Grafting technology can improve the yield and quality of crops. In this study, we investigated the effects of grafting on watermelon using transcriptomic and metabolomic analysis. A total of 216 differentially accumulated metabolites (DAMs) were identified between pumpkin-grafted watermelon and self-grafted watermelon. KO (Kyoto Encyclopedia of Genes and Genomes Orthology) analysis revealed that the DAMs were mainly enriched in the flavone and flavonol biosynthesis pathway. In addition, high levels of phloretin and citric acid were found in pumpkin-grafted watermelon, which contributes to fruit quality. Meanwhile, compounds such as olivetol and ferulaldehyde, which confer a bitter taste, were downregulated in pumpkin-grafted watermelon. The transcriptome data indicated that the differentially expressed genes (DEGs) identified in the pulp were enriched in fructose and mannose metabolism, biosynthesis of secondary metabolites, and flavone and flavonol biosynthesis pathways. Moreover, genes related to the microtubule, cell wall, and fiber were highly expressed in the stem of pumpkin-grafted watermelon, suggesting that grafting could change the structure of the stem and improve the quality of watermelon fruit. Our study provides a comprehensive picture of the transcriptional and metabolic profile of watermelon induced by grafting, which furthers our understanding of the molecular mechanisms involved in improving watermelon fruit quality by grafting.

Grafting significantly enhances plant quality, including stress resistance and fruit quality. We previously found that grafting watermelon onto pumpkin can alter the metabolite content, but the involvement of mobile RNA was unclear. Here, we established and comprehensively analyzed mobile mRNA (mb-mRNA) profiles, transcriptomes, and metabolomes between the rootstock (pumpkin) and scion (watermelon). A total of 834 mobile RNAs were identified in the pulp and stem of pumpkin-grafted watermelon. GO (Gene Ontology) and KO (Kyoto Encyclopedia of Genes and Genomes Orthology) analyses revealed photosynthesis- and carbon fixation-related mobile RNAs (e.g., Photosystem II D2, P700 chlorophyll a apoprotein) in the watermelon pulp and cell division-related mobile RNAs in the stem. Additionally, transcription factors like MADS and DNAJ exhibited mobility. The secondary structure prediction of the MADS-box transcription factor (CmoCh20G002790) showed multiple loop structures (e.g., internal and hairpin loops) related to its mobility. An integrated analysis of transcript and metabolite profiles indicated that photosynthesis-related products are regulated not only by the scion’s own RNA but also by mb-mRNA synthesized by the rootstock. This research advances our understanding of grafting’s molecular mechanisms and provides insights for improving crop quality and sustainability in agriculture.

Background: Common bean (Phaseolus vulgaris L.) is a major food legume with high nutritional value and economic importance globally. A remarkable attribute of this plant is its propensity to generate adventitious roots from petioles of detached leaves when moisture is appropriate. This distinctive feature presents promising prospects for harnessing petioles in the facilitation of transgenic hairy root production. Methods: We achieved the successful induction of transgenic hairy roots from common bean petioles through the utilization of Agrobacterium rhizogenes strain K599. Our experimentation encompassed a diverse array of common bean varieties and leaves of varying ages. Subsequently, we refined and optimized the procedure for hairy root induction. Result: Our investigations have revealed that the most conducive conditions for hairy root transformation with K599 are attained using 5-day-old leaves from the cultivar ‘Honghuaqingjia’, exhibiting a remarkable induction efficiency of 59%. The usefulness of this system was demonstrated through a subcellular localization analysis of the transcription factor PvTCP2 protein in combination with GFP (Green Fluorescent Protein).

Secondary metabolites in hemp enhance its pharmaceutical and nutraceutical value, yet the epigenetic regulatory network underlying secondary metabolite biosynthesis remains poorly understood in hemp. Here, we profiled the inflorescences of two cultivars with different trichome density by integrating metabolomics, transcriptomics and ATAC-seq. Multi-omics data revealed pronounced differences in metabolites (491 differentially accumulated metabolites (DAMs)), transcripts (8343 differentially expressed genes (DEGs)), and chromatin accessibility (11376 different accessibility genes, (DAGs)) between two cultivars. Integrated analyses reveal that increased chromatin accessibility at the promoters of several flavonoid-biosynthetic genes up-regulated their expression, resulting in the accumulation of flavonoids. Although chromatin accessibility of cannabinoid biosynthetic gene promoters modulates content, differential chromatin accessibility of the promoter of fatty acid biosynthetic and trichome density (trichome initiation, MeJA signaling, and identity of floral organ) related genes constitutes the key driver underlying cannabinoid divergence between two cultivars. Our study advances the understanding of epigenetic regulation of plant secondary metabolites and offers a novel strategy for enhancing cannabinoid and flavonoid content in Cannabis, providing efficient and precise molecular markers for the selection and breeding of new cannabis varieties.

Potato (Solanum tuberosum L.), the fourth most important food crop worldwide, serves as a multi-purpose resource for food, feed and industrial raw materials, and plays a pivotal role in safeguarding food security, diversifying dietary structure and boosting the development of agricultural economy. With increasing consumer demand for nutritional quality, elucidating the regulatory mechanisms of potato quality traits has become a research priority. In this study, three potato cultivars with distinct coloration were employed as materials. Metabolomic profiling identified a total of 1128 metabolites, and revealed that pigmented potato cultivars accumulated higher levels of flavonoids and linoleic acid derivatives compared with the white-fleshed cultivar. Transcriptomic analysis uncovered numerous differentially expressed genes (DEGs) among the three cultivars; notably, DEGs in pigmented cultivars were significantly enriched in pathways related to terpenoid backbone biosynthesis, flavonoid biosynthesis, linoleic acid metabolism, and starch and sucrose metabolism. Integrated multi-omics analysis revealed that the high expression of structural genes in the flavonoid biosynthesis pathway is strongly associated with flavonoid accumulation in pigmented potatoes, suggesting that transcriptional upregulation of these genes may be a key driver of flavonoid biosynthesis. Furthermore, several MYB and WD40 family transcription factors were identified as potential regulators of flavonoid and anthocyanin biosynthesis in potato. Collectively, our study provides insight into the regulatory mechanisms underlying the biosynthesis of secondary metabolites in potato by combining transcriptomic and metabolomic approaches, and the findings provide a valuable theoretical basis for the genetic improvement of potato nutritional quality in future breeding programs.