The Transcriptome and Metabolome Reveal Stress Responses in Sulfur-Fumigated Cucumber (Cucumis sativus L.)

Responses of differential metabolites and pathways to high temperature in cucumber anther

Cucumber is one of the most important vegetable crops, which is widely planted all over the world. Cucumber always suffers from high-temperature stress in South China in summer. In this study, liquid chromatography-mass spectrometry (LC-MS) analysis was used to study the differential metabolites of cucumber anther between high-temperature (HT) stress and normal condition (CK). After HT, the pollen fertility was significantly reduced, and abnormal anther structures were observed by the paraffin section. In addition, the metabolomics analysis results showed that a total of 125 differential metabolites were identified after HT, consisting of 99 significantly upregulated and 26 significantly downregulated metabolites. Among these differential metabolites, a total of 26 related metabolic pathways were found, and four pathways showed significant differences, namely, porphyrin and chlorophyll metabolism; plant hormone signal transduction; amino sugar and nucleotide sugar metabolism; and glycine, serine, and threonine metabolism. In addition, pollen fertility was decreased by altering the metabolites of plant hormone signal transduction and amino acid and sugar metabolism pathway under HT. These results provide a comprehensive understanding of the metabolic changes in cucumber anther under HT.

Evaluation of ethylicin as a potential soil fumigant in commercial tomato production in China

Recent increases in soil-borne plant disease have limited further expansion of some crops produced in protected agriculture. Soil fumigation effectively minimizes the impact of soil pathogens causing many diseases. We provide the first report of the efficacy of the Chinese fungicide ethylicin as a soil fumigant against the plant pathogens such as Fusarium spp. and Phytophthora spp., and against the plant parasitic nematode Meloidogyne spp. We also examined ethylicin's impact on the physicochemical properties of soil, the soil's bacterial and fungal taxonomic composition, the plant growth of tomatoes, the enzyme activity of soil and tomato yield. Ethylicin fumigation significantly decreased the abundance of Fusarium spp. and Phytophthora spp. by 67.7 %-84.0 % and 53.8 %-81.0 %, respectively. It reduced Meloidogyne spp. by 67.2 %-83.6 %. Ethylicin significantly increased the growth of tomato plants and tomato yield by 18.3 %-42.0 %. The soil's ammonium‑nitrogen concentration increased significantly in answer to ethylicin fumigation, while nitrate‑nitrogen concentration and the activity of soil urease decreased significantly. High-throughput gene sequencing had been used to show that ethylicin cut down the taxonomic soil bacteria diversity and bacterial abundance, but increased the soil fungi taxonomic diversity. Some genera of microorganisms increased, such as Firmicutes, Steroidobacter and Chytridiomycota, possibly due to changes in the physicochemical properties of soil that differentially favored their survival. We conclude that ethylicin is efficacious as a soil fumigant and it would be a useful addition to the limited number of soil fumigants currently available.

Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops

Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants.

Organic acid metabolism in Chinese dwarf cherry [Cerasus humilis (Bge.) Sok.] is controlled by a complex gene regulatory network

The acidity of Chinese dwarf cherry [Cerasus humilis (Bge.) Sok.] fruits is a key factor affecting the sensory quality of fruits, and it undergoes great changes during development. The molecular mechanisms of these changes are still unclear. In this study, fruits of high-acid 'Nongda4' and low-acid 'DS-1' varieties of Chinese dwarf cherry were used to determine the acid content at different developmental stages. We used transcriptome profiles to identify key genes related to organic acid metabolism and construct their co-expression networks, and we studied the expression patterns of key genes in 36 Chinese dwarf cherry accessions. The titratable acid content of both 'DS-1' and 'Nongda4' fruits first increased and then decreased during fruit development; however, the titratable acid content of 'DS-1' fruits changed to a minor extent. The organic acid content of 'Nongda4' was significantly higher than that of 'DS-1'. The organic acids in mature fruits were mainly malic acid and citric acid. Analysis of the differentially expressed genes related to organic acid metabolism revealed six key genes, including two MDH genes, one tDT gene, one ME gene, one PEPCK gene, and one VHA gene. Weighted gene co-expression network association analysis revealed four modules that were significantly correlated with organic acid content, and 10 key genes with high connectivity among these four modules were screened, including two PK genes, two MDH genes, two ME genes, one PEPCK gene, one VHA gene, one PEPC gene, and one tDT gene. According to the expression patterns of genes in different Chinese dwarf cherry accessions, seven genes were confirmed to represent key genes related to the regulation of organic acids during Chinese dwarf cherry fruit development. These results provide a foundation for further studies on the molecular mechanism of organic acid accumulation in Chinese dwarf cherry fruit.

Multiple Stressors in Vegetable Production: Insights for Trait-Based Crop Improvement in Cucurbits

Vegetable production is a key determinant of contribution from the agricultural sector toward national Gross Domestic Product in a country like India, the second largest producer of fresh vegetables in the world. This calls for a careful scrutiny of the threats to vegetable farming in the event of climate extremes, environmental degradation and incidence of plant pests/diseases. Cucurbits are a vast group of vegetables grown almost throughout the world, which contribute to the daily diet on a global scale. Increasing food supply to cater to the ever-increasing world population, calls for intensive, off-season and year-round cultivation of cucurbits. Current situation predisposes these crops to a multitude of stressors, often simultaneously, under field conditions. This scenario warrants a systematic understanding of the different stress specific traits/mechanisms/pathways and their crosstalk that have been examined in cucurbits and identification of gaps and formulation of perspectives on prospective research directions. The careful dissection of plant responses under specific production environments will help in trait identification for genotype selection, germplasm screens to identify superior donors or for direct genetic manipulation by modern tools for crop improvement. Cucurbits exhibit a wide range of acclimatory responses to both biotic and abiotic stresses, among which a few like morphological characters like waxiness of cuticle; primary and secondary metabolic adjustments; membrane thermostability, osmoregulation and, protein and reactive oxygen species homeostasis and turnover contributing to cellular tolerance, appear to be common and involved in cross talk under combinatorial stress exposures. This is assumed to have profound influence in triggering system level acclimation responses that safeguard growth and metabolism. The possible strategies attempted such as grafting initiatives, molecular breeding, novel genetic manipulation avenues like gene editing and ameliorative stress mitigation approaches, have paved way to unravel the prospects for combined stress tolerance. The advent of next generation sequencing technologies and big data management of the omics output generated have added to the mettle of such emanated concepts and ideas. In this review, we attempt to compile the progress made in deciphering the biotic and abiotic stress responses of cucurbits and their associated traits, both individually and in combination.