A nanopore-based cucumber genome assembly reveals structural variations at two QTLs controlling hypocotyl elongation.

The Xishuangbanna (XIS) cucumber (Cucumis sativus var. xishuangbannanesis) is a semiwild variety that has many distinct agronomic traits. Here, long reads generated by Nanopore sequencing technology helped assembling a high-quality genome (contig N50 = 8.7 Mb) of landrace XIS49. A total of 10,036 structural/sequence variations (SVs) were identified when comparing with Chinese Long (CL), and known SVs controlling spines, tubercles, and carpel number were confirmed in XIS49 genome. Two QTLs of hypocotyl elongation under low light, SH3.1 and SH6.1, were fine-mapped using introgression lines (donor parent, XIS49; recurrent parent, CL). SH3.1 encodes a red-light receptor Phytochrome B (PhyB, CsaV3_3G015190). A ∼4 kb region with large deletion and highly divergent regions (HDRs) were identified in the promoter of the PhyB gene in XIS49. Loss of function of this PhyB caused a super-long hypocotyl phenotype. SH6.1 encodes a CCCH-type zinc finger protein FRIGIDA-ESSENTIAL LIKE (FEL, CsaV3_6G050300). FEL negatively regulated hypocotyl elongation but it was transcriptionally suppressed by long terminal repeats retrotransposon insertion in CL cucumber. Mechanistically, FEL physically binds to the promoter of CONSTITUTIVE PHOTOMORPHOGENIC 1a (COP1a), regulating the expression of COP1a and the downstream hypocotyl elongation. These above results demonstrate the genetic mechanism of cucumber hypocotyl elongation under low light.

Comparative phylogenetic analysis of the mediator complex subunit in asparagus bean (Vigna unguiculata ssp. sesquipedialis) and its expression profile under cold stress.

BACKGROUND: The mediator complex subunits (MED) constitutes a multiprotein complex, with each subunit intricately involved in crucial aspects of plant growth, development, and responses to stress. Nevertheless, scant reports pertain to the VunMED gene within the context of asparagus bean (Vigna unguiculata ssp. sesquipedialis). Establishing the identification and exploring the responsiveness of VunMED to cold stress forms a robust foundation for the cultivation of cold-tolerant asparagus bean cultivars. RESULTS: Within this study, a comprehensive genome-wide identification of VunMED genes was executed in the asparagus bean cultivar 'Ningjiang3', resulting in the discovery of 36 distinct VunMED genes. A phylogenetic analysis encompassing 232 MED genes from diverse species, including Arabidopsis, tomatoes, soybeans, mung beans, cowpeas, and asparagus beans, underscored the highly conserved nature of MED gene sequences. Throughout evolutionary processes, each VunMED gene underwent purification and neutral selection, with the exception of VunMED19a. Notably, VunMED9/10b/12/13/17/23 exhibited structural variations discernible across four cowpea species. Divergent patterns of temporal and spatial expression were evident among VunMED genes, with a prominent role attributed to most genes during early fruit development. Additionally, an analysis of promoter cis-acting elements was performed, followed by qRT-PCR assessments on roots, stems, and leaves to gauge relative expression after exposure to cold stress and subsequent recovery. Both treatments induced transcriptional alterations in VunMED genes, with particularly pronounced effects observed in root-based genes following cold stress. Elucidating the interrelationships between subunits involved a preliminary understanding facilitated by correlation and principal component analyses. CONCLUSIONS: This study elucidates the pivotal contribution of VunMED genes to the growth, development, and response to cold stress in asparagus beans. Furthermore, it offers a valuable point of reference regarding the individual roles of MED subunits.

The Development and Application of Vegetable Genomics Increase the Efficiency of Exploring New Gene Resources for Vegetables.

Vegetables, as indispensable non-staple foods in people's daily diet, provide a variety of essential vitamins, minerals, and other nutrients, as well as special phytochemicals, which are recognized as functional components for human nutritional balance or medicinal purposes [...].

Molecular Regulatory Mechanism of Exogenous Hydrogen Sulfide in Alleviating Low-Temperature Stress in Pepper Seedlings.

Pepper (Capsicum annuum L.) is sensitive to low temperatures, with low-temperature stress affecting its plant growth, yield, and quality. In this study, we analyzed the effects of exogenous hydrogen sulfide (H2S) on pepper seedlings subjected to low-temperature stress. Exogenous H2S increased the content of endogenous H2S and its synthetase activity, enhanced the antioxidant capacity of membrane lipids, and protected the integrity of the membrane system. Exogenous H2S also promoted the Calvin cycle to protect the integrity of photosynthetic organs; enhanced the photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), and photosynthesis; and reduced the intercellular CO2 concentration (Ci). Moreover, the activities of superoxide dismutase, peroxidase, catalase, and anti-cyclic glutathione (ASA-GSH) oxidase were improved to decompose excess reactive oxygen species (ROS), enhance the oxidative stress and detoxification ability of pepper seedlings, and improve the resistance to low-temperature chilling injury in 'Long Yun2' pepper seedlings. In addition, the H2S scavenger hypotaurine (HT) aggravated the ROS imbalance by reducing the endogenous H2S content, partially eliminating the beneficial effects of H2S on the oxidative stress and antioxidant defense system, indicating that H2S can effectively alleviate the damage of low temperature on pepper seedlings. The results of transcriptome analysis showed that H2S could induce the MAPK-signaling pathway and plant hormone signal transduction; upregulate the expression of transcription factors WRKY22 and PTI6; induce defense genes; and activate the ethylene and gibberellin synthesis receptors ERF1, GDI2, and DELLA, enhancing the resistance to low-temperature chilling injury of pepper seedlings. The plant-pathogen interaction was also significantly enriched, suggesting that exogenous H2S also promotes the expression of genes related to plant-pathogen interaction. The results of this study provide novel insights into the molecular mechanisms and genetic modifications of H2S that mitigate the hypothermic response.

5-ALA Improves the Low Temperature Tolerance of Common Bean Seedlings through a Combination of Hormone Transduction Pathways and Chlorophyll Metabolism.

Low-temperature stress is a key factor limiting the yield and quality of the common bean. 5-aminolevulinic acid (5-ALA), an antioxidant in plants, has been shown to modulate plant cold stress responses. However, the molecular mechanisms of 5-ALA-induced physiological and chemical changes in common bean seedlings under cold stress remains unknown. This study explored the physiological and transcriptome changes of common bean seedlings in response to cold stress after 5-ALA pretreatment. Physiological results showed that exogenous 5-ALA promotes the growth of common bean plants under cold stress, increases the activity of antioxidant enzymes (superoxide dismutase: 23.8%; peroxidase: 10.71%; catalase: 9.09%) and proline content (24.24%), decreases the relative conductivity (23.83%), malondialdehyde (33.65%), and active oxygen content, and alleviates the damage caused by cold to common bean seedlings. Transcriptome analysis revealed that 214 differentially expressed genes (DEGs) participate in response to cold stress. The DEGs are mainly concentrated in indole alkaloid biosynthesis, carotenoid biosynthesis, porphyrin, and chlorophyll metabolism. It is evident that exogenous 5-ALA alters the expression of genes associated with porphyrin and chlorophyll metabolism, as well as the plant hormone signal transduction pathway, which helps to maintain the energy supply and metabolic homeostasis under low-temperature stress. The results reveal the effect that applying exogenous 5-ALA has on the cold tolerance of the common bean and the molecular mechanism of its response to cold tolerance, which provides a theoretical basis for exploring and improving plant tolerance to low temperatures.

CaSPDS, a Spermidine Synthase Gene from Pepper (Capsicum annuum L.), Plays an Important Role in Response to Cold Stress.

Spermidine synthase (SPDS) is a key enzyme in the polyamine anabolic pathway. SPDS genes help regulate plant response to environmental stresses, but their roles in pepper remain unclear. In this study, we identified and cloned a SPDS gene from pepper (Capsicum annuum L.), named CaSPDS (LOC107847831). Bioinformatics analysis indicated that CaSPDS contains two highly conserved domains: an SPDS tetramerisation domain and a spermine/SPDS domain. Quantitative reverse-transcription polymerase chain reaction results showed that CaSPDS was highly expressed in the stems, flowers, and mature fruits of pepper and was rapidly induced by cold stress. The function of CaSPDS in cold stress response was studied by silencing and overexpressing it in pepper and Arabidopsis, respectively. Cold injury was more serious and reactive oxygen species levels were greater in the CaSPDS-silenced seedlings than in the wild-type (WT) seedlings after cold treatment. Compared with the WT plants, the CaSPDS-overexpression Arabidopsis plants were more tolerant to cold stress and showed higher antioxidant enzyme activities, spermidine content, and cold-responsive gene (AtCOR15A, AtRD29A, AtCOR47, and AtKIN1) expression. These results indicate that CaSPDS plays important roles in cold stress response and is valuable in molecular breeding to enhance the cold tolerance of pepper.

Lipid-Related Domestication Accounts for the Extreme Cold Sensitivity of Semiwild and Tropic Xishuangbanna Cucumber (Cucumis sativus L. var. xishuangbannanesis).

Xishuangbanna (XIS) cucumber (Cucumis sativus L. var. xishuangbannanesis) is a semiwild variety originating from low latitude tropic areas, and therefore shows extreme cold sensitivity and heat tolerance. Here, we mapped the quantitative trait loci (QTLs) that control the cold sensitivity and heat tolerance of XIS cucumber seedlings. Using bulked segregant analysis (BSA), we identified three QTLs (HTT1.1, HTT3.1, and HTT3.2, with a total length of 11.98 Mb) for heat tolerance and two QTLs (LTT6.1 and LTT6.2, with a total length of 8.74 Mb) for cold sensitivity. The QTL LTT6.1 was then narrowed down to a length of 641 kb by using kompetitive allele-specific PCR (KASP) markers. Based on structural variants (SVs) and single-nucleotide polymorphisms (SNPs), we found the LTT6.1 is covered by a high divergent region including a 50 kb deletion in the XIS49 genome, which affects the gene structure of lipase abhydrolase domain containing 6 (ABHD6, Csa_6G032560). Accordingly, there is a very big difference in lipid composition, but not in other osmoprotectants like free amino acids and fatty acids, between XIS49 and cultivated cucumber CL. Moreover, we calculated the composite likelihood ratio (CLR) and identified selective sweeps from 115 resequencing data, and found that lipid- and fatty-acid-related processes are major aspects in the domestication of the XIS group cucumber. LTT6.1 is a particularly special region positioned nearby lipid-related selective sweeps. These studies above suggested that the lipid-related domestication of XIS cucumbers should account for their extreme cold sensitivity.

Absorption, translocation, and accumulation of the fungicide triadimefon in Pak choi (Brassica rapa var chinensis), pepper (Capsicum annuum), and cucumber (Cucumis sativus).

Triadimefon is a typical systemic fungicide that is widely used in the management of powdery mildew, rust disease, and southern blight. In this study, we measured fungicide residue to profile its absorption, translocation, and accumulation in three representative vegetable crops (Pak choi, cucumber, and pepper) after over-application. The fungicides were applied through entire-plant spraying (EPS), root-irrigation (RI), and middle-leaf-daubing (MLD). The half-life of triadimefon depends on the application method and plant species. In EPS, the half-life was 5.42 days (Pak choi), 6.86 days (cucumber), and 6.73 days (pepper), while in RI it was 4.39 days (Pak choi), 6.30 days (cucumber), and 5.98 days (pepper). In the EPS treatment, triadimefon is translocated both upward/outside and downward/inner-side from the daubed leaves in all the three vegetable crops. The transfer amount to each organ reached a peak on the 2nd day after fungicide application. The mesophyll of Pak choi exhibited a higher fungicide deposition compared to the petiole. In cucumber and pepper, the leaves demonstrated the highest accumulation of triadimefon (approximately 0.3-0.5 mg·kg-1), followed by stems. Roots and fruits displayed the lowest levels of triadimefon accumulation. Furthermore, triadimefon was found to have an impact on chlorophyll content, root activity, as well as the activity of superoxide dismutase and catalase in Pak choi, indicating its potential as a plant growth regulator. These aforementioned studies provide novel insights for the safe and efficient application of triadimefon in the production of Pak choi, cucumber, and pepper.

Genome-Wide Identification of Polyamine Oxidase (PAO) Family Genes: Roles of CaPAO2 and CaPAO4 in the Cold Tolerance of Pepper (Capsicum annuum L.).

Polyamine oxidases (PAOs), which are flavin adenine dinucleotide-dependent enzymes, catalyze polyamine (PA) catabolism, producing hydrogen peroxide (H2O2). Several PAO family members have been identified in plants, but their expression in pepper plants remains unclear. Here, six PAO genes were identified in the 'Zunla-1' pepper genome (named CaPAO1-CaPAO6 according to their chromosomal positions). The PAO proteins were divided into four subfamilies according to phylogenetics: CaPAO1 belongs to subfamily I; CaPAO3 and CaPAO5 belong to subfamily III; and CaPAO2, CaPAO4, and CaPAO6 belong to subfamily IV (none belong to subfamily II). CaPAO2, CaPAO4, and CaPAO6 were ubiquitously and highly expressed in all tissues, CaPAO1 was mainly expressed in flowers, whereas CaPAO3 and CaPAO5 were expressed at very low levels in all tissues. RNA-seq analysis revealed that CaPAO2 and CaPAO4 were notably upregulated by cold stress. CaPAO2 and CaPAO4 were localized in the peroxisome, and spermine was the preferred substrate for PA catabolism. CaPAO2 and CaPAO4 overexpression in Arabidopsis thaliana significantly enhanced freezing-stress tolerance by increasing antioxidant enzyme activity and decreasing malondialdehyde, H2O2, and superoxide accumulation, accompanied by the upregulation of cold-responsive genes (AtCOR15A, AtRD29A, AtCOR47, and AtKIN1). Thus, we identified candidate PAO genes for breeding cold-stress-tolerant transgenic pepper cultivars.

Biosynthesis and Metabolism of Garlic Odor Compounds in Cultivated Chinese Chives (Allium tuberosum) and Wild Chinese Chives (Allium hookeri).

Chinese chives is a popular herb vegetable and medicine in Asian countries. Southwest China is one of the centers of origin, and the mountainous areas in this region are rich in wild germplasm. In this study, we collected four samples of germplasm from different altitudes: a land race of cultivated Chinese chives (Allium tuberosum), wide-leaf chives and extra-wide-leaf chives (Allium hookeri), and ovoid-leaf chives (Allium funckiaefolium). Leaf metabolites were detected and compared between A. tuberosum and A. hookeri. A total of 158 differentially accumulated metabolites (DAM) were identified by Gas Chromatography-Mass Spectrometry (GC-MS) and Liquid Chromatography-Mass Spectrometry (LC-MS), among which there was a wide range of garlic odor compounds, free amino acids, and sugars. A. hookeri contains a higher content of fructose, garlic odor compounds, and amino acids than A. tuberosum, which is supported by the higher expression level of biosynthetic genes revealed by transcriptome analysis. A. hookeri accumulates the same garlic odor compound precursors that A. tuberosum does (mainly methiin and alliin). We isolated full-length gene sequences of phytochelatin synthase (PCS), γ-glutamyltranspeptidases (GGT), flavin-containing monooxygenase (FMO), and alliinase (ALN). These sequences showed closer relations in phylogenetic analysis between A. hookeri and A. tuberosum (with sequence identities ranging from 86% to 90%) than with Allium cepa or Allium sativum (which had a lower sequence identity ranging from 76% to 88%). Among these assayed genes, ALN, the critical gene controlling the conversion of odorless precursors into odor compounds, was undetected in leaves, bulbs, and roots of A. tuberosum, which could account for its weaker garlic smell. Moreover, we identified a distinct FMO1 gene in extra-wide-leaf A. hookeri that is due to a CDS-deletion and frameshift mutation. These results above reveal the molecular and metabolomic basis of impressive strong odor in wild Chinese chives.

The dissection of R genes and locus Pc5.1 in Phytophthora capsici infection provides a novel view of disease resistance in peppers.

BACKGROUND: Phytophthora capsici root rot (PRR) is a disastrous disease in peppers (Capsicum spp.) caused by soilborne oomycete with typical symptoms of necrosis and constriction at the basal stem and consequent plant wilting. Most studies on the QTL mapping of P. capsici resistance suggested a consensus broad-spectrum QTL on chromosome 5 named Pc.5.1 regardless of P. capsici isolates and resistant resources. In addition, all these reports proposed NBS-ARC domain genes as candidate genes controlling resistance. RESULTS: We screened out 10 PRR-resistant resources from 160 Capsicum germplasm and inspected the response of locus Pc.5.1 and NBS-ARC genes during P. capsici infection by comparing the root transcriptomes of resistant pepper 305R and susceptible pepper 372S. To dissect the structure of Pc.5.1, we anchored genetic markers onto pepper genomic sequence and made an extended Pc5.1 (Ext-Pc5.1) located at 8.35 Mb-38.13 Mb on chromosome 5 which covered all Pc5.1 reported in publications. A total of 571 NBS-ARC genes were mined from the genome of pepper CM334 and 34 genes were significantly affected by P. capsici infection in either 305R or 372S. Only 5 inducible NBS-ARC genes had LRR domains and none of them was positioned at Ext-Pc5.1. Ext-Pc5.1 did show strong response to P. capsici infection and there were a total of 44 differentially expressed genes (DEGs), but no candidate genes proposed by previous publications was included. Snakin-1 (SN1), a well-known antimicrobial peptide gene located at Pc5.1, was significantly decreased in 372S but not in 305R. Moreover, there was an impressive upregulation of sugar pathway genes in 305R, which was confirmed by metabolite analysis of roots. The biological processes of histone methylation, histone phosphorylation, DNA methylation, and nucleosome assembly were strongly activated in 305R but not in 372S, indicating an epigenetic-related defense mechanism. CONCLUSIONS: Those NBS-ARC genes that were suggested to contribute to Pc5.1 in previous publications did not show any significant response in P. capsici infection and there were no significant differences of these genes in transcription levels between 305R and 372S. Other pathogen defense-related genes like SN1 might account for Pc5.1. Our study also proposed the important role of sugar and epigenetic regulation in the defense against P. capsici.

MicroRNAs and their targets in cucumber shoot apices in response to temperature and photoperiod.

BACKGROUND: The cucumber is one of the most important vegetables worldwide and is used as a research model for study of phloem transport, sex determination and temperature-photoperiod physiology. The shoot apex is the most important plant tissue in which the cell fate and organ meristems have been determined. In this study, a series of whole-genome small RNA, degradome and transcriptome analyses were performed on cucumber shoot apical tissues treated with high vs. low temperature and long vs. short photoperiod. RESULTS: A total of 164 known miRNAs derived from 68 families and 203 novel miRNAs from 182 families were identified. Their 4611 targets were predicted using psRobot and TargetFinder, amongst which 349 were validated by degradome sequencing. Fourteen targets of six miRNAs were differentially expressed between the treatments. A total of eight known and 16 novel miRNAs were affected by temperature and photoperiod. Functional annotations revealed that "Plant hormone signal transduction" pathway was significantly over-represented in the miRNA targets. The miR156/157/SBP-Boxes and novel-mir153/ethylene-responsive transcription factor/senescence-related protein/aminotransferase/acyl-CoA thioesterase are the two most credible miRNA/targets combinations modulating the plant's responsive processes to the temperature-photoperiod changes. Moreover, the newly evolved, cucumber-specific novel miRNA (novel-mir153) was found to target 2087 mRNAs by prediction and has 232 targets proven by degradome analysis, accounting for 45.26-58.88% of the total miRNA targets in this plant. This is the largest sum of genes targeted by a single miRNA to the best of our knowledge. CONCLUSIONS: These results contribute to a better understanding of the miRNAs mediating plant adaptation to combinations of temperature and photoperiod and sheds light on the recent evolution of new miRNAs in cucumber.

Temperature and photoperiod changes affect cucumber sex expression by different epigenetic regulations.

BACKGROUND: Cucumbers (Cucumis sativus) are known for their plasticity in sex expression. DNA methylation status determines gene activity but is susceptible to environmental condition changes. Thus, DNA methylation-based epigenetic regulation may at least partially account for the instability of cucumber sex expression. Do temperature and photoperiod that are the two most important environmental factors have equal effect on cucumber sex expression by similar epigenetic regulation mechanism? To answer this question, we did a two-factor experiment of temperature and photoperiod and generated methylome and transcriptome data from cucumber shoot apices. RESULTS: The seasonal change in the femaleness of a cucumber core germplasm collection was investigated over five consecutive years. As a result, 71.3% of the 359 cucumber accessions significantly decreased their femaleness in early autumn when compared with spring. High temperature and long-day photoperiod treatments, which mimic early autumn conditions, are both unfavorable for female flower formation, and temperature is the predominant factor. High temperatures and long-day treatments both predominantly resulted in hypermethylation compared to demethylation, and temperature effect was decisive. The targeted cytosines shared in high-temperature and long-day photoperiod treatment showed the same change in DNA methylation level. Moreover, differentially expressed TEs (DETs) and the predicted epiregulation sites were clustered across chromosomes, and importantly, these sites were reproducible among different treatments. Essentially, the photoperiod treatment preferentially and significantly influenced flower development processes, while temperature treatment produced stronger responses from phytohormone-pathway-related genes. Cucumber AGAMOUS was likely epicontrolled exclusively by photoperiod while CAULIFLOWER A and CsACO3 were likely epicontrolled by both photoperiod and temperature. CONCLUSIONS: Seasonal change of sex expression is a germplasm-wide phenomenon in cucumbers. High temperature and long-day photoperiod might have the same effect on the methylome via the same mechanism of gene-TE interaction but resulted in different epicontrol sites that account for different mechanisms between temperature- and photoperiod-dependent sex expression changes.

Effects of living hyperaccumulator plants and their straws on the growth and cadmium accumulation of Cyphomandra betacea seedlings.

To determine whether the living hyperaccumulator plants and their straws have the same effects on the growth and heavy metal accumulation of common plants, two pot experiments (intercropping experiment and straw mulch experiment) were conducted to study the effects of living hyperaccumulator plants (Solanum photeinocarpum, Tagetes erecta, Galinsoga parviflora and Bidens pilosa) and their straws on the growth and cadmium (Cd) accumulation of common plant Cyphomandra betacea seedlings. Intercropping with T. erecta or B. pilosa promoted the growth of C. betacea seedlings compared with the monoculture, while intercropping with S. photeinocarpum or G. parviflora inhibited that. Intercropping with S. photeinocarpum decreased the Cd contents in the roots and shoots of C. betacea seedlings compared with the monoculture, but intercropping with the other plants did not. In the straw mulch experiment, the straw of S. photeinocarpum or T. erecta promoted the growth of C. betacea seedlings compared with the control, while the straw of G. parviflora or B. pilosa did not. The straw of S. photeinocarpum or T. erecta decreased the Cd contents in the shoots of C. betacea seedlings, and the straw of G. parviflora or B. pilosa increased the shoot Cd contents. Thus, intercropping with S. photeinocarpum and applying S. photeinocarpum or T. erecta straw can reduce the Cd uptake of C. betacea.

Effects of melatonin on the growth and cadmium characteristics of Cyphomandra betacea seedlings.

To determine whether the melatonin (MT) could reduce cadmium (Cd) accumulation in Cyphomandra betacea seedlings, different concentrations of MT were added to the nutrient solution and soil to study its effects on the growth and Cd characteristics of C. betacea seedlings. Fifty micromoles per liter (µmol/kg) of MT increased the biomass of C. betacea seedlings, but 100-200 µmol/L (µmol/kg) MT decreased seedling biomass in both the nutrient solution and soil cultivation experiments. The photosynthetic pigment contents showed no significant changes compared with the control when the MT dose was 150 µmol/L (µmol/kg) or less, while 200 µmol/L (µmol/kg) MT decreased the photosynthetic pigment contents. Low levels of MT improved the antioxidant enzyme activities of C. betacea seedlings, whereas high MT levels reduced them. MT increased the Cd contents in different organs of C. betacea seedlings in the nutrient solution cultivation experiment, but only 50 µmol/kg MT increased the Cd contents in stems, leaves, and shoots of C. betacea seedlings in the soil cultivation experiment. Therefore, only low levels of MT can promote the growth of C. betacea seedlings, and MT is not suitable for reducing Cd accumulation in C. betacea seedlings.

The association of changes in DNA methylation with temperature-dependent sex determination in cucumber.

Cucumber (Cucumis sativus L.) is characterized by its diverse and flexible sexual types. Here, we evaluated the effect of low temperature (LT) exposure on cucumber femaleness under short-day conditions. Shoot apices were subjected to whole-genome bisulfate sequencing (WGBS), mRNA-seq, and sRNA-seq. The results showed that temperature had a substantial and global impact on transposable element (TE)-related small RNA-directed DNA methylation (RdDM) mechanisms, resulting in large amounts of CHH-type cytosine demethylation. In the cucumber genome, TEs are common in regions near genes that are also subject to DNA demethylation. TE-gene interactions showed very strong reactions to LT treatment, as nearly 80% of the differentially methylated regions (DMRs) were distributed in genic regions. Demethylation near genes led to the co-ordinated expression of genes and TEs. More importantly, genome-wide de novo methylation changes also resulted in small amounts of CG- and CHG-type DMRs. Methylation changes in CG-DMRs located <600 bp from the transcription start and end sites (TSSs/TESs) negatively correlated with transcription changes in differentially expressed genes (DEGs), probably indicating epiregulation. Ethylene is called the 'sex hormone' of cucumbers. We observed the up-regulation of ethylene biosynthesis-related CsACO3 and the down-regulation of an Arabidopsis RAP2.4-like ethylene-responsive (AP2/ERF) transcription factor, demonstrating the inferred epiregulation. Our study characterized the response of the apex methylome to LT and predicted the possible epiregulation of temperature-dependent sex determination (TSD) in cucumber.

Uniconazole (S-3307) strengthens the growth and cadmium accumulation of accumulator plant Malachium aquaticum.

The effects of uniconazole (S-3307) application on the growth and cadmium (Cd) accumulation of accumulator plant Malachium aquaticum (L.) Fries. were studied through a pot experiment. The application of S-3307 increased the biomass and photosynthetic pigment content of M. aquaticum in Cd-contaminated soil, and also improved the superoxide dismutase (SOD) and peroxidase (POD) activities in M. aquaticum. Application of S-3307 increased Cd content in shoots and decreased Cd content in roots of M. aquaticum, but the translocation factor (TF) of M. aquaticum increased with the increase of S-3307 concentration. For phytoextraction, the application of S-3307 increased Cd extractions by roots, shoots and whole plants of M. aquaticum, and the maxima were obtained at 75 mg L-1 S-3307, which increased by 22.07%, 37.79% and 29.07%, respectively, compared with their respective controls. Therefore, S-3307 can be used for enhancing the Cd extraction ability of M. aquaticum, and 75 mg L-1 S-3307 was the optimal dose.

Effects of mutual intercropping on the cadmium accumulation in accumulator plants Stellaria media, Malachium aquaticum, and Galium aparine.

Intercropping affects heavy-metal uptake in plants. In this study, three cadmium (Cd)-accumulator species (Stellaria media, Malachium aquaticum, and Galium aparine) were intercropped together in Cd-contaminated soil to study the effects of intercropping on co-remediation. Mutual intercropping significantly increased the biomasses of S. media, M. aquaticum, and G. aparine compared with their respective monocultures. The photosynthetic pigment contents of three species were not significantly affected by mutual intercropping. Mutual intercropping did not increase the Cd contents in roots and shoots of G. aparine, but it increased the Cd contents in roots of S. media and M. aquaticum. It also decreased the Cd contents in shoots of S. media and M. aquaticum. Only G. aparine intercropped with M. aquaticum and three-species intercropping increased Cd-accumulation levels in whole plants of each species. Only S. media intercropped with M. aquaticum and three-species intercropping increased the Cd accumulation at the whole plant level in every plant in a single pot, with S. media intercropped with M. aquaticum showing the greatest increase. Therefore, S. media intercropped with M. aquaticum and three-species intercropping may improve the efficiency of phytoremediation of Cd-contaminated soil, with S. media intercropped with M. aquaticum representing the best combination.

The effects of abscisic acid (ABA) addition on cadmium accumulation of two ecotypes of Solanum photeinocarpum.

The study of the effects of exogenous abscisic acid (ABA) addition on cadmium (Cd) accumulation of two ecotypes (mining and farmland) of Solanum photeinocarpum was operated through a pot experiment. The results showed that the biomass and chlorophyll content of the two ecotypes of S. photeinocarpum increased with increasing ABA concentration. Applying exogenous ABA increased Cd content in the two ecotypes of S. photeinocarpum. The maximum Cd contents in shoots of the two ecotypes of S. photeinocarpum were obtained at 20 µmol/L ABA; shoot Cd contents respectively for the mining and farmland ecotypes were 33.92 and 24.71% higher than those for the control. Applying exogenous ABA also increased Cd extraction by the two ecotypes of S. photeinocarpum, and the highest Cd extraction was obtained at 20 µmol/L ABA with 569.42 µg/plant in shoots of the mining ecotype and 520.51 µg/plant in shoots of the farmland ecotype respectively. Therefore, exogenous ABA can be used for enhancing the Cd extraction ability of S. photeinocarpum, and 20 µmol/L ABA was the optimal dose.

Effects of grafting on the cadmium accumulation characteristics of the potential Cd-hyperaccumulator Solanum photeinocarpum.

The effects of grafting on the cadmium (Cd) accumulation characteristics of the potential Cd-hyperaccumulator Solanum photeinocarpum were studied under Cd stress in our experiment. Four treatments were used in the experiment: ungrafted (UG), self-rooted grafting by the same S. photeinocarpum seedling (SG), self-rooted grafting by two different development stages of S. photeinocarpum seedlings (DG), and grafting on the rootstock of wild potato (PG). SG and DG decreased the root, scion stem, leaf, whole shoot, and whole plant biomasses compared with UG, but increased the rootstock stem biomass, while only PG increased the root and whole plant biomasses. SG and DG increased the Cd contents in the different organs of S. photeinocarpum compared with UG, while PG decreased the Cd content compared with UG. The Cd extraction by the whole plant of S. photeinocarpum was ranked as DG > SG > UG > PG. Additionally, the antioxidant enzyme activities in SG and DG were enhanced compared with UG, while that of PG was reduced compared with UG. The grafting increased the DNA methylation levels and changed the methylation patterns of S. photeinocarpum compared with UG. Therefore, SG and DG can increase the Cd accumulation in S. photeinocarpum, which can be used for the phytoremediation of Cd-contaminated soil.