A strategy for developing representative germplasm sets for systematic QTL validation, demonstrated for apple, peach, and sweet cherry

C. P. Peace, J. J. Luby, W. E. van de Weg, M. C.A.M. Bink, A. F. Iezzoni

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49 Scopus citations


Horticultural crop improvement would benefit from a standardized, systematic, and statistically robust procedure for validating quantitative trait loci (QTLs) in germplasm relevant to breeding programs. Here, we describe and demonstrate a strategy for developing reference germplasm sets of perennial, clonally propagated crops, especially those with long juvenile periods. Germplasm is chosen to efficiently represent important members of larger pedigree-connected genepools. To facilitate validation of multiple QTLs, genome-wide representation of alleles is optimized for designated important breeding parents (IBPs) by estimating average allelic representation in relatives. The strategy and arising principles were demonstrated in a simulated germplasm set. Strong statistical power can be achieved with a carefully chosen germplasm set composed of IBPs, their numerous unselected progenies and close relatives, and all available founders and intermediate ancestors. Crop Reference Sets were developed in the marker-assisted breeding (MAB)-enabling “RosBREED” project as a base resource for QTL validation in US breeding germplasm of apple (Malus × domestica), peach (Prunus persica), and sweet cherry (Prunus avium) consisting of 467, 452, and 268 individuals, respectively. These sets adequately represent the most designated IBPs, have distinct advantages for QTL validation over other germplasm arrangements of equal size, and are recommended as a base resource for QTL validation by breeders of these US crops. The strategy described here can be used to develop efficient reference germplasm sets suiting other breeding genepools or to calculate the statistical power for QTL validation of germplasm sets already established.

Original languageEnglish (US)
Pages (from-to)1679-1694
Number of pages16
JournalTree Genetics and Genomes
Issue number6
StatePublished - Dec 2014

Bibliographical note

Funding Information:
We gratefully acknowledge RosBREED’s apple, peach, and sweet cherry “demonstration breeders” for making available vast troves of germplasm and for helping assemble pedigree information. Key germplasm was also kindly provided by interim curators of two National Plant Germplasm System collections, Gennaro Fazio of the Plant Genetic Resources Unit in Geneva, NY and Malli Aradhya of the National Clonal Germplasm Repository in Davis, CA. This work was funded by USDA’s National Institute of Food and Agriculture (NIFA)—specialty crop research initiative project, “RosBREED: Enabling marker-assisted breeding in Rosaceae” (2009-51181-05808) and was precipitated by grant number 2008-35300-04435 of the National Research Initiative of the USDA Cooperative State Research, Education and Extension Service (now NIFA).

Publisher Copyright:
© 2014, Springer-Verlag Berlin Heidelberg.


  • Crop Reference Set
  • Marker-assisted breeding
  • Marker-locus-trait associations
  • Pedigree-Based Analysis
  • RosBREED


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