Integrated transcriptome-metabolome analyses reveal regulatory networks underlying soluble solids accumulation in Capsicum chinense fruits.

The Capsicum genus shows remarkable phenotypic diversity, making it an excellent system to study non-climacteric fruit ripening. Unlike climacteric model species, such as tomato (Solanum lycopersicum), the regulatory networks linking transcriptome and metabolome to fruit quality traits remain poorly understood in non-climacteric crop species. To address this gap, we selected four contrasting C. chinense accessions and performed integrated transcriptomic and metabolomic analyses to investigate the regulation of total soluble solids (TSS) accumulation. We profiled 16 922 genes and 63 metabolic features across two fruit developmental stages (immature and mature), including sugars, organic acids, capsaicinoids, and other secondary metabolites. We identified more than 3800 differentially expressed genes and detected strong correlations between gene expression and metabolite levels. Some metabolites, including chlorophylls, carotenoids, and starch, showed consistent temporal trends across genotypes, while others showed genotype-dependent variation. Our results demonstrate that pepper fruit ripening involves a transcriptional shift toward soluble sugar accumulation, characterized by upregulation of starch-hydrolyzing enzymes (CaAMY1/2, CaBAM1), invertases (CaINV1, CaCWINV3), sucrose synthase (CaSUS2), and the sugar transporter CaSWEET10, alongside downregulation of the starch biosynthetic gene CaSBE1. Among these, CaSUS2, CaSWEET10, and CaBAM1 emerged as key candidate regulators. These results suggest that coordinated starch degradation and sucrose transport primarily drive TSS increase, while secondary metabolism undergoes independent shifts that characterize other aspects of the ripening process.