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Candidate gene database and transcript map for peach, a model species for fruit trees

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Abstract

Peach (Prunus persica) is a model species for the Rosaceae, which includes a number of economically important fruit tree species. To develop an extensive Prunus expressed sequence tag (EST) database for identifying and cloning the genes important to fruit and tree development, we generated 9,984 high-quality ESTs from a peach cDNA library of developing fruit mesocarp. After assembly and annotation, a putative peach unigene set consisting of 3,842 ESTs was defined. Gene ontology (GO) classification was assigned based on the annotation of the single “best hit” match against the Swiss-Prot database. No significant homology could be found in the GenBank nr databases for 24.3% of the sequences. Using core markers from the general Prunus genetic map, we anchored bacterial artificial chromosome (BAC) clones on the genetic map, thereby providing a framework for the construction of a physical and transcript map. A transcript map was developed by hybridizing 1,236 ESTs from the putative peach unigene set and an additional 68 peach cDNA clones against the peach BAC library. Hybridizing ESTs to genetically anchored BACs immediately localized 11.2% of the ESTs on the genetic map. ESTs showed a clustering of expressed genes in defined regions of the linkage groups. [The data were built into a regularly updated Genome Database for Rosaceae (GDR), available at (http://www.genome.clemson.edu/gdr/).]

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Acknowledgements

We would like to thank the USDA IFAFS program for supporting this research by the award of no. 2001-52100-11345, the NSF PGR program for supporting the Genome Database for Rosaceae award no. 0320544, the Clemson University for supporting the Bioinformatics analysis, the South Carolina Peach Council and the South Carolina Agricultural Experimental Station for grant SC-1700120 within the SCAFR program as well as the OECD for the fellowship to I. Verde at Clemson University under the OECD co-operative research program: “Biological resource management for sustainable agricultural systems”.

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Authors and Affiliations

  1. Department of Genetics, Biochemistry and Life Science Studies, Clemson University, Clemson, SC, 29634, USA

    Renate Horn, Anne-Claire Lecouls, Lilibeth Garay, Doreen Main, Sook Jung, Laura Georgi, Sam Forrest, Jennifer Mook, Christopher Jesudurai, Jeffrey Tomkins & Albert Glenn Abbott

  2. USDA Appalachian Fruit Research Station, Kearneysville, WV, 25430, USA

    Ann Callahan & Ralph Scorza

  3. Department of Pomology, University of California Davis, Davis, CA, 95616, USA

    Abhaya Dandekar, Helen Chan & Dan Parfitt

  4. Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA

    Per McCord & Bryon Sosinski

  5. Departament de Genètica Vegetal, Institut de Recerca I Tecnologia Agroalimentàries, 08348, Cabrilis, Spain

    Werner Howad & Pere Arús

  6. Istituto Sperimentale per la Frutticoltura (ISF), 00040, Rome, Italy

    Ignazio Verde

  7. Clemson University Genomics Institute, Clemson University, SC, 29634, USA

    Doreen Main, Sook Jung, Christopher Jesudurai & Jeffrey Tomkins

  8. Horticulture Department, Clemson University, Clemson, SC, 29634, USA

    Tatyana Zhebentyayeva, Vance Baird & Gregory Reighard

  9. Plant Sciences Department, University of Arizona, Tucson, AZ, 85721-0036, USA

    Yeisoo Yu, Hye Ran Kim & Rod Wing

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  1. Renate Horn
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  2. Anne-Claire Lecouls
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  3. Ann Callahan
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  4. Abhaya Dandekar
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  5. Lilibeth Garay
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  6. Per McCord
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  7. Werner Howad
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  8. Helen Chan
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  9. Ignazio Verde
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  10. Doreen Main
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  11. Sook Jung
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  12. Laura Georgi
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  13. Sam Forrest
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  14. Jennifer Mook
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  15. Tatyana Zhebentyayeva
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  16. Yeisoo Yu
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  17. Hye Ran Kim
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  18. Christopher Jesudurai
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  19. Bryon Sosinski
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  20. Pere Arús
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  21. Vance Baird
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  22. Dan Parfitt
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  23. Gregory Reighard
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  24. Ralph Scorza
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  27. Albert Glenn Abbott
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Correspondence to Albert Glenn Abbott.

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Communicated by H.C. Becker

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Horn, R., Lecouls, AC., Callahan, A. et al. Candidate gene database and transcript map for peach, a model species for fruit trees. Theor Appl Genet 110, 1419–1428 (2005). https://doi.org/10.1007/s00122-005-1968-x

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  • DOI: https://doi.org/10.1007/s00122-005-1968-x

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