Objective Varied pulp thickness and differentially expressed metabolites (DEMs) of Momordica charantia L. varieties and the associated metabolic pathways and regulatory networks related to the fruit development were analyzed.

Methods DEMs, KO functional annotation, KEGG pathway enrichment, and expressions of the thick-pulp M. charantia L1 and the thin-pulp L2 at different growth stages were determined to identify the differential metabolites between the two categories of bitter gourds. Comparative and regulatory network analyses based on the enrichment pathways were conducted to further analyze the differentiations.

Results At all developmental stages, L1 and L2 differed significantly in pulp thickness. For instance, the fruit pulp of L1 was significantly thicker than that of L2 at Stage S3 and S4. There were 511 DEMs found between L1S3 (i.e., L1 at Stage S3, similar for the following) and L1S1, and 545 DEMs between L2S3 and L2S1, with 44% commonly existing in the two comparing groups. The metabolic modules in both groups shown by KO annotation were those most abundantly existed in a category or pathway, while those by KEGG enrichment analysis partially overlapped and in large proportion belonged to "metabolism"-related pathways. The unique DEMs in the groups included dopamine in L1S3 vs. L1S1 and citric acid, D-erythrose-4-phosphate, and L-ornithine in L2S3 vs. L2S1 and participated in 5 or more pathways. Whereas the common DEMs, i.e., stevioside and pheophorbide A, differed more than 10-fold on FC value. The expressions of those 6 key metabolites were distinctly differentiated, reflecting a significant regulatory variation between L1 and L2.

Conclusion The thickness of fruit pulp of a M. charantia could serve as an effective visual indicator for quality and market value of the germplasm. The two different varieties of bitter gourds compared in the study showed distinctive DEMs even at developmental stages, as the plants required specific metabolites to regulate growth, quality, and stress-resistance as they grow.