Melon (Cucumis melo L.) represents an agriculturally significant horticultural crop that is widely grown for its flavorful fruits. Downy mildew (DM), a pervasive foliar disease, poses a significant threat to global melon production. Although several quantitative trait loci related to DM resistance have been identified, the comprehensive genetic underpinnings of this resistance remain largely uncharted. In this study, we utilized integrative transcriptomics and metabolomics approaches to identify potential resistance-associated genes and delineate the strategies involved in the defense against DM in two melon cultivars: the resistant ‘PI442177′ (‘K10-1′) and the susceptible ‘Huangdanzi’ (‘K10-9′), post-P. cubensis infection. Even in the absence of the pathogen, there were distinctive differentially expressed genes (DEGs) between ‘K10-1′ and ‘K10-9′. When P. cubensis was infected, certain genes, including flavin-containing monooxygenase (FMO), receptor-like protein kinase FERONIA (FER), and the HD-ZIP transcription factor member, AtHB7, displayed pronounced expression differences between the cultivars. Notably, our data suggest that following P. cubensis infection, both cultivars suppressed flavonoid biosynthesis via the down-regulation of associated genes whilst concurrently promoting lignin production. The complex interplay of transcriptomic and metabolic responses elucidated by this study provides foundational insights into melon’s defense mechanisms against DM. The robust resilience of ‘K10-1′ to DM is attributed to the synergistic interaction of its inherent transcriptomic and metabolic reactions.

Melon (Cucumis melo L.) holds significant importance as a horticultural crop, but it faces several yield-limiting factors, including salinity stress. While salinity traditionally hampers the vegetative growth of melon and detrimentally impacts fruit development and quality, certain melon cultivars exhibit the ability to flourish in conditions of relatively high soil salinity. However, truly salt-tolerant melon varieties are quite rare. In this article, we conducted seedling indoor tests, assessed morphological, physiological and biochemical indices, and explored different salt tolerance types among five melon varieties. As a result, we identified three salt-tolerant varieties, with ‘kuizilike’ (KLK) demonstrating the most impressive performance under salt stress. ‘KLK’ exhibited minimal growth and development constraints during salt stress, with the lowest Na⁺ content, the highest K⁺ content, and the highest K⁺/Na⁺ ratio. Moreover, it displayed the lowest content of malondialdehyde, the highest concentrations of osmoregulation substances, and the highest activity of antioxidant enzymes. Real-time fluorescence quantitation PCR results revealed significantly elevated gene expression levels of TPK, NHX2, LTP, POD, SuSy, HK, PRP and P5CR in ‘KLK’ compared to other varieties. These newly identified salt-tolerant melon germplasms will serve as valuable genetic resources for future studies on the mechanisms underlying melon salt tolerance, and provide insights into melon improvement and molecular breeding.