Genome-wide identification and expression analysis of genes associated with peach (Prunus persica) fruit ripening

Fruit ripening is determined by the coordinated action of multi-faceted biological processes. However, little is known about the molecular mechanism of fruit ripening in peach. To explore the genes involved into fruit ripening, in this study, transcriptome sequencing was conducted in the peach fruits at the stone hardening, the second rapid growth, and ripening stages. By comparing the expression levels of whole genes between the ripening (LYE) and developing fruits (LYD and LYC), 1 615 and 1 938 genes were up- and down-regulated in the ripening fruits. In these differential expressed genes, the PG, PL8, and XTH33 genes related to cell wall degradation were up-regulated in ripening fruits, in contrast, two GDSL genes against the xyloglucan oligosaccharides were down regulated. The CABs, photosystem I/II, and OEE genes involved in photosynthesis were detected having the lowest expression levels in the ripening fruits. The genes associated with ethylene response, biosynthesis, and auxin-responsive were remarkably increased in expression levels in ripening fruits. The stress related genes UP3, EDR2L, PR1, PR4 and programmed cell death gene ACD11 also displayed an up-regulation trends during fruit ripening. Few ripening-related transcription factors, such as NAC, MADS-box, and MYB, were also detected from the differential expressed genes. Moreover, expression patterns of the selected genes were tested by real-time quantitative PCR (qRT-PCR), and the qRT-PCR results were consistent with transcriptome data. This study provides important candidate genes for exploring the complex metabolic process involved in ripening.