Integrated analysis of ATAC-seq and transcriptomic reveals the ScDof3-ScproC molecular module regulating the cold acclimation capacity of potato

Low temperature severely affects the geographical distribution and production of potato, which may incur cold damage in early spring or winter. Cultivated potatoes, mainly derived from Solanum tuberosum, are sensitive to freezing stress, but wild species of potato such as S. commersonii exhibit both constitutive freezing tolerance and/or cold acclimation tolerance. Hence, such wild species could assist in cold hardiness breeding. Yet the key transcription factors and their downstream functional genes that confer freezing tolerance are far from clear, hindering the breeding process. Here, we used ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) alongside RNA-seq to investigate the variation in chromatin accessibility and patterns of gene expression in freezing-tolerant CMM5 (S. commersonii), before and after its cold treatment. Our results suggest that after exposure to cold, transcription factors including Dof3, ABF2, PIF4, and MYB4 were predicted to further control the genes active in the synthetic/metabolic pathways of plant hormones, namely abscisic acid, polyamine, and reductive glutathione (among others). This suggests these transcription factors could regulate freezing tolerance of CMM5 leaves. In particular, ScDof3 was proven to regulate the expression of ScproC (pyrroline-5-carboxylate reductase, P5CR) according to dual-LUC assays. Overexpressing ScDof3 in Nicotiana benthamiana leaves led to an increase in both the proline content and expression level of NbproC (homolog of ScproC). These results demonstrate the ScDof3-ScproC module regulates the proline content and thus promotes freezing tolerance in potato. Our research provides valuable genetic resources to further study the molecular mechanisms underpinning cold tolerance in potato.

MSTRG3207 promotes apoptosis in zebrafish ZF4 cells via sponging dre-miR-736/bbc3/LOC101885512 axis during cold acclimation

Long non-coding RNAs (lncRNAs) play essential roles in a variety of biological processes. It has been recently reported that lncRNAs can regulate mRNA expression by binding to microRNAs (miRNAs) as competing endogenous RNAs (ceRNAs). However, the involvement of this regulatory mechanism during cold acclimation in fish remains unclear. In this study, we constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells through bioinformatic analysis of the mRNA, miRNA, and lncRNA profiles obtained from ZF4 cells cultured at 18 °C for 30 days. A previously uncharacterized lncRNA, MSTRG3207, was selected for further analysis. MSTRG3207 was upregulated and dre-miR-736 was downregulated during cold acclimation. MSTRG3207 was cloned by rapid amplification of cDNA ends (RACE) and functionally characterized. The binding of MSTRG3207 to dre-miR-736 was validated by dual-luciferase reporter assay. Under cold acclimation, MSTRG3207 promoted apoptosis by sponging dre-miR-736 and upregulating bbc3 and LOC101885512, two apoptotic genes targeted by dre-miR-736. Taken together, our findings indicate that MSTRG3207 upregulation promotes apoptosis by sponging dre-miR-736 during cold acclimation in fish.

Vitis Myb14 confer cold and drought tolerance by activating lipid transfer protein genes expression and reactive oxygen species scavenge

The R2R3 Myb transcription factor exhibits a wide range of functions and participates in various biological processes in plant development, secondary metabolism, and abiotic stress tolerance, among others. Vitis Myb14 initially identified for its involvement in resveratrol synthesis in grapevines. In this study, we investigate its role in abiotic stress tolerance. Significant differences in expression were observed between two grape varieties, Vitis amurensis (Cold-hardy) and V. vinifera (Cold-sentitive), under abiotic and hormone treatments. Both VvMyb14 and VaMyb14 demonstrated responsiveness to cold, drought and high salt treatment, but VaMyb14 exhibited a quicker and more pronounced response. To investigate further, we overexpressed VaMyb14 in A. thalina and found that VaMyb14 OE plants showed significantly enhanced cold and drought tolerance compared to wild-type plants. Additionally, the transgenic lines exhibited increased antioxidant enzyme activity, particularly POD activity, and reduced MDA content. Microarray analysis of VaMyb14 OE plants revealed up-regulation of several ABA metabolism and signal transduction genes, including several LTPs, PP2Cs, RD29B, COR78 and other structural genes, indicating that VaMyb14 has the capacity to reprogram a significant signaling pathway. Furthermore, comparative mRNA sequencing profiling of 35S:VaMyb14 grapevine callus indicated its involvement its function involved in ROS scavenging and ABA signaling. These findings collectively demonstrate that Vitis Myb14 serves as a critical regulator in grapevine stress responses, contributing to improved defense against necrotrophic pathogens, enhanced phytoalexin resveratrol production, and increased drought or cold tolerance.

Phenotypic flexibility in metabolic adjustments and digestive function in white-shouldered starlings: responses to short-term temperature acclimation

Changing the intrinsic rate of metabolic heat production is the main adaptive strategy for small birds to cope with different ambient temperatures. In this study, we tested the hypothesis that the small passerine the white-shouldered starling (Sturnus sinensis) can modulate basal metabolism under temperature acclimation by changing the morphological, physiological and biochemical state of its tissues and organs. We measured the effects of temperature on body mass, basal metabolic rate (BMR), wet mass of various internal organs, state 4 respiration (S4R) and cytochrome c oxidase (CCO) activity in the pectoral muscle and organs, metabolites in the pectoral muscle, energy intake, histological dynamics and the activity of duodenal digestive enzymes. Warm acclimation decreased BMR to a greater extent than cold acclimation. At the organ level, birds in the cold-acclimated group had significantly heavier intestines but significantly lighter pectoral muscles. At the cellular level, birds in the cold-acclimated group showed significantly higher S4R in the liver and heart and CCO activity in the liver and kidney at both the mass-specific and whole-organ levels. A metabolomic analysis of the pectoral tissue revealed significantly higher lipid decomposition, amino acid degradation, ATP hydrolysis, and GTP and biotin synthesis in cold-acclimated birds. Acclimation to cold significantly increased the gross energy intake (GEI), feces energy (FE) and digestive energy intake (DEI) but significantly decreased the digestive efficiency of these birds. Furthermore, cold-acclimated birds had a higher maltase activity and longer villi in the duodenum. Taken together, these data show that white-shouldered starlings exhibit high phenotypic flexibility in metabolic adjustments and digestive function under temperature acclimation, consistent with the notion that small birds cope with the energy challenges presented by a cold environment by modulating tissue function in a way that would affect BMR.

Over-activation of cold tolerance in arabidopsis causes carbohydrate shortage compared with Chorispora bungeana

Many plants cope with cold stress by developing acquired freezing tolerance (AFT) through cold acclimation (CA), and some species have strong basal freezing tolerance (BFT) independent of CA. Although CA has been extensively studied, its potential in agricultural applications is still unclear. Here, carbohydrate metabolism and transcriptome in AFT plant Arabidopsis and BFT plant Chorispora bungeana were compared with each other. The results showed that, although both species were able to accumulate soluble sugars during CA, leaf starch accumulation in the daytime was almost blocked in Arabidopsis while it was greatly enhanced in C. bungeana, revealing that Arabidopsis experienced carbohydrate shortage during CA. Transcriptome and pathway enrichment analysis found that genes for photosynthesis antenna proteins were generally repressed by cold stress in both species. However, cold-up-regulated genes were enriched in protein translation in Arabidopsis, whilst they were enriched in carotenoid biosynthesis, flavonoid biosynthesis, and beta-amylases in C. bungeana. Furthermore, weighted gene co-expression network analysis (WGCNA) showed that the inhibition of starch accumulation was associated with down-regulation of genes for photosynthesis antenna proteins and up-regulation of genes for protein translation, DNA repair, and proteasome in Arabidopsis but not in C. bungeana. Taken together, our results revealed that over-activation of common tolerant mechanisms resulted in insufficient carbohydrate supplies in Arabidopsis during CA, and photoprotective mechanisms played important roles in cold adaptation of C. bungeana. These findings uncovered the drawback of CA in improving freezing tolerance and highlighted photoprotection as a possible solution for agricultural applications.

Maintenance of xylem hydraulic function during winter in the woody bamboo Phyllostachys propinqua McClure

Background

Frost is a common environmental stress for temperate plants. Xylem embolism occurs in many overwintering plants due to freeze-thaw cycles, so coping with freeze-thaw-induced embolisms is essential for the survival of temperate plants.

Methods

This study was conducted on Phyllostachys propinqua McClure, a woody bamboo species that was grown under natural frost conditions to explore its responses to winter embolisms. From autumn to the following spring, the following measurements were recorded: predawn branch and leaf embolism, branch and leaf relative water content (RWC), root pressure and soil temperature, xylem sap osmotic potential, branch and leaf electrolyte leakage (EL), branch nonstructural carbohydrate (NSC) content and leaf net photosynthetic rate.

Results

P. propinqua had a mean vessel diameter of 68.95 ±1.27 µm but did not suffer severe winter embolism, peaking around  60% in winter (January), with a distinct reduction in March when root pressure returned. Leaves had a more severe winter embolism, up to 90%. Leaf RWC was much lower in winter, and leaf EL was significantly higher than branch EL in all seasons. Root pressure remained until November when soil temperature reached 9 °C, then appeared again in March when soil temperatures increased from -6 °C (January) to 11 °C. Xylem sap osmotic potential decreased from autumn to winter, reaching a minimum in March, and then increasing again. Soluble sugar (SS) concentration increased throughout the winter, peaked in March, and then decreased.

Conclusions

These results suggest that (1) there is a hydraulic segmentation between the stem and leaf, which could prevent stem water loss and further embolization in winter; (2) maintenance of root pressure in early winter played an important role in reducing the effect of freeze-thaw cycles on the winter embolism; (3) the physiological process that resulted in a decrease in xylem sap osmotic potential and tissue water content, and an accumulation of SS associated with cold acclimation also aided in reducing the extent of freeze-thaw-induced embolism. All these strategies could be helpful for the maintenance of xylem hydraulic function of this bamboo species during winter.

Plant transcriptional memory and associated mechanism of abiotic stress tolerance

Plants face various adverse environmental conditions, particularly with the ongoing changes in global climate, which drastically affect the growth, development and productivity of crops. To cope with these stresses, plants have evolved complex mechanisms, and one of the crucial ways is to develop transcriptional memories from stress exposure. This induced learning enables plants to better and more strongly restart the response and adaptation mechanism to stress when similar or dissimilar stresses reoccur. Understanding the molecular mechanism behind plant transcriptional memory of stress can provide a theoretical basis for breeding stress-tolerant crops with resilience to future climates. Here we review the recent research progress on the transcriptional memory of plants under various stresses and the applications of underlying mechanisms for sustainable agricultural production. We propose that a thorough understanding of plant transcriptional memory is crucial for both agronomic management and resistant breeding, and thus may help to improve agricultural yield and quality under changing climatic conditions.

Molecular and genetic perspectives of cold tolerance in wheat

Environmental variation is the most crucial problem as it is causing food insecurity and negatively impacts food availability, utilization, assessment, and stability. Wheat is the largest and extensively cultivated staple food crop for fulfilling global food requirements. Abiotic stresses including salinity, heavy metal toxicity, drought, extreme temperatures, and oxidative stresses being the primary cause of productivity loss are a serious threat to agronomy. Cold stress is a foremost ecological constraint that is extremely influencing plant development, and yield. It is extremely hampering the propagative development of plant life. The structure and function of plant cells depend on the cell's immune system. The stresses due to cold, affect fluid in the plasma membrane and change it into crystals or a solid gel phase. Plants being sessile in nature have evolved progressive systems that permit them to acclimatize the cold stress at the physiological as well as molecular levels. The phenomenon of acclimatisation of plants to cold stress has been investigated for the last 10 years. Studying cold tolerance is critical for extending the adaptability zones of perennial grasses. In the present review, we have elaborated the current improvement of cold tolerance in plants from molecular and physiological viewpoints, such as hormones, the role of the posttranscriptional gene, micro RNAs, ICE-CBF-COR signaling route in cold acclimatization and how they are stimulating the expression of underlying genes encoding osmoregulatory elements and strategies to improve cold tolerance in wheat.

Phospholipid:diacylglycerol acyltransferase1-overexpression stimulates lipid turnover, oil production and fitness in cold-grown plants

BACKGROUND

Extensive population growth and climate change accelerate the search for alternative ways of plant-based biomass, biofuel and feed production. Here, we focus on hitherto unknow, new promising cold-stimulated function of phospholipid:diacylglycerol acyltransferase1 (PDAT1) - an enzyme catalyzing the last step of triacylglycerol (TAG) biosynthesis.

RESULT

Overexpression of AtPDAT1 boosted seed yield by 160% in Arabidopsis plants exposed to long-term cold compared to standard conditions. Such seeds increased both their weight and acyl-lipids content. This work also elucidates PDAT1's role in leaves, which was previously unclear. Aerial parts of AtPDAT1-overexpressing plants were characterized by accelerated growth at early and vegetative stages of development and by biomass weighing three times more than control. Overexpression of PDAT1 increased the expression of SUGAR-DEPENDENT1 (SDP1) TAG lipase and enhanced lipid remodeling, driving lipid turnover and influencing biomass increment. This effect was especially pronounced in cold conditions, where the elevated synergistic expression of PDAT1 and SDP1 resulted in double biomass increase compared to standard conditions. Elevated phospholipid remodeling also enhanced autophagy flux in AtPDAT1-overexpresing lines subjected to cold, despite the overall diminished autophagy intensity in cold conditions.

CONCLUSIONS

Our data suggest that PDAT1 promotes greater vitality in cold-exposed plants, stimulates their longevity and boosts oilseed oil production at low temperature.

Thermo-TRP channels are involved in BAT thermoregulation in cold-acclimated Brandt's voles

Transient receptor potential (TRP) channels, which can sense temperature, pressure and mechanical stimuli, were involved in many physiological and biochemical reactions. Whether thermosensitive TRP channels (Thermo-TRPs) are involved in thermoregulation in small mammals is still not clear. We measured the changes of thermo-TRPs at 4 °C, 23 °C and 30 °C in Brandt's voles (Lasiopodomys brandtii) to test the hypothesis that Thermo-TRPs are involved in cold-induced thermogenesis of brown adipose tissue (BAT) in small mammals. Results showed that air temperatures had no effect on body mass and rectal temperature, but the food intake and basal metabolic rate (BMR) in the 4 °C group were significantly higher than in the 30 °C group. Compared with 30 °C group, the protein contents of uncoupling protein 1(UCP1), TRP vanilloid 2 (TRPV2), TRP ankyrin 1 (TRPA1), TRP melastatin 2 (TRPM2), silent Information Regulator T1 (SIRT1), AMP-activated protein kinase (AMPK) and Calcium/calmodulin-dependent protein kinase II (CaMKII) in BAT increased significantly in 4 °C group, but there was no significant difference in the protein content of Thermo-TRPs in the hypothalamus among groups. Further, the expression of PRDM16 (PR domain containing 16) in inguinal white adipose tissue (iWAT) at 4 °C was significantly higher than that at 30 °C, but no difference was observed in the expression of other browning-related genes or TRPV2. In conclusion, TRP channels may participate in BAT thermoregulation through the CaMKII, AMPK, SIRT1 and UCP1 pathway in cold-acclimated Brandt's voles.

Characterization and expression analysis of basic leucine zipper (bZIP) transcription factors responsive to chilling injury in peach fruit

BACKGROUND

Peach (Prunus persica L.) is prone to chilling injury as exhibited by inhibition of the ethylene production, failure in softening, and the manifestation of internal browning. The basic leucine zipper (bZIP) transcription factors play an essential role in regulatory networks that control many processes associated with physiological, abiotic and biotic stress responses in fruits. Formerly, the underlying molecular and regulatory mechanism of (bZIP) transcription factors responsive to chilling injury in peach fruit is still elusive.

METHODS AND RESULTS

In the current experiment, the solute peach 'Zhongyou Peach No. 13' was used as the test material and cold storage at low temperature (4 °C). It was found that long-term low-temperature storage induced the production of ethylene, the hardness of the pulp decreased, and the low temperature also induced ABA accumulation. The changes of ABA and ethylene in peach fruits during low-temperature storage were clarified. Since the bZIP transcription factor is involved in the regulation of downstream pathways of ABA signals, 47 peach bZIP transcription factor family genes were identified through bioinformatics analysis. Further based on RT-qPCR analysis, 18 PpbZIP genes were discovered to be expressed in refrigerated peach fruits. Among them, the expression of PpbZIP23 and PpbZIP25 was significantly reduced during the refrigeration process, the promoter analysis of these genes found that this region contains the MYC/MYB/ABRES binding element, but not the DRES/CBFS element, indicating that the expression may be regulated by the ABA-dependent cold induction pathway, thereby responding to chilling injury in peach fruit.

CONCLUSIONS

Over investigation will provide new insights for further postharvest protocols related to molecular changes during cold storage and will prove a better cope for chilling injury.

A comparative transcriptomic analysis reveals a coordinated mechanism activated in response to cold acclimation in common vetch (Vicia sativa L.)

BACKGROUND

Due to its strong abiotic stress tolerance, common vetch is widely cultivated as a green manure and forage crop in grass and crop rotation systems. The comprehensive molecular mechanisms activated in common vetch during cold adaptation remain unknown.

RESULTS

We investigated physiological responses and transcriptome profiles of cold-sensitive (Lanjian No. 1) and cold-tolerant (Lanjian No. 3) cultivars during cold acclimation to explore the molecular mechanisms of cold acclimation. In total, 2681 and 2352 differentially expressed genes (DEGs) were identified in Lanjian No. 1 and Lanjian No. 3, respectively; 7532 DEGs were identified in both lines. DEGs involved in "plant hormone signal transduction" were significantly enriched during cold treatment, and 115 DEGs involved in cold-processed hormone signal transduction were identified. Common vetch increased the level of indoleacetic acid (IAA) by upregulating the transcriptional regulator Aux/IAA and downregulating GH3, endowing it with stronger cold tolerance. An auxin-related DEG was overexpressed in yeast and shown to possess a biological function conferring cold tolerance.

CONCLUSION

This study identifies specific genes involved in Ca²⁺ signaling, redox regulation, circadian clock, plant hormones, and transcription factors whose transcriptional differentiation during cold acclimation may improve cold tolerance and contributes to the understanding of common and unique molecular mechanisms of cold acclimation in common vetch. The candidate genes identified here also provide valuable resources for further functional genomic and breeding studies.

CROP PRODUCTION UNDER COLD STRESS: An understanding of plant responses, acclimation processes, and management strategies

In the context of climate change, the magnitude and frequency of temperature extremes (low and high temperatures) are increasing worldwide. Changes to the lower extremes of temperature, known as cold stress (CS), are one of the recurrent stressors in many parts of the world, severely limiting agricultural production. A series of plant reactions to CS could be generalized into morphological, physiological, and biochemical responses based on commonalities among crop plants. However, the differing originality of crops revealed varying degrees of sensitivity to cold and, therefore, exhibited large differences in these responses among the crops. This review discusses the vegetative and reproductive growth effects of CS and highlights the species-specific aspect of each growth stage whereby the reproductive growth CS appears more detrimental in rice and wheat, with marginal yield losses. To mitigate CS negative effects, crop plants have evolved cold-acclimation mechanisms (with differing capability), characterized by specific protein accumulation, membrane modification, regulation of signaling pathways, osmotic regulation, and induction of endogenous hormones. In addition, we reviewed a comprehensive account of management strategies for regulating tolerance mechanisms of crop plants under CS.

Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) family genes in tea plant

Background

As a type of calmodulin binding protein, CAMTAs are widely involved in vegetative and reproductive processes as well as various hormonal and stress responses in plants. To study the functions of CAMTA genes in tea plants, we investigated bioinformatics analysis and performed qRT-PCR analysis of the CAMTA gene family by using the genomes of ‘ShuChaZao’ tea plant cultivar.

Results

In this study, 6 CsCAMTAs were identified from tea plant genome. Bioinformatics analysis results showed that all CsCAMTAs contained six highly conserved functional domains. Tissue-specific analysis results found that CsCAMTAs played great roles in mediating tea plant aging and flowering periods. Under hormone and abiotic stress conditions, most CsCAMTAs were upregulated at different time points under different treatment conditions. In addition, the expression levels of CsCAMTA1/3/4/6 were higher in cold-resistant cultivar ‘LongJing43’ than in the cold-susceptible cultivar ‘DaMianBai’ at cold acclimation stage, while CsCAMTA2/5 showed higher expression levels in ‘DaMianBai’ than in ‘LongJing43’ during entire cold acclimation periods.

Conclusions

In brief, the present results revealed that CsCAMTAs played great roles in tea plant growth, development and stress responses, which laid the foundation for deeply exploring their molecular regulation mechanisms.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08894-x.

Iso-Seq and RNA-Seq analyses uncover the molecular response of Dalbergia odorifera T. Chen to low temperature

In previous studies, we found young plants propagated from acclimated D. odorifera T. Chen trees displayed increased cold tolerance. To understand the molecular and physiological mechanisms underlying this phenomenon, we prepared acclimated and non-acclimated young D. odorifera T. Chen trees for physiological, RNA-Seq, and Iso-Seq analyses. First, both the acclimated and non-acclimated young trees were grown in 10 ℃ condition, then treated at -3 ℃ for one day, and finally recovered at 10 ℃. The measurement of physiological parameters, including superoxide dismutase, peroxidase, malondialdehyde, thiobarbituric acid, and soluble sugar, showed that the physiological change of acclimated plants is smoother than non-acclimated plants. The RNA-Seq analyses pointed out that cold acclimation already fixed the different gene expression patterns of D. odorifera T. Chen trees. The hormone-related, secondary metabolic, and signal transduction related biological genes tend to show different expressions between the acclimated and non-acclimated D. odorifera T. Chen trees. Moreover, the change of gene expression for some biological processes, such as alpha-Linolenic acid metabolism and its response to hydrogen peroxide, seems to occur earlier in non-acclimated than acclimated plants. The ISO-Seq analyses pointed out that alternative splicing (AS) of some genes was also found, and these AS events were predicted to play important roles in regulating different expression patterns between non-acclimated and acclimated plants. Therefore, according to the performance of this study, we are able to provide some novel understanding of cold tolerance enhanced by cold acclimation in perennial trees.

How does mitochondrial function relate to thermogenic capacity and basal metabolic rate in small birds?

We investigated the role of mitochondrial function in the avian thermoregulatory response to a cold environment. Using black-capped chickadees (Poecile atricapillus) acclimated to cold (-10°C) and thermoneutral (27°C) temperatures, we expected to observe an upregulation of pectoralis muscle and liver respiratory capacity that would be visible in mitochondrial adjustments in cold-acclimated birds. We also predicted that these adjustments would correlate with thermogenic capacity (Msum) and basal metabolic rate (BMR). Using tissue high-resolution respirometry, mitochondrial performance was measured as respiration rate triggered by proton leak and the activity of complex I (OXPHOSCI) and complex I+II (OXPHOSCI+CII) in the liver and pectoralis muscle. The activity of citrate synthase (CS) and cytochrome c oxidase (CCO) was also used as a marker of mitochondrial density. We found 20% higher total CS activity in the whole pectoralis muscle and 39% higher total CCO activity in the whole liver of cold-acclimated chickadees relative to that of birds kept at thermoneutrality. This indicates that cold acclimation increased overall aerobic capacity of these tissues. Msum correlated positively with mitochondrial proton leak in the muscle of cold-acclimated birds while BMR correlated with OXPHOSCI in the liver with a pattern that differed between treatments. Consequently, this study revealed a divergence in mitochondrial metabolism between thermal acclimation states in birds. Some functions of the mitochondria covary with thermogenic capacity and basal maintenance costs in patterns that are dependent on temperature and body mass.

Temperature-phase transcriptomics reveals that hormones and sugars in the phloem of grape participate in tolerance during cold acclimation

Most of the upregulated genes contributed to the accumulation of soluble sugars and ABA in the phloem of 'Vitis amurensis' compared to 'Merlot' during cold acclimation. Extreme cold is one of the dominant abiotic factors affecting grape yield and quality. However, the changes in sugars, phytohormones, and gene expression in the branch phloem of different tolerant grape varieties during cold acclimation remain elusive. The data supported that with decreasing temperature, the contents of fructose, sucrose, and ABA in the phloem of Vitis amurensis (cold-tolerant, T) and 'Merlot' (cold-sensitive, S) increased during cold acclimation, and these indicators were higher in T than in S. Furthermore, the activities of sucrose synthetase, sucrose phosphate synthetase, and acid invertase peaked in the early phase of cold acclimation (approximately 5 °C) compared to other phases (approximately 28 °C, 0 °C, - 5 °C and - 10 °C). Moreover, the RNA sequencing results helped identify a total of 11,343 differentially expressed genes in the phloem of T and S, among which 4912 were upregulated and 6431 were downregulated. In the abscisic acid pathway, CRTISO, PSPY1-1, CYCP707A4-2, PYL4-1, PYL4-2, P2C08, SAPK2, TARAB1, and DBF3 were more highly expressed in T than in S. In the starch and sucrose metabolism pathway, HXK1, PGMP, GLGL1, SUS6, VCINV, BGL11, SSY1, GPS, BAM1 and BAM3 were also more highly expressed in T than in S. Moreover, the genes related to oxidative phosphorylation, such as NDHF, ND4, ND1, NAD7, NAD2, ATPB, YMF19, ATP9, PMA1 and AHA8, were upregulated in T. These results will be beneficial for understanding the potential differences in tolerance across two different cold-tolerant grapes with respect to sugar metabolism and gene expression.

Transcriptome sequencing reveals the differentially expressed lncRNAs and mRNAs in response to cold acclimation and cold stress in Pomacea canaliculata

Background

Tolerance of low temperature has a significant impact on survival and expansion of invasive snail Pomacea canalicuata. Cold acclimation can enhance cold tolerance of Pomacea canalicuata. To elucidate the molecular mechanism of P. canaliculata’s responses to cold acclimation and cold stress, a high-throughput transcriptome analysis of P. canaliculata was performed, and gene expression following artificial cold acclimation and then cold stress at 0 °C for 24 h was compared using RNA sequencing.

Results

Using the Illumina platform, we obtained 151.59 G subreads. A total of 5,416 novel lncRNAs were identified, and 3166 differentially expressed mRNAs and 211 differentially expressed lncRNAs were screened with stringent thresholds. The potential antisense, cis and trans targets of lncRNAs were predicted. Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that many target genes were involved in proteasome, linoleic acid metabolism and retinol metabolism under cold acclimation. The lncRNA of P. canaliculata could participate in cold acclimation by regulating the expression of E3 ubiquitin protein ligase, 26S proteasome non-ATPase dependent regulation subunit, glutathione S-transferase, sodium/glucose cotransporter and cytochrome P450.

Conclusions

These results broaden our understanding of cold acclimation and cold stress associated lncRNAs and mRNAs, and provide new insights into lncRNA mediated regulation of P. canaliculata cold acclimation and cold stress response.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08622-5.

Genome-wide identification of CBF genes and their responses to cold acclimation in Taraxacum kok-saghyz

C-repeat binding factors (CBFs) are transcription factors that are known to play important roles in plant cold acclimation. They are highly conserved in most higher plants. Taraxacum kok-saghyz (TKS) is an herb native to China and Kazakhstan and is well-known for its production of rubber silk with industrial and economic value. To understand cold acclimation mechanisms, we conducted a genome-wide discovery of the CBF family genes in TKS and revealed ten CBF genes. A bioinformatic analysis of the CBF genes was carried out to analyze the phylogenetic relationship, protein conservative motifs, protein physicochemical properties, gene structure, promoter cis-acting elements, and the gene expression patterns under cold acclimation and control conditions. It was found that most of these genes were highly responsive at the late stage of cold acclimation, indicating that they play important roles in the cold acclimation processes of TKS. This study provides a theoretical basis for the study of the molecular functions of the CBF gene family in TKS, and a useful guidance for the genetic improvement of the cold tolerance traits of TKS and other plants, including crops.

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.

Responses of the Plant Cell Wall to Sub-Zero Temperatures: A Brief Update

Our general understanding of plant responses to sub-zero temperatures focuses on mechanisms that mitigate stress to the plasma membrane. The plant cell wall receives comparatively less attention, and questions surrounding its role in mitigating freezing injury remain unresolved. Despite recent molecular discoveries that provide insight into acclimation responses, the goal of reducing freezing injury in herbaceous and woody crops remains elusive. This is likely due to the complexity associated with adaptations to low temperatures. Understanding how leaf cell walls of herbaceous annuals promote tissue tolerance to ice does not necessarily lead to understanding how meristematic tissues are protected from freezing by tissue-level barriers formed by cell walls in overwintering tree buds. In this mini-review, we provide an overview of biological ice nucleation and explain how plants control the spatiotemporal location of ice formation. We discuss how sugars and pectin side chains alleviate adhesive injury that develops at sub-zero temperatures between the matrix polysaccharides and ice. The importance of site-specific cell-wall elasticity to promote tissue expansion for ice accommodation and control of porosity to impede ice growth and promote supercooling will be presented. How specific cold-induced proteins modify plant cell walls to mitigate freezing injury will also be discussed. The opinions presented in this report emphasize the importance of a plant's developmental physiology when characterizing mechanisms of freezing survival.

Genome-wide identification and functional analysis of the glutathione S-transferase (GST) family in Pomacea canaliculata

Cold causes oxidative stress in living organisms, mainly caused by the accumulation of reactive oxygen species (ROS). In the antioxidant defense systems, Glutathione S-transferases (GSTs) play a vital role in the regulation of detoxification and redox balance of ROS. In this study, the P. canaliculata GST gene family were characterized using a genome-wide search of the conserved domain. Phylogenetic tree and domain composition analysis revealed that 30 PcGSTs belong to seven classes, including five in MAPEG, two in Mu, nine in Omega, 11 in Sigma, one in Rho, Theta and Alpha class, respectively. RNA-seq analysis revealed that most PcGSTs localized in mitochondria highly expressed in hepatopancreas, and most PcGSTs localized in cytoplasm highly expressed in kidney. A total of 12 PcGST genes were significantly up-regulated and PcGST12 was significantly down-regulated after cold acclimation. Ten PcGSTs were identified as DEGs under cold stress after cold acclimation. qRT-PCR revealed that the expression level of five PcGST genes were significantly varied during the cold acclimation. The present study investigated the characterization of the P. canaliculata GST gene family, extending our understanding of GST mediated cold acclimation and cold stress-response mechanisms in this invasive snail.

Physiological and biochemical responses of strawberry crown and leaf tissues to freezing stress

BACKGROUND

In northern Iran and other cold regions, winter freezing injury and resultant yield instability are major limitations to strawberry production. However, there is scarcity of information on the physiological and biochemical responses of strawberry cultivars to freezing stress. This study aimed to investigate the physiological and biochemical responses of strawberry cultivars (Tennessee Beauty, Blakemore, Kurdistan, Queen Elisa, Chandler, Krasnyy Bereg, and Yalova) to different freezing temperature treatments (- 5, - 10, - 15, - 20, and - 25 °C) under controlled conditions.

RESULTS

All measured physiological and biochemical features were significantly affected by the interaction effect between low temperatures and cultivars. Tennessee Beauty showed the highest RWC at - 25 °C. The highest Fv/Fm was observed in Queen Elisa. Krasnyy Bereg had the least freezing injury (FI) in crown and leaf, while Yalova and Chandler showed the highest crown and leaf FI, respectively. At - 20 to - 25 °C, the highest carbohydrates contents of crown and leaf were noted in Blakemore and Krasnyy Bereg cultivars, respectively. The Yalova showed the highest protein content in both crown and leaf tissues at - 25 °C. The Tennessee Beauty and Blackmore cultivars showed the highest proline in crowns and leaves at - 15 °C, respectively. The highest ThioBarbituric Acid Reactive Substances (TBARS) contents in the crown and leaf were observed in Kurdistan and Queen Elisa, respectively. Queen Elisa and Krasnyy Bereg cultivars showed SOD and POD peaks in the crown at - 15 °C, respectively.

CONCLUSION

Freezing stress was characterized by decreased Fv/Fm and RWC, and increased FI, TBARS, total carbohydrates, total proteins, proline content, and antioxidant enzyme activity. The extent of changes in above mentioned traits was cultivar dependent. FI and TBARS were the best traits among destructive parameters for evaluating freezing tolerance. Moreover, maximum quantum yield of PSII (Fv/Fm index), as non-destructive parameters, showed a significant efficiency in rapid assessment for screening of freezing tolerant strawberry cultivars. The cultivars Krasnyy Bereg, Queen Elisa, and Kurdistan were the most tolerant cultivars to freezing stress. These cultivars can be used as parents in breeding programs to develop new freezing tolerant cultivars.

Temporal expression study of miRNAs in the crown tissues of winter wheat grown under natural growth conditions

BACKGROUND

Winter wheat requires prolonged exposure to low temperature to initiate flowering (vernalization). Shoot apical meristem of the crown is the site of cold perception, which produces leaf primordia during vegetative growth before developing into floral primordia at the initiation of the reproductive phase. Although many essential genes for winter wheat cold acclimation and floral initiation have been revealed, the importance of microRNA (miRNA) meditated post-transcriptional regulation in crowns is not well understood. To understand the potential roles of miRNAs in crown tissues, we performed a temporal expression study of miRNAs in crown tissues at the three-leaf stage, winter dormancy stage, spring green-up stage, and jointing stage of winter wheat grown under natural growth conditions.

RESULTS

In total, 348 miRNAs belonging to 298 miRNA families, were identified in wheat crown tissues. Among them, 92 differentially expressed miRNAs (DEMs) were found to be significantly regulated from the three-leaf stage to the jointing stage. Most of these DEMs were highly expressed at the three-leaf stage and winter dormancy stage, and then declined in later stages. Six DEMs, including miR156a-5p were markedly induced during the winter dormancy stage. Eleven DEMs, including miR159a.1, miR390a-5p, miR393-5p, miR160a-5p, and miR1436, were highly expressed at the green-up stage. Twelve DEMs, such as miR172a-5p, miR394a, miR319b-3p, and miR9676-5p were highly induced at the jointing stage. Moreover, 14 novel target genes of nine wheat or Pooideae-specific miRNAs were verified using RLM-5' RACE assay. Notably, six mTERFs and two Rf1 genes, which are associated with mitochondrial gene expression, were confirmed as targets of three wheat-specific miRNAs.

CONCLUSIONS

The present study not only confirmed the known miRNAs associated with phase transition and floral development, but also identified a number of wheat or Pooideae-specific miRNAs critical for winter wheat cold acclimation and floral development. Most importantly, this study provided experimental evidence that miRNA could regulate mitochondrial gene expression by targeting mTERF and Rf1 genes. Our study provides valuable information for further exploration of the mechanism of miRNA mediated post-transcriptional regulation during winter wheat vernalization and inflorescent initiation.

Winter survival of the unicellular green alga Micrasterias denticulata: insights from field monitoring and simulation experiments

Peat bog pools around Tamsweg (Lungau, Austria) are typical habitats of the unicellular green alga Micrasterias denticulata. By measurement of water temperature and irradiation throughout a 1-year period (2018/2019), it was intended to assess the natural environmental strain in winter. Freezing resistance of Micrasterias cells and their ability to frost harden and become tolerant to ice encasement were determined after natural hardening and exposure to a cold acclimation treatment that simulated the natural temperature decrease in autumn. Transmission electron microscopy (TEM) was performed in laboratory-cultivated cells, after artificial cold acclimation treatment and in cells collected from field. Throughout winter, the peat bog pools inhabited by Micrasterias remained unfrozen. Despite air temperature minima down to -17.3 °C, the water temperature was mostly close to +0.8 °C. The alga was unable to frost harden, and upon ice encasement, the cells showed successive frost damage. Despite an unchanged freezing stress tolerance, significant ultrastructural changes were observed in field-sampled cells and in response to the artificial cold acclimation treatment: organelles such as the endoplasmic reticulum and thylakoids of the chloroplast showed distinct membrane bloating. Still, in the field samples, the Golgi apparatus appeared in an impeccable condition, and multivesicular bodies were less frequently observed suggesting a lower overall stress strain. The observed ultrastructural changes in winter and after cold acclimation are interpreted as cytological adjustments to winter or a resting state but are not related to frost hardening as Micrasterias cells were unable to improve their freezing stress tolerance.

Monitoring Seasonal Bud Set, Bud Burst, and Cold Hardiness in Populus

Using a perennial model plant allows the study of reoccurring seasonal events in a way that is not possible using a fast-growing annual such as A. thaliana (Arabidopsis). In this study, we present a hybrid aspen (Populus tremula × P. tremuloides) as our perennial model plant. These plants can be grown in growth chambers to shorten growth periods and manipulate day length and temperature in ways that would be impossible under natural conditions. In addition, the use of growth chambers allows easy monitoring of height and diameter expansion, accelerating the collection of data from new strategies that allow evaluation of promoters or inhibitors of growth. Here, we describe how to study and quantify responses to seasonal changes (mainly using P. tremula × P. tremuloides) by measuring growth rate and key events under different photoperiodic cycles.

Transcriptional memory and response to adverse temperatures in plants

Temperature is one of the major environmental signals controlling plant development, geographical distribution, and seasonal behavior. Plants perceive adverse temperatures, such as high, low, and freezing temperatures, as stressful signals that can cause physiological defects and even death. As sessile organisms, plants have evolved sophisticated mechanisms to adapt to recurring stressful environments through changing gene expression or transcriptional reprogramming. Transcriptional memory refers to the ability of primed plants to remember previously experienced stress and acquire enhanced tolerance to similar or different stresses. Epigenetic modifications mediate transcriptional memory and play a key role in adapting to adverse temperatures. Understanding the mechanisms of the formation, maintenance, and resetting of stress-induced transcriptional memory will not only enable us to understand why there is a trade-off between plant defense and growth, but also provide a theoretical basis for generating stress-tolerant crops optimized for future climate change. In this review, we summarize recent advances in dissecting the mechanisms of plant transcriptional memory in response to adverse temperatures, based mainly on studies of the model plant Arabidopsis thaliana. We also discuss remaining questions that are important for further understanding the mechanisms of transcriptional memory during the adverse temperature response.

Physiological and transcriptome analysis of Magnolia denudata leaf buds during long-term cold acclimation

BACKGROUND

Magonlia denudata is an important perennial tree species of the Magnoliaceae family, known for its ornamental value, resistance to smoke pollution and wind, role in air purification, and robust cold tolerance. In this study, a high-throughput transcriptome analysis of leaf buds was performed, and gene expression following artificial acclimation 22 °C, 4 °C and 0 °C, was compared by RNA sequencing.

RESULTS

Over 426 million clean reads were produced from three libraries (22 °C, 4 °C and 0 °C). A total of 74,503 non-redundant unigenes were generated, with an average length of 1173.7 bp (N50 = 1548). Based on transcriptional results, 357 and 235 unigenes were identified as being upregulated and downregulated under cold stress conditions, respectively. Differentially expressed genes were annotated using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway analyses. The transcriptomic analysis focused on carbon metabolism and plant hormone signal transduction associated with cold acclimation. Transcription factors such as those in the basic helix-loop-helix and AP2/ERF families were found to play an important role in M. denudata cold acclimation.

CONCLUSION

M. denudata exhibits responses to non-freezing cold temperature (4 °C) to increase its cold tolerance. Cold resistance was further strengthened with cold acclimation under freezing conditions (0 °C). Cold tolerance genes, and cold signaling transcriptional pathways, and potential functional key components for the regulation of the cold response were identified in M. denudata. These results provide a basis for further studies, and the verification of key genes involved in cold acclimation responses in M. denudata lays a foundation for developing breeding programs for Magnoliaceae species.

Proteome analysis reveals a systematic response of cold-acclimated seedlings of an exotic mangrove plant Sonneratia apetala to chilling stress

Low temperature in winter was the most crucial abiotic stress that limits the mangrove afforestation northward. Previous study demonstrated that Sonneratia apetala initially transplanted to high latitude area exhibited a stronger plasticity of cold tolerance. To clarify the underlying mechanism, the physiological and proteomic responses to chilling stress were investigated in S. apetala leaves. Our results found that cold-acclimated seedlings had lower relative electrolyte leakage and MDA content than non-acclimated seedlings. On the contrary, higher chlorophyll content and photosynthetic capacity were observed in cold-acclimated seedlings. With proteomic analyses, the differentially accumulated proteins (DAPs) involved in ROS scavenging, photosynthesis and energy metabolism, carbohydrate metabolism, cofactor biosynthesis, and protein folding were suggested to play important roles in enhancing the cold tolerance of S. apetala. However, the down-regulation DAPs were suggested as a tradeoff between plant growth and chilling response. By the protein-protein interaction analyses, translation elongation factor G, chlorophyll A-B binding protein and ascorbate peroxidase 1 were suggested as the important regulators in cold-acclimated S. apetala seedlings under chilling stress. Based on the above results, a schematic diagram describing the mechanism of cold tolerance of exotic mangrove species S. apetala that was achieved by cold acclimation was presented in this study. SIGNIFICANCE: The major environmental factor limits the mangrove afforestation northward is the low temperature in winter. Previous study reported that Sonneratia apetala grew in high latitude exhibited a higher cold tolerance than that in low latitude, which was suggested as a result of cold acclimation. To further understand "how cold acclimation enhance the cold tolerance in S. apetala", the response of S. apetala subjected to chilling stress with or without cold acclimation was investigated in this study at the physiological and proteomic aspects. Our physiological results showed that S. apetala seedlings treated with cold acclimation exhibited a higher tolerance under chilling stress than that without cold acclimation. By using the comparative proteomic approaches and bioinformatic analyses, various biological processes were suggested to play an important role in enhancing the cold tolerance of S. apetala under chilling stress, such as ROS scavenging, photosynthesis and energy metabolism, carbohydrate metabolism, cofactor biosynthesis, and protein folding. Among these differentially accumulated proteins, translation elongation factor G (eEF-G), chlorophyll A-B binding protein (CAB) and ascorbate peroxidase 1 (APX1) were identified as the hub proteins function in coordinated regulating ROS scavenging, photosynthesis and protein biosynthesis in chloroplast and subsequently enhanced the cold tolerance of S. apetala under chilling stress. Our results provided a further understanding of cold acclimation in improving the cold tolerance in exotic mangrove species S. apetala.

The effect of long-term cold acclimation on redox state and antioxidant defense in the high-altitude frog, Nanorana pleskei

Cold hardiness is a key determinant of the distribution and abundance of ectothermic animals, and thermal acclimation can strongly influence stress tolerance phenotypes. However, the effect of cold acclimation on oxidative stress and antioxidant defenses is still not well understood. Here, we investigated the effects of long-term cold exposure (30 days at 4 °C in darkness versus 30 days at 20 °C in natural light) on the redox state and antioxidant defenses of the high-altitude frog, Nanorana pleskei, indigenous to the Tibetan plateau. We found that cold acclimation, under conditions mimicking winter, led to a significant increase in the ratio of oxidized glutathione (GSSG) to its reduced form (GSH) in liver and skeletal muscle tissues, suggesting that cold exposure induced oxidative stress in this species. Furthermore, malondialdehyde (MDA) contents were significantly augmented in heart, liver and muscle, indicating cold-related oxidative damage in these tissues. In the brain, GST activity, total antioxidant capacity (T-AOC), and vitamin C content showed a significant reduction after cold acclimation. In liver, an apparent decrease was also observed in the activities of SOD and GST, as well as T-AOC, whereas CAT and GPX activities showed a prominent increase in cold-acclimated groups. In kidney, there was a significant decrease in most antioxidant enzyme activities except for SOD and GST activity. In skeletal muscle, the activity of SOD, CAT, GR as well as T-AOC significantly decreased but GPX activity showed a significant increase in cold-acclimated frogs. These findings indicate that, in general, cold acclimation induces a suppression of the antioxidant defense system. Overall, our present study systematically describes the responses of antioxidant defenses to long-term cold acclimation and these findings contribute to extending the current understanding of the mechanisms of cold tolerance in high-altitude frogs.

Effects of MPK3 and MPK6 kinases on the chloroplast architecture and function induced by cold acclimation in Arabidopsis

Exposure to low, non-freezing temperatures develops freezing tolerance in many plant species. Such process is called cold acclimation. Molecular changes undergone during cold acclimation are orchestrated by signalling networks including MAP kinases. Structure and function of chloroplasts are affected by low temperatures. The aim of this work was to study how the MAP kinases MPK3 and MPK6 are involved in the chloroplast performance upon a long period of cold acclimation. We used Arabidopsis thaliana wild type and mpk3 and mpk6 mutants. Adult plants were acclimated during 7 days at 4 °C and then measurements of PSII performance and chloroplast ultrastructure were carried out. Only the mpk6 acclimated plants showed a high freezing sensitivity. No differences in the PSII function were observed in the plants from the three genotypes exposed to non-acclimated or acclimated conditions. The acclimation of wild-type plants produced severe alterations in the ultrastructure of chloroplast and thylakoids, which was more accentuated in the mpk plants. However, only the mpk6 mutant was unable to internalize the damaged chloroplasts into the vacuole. These results indicate that cold acclimation induces alterations in the chloroplast architecture leading to preserve an optimal performance of PSII. MPK3 and MPK6 are necessary to regulate these morphological changes, but besides, MPK6 is needed to the vacuolization of the damaged chloroplasts, suggesting a role in the chloroplast recycling during cold acclimation. The latter could be quite relevant, since it could explain why this mutant is the only one showing an extremely low freezing tolerance.

Identification of microRNAs and their target genes related to needle discoloration of evergreen tree Chinese cedar (Cryptomeria fortunei) in cold winters

Comparative analysis of miRNAs and their gene targets between the evergreen and yellowish-brown Cryptomeria fortunei phenotypes in cold winters suggests a possible role of miRNA-regulated pathways in needle color. Cryptomeria fortunei (Chinese cedar) is a conifer tree of considerable economic, ornamental and ecological importance. Despite the evergreen nature of C. fortunei, most needles turn yellowish- or reddish-brown in winter. The roles of microRNAs (miRNAs) in regulating pigment biosynthesis in color-leafed plants have been widely investigated. However, whether or not an miRNA-mediated staged discoloration mechanism exists in evergreen C. fortunei is currently unknown. In this study, we deciphered the microRNAs landscape in overwintering C. fortunei needles using high-throughput sequencing. A total of 517 known and 212 novel miRNA mature/star sequences, including 233 differentially expressed miRNAs, were identified. Based on integrated transcriptome and miRNA analysis, 2702 target unigenes of the miRNAs were predicted and these targets were significantly enriched in pigment-related biosynthesis pathways. A miRNA-target pigment biosynthesis regulatory network was then constructed, and its module miRNA (ath-miR858b, aly-miR858-3p, cme-miR828 and novel33_mature)-MYBs (v-myb avian myeloblastosis viral oncogene homolog) appeared to be a key factor regulating needle discoloration in C. fortunei. These miRNA-MYBs were further confirmed by degradome sequencing. Overall, these findings provide new insight into the posttranscriptional regulatory mechanism of leaf/needle discoloration in gymnosperms and may contribute to the miRNA-mediated genetic improvement of evergreen C. fortunei needles.

Natural Variation among Arabidopsis Accessions in the Regulation of Flavonoid Metabolism and Stress Gene Expression by Combined UV Radiation and Cold

Plants are constantly exposed to stressful environmental conditions. Plant stress reactions were mainly investigated for single stress factors. However, under natural conditions plants may be simultaneously exposed to different stresses. Responses to combined stresses cannot be predicted from the reactions to the single stresses. Flavonoids accumulate in Arabidopsis thaliana during exposure to UV-A, UV-B or cold, but the interactions of these factors on flavonoid biosynthesis were unknown. We therefore investigated the interaction of UV radiation and cold in regulating the expression of well-characterized stress-regulated genes, and on transcripts and metabolites of the flavonoid biosynthetic pathway in 52 natural Arabidopsis accessions that differ widely in their freezing tolerance. The data revealed interactions of cold and UV on the regulation of stress-related and flavonoid biosynthesis genes, and on flavonoid composition. In many cases, plant reactions to a combination of cold and UV were unique under combined stress and not predictable from the responses to the single stresses. Strikingly, all correlations between expression levels of flavonoid biosynthesis genes and flavonol levels were abolished by UV-B exposure. Similarly, correlations between transcript levels of flavonoid biosynthesis genes or flavonoid contents, and freezing tolerance were lost in the presence of UV radiation, while correlations with the expression levels of cold-regulated genes largely persisted. This may indicate different molecular cold acclimation responses in the presence or absence of UV radiation.

Cold response and tolerance in cereal roots

Cold stress adversely affects plant growth and is a limiting factor in crop productivity. Temperature volatility as a consequence of climate change will increase the effects of cold stress on crop cultivation. Low temperatures frequently occur early after planting in temperate climates and severely affect root development in cereals. In this review we address the question how cereal root systems respond to cold on different scales. First, we summarize the morphological, physiological and cellular responses of cereal roots to cold stress and how these processes are regulated by phytohormones. Subsequently, we highlight the status of the genetic and molecular dissection of cold tolerance with emphasis on the role of cold-responsive genes in improving cold tolerance in cereal roots. Finally, we discuss the role of beneficial microorganisms and mineral nutrients in ameliorating the effects of cold stress in cereal roots. A comprehensive knowledge of the molecular mechanisms underlying cold tolerance will ensure yield stability by enabling the generation of cold-tolerant crop genotypes.

The role of antioxidant defense in freezing tolerance of resurrection plant Haberlea rhodopensis

Haberlea rhodopensis Friv. is unique with its ability to survive two extreme environmental stresses-desiccation to air-dry state and subzero temperatures. In contrast to desiccation tolerance, the mechanisms of freezing tolerance of resurrection plants are scarcely investigated. In the present study, the role of antioxidant defense in the acquisition of cold acclimation and freezing tolerance in this resurrection plant was investigated comparing the results of two sets of experiments-short term freezing stress after cold acclimation in controlled conditions and long term freezing stress as a part of seasonal temperature fluctuations in an outdoor ex situ experiment. Significant enhancement in flavonoids and anthocyanin content was observed only as a result of freezing-induced desiccation. The total amount of polyphenols increased upon cold acclimation and it was similar to the control in post freezing stress and freezing-induced desiccation. The main role of phenylethanoid glucoside, myconoside and hispidulin 8-C-(2-O-syringoyl-b-glucopyranoside) in cold acclimation and freezing tolerance was elucidated. The treatments under controlled conditions in a growth chamber showed enhancement in antioxidant enzymes activity upon cold acclimation but it declined after subsequent exposure to -10 °C. Although it varied under ex situ conditions, the activity of antioxidant enzymes was high, indicating their important role in overcoming oxidative stress under all treatments. In addition, the activity of specific isoenzymes was upregulated as compared to the control plants, which could be more useful for stress counteraction compared to changes in the total enzyme activity, due to the action of these isoforms in the specific cellular compartments.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-00998-0.

Cold acclimation can specifically inhibit chlorophyll biosynthesis in young leaves of Pakchoi

BACKGROUND

Leaf color is an important trait in breeding of leafy vegetables. Y-05, a pakchoi (Brassica rapa ssp. chinensis) cultivar, displays yellow inner (YIN) and green outer leaves (GOU) after cold acclimation. However, the mechanism of this special phenotype remains elusive.

RESULTS

We assumed that the yellow leaf phenotype of Y-05 maybe caused by low chlorophyll content. Pigments measurements and transmission electron microscopy (TEM) analysis showed that the yellow phenotype is closely related with decreased chlorophyll content and undeveloped thylakoids in chloroplast. Transcriptomes and metabolomes sequencing were next performed on YIN and GOU. The transcriptomes data showed that 4887 differentially expressed genes (DEGs) between the YIN and GOU leaves were mostly enriched in the chloroplast- and chlorophyll-related categories, indicating that the chlorophyll biosynthesis is mainly affected during cold acclimation. Together with metabolomes data, the inhibition of chlorophyll biosynthesis is contributed by blocked 5-aminolevulinic acid (ALA) synthesis in yellow inner leaves, which is further verified by complementary and inhibitory experiments of ALA. Furthermore, we found that the blocked ALA is closely associated with increased BrFLU expression, which is indirectly altered by cold acclimation. In BrFLU-silenced pakchoi Y-05, cold-acclimated leaves still showed green phenotype and higher chlorophyll content compared with control, meaning silencing of BrFLU can rescue the leaf yellowing induced by cold acclimation.

CONCLUSIONS

Our findings suggested that cold acclimation can indirectly promote the expression of BrFLU in inner leaves of Y-05 to block ALA synthesis, resulting in decreased chlorophyll content and leaf yellowing. This study revealed the underlying mechanisms of leaves color change in cold-acclimated Y-05.

Thermal tolerance variations and physiological adjustments in a winter active and a summer active aphid species

The Russian wheat aphid Diuraphis noxia (Kurdjumov) and melon aphid Aphis gossypii Glover are known as winter and summer active species, respectively. It is hypothesized that differences in the aphids' seasonal activities might be related to their response to temperature extremes and different physiological mechanisms. To study the aphids' thermal tolerance variations and mode of their physiological basis, they were cold acclimated at 20, 15, 10, 5, and 0 °C for 168 h (7 days) and heat acclimated at 20, 25, 30 °C for 168 h and 35 °C for 48 h. At the end of each thermal regime, survival at low and high temperatures was determined, and changes in sugars and polyols and heat shock protein 70 (Hsp70) were investigated. D. noxia was more cold-tolerant, while A. gossypii was a more heat-tolerant insect. The type and pattern of sugars and polyols were similar in both species under cold acclimation (ACC) and heat acclimation (HCC). In both species, glucose and mannitol were the major identified compounds involved in cold and heat tolerance. However, they showed different patterns of Hsp70 level, with D. noxia having a higher level of Hsp70 under ACC and A. gossypii having a higher level of Hsp70 under HCC. These results demonstrated that their differences in thermal tolerance might explain the seasonal activities of the aphids.

In Planta Monitoring of Cold-Responsive Promoter Activity Reveals a Distinctive Photoperiodic Response in Cold Acclimation

Plant cold acclimation involves complicated pathways that integrate signals from temperature changes and light conditions. To understand plant responses to environmental signals in detail, molecular events that are regulated by temperature and light must be investigated at the whole-plant level in a nondestructive way. Using the promoter of COR15A connected to the luciferase reporter gene as a cold-responsive indicator, we developed an in planta monitoring system for gene expression under controlled temperature and photoperiod conditions. COR15A promoter activity was intensified by day-night cycles at 2�C, while its induction was abruptly suppressed in the dark at 8�C or higher, indicating a difference in responsiveness to photocycle between these two acclimation conditions. Freeze-thawing tests of whole plants proved that lower acclimation temperature resulted in higher tolerance to freezing, consistent with the temperature-dependent induction of COR15A. Inhibition of photosynthetic electron transport by 3-(3,4-dichlorophenyl)-1,1-dimethylurea eliminated the responsiveness to the day-night cycles at 2�C, indicating a possibility that the photosynthetic redox and/or the accumulation of photosynthates modulate COR15A responsiveness to photoperiod during cold acclimation, in addition to the well-known regulation by CBF (C-repeat binding factor) genes. These findings indicate that the cold-responsive promoter is regulated by distinctive mechanisms dependent on temperature and simultaneously affected by photocycle and photosynthesis.

Transcriptional reprogramming caused by cold acclimation in Meloidogyne incognita eggs

BACKGROUND

Egg hatching in Meloidogyne incognita is a highly regulated developmental event and is strictly correlated with temperature. It has been demonstrated that exposure of M. incognita eggs to low temperature seriously affects their embryonic development. On the other hand, clear evidence has shown that M. incognita is able to overwinter at subzero soil temperatures in certain open fields. Therefore, subtle physiological and genetic adaptations may occur in M. incognita to minimize freezing injuries.

OBJECTIVE

A growing body of evidence indicates that cold acclimation plays a large role in an individual organism's ability to cope with freezing-induced cellular damage. Given the decreasing temperatures in late autumn or early winter, we hypothesize that natural cold acclimation occurring during these periods may assist M. incognita in overwintering.

METHODS

Transcriptomic analysis and functional enrichment analyses were used to identify and annotate differentially expressed genes (DEGs) in acclimated eggs. The expression of DEGs involved in signal transduction and protein assembly was subsequently validated by reverse transcription quantitative PCR (RT-qPCR).

RESULTS

Relatively long-term preacclimation at 4 °C significantly accelerated the hatching of M. incognita eggs that were subjected to freezing at - 1 °C. Using a transcriptomic approach, we further identified 686 and 460 up- and downregulated transcripts, respectively, in pre-cold-acclimated eggs. Additionally, we used Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology annotations for functional enrichment analyses of the differentially expressed genes (DEGs).

CONCLUSION

The phenomenon in which M. incognita safely overwinters at subzero soil temperatures in certain areas may be attributed to the natural cold acclimation occurring in late autumn. Here, the identification of DEGs between acclimated and nonacclimated eggs will provide us with promising directions for future studies on the mechanisms of M. incognita freezing tolerance.

Mapping of Quantitative Trait Loci (QTL) Associated with Plant Freezing Tolerance and Cold Acclimation

Most agronomic traits are determined by quantitative trait loci (QTL) and exhibit continuous distribution in natural or especially built segregating populations. The genetic architecture and the hereditary characteristics of these traits are much more complicated than those of oligogenic traits and need adapted strategies for deciphering. The model plant Arabidopsis thaliana is widely studied for quantitative traits, especially via the utilization of genetic natural diversity. Here we describe a QTL-mapping protocol for analyzing freezing tolerance after cold acclimation in this species, based on its specific genetic tools. Nevertheless, this approach can be applied for the elucidation of complex traits in others species.

Genome-wide identification, characterization, and expression analysis of tea plant autophagy-related genes (CsARGs) demonstrates that they play diverse roles during development and under abiotic stress

Background

Autophagy, meaning ‘self-eating’, is required for the degradation and recycling of cytoplasmic constituents under stressful and non-stressful conditions, which helps to maintain cellular homeostasis and delay aging and longevity in eukaryotes. To date, the functions of autophagy have been heavily studied in yeast, mammals and model plants, but few studies have focused on economically important crops, especially tea plants (Camellia sinensis). The roles played by autophagy in coping with various environmental stimuli have not been fully elucidated to date. Therefore, investigating the functions of autophagy-related genes in tea plants may help to elucidate the mechanism governing autophagy in response to stresses in woody plants.

Results

In this study, we identified 35 C. sinensis autophagy-related genes (CsARGs). Each CsARG is highly conserved with its homologues from other plant species, except for CsATG14. Tissue-specific expression analysis demonstrated that the abundances of CsARGs varied across different tissues, but CsATG8c/i showed a degree of tissue specificity. Under hormone and abiotic stress conditions, most CsARGs were upregulated at different time points during the treatment. In addition, the expression levels of 10 CsARGs were higher in the cold-resistant cultivar ‘Longjing43’ than in the cold-susceptible cultivar ‘Damianbai’ during the CA period; however, the expression of CsATG101 showed the opposite tendency.

Conclusions

We performed a comprehensive bioinformatic and physiological analysis of CsARGs in tea plants, and these results may help to establish a foundation for further research investigating the molecular mechanisms governing autophagy in tea plant growth, development and response to stress. Meanwhile, some CsARGs could serve as putative molecular markers for the breeding of cold-resistant tea plants in future research.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07419-2.

Impaired chloroplast positioning affects photosynthetic capacity and regulation of the central carbohydrate metabolism during cold acclimation

Photosynthesis and carbohydrate metabolism of higher plants need to be tightly regulated to prevent tissue damage during environmental changes. The intracellular position of chloroplasts changes due to a changing light regime. Chloroplast avoidance and accumulation response under high and low light, respectively, are well known phenomena, and deficiency of chloroplast movement has been shown to result in photodamage and reduced biomass accumulation. Yet, effects of chloroplast positioning on underlying metabolic regulation are less well understood. Here, we analysed photosynthesis together with metabolites and enzyme activities of the central carbohydrate metabolism during cold acclimation of the chloroplast unusual positioning 1 (chup1) mutant of Arabidopsis thaliana. We compared cold acclimation under ambient and low light and found that maximum quantum yield of PSII was significantly lower in chup1 than in Col-0 under both conditions. Our findings indicated that net CO₂ assimilation in chup1 is rather limited by biochemistry than by photochemistry. Further, cold-induced dynamics of sucrose phosphate synthase differed significantly between both genotypes. Together with a reduced rate of sucrose cycling derived from kinetic model simulations our study provides evidence for a central role of chloroplast positioning for photosynthetic and metabolic acclimation to low temperature.

Simultaneous Occurrence of Diapause and Cold Hardiness in Overwintering Eggs of the Apple Oystershell Scale, Lepidosaphes Malicola Borchsenius (Hem.: Diaspididae)

As the key pest of apple fruits, the oystershell scale, Lepidosaphes malicola Borchsenius (Hem.: Diaspididae), overwinters as diapausing eggs under the protective, waxy cover of females. In this research, the effects of diapause development, cold acclimation, and rapid cold hardening were studied on the cold hardiness of the eggs. The changes in some physiological components were also investigated. The results indicated cold exposure to be a prerequisite for the survival of the diapausing eggs of L. malicola. No eggs hatched without exposure to cold. In addition, a direct relationship was observed among cold hardiness, cold acclimation, and diapause of the eggs based on the results. The highest level of hatching (the highest cold hardiness) of the eggs (80%) occurred in the cold-acclimated eggs at the end of diapause (March). Rapid cold hardening also influenced the cold hardiness of the eggs with diapause development. At the end of diapause, the lowest (61%) and the highest (77%) rates of egg survival were observed when the eggs were exposed to 5 and -10°C for 24 h, respectively. Cold hardiness of the diapausing eggs of L. malicola was also accompanied by some physiological changes, i.e., a decrease in glycogen content and an increase in simple sugar, lipid, and protein contents. The lowest glycogen content (about 50 μg/g) and the highest amounts of total simple sugars (454 μg/g) of lipids (542 μg/g) and proteins (84 μg/g) were observed in the cold-acclimated eggs at the end of diapause.

miR-31-5p regulates cold acclimation of the wood-boring beetle Monochamus alternatus via ascaroside signaling

BACKGROUND

Survival to cold stress in insects living in temperate environments requires the deployment of strategies that lead to physiological changes involved in freeze tolerance or freeze avoidance. These strategies may consist of, for instance, the induction of metabolic depression, accumulation of cryoprotectants, or the production of antifreeze proteins, however, little is known about the way such mechanisms are regulated and the signals involved in their activation. Ascarosides are signaling molecules usually known to regulate nematode behavior and development, whose expression was recently found to relate to thermal plasticity in the Japanese pine sawyer beetle Monochamus alternatus. Accumulating evidence also points to miRNAs as another class of regulators differentially expressed in response to cold stress, which are predicted to target genes involved in cold adaptation of insects. Here, we demonstrate a novel pathway involved in insect cold acclimation, through miRNA-mediated regulation of ascaroside function.

RESULTS

We initially discovered that experimental cold acclimation can enhance the beetle's cold hardiness. Through screening and functional verification, we found miR-31-5p, upregulated under cold stress, significantly contributes to this enhancement. Mechanistically, miR-31-5p promotes production of an ascaroside (asc-C9) in the beetle by negatively targeting the rate-limiting enzyme, acyl-CoA oxidase in peroxisomal β-oxidation cycles. Feeding experiments with synthetic asc-C9 suggests it may serve as a signal to promote cold acclimation through metabolic depression and accumulation of cryoprotectants with specific gene expression patterns.

CONCLUSIONS

Our results point to important roles of miRNA-mediated regulation of ascaroside function in insect cold adaptation. This enhanced cold tolerance may allow higher survival of M. alternatus in winter and be pivotal in shaping its wide distribution range, greatly expanding the threat of pine wilt disease, and thus can also inspire the development of ascaroside-based pest management strategies.

Low temperature tolerance of three Aedes albopictus strains (Diptera: Culicidae) under constant and fluctuating temperature scenarios

Background

Aedes albopictus, a vector of numerous viruses and filarial worms, has already established in 20 countries in Europe, mainly colonising subtropical regions. Continuing adaptation to climatic conditions in temperate areas would probably result in a spread to more northern European countries, producing an increasing risk of mosquito-borne pathogen transmission over a much greater area. Based on previous studies showing that Ae. albopictus is able to overwinter in Germany, this study aims to determine more exactly its ecological limits of enduring low temperatures.

Methods

Non-diapausing and experimentally induced diapausing eggs of three different Ae. albopictus strains (tropical, subtropical and temperate origins) were exposed to four different regimes with constant temperatures and three different regimes with fluctuating temperatures in a course of a day for a minimum of 2 and a maximum of 30 days. The hatching rate of larvae after cold exposure of the eggs was taken as a measure of cold tolerance.

Results

The experiments showed that the tropical Ae. albopictus strain had a lower cold tolerance than the subtropical and the temperate strains. The eggs of all used strains were able to survive constant temperatures as low as −5 °C for an exposure period of 30 days, while constant temperatures as low as −10 °C were endured for 2 days by the tropical strain and for 10 and 20 days by the subtropical and temperate strains, respectively. At fluctuating temperatures, both the subtropical and the temperate strains exhibited hatching under all temperature regimes, even with a minimum temperature of −10 °C, whereas the tropical strain ceased hatching after an exposure period of 30 days under the temperature regime with a minimum temperature of −10 °C. The analyses showed that the temperature played the major role in interpreting the hatching rates of the eggs. The condition, whether the eggs were diapausing or not, had no significant influence, although results indicated a slightly higher cold tolerance of diapausing eggs at −10 °C.

Conclusions

It must be expected that subtropical and temperate strains of Ae. albopictus are able to withstand common central European winters and are able to establish in considerable parts of the continent.

Comparative transcriptome analysis of human skeletal muscle in response to cold acclimation and exercise training in human volunteers

Background

Cold acclimation and exercise training were previously shown to increase peripheral insulin sensitivity in human volunteers with type 2 diabetes. Although cold is a potent activator of brown adipose tissue, the increase in peripheral insulin sensitivity by cold is largely mediated by events occurring in skeletal muscle and at least partly involves GLUT4 translocation, as is also observed for exercise training.

Methods

To investigate if cold acclimation and exercise training overlap in the molecular adaptive response in skeletal muscle, we performed transcriptomics analysis on vastus lateralis muscle collected from human subjects before and after 10 days of cold acclimation, as well as before and after a 12-week exercise training intervention.

Results

Cold acclimation altered the expression of 756 genes (422 up, 334 down, P < 0.01), while exercise training altered the expression of 665 genes (444 up, 221 down, P < 0.01). Principal Component Analysis, Venn diagram, similarity analysis and Rank–rank Hypergeometric Overlap all indicated significant overlap between cold acclimation and exercise training in upregulated genes, but not in downregulated genes. Overlapping gene regulation was especially evident for genes and pathways associated with extracellular matrix remodeling. Interestingly, the genes most highly induced by cold acclimation were involved in contraction and in signal transduction between nerve and muscle cells, while no significant changes were observed in genes and pathways related to insulin signaling or glucose metabolism.

Conclusions

Overall, our results indicate that cold acclimation and exercise training have overlapping effects on gene expression in human skeletal muscle, but strikingly these overlapping genes are designated to pathways related to tissue remodeling rather than metabolic pathways.

Cold acclimation and freezing tolerance in three Eucalyptus species: A metabolomic and proteomic approach

The ability of plants to cope with frost events relies on the physiological and molecular responses triggered by cold temperatures. This process, named acclimation, involves reprogramming gene expression in order to adjust metabolism. Planted Eucalyptus species are highly productive but most of them are frost sensitive. However, acclimation process varies among species and environmental conditions, promoting more or less frost damage in young plantations of frost-prone areas. To identify metabolites and proteins responsible for these differences, two acclimation regimes were imposed to seedling of Eucalyptus grandis Hill ex Maiden (Eg), Eucalyptus dunnii Maiden (Ed) and Eucalyptus benthamii Maiden Cambage (Eb), and leaves submitted to biochemical and molecular analyses. Further, seedlings were used for simulated frosts in order to test the acclimation status effect on frost tolerance. Eb showed higher frost tolerance than Ed and Eg under control and acclimation scenarios, possibly due to its higher accumulation of phenolics, anthocyanins and soluble sugars as well as lower levels of photosynthetic pigments and related proteins. Also, a rise in frost tolerance and in osmoprotectants and antioxidants was observed for all the species due to cold acclimation treatment. Interestingly, metabolic profiles differed among species, suggesting different mechanisms to endure frosts and, probably, different requirements for cold acclimation. Shotgun proteomics reinforced differences and commonalities and supported metabolome observations. An in depth understanding of these responses could help to safeguard planted forests productivity through breeding of tolerant genetic material.

Transcriptomic profiling revealed key signaling pathways for cold tolerance and acclimation of two carp species

Background

Closely related species of the carp family (Cyprinidae) have evolved distinctive abilities to survive under cold stress, but molecular mechanisms underlying the generation of cold resistance remain largely unknown. In this study, we compared transcriptomic profiles of two carp species to identify key factors and pathways for cold tolerance and acclimation.

Results

Larvae of Songpu mirror carp and Barbless carp that were pretreated at 18 °C for 24 h significantly improved their survival rates under lethal cold temperature at 8 °C or 10 °C, indicating that two carp species possess the ability of cold acclimation. However, Songpu mirror carp exhibited stronger abilities of cold tolerance and acclimation than Barbless carp. Transcriptomic profiles of Songpu mirror carp and Barbless carp larvae at 28 °C and 18 °C were compared during cold acclimation through RNA-seq. Differentially expressed genes that are closely associated with the differences in cold acclimation between two carp species were identified through bioinformatics and Venn’s diagram analysis. GO enrichment analysis of these genes indicated that cellular component assembly involved in morphogenesis, secondary alcohol metabolism and drug transport were the most up-regulated biological processes during cold acclimation of Songpu mirror carp. Conversely, positive regulation of macroautophagy, intracellular protein transport, and organonitrogen compound catabolism were the most down-regulated biological processes during cold acclimation of Barbless carp. KEGG enrichment analysis revealed that factors in the FoxO-related signaling pathways are mainly responsible for the development of differences in cold tolerance and acclimation between two carp species since altering the phosphorylation of key proteins in the FoxO-related signaling pathways with inhibitors or an activator significantly decreased the cold tolerance and acclimation of Songpu mirror carp. These data provided key clues for dissection of molecular mechanisms underlying the development of cold tolerance and acclimation in carps.

Conclusions

These findings indicate that larvae of two carp species possess different abilities of cold tolerance and can build cold acclimation under mild low temperature. Multiple biological processes and FoxO-related signaling pathways are closely associated with the development of differences in cold tolerance and acclimation between two carp species.

Proteomic Approaches to Identify Cold-Regulated Plasma Membrane Proteins

Plasma membrane is the primary determinant of freezing tolerance in plants because of its central role in freeze-thaw cycle. Changes in plasma membrane protein composition have been one of the major research areas in plant cold acclimation. To obtain comprehensive profiles of the plasma membrane proteomes and their changes during the cold acclimation process, a plasma membrane purification method using a dextran-polyethylene glycol two polymer system and a mass spectrometry-based shotgun proteomics method using nano-LC-MS/MS for the plasma membrane proteins are described. The proteomic results obtained are further applied to label-free protein semiquantification.

Subcellular Compartmentation of Metabolites Involved in Cold Acclimation

Plant cells are heavily compartmentalized, and metabolite concentrations in the various compartments differ significantly. Thus, determination of metabolite abundance in whole-cell extracts may be misleading, when the role of a compound in plant freezing tolerance shall be evaluated. Here, we describe a method for the separation of the largest compartments of plant cells, the vacuole, plastid, and cytosol. With more elaborate analysis, this method can be expanded to also resolve mitochondria and other compartments.