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QTL mapping of pomological traits in peach and related species breeding germplasm

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Abstract

Peach is an economically important fruit tree crop that exhibits high phenotypic variability yet suffers from diversity-limited gene pool. Genetic introgression of novel alleles from related species is being pursued to expand genetic diversity. This process is, however, challenging and requires the incorporation of innovative genomic and statistical tools to facilitate efficient transfer of these exotic alleles across the multiple generations required for introgression. In this study, pedigree-based analysis (PBA) in a Bayesian QTL mapping framework was applied to a diverse peach pedigree introgressed with almond and other related Prunus species. The aim was to investigate the genetic control of eight commercially important fruit productivity and fruit quality traits over two subsequent years. Fifty-two QTLs with at least positive evidence explaining up to 98 % of the phenotypic variance across all trait/year combinations were mapped separately per trait and year. Several QTLs exhibited variable association with traits between years. By using the peach genome sequence as a reference, the intrachromosomal positions for several QTLs were shown to differ from those previously reported in peach. The inclusion of introgressed germplasm and the explicit declaration of the genetic structure of the pedigree as covariate in PBA enhanced the mapping and interpretation of QTLs. This study serves as a model study for PBA in a diverse peach breeding program, and the results highlight the ability of this strategy to identify genomic resources for direct utilization in marker-assisted breeding.

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Acknowledgments

This study was funded by USDA’s National Institute of Food and Agriculture—Specialty Crop Research Initiative project, ‘RosBREED: Enabling marker-assisted breeding in Rosaceae’ (2009-51181-05808). Jonathan Fresnedo Ramírez was supported by a CONACYT-UCMEXUS (Mexican Council of Science and Technology and University of California Institute for Mexico and the United States) Doctoral fellowship at the University of California, Davis. The contributions of M.C.A.M. Bink & E.W. van de Weg were also supported by the EU-FruitBreedomics project funded by the Commission of the European Communities (Contract FP7-KBBE-2010-265582). Thanks to Dr. Pedro J. Martínez-García for his helpful comments about the organization of the manuscript. Special thanks for their valuable help during the phenotyping of the accessions to the field crew of the Processing Peach Breeding Program at UC Davis, supervised by Mary Ann Thorpe, Sabrina Marchand, Helen Chan and Rachel Williams. Likewise, thanks to Palma Lower, writing specialist at UC Davis, for her valuable comments and corrections during early drafts of the manuscript.

Data archiving

The genotypic and phenotypic datasets of the UC Davis pedigree-connected germplasm can be accessed through the Breeders Toolbox available at the Genome Database for Rosaceae (http://www.rosaceae.org/breeders_toolbox). The QTL information is accessible through the Trait Loci search tool at GDR. (http://www.rosaceae.org/search/qtl).

Authors’ contributions

J.F.R. carried out the analyzes and drafted the manuscript, M.C.A.M.B. and E.V.W. provided support for implementation and performing of PBA as well as for the interpretation of the results, also helped in drafting the manuscript, T.R.F. helped to perform pedigree pruning and determination of genetic structure, C.H.C. provided support for phenotypic evaluation and analyzes, T.J.F., K.G. and C.P.P. developed the SNP genotyping and database for the peach set in RosBREED and helped in drafting the manuscript, and T.M.G. provided the genetic materials, coordinated the study and elaborated on manuscripts. All authors read and approved the final and reviewed manuscript.

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Author notes

  1. Jonathan Fresnedo-Ramírez

    Present address: BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA

  2. Terrence J. Frett

    Present address: Horticulture Department, University of Arkansas, Fayetteville, AR, 72701, USA

Authors and Affiliations

  1. Department of Plant Sciences, University of California, Davis, CA, 95616, USA

    Jonathan Fresnedo-Ramírez, Carlos H. Crisosto & Thomas M. Gradziel

  2. Biometris, Wageningen University and Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands

    Marco C. A. M. Bink

  3. Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands

    Eric van de Weg

  4. Department of Animal Science, University of California, Davis, CA, 95616, USA

    Thomas R. Famula

  5. Department of Agricultural and Environmental Sciences, Clemson University, Clemson, SC, 29634, USA

    Terrence J. Frett & Ksenija Gasic

  6. Department of Horticulture, Washington State University, Pullman, WA, 99164, USA

    Cameron P. Peace

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  1. Jonathan Fresnedo-Ramírez
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Correspondence to Thomas M. Gradziel.

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Fresnedo-Ramírez, J., Bink, M.C.A.M., van de Weg, E. et al. QTL mapping of pomological traits in peach and related species breeding germplasm. Mol Breeding 35, 166 (2015). https://doi.org/10.1007/s11032-015-0357-7

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