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

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Abstract

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.

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Acknowledgments

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).

Data archiving statement

A matrix of the AAR units provided by each individual included in the apple, peach, and sweet cherry Crop Reference Sets for each of the other individuals and ancestors of the sets was submitted to the Genome Database for Rosaceae (www.rosaceae.org).

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Authors and Affiliations

  1. Department of Horticulture, Washington State University, Pullman, WA, USA

    C. P. Peace

  2. Department of Horticultural Science, University of Minnesota, St. Paul, Minneapolis, MN, 55455, USA

    J. J. Luby

  3. Plant Breeding, Wageningen UR, Wageningen, The Netherlands

    W. E. van de Weg

  4. Biometris, Wageningen UR, Wageningen, The Netherlands

    M. C. A. M. Bink

  5. Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA

    A. F. Iezzoni

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  1. C. P. Peace
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  2. J. J. Luby
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  3. W. E. van de Weg
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  4. M. C. A. M. Bink
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Corresponding author

Correspondence to C. P. Peace.

Additional information

Communicated by E. Dirlewanger

Electronic supplementary material

Below is the link to the electronic supplementary material.

Online Resource 1

Spreadsheet-based procedure to calculate average allelic representation of germplasm individuals, demonstrated with a simulated germplasm set (XLSX 324 kb)

Online Resource 2

The US Apple Crop Reference Set of 467 individuals, chosen to be representative of 57 important breeding parents (underlined), and their 70 known ancestors. Parentage according to pedigree records is indicated (“-” = unknown). Number of seedlings included for each family is indicated. For the cultivar McIntosh, two distinct types were included: ‘Marshall McIntosh’ and ‘Wijcik McIntosh’. AAR = average allelic representation of each individual achieved by the Set; Bal. = balanced, Uns. = unselected for typical breeding traits (PDF 768 kb)

Online Resource 3

The U.S. Peach Crop Reference Set of 452 individuals, chosen to be representative of 38 important breeding parents (underlined), and their 331 known ancestors. Parentage according to pedigree records is indicated (“-” = unknown). Number of seedlings included for each family is indicated. AAR = average allelic representation of each individual achieved by the Set; Bal. = balanced, Uns. = unselected for typical breeding traits (PDF 977 kb)

Online Resource 4

The U.S. Sweet Cherry Crop Reference Set of 268 individuals, chosen to be representative of 25 important breeding parents (underlined), and their 15 known ancestors. Parentage according to pedigree records is indicated (“-” = unknown). Number of seedlings included for each family is indicated. AAR = average allelic representation of each individual achieved by the Set; Bal. = balanced, Uns. = unselected for typical breeding traits (PDF 595 kb)

Online Resource 5

Guiding principles for establishing efficient germplasm sets for (discovery and) validation of existing alleles of a breeding program (PDF 83 kb)

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Peace, C.P., Luby, J.J., van de Weg, W.E. et al. A strategy for developing representative germplasm sets for systematic QTL validation, demonstrated for apple, peach, and sweet cherry. Tree Genetics & Genomes 10, 1679–1694 (2014). https://doi.org/10.1007/s11295-014-0788-z

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  • DOI: https://doi.org/10.1007/s11295-014-0788-z

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