Investigating the Molecular Mechanisms of Pepper Fruit Tolerance to Storage via Transcriptomics and Metabolomics

Pepper is one of the most important vegetable crops in China and has high economic value. However, the pepper fruit is easily softened and spoiled after harvest, which seriously affects its flavor, transportation, and economic value. In this study, we used pepper lines with different levels of storage resistance, A144 and A361, and performed physiological examination, transcriptomics, and metabolomics on them at 0 and 3 days after harvest in order to analyze their gene expression patterns and molecular regulatory mechanisms for storage tolerance. A total of 23,477 genes and 985 metabolites were identified. After comparing and analyzing each sample, we identified 7829 differentially expressed genes and 296 differential metabolites. We found that the genes such as ethylene-responsive transcriptional factor (ERFs), polygalacturonase (PG), cellulose synthase (CESA), abscisic acid insensitive (ABI), protein kinase 2 (SnRK2), and protein phosphatase 2C (PP2C) and metabolites such as phenylalanine and glycyl-tyrosine were differentially expressed between different storage times in the two materials. Through GO and KEGG enrichment analysis, we found that the differential genes were mainly enriched in carbohydrate metabolism, small molecule metabolism, and plant hormone signal transduction, and the differential metabolites were mainly enriched in flavonoid biosynthesis, glutathione metabolism, and cysteine and methionine metabolism pathways. This study provides a scientific basis for investigating the molecular mechanisms of storage tolerance and developing new pepper varieties with improved storage resistance.