Physiological and transcriptome analysis of Poa pratensis var. anceps cv. Qinghai in response to cold stress

Tissue-specific transcriptomic analysis reveals the molecular mechanisms responsive to cold stress in Poa crymophila, and development of EST-SSR markers linked to cold tolerance candidate genes

BACKGROUND

Poa crymophila is a perennial, cold-tolerant, native grass species, widely distributed in the Qinghai-Tibet Plateau. However, the tissue-specific regulatory mechanisms and key regulatory genes underlying its cold tolerance remain poorly characterized. Therefore, in this study, based on the screening and evaluation of cold tolerance of four Poa species, the cold tolerance mechanism of P. crymophila's roots, stems, and leaves and its cold tolerance candidate genes were investigated through physiological and transcriptomic analyses.

RESULTS

Results of the present study suggested that the cold tolerance of the four Poa species was in the following order: P. crymophila > P. botryoides > P. pratensis var. anceps > P. pratensis. Cold stress significantly changed the physiological characteristics of roots, stems, and leaves of P. crymophila in this study. In addition, the transcriptome results showed that 4434, 8793, and 14,942 differentially expressed genes (DEGs) were identified in roots, stems, and leaves, respectively; however, 464 DEGs were commonly identified in these three tissues. KEGG enrichment analysis showed that these DEGs were mainly enriched in the phenylpropanoid biosynthesis pathway (roots), photosynthesis pathway (stems and leaves), circadian rhythm-plant pathway (stems and leaves), starch and sucrose metabolism pathway (roots, stems, and leaves), and galactose metabolism pathway (roots, stems, and leaves). A total of 392 candidate genes involved in Ca2+ signaling, ROS scavenging system, hormones, circadian clock, photosynthesis, and transcription factors (TFs) were identified in P. crymophila. Weighted gene co-expression network analysis (WGCNA) identified nine hub genes that may be involved in P. crymophila cold response. A total of 200 candidate gene-based EST-SSRs were developed and characterized. Twenty-nine polymorphic EST-SSRs primers were finally used to study genetic diversity of 40 individuals from four Poa species with different cold tolerance characteristics. UPGMA cluster and STRUCTURE analysis showed that the 40 Poa individuals were clustered into three major groups, individual plant with similar cold tolerance tended to group together. Notably, markers P37 (PcGA2ox3) and P148 (PcERF013) could distinguish P. crymophila from P. pratensis var. anceps, P. pratensis, and P. botryoides.

CONCLUSIONS

This study provides new insights into the molecular mechanisms underlying the cold tolerance of P. crymophila, and also lays a foundation for molecular marker-assisted selection for cold tolerance improvement in Poa species.

Multiomic analysis reveals that the flavonoid biosynthesis pathway is associated with cold tolerance in Heracleum moellendorffii Hance

Heracleum moellendorffii Hance is a perennial herbaceous plant that is adaptable to cold environments and has both edible and medicinal value. Given that no reference genome for this species is available, we constructed a high-quality transcript isoform library using full-length transcriptome sequencing and conducted a comparative genomic analysis. Samples were obtained from plants that had been subjected to cold stress for 12, 24 and 36 hours (Cold_12, Cold_24, and Cold_36, respectively) and from control plants (Cold_0) that were not subjected to cold stress and used in transcriptome and nontargeted metabolome analyses. Compared with the genes expressed in CK (Cold_0), the number of differentially expressed genes (DEGs) in Cold 12, Cold_24, and Cold_36 increased gradually over time; plants subjected to 12, 24 and 36 hours of cold stress displayed 669, 6084, and 24,129 DEGs, respectively. The DEGs were clustered into 8 subclasses by k-means clustering; subclasses 2, 3, 4, and 7 were enriched in pathways related to "flavonoid biosynthesis". Nontargeted metabolome analysis revealed that 3719 annotated metabolites were shared by all four groups of samples. We identified 1186, 1087, and 1097 differentially accumulated metabolites (DAMs) in three comparisons: Cold_12 vs. CK, Cold_24 vs. CK, and Cold_36 vs. CK, respectively. The DAMs were predominantly enriched in the "flavonoid biosynthesis pathway". Through WGCNA, we obtained five modules and 29 flavonoid-related metabolites with extremely significant module-metabolite paired relationships (|correlation coefficient|> 0.9, P < 0.01). We analysed the DEGs and DAMs of the flavonoid biosynthetic pathway in H. moellendorffii Hance under cold stress and constructed a correlation network between transcription factors (TFs) and structural genes in the pathway. RT-qPCR was used to confirm the expression of four hub genes from the WGCNA, six TFs, and 15 structural genes of the flavonoid biosynthetic pathway. These data provide a foundation for functional genomics studies of H. moellendorffii Hance and contribute to the study of the molecular mechanisms and transcriptional regulation of flavonoid accumulation by TFs under cold stress conditions in plants.

Comparative transcriptome analysis and meta-QTLs mapping reveal the regulatory mechanism of cold tolerance in rice at the budding stage

Rice (Oryza sativa L.) is one of the most extensively farmed food crops, but its development and productivity are significantly impacted by cold stress during the budding period. In this study, transcriptome sequencing was conducted on two types of rice: the cold-sensitive indica rice A117 and the substantially cold-tolerant japonica rice B106 under control and cold treatments. Differentially expressed genes between the two materials under cold conditions were analyzed using GO and KEGG enrichment analyses. The results revealed that processes such as the TCA cycle, glycolysis/glycogenesis, oxidative phosphorylation, and glutathione metabolism contribute to B106's cold tolerance. Additionally, an enrichment analysis of cold-induced genes in each material and shared genes identified significant enrichment in pathways such as glutathione metabolism, phenylpropanoid biosynthesis, and photosynthesis-antenna proteins. Initial cold tolerance QTLs at the rice bud stage were collected from published literature, and meta-QTL mapping identified 9 MQTLs. Gene expression profiling led to the identification of 75 potential DEGs within the 9 MQTLs region, from which four candidate genes (Os02g0194100, Os03g0802500, Os05g0129000, and Os07g0462000) were selected using qRT-PCR and gene annotation. These findings provide genetic resources for further research on the molecular mechanisms underlying rice's response to cold stress during the bud stage.

Transcriptomic analysis of Asparagus officinalis cultivars with varying levels of freezing tolerance over fall acclimation and spring deacclimation periods

Asparagus (Asparagus officinalis L.) is an important vegetable crop in southern Ontario, Canada, where winter air and soil temperatures below 0°C are common. Consequently, cultivars growing in this area must possess winterhardiness and freezing tolerance for survival. Asparagus acquires freezing tolerance in the fall through cold acclimation and loses freezing tolerance in the spring through deacclimation. To understand the molecular bases of these processes, transcriptomic analysis (RNA-Seq) was conducted on two cultivars, one adapted, 'Guelph Millennium' (GM), and one unadapted, 'UC157' (UC), to the winter conditions of southern Ontario. RNA extracted from bud and rhizome tissues, sampled on three dates during early spring and late fall, was subjected to sequencing. In the fall, the numbers of differentially expressed (DE) genes at the second and third harvests increased, relative to the first harvest, in dormant buds and rhizomes as freezing tolerance of cultivars increased, and the majority of DE genes were downregulated. In spring, freezing tolerance decreased as plants deacclimated and most genes DE at second and third harvests were upregulated in both cultivars. GM had lower LT50 (lethal temperature at which 50% of plants die) values and hence higher freezing tolerance than UC on specific sampling dates during both spring and fall, and expression patterns of specific genes were correlated with LT50 differences. Functional analysis revealed that these genes were involved in carbohydrate metabolic process, plant hormone signal transduction (auxin and gibberellin), proline metabolism, biosynthesis of secondary metabolites, circadian rhythm, and late embryogenesis abundant proteins and could be associated with cold acclimation and deacclimation processes. These findings will help researchers understand the molecular mechanisms of freezing tolerance in asparagus, leading to breeding and genetic strategies to improve the trait.

Comparative Metabolome and Transcriptome Analysis of Rapeseed (Brassica napus L.) Cotyledons in Response to Cold Stress

Cold stress affects the seed germination and early growth of winter rapeseed, leading to yield losses. We employed transmission electron microscopy, physiological analyses, metabolome profiling, and transcriptome sequencing to understand the effect of cold stress (0 °C, LW) on the cotyledons of cold-tolerant (GX74) and -sensitive (XY15) rapeseeds. The mesophyll cells in cold-treated XY15 were severely damaged compared to slightly damaged cells in GX74. The fructose, glucose, malondialdehyde, and proline contents increased after cold stress in both genotypes; however, GX74 had significantly higher content than XY15. The pyruvic acid content increased after cold stress in GX74, but decreased in XY15. Metabolome analysis detected 590 compounds, of which 32 and 74 were differentially accumulated in GX74 (CK vs. cold stress) and XY15 (CK vs. cold stressed). Arachidonic acid and magnoflorine were the most up-accumulated metabolites in GX74 subjected to cold stress compared to CK. There were 461 and 1481 differentially expressed genes (DEGs) specific to XY15 and GX74 rapeseeds, respectively. Generally, the commonly expressed genes had higher expressions in GX74 compared to XY15 in CK and cold stress conditions. The expression changes in DEGs related to photosynthesis-antenna proteins, chlorophyll biosynthesis, and sugar biosynthesis-related pathways were consistent with the fructose and glucose levels in cotyledons. Compared to XY15, GX74 showed upregulation of a higher number of genes/transcripts related to arachidonic acid, pyruvic acid, arginine and proline biosynthesis, cell wall changes, reactive oxygen species scavenging, cold-responsive pathways, and phytohormone-related pathways. Taken together, our results provide a detailed overview of the cold stress responses in rapeseed cotyledons.

Integrated anatomical structure, physiological, and transcriptomic analyses to identify differential cold tolerance responses of Ziziphus jujuba mill. 'Yueguang' and its autotetraploid 'Hongguang'

Cold stress is a limiting stress factor that limits plant distribution and development; however, polyploid plants have specific characteristics such as higher resistance to abiotic stress, especially cold stress, that allow them to overcome this challenge. The cultivated cultivar Ziziphus jujuba Mill. 'Yueguang' (YG) and its autotetraploid counterpart 'Hongguang' (HG) exhibit differential cold tolerance. However, the underlying molecular mechanism and methods to enhance their cold tolerance remain unknown. Anatomical structure and physiological analysis indicated YG had a higher wood bark ratio, and xylem ratio under cold treatment compared to HG. However, the half-lethal temperature (LT50), cortex ratio, and malondialdehyde (MDA) content were significantly decreased in YG than HG, which indicated YG was cold tolerant than HG. Transcriptome analysis showed that 2084, 1725, 2888, and 2934 differentially expressed genes (DEGs) were identified in HC vs YC, H20 vs Y20, Y20 vs YC, and H20 vs HC treatment, respectively. Meanwhile, KEGG enrichment analysis of DEGs showed that several metabolic pathways, primarily plant hormone signal transduction and the MAPK signaling pathway, were involved in the differential regulation of cold tolerance between YG and HG. Furthermore, exogenous abscisic acid (ABA) and brassinolide (BR) treatments could improve their cold tolerance through increased SOD and POD activities, decreased relative electrical conductivity, and MDA content. All of these findings suggested that plant hormone signal transduction, particularly ABA and BR, might have an important role in the regulation of differential cold tolerance between YG and HG, laying the foundation for further improving cold tolerance in jujube and examining the molecular mechanisms underlying differences in cold tolerance among different ploidy cultivars.

Metabolic profiling of Oryza sativa seedlings under chilling stress using nanoliter electrospray ionization mass spectrometry

Low temperatures significantly impact on rice (Oryza sativa) yield and quality. Traditional metabolomic techniques, often involving time-consuming chromatography-mass spectrometry procedures, are currently in use. This study investigated metabolomic responses of rice seedlings under low-temperature stress using nanoliter electrospray ionization mass spectrometry (nanoESI-MS) in combination with multivariate analysis. Results revealed distinct metabolic profiles in 'Qiutianxiaoting' (japonica) and '93-11' (indica) rice seedlings. Among the 36 identified compounds in rice, seven key metabolites, comprising l-glutamic acid, asparagine, tryptophan, citric acid, α-linolenic acid, malic acid, and inositol, were identified as responsive to cold stress. Notably, malic acid content reached 1332.40 μg/g dry weight in Qiutianxiaoting and 1444.13 μg/g in 93-11. Both the qualitative and quantitative results of nanoESI-MS were further confirmed through gas chromatography-mass spectrometry validation. The findings highlight the potential of nanoESI-MS for rapidly characterizing crucial metabolites across diverse plant species under exposure to stress.

DIA-Based Quantitative Proteomics in the Flower Buds of Two Malus sieversii (Ledeb.) M. Roem Subtypes at Different Overwintering Stages

Malus sieversii is considered the ancestor of the modern cultivated apple, with a high value for apple tolerance breeding. Despite studies on the temperature adaptability of M. sieversii carried out at a physiological response and the genome level, information on the proteome changes of M. sieversii during dormancy is limited, especially about the M. sieversii subtypes. In this study, a DIA-based approach was employed to screen and identify differential proteins involved in three overwintering periods of flower buds in two M. sieversii subtypes (Malus sieversii f. luteolus, GL; Malus sieversii f. aromaticus, HC) with different overwintering adaptabilities. The proteomic analysis revealed that the number of the down-regulated differential expression proteins (DEPs) was obviously higher than that of the up-regulated DEPs in the HC vs. GL groups, especially at the dormancy stage and dormancy-release stage. Through functional classification of those DEPs, the majority of the DEPs in the HC vs. GL groups were associated with protein processing in the endoplasmic reticulum, oxidative phosphorylation, starch and sucrose metabolism and ribosomes. Through WGCNA analysis, tricarboxylic acid cycle and pyruvate metabolism were highly correlated with the overwintering stages; oxidative phosphorylation and starch and sucrose metabolism were highly correlated with the Malus sieversii subtypes. This result suggests that the down-regulation of DEPs, which are predominantly enriched in these pathways, could potentially contribute to the lower cold tolerance observed in HC during overwintering stage.

Insights into the molecular network underlying phytotoxicity and phytoaccumulation of ciprofloxacin

Ciprofloxacin (CIP) is frequently detected in agricultural soils and can be accumulated by crops, causing phytotoxicities and food safety concerns. However, the molecular basis of its phytotoxicity and phytoaccumulation is hardly known. Here, we analyzed physiological and molecular responses of choysum (Brassica parachinensis) to CIP stress by comparing low CIP accumulation variety (LAV) and high accumulation variety (HAV). Results showed that the LAV suffered more severe inhibition of growth and photosynthesis than the HAV, exhibiting a lower tolerance to CIP toxicity. Integrated transcriptome and proteome analyses suggested that more differentially expressed genes/proteins (DEGs/DEPs) involved in basic metabolic processes were downregulated to a larger extent in the LAV, explaining its lower CIP tolerance at molecular level. By contrast, more DEGs/DEPs involved in defense responses were upregulated to a larger extent in the HAV, showing the molecular basis of its stronger CIP tolerance. Further, a CIP phytotoxicity-responsive molecular network was constructed for the two varieties to better understand the molecular mechanisms underlying the variety-specific CIP tolerance and accumulation. The results present the first comprehensive molecular profile of plant response to CIP stress for molecular-assisted breeding to improve CIP tolerance and minimize CIP accumulation in crops.

CsBPC2 is essential for cucumber survival under cold stress

Cold stress affects the growth and development of cucumbers. Whether the BPC2 transcription factor participates in cold tolerance and its regulatory mechanism in plants have not been reported. Here, we used wild-type (WT) cucumber seedlings and two mutant Csbpc2 lines as materials. The underlying mechanisms were studied by determining the phenotype, physiological and biochemical indicators, and transcriptome after cold stress. The results showed that CsBPC2 knockout reduced cucumber cold tolerance by increasing the chilling injury index, relative electrical conductivity and malondialdehyde (MDA) content and decreasing antioxidant enzyme activity. We then conducted RNA sequencing (RNA-seq) to explore transcript-level changes in Csbpc2 mutants. A large number of differentially expressed genes (1032) were identified and found to be unique in Csbpc2 mutants. However, only 489 down-regulated genes related to the synthesis and transport of amino acids and vitamins were found to be enriched through GO analysis. Moreover, both RNA-seq and qPT-PCR techniques revealed that CsBPC2 knockout also decreased the expression of some key cold-responsive genes, such as CsICE1, CsCOR413IM2, CsBZR1 and CsBZR2. These results strongly suggested that CsBPC2 knockout not only affected cold function genes but also decreased the levels of some key metabolites under cold stress. In conclusion, this study reveals for the first time that CsBPC2 is essential for cold tolerance in cucumber and provides a reference for research on the biological function of BPC2 in other plants.

Transcriptome analysis revealed molecular basis of cold response in Prunus mume

Japanese apricot (Prunus mume Sieb. et Zucc.) is a traditional woody flower and fruit tree restrictedly cultivated in northern area due to its inability to survive harsh winters and early springs. In the current study, RNA-seq and physiological assay were used to study the cold response of P. mume 'Xuemei'. A total of 4705 genes were identified as differentially expressed genes (DEGs) in the 21 pairwise comparisons among seven time points under 0 °C cold treatment, and 3678 of them showed differential levels compared with control at normal temperature. The gene expression profiles indicated that the number of upregulated genes increased with prolongation of treatment time throughout the whole 48 h. Hierarchical clustering suggested three obvious phases of the gene expression profiles. Gene ontology (GO) analysis of the 4705 DEGs resulted in 102 significantly enriched GO items in which the transcription activity was dominant. 225 DEGs were predicted to encode transcription factor (TF) genes. Some important TFs (ERF, CBF, WRKY, NAC, MYB, bHLH) were strongly induced during the whole cold treatment. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that plant signal transduction pathways such as plant hormone and calcium (Ca2+) were notable. Metabolic pathways such as sugar metabolism, especially RFOs (raffinose family oligosaccharides) were activated, which was accompanied by the accumulation of soluble sugars. SOD and POD enzyme activities coupled with reactive oxygen species (ROS)-related gene expression profile implied a gradually induced ROS scavenging system under cold treatment. These results might shed light on the sensitivity to cold stress in Japanese apricot and provide new insights into hardiness studies in P. mume and its related species.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01376-2.

Nitric oxide promotes adventitious root formation in cucumber under cadmium stress through improving antioxidant system, regulating glycolysis pathway and polyamine homeostasis

Cadmium (Cd) as a potentially toxic heavy metal that not only pollutes the environment but also interferes with plant growth. Nitric oxide (NO) regulates plant growth and development as well as abiotic stress response. However, the mechanism underpinning NO-induced adventitious root development under Cd stress remains unclear. In this study, cucumber (Cucumis sativus 'Xinchun No. 4') was used as the experimental material to investigate the effect of NO on the development of adventitious roots in cucumber under Cd stress. Our results revealed that, as compared to Cd stress, 10 μM SNP (a NO donor) could considerably increase the number and length of adventitious roots by 127.9% and 289.3%, respectively. Simultaneously, exogenous SNP significantly increased the level of endogenous NO in cucumber explants under Cd stress. Our results revealed that supplementation of Cd with SNP significantly increased endogenous NO content by 65.6% compared with Cd treatment at 48 h. Furthermore, our study indicated that SNP treatment could improve the antioxidant capacity of cucumber explants under Cd stress by up-regulating the gene expression level of antioxidant enzymes, as well as reducing the levels of malondialdehyde (MDA), hydrogen peroxide (H₂O₂) and superoxide anion (  O 2    · - ) to alleviate oxidative damage and membrane lipid peroxidation. Application of NO resulted in a decrease of the  O 2    · - , MDA, and H₂O₂ level by 39.6%, 31.4% and 60.8% as compared to Cd-alone treatment, respectively. Besides that, SNP treatment significantly increased the expression level of related genes involved in glycolysis processes and polyamine homeostasis. However, application of NO scavenger 2-(4-carboxy -2-phenyl)-4, 4, 5, 5-tetramethy limidazoline -1-oxyl -3-oxide (cPTIO) and the inhibitor tungstate significantly reversed the positive role of NO in promoting the adventitious root formation under Cd stress. These results suggest that exogenous NO can increase the level of endogenous NO, improve antioxidation ability, promote glycolysis pathway and polyamine homeostasis to enhance the occurrence of adventitious roots in cucumber under Cd stress. In summary, NO can effectively alleviate the damage of Cd stress and significantly promote the development of adventitious root of cucumber under Cd stress.

Comparative transcriptome analysis reveals the regulatory mechanisms of two tropical water lilies in response to cold stress

BACKGROUND

Tropical water lily is an aquatic plant with high ornamental value, but it cannot overwinter naturally at high latitudes. The temperature drop has become a key factor restricting the development and promotion of the industry.

RESULTS

The responses of Nymphaea lotus and Nymphaea rubra to cold stress were analyzed from the perspective of physiology and transcriptomics. Under the cold stress, Nymphaea rubra had obvious leaf edge curling and chlorosis. The degree of peroxidation of its membrane was higher than that of Nymphaea lotus, and the content of photosynthetic pigments also decreased more than that of Nymphaea lotus. The soluble sugar content, SOD enzyme activity and CAT enzyme activity of Nymphaea lotus were higher than those of Nymphaea rubra. This indicated that there were significant differences in the cold sensitivity of the two varieties. GO enrichment and KEGG pathway analysis showed that many stress response genes and pathways were affected and enriched to varying degrees under the cold stress, especially plant hormone signal transduction, metabolic pathways and some transcription factor genes were from ZAT gene family or WKRY gene family. The key transcription factor ZAT12 protein in the cold stress response process has a C₂H₂ conserved domain, and the protein is localized in the nucleus. Under the cold stress, overexpression of the NlZAT12 gene in Arabidopsis thaliana increased the expression of some cold-responsive protein genes. The content of reactive oxygen species and MDA in transgenic Arabidopsis thaliana was lower, and the content of soluble sugar was higher, indicating that overexpression of NlZAT12 can improve the cold tolerance of Arabidopsis thaliana.

CONCLUSION

We demonstrate that ethylene signalling and reactive oxygen species signalling play critical roles in the response of the two cultivars to cold stress. The key gene NlZAT12 for improving cold tolerance was identified. Our study provides a theoretical basis for revealing the molecular mechanism of tropical water lily in response to cold stress.

Transcriptomic and metabolomic insights on the molecular mechanisms of flower buds in responses to cold stress in two Camellia oleifera cultivars

INTRODUCTION

The Camellia oleifera (C. oleifera) cultivars 'Huashuo' (HS) and 'Huaxin' (HX) are new high-yielding and economically valuable cultivars that frequently encounter prolonged cold weather during the flowering period, resulting in decreased yields and quality. The flower buds of HS sometimes fail to open or open incompletely under cold stress, whereas the flower buds of HX exhibit delayed opening but the flowers and fruits rarely drop.

METHODS

In this study, flower buds at the same development stage of two C. oleifera cultivars were used as test materials for a combination of physiological, transcriptomic and metabolomic analyses, to unravel the different cold regulatory mechanisms between two cultivars of C. oleifera.

RESULTS AND DISCUSSION

Key differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) involved in sugar metabolism, phenylpropanoid biosynthesis, and hormone signal transduction were significantly higher in HX than in HS, which is consistent with phenotypic observations from a previous study. The results indicate that the flower buds of HX are less affected by long-term cold stress than those of HS, and that cold resistance in C. oleifera cultivars varies among tissues or organs.This study will provide a basis for molecular markers and molecular breeding of C. oleifera.

Testing the chilling- before drought-tolerance hypothesis in Pooideae grasses

Temperate Pooideae are a large clade of economically important grasses distributed in some of the Earth's coldest and driest terrestrial environments. Previous studies have inferred that Pooideae diversified from their tropical ancestors in a cold montane habitat, suggesting that above-freezing cold (chilling) tolerance evolved early in the subfamily. By contrast, drought tolerance is hypothesized to have evolved multiple times independently in response to global aridification that occurred after the split of Pooideae tribes. To independently test predictions of the chilling-before-drought hypothesis in Pooideae, we assessed conservation of whole plant and gene expression traits in response to chilling vs. drought. We demonstrated that both trait responses are more similar across tribes in cold as compared to drought, suggesting that chilling responses evolved before, and drought responses after, tribe diversification. Moreover, we found significantly more overlap between drought and chilling responsive genes within a species than between drought responsive genes across species, providing evidence that chilling tolerance genes acted as precursors for the novel acquisition of increased drought tolerance multiple times independently, partially through the cooption of chilling responsive genes.

Combined Transcriptome and Metabolome Profiling Provide Insights into Cold Responses in Rapeseed (Brassica napus L.) Genotypes with Contrasting Cold-Stress Sensitivity

Low temperature is a major environmental factor, which limits rapeseed (Brassica napus L.) growth, development, and productivity. So far, the physiological and molecular mechanisms of rapeseed responses to cold stress are not fully understood. Here, we explored the transcriptome and metabolome profiles of two rapeseed genotypes with contrasting cold responses, i.e., XY15 (cold-sensitive) and GX74 (cold-tolerant). The global metabolome profiling detected 545 metabolites in siliques of both genotypes before (CK) and after cold-stress treatment (LW). The contents of several sugar metabolites were affected by cold stress with the most accumulated saccharides being 3-dehydro-L-threonic acid, D-xylonic acid, inositol, D-mannose, D-fructose, D-glucose, and L-glucose. A total of 1943 and 5239 differentially expressed genes were identified from the transcriptome sequencing in XY15CK_vs_XY15LW and GX74CK_vs_GX74LW, respectively. We observed that genes enriched in sugar metabolism and biosynthesis-related pathways, photosynthesis, reactive oxygen species scavenging, phytohormone, and MAPK signaling were highly expressed in GX74LW. In addition, several genes associated with cold-tolerance-related pathways, e.g., the CBF-COR pathway and MAPK signaling, were specifically expressed in GX74LW. Contrarily, genes in the above-mentioned pathways were mostly downregulated in XY15LW. Thus, our results indicate the involvement of these pathways in the differential cold-stress responses in XY15 and GX74.

Transcriptome Analysis of Low-Temperature-Treated Tetraploid Yellow Actinidia chinensis Planch. Tissue Culture Plantlets

Simple Summary

Yellow kiwifruit (Actinidia chinensis Planch.) is popular in the market. However, it is highly susceptible to severe weather, including as low temperatures and frost, which may affect its production in the coming year. The cold-resistant mechanism of yellow kiwifruit associated with gene regulation is poorly investigated. To better understand cold-adaptive mechanisms, we grew plants under low-temperature conditions, which was followed by transcriptome analysis to discern the genes that play an active role in growth under low temperatures. The findings and dataset obtained in this study advance our knowledge of the cold-adaptive genes in regulatory networks and helps us to understand the cold-tolerance mechanisms in the tetraploid yellow kiwifruit.

Abstract

The cold-resistant mechanism of yellow kiwifruit associated with gene regulation is poorly investigated. In this study, to provide insight into the causes of differences in low-temperature tolerance and to better understand cold-adaptive mechanisms, we treated yellow tetraploid kiwifruit ‘SWFU03’ tissue culture plantlets at low temperatures, used these plantlets for transcriptome analysis, and validated the expression levels of ten selected genes by real-time quantitative polymerase chain reaction (RT-qPCR) analysis. A number of 1630 differentially expressed genes (DEGs) were identified, of which 619 pathway genes were up-regulated, and 1011 were down-regulated in the cold treatment group. The DEGs enriched in the cold tolerance-related pathways mainly included the plant hormone signal transduction and the starch and sucrose metabolism pathway. RT-qPCR analysis confirmed the expression levels of eight up-regulated genes in these pathways in the cold-resistant mutants. In this study, cold tolerance-related pathways (the plant hormone signal transduction and starch and sucrose metabolism pathway) and genes, e.g., CEY00_Acc03316 (abscisic acid receptor PYL), CEY00_Acc13130 (bZIP transcription factor), CEY00_Acc33627 (TIFY protein), CEY00_Acc26744 (alpha-trehalose-phosphate synthase), CEY00_Acc28966 (beta-amylase), CEY00_Acc16756 (trehalose phosphatase), and CEY00_Acc08918 (beta-amylase 4) were found.

Comparative transcriptomic and lipidomic analyses indicate that cold stress enhanced the production of the long C18–C22 polyunsaturated fatty acids in Aurantiochytrium sp

Aurantiochytrium sp. belonging to Thraustochytrids are known for their capacity to produce long-chain polyunsaturated fatty acids (PUFAs). However, effects of cold stress accompanied with staged-temperature control on the fatty acid metabolism in Aurantiochytrium sp. were rarely studied. In this study, cold stress (15°C, 5°C) was applied for Aurantiochytrium sp., with the physiological responses (morphology, growth, fatty acid profiling) and gene expression related FA synthesis, lipid metabolism, and regulatory processes was observed. Results showed that there is a significant change for the lipid types under 5°C (251 species) and 15°C (97 species) treatment. The 5°C treatment was benefit for the C18–C22 PUFAs with the yield of docosahexaenoic acid (DHA) increased to 1.25 times. After incubation at 15°C, the accumulation of eicosadienoic acid (EA) (20:2) was increased to 2.00-fold. Based on transcriptomic and qPCR analysis, an increase in genes involved in fatty acid synthase (FAS) and polyketide synthase (PKS) pathways was observed under low-temperature treatment. With upregulation of 3-ketoacyl-CoA synthase (2.44-fold), ketoreductase (2.50-fold), and dTDP-glucose 4,6-Dehydratase (rfbB) (2.31-fold) involved in PKS pathway, the accumulation of DHA was enhanced under 5°C. While, FAS and fatty elongase 3 (ELO) involved in the FAS pathway were upregulated (1.55-fold and 2.45-fold, respectively) to accumulate PUFAs at 15°C. Additionally, glycerol-3-phosphate acyltransferase (GPAT), lysophospholipid acyltransferase (LPAT), phosphatidic acid phosphatase (PAP), phosphatidylserine synthase (PSS), and phosphatidylserine decarboxylase (PSD) involved in glycerophospholipid biosynthesis were upregulated at 5°C increasing the accumulation of phosphatidic acid (PA), phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and phosphatidylinositol (PI). However, glycolysis and the TCA cycle were inhibited under 5°C. This study provides a contribution to the application of two-staged temperature control in the Aurantiochytrium sp. fermentation for producing cold stress-enhancing PUFAs, in order to better understand the function of the key genes for future genetic engineering.

Transcriptome analysis of the winter wheat Dn1 in response to cold stress

BACKGROUND

Heilongjiang Province has a long and cold winter season (the minimum temperature can reach -30 ℃), and few winter wheat varieties can safely overwinter. Dongnongdongmai1 (Dn1) is the first winter wheat variety that can safely overwinter in Heilongjiang Province. This variety fills the gap for winter wheat cultivation in the frigid region of China and greatly increases the land utilization rate. To understand the molecular mechanism of the cold response, we conducted RNA-sequencing analysis of Dn1 under cold stress.

RESULTS

Approximately 120,000 genes were detected in Dn1 under cold stress. The numbers of differentially expressed genes (DEGs) in the six comparison groups (0 ℃ vs. 5 ℃, -5 ℃ vs. 5 ℃, -10 ℃ vs. 5 ℃, -15 ℃ vs. 5 ℃, -20 ℃ vs. 5 ℃ and -25 ℃ vs. 5 ℃) were 11,313, 8313, 15,636, 13,671, 14,294 and 13,979, respectively. Gene Ontology functional annotation suggested that the DEGs under cold stress mainly had "binding", "protein kinase" and "catalytic" activities and were involved in "oxidation-reduction", "protein phosphorylation" and "carbohydrate metabolic" processes. Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that the DEGs performed important functions in cold signal transduction and carbohydrate metabolism. In addition, major transcription factors (AP2/ERF, bZIP, NAC, WRKY, bHLH and MYB) participating in the Dn1 cold stress response were activated by low temperature.

CONCLUSION

This is the first study to explore the Dn1 transcriptome under cold stress. Our study comprehensively analysed the key genes involved in cold signal transduction and carbohydrate metabolism in Dn1 under cold stress. The results obtained by transcriptome analysis could help to further explore the cold resistance mechanism of Dn1 and provide basis for breeding of cold-resistant crops.

Increasing Interspecific Difference of Alpine Herb Phenology on the Eastern Qinghai-Tibet Plateau

The phenology of alpine grassland on the Qinghai-Tibet Plateau (QTP) is critical to regional climate change through climate-vegetation feedback. Although many studies have examined QTP vegetation dynamics and their climate sensitivities, the interspecific difference in the phenology response to climate change between alpine species is poorly understood. Here, we used a 30-year (1989-2018) record of in situ phenological observation for five typical alpine herbs (Elymus nutans, Kobresia pygmaea, Plantago asiatica, Puccinellia tenuiflora, and Scirpus distigmaticus) and associated climatic records at Henan Station in the eastern QTP to examine the species-level difference in spring and autumn phenology and then quantify their climate sensitivities. Our results show that with significantly warming, the green-up dates of herbs were insignificantly shifted, while the brown-off dates in four out of the five herbs were significantly delayed. Meanwhile, the interspecific difference in brown-off dates significantly increased at a rate of 0.62 days/annual from 1989 to 2016, which was three times larger than that in green-up dates (0.20 days/annual). These diverse rates were attributed to the different climate controls on spring and autumn phenology. In particular, green-up dates in most herbs were sensitive to mean surface temperature, while brown-off dates were sensitive to the night surface temperature. Furthermore, brown-off dates are less sensitive to the warming in high ecological niche (with higher herb height and aboveground biomass) herbs than low niche herbs (with lower herb height and aboveground biomass). The increased phenology interspecific difference highlights the complex responses of herbs to future climate change even under the same alpine environment and indicates a potential alternation in the plants community of alpine QTP, which may further influence the regional climate-vegetation feedback.

Transcriptome analysis and differential gene expression profiling of wucai (Brassica campestris L.) in response to cold stress

Background

Wucai suffers from low temperature during the growth period, resulting in a decline in yield and poor quality. But the molecular mechanisms of cold tolerance in wucai are still unclear.

Results

According to the phenotypes and physiological indexes, we screened out the cold-tolerant genotype “W18” (named CT) and cold-sensitive genotype “Sw-1” (named CS) in six wucai genotypes. We performed transcriptomic analysis using seedling leaves after 24 h of cold treatment. A total of 3536 and 3887 differentially expressed genes (DEGs) were identified between the low temperature (LT) and control (NT) comparative transcriptome in CT and CS, respectively, with 1690 DEGs specific to CT. The gene ontology (GO) analysis showed that the response to cadmium ion (GO:0,046,686), response to jasmonic acid (GO:0,009,753), and response to wounding (GO:0,009,611) were enriched in CT (LT vs NT). The DEGs were enriched in starch and sucrose metabolism and glutathione metabolism in both groups, and α-linolenic acid metabolism was enriched only in CT (LT vs NT). DEGs in these processes, including glutathione S-transferases (GSTs), 13S lipoxygenase (LOX), and jasmonate ZIM-domain (JAZ), as well as transcription factors (TFs), such as the ethylene-responsive transcription factor 53 (ERF53), basic helix-loop-helix 92 (bHLH92), WRKY53, and WRKY54.We hypothesize that these genes play important roles in the response to cold stress in this species.

Conclusions

Our data for wucai is consistent with previous studies that suggest starch and sucrose metabolism increased the content of osmotic substances, and the glutathione metabolism pathway enhance the active oxygen scavenging. These two pathways may participated in response to cold stress. In addition, the activation of α-linolenic acid metabolism may promote the synthesis of methyl jasmonate (MeJA), which might also play a role in the cold tolerance of wucai.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08311-3.

Comparative transcriptomic and physiological analyses of weedy rice and cultivated rice to identify vital differentially expressed genes and pathways regulating the ABA response

Weedy rice is a valuable germplasm resource characterized by its high tolerance to both abiotic and biotic stresses. Abscisic acid (ABA) serves as a regulatory signal in plant cells as part of their adaptive response to stress. However, a global understanding of the response of weedy rice to ABA remains to be elucidated. In the present study, the sensitivity to ABA of weedy rice (WR04-6) was compared with that of temperate japonica Shennong9816 (SN9816) in terms of seed germination and post-germination growth via the application of exogenous ABA and diniconazole, an inhibitor of ABA catabolism. Physiological analysis and a transcriptomic comparison allowed elucidation of the molecular and physiological mechanisms associated with continuous ABA and diniconazole treatment. WR04-6 was found to display higher ABA sensitivity than SN9816, resulting in the rapid promotion of antioxidant enzyme activity. Comparative transcriptomic analyses indicated that the number of differentially expressed genes (DEGs) in WR04-6 seedlings treated with 2 μM ABA or 10 μM diniconazole was greater than that in SN9816 seedlings. Genes involved in stress defense, hormone signal transduction, and glycolytic and citrate cycle pathways were highly expressed in WR04-6 in response to ABA and diniconazole. These findings provide new insight into key processes mediating the ABA response between weedy and cultivated rice.