Tree Genetics & Genomes

, Volume 9, Issue 1, pp 19–36 | Cite as

High density SNP mapping and QTL analysis for fruit quality characteristics in peach (Prunus persica L.)

  • Pedro J. Martínez-GarcíaEmail author
  • Dan E. Parfitt
  • Ebenezer A. Ogundiwin
  • Joseph Fass
  • Helen M. Chan
  • Riaz Ahmad
  • Susan Lurie
  • Abhaya Dandekar
  • Thomas M. Gradziel
  • Carlos H. Crisosto
Original Paper


Single nucleotide polymorphisms (SNPs) were used to construct an integrated SNP linkage map of peach (Prunus persica (L.) Batsch). A set of 1,536 SNPs were evaluated with the GoldenGate® Genotyping assay in two mapping populations, Pop-DF, and Pop-DG. After genotyping and filtering, a final set of 1,400 high quality SNPs in Pop-DF and 962 in Pop-DG with full map coverage were selected and used to construct two linkage maps with JoinMap®4.0. The Pop-DF map covered 422 cM of the peach genome and included 1,037 SNP markers, and Pop-DG map covered 369 cM and included 738 SNPs. A consensus map was constructed with 588 SNP markers placed in eight linkage groups (n = 8 for peach), with map coverage of 454 cM and an average distance of 0.81 cM/marker site. Placements of SNPs on the “peach v1.0” physical map were compared to placement on the linkage maps and several differences were observed. Using the SNP linkage map of Pop-DG and phenotypic data collected for three harvest seasons, a QTL analysis for fruit quality traits and chilling injury symptoms was carried out with the mapped SNPs. Significant QTL effects were detected for mealiness (M) and flesh bleeding (FBL) QTLs on linkage group 4 and flesh browning (FBr) on linkage group 5. This study represents one of the first examples of QTL detection for quality traits and chilling injury symptoms using a high-density SNP map in a single peach F1 family.


Single nucleotide polymorphism Prunus Linkage map SNP effects “Lovell” sequence Peach v1.0 Quantitative trait loci Chilling injury symptoms 



We gratefully acknowledge the assistance of DNA Technologies Core at the University of California, Davis as well as the support of the National Research Initiative of USDA’s National Institute of Food and Agriculture (NIFA) grant # 2008-35300-04432 and US-Israel Bi-national Agriculture Research and Development Fund (BARD) Grant no. US-4027-07 for provided financial support to this project, as well as UC Davis, UC Agricultural Experiment Station and USDA-CREES (Hatch Experiment Station funding). We would especially like to thank Maria J. Truco from UC Davis Genome Center for helpful comments on JoinMap®4.0, Jonathan Fresnedo-Ramírez, PhD student at UC Davis, for his collaboration in data processing and we gratefully, acknowledge Dr. Cameron Peace for his contributions to our earlier discussion of potential traits for peach marker assistance selection.

Supplementary material

11295_2012_522_MOESM1_ESM.xls (920 kb)
ESM 1 (XLS 920 kb)
11295_2012_522_MOESM2_ESM.xls (664 kb)
ESM 2 (XLS 664 kb)


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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Pedro J. Martínez-García
    • 1
    Email author
  • Dan E. Parfitt
    • 1
  • Ebenezer A. Ogundiwin
    • 1
  • Joseph Fass
    • 2
  • Helen M. Chan
    • 1
  • Riaz Ahmad
    • 1
  • Susan Lurie
    • 3
  • Abhaya Dandekar
    • 1
  • Thomas M. Gradziel
    • 1
  • Carlos H. Crisosto
    • 1
  1. 1.Department of Plant SciencesUniversity of CaliforniaDavisUSA
  2. 2.Bioinformatics CoreUniversity of CaliforniaDavisUSA
  3. 3.Department of Postharvest Science of Fresh Produce, Agricultural Research OrganizationVolcani CenterBet DaganIsrael

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