So what's new in the field of plant cold acclimation? Lots!

Genome-wide analysis of apple histone acetyltransferases reveals the regulatory roles of MdHAG1 and MdHAM1 in response to abiotic stresses

It is known that histone acetyltransferases (HATs) are involved in a wide range of biological processes by activating gene expression. However, the regulatory role of HATs in apple remains to be elucidated. This study identified 58 HATs from the apple genome (named MdHATs) and performed comprehensive analyses of these MdHATs, given their involvements in plant development and stress response. Firstly, we classified 58 predicted MdHATs into four different categories based on the phylogenetic analyses. Then, the intron/exon structures, conserved motifs, and structural domain organization of MdHAT genes and predicted proteins were further analyzed. Next, we investigated the expression patterns of MdHATs during apple plants' development process and stress responses. Moreover, according to these findings, we selected two candidate genes, MdHAG1 and MdHAM1, and ectopically expressed them in tobacco to investigate their function in response to drought and low-temperature stress, respectively. The results showed that overexpression of MdHAG1 in tobacco negatively regulated drought tolerance and cold tolerance of transgenic tobacco, and overexpression of MdHAM1 in tobacco improved drought tolerance and cold tolerance of transgenic tobacco. In summary, our study provides a comprehensive analysis of the MdHAT family and insights into the epigenetic mechanisms of histone acetylases under abiotic stress.

Naganishia liquefaciens ARY7, a Psychrophilic Yeast Endophyte Improves Plant Low Temperature Acclimation Through Auxin and Salicylic Acid Signaling

Understanding how plant-associated yeasts mediate plant fitness under environmental stress remains mostly elusive. Here, the role of auxin and salicylic acid (SA)-producing psychrophilic yeast endophyte Naganishia liquefaciens strain ARY7, isolated from the roots of cold-desert plant Arnebia euchroma, was investigated for low temperature (LT; 10°C) tolerance in Arabidopsis thaliana. ARY7-inoculated plants had higher biomass, exhibited higher photosynthetic efficiency, starch accumulation, and reduced stress-responsive parameters at 10°C than their non-inoculated controls. ARY7-inoculation in the Arabidopsis enhanced auxin signaling in the roots, leading to more lateral roots and root hair development at 10°C. Increased exopolysaccharide (EPS) accumulation around roots and root colonization by ARY7 at 10°C also suggested its role in cold tolerance. The SA-production ability of ARY7 was supported by the elevated SA levels and upregulation of key SA biosynthesis genes (SID2 and PBS3) in ARY7-inoculated plants at 10°C. In addition, an improved seedling phenotype in ARY7-inoculated sid2 (SA-deficient) mutants of Arabidopsis further confirmed the role of ARY7-produced SA-mediated plant fitness. The downregulated expression of key cold-responsive genes (CBF, COR, RD29A, and P5CS1) in the leaves of ARY7-inoculated plants indicated reduced sensitivity to LT. This study established that the ARY7-mediated plant cold tolerance is due to the increased ARY7-root colonization through EPS production and involves auxin and SA signaling. This study provides valuable insights to explore plant-associated psychrophilic yeasts for protecting plants from various abiotic stresses, including cold temperature.

Cold-related genes BcCOR15B and BcCOR15A have environment adapted expression pattern in non-heading Chinese cabbage

In this work, two cold-related (COR) genes, BcCOR15B and BcCOR15A, were isolated from non-heading Chinese cabbage (Brassica rapa ssp. chinensis cv. Suzhouqing). Their open reading frames (ORFs) are 429 and 390 base pairs (bp) in length, which encode 142 and 129 amino acids (aa), respectively. The predicted amino acid sequences of BcCOR15B and BcCOR15A share the respective 99.30% and 95.56% highest homology with the amino acid sequences of the corresponding BrCOR15B and BrCOR15A in Chinese cabbage (Brassica rapa). Sequence and phylogenetic analysis showed that the relationship between BcCOR15 B/A and BrCOR15 B/A was relatively close. Structural analysis showed that the structure of BcCOR15 B/A proteins was both relatively stable and conservative. Subcellular localization indicated that BcCOR15B and BcCOR15A proteins were both localized on the chloroplast. Real-time quantitative polymerase chain reaction (RT-qPCR) analysis showed that BcCOR15 B/A were both induced to express by cold and other abiotic stresses. Prokaryotic expression and Western blot analysis revealed that the two proteins were both hydrophilic. The identification and analysis of cold-related genes BcCOR15 B/A from non-heading Chinese cabbage might provide a reference for further study on agronomic traits of vegetable and crop plants in cold environments.

Chemical genetics reveals cross-regulation of plant developmental signaling by the immune peptide-receptor pathway

Cells sense and integrate multiple signals to coordinate a response. A receptor-kinase signaling pathway for plant stomatal development shares components with the immunity pathway. The mechanism ensuring their signal specificities remains unclear. Using chemical genetics, here, we report the identification of a small molecule, kC9, that triggers excessive stomatal differentiation by inhibiting the canonical ERECTA pathway. kC9 binds to and inhibits the downstream mitogen-activated protein kinase MPK6, perturbing its substrate interaction. Notably, activation of immune signaling by a bacterial flagellin peptide nullified kC9's effects on stomatal development. This cross-regulation depends on the immune receptor FLS2 (FLAGELLIN SENSING 2) and occurs even in the absence of kC9 if the ERECTA family receptor population becomes suboptimal. Proliferating stomatal lineage cells are vulnerable to this immune signal penetration. Our findings suggest that the signal specificity between development and immunity can be ensured by mitogen-activated protein kinase homeostasis, reflecting the availability of upstream receptors, thereby providing an unanticipated view on signal specificity.

Exogenous diethyl aminoethyl hexanoate alleviates the damage caused by low-temperature stress in Phaseolus vulgaris L. seedlings through photosynthetic and antioxidant systems

BACKGROUND

Phaseolus vulgaris is a warm-season crop sensitive to low temperatures, which can adversely affect its growth, yield, and market value. Exogenous growth regulators, such as diethyl aminoethyl hexanoate (DA-6), have shown potential in alleviating stress caused by adverse environmental conditions. However, the effects that DA-6 has on P. vulgaris plants subjected to low-temperature stress are not well understood. This study aimed to investigate the impact DA-6 has on the growth, photosynthesis, antioxidant system, and gene expression in cold-tolerant (YJ009763) and cold-sensitive (Baibulao) P. vulgaris seedlings under low-temperature stress.

RESULTS

To simulate low-temperature stress, P. vulgaris seedlings were exposed to 5 °C, and 25 mg/L DA-6 solution applied to their leaves. This study revealed that DA-6 significantly enhanced the growth and photosynthetic performance of P. vulgaris seedlings under low-temperature stress. Specifically, DA-6 increased chlorophyll content and photosynthetic rates, reducing stomatal limitation and enhancing carbon assimilation. It also improved the photosynthetic efficiency by boosting electron transport in the reaction center. The antioxidant enzyme activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were markedly increased following DA-6 treatment. After 24 h of low-temperature stress, the cold-tolerant seedlings showed a 68.95% increase in POD activity, whereas the cold-sensitive seedlings displayed a 160.63% increase in SOD activity and an 85.56% increase in CAT activity. In addition, DA-6 significantly reduced the production rate of superoxide anion radical generation, with a 25.24% reduction in cold-tolerant seedlings and a 49.38% reduction in cold-sensitive seedlings. Under low-temperature stress, exogenous DA-6 could upregulate the relative expression of antioxidant enzyme-related genes, such as PvSOD and PvAPX. DA-6 also promoted the expression of key antioxidant genes, including PvMDHAR and PvDHAR2, which accelerated the ascorbate-glutathione cycle and mitigated oxidative stress.

CONCLUSION

Exogenous application of DA-6 effectively alleviates low-temperature stress in P. vulgaris by enhancing photosynthetic capacity and regulating the antioxidant defense system. Cold-tolerant varieties exhibited a stronger response to DA-6, demonstrating a greater ability to withstand cold stress. These findings suggest that DA-6 treatment could serve as a promising approach for improving the resilience of P. vulgaris to low temperatures.

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.

VvbHLH036, a basic helix-loop-helix transcription factor regulates the cold tolerance of grapevine

Cold stress is an adverse environmental factor that limits the growth and productivity of horticulture crops such as grapes (Vitis vinifera). In this study, we identified a grapevine cold-induced basic helix-loop-helix (bHLH) transcription factor (VvbHLH036). Overexpression and CRISPR/Cas9-mediated knockout (KO) of VvbHLH036 enhanced and decreased cold tolerance in grapevine roots, respectively. Transcriptome analysis of VvbHLH036-overexpressed roots identified threonine synthase (VvThrC1) as a potential downstream target of VvbHLH036. We confirmed that VvbHLH036 could bind the VvThrC1 promoter and activate its expression. Both the transcripts of VvThrC1 and the content of threonine were significantly induced in the leaves and roots of grapevine under cold treatment compared to controls. Conversely, these dynamics were significantly suppressed in the roots of CRISPR/Cas9-induced KO of VvbHLH036. These observations support the regulation of threonine accumulation by VvbHLH036 through VvThrC1 during cold stress in grapevine. Furthermore, overexpression and CRISPR/Cas9-mediated KO of VvThrC1 also confirmed its role in regulating threonine content and cold tolerance in transgenic roots at low temperature. Exogenous threonine treatment increased cold tolerance and reduced the accumulation of superoxide anions and hydrogen peroxide in grapevine leaves. Together, these findings point to the pivotal role of VvbHLH036 and VvThrC1 in the cold stress response in grapes by regulating threonine biosynthesis.

Cold mediates maize root hair developmental plasticity via epidermis-specific transcriptomic responses

Cold stress during early development limits maize (Zea mays L.) production in temperate zones. Low temperatures restrict root growth and reprogram gene expression. Here, we provide a systematic transcriptomic landscape of maize primary roots, their tissues, and cell types in response to cold stress. The epidermis exhibited a unique transcriptomic cold response, and genes involved in root hair formation were dynamically regulated in this cell type by cold. Consequently, activation of genes involved in root hair tip growth contributed to root hair recovery under moderate cold conditions. The maize root hair defective mutants roothair defective 5 (rth5) and roothair defective 6 (rth6) displayed enhanced cold tolerance with respect to primary root elongation. Furthermore, DEHYDRATION RESPONSE ELEMENT-BINDING PROTEIN 2.1 (DREB2.1) was the only member of the dreb subfamily of AP2/EREB transcription factor genes upregulated in primary root tissues and cell types but exclusively downregulated in root hairs upon cold stress. Plants overexpressing dreb2.1 significantly suppressed root hair elongation after moderate cold stress. Finally, the expression of rth3 was regulated by dreb2.1 under cold conditions, while rth6 transcription was regulated by DREB2.1 irrespective of the temperature regime. We demonstrated that dreb2.1 negatively regulates root hair plasticity at low temperatures by coordinating the expression of root hair defective genes in maize.

Freezing treatment under light conditions leads to a dramatic enhancement of freezing tolerance in cold-acclimated Arabidopsis

Overwintering plants survive subzero temperatures by cold acclimation (CA), wherein they acquire freezing tolerance through short-term exposure to low temperatures above 0°C. The freezing tolerance of CA plants increases when they are subsequently exposed to mild subzero temperatures, a phenomenon known as second-phase cold hardening (2PH). Here, we explored the molecular mechanism and physiological conditions of 2PH. The results show that, compared with supercooling, a freezing treatment during 2PH after CA enhanced the freezing tolerance of Arabidopsis. This required CA as a pretreatment, and was designated as second-phase freezing acclimation (2PFA). Light increased the effect of 2PFA to enhance freezing tolerance after CA. C-repeat binding factor and cold-regulated genes were downregulated by light during the 2PFA treatment, a different transcription profile from that during CA. The freezing tolerance of 2PFA plants was decreased by the presence of the photosynthetic electron transfer inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea during the 2PFA treatment. Compared with wild-type plants, phototropin1,2 and phyb mutants showed lower freezing tolerance after 2PFA treatment. These results show that exposure to freezing after CA increases freezing tolerance as a secondary process, and that freezing under light conditions further increases freezing tolerance via pathways involving photoreceptors and photosynthetic electron transfer.

Chemical genetics reveals cross-activation of plant developmental signaling by the immune peptide-receptor pathway

Cells sense and integrate multiple signals to coordinate development and defence. A receptor-kinase signaling pathway for plant stomatal development shares components with the immunity pathway. The mechanism ensuring their signal specificities remains unclear. Using chemical genetics, here we report the identification of a small molecule, kC9, that triggers excessive stomatal differentiation by inhibiting the canonical ERECTA receptor-kinase pathway. kC9 binds to and inhibits the downstream MAP kinase MPK6, perturbing its substrate interaction. Strikingly, activation of immune signaling by a bacterial flagellin peptide nullified kC9's effects on stomatal development. This cross-activation of stomatal development by immune signaling depends on the immune receptor FLS2 and occurs even in the absence of kC9 if the ERECTA-family receptor population becomes suboptimal. Furthermore, proliferating stomatal-lineage cells are vulnerable to the immune signal penetration. Our findings suggest that the signal specificity between development and immunity can be ensured by MAP Kinase homeostasis reflecting the availability of upstream receptors, thereby providing a novel view on signal specificity.

Integrated transcriptomic and metabolomic analysis provides insights into cold tolerance in lettuce (Lactuca sativa L.)

The popular leafy vegetable lettuce (Lactuca sativa L.) is susceptible to cold stress during the growing season, which slows growth rate, causes leaf yellowing and necrosis, and reduced yield and quality. In this study, transcriptomic and metabolomic analyses of two cold-resistant lettuce cultivars (GWAS-W42 and F11) and two cold-sensitive lettuce cultivars (S13K079 and S15K058) were performed to identify the mechanisms involved in the cold response of lettuce. Overall, transcriptome analysis identified 605 differentially expressed genes (DEGs), including significant enrichment of genes involved in the flavonoid and flavonol (CHS, CHI, F3H, FLS, CYP75B1, HCT, etc.) biosynthetic pathways related to oxidation-reduction and catalytic activity. Untargeted metabolomic analysis identified fifteen flavonoid metabolites and 28 other metabolites potentially involved in the response to cold stress; genistein, quercitrin, quercetin derivatives, kaempferol derivatives, luteolin derivatives, apigenin and their derivatives accumulate at higher levels in cold-resistant cultivars. Moreover, MYBs, bHLHs, WRKYs and Dofs also play positive role in the low temperature response, which affected the expression of structural genes contributing to the variation of metabolites between the resistant and sensitive. These results provide valuable evidence that the metabolites and genes involved in the flavonoid biosynthetic pathway play important roles in the response of lettuce to cold stress.

The histone deacetylase SRT2 enhances the tolerance of chrysanthemum to low temperatures through the ROS scavenging system

Low temperatures can severely affect plant growth and reduce their ornamental value. A family of plant histone deacetylases allows plants to cope with both biotic and abiotic stresses. In this study, we screened and cloned the cDNA of DgSRT2 obtained from transcriptome sequencing of chrysanthemum leaves under low-temperature stress. Sequence analysis showed that DgSRT2 belongs to the sirtuin family of histone deacetylases. We obtained the stable transgenic chrysanthemum lines OE-2 and OE-12. DgSRT2 showed tissue specificity in wild-type chrysanthemum and was most highly expressed in leaves. Under low-temperature stress, the OE lines showed higher survival rates, proline content, solute content, and antioxidant enzyme activities, and lower relative electrolyte leakage, malondialdehyde, hydrogen peroxide, and superoxide ion accumulation than the wild-type lines. This work suggests that DgSRT2 can serve as an essential gene for enhancing cold resistance in plants. In addition, a series of cold-responsive genes in the OE line were compared with WT. The results showed that DgSRT2 exerted a positive regulatory effect by up-regulating the transcript levels of cold-responsive genes. The above genes help to increase antioxidant activity, maintain membrane stability and improve osmoregulation, thereby enhancing survival under cold stress. It can be concluded from the above work that DgSRT2 enhances chrysanthemum tolerance to low temperatures by scavenging the ROS system.

Do diverse wheat genotypes unleash their biochemical arsenal differentially to conquer cold stress? A comprehensive study in the Western Himalayas

Wheat is one of the most important cereal crops in the world. Cold stress is a major constraint in production of wheat grown in cold climate regions. In this study, we conducted a comprehensive assessment of cold stress tolerance in wheat genotypes through field screening, cell membrane stability through electrolyte leakage assay and biochemical profiling. A core set comprising 4560 genotypes was evaluated for two years (2021-2022), revealing substantial genetic variation for cold stress tolerance. Most genotypes exhibited moderate tolerance, while a smaller proportion showed susceptibility to cold stress. Based on the cold screening data in the field, a mini-core set of 350 genotypes was selected for membrane stability analysis using electrical conductivity assays. Significant differences were observed in membrane stability among the genotypes, indicating the presence of genetic variation for this trait. Furthermore, a mini-core set was narrowed down to 50 diverse candidate genotypes that were subsequently profiled for various biochemicals, including reactive oxygen species (ROS) like lipid peroxidation (MDA) and hydrogen peroxide (H2 02 ), osmoprotectant (proline) and enzymatic antioxidants including ascorbate peroxidase (APX), superoxide dismutase (SOD), guaiacol peroxidase (GPX), and catalase (CAT). Correlation analysis of the biochemicals revealed negative associations between antioxidants and reactive oxygen species (ROS), highlighting their role in mitigating oxidative damage under cold stress. This study enhances our understanding of the physiological and biochemical mechanisms underlying cold stress tolerance in wheat. The identified genotypes with superior cold stress tolerance can serve as valuable genetic resources for wheat breeding.

Oligogalactolipid production during cold challenge is conserved in early diverging lineages

Severe cold, defined as a damaging cold beyond acclimation temperatures, has unique responses, but the signaling and evolution of these responses are not well understood. Production of oligogalactolipids, which is triggered by cytosolic acidification in Arabidopsis (Arabidopsis thaliana), contributes to survival in severe cold. Here, we investigated oligogalactolipid production in species from bryophytes to angiosperms. Production of oligogalactolipids differed within each clade, suggesting multiple evolutionary origins of severe cold tolerance. We also observed greater oligogalactolipid production in control samples than in temperature-challenged samples of some species. Further examination of representative species revealed a tight association between temperature, damage, and oligogalactolipid production that scaled with the cold tolerance of each species. Based on oligogalactolipid production and transcript changes, multiple angiosperm species share a signal of oligogalactolipid production initially described in Arabidopsis, namely cytosolic acidification. Together, these data suggest that oligogalactolipid production is a severe cold response that originated from an ancestral damage response that remains in many land plant lineages and that cytosolic acidification may be a common signaling mechanism for its activation.

Molecular mechanisms of low-temperature sensitivity in tropical/subtropical plants: a case study of Casuarina equisetifolia

Low temperature is a limiting factor affecting plant growth and development. Casuarina equisetifolia, a typical tropical and subtropical tree important for the ecological restoration of coastal beaches, is sensitive to cold stress. By comparing cold tolerance between C. equisetifolia and Arabidopsis, we investigated the molecular basis underlying the cold sensitivity of C. equisetifolia. Transcriptomic analysis showed that the number of cold-induced genes in C. equisetifolia was significantly less than that in Arabidopsis, and notably, the response of cold-induced genes was also delayed in C. equisetifolia. Among the cold-induced genes, C-repeat binding factors (CBFs), the major transcription factors in cold acclimation in Arabidopsis, showed a delayed cold-induced expression in C. equisetifolia, despite that C. equisetifolia CBFs could restore the low temperature-sensitive phenotype of Arabidopsis cbfs triple mutants. Interestingly, some key cold-responsive genes (e.g., COR15A and COR15B) targeted by Arabidopsis CBF were absent in the C. equisetifolia genome and many cold-responsive genes in C. equisetifolia lacked the DRE element (i.e., CBF binding cis-element). Moreover, like in C. equisetifolia, many COR genes in other tropical/subtropical plants lacked the DRE element or were directly missing. These two factors could be the underlying reasons for the low-temperature sensitivity of C. equisetifolia and other tropical/subtropical plants.

Chemical screening approach using single leaves identifies compounds that affect cold signaling in Arabidopsis

The identification of chemical compounds that affect intracellular processes has greatly contributed to our understanding of plant growth and development. In most cases, these compounds have been identified in germinated seedlings. However, chemical screening using mature plants would benefit and advance our understanding of environmental responses. In this study, we developed a high-throughput screening method using single leaves of mature plants to identify small molecules that affect cold-regulated gene expression. A single excised leaf of Arabidopsis (Arabidopsis thaliana) grown in submerged cultures responded to low temperatures in terms of COLD-REGULATED (COR) gene expression. We used transgenic Arabidopsis harboring a COLD-REGULATED 15A (COR15A) promoter::luciferase (COR15Apro::LUC) construct to screen natural compounds that affect the cold induction of COR15Apro::LUC. This approach allowed us to identify derivatives of 1,4-naphthoquinone as specific inhibitors of COR gene expression. Moreover, 1,4-naphthoquinones appeared to inhibit the rapid induction of upstream C-REPEAT BINDING FACTOR (CBF) transcription factors upon exposure to low temperature, suggesting that 1,4-naphthoquinones alter upstream signaling processes. Our study offers a chemical screening scheme for identifying compounds that affect environmental responses in mature plants. This type of analysis is likely to reveal an unprecedented link between certain compounds and plant environmental responses.

Arundo donax L. growth potential under different abiotic stress

Arundo donax L. (giant reed) is a fast-growing, vegetatively multiplying, and rhizomatous perennial grass. It is considered a leading crop for biomass production on marginal and degraded lands under different adverse conditions such as drought, salinity, waterlogging, high and low temperatures, and heavy metal stress. The giant reed tolerance to those stresses is reviewed based on its effects on photosynthetic capacity and biomass production. Possible explanations for the giant reed tolerance against each particular stress were elucidated, as well as changes shown by the plant at a biochemical, physiological and morphological level, that may directly affect its biomass production. The use of giant reed in other areas of interest such as bioconstruction, phytoremediation, and bioremediation, is also reviewed. Arundo donax can be key for circular economy and global warming mitigation.

Mdm-miR160-MdARF17-MdWRKY33 module mediates freezing tolerance in apple

Apple (Malus domestica) trees are vulnerable to freezing temperatures. Cold resistance in woody perennial plants can be improved through biotechnological approaches. However, genetic engineering requires a thorough understanding of the molecular mechanisms of the tree's response to cold. In this study, we demonstrated that the Mdm-miR160-MdARF17-MdWRKY33 module is crucial for apple freezing tolerance. Mdm-miR160 plays a negative role in apple freezing tolerance, whereas MdARF17, one of the targets of Mdm-miR160, is a positive regulator of apple freezing tolerance. RNA sequencing analysis revealed that in apple, MdARF17 mediates the cold response by influencing the expression of cold-responsive genes. EMSA and ChIP-qPCR assays demonstrated that MdARF17 can bind to the promoter of MdWRKY33 and promotes its expression. Overexpression of MdWRKY33 enhanced the cold tolerance of the apple calli. In addition, we found that the Mdm-miR160-MdARF17-MdWRKY33 module regulates cold tolerance in apple by regulating reactive oxygen species (ROS) scavenging, as revealed by (i) increased H₂ O₂ levels and decreased peroxidase (POD) and catalase (CAT) activities in Mdm-miR160e OE plants and MdARF17 RNAi plants and (ii) decreased H₂ O₂ levels and increased POD and CAT activities in MdmARF17 OE plants and MdWRKY33 OE calli. Taken together, our study uncovered the molecular roles of the Mdm-miR160-MdARF17-MdWRKY33 module in freezing tolerance in apple, thus providing support for breeding of cold-tolerant apple cultivars.

Comprehensive Transcriptome Analysis of Responses during Cold Stress in Wheat (Triticum aestivum L.)

Wheat production is often impacted by pre-winter freezing damage and cold spells in later spring. To study the influences of cold stress on wheat seedlings, unstressed Jing 841 was sampled once at the seedling stage, followed by 4 °C stress treatment for 30 days and once every 10 days. A total of 12,926 differentially expressed genes (DEGs) were identified from the transcriptome. K-means cluster analysis found a group of genes related to the glutamate metabolism pathway, and many genes belonging to the bHLH, MYB, NAC, WRKY, and ERF transcription factor families were highly expressed. Starch and sucrose metabolism, glutathione metabolism, and plant hormone signal transduction pathways were found. Weighted Gene Co-Expression Network Analysis (WGCNA) identified several key genes involved in the development of seedlings under cold stress. The cluster tree diagram showed seven different modules marked with different colors. The blue module had the highest correlation coefficient for the samples treated with cold stress for 30 days, and most genes in this module were rich in glutathione metabolism (ko00480). A total of eight DEGs were validated using quantitative real-time PCR. Overall, this study provides new insights into the physiological metabolic pathways and gene changes in a cold stress transcriptome, and it has a potential significance for improving freezing tolerance in wheat.

Dissecting the effect of ethylene in the transcriptional regulation of chilling treatment in grapevine leaves

Ethylene (ETH) plays important roles in various development programs and stress responses in plants. In grapevines, ETH increased dramatically under chilling stress and is known to positively regulate cold tolerance. However, the role of ETH in transcriptional regulation during chilling stress of grapevine leaves is still not clear. To address this gap, targeted hormone profiling and transcriptomic analysis were performed on leaves of Vitis amurensis under chilling stress with and without aminoethoxyvinylglycine (AVG, a inhibitor of ETH synthesis) treatment. APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) and WRKY transcription factors (TF) were only the two highly enriched TF families that were consistently up-regulated during chilling stress but inhibited by AVG. The comparison of leaf transcriptomes between chilling treatment and chilling with AVG allowed the identification of potential ETH-regulated genes. Potential genes that are positively regulated by ETH are enriched in solute transport, protein biosynthesis, phytohormone action, antioxidant and carbohydrate metabolism. Conversely, genes related to the synthesis and signaling of ETH, indole-3-acetic acid (IAA), abscisic acid (ABA) were up-regulated by chilling treatment but inhibited by AVG. The contents of ETH, ABA and IAA also paralleled with the transcriptome data, which suggests that the response of ABA and IAA during chilling stress may regulate by ETH signaling, and together may belong to an integrated network of hormonal signaling pathways underpinning chilling stress response in grapevine leaves. Together, these findings provide new clues for further studying the complex regulatory mechanism of ETH under low-temperature stress in plants more generally and new opportunities for breeding cold-resilient grapevines.

Cold-Induced Physiological and Biochemical Alternations and Proteomic Insight into the Response of Saccharum spontaneum to Low Temperature

Sugarcane, a cash crop, is easily affected by low temperature, which results in a decrease in yield and sugar production. Breeding a new variety with cold tolerance is an essential strategy to reduce loss from cold stress. The identification of germplasms and genes/proteins with cold tolerance is a vital step in breeding sugarcane varieties with cold tolerance via a conventional program and molecular technology. In this study, the physiological and biochemical indices of 22 genotypes of S. spontaneum were measured, and the membership function analysis method was used to comprehensively evaluate the cold tolerance ability of these genotypes. The physiological and biochemical indices of these S. spontaneum genotypes showed a sophisticated response to low temperature. On the basis of the physiological and chemical indices, the genotypes were classified into different cold tolerance groups. Then, the high-tolerance genotype 1027 and the low-tolerance genotype 3217 were selected for DIA-based proteomic analysis by subjecting them to low temperature. From the four comparison groups, 1123, 1341, 751, and 1693 differentially abundant proteins (DAPs) were identified, respectively. The DAPs based on genotypes or treatments participated in distinct metabolic pathways. Through detailed analysis of the DAPs, some proteins related to protein homeostasis, carbohydrate and energy metabolism, amino acid transport and metabolism, signal transduction, and the cytoskeleton may be involved in sugarcane tolerance to cold stress. Furthermore, five important proteins related to cold tolerance were discovered for the first time in this study. This work not only provides the germplasms and candidate target proteins for breeding sugarcane varieties with cold tolerance via a conventional program and molecular breeding, but also helps to accelerate the determination of the molecular mechanism underlying cold tolerance in sugarcane.

Integrated Transcriptome and Metabolome Analysis of Color Change and Low-Temperature Response during Flowering of Prunus mume

In China, Prunus mume is a famous flowering tree that has been cultivated for 3000 years. P. mume grows in tropical and subtropical regions, and most varieties lack cold resistance; thus, it is necessary to study the low-temperature response mechanism of P. mume to expand the scope of its cultivation. We used the integrated transcriptomic and metabolomic analysis of a cold-resistant variety of P. mume 'Meiren', to identify key genes and metabolites associated with low temperatures during flowering. The 'Meiren' cultivar responded in a timely manner to temperature by way of a low-temperature signal transduction pathway. After experiencing low temperatures, the petals fade and wilt, resulting in low ornamental value. At the same time, in the cold response pathway, the activities of related transcription factors up- or downregulate genes and metabolites related to low temperature-induced proteins, osmotic regulators, protective enzyme systems, and biosynthesis and metabolism of sugars and acids. Our findings promote research on the adaptation of P. mume to low temperatures during wintering and early flowering for domestication and breeding.

Overexpression of a Fragaria vesca MYB Transcription Factor Gene (FvMYB82) Increases Salt and Cold Tolerance in Arabidopsis thaliana

The MYB transcription factor (TF) family is one of the largest transcription families in plants, which is widely involved in the responses to different abiotic stresses, such as salt, cold, and drought. In the present study, a new MYB TF gene was cloned from Fragaria vesca (a diploid strawberry) and named FvMYB82. The open reading frame (ORF) of FvMYB82 was found to be 960 bp, encoding 319 amino acids. Sequence alignment results and predictions of the protein structure indicated that the FvMYB82 contained the conserved R2R3-MYB domain. Subcellular localization analysis showed that FvMYB82 was localized onto the nucleus. Furthermore, the qPCR showed that the expression level of FvMYB82 was higher in new leaves and roots than in mature leaves and stems. When dealing with different stresses, the expression level of FvMYB82 in F. vesca seedlings changed markedly, especially for salt and cold stress. When FvMYB82 was introduced into Arabidopsis thaliana, the tolerances to salt and cold stress of FvMYB82-OE A. thaliana were greatly improved. When dealt with salt and cold treatments, compared with wild-type and unloaded line (UL) A. thaliana, the transgenic lines had higher contents of proline and chlorophyll, as well as higher activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). However, the transgenic A. thaliana had lower level of malondialdehyde (MDA) and electrolytic leakage (EL) than wild-type and UL A. thaliana under salt and cold stress. Meanwhile, FvMYB82 can also regulate the expression of downstream genes associated with salt stress (AtSnRK2.4, AtSnRK2.6, AtKUP6, and AtNCED3) and cold stress (AtCBF1, AtCBF2, AtCOR15a, and AtCOR78). Therefore, these results indicated that FvMYB82 probably plays an important role in the response to salt and cold stresses in A. thaliana by regulating downstream related genes.

Transcriptomic Analysis Reveals the Correlation between End-of-Day Far Red Light and Chilling Stress in Setaria viridis

Low temperature and end-of-day far-red (EOD-FR) light signaling are two key factors limiting plant production and geographical location worldwide. However, the transcriptional dynamics of EOD-FR light conditions during chilling stress remain poorly understood. Here, we performed a comparative RNA-Seq-based approach to identify differentially expressed genes (DEGs) related to EOD-FR and chilling stress in Setaria viridis. A total of 7911, 324, and 13431 DEGs that responded to low temperature, EOD-FR and these two stresses were detected, respectively. Further DEGs analysis revealed that EOD-FR may enhance cold tolerance in plants by regulating the expression of genes related to cold tolerance. The result of weighted gene coexpression network analysis (WGCNA) using 13431 nonredundant DEGs exhibited 15 different gene network modules. Interestingly, a CO-like transcription factor named BBX2 was highly expressed under EOD-FR or chilling conditions. Furthermore, we could detect more expression levels when EOD-FR and chilling stress co-existed. Our dataset provides a valuable resource for the regulatory network involved in EOD-FR signaling and chilling tolerance in C₄ plants.

Root Breeding in the Post-Genomics Era: From Concept to Practice in Apple

The development of rootstocks with a high-quality dwarf-type root system is a popular research topic in the apple industry. However, the precise breeding of rootstocks is still challenging, mainly because the root system is buried deep underground, roots have a complex life cycle, and research on root architecture has progressed slowly. This paper describes ideas for the precise breeding and domestication of wild apple resources and the application of key genes. The primary goal of this research is to combine the existing rootstock resources with molecular breeding and summarize the methods of precision breeding. Here, we reviewed the existing rootstock germplasm, high-quality genome, and genetic resources available to explain how wild resources might be used in modern breeding. In particular, we proposed the 'from genotype to phenotype' theory and summarized the difficulties in future breeding processes. Lastly, the genetics governing root diversity and associated regulatory mechanisms were elaborated on to optimize the precise breeding of rootstocks.

Can we improve the chilling tolerance of maize photosynthesis through breeding?

Chilling tolerance is necessary for crops to thrive in temperate regions where cold snaps and lower baseline temperatures place limits on life processes; this is particularly true for crops of tropical origin such as maize. Photosynthesis is often adversely affected by chilling stress, yet the maintenance of photosynthesis is essential for healthy growth and development, and most crucially for yield. In this review, we describe the physiological basis for enhancing chilling tolerance of photosynthesis in maize by examining nine key responses to chilling stress. We synthesize current knowledge of genetic variation for photosynthetic chilling tolerance in maize with respect to each of these traits and summarize the extent to which genetic mapping and candidate genes have been used to understand the genomic regions underpinning chilling tolerance. Finally, we provide perspectives on the future of breeding for photosynthetic chilling tolerance in maize. We advocate for holistic and high-throughput approaches to screen for chilling tolerance of photosynthesis in research and breeding programmes in order to develop resilient crops for the future.

Proteomic analysis reveals the molecular mechanism underlying the cold acclimation and freezing tolerance of wheat (Triticum aestivum L.)

Cold acclimation (CA) is an important evolutionary adaptive mechanism for wheat freezing resistence. To clarify the molecular basis of wheat CA and freezing tolerance, the effects of CA (4 °C) and non-CA (20 °C) treatments and freezing stress (-5 °C) on the proteins in the wheat crown were characterized via an iTRAQ-based proteomic analysis. A total of 669 differentially accumulated proteins (DAPs) were identified after the CA, of which seven were also DAPs in the CA plants exposed to freezing stress. Additionally, the 15 DAPs in the CA group and the 23 DAPs in the non-CA group after the freezing treatment differed substantially. Functional analyses indicated that CA enhanced freezing tolerance by regulating proteins involved in signal transduction, carbohydrate metabolism, stress and defense responses, and phenylpropanoid biosynthesis. An integrated transcriptomic, proteomic, and metabolomic analysis revealed significant changes in various components of the glutathione metabolic pathway. The overexpression and silencing of Wdhn13 in Arabidopsis and wheat resulted in increased tolerance and sensitivity to freezing stress, respectively, suggesting Wdhn13 promotes freezing tolerance. Overall, our study offers insights into the regulatory network underlying the CA and freezing tolerance of wheat, which may be useful for elucidating wheat freezing resistance.

Molecular Cloning and Characterization of MbMYB108, a Malus baccata MYB Transcription Factor Gene, with Functions in Tolerance to Cold and Drought Stress in Transgenic Arabidopsis thaliana

The MYB transcription factor (TF) family is one of the largest transcription families in plants, which is widely involved in the responses of plants to biotic and abiotic stresses, as well as plant growth, development, and metabolic regulation. In the present study, a new MYB TF gene, MbMYB108, from Malus baccata (L.) Borkh, was identified and characterized. The open reading frame (ORF) of MbMYB108 was found to be 903 bp, encoding 300 amino acids. Sequence alignment results and predictions of the protein structure indicated that the MbMYB108 protein contained the conserved MYB domain. Subcellular localization showed that MbMYB108 was localized to the nucleus. The expression of MbMYB108 was enriched in young and mature leaves, and was highly affected by cold and drought treatments in M. baccata seedlings. When MbMYB108 was introduced into Arabidopsis thaliana, it greatly increased the cold and drought tolerances in the transgenic plant. Increased expression of MbMYB108 in transgenic A. thaliana also resulted in higher activities of peroxidase (POD) and catalase (CAT), higher contents of proline and chlorophyll, while malondialdehyde (MDA) content and relative conductivity were lower, especially in response to cold and drought stresses. Therefore, these results suggest that MbMYB108 probably plays an important role in the response to cold and drought stresses in A. thaliana by enhancing the scavenging capability for reactive oxygen species (ROS).

Comparative transcriptomic analyses of citrus cold-resistant vs. sensitive rootstocks might suggest a relevant role of ABA signaling in triggering cold scion adaption

BACKGROUND

The citrus genus comprises a number of sensitive tropical and subtropical species to cold stress, which limits global citrus distribution to certain latitudes and causes major economic loss. We used RNA-Seq technology to analyze changes in the transcriptome of Valencia delta seedless orange in response to long-term cold stress grafted on two frequently used citrus rootstocks: Carrizo citrange (CAR), considered one of the most cold-tolerant accessions; C. macrophylla (MAC), a very sensitive one. Our objectives were to identify the genetic mechanism that produce the tolerant or sensitive phenotypes in citrus, as well as to gain insights of the rootstock-scion interactions that induce the cold tolerance or sensitivity in the scion.

RESULTS

Plants were kept at 1 ºC for 30 days. Samples were taken at 0, 15 and 30 days. The metabolomic analysis showed a significant increase in the concentration of free sugars and proline, which was higher for the CAR plants. Hormone quantification in roots showed a substantially increased ABA concentration during cold exposure in the CAR roots, which was not observed in MAC. Different approaches were followed to analyze gene expression. During the stress treatment, the 0-15-day comparison yielded the most DEGs. The functional characterization of DEGs showed enrichment in GO terms and KEGG pathways related to abiotic stress responses previously described in plant cold adaption. The DEGs analysis revealed that several key genes promoting cold adaption were up-regulated in the CAR plants, and those repressing it had higher expression levels in the MAC samples.

CONCLUSIONS

The metabolomic and transcriptomic study herein performed indicates that the mechanisms activated in plants shortly after cold exposure remain active in the long term. Both the hormone quantification and differential expression analysis suggest that ABA signaling might play a relevant role in promoting the cold hardiness or sensitiveness of Valencia sweet orange grafted onto Carrizo citrange or Macrophylla rootstocks, respectively. Our work provides new insights into the mechanisms by which rootstocks modulate resistance to abiotic stress in the production variety grafted onto them.

Temperature-mediated regulation of flowering time in Arabidopsis thaliana

Throughout a plant's life cycle, temperature plays a major role in development. Regulatory modules use temperature cues to control gene expression, facilitating physiological change from germination to flowering. These regulatory modules control morphological and molecular responses to temperature changes caused by seasonal changes or by temporary fluctuations, providing a versatile plasticity of plants. In this review, we outline how temperature changes affect the regulatory modules that induce and repress flowering, in addition to general temperature regulation. Recent studies have identified several regulatory modules by which floral transition and growth responses are controlled in a temperature-dependent manner. This review will report on recent studies related to floral transition and ambient temperature response.

Salicylic acid induces tolerance of Vitisriparia×V.labrusca to chilling stress by altered photosynthetic, antioxidant mechanisms and expression of cold stress responsive genes

The yield and quality of wine grapes are severely persecuted by low-temperaturestresses. Salicylic acid (SA) assists plants in coping with abiotic stresses such as drought, heavy metal toxicity, and osmotic stress. The objective of this study was to evaluate the effect of foliar spraying of different concentrations of SA on the mitigation of cold damage in grapes, which is useful for the cultivation of wine grapes.Vitisriparia×V.labruscaseedlings were treated with foliar-sprayedSA at concentrations of 0-2 mM and then subjected to chilling stress at 4°C for 2 or 4 days, while the expression of relevant physiological indicators and cold response genes (CBF1, CBF2, CBF3) were measured. The findings indicated that low temperature stresses markedly reduced chlorophyll content, and increased proline as well as soluble sugar content, enhanced superoxide dismutase (SOD) and peroxidase (POD) activities, decreased catalase (CAT) activity and inducedCBFgene expression in leaves. Physiologically, foliar spraying of different concentrations of SA greatly increased antioxidant enzyme activity (P < .05), soluble sugars, proline, and chlorophyll content of grapes leave under low temperature stress. With regard to gene expression, SA has significantly regulated the cold response genesCBF1, CBF2, andCBF3. Therefore, SA could reduce cold damage in grapevines under low-temperaturestress, and the effect of SA was most pronounced in the 1 and 2 mM concentrates.

Harnessing translational research in wheat for climate resilience

Despite being the world's most widely grown crop, research investments in wheat (Triticum aestivum and Triticum durum) fall behind those in other staple crops. Current yield gains will not meet 2050 needs, and climate stresses compound this challenge. However, there is good evidence that heat and drought resilience can be boosted through translating promising ideas into novel breeding technologies using powerful new tools in genetics and remote sensing, for example. Such technologies can also be applied to identify climate resilience traits from among the vast and largely untapped reserve of wheat genetic resources in collections worldwide. This review describes multi-pronged research opportunities at the focus of the Heat and Drought Wheat Improvement Consortium (coordinated by CIMMYT), which together create a pipeline to boost heat and drought resilience, specifically: improving crop design targets using big data approaches; developing phenomic tools for field-based screening and research; applying genomic technologies to elucidate the bases of climate resilience traits; and applying these outputs in developing next-generation breeding methods. The global impact of these outputs will be validated through the International Wheat Improvement Network, a global germplasm development and testing system that contributes key productivity traits to approximately half of the global wheat-growing area.

Cold Stress in Wheat: Plant Acclimation Responses and Management Strategies

Unpredicted variability in temperature is associated with frequent extreme low-temperature events. Wheat is a leading crop in fulfilling global food requirements. Climate-driven temperature extremes influence the vegetative and reproductive growth of wheat, followed by a decrease in yield. This review describes how low temperature induces a series of modifications in the morphophysiological, biochemical, and molecular makeup of wheat and how it is perceived. To cope with these modifications, crop plants turn on their cold-tolerance mechanisms, characterized by accumulating soluble carbohydrates, signaling molecules, and cold tolerance gene expressions. The review also discusses the integrated management approaches to enhance the performance of wheat plants against cold stress. In this review, we propose strategies for improving the adaptive capacity of wheat besides alleviating risks of cold anticipated with climate change.

Salicylic Acid Is Involved in Rootstock-Scion Communication in Improving the Chilling Tolerance of Grafted Cucumber

Salicylic acid (SA) has been proven to be a multifunctional signaling molecule that participates in the response of plants to abiotic stresses. In this study, we used cold-sensitive cucumber and cold-tolerant pumpkin as experimental materials to examine the roles of SA in root-shoot communication responses to aerial or/and root-zone chilling stress in own-root and hetero-root grafted cucumber and pumpkin plants. The results showed that pumpkin (Cm) rootstock enhanced the chilling tolerance of grafted cucumber, as evidenced by the observed lower levels of electrolyte leakage (EL), malondialdehyde (MDA), and higher photosynthetic rate (Pn) and gene expression of Rubisco activase (RCA). However, cucumber (Cs) rootstock decreased the chilling tolerance of grafted pumpkins. Cs/Cm plants showed an increase in the mRNA expression of C-repeat-binding factor (CBF1), an inducer of CBF expression (ICE1), and cold-responsive (COR47) genes and CBF1 protein levels in leaves under 5/25 and 5/5°C stresses, or in roots under 25/5 and 5/5°C stresses, respectively, compared with the Cs/Cs. Chilling stress increased the endogenous SA content and the activity of phenylalanine ammonia-lyase (PAL), and the increase in SA content and activity of PAL in Cs/Cm plants was much higher than in Cs/Cs plants. Transcription profiling analysis revealed the key genes of SA biosynthesis, PAL, ICS, and SABP2 were upregulated, while SAMT, the key gene of SA degradation, was downregulated in Cs/Cm leaves, compared with Cs/Cs leaves under chilling stress. The accumulation of SA in the Cs/Cm leaves was mainly attributed to an increase in SA biosynthesis in leaves and that in transport from roots under aerial and root-zone chilling stress, respectively. In addition, exogenous SA significantly upregulated the expression level of cold-responsive (COR) genes, enhanced actual photochemical efficiency (Φ _PSII), maximum photochemical efficiency (F _v/F _m), and Pn, while decreased EL, MDA, and CI in grafted cucumber. These results suggest that SA is involved in rootstock-scion communication and grafting-induced chilling tolerance by upregulating the expression of COR genes in cucumber plants under chilling stress.

Updated Mechanisms of GCN5-The Monkey King of the Plant Kingdom in Plant Development and Resistance to Abiotic Stresses

Histone modifications are the main epigenetic mechanisms that regulate gene expression, chromatin structure, and plant development, among which histone acetylation is one of the most important and studied epigenetic modifications. Histone acetylation is believed to enhance DNA access and promote transcription. GENERAL CONTROL NON-REPRESSIBLE 5 (GCN5), a well-known enzymatic protein responsible for the lysine acetylation of histone H3 and H4, is a universal and crucial histone acetyltransferase involved in gene transcription and plant development. Many studies have found that GCN5 plays important roles in the different development stages of Arabidopsis. In terms of exogenous stress conditions, GCN5 is also involved in the responses to heat stress, cold stress, and nutrient element deficiency by regulating the related gene expression to maintain the homeostasis of some key metabolites (e.g., cellulose) or ions (e.g., phosphate, iron); in addition, GCN5 is involved in the phytohormone pathways such as ethylene, auxin, and salicylic acid to play various roles during the plant lifecycle. Some of the pathways involved by GCN5 also interwind to regulate specific physiological processes or developmental stages. Here, interactions between various developmental events and stress-resistant pathways mediated by GCN5 are comprehensively addressed and the underlying mechanisms are discussed in the plant. Studies with some interacting factors such as ADA2b provided valuable information for the complicated histone acetylation mechanisms. We also suggest the future focuses for GCN5 functions and mechanisms such as functions in seed development/germination stages, exploration of novel interaction factors, identification of more protein substrates, and application of advanced biotechnology-CRISPR in crop genetic improvement, which would be helpful for the complete illumination of roles and mechanisms of GCN5.

Genome-Wide Identification and Low Temperature Responsive Pattern of Actin Depolymerizing Factor (ADF) Gene Family in Wheat (Triticum aestivum L.)

The actin depolymerizing factor (ADF) gene family, which is conserved in eukaryotes, is important for plant development, growth, and stress responses. Cold stress restricts wheat growth, development, and distribution. However, genome-wide identification and functional analysis of the ADF family in wheat is limited. Further, because of the promising role of ADF genes in cold response, there is need for an understanding of the function of this family on wheat under cold stress. In this study, 25 ADF genes (TaADFs) were identified in the wheat genome and they are distributed on 15 chromosomes. The TaADF gene structures, duplication events, encoded conversed motifs, and cis-acting elements were investigated. Expression profiles derived from RNA-seq data and real-time quantitative PCR analysis revealed the tissue- and temporal-specific TaADF expression patterns. In addition, the expression levels of TaADF13/16/17/18/20/21/22 were significantly affected by cold acclimation or freezing conditions. Overexpression of TaADF16 increased the freezing tolerance of transgenic Arabidopsis, possibly because of enhanced ROS scavenging and changes to the osmotic regulation in cells. The expression levels of seven cold-responsive genes were up-regulated in the transgenic Arabidopsis plants, regardless of whether the plants were exposed to low temperature. These findings provide fundamental information about the wheat ADF genes and may help to elucidate the regulatory effects of the encoded proteins on plant development and responses to low-temperature stress.

CRISPR/Cas9-Mediated Knockout of HOS1 Reveals Its Role in the Regulation of Secondary Metabolism in Arabidopsis thaliana

In Arabidopsis, the RING finger-containing E3 ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1 (HOS1) functions as a main regulator of the cold signaling. In this study, CRISPR/Cas9-mediated targeted mutagenesis of the HOS1 gene in the first exon was performed. DNA sequencing showed that frameshift indels introduced by genome editing of HOS1 resulted in the appearance of premature stop codons, disrupting the open reading frame. Obtained hos1^Cas9 mutant plants were compared with the SALK T-DNA insertion mutant, line hos1-3, in terms of their tolerance to abiotic stresses, accumulation of secondary metabolites and expression levels of genes participating in these processes. Upon exposure to cold stress, enhanced tolerance and expression of cold-responsive genes were observed in both hos1-3 and hos1^Cas9 plants. The hos1 mutation caused changes in the synthesis of phytoalexins in transformed cells. The content of glucosinolates (GSLs) was down-regulated by 1.5-times, while flavonol glycosides were up-regulated by 1.2 to 4.2 times in transgenic plants. The transcript abundance of the corresponding MYB and bHLH transcription factors, which are responsible for the regulation of secondary metabolism in Arabidopsis, were also altered. Our data suggest a relationship between HOS1-regulated downstream signaling and phytoalexin biosynthesis.

Role of Glycine max ABSCISIC ACID INSENSITIVE 3 (GmABI3) in lipid biosynthesis and stress tolerance in soybean

Soybean is an important oilseed crop and primary dietary protein resource. The limited understanding of soybean oil biosynthesis has become a significant obstacle for the improvement of soybean oil production. A transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3) is known for its role in plant development and seed dormancy in many crops. The current study was aimed to functionally characterise ABI3 homologue in Glycine max L. For this purpose, the GmABI3 gene was cloned and ectopically expressed in wildtype and abi3 mutant Arabidopsis. The GmABI3 expression in the atabi3 mutant enhanced the triacylglycerol (TAG) content (7.3%) in addition to modified fatty acid composition. The GmABI3 increased eicosenoic acid (20:1) up to 6.5% in genetically complemented Arabidopsis mutant seeds, which is essential for long-chain fatty acid synthesis. The transgenic GmABI3/wildtype seeds contain 34.9% more TAG content compared with wildtype seeds. The results showed that GmABI3 is responsible for seed-specific TAG and long-chain fatty acid biosynthesis in soybean. The exposure to cold and heat stress and exogenous supply of abscisic acid and jasmonic acid altered the level of GmABI3 in treated seeds and leaves. It also concluded that GmABI3 could regulate stress tolerance in soybean, which applies to a wide variety of crops to deal with biological stresses.

Nitric Oxide Functions as a Downstream Signal for Melatonin-Induced Cold Tolerance in Cucumber Seedlings

Melatonin (MT) and nitric oxide (NO) are two multifunctional signaling molecules that are involved in the response of plants to abiotic stresses. However, how MT and NO synergize in response to cold stress affecting plants is still not clear. In this study, we found that endogenous MT accumulation under cold stress was positively correlated with cold tolerance in different varieties of cucumber seedlings. The data presented here also provide evidence that endogenous NO is involved in the response to cold stress. About 100 μM MT significantly increased the nitrate reductase (NR) activity, NR-relative messenger RNA (mRNA) expression, and endogenous NO accumulation in cucumber seedlings. However, 75 μM sodium nitroprusside (SNP, a NO donor) showed no significant effect on the relative mRNA expression of tryptophan decarboxylase (TDC), tryptamine-5-hydroxylase (T5H), serotonin-N-acetyltransferase (SNAT), or acetylserotonin O-methyltransferase (ASMT), the key genes for MT synthesis and endogenous MT levels. Compared with H₂O treatment, both MT and SNP decreased electrolyte leakage (EL), malondialdehyde (MDA), and reactive oxygen species (ROS) accumulation by activating the antioxidant system and consequently mitigated cold damage in cucumber seedlings. MT and SNP also enhanced photosynthetic carbon assimilation, which was mainly attributed to an increase in the activity and mRNA expression of the key enzymes in the Calvin-Benson cycle. Simultaneously, MT- and SNP-induced photoprotection for both photosystem II (PSII) and photosystem I (PSI) in cucumber seedlings, by stimulating the PsbA (D1) protein repair pathway and ferredoxin-mediated NADP⁺ photoreduction, respectively. Moreover, exogenous MT and SNP markedly upregulated the expression of chilling response genes, such as inducer of CBF expression (ICE1), C-repeat-binding factor (CBF1), and cold-responsive (COR47). MT-induced cold tolerance was suppressed by 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO, a specific scavenger of NO). However, p-chlorophenylalanine (p-CPA, a MT synthesis inhibitor) did not affect NO-induced cold tolerance. Thus, novel results suggest that NO acts as a downstream signal in the MT-induced plant tolerance to cold stress.

Activation tagging identifies Arabidopsis transcription factor AtMYB68 for heat and drought tolerance at yield determining reproductive stages

Heat stress occurring at reproductive stages can result in significant and permanent damage to crop yields. However, previous genetic studies in understanding heat stress response and signaling were performed mostly on seedling and plants at early vegetative stages. Here we identify, using a developmentally defined, gain-of-function genetic screen with approximately 18 000 Arabidopsis thaliana activation-tagged lines, a mutant that maintained productive seed set post-severe heat stress during flowering. Genome walking indicated this phenotype was caused by the insertion of 35S enhancers adjacent to a nuclear localized transcription factor AtMYB68. Subsequent overexpression analysis confirmed that AtMYB68 was responsible for the reproductive heat tolerance of the mutant. Furthermore, these transgenic Arabidopsis plants exhibited enhanced abscisic acid sensitivity at and post-germination, reduced transpirational water loss during a drought treatment, and enhanced seed yield under combined heat and drought stress during flowering. Ectopic expression of AtMYB68 in Brassica napus driven either by 35S or by heat-inducible promoter recapitulated the enhanced reproductive heat stress and drought tolerance phenotypes observed in the transgenic Arabidopsis. The improvement to heat stress is likely due to enhanced pollen viability observed in the transgenic plants. More importantly, the transgenic canola showed significant yield advantages over the non-transgenic controls in multiple locations, multiple season field trials under various drought and heat stress conditions. Together these results suggest that AtMYB68 regulate plant stress tolerance at the most important yield determining stage of plant development, and is an effective target for crop yield protection under current global climate volatility.

Varying Atmospheric CO2 Mediates the Cold-Induced CBF-Dependent Signaling Pathway and Freezing Tolerance in Arabidopsis

Changes in the stomatal aperture in response to CO₂ levels allow plants to manage water usage, optimize CO₂ uptake and adjust to environmental stimuli. The current study reports that sub-ambient CO₂ up-regulated the low temperature induction of the C-repeat Binding Factor (CBF)-dependent cold signaling pathway in Arabidopsis (Arabidopsis thaliana) and the opposite occurred in response to supra-ambient CO₂. Accordingly, cold induction of various downstream cold-responsive genes was modified by CO₂ treatments and expression changes were either partially or fully CBF-dependent. Changes in electrolyte leakage during freezing tests were correlated with CO_2′s effects on CBF expression. Cold treatments were also performed on Arabidopsis mutants with altered stomatal responses to CO₂, i.e., high leaf temperature 1-2 (ht1-2, CO₂ hypersensitive) and β-carbonic anhydrase 1 and 4 (ca1ca4, CO₂ insensitive). The cold-induced expression of CBF and downstream CBF target genes plus freezing tolerance of ht1-2 was consistently less than that for Col-0, suggesting that HT1 is a positive modulator of cold signaling. The ca1ca4 mutant had diminished CBF expression during cold treatment but the downstream expression of cold-responsive genes was either similar to or greater than that of Col-0. This finding suggested that βCA1/4 modulates the expression of certain cold-responsive genes in a CBF-independent manner. Stomatal conductance measurements demonstrated that low temperatures overrode low CO₂-induced stomatal opening and this process was delayed in the cold tolerant mutant, ca1ca4, compared to the cold sensitive mutant, ht1-2. The similar stomatal responses were evident from freezing tolerant line, Ox-CBF, overexpression of CBF3, compared to wild-type ecotype Ws-2. Together, these results indicate that CO₂ signaling in stomata and CBF-mediated cold signaling work coordinately in Arabidopsis to manage abiotic stress.

Overestimation of the effect of climatic warming on spring phenology due to misrepresentation of chilling

Spring warming substantially advances leaf unfolding and flowering time for perennials. Winter warming, however, decreases chilling accumulation (CA), which increases the heat requirement (HR) and acts to delay spring phenology. Whether or not this negative CA-HR relationship is correctly interpreted in ecosystem models remains unknown. Using leaf unfolding and flowering data for 30 perennials in Europe, here we show that more than half (7 of 12) of current chilling models are invalid since they show a positive CA-HR relationship. The possible reason is that they overlook the effect of freezing temperature on dormancy release. Overestimation of the advance in spring phenology by the end of this century by these invalid chilling models could be as large as 7.6 and 20.0 days under RCPs 4.5 and 8.5, respectively. Our results highlight the need for a better representation of chilling for the correct understanding of spring phenological responses to future climate change.

Climate warming is advancing spring leaf unfolding, but it is also reducing the cold periods that many trees require to break winter dormancy. Here, the authors show that 7 of 12 current chilling models fail to account for the correct relationship between chilling accumulation and heat requirement, leading to substantial overestimates of the advance of spring phenology under climate change.

PuMYB21/PuMYB54 coordinate to activate PuPLDβ1 transcription during peel browning of cold-stored "Nanguo" pears

Refrigeration is commonly used to extend the storage life of "Nanguo" pears, but fruit in long-term refrigeration is prone to peel browning, which is related to membrane lipid degradation. To determine the mechanism of membrane lipid degradation, we identified two R2R3-MYB transcription factors (TFs), PuMYB21 and PuMYB54, from "Nanguo" pears, which were notably expressed in response to cold stress and during the peel-browning process. The results from yeast one-hybrid, electrophoretic mobility shift, and transient expression assays indicated that both PuMYB21 and PuMYB54 directly bind to the promoter of PuPLDβ1 (a key enzyme catalyzing the hydrolysis of membrane phospholipids) and activate its expression, which probably enhances the degradation of membrane phospholipids and eventually results in peel browning. Moreover, the overexpression of PuMYB21 and PuMYB54 can greatly activate the transcription of endogenous PuPLDβ1 in both "Nanguo" pear fruits and calli, and their silencing can inhibit its transcription. Furthermore, yeast two-hybrid, bimolecular fluorescence complementation, and pull-down assays verified that PuMYB21 interacts with PuMYB54 to enhance the expression of PuPLDβ1. In summary, we demonstrate that PuMYB21 and PuMYB54 may have roles in membrane lipid metabolism by directly binding to the downstream structural gene PuPLDβ1 during the low temperature-induced peel browning of "Nanguo" pears.

SlGRAS4 mediates a novel regulatory pathway promoting chilling tolerance in tomato

Tomato (Solanum lycopersicum L.) plants are cold-sensitive, and the fruit are susceptible to postharvest chilling injury when stored at low temperature. However, the mechanisms underlying cold stress responses in tomato are poorly understood. We demonstrate that SlGRAS4, encoding a transcription factor induced by low temperature, promotes chilling tolerance in tomato leaves and fruit. Combined genome-wide ChIP-seq and RNA-seq approaches identified among cold stress-associated genes those being direct targets of SlGRAS4 and protein studies revealed that SlGRAS4 forms a homodimer to self-activate its own promoter. SlGRAS4 can also directly bind tomato SlCBF promoters to activate their transcription without inducing any growth retardation. The study identifies the SlGRAS4-regulon as a new cold response pathway conferring cold stress tolerance in tomato independently of the ICE1-CBF pathway. This provides new track for breeding strategies aiming to improve chilling tolerance of cultivated tomatoes and to preserve sensory qualities of tomato fruit often deteriorated by storage at low temperatures.

Molecular genetic analyses of abiotic stress responses during plant reproductive development

Plant responses to abiotic stresses during vegetative growth have been extensively studied for many years. Daily environmental fluctuations can have dramatic effects on plant vegetative growth at multiple levels, resulting in molecular, cellular, physiological, and morphological changes. Plants are even more sensitive to environmental changes during reproductive stages. However, much less is known about how plants respond to abiotic stresses during reproduction. Fortunately, recent advances in this field have begun to provide clues about these important processes, which promise further understanding and a potential contribution to maximize crop yield under adverse environments. Here we summarize information from several plants, focusing on the possible mechanisms that plants use to cope with different types of abiotic stresses during reproductive development, and present a tentative molecular portrait of plant acclimation during reproductive stages. Additionally, we discuss strategies that plants use to balance between survival and productivity, with some comparison among different plants that have adapted to distinct environments.

An eggplant SmICE1a gene encoding MYC-type ICE1-like transcription factor enhances freezing tolerance in transgenic Arabidopsis thaliana

Low temperature is a crucial environmental factor affecting the quality and production of eggplant. Therefore, it is necessary to explore the molecular mechanisms of low temperature response. We isolated an ICE (inducer of CBF expression) gene from Solanum melongena, named SmICE1a. We then analysed structure, transcriptional activity and expression patterns of SmICE1a. Moreover, we also expressed SmICE1a in Arabidopsis thaliana. Bioinformatics and expression analysis showed that SmICE1a has a typical S-rich motif, ZIP region, bHLH and ACT-like domain. The gene SmICE1a had transcriptional activity in yeast and was localized to the nucleus following transient expression in tobacco leaves, which suggests that SmICE1a is a transcription factor. A dual-LUC assay revealed that SmICE1a can enhance expression of SmCBF. Overexpression of SmICE1a in Arabidopsis increased freezing tolerance and caused multiple biochemical changes: transgenic lines have higher proline content and lower electrolyte leakage and malondialdehyde than the wild type in cold conditions. The expression of AtCBF and their target genes, AtCOR15A, AtCOR47, AtKIN1 and AtRD29A, were up-regulated in SmICE1a-overexpressing plants under low temperatures. Based on these results, we suggest that SmICE1a plays an important role in cold response, which may help to understand the cold response mechanism in eggplant and could be used to enhance cold tolerance of eggplant in future.

Plasma Membrane Aquaporin Members PIPs Act in Concert to Regulate Cold Acclimation and Freezing Tolerance Responses in Arabidopsis thaliana

Aquaporins play a major role in plant water uptake at both optimal and environmentally stressed conditions. However, the functional specificity of aquaporins under cold remains obscure. To get a better insight to the role of aquaporins in cold acclimation and freezing tolerance, we took an integrated approach of physiology, transcript profiling and cell biology in Arabidopsis thaliana. Cold acclimation resulted in specific upregulation of PIP1;4 and PIP2;5 aquaporin (plasma membrane intrinsic proteins) expression, and immunoblotting analysis confirmed the increase in amount of PIP2;5 protein and total amount of PIPs during cold acclimation, suggesting that PIP2;5 plays a major role in tackling the cold milieu. Although single mutants of pip1;4 and pip2;5 or their double mutant showed no phenotypic changes in freezing tolerance, they were more sensitive in root elongation and cell survival response under freezing stress conditions compared with the wild type. Consistently, a single mutation in either PIP1;4 or PIP2;5 altered the expression of a number of aquaporins both at the transcriptional and translational levels. Collectively, our results suggest that aquaporin members including PIP1;4 and PIP2;5 function in concert to regulate cold acclimation and freezing tolerance responses.

Individual Cryptomeria fortunei Hooibrenk Clones Show Varying Degrees of Chilling Stress Resistance

Low temperature (LT) is an important abiotic factor affecting plant survival, growth and distribution. The response of Cryptomeria fortunei (Chinese cedar) to LT is not well known, limiting its application in production and ornamental value. In this study, we first screened ten clones (#3, #25, #32, #42, #54, #57, #68, #66, #74, #X1), originating from five different locations in China, for their degrees of cold resistance. We then selected the two showing the highest (#32) and lowest (#42) cold resistance to see the physiological and morphological response of different cold-resistant C. fortunei clones to LT. We found that the electrolyte leakage of all ten clones increased strongly between 0 and −8 °C, while below −8 or between 4 and 0 °C did not yield additional increases. Under cold stress, clones #32 and #42 showed different degrees of needle browning. From 25 to −20 °C, maximum and effective quantum yields of photosystem II (Fv/Fm and YII) and photochemical and non-photochemical quenching (qP and NPQ) decreased continuously in two clones with decreasing temperature, where #42 was more strongly affected compared with #32. The chlorophyll content first decreased significantly to the lowest from 25 to −12 °C, then increased significantly at −16/−20 °C compared with −12 °C. We observed changes in needle cellular ultrastructure at −8 °C, with chloroplasts of #32 swelling, while those of #42 were destroyed. Correlation analysis indicated that needle browning and chlorophyll fluorescence were closely related to temperature, and cellular ultrastructure changed notably around semi-lethal temperature (LT50), which can be used as physiological indicators for the identification of cold resistance. We found a clear difference in cold tolerance between clones of #32 and #42, with #32 being more tolerant, which can be exploited in breeding programs. We conclude that strongly cold-resistant clones have more stable physiological states and a wider adaptability to LT compared with weak ones.

Genome-wide expression of low temperature response genes in Rosa hybrida L

Plants respond to low temperature stress during cold acclimation, a complex process involving changes in physiological and biochemical modifications. The rose serves as a good model to investigate low temperature responses in perennial ornamentals. In this study, a heterologous apple microarray is used to investigate genome-wide expression profiles in Rosa hybrida subjected to low temperature dark treatment. Transcriptome profiles are determined in floral buds at 0h, 2h, and 12h of low temperature treatment (4 °C). It is observed that a total of 134 transcripts are up-regulated and 169 transcripts are down-regulated in response to low temperature. Interestingly, a total of eight up-regulated genes, including those coding for two cytochrome P450 proteins, two ankyrin repeat family proteins, two metal ion binding proteins, and two zinc finger protein-related transcription factors, along with a single down-regulated gene, coding for a dynamin-like protein, are detected. Transcript profiles of 12 genes known to be involved in cold stress response are also validated using qRT-PCR. Furthermore, expression patterns of the AP2/ERF gene family of transcription factors are investigated in both floral buds and leaves. Overall, AP2/ERFs genes are more rapidly induced in leaves than in floral buds. Moreover, differential expression of several AP2/ERF genes are detected earlier in vegetative rather than in reproductive tissues. These findings highlight important roles of various low temperature response genes in mediating cold acclimation, thereby allowing roses to adapt to low temperatures, but without adversely affecting flower bud development and subsequent flowering, while vegetative tissues undergo early adaptation to low temperatures.

Genetic Architecture of Chilling Tolerance in Sorghum Dissected with a Nested Association Mapping Population

Dissecting the genetic architecture of stress tolerance in crops is critical to understand and improve adaptation. In temperate climates, early planting of chilling-tolerant varieties could provide longer growing seasons and drought escape, but chilling tolerance (<15°) is generally lacking in tropical-origin crops. Here we developed a nested association mapping (NAM) population to dissect the genetic architecture of early-season chilling tolerance in the tropical-origin cereal sorghum (Sorghum bicolor [L.] Moench). The NAM resource, developed from reference line BTx623 and three chilling-tolerant Chinese lines, is comprised of 771 recombinant inbred lines genotyped by sequencing at 43,320 single nucleotide polymorphisms. We phenotyped the NAM population for emergence, seedling vigor, and agronomic traits (>75,000 data points from ∼16,000 plots) in multi-environment field trials in Kansas under natural chilling stress (sown 30-45 days early) and normal growing conditions. Joint linkage mapping with early-planted field phenotypes revealed an oligogenic architecture, with 5-10 chilling tolerance loci explaining 20-41% of variation. Surprisingly, several of the major chilling tolerance loci co-localize precisely with the classical grain tannin (Tan1 and Tan2) and dwarfing genes (Dw1 and Dw3) that were under strong directional selection in the US during the 20^th century. These findings suggest that chilling sensitivity was inadvertently selected due to coinheritance with desired nontannin and dwarfing alleles. The characterization of genetic architecture with NAM reveals why past chilling tolerance breeding was stymied and provides a path for genomics-enabled breeding of chilling tolerance.