Apple whole genome sequences: recent advances and new prospects
Luca Bianco1 , Michela Troggio2 , Eric van de Weg3 , Nicholas P. Howard4,5 , Amandine Cornille6 , Charles-Eric Durel7 , Sean Myles8 , Zoë Migicovsky8 , Robert J. Schaffer9,10 , Evelyne Costes11 , Gennaro Fazio12 , Hisayo Yamane13 , Steve van Nocker14 , Chris Gottschalk14 , Fabrizio Costa2 , David Chagné15 , Xinzhong Zhang16 , Andrea Patocchi17 , Susan E. Gardiner15 , Craig Hardner18 , Satish Kumar19 , François Laurens7 , Etienne Bucher7,20 and Dorrie Main21 , Sook Jung21 , Stijn Vanderzande21 , Cameron P. Peace,21,
1Computational Biology, Fondazione Edmund Mach, San Michele all’Adige, TN 38010, Italy 2Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, San Michele all’Adige, TN 38010, Italy 3Plant Breeding, Wageningen University and Research, Wageningen 6708PB, The Netherlands 4Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA 5Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Universität, 26129 Oldenburg, Germany 6GQE – Le Moulon, Institut National de la Recherche Agronomique, University of Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France 7Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France 8Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada 9The New Zealand Institute for Plant and Food Research Ltd, Motueka 7198, New Zealand 10School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand 11AGAP, INRA, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France 12Plant Genetic Resources Unit, USDA ARS, Geneva, NY 14456, USA 13Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan 14Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA 15The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North 4474, New Zealand 16College of Horticulture, China Agricultural University, 100193 Beijing, China 17Agroscope, 8820 Wädenswil, Switzerland 18Queensland Alliance of Agriculture and Food Innovation, University of Queensland, St Lucia 4072, Australia 19New Cultivar Innovation, Plant and Food Research, Havelock North 4130, New Zealand 20Agroscope, 1260 Changins, Switzerland 21Department of Horticulture, Washington State University, Pullman, WA 99164, USA *Corresponding author. E-mail: cpeace@wsu.edu
Received: 19 Feb 2019 Revised: 15 Mar 2019 Accepted: 15 Mar 2019 Published online: 05 Apr 2019
Abstract
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.
