species (ROS) scavenging. RNA sequencing revealed that OsZOS2-19 overexpression interfered with key stress-response pathways, including those associated with sugar metabolism and glutathione biosynthesis. These findings suggest that OsZOS2-19 negatively regulates cold tolerance and ABA sensitivity by modulating ROS accumulation and osmotic balance, offering new insights into cold adaptation in rice.

Inheritance of acquired adaptive cold tolerance in rice through DNA methylation

Epigenetic pathways could provide a mechanistic explanation for the inheritance of acquired characteristics, as proposed by Lamarck in 1802, but epigenetic alterations that endow adaptive hereditary traits have rarely been observed. Here, in cultivated Asian rice (Oryzasativa L.), we identified an epiallele conferring acquired and heritable cold tolerance, an adaptive trait enabling northward spread from its tropical origins. We subjected cold-sensitive rice to multigenerational cold stress and identified a line with acquired stable inheritance of cold tolerance. DNA-hypomethylation variation in the acquiredcoldtolerance 1 (ACT1) promoter region rendered its expression insensitive to cold. This change is, in large part, responsible for the acquired cold tolerance, as confirmed by DNA-methylation editing. Natural variation in ACT1 DNA hypomethylation is associated with cold tolerance and rice geographic distribution. Hypomethylation at ACT1 triggers adaptive cold tolerance, presenting a route to epigenetic-variation-driven inheritance of acquired characteristics.

Suppressing an auxin efflux transporter enhances rice adaptation to temperate habitats

Rice (Oryza sativa L.), a chilling-sensitive staple crop originating from tropical and subtropical Asia, can be cultivated in temperate regions through the introduction of chilling tolerance traits. However, the molecular mechanisms underlying this adaptation remain largely unknown. Herein, we show that HAN2, a quantitative trait locus, confers chilling tolerance in temperate japonica rice. HAN2 encodes an auxin efflux transporter (OsABCB5) and negatively regulates chilling tolerance, potentially via auxin-mediated signaling pathway. During rice domestication, HAN2 has undergone selective divergence between the indica and temperate japonica subspecies. In temperate japonica rice, the insertion of a Copia long terminal repeat retrotransposon downstream of HAN2 reduces its expression, thereby enhancing chilling tolerance and facilitating adaptation to temperate climates. Introgression of the temperate japonica HAN2 allele into indica rice significantly improves chilling tolerance at both seedling and booting stages. These findings advance our understanding of rice northward expansion and provide a valuable genetic resource for improving yield stability under chilling stress.

Photosynthetic variation for climate-resilient crops: photosynthetic responses to fluctuating light and chilling in tomato

An increase in global demand for crop-based products necessitates an increased crop yield. Optimizing photosynthesis, which is sensitive to environmental fluctuations, offers a promising strategy to improve crop yield and resilience. Photosynthetic responses often lag behind changes in irradiance, resulting in the loss of potential carbon gain. Additionally, global warming is accompanied by unexpected chilling spells, further affecting photosynthesis. Thus, developing chilling-resilient crops and optimizing photosynthetic responses to fluctuating light is critical. This can be achieved by identifying genetic markers associated with desirable photosynthetic traits in plant populations. However, the combined effect of chilling and photosynthetic responses to fluctuating light remains unexplored, and there is a lack in populations designed to explore these responses. Thus, exploration needs to be done in pre-existing populations where there is phenotypic variation in photosynthetic responses and in how chilling affects these responses within parental lines. This study examined the variation in photosynthetic responses of the parental lines of a Multi-parent-Advanced-Generation Inter-Cross (MAGIC) population of tomato (Solanum lycopersicum) under fluctuating light and suboptimal temperatures. Photosynthetic responses to step increases and step decreases in irradiance were measured using modulated chlorophyll fluorescence and the effect of lowered temperature (14°C) on these responses was investigated. The results showed variation in the kinetics of the response of quantum efficiency of PSII (ΦPSII) to step changes in irradiance under control and chilling conditions. Chilling had a minimal effect on the photosynthetic responses of some parental lines, indicating resilience to chilling. These findings highlight the potential of exploring genetic components to breed climate-resilient crops.

Strategies for plant-microbe symbiosis: Mycorrhizal fungi and helper bacteria to improve cold tolerance in rice

Cold stress is a limiting factor for rice yield. Empirical evidence has demonstrated that arbuscular mycorrhizal fungi (AMF) can bolster the cold resilience of plants. In barren environments, AMF can promote host plant growth and resistance. However, whether the addition of mycorrhizal helper bacteria (MHB) can further enhance AMF's ability to improve cold tolerance in plants remains unclear. In this study, we set up an uninoculated group, a separately inoculated group, and a compound inoculated group and incubated rice at 25 °C until the three-leaf stage, and then each group was equally divided into four portions for treatment at 25 °C, 12 °C, 8 °C, and 4 °C, respectively. The results showed that: (1) Under cold stress conditions, the biomass of rice plants inoculated with AMF was significantly higher than that of the non-inoculated group; (2) AMF and MHB effectively activated the antioxidant enzyme system in rice plants and improved their osmoregulatory capacity under cold stress; (3) The presence of AMF and MHB stimulated and modulated the upregulation of genes related to photosynthesis and cold tolerance in rice plants, thereby enhancing their resilience against cold stress. Our findings corroborate that MHB can further enhance the cold tolerance of rice by promoting the functions of AMF. This study lays the foundation for expanding rice cultivation areas, and ensuring food production security.

An RNA helicase coordinates with iron signal regulators to alleviate chilling stress in Arabidopsis

Chilling stress is one of the major environmental stresses that restrains plant development and growth. Our previous study showed that a potential iron sensor BTS (BRUTUS) was involved in temperature response in Arabidopsis plants. However, whether plant iron homeostasis is involved in plant response to temperature fluctuation is not known. In this study, we discover that BTS mutant bts-2 is sensitive to chilling stress, and the sensitivity is attributed to the accumulation of iron. The suppressor screening of bts-2 led to the discovery of RH24, a DEAD-box RNA helicase, that fully suppresses bts-2 chilling sensitivity. RH24 is accumulated under low temperatures, where it unwinds the iron regulator ILR3 (IAA-leucine resistant 3) mRNA and increases the ILR3 protein levels. Intriguingly, RH24 sequesters ILR3 in phase-separated condensates to reduce ILR3-mediated iron overload, and BTS or cold treatments further facilitated the condensate formation. Therefore, RH24 and BTS coordinately control ILR3 to reduce iron uptake under chilling stress. Our findings reveal that the RNA helicase RH24 and BTS finetunes ILR3 to maintain plant iron homeostasis in response to temperature fluctuations.

Differential resilience of chickpea's reproductive organs to cold stress across developmental stages: insights into antioxidant strategies for enhanced fertility

Chickpea is highly sensitive to cold stress during its reproductive stages, leading to significant reductions in potential pod formation due to decreased reproductive success. This study aimed to investigate the specific responses of anthers and ovules to cold stress, explore the role of oxidative stress and antioxidant mechanisms, and understand the relationship between oxidative stress and reproductive function to enhance our understanding of chickpea responses to cold stress. Chickpea seeds of contrasting genotypes-cold-tolerant (ICC 17258, ICC 16349) and cold-sensitive (ICC 15567, GPF 2)-were sown outdoors in early November under optimal conditions (25.5/15.4°C mean day/night temperatures). At 50 days after sowing, plants were subjected to 13/7°C cold stress (12 h light/dark in walk-in growth chambers. Cold stress significantly increased membrane damage and reduced cellular viability in anthers and ovules, particularly in cold-sensitive (CS) genotypes. Oxidative damage was more pronounced in anthers, particularly at anthesis (stage 2), as indicated by elevated malondialdehyde and hydrogen peroxide levels. Cold-tolerant (CT) genotypes exhibited increased antioxidant activity under stress, especially at pre-anthesis (stage 1), followed by declines at later stage, although responses varied by genotype. Anthers exhibited higher overall antioxidants activity than ovules, while ovules demonstrated notably high catalase activity. Among the antioxidants studied, ascorbate peroxidase and glutathione reductase were most prominent in the CT genotype, along with higher levels of ascorbate (AsA) and glutathione (GSH), highlighting the critical role of the AsA-GSH cycle in conferring cold tolerance to chickpea. Exogenous supplementation with 1 mM ascorbate (AsA) and glutathione (GSH) significantly stimulated pollen germination in cold-stressed plants under in vitro conditions, with a greater effect observed in CS genotypes. Furthermore, antioxidant activity strongly correlated with key reproductive traits such as pollen germination and ovule viability. This study revealed that the anthers and ovules exhibited distinct responses to cold stress, with significant genotypic differences across key reproductive stages. These insights provide a deeper understanding of cold tolerance mechanisms in chickpea and provide vital clues for breeding strategies to enhance resilience and reproductive success under cold stress.

Utilization of natural alleles and haplotypes of Ctb1 for rice cold adaptability

Cold stress during the booting stage of rice (Oryza sativa) significantly reduces yields, particularly in temperate and high-altitude regions. This study investigates the Ctb1 gene, critical for booting-stage cold tolerance, to improve breeding of resilient rice varieties. Re-sequencing the Ctb1 promoter in 202 accessions identified six Insertions and/or deletions (InDels) and four Single nucleotide polymorphisms (SNPs), with an InDel at -1,302 bp significantly boosting Ctb1 expression and cold tolerance. Accessions carrying this InDel (Haplotype I) exhibited the highest tolerance. Near-isogenic lines (NIL-Ctb1HapI) introduced Haplotype I into the cold-sensitive Huazhan (HZ) variety, resulting in a 5.9-fold increase in Ctb1 expression, higher seedling survival, improved pollen fertility, a 64.2 % increase in seed setting rate, and a 12 g per plant yield boost under cold stress. These findings confirm the critical role of the -1,302 InDel in cold tolerance and establish NIL-Ctb1HapI as a valuable breeding tool for cold-resilient rice.

Brassica rapa receptor-like cytoplasmic kinase BrRLCK1 negatively regulates freezing tolerance in transgenic Arabidopsis via the CBF pathway

Some winter rapeseed (Brassica rapa) varieties can endure extremely low temperatures (-20°C to -32°C). However, because of a lack of mutant resources, the molecular mechanisms underlying cold tolerance in B. rapa remain unclear. In this study, we identified a low-temperature-sensitive mutant receptor-like cytoplasmic kinase (RLCK), BrRLCK1, using the B. rapa--Arabidopsis (Arabidopsis thaliana) full-length cDNA-overexpressing gene hunting system mutant library. BrRLCK1, localized to the plasma membrane and retained its localization under low temperatures. Phylogenetic analysis showed that BrRLCK1 is highly conserved across six widely cultivated Brassica species, but exhibits complexity due to genome hybridization and polyploidization. Notably, β-glucuronidase activity and qRT-PCR analysis showed that B. rapa BrRLCK1 and its homologous gene BrRLCK2 were mainly expressed in the main root, shoot, and leaves, with their expression being activated by low temperatures. Transgenic Arabodipsis expressing BrRLCK1 and BrRLCK2 reduced freezing tolerance and promoted root elongation. These combined results indicated that low temperatures can activate the expression of BrRLCK1 and BrRLCK2, negatively regulating freezing tolerance via the C-repeat-binding factor (CBF) pathway.

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.

Natural variation of indels in the CTB3 promoter confers cold tolerance in japonica rice

Improvement of cold tolerance at the booting stage (CTB) in rice is a key strategy for cultivation in high-altitude and high-latitude regions. Here, we identify CTB3 gene, encoding a calmodulin-binding transcriptional activator that positively regulates cold tolerance at the booting stage in japonica rice. Two indels (57-bp and 284-bp) in the CTB3 promoter confer a differential transcriptional response to cold between the japonica and indica subspecies. OsTCP19 suppresses CTB3 expression by binding to these indels, negatively regulating cold tolerance. CTB3 activates the expression of TREHALOSE-6-PHOSPHATE PHOSPHATASE1 (OsTPP1), reducing trehalose 6-phosphate (Tre6P) levels, which increases sugar accumulation in panicles and improves cold tolerance. Additionally, favorable alleles of OsTCP19 and CTB3 are selected in japonica rice for cold adaptation. These findings highlight the important role of CTB3 in cold adaptation and its potential for improving cold tolerance in rice breeding.

Molecular and Physiological Responses of Plants that Enhance Cold Tolerance

Low-temperature stress, including chilling and freezing injuries, significantly impacts plant growth in tropical and temperate regions. Plants respond to cold stress by activating mechanisms that enhance freezing tolerance, such as regulating photosynthesis, metabolism, and protein pathways and producing osmotic regulators and antioxidants. Membrane stability is crucial, with cold-resistant plants exhibiting higher lipid unsaturation to maintain fluidity and normal metabolism. Low temperatures disrupt reactive oxygen species (ROS) metabolism, leading to oxidative damage, which is mitigated by antioxidant defenses. Hormonal regulation, involving ABA, auxin, gibberellins, and others, further supports cold adaptation. Plants also manage osmotic balance by accumulating osmotic regulators like proline and sugars. Through complex regulatory pathways, including the ICE1-CBF-COR cascade, plants optimize gene expression to survive cold stress, ensuring adaptability to freezing conditions. This study reviews the recent advancements in genetic engineering technologies aimed at enhancing the cold resistance of agricultural crops. The goal is to provide insights for further improving plant cold tolerance and developing new cold-tolerant varieties.

The RAD6-like Ubiquitin Conjugase Gene OsUBC7 Has a Positive Role in the Early Cold Stress Tolerance Response of Rice

BACKGROUND/OBJECTIVES

Cold stress poses a significant threat to Asian rice cultivation, disrupting important physiological processes crucial for seedling establishment and overall plant growth. It is, thus, crucial to elucidate genetic pathways involved in cold stress tolerance response mechanisms.

METHODS

We mapped OsUBC7, a Radiation-sensitive 6 (RAD6)-type homolog of rice, to a low-temperature seedling survivability (LTSS) QTL and used genomics, molecular genetics, and physiological assays to assess its role in plant resilience against low-temperature stress.

RESULTS

OsUBC7 is cold responsive and has higher expression levels in cold-tolerant japonica than cold-sensitive indica. Overexpression of OsUBC7 enhances LTSS of indica and freezing tolerance of Arabidopsis, increases levels of soluble sugars and chlorophyll A, boosts leaf development after cold exposure, and increases leaf cell numbers and plants size, but it does not affect membrane stability after cold stress exposure. Additionally, OsUBC7 has a positive role for germinability in the presence of salt and for flowering and yield-related traits. The OsUBC7 protein physically interacts with the developmental stage-specific and histone-modifying E3 ligases OsRFPH2-12 and OsHUB1/2, respectively, and potential target genes such as cell cycle dependent kinases were identified.

CONCLUSIONS

OsUBC7 might contribute to cold resilience by regulating sugar metabolism to provide energy for promoting cellular homeostasis restoration after cold stress exposure via new cell growth, particularly in leaf cells crucial for photosynthesis and metabolic activity, possibly by interacting with cell cycle regulating proteins. Overall, the present study suggests that OsUBC7 may be involved in plant development, reproduction, and stress adaptation, and contributes to a deeper understanding of rice plant cold stress tolerance response mechanisms. OsUBC7 may be a promising candidate for improving crop productivity and resilience to stressful environments.

Unlocking ABA's role in rice cold tolerance: insights from Zhonghua 11 and Kasalath

KEY MESSAGE

Unraveling key ABA pathways, including OsWRKY71-OsABA8ox1 and OsbZIP73-OsNCED5, provides valuable insights for improving cold tolerance in rice breeding for cold-prone regions. Cold stress limits rice (Oryza sativa L.) production in cooler climates. This study uncovers how abscisic acid (ABA) signaling enhances cold tolerance in the rice variety Zhonghua 11 (ZH11) compared to the cold-sensitive Kasalath. Under cold stress, ZH11 rapidly accumulates ABA through efficient regulation of key genes. The transcription factor OsWRKY71ZH11 represses the ABA catabolism gene OsABA8ox1 during early stress, enabling quick ABA accumulation. Additionally, OsbZIP73 regulates the ABA synthesis gene OsNCED5 to maintain ABA balance during prolonged stress. Transgenic ZH11 plants overexpressing OsWRKY71ZH11 exhibited enhanced cold tolerance, while overexpression of OsWRKY71Ka did not confer benefits. Haplotype analysis linked allelic variations in OsWRKY71 and OsNCED5 to differences in cold tolerance. Our findings highlight critical ABA signaling pathways that enhance cold tolerance in rice. Targeting these pathways offers promising strategies for breeding cold-resistant rice varieties, improving resilience in cold-prone regions.

Subtilisin-like protease 4 regulates cold tolerance through cell wall modification in rice

Rice is susceptible to cold temperatures, especially during the seedling stage. Despite extensive research into the cold tolerance mechanisms of rice, the number of cloned genes remains limited. Plant subtilisin-like proteases (SUBs or SBTs) are protein-hydrolyzing enzymes which play important roles in various aspects of plant growth as well as the plant response to biotic and abiotic stress. The rice SUB gene family consists of 62 members, but it is unknown whether they are involved in the response to cold stress. In this study, we observed that a loss-of-function SUB4 mutant exhibited enhanced cold tolerance at the seedling stage. The sub4 mutant seedlings exhibited improved survival rates and related physiological parameters, including relative electrolyte conductivity, chlorophyll content, malondialdehyde content, and antioxidant enzyme activity. Transcriptomic analysis revealed that differentially expressed genes responsive to cold stress in the sub4 mutants were primarily associated with metabolism and signal transduction. Notably, the majority of cold-responsive genes were associated with cell wall functions, including those related to cell wall organization, chitin catabolic processes, and oxidoreductases. Our findings suggest that SUB4 negatively regulates the cold response in rice seedlings, possibly by modifying the properties of the cell wall.

ERD14 regulation by the HY5- or HY5-MED2 module mediates the cold signal transduction of asparagus bean

Cold stress affects the growth, development, and yield of asparagus bean (Vigna unguiculata subsp. sesquipedalis). Mediator (MED) complex subunits regulate the cold tolerance of asparagus bean, but the underlying regulatory mechanisms remain unclear. Here, VunMED2 positively responds to cold stress of asparagus beans. Under cold acclimation and freezing treatment, the survival rate, ROS scavenging activity, and expression levels of VunMED2 were increased in VunMED2 transgenic plants. Natural variation in the promoter of VunMED2 in two different cold-tolerant asparagus beans was observed. Under cold stress, the expression of the GUS reporter gene was higher in cold-tolerant plants than in cold-sensitive plants, and the expression of the GUS reporter gene was tissue-specific. VunHY5 positively influenced the expression of VunMED2 by binding to the E-box motif, and the transcriptional activation of the promoter was stronger in the cold-tolerant variety than in cold-sensitive plants. VunHY5 overexpression improved plant freezing resistance by increasing the antioxidant capacity and expression of dehydrin genes. VunHY5 and VunMED2 play a synergistic role in binding to the G-box/ABRE motif and transcriptionally activating the expression of VunERD14. VunERD14 complemented the med2 mutant, which could positively respond to plant freezing resistance by reducing membrane lipid peroxidation and improving the antioxidant capacity. Therefore, the VunHY5-VunERD14 module and the VunHY5-VunMED2-VunERD14 positive cascade effect are involved in the cold signal transduction in asparagus bean. Our findings have implications for the breeding of asparagus bean varieties with improved cold tolerance.

Editorial for the Special Issue 'Molecular Breeding and Genetics Research in Plants'

Despite significant advancements in plant breeding research, the challenges posed by a growing global population, the impact of abiotic and biotic stresses, and the uncertainties of climate change necessitate continued focus and innovation in plant breeding and genetic studies [...].

The seed endophytic microbe Microbacterium testaceum M15 enhances the cold tolerance and growth of rice (Oryza sativa L.)

The potential of seed endophytic microbes to enhance plant growth and resilience is well recognized, yet their role in alleviating cold stress in rice remains underexplored due to the complexity of these microbial communities. In this study, we investigated the diversity of seed endophytic microbes in two rice varieties, the cold-sensitive CB9 and the cold-tolerant JG117. Our results revealed significant differences in the abundance of Microbacteriaceae, with JG117 exhibiting a higher abundance under both cold stress and room temperature conditions compared to CB9. Further analysis led to the identification of a specific cold-tolerant microbe, Microbacterium testaceum M15, in JG117 seeds. M15-inoculated CB9 plants showed enhanced growth and cold tolerance, with a germination rate increase from 40 % to 56.67 % at 14℃ and a survival rate under cold stress (4℃) doubling from 22.67 % to 66.67 %. Additionally, M15 significantly boosted chlorophyll content by over 30 %, increased total protein by 16.31 %, reduced malondialdehyde (MDA) levels by 37.76 %, and increased catalase activity by 26.15 %. Overall, our study highlights the potential of beneficial endophytic microbes like M. testaceum M15 in improving cold tolerance in rice, which could have implications for sustainable agricultural practices and increased crop productivity in cold-prone regions.

Domestication-selected COG4-OsbZIP23 module regulates chilling tolerance in rice

Identifying excellent natural variations is the foundation for breeding. Several major genes of quantitative trait loci for chilling tolerance at the seedling stage (qCTS) have been identified. However, less is known about the dual elite modules for the tolerance. Here, we report the major gene of qCTS1-2, Chilling-tolerance in Geng/japonica rice 4 (COG4), encoding the transcription factor ENAC1, coupled with OsbZIP23 to positively regulate chilling tolerance. The haplotype analysis and geographical distribution show that most of the chilling-tolerant japonica varieties carry Var9(CT) at -317 in COG4 (COG4jap). The COG4jap promoter is preferentially bound by cold-induced OsbZIP23 to cause a higher expression of COG4jap compared to COG4ind, which promotes multiple pathways for the tolerance. Both COG4jap and OsbZIP23jap are artificially selected and retained in japonica varieties during domestication. These results not only reveal the regulatory mechanism of OsbZIP23jap-COG4jap module but also provide valuable variations for molecular design breeding.

COLD6-OSM1 module senses chilling for cold tolerance via 2',3'-cAMP signaling in rice

While it is known that temperature sensors trigger calcium (Ca2+) signaling to confer cold tolerance in cells, less is known about sensors that couple with other secondary messengers. Here, we identify a cold sensor complex of CHILLING-TOLERANCE DIVERGENCE 6 (COLD6) and osmotin-like 1 (OSM1), which triggers 2',3'-cyclic adenosine monophosphate (2',3'-cAMP) production to enhance cold tolerance in rice. COLD6, which is encoded by a major quantitative trait locus (QTL) gene, interacts with the rice G protein α subunit (RGA1) at the plasma membrane under normal conditions. Upon exposure to chilling, cold-induced OSM1 binds to COLD6, kicking out RGA1 from interaction. This triggers an elevation of 2',3'-cAMP levels for enhancing chilling tolerance. Genetic data show that COLD6 negatively regulates cold tolerance and functionally depends on OSM1 in chilling stress. COLD6 alleles were selected during rice domestication. Knockout and natural variation of COLD6 in hybrid rice enhanced chilling tolerance, hinting design potential for breeding. This highlighted a module triggering 2',3'-cAMP to improve chilling tolerance in crops.

Inducing rice chilling tolerance by the second messenger 2',3'-cAMP

In this issue of Molecular Cell, Luo et al.1 identify a signaling pathway, OSM1-COLD6, that induces cold tolerance in rice by promoting production of the non-canonical cyclic nucleotide 2',3'-cAMP. The study opens new avenues for enhancing cold tolerance in rice breeding.

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.

The OsSRO1c-OsDREB2B complex undergoes protein phase transition to enhance cold tolerance in rice

Cold stress is one of the major abiotic stress factors affecting rice growth and development, leading to significant yield loss in the context of global climate change. Exploring natural variants that confer cold resistance and the underlying molecular mechanism responsible for this is the major strategy to breed cold-tolerant rice varieties. Here, we show that natural variations of a SIMILAR to RCD ONE (SRO) gene, OsSRO1c, confer cold tolerance in rice at both seedling and booting stages. Our in vivo and in vitro experiments demonstrated that OsSRO1c possesses intrinsic liquid-liquid phase-separation ability and recruits OsDREB2B, an AP2/ERF transcription factor that functions as a positive regulator of cold stress, into its biomolecular condensates in the nucleus, resulting in elevated transcriptional activity of OsDREB2B. We found that the OsSRO1c-OsDREB2B complex directly responds to low temperature through dynamic phase transitions and regulates key cold-response genes, including COLD1. Furthermore, we showed that introgression of an elite haplotype of OsSRO1c into a cold-susceptible indica rice could significantly increase its cold resistance. Collectively, our work reveals a novel cold-tolerance regulatory module in rice and provides promising genetic targets for molecular breeding of cold-tolerant rice varieties.

Rice BARENTSZ genes are required to maintain floral developmental stability against temperature fluctuations

BARENTSZ (BTZ), a core component of the exon junction complex, regulates diverse developmental processes in animals. However, its evolutionary and developmental roles in plants remain elusive. Here, we revealed that three groups of paralogous BTZ genes existed in Poaceae, and Group 2 underwent loss-of-function mutations during evolution. They showed surprisingly low (~33%) sequence identities, implying functional divergence. Two genes retained in rice, OsBTZ1 and OsBTZ3, were edited; however, the resultant osbtz1 and osbtz3 mutants showed similar floral morphological and functional defects at a low frequency. When growing under low-temperature conditions, developmental abnormalities became pronounced, and new floral variations were induced. In particular, stamen and carpel functionality was impaired in these rice btz mutants. The double-gene mutant osbtz1/3 shared these floral defects with an increased frequency, which was further induced under low-temperature conditions. OsBTZs interacted with OsMADS7 and OsMADS8, and the floral expressions of the OsTGA10 and MADS-box genes were correlatively altered in these osbtz mutants and responded to low-temperature treatment. These novel findings demonstrate that two highly diverged OsBTZs are required to maintain floral developmental stability under low-temperature conditions, and play an integral role in male and female fertility, thus providing new insights into the indispensable roles of BTZ genes in plant development and adaptive evolution.

LUX ARRHYTHMO links CBF pathway and jasmonic acid metabolism to regulate cold tolerance of tea plants

Cold stress declines the quality and yield of tea, yet the molecular basis underlying cold tolerance of tea plants (Camellia sinensis) remains largely unknown. Here, we identified a circadian rhythm component LUX ARRHYTHMO (LUX) that potentially regulates cold tolerance of tea plants through a genome-wide association study and transcriptomic analysis. The expression of CsLUX phased with sunrise and sunset and was strongly induced by cold stress. Genetic assays indicated that CsLUX is a positive regulator of freezing tolerance in tea plants. CsLUX was directly activated by CsCBF1 and repressed the expression level of CsLOX2, which regulates the cold tolerance of tea plants through dynamically modulating jasmonic acid content. Furthermore, we showed that the CsLUX-CsJAZ1 complex attenuated the physical interaction of CsJAZ1 with CsICE1, liberating CsICE1 with transcriptional activities to withstand cold stress. Notably, a single-nucleotide variation of C-to-A in the coding region of CsLUX was functionally validated as the potential elite haplotype for cold response, which provided valuable molecular markers for future cold resistance breeding in tea plants.

Impact of Abiotic Stress on Rice and the Role of DNA Methylation in Stress Response Mechanisms

With the intensification of global climate change and the increasing complexity of agricultural environments, the improvement of rice stress tolerance is an important focus of current breeding research. This review summarizes the current knowledge on the impact of various abiotic stresses on rice and the associated epigenetic responses (DNA methylation). Abiotic stress factors, including high temperature, drought, cold, heavy metal pollution, and high salinity, have a negative impact on crop productivity. Epigenetic changes are key regulatory factors in plant stress responses, and DNA methylation is one of the earliest discovered and thoroughly studied mechanisms in these epigenetic regulatory mechanisms. The normal growth of rice is highly dependent on the environment, and changes in the environment can lead to rice sterility and severe yield loss. Changes in the regulation of the DNA methylation pathway are involved in rice's response to stress. Various DNA methylation-regulating protein complexes that function during rice development have been identified. Significant changes in DNA methylation occur in numerous stress-responsive genes, particularly those in the abscisic acid signaling pathway. These findings underscore the complex mechanisms of the abiotic stress response in rice. We propose the effective improvement of tolerance traits by regulating the epigenetic status of rice and emphasize the role of DNA methylation in abiotic stress tolerance, thereby addressing global climate change and ensuring food security.

OsEIN2-OsEIL1/2 pathway negatively regulates chilling tolerance by attenuating OsICE1 function in rice

Low temperature severely affects rice development and yield. Ethylene signal is essential for plant development and stress response. Here, we reported that the OsEIN2-OsEIL1/2 pathway reduced OsICE1-dependent chilling tolerance in rice. The overexpressing plants of OsEIN2, OsEIL1 and OsEIL2 exhibited severe stress symptoms with excessive reactive oxygen species (ROS) accumulation under chilling, while the mutants (osein2 and oseil1) and OsEIL2-RNA interference plants (OsEIL2-Ri) showed the enhanced chilling tolerance. We validated that OsEIL1 and OsEIL2 could form a heterxodimer and synergistically repressed OsICE1 expression by binding to its promoter. The expression of OsICE1 target genes, ROS scavenging- and photosynthesis-related genes were downregulated by OsEIN2 and OsEIL1/2, which were activated by OsICE1, suggesting that OsEIN2-OsEIL1/2 pathway might mediate ROS accumulation and photosynthetic capacity under chilling by attenuating OsICE1 function. Moreover, the association analysis of the seedling chilling tolerance with the haplotype showed that the lower expression of OsEIL1 and OsEIL2 caused by natural variation might confer chilling tolerance on rice seedlings. Finally, we generated OsEIL2-edited rice with an enhanced chilling tolerance. Taken together, our findings reveal a possible mechanism integrating OsEIN2-OsEIL1/2 pathway with OsICE1-dependent cascade in regulating chilling tolerance, providing a practical strategy for breeding chilling-tolerant rice.

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.

Knockout of the Chlorophyll a Oxygenase Gene OsCAO1 Reduces Chilling Tolerance in Rice Seedlings

Chilling stress is one of the main abiotic factors affecting rice growth and yield. In rice, chlorophyllide a oxygenase encoded by OsCAO1 is responsible for converting chlorophyllide a to chlorophyllide b, playing a crucial role in photosynthesis and thus rice growth. However, little is known about the function of OsCAO1 in chilling stress responses. The presence of the cis-acting element involved in low-temperature responsiveness (LTR) in the OsCAO1 promoter implied that OsCAO1 probably is a cold-responsive gene. The gene expression level of OsCAO1 was usually inhibited by low temperatures during the day and promoted by low temperatures at night. The OsCAO1 knockout mutants generated by the CRISPR-Cas9 technology in rice (Oryza sativa L.) exhibited significantly weakened chilling tolerance at the seedling stage. OsCAO1 dysfunction led to the accumulation of reactive oxygen species and malondialdehyde, an increase in relative electrolyte leakage, and a reduction in antioxidant gene expression under chilling stress. In addition, the functional deficiency of OsCAO1 resulted in more severe damage to chloroplast morphology, such as abnormal grana thylakoid stacking, caused by low temperatures. Moreover, the rice yield was reduced in OsCAO1 knockout mutants. Therefore, the elevated expression of OsCAO1 probably has the potential to increase both rice yield and chilling tolerance simultaneously, providing a strategy to cultivate chilling-tolerant rice varieties with high yields.

Acyl carrier protein OsMTACP2 confers rice cold tolerance at the booting stage

Low temperatures occurring at the booting stage in rice (Oryza sativa L.) often result in yield loss by impeding male reproductive development. However, the underlying mechanisms by which rice responds to cold at this stage remain largely unknown. Here, we identified MITOCHONDRIAL ACYL CARRIER PROTEIN 2 (OsMTACP2), the encoded protein of which mediates lipid metabolism involved in the cold response at the booting stage. Loss of OsMTACP2 function compromised cold tolerance, hindering anther cuticle and pollen wall development, resulting in abnormal anther morphology, lower pollen fertility, and seed setting. OsMTACP2 was highly expressed in tapetal cells and microspores during anther development, with the encoded protein localizing to both mitochondria and the cytoplasm. Comparative transcriptomic analysis revealed differential expression of genes related to lipid metabolism between the wild type and the Osmtacp2-1 mutant in response to cold. Through a lipidomic analysis, we demonstrated that wax esters, which are the primary lipid components of the anther cuticle and pollen walls, function as cold-responsive lipids. Their levels increased dramatically in the wild type but not in Osmtacp2-1 when exposed to cold. Additionally, mutants of two cold-induced genes of wax ester biosynthesis, ECERIFERUM1 and WAX CRYSTAL-SPARSE LEAF2, showed decreased cold tolerance. These results suggest that OsMTACP2-mediated wax ester biosynthesis is essential for cold tolerance in rice at the booting stage.

OsNAC5 orchestrates OsABI5 to fine-tune cold tolerance in rice

Due to its tropical origins, rice (Oryza sativa) is susceptible to cold stress, which poses severe threats to production. OsNAC5, a NAC-type transcription factor, participates in the cold stress response of rice, but the detailed mechanisms remain poorly understood. Here, we demonstrate that OsNAC5 positively regulates cold tolerance at germination and in seedlings by directly activating the expression of ABSCISIC ACID INSENSITIVE 5 (OsABI5). Haplotype analysis indicated that single nucleotide polymorphisms in a NAC-binding site in the OsABI5 promoter are strongly associated with cold tolerance. OsNAC5 also enhanced OsABI5 stability, thus regulating the expression of cold-responsive (COR) genes, enabling fine-tuned control of OsABI5 action for rapid, precise plant responses to cold stress. DNA affinity purification sequencing coupled with transcriptome deep sequencing identified several OsABI5 target genes involved in COR expression, including DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR 1A (OsDREB1A), OsMYB20, and PEROXIDASE 70 (OsPRX70). In vivo and in vitro analyses suggested that OsABI5 positively regulates COR gene transcription, with marked COR upregulation in OsNAC5-overexpressing lines and downregulation in osnac5 and/or osabi5 knockout mutants. This study extends our understanding of cold tolerance regulation via OsNAC5 through the OsABI5-CORs transcription module, which may be used to ameliorate cold tolerance in rice via advanced breeding.

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.

Identification of hub genes that variate the qCSS12-mediated cold tolerance between indica and japonica rice using WGCNA

KEY MESSAGE

Cold-tolerant QTL qCSS12-regulated 14 hub genes are involved in the chloroplastic biological processes and in the protein synthesis and degradation processes in japonica rice. Low temperature is a main constraint factor for rice growth and production. To better understand the regulatory mechanisms underlying the cold tolerance phenotype in rice, here, we selected a cold-sensitive nearly isogenic line (NIL) NIL(qcss12) as materials to identify hub genes that are mediated by the cold-tolerant locus qCSS12 through weighted gene co-expression network analysis (WGCNA). Fourteen cold-responsive genes were identified, of which, 6 are involved in regulating biological processes in chloroplasts, including the reported EF-Tu, Prk, and ChlD, and 8 are involved in the protein synthesis and degradation processes. Differential expression of these genes between NIL(qcss12) and its controls under cold stress may be responsible for qCSS12-mediated cold tolerance in japonica rice. Moreover, natural variations in 12 of these hub genes are highly correlated with the cold tolerance divergence in two rice subspecies. The results provide deep insights into a better understanding of the molecular basis of cold adaptation in rice and provide a theoretical basis for molecular breeding.

Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genes

Due to global climate change resulting in extreme temperature fluctuations, it becomes increasingly necessary to explore the natural genetic variation in model crops such as rice to facilitate the breeding of climate-resilient cultivars. To uncover genomic regions in rice involved in managing cold stress tolerance responses and to identify associated cold tolerance genes, two inbred line populations developed from crosses between cold-tolerant and cold-sensitive parents were used for quantitative trait locus (QTL) mapping of two traits: degree of membrane damage after 1 week of cold exposure quantified as percent electrolyte leakage (EL) and percent low-temperature seedling survivability (LTSS) after 1 week of recovery growth. This revealed four EL QTL and 12 LTSS QTL, all overlapping with larger QTL regions previously uncovered by genome-wide association study (GWAS) mapping approaches. Within the QTL regions, 25 cold-tolerant candidate genes were identified based on genomic differences between the cold-tolerant and cold-sensitive parents. Of those genes, 20% coded for receptor-like kinases potentially involved in signal transduction of cold tolerance responses; 16% coded for transcription factors or factors potentially involved in regulating cold tolerance response effector genes; and 64% coded for protein chaperons or enzymes potentially serving as cold tolerance effector proteins. Most of the 25 genes were cold temperature regulated and had deleterious nucleotide variants in the cold-sensitive parent, which might contribute to its cold-sensitive phenotype.

Genetics of chilling response at early growth stage in rice: a recessive gene for tolerance and importance of acclimation

Low-temperature adaptation in rice is mediated by the ability of a genotype to tolerate chilling temperatures. A genetic locus on chromosome 11 was analysed for chilling tolerance at the plumule stage in rice. The tolerant allele of A58, a japonica landrace in Japan, was inherited as a recessive gene (ctp-1A58), whereas the susceptible alleles from wild rice (Ctp-1W107) and modern variety (Ctp-1HY) were the dominant genes. Another recessive tolerant allele (ctp-1Silewah) was found in a tropical japonica variety (Silewah). Fine-mapping revealed that a candidate gene for the ctp-1 locus encoded a protein similar to the nucleotide-binding domain and leucine-rich repeat (NLR) protein, in which frameshift mutation by a 73 bp-deletion might confer chilling tolerance in ctp-1A58. Analysis of near-isogenic lines demonstrated that ctp-1A58 imparted tolerance effects only at severe chilling temperatures of 0.5 °C and 2 °C, both at plumule and seedling stages. Chilling acclimation treatments at a wide range of temperatures (8 °C-16 °C) for 72 h concealed the susceptible phenotype of Ctp-1W107 and Ctp-1HY. Furthermore, short-term acclimation treatment of 12 h at 8 °C was enough to be fully acclimated. These results suggest that the NLR gene induces a susceptible response upon exposure to severe chilling stress, however, another interacting gene(s) for acclimation response could suppress the maladaptive phenotype caused by the Ctp-1 allele. This study provides new insights for the adaptation and breeding of rice in a low-temperature environment.

MdNAC104 positively regulates apple cold tolerance via CBF-dependent and CBF-independent pathways

Low temperature is the main environmental factor affecting the yield, quality and geographical distribution of crops, which significantly restricts development of the fruit industry. The NAC (NAM, ATAF1/2 and CUC2) transcription factor (TF) family is involved in regulating plant cold tolerance, but the mechanisms underlying these regulatory processes remain unclear. Here, the NAC TF MdNAC104 played a positive role in modulating apple cold tolerance. Under cold stress, MdNAC104-overexpressing transgenic plants exhibited less ion leakage and lower ROS (reactive oxygen species) accumulation, but higher contents of osmoregulatory substances and activities of antioxidant enzymes. Transcriptional regulation analysis showed that MdNAC104 directly bound to the MdCBF1 and MdCBF3 promoters to promote expression. In addition, based on combined transcriptomic and metabolomic analyses, as well as promoter binding and transcriptional regulation analyses, we found that MdNAC104 stimulated the accumulation of anthocyanin under cold conditions by upregulating the expression of anthocyanin synthesis-related genes, including MdCHS-b, MdCHI-a, MdF3H-a and MdANS-b, and increased the activities of the antioxidant enzymes by promoting the expression of the antioxidant enzyme-encoding genes MdFSD2 and MdPRXR1.1. In conclusion, this study revealed the MdNAC104 regulatory mechanism of cold tolerance in apple via CBF-dependent and CBF-independent pathways.

Extra-large G proteins have extra-large effects on agronomic traits and stress tolerance in maize and rice

Heterotrimeric G proteins - comprising Gα, Gβ, and Gγ subunits - are ubiquitous elements in eukaryotic cell signaling. Plant genomes contain both canonical Gα subunit genes and a family of plant-specific extra-large G protein genes (XLGs) that encode proteins consisting of a domain with Gα-like features downstream of a long N-terminal domain. In this review we summarize phenotypes modulated by the canonical Gα and XLG proteins of arabidopsis and highlight recent studies in maize and rice that reveal dramatic phenotypic consequences of XLG clustered regularly interspaced short palindromic repeats (CRISPR) mutagenesis in these important crop species. XLGs have both redundant and specific roles in the control of agronomically relevant plant architecture and resistance to both abiotic and biotic stresses. We also point out areas of current controversy, suggest future research directions, and propose a revised, phylogenetically-based nomenclature for XLG protein genes.

Integration of Metabolome and Transcriptome Reveals the Major Metabolic Pathways and Potential Biomarkers in Response to Freeze-Stress Regulation in Apple (Malus domestica)

Freezing stress is the main factor affecting the normal growth and distribution of plants. The safe overwintering of a perennial deciduous plant is a crucial link to ensuring its survival and yield. However, little is known about the molecular mechanism of its gene regulation metabolites as related to its freeze-tolerance. In order to enhance our comprehension of freeze-tolerance metabolites and gene expression in dormant apple trees, we examined the metabolic and transcriptomic differences between 'Ralls' and 'Fuji', two apple varieties with varying degrees of resistance to freezing. The results of the freezing treatment showed that 'Ralls' had stronger freeze-tolerance than 'Fuji'. We identified 302, 334, and 267 up-regulated differentially accumulated metabolites (DAMs) and 408, 387, and 497 down-regulated DAMs between 'Ralls' and 'Fuji' under -10, -15, and -20 °C treatment, respectively. A total of 359 shared metabolites were obtained in the upward trend modules, of which 62 metabolites were associated with 89 pathways. The number of up-regulated genes accounted for 50.2%, 45.6%, and 43.2% of the total number of differentially expressed genes (DEGs), respectively, at -10, -15, and -20 °C. Through combined transcriptome and metabolome analysis, we identified 12 pathways that included 16 DAMs and 65 DEGs. Meanwhile, we found that 20 DEGs were identified in the phenylpropanoid biosynthesis pathway and its related pathways, involving the metabolism of p-Coumaroyl-CoA, 7, 4'-Dihydroxyflavone, and scolymoside. These discoveries advance our comprehension of the molecular mechanism underlying apple freeze-tolerance and provide genetic material for breeding apple cultivars with enhanced freeze-tolerance.

Transcriptomic Profiling of Cold Stress-Induced Differentially Expressed Genes in Seedling Stage of Indica Rice

Cold stress significantly constrains the growth, development, productivity, and distribution of rice, particularly the indica cultivar, known for its susceptibility to cold, limiting its cultivation to specific regions. This study investigated the genes associated with cold responsiveness in the roots of two indica cultivars, SQSL (cold-tolerant) and XZX45 (cold-susceptible), through transcriptome dynamics analysis during the seedling stage. The analysis identified 8144 and 6427 differentially expressed genes (DEGs) in XZX45 and SQSL, respectively. Among these DEGs, 4672 (G2) were shared by both cultivars, while 3472 DEGs (G1) were specific to XZX45, and 1755 DEGs (G3) were specific to SQSL. Additionally, 572 differentially expressed transcription factors (TFs) from 48 TF families, including WRKY, NAC, bHLH, ERF, bZIP, MYB, C2H2, and GRAS, were identified. Gene Ontology (GO) enrichment analysis revealed significant enrichment of DEGs in the G3 group, particularly in the "response to cold" category, highlighting the crucial role of these specific genes in response to cold stress in SQSL. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated pronounced enrichment of DEGs in the G3 group in metabolic pathways such as "Pyruvate metabolism", "Glycolysis/Gluconeogenesis", and "Starch and sucrose metabolism", contributing to cold tolerance mechanisms in SQSL. Overall, this study provides comprehensive insights into the molecular mechanisms underlying cold responses in the indica cultivar, informing future genetic improvement strategies to enhance cold tolerance in susceptible indica rice cultivars.

Foliar Spraying of Glycine Betaine Alleviated Growth Inhibition, Photoinhibition, and Oxidative Stress in Pepper (Capsicum annuum L.) Seedlings under Low Temperatures Combined with Low Light

Low temperature combined with low light (LL stress) is a typical environmental stress that limits peppers' productivity, yield, and quality in northwestern China. Glycine betaine (GB), an osmoregulatory substance, has increasingly valuable effects on plant stress resistance. In this study, pepper seedlings were treated with different concentrations of GB under LL stress, and 20 mM of GB was the best treatment. To further explore the mechanism of GB in response to LL stress, four treatments, including CK (normal temperature and light, 28/18 °C, 300 μmol m^-2 s^-1), CB (normal temperature and light + 20 mM GB), LL (10/5 °C, 100 μmol m^-2 s^-1), and LB (10/5 °C, 100 μmol m^-2 s^-1 + 20 mM GB), were investigated in terms of pepper growth, biomass accumulation, photosynthetic capacity, expression levels of encoded proteins Capsb, cell membrane permeability, antioxidant enzyme gene expression and activity, and subcellular localization. The results showed that the pre-spraying of GB under LL stress significantly alleviated the growth inhibition of pepper seedlings; increased plant height by 4.64%; increased root activity by 63.53%; and decreased photoinhibition by increasing the chlorophyll content; upregulating the expression levels of encoded proteins Capsb A, Capsb B, Capsb C, Capsb D, Capsb S, Capsb P1, and Capsb P2 by 30.29%, 36.69%, 18.81%, 30.05%, 9.01%, 6.21%, and 16.45%, respectively; enhancing the fluorescence intensity (OJIP curves), the photochemical efficiency (Fv/Fm, Fv'/Fm'), qP, and NPQ; improving the light energy distribution of PSΠ (Y(II), Y(NPQ), and Y(NO)); and increasing the photochemical reaction fraction and reduced heat dissipation, thereby increasing plant height by 4.64% and shoot bioaccumulation by 13.55%. The pre-spraying of GB under LL stress also upregulated the gene expression of CaSOD, CaPOD, and CaCAT; increased the activity of the ROS-scavenging ability in the pepper leaves; and coordinately increased the SOD activity in the mitochondria, the POD activity in the mitochondria, chloroplasts, and cytosol, and the CAT activity in the cytosol, which improved the LL resistance of the pepper plants by reducing excess H₂O₂, O₂^-, MDA, and soluble protein levels in the leaf cells, leading to reduced biological membrane damage. Overall, pre-spraying with GB effectively alleviated the negative effects of LL stress in pepper seedlings.

qCTB7 positively regulates cold tolerance at booting stage in rice

KEY MESSAGE

LOC_Os07g07690 on qCTB7 is associated with cold tolerance at the booting stage in rice, and analysis of transgenic plants demonstrated that qCTB7 influenced cold tolerance by altering the morphology and cytoarchitecture of anthers and pollen. Cold tolerance at the booting stage (CTB) in rice can significantly affect yield in high-latitude regions. Although several CTB genes have been isolated, their ability to induce cold tolerance is insufficient to ensure adequate rice yields in cold regions at high latitudes. Here, we identified the PHD-finger domain-containing protein gene qCTB7 using QTL-seq and linkage analysis through systematic measurement of CTB differences and the spike fertility of the Longjing31 and Longdao3 cultivars, resulting in the derivation of 1570 F2 progeny under cold stress. We then characterized the function of qCTB7 in rice. It was found that overexpression of qCTB7 promoted CTB and the same yield as Longdao3 under normal growing conditions while the phenotype of qctb7 knockout showed anther and pollen failure under cold stress. When subjected to cold stress, the germination of qctb7 pollen on the stigma was reduced, resulting in lower spike fertility. These findings indicate that qCTB7 regulates the appearance, morphology, and cytoarchitecture of the anthers and pollen. Three SNPs in the promoter region and coding region of qCTB7 were identified as recognition signals for CTB in rice and could assist breeding efforts to improve cold tolerance for rice production in high latitudes.

OsLUX Confers Rice Cold Tolerance as a Positive Regulatory Factor

During the early seedling stage, rice (Oryza sativa L.) must overcome low-temperature stress. While a few cold-tolerance genes have been characterized, further excavation of cold-resistance genes is still needed. In this study, we identified a cold-induced transcription factor—LUX ARRHYTHMO (LUX)—in rice. OsLUX was found to be specifically expressed in leaf blades and upregulated by both cold stress and circadian rhythm. The full-length OsLUX showed autoactivation activity, and the OsLUX protein localized throughout the entire onion cell. Overexpressing OsLUX resulted in increased cold tolerance and reduced ion leakage under cold-stress conditions during the seedling stage. In contrast, the knockout of OsLUX decreased seedling cold tolerance and showed higher ion leakage compared to the wild type. Furthermore, overexpressing OsLUX upregulated the expression levels of oxidative stress-responsive genes, which improved reactive oxygen species (ROS) scavenging ability and enhanced tolerance to chilling stress. Promoter analysis showed that the OsLUX promoter contains two dehydration-responsive element binding (DREB) motifs at positions −510/−505 (GTCGGa) and −162/−170 (cCACCGccc), which indicated that OsDREB1s and OsDREB2s probably regulate OsLUX expression by binding to the motif to respond to cold stress. Thus, OsLUX may act as a downstream gene of the DREB pathway. These results demonstrate that OsLUX serves as a positive regulatory factor of cold stress and that overexpressing OsLUX could be used in rice breeding programs to enhance abiotic stress tolerance.

Comparative transcriptomics and co-expression networks reveal cultivar-specific molecular signatures associated with reproductive-stage cold stress in rice

The resistance of Huaidao5 results from the high constitutive expression of tolerance genes, while that of Huaidao9 is due to the cold-induced resistance in flag leaves and panicles. The regulation mechanism of rice seedlings' cold tolerance is relatively clear, and knowledge of its underlying mechanisms at the reproductive stage is limited. We performed differential expression and co-expression network analyses to transcriptomes from panicle and flag leaf tissues of a cold-tolerant cultivar (Huaidao5), and a sensitive cultivar (Huaidao9), under reproductive-stage cold stress. The results revealed that the expression levels of genes in stress-related pathways such as MAPK signaling pathway, diterpenoid biosynthesis, glutathione metabolism, plant-pathogen interaction and plant hormone signal transduction were constitutively highly expressed in Huaidao5, especially in panicles. Moreover, the Hudaidao5's panicle sample-specific (under cold) module contained some genes related to rice yield, such as GW5L, GGC2, SG1 and CTPS1. However, the resistance of Huaidao9 was derived from the induced resistance to cold in flag leaves and panicles. In the flag leaves, the responses included a series of stress response and signal transduction, while in the panicles nitrogen metabolism was severely affected, especially 66 endosperm-specific genes. Through integrating differential expression with co-expression networks, we predicted 161 candidate genes (79 cold-responsive genes common to both cultivars and 82 cold-tolerance genes associated with differences in cold tolerance between cultivars) potentially affecting cold response/tolerance, among which 85 (52.80%) were known to be cold-related genes. Moreover, 52 (65.82%) cold-responsive genes (e.g., TIFY11C, LSK1 and LPA) could be confirmed by previous transcriptome studies and 72 (87.80%) cold-tolerance genes (e.g., APX5, OsFbox17 and OsSTA109) were located within QTLs associated with cold tolerance. This study provides an efficient strategy for further discovery of mechanisms of cold tolerance in rice.

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.

Transcriptomic profiling of wheat stem during meiosis in response to freezing stress

Low temperature injury in spring has seriously destabilized the production and grain quality of common wheat. However, the molecular mechanisms underlying spring frost tolerance remain elusive. In this study, we investigated the response of a frost-tolerant wheat variety Zhongmai8444 to freezing stress at the meiotic stage. Transcriptome profiles over a time course were subsequently generated by high-throughput sequencing. Our results revealed that the prolonged freezing temperature led to the significant reductions in plant height and seed setting rate. Cell wall thickening in the vascular tissue was also observed in the stems. RNA-seq analyses demonstrated the identification of 1010 up-regulated and 230 down-regulated genes shared by all time points of freezing treatment. Enrichment analysis revealed that gene activity related to hormone signal transduction and cell wall biosynthesis was significantly modulated under freezing. In addition, among the identified differentially expressed genes, 111 transcription factors belonging to multiple gene families exhibited dynamic expression pattern. This study provided valuable gene resources beneficial for the breeding of wheat varieties with improved spring frost tolerance.

COG2 negatively regulates chilling tolerance through cell wall components altered in rice

Chilling-tolerant QTL gene COG2 encoded an extensin and repressed chilling tolerance by affecting the compositions of cell wall. Rice as a major crop is susceptible to chilling stress. Chilling tolerance is a complex trait controlled by multiple quantitative trait loci (QTLs). Here, we identify a QTL gene, COG2, that negatively regulates cold tolerance at seedling stage in rice. COG2 overexpression transgenic plants are sensitive to cold, whereas knockout transgenic lines enhance chilling tolerance. Natural variation analysis shows that Hap1 is a specific haplotype in japonica/Geng rice and correlates with chilling tolerance. The SNP1 in COG2 promoter is a specific divergency and leads to the difference in the expression level of COG2 between japonica/Geng and indica/Xian cultivars. COG2 encodes a cell wall-localized extensin and affects the compositions of cell wall, including pectin and cellulose, to defense the chilling stress. The results extend the understanding of the adaptation to the environment and provide an editing target for molecular design breeding of cold tolerance in rice.

Genome-Wide Association Mapping Identifies New Candidate Genes for Cold Stress and Chilling Acclimation at Seedling Stage in Rice (Oryza sativa L.)

Rice (Oryza sativa L.) is a chilling-sensitive staple food crop, and thus, low temperature significantly affects rice growth and yield. Many studies have focused on the cold shock of rice although chilling acclimation is more likely to happen in the field. In this paper, a genome-wide association study (GWAS) was used to identify the genes that participated in cold stress and chilling accumulation. A total of 235 significantly associated single-nucleotide polymorphisms (SNPs) were identified. Among them, we detected 120 and 88 SNPs for the relative shoot fresh weight under cold stress and chilling acclimation, respectively. Furthermore, 11 and 12 quantitative trait loci (QTLs) were identified for cold stress and chilling acclimation, respectively, by integrating the co-localized SNPs. Interestingly, we identified 10 and 15 candidate genes in 11 and 12 QTLs involved in cold stress and chilling acclimation, respectively, and two new candidate genes (LOC_Os01g62410, LOC_Os12g24490) were obviously up-regulated under chilling acclimation. Furthermore, OsMYB3R-2 (LOC_Os01g62410) that encodes a R1R2R3 MYB gene was associated with cold tolerance, while a new C3HC4-type zinc finger protein-encoding gene LOC_Os12g24490 was found to function as a putative E3 ubiquitin-protein ligase in rice. Moreover, haplotype, distribution, and Wright’s fixation index (FST) of both genes showed that haplotype 3 of LOC_Os12g24490 is more stable in chilling acclimation, and the SNP (A > T) showed a difference in latitudinal distribution. FST analysis of SNPs in OsMYB3R-2 (LOC_Os01g62410) and LOC_Os12g24490 indicated that several SNPs were under selection in rice indica and japonica subspecies. This study provided new candidate genes in genetic improvement of chilling acclimation response in rice.

The OsWRKY63-OsWRKY76-OsDREB1B module regulates chilling tolerance in rice

Rice (Oryza sativa) is sensitive to low temperatures, which affects the yield and quality of rice. Therefore, uncovering the molecular mechanisms behind chilling tolerance is a critical task for improving cold tolerance in rice cultivars. Here, we report that OsWRKY63, a WRKY transcription factor with an unknown function, negatively regulates chilling tolerance in rice. OsWRKY63-overexpressing rice lines are more sensitive to cold stress. Conversely, OsWRKY63-knockout mutants generated using a CRISPR/Cas9 genome editing approach exhibited increased chilling tolerance. OsWRKY63 was expressed in all rice tissues, and OsWRKY63 expression was induced under cold stress, dehydration stress, high salinity stress, and ABA treatment. OsWRKY63 localized in the nucleus plays a role as a transcription repressor and downregulates many cold stress-related genes and reactive oxygen species scavenging-related genes. Molecular, biochemical, and genetic assays showed that OsWRKY76 is a direct target gene of OsWRKY63 and that its expression is suppressed by OsWRKY63. OsWRKY76-knockout lines had dramatically decreased cold tolerance, and the cold-induced expression of five OsDREB1 genes was repressed. OsWRKY76 interacted with OsbHLH148, transactivating the expression of OsDREB1B to enhance chilling tolerance in rice. Thus, our study suggests that OsWRKY63 negatively regulates chilling tolerance through the OsWRKY63-OsWRKY76-OsDREB1B transcriptional regulatory cascade in rice.