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Towards genomic selection in apple (Malus × domestica Borkh.) breeding programmes: Prospects, challenges and strategies

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Abstract

The apple genome sequence and the availability of high-throughput genotyping technologies have initiated a new era where SNP markers are abundant across the whole genome. Genomic selection (GS) is a statistical approach that utilizes all available genome-wide markers simultaneously to estimate breeding values or total genetic values. For breeding programmes, GS is a promising alternative to the traditional marker-assisted selection for manipulating complex polygenic traits often controlled by many small-effect genes. Various factors, such as genetic architecture of selection traits, population size and structure, genetic evaluation systems, density of SNP markers and extent of linkage disequilibrium, have been shown to be the key drivers of the accuracy of GS. In this paper, we provide an overview of the status of these aspects in current apple-breeding programmes. Strategies for GS for fruit quality and disease resistance are discussed, and an update on an empirical genomic selection study in a New Zealand apple-breeding programme is provided, along with a foresight of expected accuracy from such selection.

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Acknowledgements

This work was partially funded by Prevar™ Limited under contract from the New Zealand Foundation for Research, Science and Technology. Luis Gea and Ron Beatson made many useful comments on an earlier version of this manuscript. D Chagné acknowledge support by USDA’s National Institute of Food and Agriculture—Speciality Crop Research Initiative RosBREED (2009-51181-05808) and European Framework Program 7 FruitBreedomics projects. The contribution of M. Bink was carried out as part of the EU COST Action TD0801 “StatSeq” and the FruitBreedomics project funded by the Commission of the European Communities (Contract FP7-KBBE-2010-265582). It does not necessarily reflect the Commission’s views and in no way anticipates its future policy in this area. Its content is the sole responsibility of the authors. We thank the anonymous reviewers and the Associate Editor for their suggestions on the manuscript.

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Kumar, S., Bink, M.C.A.M., Volz, R.K. et al. Towards genomic selection in apple (Malus × domestica Borkh.) breeding programmes: Prospects, challenges and strategies. Tree Genetics & Genomes 8, 1–14 (2012). https://doi.org/10.1007/s11295-011-0425-z

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