Comparative Transcriptome Analysis Identified Key Pathways and Genes Regulating Differentiated Stigma Color in Melon (Cucumis melo L.)

Abstract

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.

Map-based cloning of the APRR2 gene controlling green stigma in bitter gourd (Momordica charantia)

“…The green color of stigmas is likely caused by accumulation of chlorophyll, the same pigment that gives plants leaves and fruits their characteristic green appearance. The genetic study for melon ( Cucumis melo ) stigma color showed that green stigma is dominant over the yellow one; transcriptomic analysis proposed that the yellow color is probably due to the break-down of chloroplast structure interfering with chlorophyll biosynthesis; in contrast, the green stigmas are a functional accumulation of chlorophyll ( Lv et al., 2022a ; Lv et al., 2022b ). This might also be true for the green/yellow stigma of bitter gourd.…”

“…In a rice indica cultivar, its purple apiculi and stigma were genetic regulated by the interaction of two genes involved the anthocyanin biosynthesis pathway: OsC1 (encoding a R2R3-MYB transcription factor) and OsDFR (encoding a dihyroflavonol 4-reductase) ( Meng et al., 2021 ). Recent two transcriptomic studies aimed at revealing the gene network were conducted and showed that the yellow stigma in tomato is very likely due to the accumulation of yellow-colored flavonoid naringenin chalcone, whereas the melon yellow stigma is due to break-down of chloroplast structure interfering chlorophyll biosynthesis ( Zhang et al., 2017 ; Lv et al., 2022a ). Despite the crucial functional roles of stigmas play in plant reproduction, there has not been sufficient researches dedicated to the color of stigma.…”

Deciphering the Genomic Characterization of the GGP Gene Family and Expression Verification of CmGGP1 Modulating Ascorbic Acid Biosynthesis in Melon Plants

“…All the gene primer information can be seen in Supplementary Table S2. qRT-PCR analysis was performed by following three biological replicates per sample, as reported earlier [54]. The relative expression levels of putative identified CmGGP1 and associated genes were determined using an earlier reported method [55], respectively.…”

Genetic Diversity and Molecular Breeding of Melon (Cucumis melo L.): A review

“…Data from the transmission electron microscopy of chloroplast structures, RNA sequencing and transcriptome analysis, and qRT-PCR analysis, altogether concluded that relative expression of five key genes (CAO, CHLH, CRD, HEMA, POR) of chlorophyll biosynthesis pathway were observed to be highly expressed in green stigma melon than the yellow one. 16 The future breeding programmes aiming to increase the extent of natural pollination in melon by the insects could target the expression of these key genes. In addition, the recently identified QTLs linked to stigma color namely, SC2.1 and SC8.1 would further help in marker-assisted selection of a particular type of melon stigma color cultivars.…”

“…(a) Extraction of the total RNA of an individual plant, (b) cDNA libraries construction and resequencing, (c) Quantitative Reverse Transcription PCR (qRT-PCR) using the primers designed for candidate genes based on the known genome sequence, (d) Identification and annotation of differentially expressed genes. [13][14][15][16][17] Altogether, these molecular studies would provide valuable genetic resources that can be directly used in molecular breeding for melon crop improvement.…”