Transcriptomics and Metabolomics Reveal Biosynthetic Pathways and Regulatory Mechanisms of Phenylpropanes in Different Ploidy of Capsicum frutescens

Pepper is a significant cash crop, and <i>Capsicum frutescens</i> is an exemplary variety of pepper cultivated for its distinctive flavor and substantial nutritional value. Polyploidization of plants often leads to an increase in their biomass and improved stress tolerance, and thus has important applications in plant breeding and improvement. In this study, germplasm innovation was carried out by polyploidy induction of <i>C. frutescens</i> by colchicine. To investigate the effects of polyploidization on <i>C. frutescens</i>, we conducted transcriptomic and metabolomic analyses of diploids and homotetraploids of <i>C. frutescens</i> to gain insights into the mechanisms of metabolite composition and molecular regulation of <i>C. frutescens</i> by polyploidization. Based on the analysis of metabolomics and transcriptomics data, a total of 551 differential metabolites were identified in the leaves of <i>C. frutescens</i> of different ploidy and 634 genes were significantly differentially expressed. In comparison, 241 differential metabolites and 454 genes were significantly differentially expressed in the mature fruits of <i>C. frutescens</i> of different ploidy. Analysis of KEGG enrichment of differentially expressed genes and differential metabolites revealed that both differential metabolites and differentially expressed genes were highly enriched in the phenylalanine metabolic pathway. It is worth noting that phenylpropanoids are highly correlated with capsaicin synthesis and also have an effect on fruit development. Therefore, we comprehensively analyzed the phenylalanine metabolic pathway and found that chromosome doubling significantly down-regulated the expression of genes upstream of phenylalanine (<i>PAL</i>, <i>4CL</i>), which promoted lignin accumulation, and we suggested that this might have led to the enlargement of polyploid <i>C. frutescens</i> fruits. This study provides some references for further research on the phenotypic traits of different ploidy of <i>C. frutescens</i>, cloning of key regulatory genes, and using genetic engineering techniques in <i>C. frutescens</i> breeding for germplasm improvement.