RNA-Seq analysis of gene expression during the yellowing developmental process of fresh-cut Chinese water chestnuts

Abstract

Fresh-cut corms of Chinese water chestnut (CWC) have become a very popular ready-to-eat fruit in Asian countries. However, the surface of fresh-cut CWC is prone to yellowing during storage, and the mechanism underlying this process remains unclear. In this study, RNA-Seq was used to identify the differentially expressed genes (DEGs) between the fresh-cut CWC exposed to 10 mM ferulic acid (FA) or 10 mM salicylic acid (SA) and the control (Ct) CWC. Abundance analysis identified 22,232, 11,066 and 16,165 DEGs in the comparisons between the control at 0 d (0d Ct) and the control at 3 d (3d Ct), 3d Ct and the FA treatment at 3 d (3d FA), and 3d Ct and the SA treatment at 3 d (3d SA). The expression level of most DEGs involved in the shikimate-phenylpropanoid pathway was upregulated in the 3d Ct group compared with that in the 0d Ct group. However, the expression of these DEGs was significantly downregulated in the 3d FA and 3d SA groups compared with that in the 3d Ct group. Some transcription factor (TF)-related DEGs, including five MYB-like and eight bHLH-like genes, were identified as candidate genes associated with the CWC yellowing process. In addition, the expression levels of jasmonate biosynthesis-related genes were upregulated in the 3d Ct group compared with those in the 0d Ct group, but most of these genes were repressed by exogenous SA. Our results provide comprehensive insights into the fresh-cut CWC yellowing process and provide abundant sequence resources for studying the molecular mechanisms of the phenylpropanoid pathway.