Identification of volatile and softening-related genes using digital gene expression profiles in melting peach

To reveal the comprehensive mechanism which is associated with the biosynthesis of volatile compounds and the accompanying texture change, RNA-seq was employed to survey the differentially expressed genes (DEGs), at the transcriptional level, of one cultivar at three stages of ripening and of four melting peach cultivars at harvest stage. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that highly ranked genes are involved in “Ribosome” and “Plant-pathogen interaction,” “Flavonoid biosynthesis,” “Linoleic acid metabolism,” and “Flavone and flavonol biosynthesis” during the fruit-ripening process. The quantitative real-time PCR (qRT-PCR) validation with 15 aroma and softening-related genes showed high correlation with the RNA-seq results. Transcripts of a nonspecific lipid transfer protein (nsLTP, ppa013554) and an ATP-binding cassette transporter (ABC, ppa002351) increased from the early ripening stage to the commercial harvest stage and then declined in the fully ripening stage. The highest transcript abundance was in the aroma-enriched cv. “Hu Jing Mi Lu” (HJ) and lowest in the cv. “Zhong Hua Shou Tao” with slight aroma. Fifty gene families related to the formation of aroma compounds were found. For peach lactone biosynthesis, we inferred that ppa002510 and ppa002282 may be the two important acyl-CoA oxidase genes correlating with the difference in γ-decalactone concentrations among the four cultivars. The expression of one 3-hydroxyacyl-CoA dehydrogenase gene (HCAD, ppa008854) was upregulated during ripening. Thirteen gene families were associated to fruit softening. Four aquaporin (AQP) genes showed cultivar-specificity for HJ, and one of them, ppa009506, reached maximum accumulation of transcripts at harvest stage. The batch of novel genes (nsLTP, ACX, AOC, ABC, HCAD, AQP) found here facilitates understanding of the molecular mechanism of melting peach aroma biosynthesis and fruit softening.