Transcriptomic and metabolomic analyses reveal key factors regulating chilling stress-induced softening disorder in papaya fruit

Chilling injury (CI) severely affects the transportation, storage, and marketing of fruit. Papaya is a typical tropical/subtropical fruit susceptible to CI. Generally, fruit stored below 12 °C exhibit CI symptoms and softening disorder after returning to room temperature. In this study, papaya stored at 7 °C showed slight injury after 15 d and severe injury after 25 d, while no CI occurred under 12 °C storage. Transcriptome analysis identified 7710 differential expressed genes (DEGs) between fruit stored at 7 °C and 12 °C. Further KEGG analysis revealed that these DEGs mainly enriched pathways associated with folding, sorting and degradation, lipid metabolism, carbohydrate metabolism, and biosynthesis of other secondary metabolites. Besides, we found that 69 DEGs with expression patterns highly correlated with the CI were associated with lignin synthesis, cellulose, hemicellulose, and pectin degradation pathways and subsequently screened out eight intermediate metabolites of these pathways. The low-temperature storage induced CI inhibited the degradation of lignin, cellulose and total pectin. Further metabolome analysis identified 198 differentially accumulated metabolites (DAMs) between the fruit at 7 °C and 12 °C at 25 d of storage. Metabolic pathways enriched by these DAMs included phenylpropanoid biosynthesis, biosynthesis of secondary metabolites, starch and sucrose metabolism, and plant hormone signal transduction. Weighted gene co-expression network analysis (WGCNA) identified five transcription factors (RAP2–7, bHLH74, AGL9, MYB33, and SRM1-like) and their predicted downstream target genes closely related to fruit softening. Finally, RT-qPCR analysis of 15 genes validated the transcriptome sequencing data. Thus, our findings collectively prove that CI severely represses the expression of key TFs and their target genes involved in cellulose, hemicellulose, and pectin degradation and their metabolic pathways, resulting in the softening disorder.