Molecular Breeding, August 2015, 35:166

Jonathan Fresnedo-Ramírez1, Marco C. A. M. Bink2, Eric van de Weg3, Thomas R. Famula4, Carlos H. Crisosto5, Terrence J. Frett6, Ksenija Gasic7, Cameron P. Peace8, Thomas M. Gradzie9

1Department of Plant Sciences, University of California, BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University
2Biometris, Wageningen University and Research Centre
3Wageningen UR Plant Breeding, Wageningen University and Research Centre
4Department of Animal Science, University of California
5Department of Plant Sciences, University of California
6Department of Agricultural and Environmental Sciences, Clemson University and Horticulture Department, University of Arkansas
7Department of Agricultural and Environmental Sciences, Clemson University
8Department of Horticulture, Washington State University
9Department of Plant Sciences, University of California


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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