Pericarp colors are critical agronomic traits that affect the quality and economic values of fruits. Although a diversity of bitter melon pericarp (BMP) colors is available, the fruit pigmentation mechanisms remain elusive. Hence, this study aimed to unveil the key metabolites and molecular mechanisms underlying variation in BMP coloration through integrative metabolomics and transcriptomics analyses of four differently colored genotypes, including K1102 (grayish orange), 262 (grayish yellow), 1392 (very soft green), and K115 (dark grayish cyan). The four BMPs exhibited significant metabolite profile and transcriptional differences, as over 112 and 1865 DAMs (differentially accumulated metabolites) and DEGs (differentially expressed genes), respectively, were identified. The variation in the content of six anthocyanins, including malvidin 3-O-glucoside, petunidin 3-O-glucoside, rosinidin O-hexoside, cyanidin, cyanidin 3-p-hydroxybenzoylsophoroside-5-glucoside, and pelargonidin 3-O-beta-D-glucoside, might be the major driving factor of BMP color changes. Notably, malvidin 3-O-glucoside, rosinidin O-hexoside, and petunidin 3-O-glucoside are the dominant pigments in K115, while carotenoids and other flavonoids may contribute to other colors. Candidate flavonoid structural and regulatory (MYBs, NACs, MADSs, bHLHs, and bZIPs) genes were identified. Of them, gene13201 (anthocyanin reductase), gene8173 (polyphenol oxidase), gene2136 (NAC43), gene19593 (NAC104), and gene15171 (tetrapyrrole-binding protein) might play essential roles in K115 pericarp color development. Our findings deepen our understanding of BMP pigmentation and provide fundamental resources for higher-valued bitter melon breeding perspectives.

In flowering plants, MADS-box genes play regulatory roles in flower induction, floral initiation, and floral morphogenesis. Isatis indigotica (I. indigotica) is a traditional Chinese medicinal plant. However, available information concerning MADS-box genes in I. indigotica is insufficient. Based on the sequencing data of the I. indigotica transcriptome, we identified MADS-box gene-encoding transcription factors that have been shown to play critical roles in developmental processes. In this study, 102 I. indigotica MADS-box genes were identified and categorized into type I (Mα, Mβ, and Mγ) and type II (MIKC^C and MIKC*) subfamilies. IiMADS proteins in the same cluster had similar motifs and gene structures. In total, 102 IiMADS-box genes were unevenly distributed across seven chromosomes. APETALA1 (AP1) encodes a MADS-box transcription factor which plays a pivotal role in determining floral meristem identity and also modulates developmental processes within the perianth. We then selected IiAP1 for functional studies and found that it is localized to the nucleus and highly expressed in inflorescence, sepals, and petals. The ectopic expression of IiAP1 in Arabidopsis resulted in early flowering and abnormal development of floral organs. Taken together, this research study carried out a systematic identification of MADS-box genes in I. indigotica and demonstrated that IiAP1 takes part in the regulation of floral transition and formation.

Across plants, the PEBP gene family is reported to regulate storage organ formation, developmental plasticity, and floral transitioning. However, its evolutionary dynamics and functional diversification within Allium species remain poorly understood. In this study, we performed genomic and transcriptomic analyses of the PEBP gene family across three economically important Allium species, including Allium fistulosum (bunching onion), Allium sativum (garlic), and Allium cepa (onion), identifying 19, 17, and 21 PEBP genes, respectively. The genes were assigned into five subfamilies (FT-like, TFL1-like, MFT-like, BFT-like, and PEBP-like), with MFT-like members being the most abundant. Structural analysis revealed strong conservation of key motifs (e.g., GxHR and DPDxP) across species, while substantial variation in intron–exon organization suggested subfunctionalization. Collinearity analysis indicated that segmental duplication primarily drove PEBP gene expansion in garlic and onion, whereas tandem duplication was absent in bunching onion. Promoter analysis showed enrichment of light- and hormone-related cis-regulatory elements, implicating their involvement in environmental and hormonal regulation. Expression profiling demonstrated clear tissue specificity, with AsPEBP11/13/14/16/19 exhibiting significantly higher expression in normal flowers than in abnormal ones, suggesting key roles in floral morphogenesis. Together, these findings will prove useful for future breeding programs aimed at improving reproductive development and fertility in Allium species.