Stigma color is an important morphological trait in many flowering plants. Visual observations in different field experiments have shown that a green stigma in melons is more attractive to natural pollinators than a yellow one. In the current study, we evaluated the characterization of two contrasted melon lines (MR-1 with a green stigma and M4-7 with a yellow stigma). Endogenous quantification showed that the chlorophyll and carotenoid content in the MR-1 stigmas was higher compared to the M4-7 stigmas. The primary differences in the chloroplast ultrastructure at different developmental stages depicted that the stigmas of both melon lines were mainly enriched with granum, plastoglobulus, and starch grains. Further, comparative transcriptomic analysis was performed to identify the candidate pathways and genes regulating melon stigma color during key developmental stages (S1–S3). The obtained results indicated similar biological processes involved in the three stages, but major differences were observed in light reactions and chloroplast pathways. The weighted gene co-expression network analysis (WGCNA) of differentially expressed genes (DEGs) uncovered a “black” network module (655 out of 5302 genes), mainly corresponding to light reactions, light harvesting, the chlorophyll metabolic process, and the chlorophyll biosynthetic process, and exhibited a significant contribution to stigma color. Overall, the expression of five key genes of the chlorophyll synthesis pathway—CAO (MELO03C010624), CHLH (MELO03C007233), CRD (MELO03C026802), HEMA (MELO03C011113), POR (MELO03C016714)—were checked at different stages of stigma development in both melon lines using quantitative real time polymerase chain reaction (qRT-PCR). The results exhibited that the expression of these genes gradually increased during the stigma development of the MR-1 line but decreased in the M4-7 line at S2. In addition, the expression trends in different stages were the same as RNA-seq, indicating data accuracy. To sum up, our research reveals an in-depth molecular mechanism of stigma coloration and suggests that chlorophyll and related biological activity play an important role in differentiating melon stigma color.

Introduction: Melon ( Cucumis melo L.) is an important economic crop, yet its cultivation relies heavily on manual pruning to regulate branching, which limits melon industrialization. Branching originates from axillary bud development, a process regulated by polar auxin transport, in which ABCB proteins serve as key auxin transporters. However, systematic identification of the ABCB gene family in melon and the functional roles of its members in axillary bud development have not been systematically elucidated. Methods: We performed a genome-wide identification of the ABCB gene family from the latest melon genome using bioinformatics approaches. We systematically analyzed the physicochemical properties and other characteristics of the identified CmABCB genes. Additionally, RNA sequencing (RNA-seq) and qRT-PCR were employed to investigate the expression patterns of these genes in axillary buds under IAA treatment. Results: Through this genome-wide identification, we identified a total of 39 CmABCB genes in the melon genome. Phylogenetic analysis classified them into five subgroups, with Group I being unique to melon. Collinearity analysis revealed a close evolutionary relationship between melon and cucumber. Expression profiling revealed that several genes responded specifically to IAA treatment. Notably, CmABCB14 , CmABCB20 , and CmABCB21 exhibited a statistically significant positive correlation between their expression levels and IAA concentration. Discussion: Collectively, these findings suggest that CmABCB14 , CmABCB20 , and CmABCB21 may function as auxin efflux carriers that suppress axillary bud growth. This study therefore provides a theoretical basis for understanding the molecular mechanisms underlying branching regulation in melon and offers a valuable framework for the precise improvement of plant architecture and the reduction of production costs through molecular breeding.