Apple whole genome sequences: recent advances and new prospects

Cameron P. Peace*, Luca Bianco, Michela Troggio, Eric van de Weg, Nicholas P. Howard, Amandine Cornille, Charles Eric Durel, Sean Myles, Zoë Migicovsky, Robert J. Schaffer, Evelyne Costes, Gennaro Fazio, Hisayo Yamane, Steve van Nocker, Chris Gottschalk, Fabrizio Costa, David Chagné, Xinzhong Zhang, Andrea Patocchi, Susan E. GardinerCraig Hardner, Satish Kumar, Francois Laurens, Etienne Bucher, Dorrie Main, Sook Jung, Stijn Vanderzande

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

14 Citations (Scopus)


In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for “what’s next” focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.

Original languageEnglish
Article number59
JournalHorticulture Research
Issue number1
Publication statusPublished - 5 Apr 2019

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