Abstract
The narrow genetic base of peach (Prunus persica L. Batsch) challenges efforts to accurately dissect the genetic architecture of complex traits. Standardized phenotypic assessment of pedigree-linked breeding germplasm and new molecular strategies and analytical approaches developed and conducted during the RosBREED project for enabling marker-assisted breeding (MAB) in Rosaceae crops has overcome several aspects of this challenge. The genetic underpinnings of fruit size (fruit equatorial diameter (FD)) and weight (fresh weight (FW)), two most important components of yield, were investigated using the pedigree-based analysis (PBA) approach under a Bayesian framework which has emerged as an alternative strategy to study the genetics of quantitative traits within diverse breeding germplasm across breeding programs. In this study, a complex pedigree with the common founder “Orange Cling” was identified and FD and FW data from 2011 and 2012 analyzed. A genetic model including genetic additive and dominance effects was considered, and its robustness was evaluated by using various prior and initial values in the Markov chain Monte Carlo procedure. Five QTLs were identified which accounted for up to 29 and 17 % of the phenotypic variation for FD and FW, respectively. Additionally, genomic breeding values were obtained for both traits, with accuracies >85 %. This approach serves as a model study for performing PBA across diverse pedigrees. By incorporating multiple breeding programs, the method and results presented support and highlight the ability of this strategy to identify genomic resources as targets for DNA marker development and subsequent MAB within each program.
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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 (the lead author) 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 University of California, Davis.
Special thanks are given to Palma Lower, writing specialist at UC Davis, for her valuable comments and corrections during early stages of redaction of the manuscript.
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Authors’ contributions
JFR phenotyped the accessions from UC Davis, carried out the analysis, and led the drafting of the manuscript. KG provided initial marker analysis IPSC 9K peach SNP array. TJF, PJS, and ASR helped in the selection of markers; phenotyped the selections from Clemson University, University of Arkansas; and drafted the manuscript. NA and TPH phenotyped the selections from Texas A&M University. MCAMB and EVW provided support for implementation and performing of PBA as well as for the interpretation of the results. CHC provided support for phenotypic evaluation and analyses. DHB, JRC, KG, and TMG provided the genetic materials and helped draft the manuscript. TMG coordinated the study and elaborated on the manuscript. All authors read and approved the final and reviewed manuscript.
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The QTL data and genomic breeding values (GBVs) reported in this manuscript will be made publicly available through the Genome Database for Rosaceae (www.rosaceae.org).
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Communicated by C. Dardick
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Number of progenies, maximum generation coefficient and contributing founders from each peach breeding program. (PDF 107 kb)
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Polynomial equations and supplemental figures and table. (PDF 396 kb)
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Genomic breeding values (GBVs) per accession per trait per year, and additional statistics. (PDF 265 kb)
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Fresnedo-Ramírez, J., Frett, T.J., Sandefur, P.J. et al. QTL map** and breeding value estimation through pedigree-based analysis of fruit size and weight in four diverse peach breeding programs. Tree Genetics & Genomes 12, 25 (2016). https://doi.org/10.1007/s11295-016-0985-z
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DOI: https://doi.org/10.1007/s11295-016-0985-z