Skip to main content
SpringerLink
Log in

Development and mapping of peach candidate genes involved in fruit quality and their transferability and potential use in other Rosaceae species

  • Original Paper
  • Published:
Tree Genetics & Genomes Aims and scope Submit manuscript

Abstract

The goal of the present study was to identify candidate genes (CGs) involved in fruit quality in peach that can be transferred to other Rosaceae species. Two cDNA libraries from fruit of the “Fantasia” peach cultivar, constructed at two stages of development, were used to generate a set of expressed sequence tag sequences. A total of 1,730 peach unigenes were obtained after clustering. Sequences and corresponding annotations were stored in a relational database and are available through a web interface. Fifty-nine CGs involved in fruit growth and development or fruit quality at maturity, focusing on sweetness, acidity, and phenolic compound content, were selected according to their annotation. Fifty-five primer pairs, designed from peach CG sequences and giving PCR products in peach, were tested in strawberry and 36 gave amplified products. Eight CGs were mapped in peach, 14 in strawberry, four in both species and confirmed the pattern of synteny already proposed using comparative mapping. In peach, the CGs are located in three linkage groups (3, 5, 7), and in strawberry they are distributed in all seven Fragaria linkage groups. Colocalization between some of these CGs and quantitative trait loci for fruit quality traits were identified and are awaiting confirmation in further analyses.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Abbott AG, Lecouls AC, Wang Y, Georgi L, Scorza R, Reighard G (2002) Peach: the model genome for Rosaceae genomics. Acta Hortic 592:199–203

    CAS  Google Scholar 

  • Akiyama Y, Yamamoto Y, Ohmido N, Ohshima M, Fukui K (2001) Estimation of the nuclear DNA content of strawberries (Fragaria spp.) compared with Arabidopsis thaliana by using dual-step flow cytometry. Cytologia (Tokyo) 66:431–436

    Google Scholar 

  • Baird WV, Estager AS, Wells JK (1994) Estimating nuclear-DNA content in peach and related diploid species using laser flow-cytometry and DNA hybridization. J Am Soc Hortic Sci 119:1312–1316

    Google Scholar 

  • Bliss FA, Arulsekar S, Foolad MR, Becerra V, Gillen AM, Warburton ML, Dandekar AM, Kocsisne GM, Mydin KK (2002) An expanded genetic linkage map of Prunus based on an interspecific cross between almond and peach. Genome 45:520–529

    Article  CAS  PubMed  Google Scholar 

  • Burke J, Wang H, Hide W, Davison DB (1998) Alternative gene form discovery and candidate gene selection from gene indexing projects. Genome Res 8:276–290

    CAS  PubMed  Google Scholar 

  • Burke J, Davison D, Hide W (1999) d2_cluster: a validated method for clustering EST and full-length cDNA sequences. Genome Res 9:1135–1142

    Article  CAS  PubMed  Google Scholar 

  • Causse M, Duffe P, Gomez MC, Buret M, Damidaux R, Zamir D, Gur A, Chevalier C, Lemaire-Chamley M, Rothan C (2004) A genetic map of candidate genes and QTLs involved in tomato fruit size and composition. J Exp Bot 55:1671–1685

    Article  CAS  PubMed  Google Scholar 

  • Chaparro JX, Werner DJ, Omalley D, Sederoff RR (1994) Targeted mapping and linkage analysis of morphological isozyme, and RAPD markers in peach. Theor Appl Genet 87:805–815

    Article  CAS  Google Scholar 

  • Clifford MN, Scalbert A (2000) Ellagitannins—nature, occurrence and dietary burden. J Sci Food Agric 80:1118–1125

    Article  CAS  Google Scholar 

  • Deluc L, Barrieu F, Marchive C, Lauvergeat V, Decendit A, Richard T, Carde JP, Merillon JM, Hamdi S (2006) Characterization of a grapevine R2R3-MYB transcription factor that regulates the phenylpropanoid pathway. Plant Physiol 140:499–511

    Article  CAS  PubMed  Google Scholar 

  • Dettori MT, Quarta R, Verde I (2001) A peach linkage map integrating RFLPs, SSRs, RAPDs, and morphological markers. Genome 44:783–790

    Article  CAS  PubMed  Google Scholar 

  • Dirlewanger E, Moing A, Rothan C, Svanella L, Pronier V, Guye A, Plomion C, Monet R (1999) Mapping QTLs controlling fruit quality in peach (Prunus persica (L.) Batsch). Theor Appl Genet 98:18–31

    Article  CAS  Google Scholar 

  • Dirlewanger E, Graziano E, Joobeur T, Garriga-Caldere F, Cosson P, Howad W, Arús P (2004) Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc Natl Acad Sci U S A 101:9891–9896

    Article  CAS  PubMed  Google Scholar 

  • Dirlewanger E, Cosson P, Renaud C, Monet R, Poëssel JL, Moing A (2005) New detection of QTLs controlling major fruit quality components in peach. Acta Hortic 713:65–72

    Google Scholar 

  • Dirlewanger E, Cosson P, Boudehri K, Renaud C, Capdeville G, Tauzin Y, Laigret F, Moing A (2006) Development of a second-generation genetic linkage map for peach [Prunus persica (L.) Batsch] and characterization of morphological traits affecting flower and fruit. Tree Genet Genomes 3:1–13

    Article  Google Scholar 

  • Etienne C, Moing A, Dirlewanger E, Raymond P, Monet R, Rothan C (2002a) Isolation and characterization of six peach cDNAs encoding key proteins in organic acid metabolism and solute accumulation: involvement in regulating peach fruit acidity. Physiol Plant 114:259–270

    Article  CAS  PubMed  Google Scholar 

  • Etienne C, Rothan C, Moing A, Plomion C, Bodenes C, Svanella-Dumas L, Cosson P, Pronier V, Monet R, Dirlewanger E (2002b) Candidate genes and QTLs for sugar and organic acid content in peach [Prunus persica (L.) Batsch]. Theor Appl Genet 105:145–159

    Article  CAS  PubMed  Google Scholar 

  • Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194

    CAS  PubMed  Google Scholar 

  • Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175–185

    CAS  PubMed  Google Scholar 

  • Feltus FA, Singh HP, Lohithaswa HC, Schulze SR, Silva TD, Paterson AH (2006) A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops. Plant Physiol 140:1183–1191

    Article  CAS  PubMed  Google Scholar 

  • Folta KM, Davis TM (2006) Strawberry genes and genetics. Crit Rev Plant Sci 25:399–415

    Article  CAS  Google Scholar 

  • Fraser CM, Rider LW, Chapple C (2005) An expression and bioinformatics analyses of the Arabidopsis serine carboxypeptidase-like gene family. Plant Physiol 138:1136–1148

    Article  CAS  PubMed  Google Scholar 

  • Gaxiola RA, Palmgren MG, Schumacher K (2007) Plant proton pumps. FEBS Lett 581:2204–2214

    Article  CAS  PubMed  Google Scholar 

  • Georgi LL, Wang Y, Reighard GL, Mao L, Wing RA, Abbott AG (2003) Comparison of peach and Arabidopsis genomic sequences: fragmentary conservation of gene neighborhoods. Genome 46:268–276

    Article  CAS  PubMed  Google Scholar 

  • Gil MI, Tomas-Barberan FA, Hess-Pierce B, Kader AA (2002) Antioxidant capacities, phenolic compounds, carotenoids, and vitamin C contents of nectarine, peach, and plum cultivars from California. J Agric Food Chem 50:4976–4982

    Article  CAS  PubMed  Google Scholar 

  • Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8:195–202

    CAS  PubMed  Google Scholar 

  • Hesse CO (1975) Peaches. In: Janick J, Moore JN (eds) Advances in fruit breeding. Purdue Univ Press, West Lafayette, pp 285–335

    Google Scholar 

  • Hiwasa K, Nakano R, Inaba A, Kubo Y (2003) Expression analysis of genes encoding xyloglucan endotransglycosylase during ripening in pear fruit. Acta Hortic 628:549–553

    CAS  Google Scholar 

  • Howad W, Yamamoto T, Dirlewanger E, Testolin R, Cosson P, Cipriani G, Monforte AJ, Georgi L, Abbott AG, Arús P (2005) Mapping with a few plants: using selective mapping for microsatellite saturation of the Prunus reference map. Genetics 171:1305–1309

    Article  CAS  PubMed  Google Scholar 

  • Hu CG, Hao YJ, Honda C, Kita M, Moriguchi T (2003) Putative PIP1 genes isolated from apple: expression analyses during fruit development and under osmotic stress. J Exp Bot 54:2193–2194

    Article  CAS  PubMed  Google Scholar 

  • Jung S, Main D, Staton M, Cho I, Zhebentyayeva T, Arús P, Abbott A (2006) Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomes. BMC Genomics 7:81

    Article  PubMed  Google Scholar 

  • Jung S, Staton M, Lee T, Blenda A, Svancara R, Abbott A, Main D (2008) GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Res 36:D1034–D1040

    Article  CAS  PubMed  Google Scholar 

  • Kubota N, Mimura H, Shimamura K (2000) Differences in phenolic levels among mature peach and nectarine cultivars and their relation to astringency. J Japan Soc Hort Sci 69:35–39

    Article  CAS  Google Scholar 

  • Kubota N, Yakushiji H, Nishiyama N, Mimura H, Shimamura K (2001) Phenolic contents and l-phenylalanine ammonia-lyase activity in peach fruit as affected by rootstocks. J Japan Soc Hort Sci 70:151–156

    Article  CAS  Google Scholar 

  • Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    Article  CAS  PubMed  Google Scholar 

  • Le Dantec L, Chagne D, Pot D, Cantin O, Garnier-Gere P, Bedon F, Frigerio JM, Chaumeil P, Leger P, Garcia V, Laigret F, De Daruvar A, Plomion C (2004) Automated SNP detection in expressed sequence tags: statistical considerations and application to maritime pine sequences. Plant Mol Biol 54:461–470

    Article  PubMed  Google Scholar 

  • Lea MA, Ibeh C, desBordes C, Vizzotto M, Cisneros-Zevallos L, Byrne DH, Okie WR, Moyer MP (2008) Inhibition of growth and induction of differentiation of colon cancer cells by peach and plum phenolic compounds. Anticancer Res 28:2067–2076

    CAS  PubMed  Google Scholar 

  • Lerceteau-Kohler E, Moing A, Guerin G, Renaud C, Maucourt M, Rolin D, Roudeillac P, Denoyes-Rothan B (2006) QTL analysis for sugars and organic acids in strawberry fruits. Acta Hortic 708:573–577

    CAS  Google Scholar 

  • Lewers KS, Saski CA, Cuthbertson BJ, Henry DC, Staton ME, Main DS, Dhanaraj AL, Rowland LJ, Tomkins JP (2008) A blackberry (Rubus L.) expressed sequence tag library for the development of simple sequence repeat markers. BMC Plant Biol 8:69

    Article  PubMed  Google Scholar 

  • Marth GT, Korf I, Yandell MD, Yeh RT, Gu Z, Zakeri H, Stitziel NO, Hillier L, Kwok PY, Gish WR (1999) A general approach to single-nucleotide polymorphism discovery. Nat Genet 23:452–456

    Article  CAS  PubMed  Google Scholar 

  • Masia A, Zanchin A, Rascio N, Ramina A (1992) Some biochemical and ultrastructural aspects of peach fruit-development. J Am Soc Hortic Sci 117:808–815

    CAS  Google Scholar 

  • Miller RT, Christoffels AG, Gopalakrishnan C, Burke J, Ptitsyn AA, Broveak TR, Hide WA (1999) A comprehensive approach to clustering of expressed human gene sequence: the sequence tag alignment and consensus knowledge base. Genome Res 9:1143–1155

    Article  CAS  PubMed  Google Scholar 

  • Moing A (2000) Sugar alcohols as carbohydrate reserves in some higher plants. In: Gupta AK, Kaur N (eds) Carbohydrate reserves in plants—synthesis and regulation, vol 26. Elsevier Ludhiana, India, p 380

    Chapter  Google Scholar 

  • Moing A, Svanella L, Rolin D, Gaudillere M, Gaudillere JP, Monet R (1998) Compositional changes during the fruit development of two peach cultivars differing in juice acidity. J Am Soc Hortic Sci 123:770–775

    CAS  Google Scholar 

  • Monet R, Guye A, Roy M, Dachary N (1996) Peach Mendelian genetics: a short review and new results. Agronomie 16:321–329

    Article  Google Scholar 

  • Nickerson DA, Tobe VO, Taylor SL (1997) PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res 25:2745–2751

    Article  CAS  PubMed  Google Scholar 

  • Ogundiwin EA, Marti C, Forment J, Pons C, Granell A, Gradziel TM, Peace CP, Crisosto CH (2008) Development of ChillPeach genomic tools and identification of cold-responsive genes in peach fruit. Plant Mol Biol 68:379–397

    Article  CAS  PubMed  Google Scholar 

  • Peace CP, Crisosto CH, Gradziel TM (2005) Endopolygalacturonase: a candidate gene for Freestone and Melting flesh in peach. Mol Breed 16:21–31

    Article  CAS  Google Scholar 

  • Perkins-Veazie P (1995) Growth and ripening of strawberry fruit. Hort Rev 17:267–297

    Google Scholar 

  • Quilot B, Wu BH, Kervella J, Genard M, Foulongne M, Moreau K (2004) QTL analysis of quality traits in an advanced backcross between Prunus persica cultivars and the wild relative species P. davidiana. Theor Appl Genet 109:884–897

    Article  CAS  PubMed  Google Scholar 

  • Rajapakse S, Belthoff LE, He G, Estager AE, Scorza R, Verde I, Ballard RE, Baird WV, Callahan A, Monet R, Abbott AG (1995) Genetic-linkage mapping in peach using morphological, RFLP and RAPD markers. Theor Appl Genet 90:503–510

    Article  CAS  Google Scholar 

  • Roberts MR (2003) 14–3–3 proteins find new partners in plant cell signalling. Trends Plant Sci 8:218–223

    Article  CAS  PubMed  Google Scholar 

  • Rothan C, Etienne C, Moing A, Dirlewanger E, Raymond P, Monet R (1999) Plant gene register PGR 99-126. Isolation of a cDNA encoding a metallothionein-like protein (accession no. AJ243532) expressed during peach fruit development. Plant Physiol 121:311 (Electronic Plant Gene Register)

    Article  Google Scholar 

  • Rousseau-Gueutin M, Lerceteau-Kohler E, Barrot L, Sargent DJ, Monfort A, Simpson D, Arus P, Guerin G, Denoyes-Rothan B (2008) Comparative genetic mapping between octoploid and diploid Fragaria species reveals a high level of collinearity between their genomes and the essentially disomic behavior of the cultivated octoploid strawberry. Genetics 179:2045–2060

    Article  PubMed  Google Scholar 

  • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Meth Mol Biol 132:365–386

    CAS  Google Scholar 

  • Sargent DJ, Rys A, Nier S, Simpson DW, Tobutt KR (2007) The development and mapping of functional markers in Fragaria and their transferability and potential for mapping in other genera. Theor Appl Genet 114:373–384

    Article  CAS  PubMed  Google Scholar 

  • Sargent DJ, Cipriani G, Vilanova S, Gil-Ariza D, Arus P, Simpson DW, Tobutt KR, Monfort A (2008) The development of a bin mapping population and the selective mapping of 103 markers in the diploid Fragaria reference map. Genome 51:120–127

    Article  CAS  PubMed  Google Scholar 

  • Sargent DJ, Marchese A, Simpson DW, Howad W, Fernández-Fernández F, Monfort A, Arús P, Evans KM, Tobutt KR (2009) Development of “universal” gene-specific markers from Malus spp. cDNA sequences, their mapping and use in synteny studies within Rosaceae. Tree Genet Genomes 5:133–145

    Article  Google Scholar 

  • Senter SD, Callahan A (1990) Variability in the quantities of condensed tannins and other major phenols in peach fruit during maturation. J Food Sci 55:1585–1587

    Article  CAS  Google Scholar 

  • Shiratake K, Martinoia E (2007) Transporters in fruit vacuoles. Plant Biotechnol 24:127–133

    CAS  Google Scholar 

  • Shulaev V, Korban SS, Sosinski B, Abbott AG, Aldwinckle HS, Folta KM, Iezzoni A, Main D, Arus P, Dandekar AM, Lewers K, Brown SK, Davis TM, Gardiner SE, Potter D, Veilleux RE (2008) Multiple models for Rosaceae genomics. Plant Physiol 147:985–1003

    Article  CAS  PubMed  Google Scholar 

  • Takahashi M, Matsuda F, Margetic N, Lathrop M (2003) Automated identification of single nucleotide polymorphisms from sequencing data. J Bioinform Comput Biol 1:253–265

    Article  CAS  PubMed  Google Scholar 

  • Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB et al (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132:1141–1160

    CAS  PubMed  Google Scholar 

  • Tomas-Barberan FA, Gil MI, Cremin P, Waterhouse AL, Hess-Pierce B, Kader AA (2001) HPLC-DAD-ESIMS analysis of phenolic compounds in nectarines, peaches, and plums. J Agric Food Chem 49:4748–4760

    Article  CAS  PubMed  Google Scholar 

  • Tsuda T, Yamaguchi M, Honda C, Moriguchi T (2004) Expression of anthocyanin biosynthesis genes in the skin of peach and nectarine fruit. J Am Soc Hortic Sci 129:857–862

    CAS  Google Scholar 

  • Tucker GA (1993) Introduction. In: Seymour GB, Taylor JE, Tucker GA (eds) Biochemistry of fruit ripening. Chapman & Hall, London, pp 3–43

    Google Scholar 

  • Urbanczyk-Wochniak E, Usadel B, Thimm O, Nunes-Nesi A, Carrari F, Davy M, Blasing O, Kowalczyk M, Weicht D, Polinceusz A, Meyer S, Stitt M, Fernie AR (2006) Conversion of MapMan to allow the analysis of transcript data from Solanaceous species: effects of genetic and environmental alterations in energy metabolism in the leaf. Plant Mol Biol 60:773–792

    Article  CAS  PubMed  Google Scholar 

  • Vilanova S, Sargent DJ, Arus P, Monfort A (2008) Synteny conservation between two distantly-related Rosaceae genomes: Prunus (the stone fruits) and Fragaria (the strawberry). BMC Plant Biol 8:12

    Article  Google Scholar 

  • Warburton ML, Becerra-Velasquez VL, Goffreda JC, Bliss FA (1996) Utility of RAPD markers in identifying genetic linkages to genes of economic interest in peach. Theor Appl Genet 93:920–925

    Article  CAS  Google Scholar 

  • Yang L, Jin G, Zhao X, Zheng Y, Xu Z, Wu W (2007) PIP: a database of potential intron polymorphism markers. Bioinformatics 23:2174–2177

    Article  CAS  PubMed  Google Scholar 

  • Zhebentyayeva TN, Swire-Clark G, Georgi LL, Garay L, Jung S, Forrest S, Blenda AV, Blackmon B, Mook J, Horn R, Howad W, Arus P, Main D, Tomkins JP, Sosinski B, Baird WV, Reighard GL, Abbott AG (2008) A framework physical map for peach, a model Rosaceae species. Tree Genet Genomes 4:745–756

    Article  Google Scholar 

Download references

Acknowledgements

This research was partially funded by the European ISAFRUIT Integrated Project. The ISAFRUIT project is funded by the European Commission under the Thematic Priority 5—Food Quality and Safety of the 6th Framework Programme of RTD (contract number FP6-FOOD-CT-2006-016279). We thank Dr. Christophe Rothan for his involvement in the construction of the cDNA libraries and Christel Renaud for her participation in the preparation of EST clones for sequencing. The strawberry research was supported in part with funds from the Spanish Ministry of Science and Innovation project INIA (RTA2007-00063-00-00) and Euroberry COST Action 863. JB was supported by a fellowship from AGAUR.

Author information

Authors and Affiliations

  1. INRA, UR419, Unité de Recherches sur les Espèces Fruitières, BP 81, F-33140, Villenave d’Ornon, France

    Loïck Le Dantec, Gaelle Cardinet, Mathieu Fouché, Karima Boudehri & Elisabeth Dirlewanger

  2. IRTA, Centre de Recerca en Agrogenòmica CSIC-IRTA-UAB, Carretera de Cabrils Km 2, 08348, Cabrils, Barcelona, Spain

    Julio Bonet & Amparo Monfort

  3. INRA, UR1052, Unité de Génétique et d’Amélioration des Fruits et Légumes, F-84000, Avignon, France

    Jean-Luc Poëssel

  4. INRA, UMR619 Fruit Biology, BP 81, F-33140, Villenave d’Ornon, France

    Annick Moing

Authors
  1. Loïck Le Dantec
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Gaelle Cardinet
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Julio Bonet
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mathieu Fouché
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Karima Boudehri
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Amparo Monfort
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Jean-Luc Poëssel
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Annick Moing
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Elisabeth Dirlewanger
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Elisabeth Dirlewanger.

Additional information

Communicated by A. Abbott

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplemental Table 1

Annotation of peach candidate genes (XLS 76 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Le Dantec, L., Cardinet, G., Bonet, J. et al. Development and mapping of peach candidate genes involved in fruit quality and their transferability and potential use in other Rosaceae species. Tree Genetics & Genomes 6, 995–1012 (2010). https://doi.org/10.1007/s11295-010-0308-8

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11295-010-0308-8

Keywords

Search

Navigation