Plant Molecular Biology

, Volume 91, Issue 1–2, pp 97–114 | Cite as

The peach HECATE3-like gene FLESHY plays a double role during fruit development

  • Alessandro Botton
  • Angela Rasori
  • Fiorenza Ziliotto
  • Annick Moing
  • Mickaël Maucourt
  • Stéphane Bernillon
  • Catherine Deborde
  • Anna Petterle
  • Serena Varotto
  • Claudio Bonghi


Tight control of cell/tissue identity is essential for a correct and functional organ patterning, an important component of overall fruit development and eventual maturation and ripening. Despite many investigations regarding the molecular determinants of cell identity in fruits of different species, a useful model able to depict the regulatory networks governing this relevant part of fruit development is still missing. Here we described the peach fruit as a system to link the phenotype of a slow ripening (SR) selection to an altered transcriptional regulation of genes involved in determination of mesocarp cell identity providing insight toward molecular regulation of fruit tissue formation. Morpho-anatomical observations and metabolomics analyses performed during fruit development on the reference cultivar Fantasia, compared to SR, revealed that the mesocarp of SR maintained typical immaturity traits (e.g. small cell size, high amino acid contents and reduced sucrose) throughout development, along with a strong alteration of phenylpropanoid contents, resulting in accumulation of phenylalanine and lignin. These findings suggest that the SR mesocarp is phenotypically similar to a lignifying endocarp. To test this hypothesis, the expression of genes putatively involved in determination of drupe tissues identity was assessed. Among these, the peach HEC3-like gene FLESHY showed a strongly altered expression profile consistent with pit hardening and fruit ripening, generated at a post-transcriptional level. A double function for FLESHY in channelling the phenylpropanoid pathway to either lignin or flavour/aroma is suggested, along with its possible role in triggering auxin-ethylene cross talk at the start of ripening.


Fruit patterning Mesocarp identity Metabolomics MicroRNA Phenylpropanoid pathway Post-transcriptional regulation 



This article is dedicated to the memory of our friend and colleague Angelo Ramina. We thank Daniel Jacob for developing and maintaining MeRy-B knowledge base and database. This research was financially supported by Project ex60 % (2013 and 2014) funded by the University of Padova.

Authors’ contributions

Claudio Bonghi conceived the study. Angela Rasori and Fiorenza Ziliotto made the molecular analyses, while Anna Petterle performed the histochemical assessments and microscopic analyses. Annick Moing, Stéphane Bernillon, Catherine Deborde and Mickaël Maucourt supervised and carried out the metabolomic analyses together with Angela Rasori and performed the related data mining. Alessandro Botton carried out the bioinformatic and statistical analyses and prepared the graphics. Serena Varotto gave useful advices and contributed to experiments. Claudio Bonghi and Alessandro Botton interpreted the results and wrote the paper.

Supplementary material

11103_2016_445_MOESM1_ESM.pdf (6.7 mb)
Supplementary material 1 (PDF 6835 kb)
11103_2016_445_MOESM2_ESM.pdf (259 kb)
Supplementary material 2 (PDF 259 kb)
11103_2016_445_MOESM3_ESM.pdf (121 kb)
Supplementary material 3 (PDF 120 kb)


  1. Bassi D, Monet R (2008) Botany and taxonomy. In: Layne DR, Bassi D (eds) The peach, botany, production and uses. CAB Intl, Wallingford, pp 1–36CrossRefGoogle Scholar
  2. Begheldo M, Ziliotto F, Rasori A, Bonghi C (2007) The use of μPEACH 1.0 to investigate the role of ethylene in the initiation of peach fruit ripening. In: Ramina A, Chang C, Giovannoni J, Klee H, Perata P, Woltering E (eds) Advances in plant ethylene research. Springer, Berlin, pp 265–267CrossRefGoogle Scholar
  3. Bemer M, Karlova R, Ballester AR, Tikunov YM, Bovy AG, Wolters-Arts M, Rossetto Pde B, Angenent GC, de Maagd RA (2012) The tomato FRUITFULL homologs TDR4/FUL1 and MBP7/FUL2 regulate ethylene-independent aspects of fruit ripening. Plant Cell 24:4437–4451CrossRefPubMedPubMedCentralGoogle Scholar
  4. Biais B, Allwood JW, Deborde C et al (2009) 1H NMR, GC–EI-TOFMS, and data set correlation for fruit metabolomics, Application to spatial metabolite analysis in melon. Anal Chem 81:2884–2894CrossRefPubMedGoogle Scholar
  5. Bonghi C, Trainotti L, Botton A, Tadiello A, Rasori A, Ziliotto F, Zaffalon V, Casadoro G, Ramina A (2011) A microarray approach to identify genes involved in seed-pericarp cross-talk and development in peach. BMC Plant Biol 11:107CrossRefPubMedPubMedCentralGoogle Scholar
  6. Botton A, Vegro M, De Franceschi F, Ramina A, Gemignani C, Marcer G, Pasini G, Tonutti P (2006) Different expression of Pp-LTP1 and accumulation of Pru p 3 in fruits of two Prunus persica L. Batsch genotypes. Plant Sci 171:106–113CrossRefGoogle Scholar
  7. Brecht KJ, Kader AA (1984) Ethylene production by fruit of some slow-ripening nectarine genotypes. J Am Soc Hortic Sci 109:763–767Google Scholar
  8. Brecht KJ, Kader AA, Ramming DW (1984) Description and postharvest physiology of some slow-ripening nectarine genotypes. J Am Soc Hortic Sci 109:509–600Google Scholar
  9. Callahan AM, Dardick C, Scorza R (2009) Characterization of ‘Stoneless’, A naturally occurring, partially stoneless plum cultivar. J Am Soc Hortic Sci 134:120–125Google Scholar
  10. Carceller M, Davey MR, Fowler MW, Street HE (1971) The influence of sucrose, 2,4-D and kinetin on the growth, fine structure and lignin content of cultured SYCAMORE cells. Protoplasma 73:367–385CrossRefPubMedGoogle Scholar
  11. Chang WC, Lee TY, Huang HD, Huang HY, Pan RL (2008) PlantPAN, Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene group. BMC Genom 9:561CrossRefGoogle Scholar
  12. Cline MS, Smoot M, Cerami E et al (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2:2366–2382CrossRefPubMedPubMedCentralGoogle Scholar
  13. Dardick C, Callahan A (2014) Evolution of the fruit endocarp, molecular mechanisms underlying adaptations in seed protection and dispersal strategies. Front Plant Sci 5:284CrossRefPubMedPubMedCentralGoogle Scholar
  14. Dardick CD, Callahan AM, Chiozzotto R, Schaffer RJ, Piagnani MC, Scorza R (2010) Stone formation in peach fruit exhibits spatial coordination of the lignin and flavonoid pathways and similarity to Arabidopsis dehiscence. BMC Biol 8:13CrossRefPubMedPubMedCentralGoogle Scholar
  15. Eccher G, Botton A, Di Mauro M, Boschetti A, Ruperti B, Ramina A (2013) Early induction of apple fruitlet abscission is characterized by an increase of both isoprene emission and abscisic acid content. Plant Physiol 161:1952–1969CrossRefGoogle Scholar
  16. Eduardo I, Picañol R, Rojas E, Batlle I, Howad W, Aranzana MJ, Arùs P (2015) Mapping of a major gene for the slow ripening character in peach: co-location with the maturity date gene and development of a candidate gene-based diagnostic marker for its selection. Euphytica 205:627–636CrossRefGoogle Scholar
  17. El-Sharkawy I, Mila I, Bouzayen M, Jayasankar S (2010) Regulation of two germin-like protein genes during plum fruit development. J Exp Bot 61:1761–1770CrossRefPubMedPubMedCentralGoogle Scholar
  18. Fasoli M, Santo SD, Zenoni S, Tornielli GB et al (2012) The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program. Plant Cell 24:3489–3505CrossRefPubMedPubMedCentralGoogle Scholar
  19. Ferrándiz C, Liljegren SJ, Yanofsky MF (2000) Negative regulation of the SHATTERPROOF genes by FRUITFULL during Arabidopsis fruit development. Science 289:436–438CrossRefPubMedGoogle Scholar
  20. Ferrándiz C, Fourquin C, Prunet N, Scutt CP, Sundberg E, Trehin C, Vialette-Guiraud ACM (2010) Carpel development. In: Kader JC, Delseny M (eds) Advances in botanical research. Academic Press, Burlington, pp 1–73Google Scholar
  21. Ferry-Dumazet H, Gil L, Deborde C, Moing A, Bernillon S, Rolin D, Nikolski M, de Daruvar A, Jacob D (2011) MeRy-B, a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles. BMC Plant Biol 11:104CrossRefPubMedPubMedCentralGoogle Scholar
  22. Gabotti D, Negrini N, Morgutti S, Nocito FF, Cocucci M (2015) Cinnamyl alcohol dehydrogenases in the mesocarp of ripening fruit of Prunus persica genotypes with different flesh characteristics, changes in activity and protein and transcript levels. Physiol Plantarum 154:329–348CrossRefGoogle Scholar
  23. 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 endopolygalacturonase (endo-PG) is mainly involved in pericarp textural changes, not in firmness reduction. J Exp Bot 62:4043–4054CrossRefPubMedGoogle Scholar
  24. Hagendoorn MJM, Traas TP, Boon JJ, van der Plas LHW (1990) Orthovanadate induced lignin production, in Batch and continuous cultures of Petunia hybrida. J Plant Physiol 137:72–80CrossRefGoogle Scholar
  25. Hayama H, Tatsuki M, Yoshioka H, Nakamura Y (2008) Regulation of stony hard peach softening with ACC treatment. Postharvest Biol Technol 50:231–232CrossRefGoogle Scholar
  26. Kay P, Groszmann M, Ross JJ, Parish RW, Swain SM (2012) Modifications of a conserved regulatory network involving INDEHISCENT controls multiple aspects of reproductive tissue development in Arabidopsis. New Phytol 197:73–87CrossRefPubMedGoogle Scholar
  27. Klie S, Osorio S, Tohge T, Drincovich MF, Fait A, Giovannoni JJ, Fernie AR, Nikoloski Z (2013) Conserved changes in the dynamics of metabolic processes during fruit development and ripening across species. Plant Physiol 164:55–68CrossRefPubMedPubMedCentralGoogle Scholar
  28. Knapp S (2002) Tobacco to tomatoes, a phylogenetic perspective on fruit diversity in the Solanaceae. J Exp Bot 53:2001–2022CrossRefPubMedGoogle Scholar
  29. Kroon PA, Williamson G (1999) Hydroxycinnamates in plants and food, current and future perspectives. J Sci Food Agric 79:355–361CrossRefGoogle Scholar
  30. Kumar A, Ellis BE (2003) 4-Coumarate: CoA ligase gene family in Rubus idaeus, cDNA structures, evolution, and expression. Plant Mol Biol 31:327–340CrossRefGoogle Scholar
  31. Lester DR, Sherman WB, Atwell BJ (1996) Endopolygalacturonase and the melting flesh (M) locus in peach. J Am Soc Hortic Sci 121:231–235Google Scholar
  32. Liljegren SJ, Ditta GS, Eshed Y, Savidge B, Bowman JL, Yanofsky MF (2000) SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis. Nature 404:766–770CrossRefPubMedGoogle Scholar
  33. Liljegren SJ, Roeder AH, Kempin SA, Gremski K, Ostergaard L, Guimil S, Reyes DK, Yanofsky MF (2004) Control of fruit patterning in Arabidopsis by INDEHISCENT. Cell 116:843–853CrossRefPubMedGoogle Scholar
  34. Mack AL (2000) Did fleshy fruit pulp evolve as a defence against seed loss rather as dispersal mechanism? J Biosci 25:93–97CrossRefPubMedGoogle Scholar
  35. Masia A, Zanchin A, Rascio N, Ramina A (1992) Some biochemical and ultrastructural aspects of peach fruit development. J Am Soc Hortic Sci 117:808–815Google Scholar
  36. Moing A, Aharoni A, Biais B et al (2011) Extensive metabolic crosstalk in melon fruit revealed by spatial and developmental combinatorial metabolomics. New Phytol 190:683–696CrossRefPubMedGoogle Scholar
  37. Mounet F, Lemaire-Chamley M, Maucourt M et al (2007) Quantitative metabolic profiles of tomato flesh and seeds during fruit development, complementary analysis with ANN and PCA. Metabolomics 3:273–288CrossRefGoogle Scholar
  38. Nuñez-LilloG Cifuentes-Esquivel A, Troggio M et al (2015) Identification of candidate genes associated with mealiness and maturity date in peach [Prunus persica (L.) Batsch] using QTL analysis and deep sequencing. Tree Genet Genomes 11:86CrossRefGoogle Scholar
  39. Pascual L, Xu J, Biais B et al (2013) Deciphering genetic diversity and inheritance of tomato fruit weight and composition through a systems biology approach. J Exp Bot 64:5737–5752CrossRefPubMedPubMedCentralGoogle Scholar
  40. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:e45–e50CrossRefPubMedPubMedCentralGoogle Scholar
  41. Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP (2004) Determination of stable housekeeping genes, differentially regulated target genes and sample integrity, BestKeeper–Excel-based tool using pair-wise correlations. Biotechnol Lett 26:509–515CrossRefPubMedGoogle Scholar
  42. Qiao H, Chang KN, Yazaki J, Ecker JR (2009) Interplay between ethylene, ETP1/ETP2 F-box proteins, and degradation of EIN2 triggers ethylene responses in Arabidopsis. Gene Dev 23:512–521CrossRefPubMedPubMedCentralGoogle Scholar
  43. Rajani S, Sundaresan V (2001) The Arabidopsis myc/bHLH gene ALCATRAZ enables cell separation in fruit dehiscence. Curr Biol 11:1914–1922CrossRefPubMedGoogle Scholar
  44. Ramming D (1991) Genetic-control of a slow-ripening fruit trait in nectarine. Can J Plant Sci 71:601–603CrossRefGoogle Scholar
  45. Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R (2004) Fast and effective prediction of microRNA/target duplexes. RNA 10:1507–1517CrossRefPubMedPubMedCentralGoogle Scholar
  46. Ruperti B, Bonghi C, Rasori A, Ramina A, Tonutti P (2001) Characterization and expression of two members of the peach 1-aminocyclopropane-1-carboxylate oxidase gene family. Physiol Planturum 111:336–344CrossRefGoogle Scholar
  47. Salentijn EMJ, Aharoni A, Schaart JG, Boone MJ, Krens FA (2003) Differential gene expression analysis of strawberry cultivars that differ in fruit firmness. Physiol Plantarum 118:571–578CrossRefGoogle Scholar
  48. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning, a laboratory manual. Harbor Laboratory, Cold Spring New YorkGoogle Scholar
  49. Scutt CP, Vinauger-Douard M, Fourquin C, Finet C, Dumas C (2006) An evolutionary perspective on the regulation of carpel development. J Exp Bot 57:2143–2152CrossRefPubMedGoogle Scholar
  50. Simon P (2003) Q-Gene, processing quantitative real-time RT-PCR data. Bioinformatics 19:1439–1440CrossRefPubMedGoogle Scholar
  51. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599CrossRefPubMedGoogle Scholar
  52. Tao S, Khanizadeh S, Zhang H, Zhang S (2009) Anatomy, ultrastructure and lignin distribution of stone cells in two Pyrus species. Plant Sci 176:413–419CrossRefGoogle Scholar
  53. Tataranni G, Spada A, Pozzi C, Bassi D (2010) AFLP-based bulk segregant analysis for tagging the slow-ripening trait in peach [Prunus persica (L.) Batsch]. J Hortic Sci Biotech 85:78–82CrossRefGoogle Scholar
  54. Tatsuki M, Haji T, Yamaguchi M (2006) The involvement of 1-aminocyclopropane-1-carboxylic acid synthase isogene, Pp-ACS1, in peach fruit softening. J Exp Bot 57:1281–1289CrossRefPubMedGoogle Scholar
  55. Tong Z, Gao Z, Wang F, Zhou J, Zhang Z (2009) Selection of reliable reference genes for gene expression studies in peach using real-time PCR. BMC Mol Biol 10:71CrossRefPubMedPubMedCentralGoogle Scholar
  56. Tonutti P, Bonghi C, Ruperti B, Tornielli GB, Ramina A (1997) Ethylene evolution and 1-aminocyclopropane-1-carboxylate oxidase gene expression during early development and ripening of peach fruit. J Am Soc Hortic Sci 122:642–647Google Scholar
  57. Trainotti L, Tadiello A, Casadoro G (2007) The involvement of auxin in the ripening of climacteric fruits comes of age, the hormone plays a role of its own and has an intense interplay with ethylene in ripening peaches. J Exp Bot 58:3299–3308CrossRefPubMedGoogle Scholar
  58. Van der Rest B, Danoun S, Boudet A-M, Rochange SF (2006) Down-regulation of cinnamoyl-CoA reductase in tomato (Solanum lycopersicum L.) induces dramatic changes in soluble phenolic pools. J Exp Bot 57:1399–1411CrossRefPubMedGoogle Scholar
  59. Varotto S, Locatelli S, Canova S, Pipal A, Motto M, Rossi V (2003) Expression profile and cellular localization of maize rpd3-type histone deacetylases during plant development. Plant Physiol 133:606–617CrossRefPubMedPubMedCentralGoogle Scholar
  60. Vendramin E, Pea G, Dondini L et al (2014) A unique mutation in a MYB gene cosegregates with the nectarine phenotype in peach. PLoS One 9(10):e0090574Google Scholar
  61. Vrebalov J, Pan IL, Arroyo AJM et al (2009) Fleshy fruit expansion and ripening are regulated by the tomato SHATTERPROOF gene TAGL1. Plant Cell 21:3041–3062CrossRefPubMedPubMedCentralGoogle Scholar
  62. Ziliotto F, Begheldo M, Rasori A, Bonghi C, Ramina A, Tonutti P (2005) Molecular and genetic aspects of ripening and qualitative traits in peach and nectarine fruits. Acta Hortic 682:237–246CrossRefGoogle Scholar
  63. Ziliotto F, Corso M, Rizzini FM, Rasori A, Botton A, Bonghi C (2012) Grape berry ripening delay induced by a pre-véraison NAA treatment is paralleled by a shift in the expression pattern of auxin- and ethylene-related genes. BMC Plant Biol 12:185CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Alessandro Botton
    • 1
  • Angela Rasori
    • 1
  • Fiorenza Ziliotto
    • 1
  • Annick Moing
    • 2
    • 3
  • Mickaël Maucourt
    • 3
    • 4
  • Stéphane Bernillon
    • 2
    • 3
  • Catherine Deborde
    • 2
    • 3
  • Anna Petterle
    • 1
  • Serena Varotto
    • 1
  • Claudio Bonghi
    • 1
  1. 1.Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE)University of PadovaLegnaroItaly
  2. 2.UMR1332 Biologie du Fruit et PathologieINRAVillenave d’OrnonFrance
  3. 3.Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, MetaboHUB, IBVMCentre INRA BordeauxVillenave d’OrnonFrance
  4. 4.UMR1332 Biologie du Fruit et PathologieUniversity of BordeauxVillenave d’OrnonFrance

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