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Title: Apple whole genome sequences: recent advances and new prospects

item PEACE, CAMERON - Washington State University
item BIANCO, LUCA - Fondazione Edmund Mach
item TROGGIO, MICHELA - Fondazione Edmund Mach
item VAN DE WEG, ERIC - Wageningen University And Research Center
item HOWARD, NICHOLAS - University Of Minnesota
item CORNILLE, AMANDINE - University Of Paris
item DUREL, CHARLES-ERIC - Institut National De La Recherche Agronomique (INRA)
item MYLES, SEAN - Dalhousie University
item MIGICOVSKV, ZOE - Dalhousie University
item SCHAFFER, ROBERT - New Zealand Institute Of Plant & Food Research
item COSTES, EVELYNE - University Of Montpellier
item Fazio, Gennaro
item YAMANE, HISAYO - Kyoto University
item VAN NOCKER, STEVE - Michigan State University
item GOTTSCHALK, CHRIS - New Zealand Institute Of Plant & Food Research
item COSTA, FABRIZIO - Fondazione Edmund Mach
item CHAGNE, DAVID - New Zealand Institute Of Plant & Food Research
item ZHANG, XINZHONG - China Agriculture University
item PATOCCHI, ANDREA - Agroscope
item GARDINER, SUSAN - New Zealand Institute Of Plant & Food Research
item HARDNER, CRAIG - University Of Queensland
item KUMAR, SATISH - Plant And Food Research
item LAURENS, FRANCOIS - Institut National De La Recherche Agronomique (INRA)
item BUCHER, ETIENNE - Institut National De La Recherche Agronomique (INRA)
item MAIN, DORRIE - Washington State University
item JUNG, SOOK - Washington State University
item VANDERZANDE, STIJN - Washington State University

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/15/2019
Publication Date: 3/30/2019
Citation: Peace, C.P., Bianco, L., Troggio, M., Van De Weg, E., Howard, N.P., Cornille, A., Durel, C., Myles, S., Migicovskv, Z., Schaffer, R., Costes, E., Fazio, G., Yamane, H., Van Nocker, S., Gottschalk, C., Costa, F., Chagne, D., Zhang, X., Patocchi, A., Gardiner, S.E., Hardner, C., Kumar, S., Laurens, F., Bucher, E., Main, D., Jung, S., Vanderzande, S. 2019. Apple whole genome sequences: recent advances and new prospects. Horticulture Research. 6:59.

Interpretive Summary: Assembled DNA sequences of entire chromosomes contained in cells of living organisms also referred to as Whole Genome Sequences (WGS) have had tremendous impact on understanding the complex landscape of biological interactions. Often compared to roadmaps, WGS have allowed major technological and scientific advances in human biology that are nowadays being translated into gene therapy, cancer recognition/cures, genetic risk assessment, etc. Whole genome sequence research and development on the cultivated apple, is approaching similar impacts in addressing problems like diseases which require pesticides, improving fruit quality on store shelves and in-home fruit baskets, growing apple trees in stresses caused by climate change and improving the nutrition value of apples. Many of the solutions to these problems have received an enabling benefit from the development of apple WGS and associated techniques which connect genes and traits to them. This is an important read for those who want to know about the state of the art of apple genome research, technological advancements and future research directions.

Technical 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.