Integrated transcriptomic and metabolomic analyses of developing seed coats reveals metabolic reprogramming linked to the hull-less phenotype in Cucurbita moschata

Cucurbita moschata seeds are globally esteemed as a functional food for their nutrition and health benefits. Hull-less genotypes obviate the need for mechanical dehulling, offering both practical and economic advantages. However, the phytochemical basis and genetic regulation of seed coat development in C. moschata remain ambiguous. We conducted a comparison between two C. moschata genotypes: a completely hull-less (RHLS-g) and a partially hull-less (RHLS-m). Employing LC-MS/MS-based metabolomics and RNA-seq based transcriptomics, we comparatively characterized the dynamics of metabolite and gene expression during seed coat development of these two genotypes. Integrative analysis revealed that seed coat development entails significant alterations in primary and secondary metabolism. Significantly, we identified a metabolic trade-off between the biosynthesis of structural polymers and the accumulation of soluble metabolites, which governs the seed coat phenotype. In hull-less lines, the carbon flux diverts from phenylpropanoid-derived polymers (e.g., lignin and cellulose) towards soluble sugars (e.g., glucose, sucrose, and sugar phosphates) at specific developmental stages and sinapic acid derivatives. This shift is manifested in the suppression of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) in phenylpropanoid, flavonoid, cellulose, and hemicellulose pathways, as well as the enhanced accumulation of sinapic acid derivatives and stage-specific increases in soluble sugars. Key transcription factors (TFs), including NAC, MYB, and WRKY, exhibited a strong correlation with DEGs in these pathways, suggesting a complex regulatory network for seed coat development in C. moschata . Collectively, these findings reveal the key molecular mechanisms of seed coat development in C. moschata , enhance the understanding of seed coat formation in plants, and underpin the genetic breeding and commercial application of hull-less varieties.