Identification of volatile and softening-related genes using digital gene expression profiles in melting peach
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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.
KeywordsDigital gene expression Aroma Nonspecific lipid transfer protein Acyl-CoA oxidase Polygalacturonase
Digital gene expression
Differentially expressed genes
Kyoto Encyclopedia of Genes and Genomes
This work was supported by the State Ministry of Science and Technology of China (2011AA100206 and International Cooperation 1114), China Natural Science Foundation (31372040 and 31401833), The Key Project for New Agricultural Cultivar Breeding in Zhejiang Province, China (2012C12904), and the Scientific Fund for Young Scholars in Shanghai Municipal Agricultural Commission(2014:1–27). We acknowledge Mei-dan Lu for lab work on RNA extraction.
Conflict of interest
The authors declare that they have no conflict of interest.
XWL, YY, JJ, and LPZ performed the experiments, analyzed the data, and drafted the manuscript. XWL, JJ, MLC, and HQZ performed the RNA-seq data analysis. YY contributed to the RNA extraction, qPCR implementation, and data analysis. ZWY, XMW, and JYZ were involved in selection and preparation of fruit samples and quality evaluation. ZSG, HJJ, and PA initiated the project, designed the experiment, and reviewed the manuscript. All authors read and approved the manuscript.
Data archiving statement
For each sample, the raw data files containing reads and quality scores have been deposited to the NCBI’s GEO database (http://www.ncbi.nlm.nih.gov/geo/) and will be submitted to the NCBI Sequence Read Archive (SRA) database by the GEO administrator. As required by GEO, the submitted data included three components: (1) metadata_spreadsheet_peach_DGE (indicating the research title, sample name, sample characteristic, experiment design methods, data processing methods, etc.), (2) processed data files (including all the RPKM value for each gene of each sample, e.g., HJ1_rep1_RPKM), and (3) raw reads data files (e.g., HJ1_rep1.fq). The accession number for each raw read file supplied by SRA is as follows: GSM1574411(HJ1 rep1), GSM1574412(HJ1 rep2), GSM1574413(HJ2 rep1),GSM1574414(HJ2 rep2), GSM1574415(HJ3 rep1), GSM1574416 (HJ3 rep2), GSM1574417(YL2 rep1), GSM1574418(YL2 rep2), GSM1574419(JX2 rep1), GSM1574420(JX2 rep2), GSM1574421(ZH2 rep1), and GSM1574422(ZH2 rep2).
- Atkinson RG, Sutherland PW, Johnston SL, Gunaseelan K, Hallett IC, Mitra D, Brummell DA, Schroder R, Johnston JW, Schaffer RJ (2012) Down-regulation of POLYGALACTURONASE 1 alters firmness, tensile strength and water loss in apple (Malus x domestica) fruit. BMC Plant Biol 12(1):129PubMedCentralPubMedCrossRefGoogle Scholar
- Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol 57:289–300Google Scholar
- Eduardo I, Chietera G, Pirona R, Pacheco I, Troggio M, Banchi E, Bassi D, Rossini L, Vecchietti A, Pozzi C (2013) Genetic dissection of aroma volatile compounds from the essential oil of peach fruit: QTL analysis and identification of candidate genes using dense SNP maps. Tree Genet Genomes 9(1):189–204CrossRefGoogle Scholar
- Ghiani A, Onelli E, Aina R, Cocucci M, Citterio S (2011) A comparative study of melting and non-melting flesh peach cultivars reveals that during fruit ripening endo-polygalacturonase (endo-PG) is mainly involved in pericarp textural changes, not in firmness reduction. J Exp Bot 62(11):4043–4054PubMedCrossRefGoogle Scholar
- Kao MWS, Brecht JK, Williamson JG, Huber DJ (2012) Ripening Development and Quality of Melting and Non-melting Flesh Peach Cultivars. HortSci 47(7):879–885Google Scholar
- Rea PA (2007) Plant ATP-binding cassette transporters. Annu Rev Plant Biol 58:347–375Google Scholar
- Verde I, Abbott AG, Scalabrin S, Jung S, Shu SQ, Marroni F, Zhebentyayeva T, Dettori MT, GrimwoodB J, Cattonaro F, Zuccolo A, Rossini L, Jenkins J, Vendramin E, Meisel LA, Decroocq V, Sosinski B, Prochnik S, Mitros T, Policriti A, Cipriani G, Dondini L, Ficklin S, Goodstein DM, Xuan P, Fabbro CD, Aramini V, Copetti D, Gonzalez S, Horner DS, Falchi R, Lucas S, Mica E, Maldonado J, Lazzari B, Bielenberg D, Pirona R, Miculan M, Barakat A, Testolin R, Stella A, Tartarini S, Tonutti P, Arús P, Orellana A, Wells C, Main D, Vizzotto G, Silva H, Salamini F, Schmutz J, Morgante M, Rokhsar DS (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45:487–494PubMedCrossRefGoogle Scholar
- Vizoso P, Meisel LA, Tittarelli A, Latorre M, Saba J, Caroca R, Maldonado J, Cambiazo V, Campos-Vargas R, Gonzalez M (2009) Comparative EST transcript profiling of peach fruits under different post-harvest conditions reveals candidate genes associated with peach fruit quality. BMC Genomics 10(1):423PubMedCentralPubMedCrossRefGoogle Scholar
- Waché Y, Aguedo M, LeDall MT, Nicaud JM, Belin JM (2002) Optimization of Yarrowia lipolytica’s β-oxidation pathway for γ-decalactone production. J Mol Catal B-Enzym 19–20(0):347–351Google Scholar