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Genetic diversity, population structure, and linkage disequilibrium of elite and local apple accessions from Belgium using the IRSC array

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Abstract

The identification of molecular markers associated with economic and quality traits will help improve breeding for new apple (Malus × domestica Borkh.) cultivars. Tools such as the 8K apple SNP array developed by the RosBREED consortium allow for high-throughput genotyping of SNP polymorphisms within collections. However, genetic characterization and the identification of population stratification and kinship within germplasm collections is a fundamental prerequisite for identifying robust marker–trait associations. In this study, a collection of apple germplasm originally developed for plant architectural studies and consisting of both non-commercial/local and elite accessions was genotyped using the 8K apple SNP array to identify cryptic relationships between accessions, to analyze population structure and to calculate the linkage disequilibrium (LD). A total of nine pairs of synonyms and several triploids accessions were identified within the 130 accessions genotyped. In addition, most of the known parent-child relations were confirmed, and several putative, previously unknown parent-child relations were identified among the local accessions. No clear subgroups could be identified although some separation between local and elite accessions was evident. The study of LD showed a rapid decay in our collection, indicating that a larger number of SNPs is necessary to perform whole genome association mapping. Finally, an association mapping effort for architectural traits was carried out on a small number of accessions to estimate the feasibility of this approach.

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Acknowledgements

The authors would like to thank Better3Fruit, the Centre Wallon de Recherches Agronomiques, and the Nationale Boomgaardenstichting for supplying the budwood for the plants used in this study. This study is part of a project that was funded by the IWT (IWT LO-080510).

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  1. Laboratory for Fruit Breeding and Biotechnology, Department of Biosystems, Katholieke Universiteit Leuven, Willem De Croylaan 42, Heverlee, Leuven, Belgium

    Stijn Vanderzande & Johan Keulemans

  2. Department of Horticulture, Washington State University, PO Box 646414, Pullman, WA, 99164, USA

    Stijn Vanderzande

  3. Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy

    Diego Micheletti & Michela Troggio

  4. Innovation Center, Bayer CropScience NV, Technologiepark 38, 9052, Zwijnaarde, Belgium

    Mark W. Davey

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  1. Stijn Vanderzande
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Correspondence to Stijn Vanderzande.

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Communicated by V. Decroocq

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Vanderzande, S., Micheletti, D., Troggio, M. et al. Genetic diversity, population structure, and linkage disequilibrium of elite and local apple accessions from Belgium using the IRSC array. Tree Genetics & Genomes 13, 125 (2017). https://doi.org/10.1007/s11295-017-1206-0

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