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ARS Home » Northeast Area » Geneva, New York » Plant Genetic Resources Unit (PGRU) » Research » Publications at this Location » Publication #325688

Research Project: Management of Apple, Cold-Hardy Grape, and Tart Cherry Genetic Resources and Associated Information

Location: Plant Genetic Resources Unit (PGRU)

Title: Genome to phenome mapping in apple using historical data

item MIGICOVSKY, ZOE - Dalhousie University
item GARDNER, KYLE - Dalhousie University
item MONEY, DANIEL - Dalhousie University
item SAWLER, JASON - Dalhousie University
item BLOOM, JOSHUA - Howard Hughes Medical Institute
item MOFFETT, PETER - Universite De Sherbrooke
item Chao, Chihcheng
item Schwaninger, Heidi
item Fazio, Gennaro
item Zhong, Gan-Yuan
item MYLES, SEAN - Dalhousie University

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/15/2016
Publication Date: 3/31/2016
Citation: Migicovsky, Z., Gardner, K., Money, D., Sawler, J., Bloom, J., Moffett, P., Chao, C.T., Schwaninger, H.R., Fazio, G., Zhong, G., Myles, S. 2016. Genome to phenome mapping in apple using historical data. The Plant Genome. 9(2). doi: 10.3835/plantgenome2015.11.0113.

Interpretive Summary: Apple is one of the world’s most valuable fruit crops. Because apple has large tree size and long juvenile phase, the breeding process for development of new apple cultivars can take a long time. To improve breeding efficiency, scientists often identify and use molecular markers to help make selection at early stages without going through the lengthy evaluation processes. One prerequisite for such practice is to identify molecular markers which are tightly linked with traits of interest which we want to select for development of a new apple cultivar. This study contributed to the research in this area. Specifically, the study used the trait information of apple germplasm preserved in the USDA-ARS apple germplasm repository, Geneva, NY and associated the trait variants with molecular markers. Interesting association results were obtained for several important apple fruit quality traits such as fruit firmness and fruit size.

Technical Abstract: Apple (Malus domestica) is one of the world’s most valuable fruit crops. Its large size and long juvenile phase make it a particularly promising candidate for marker-assisted selection (MAS). However, advances in MAS in apple have been limited by a lack of phenotype and genotype data from sufficiently large samples. To establish genotype-phenotype relationships and advance MAS in apple, we extracted over 24,000 phenotype scores from the USDA-Germplasm Resources Information Network (GRIN) database and linked them with over 8,000 single nucleotide polymorphisms (SNPs) from 689 apple accessions from the USDA apple germplasm collection clonally preserved in Geneva, NY. We find significant genetic differentiation between Old World and New World cultivars and demonstrate that the genetic structure of the domesticated apple also reflects the time required for ripening. A genome-wide association study (GWAS) of 36 phenotypes confirms the association between fruit color and the MYB1 locus, and we also report a novel association between the transcription factor, NAC18.1, and harvest date and fruit firmness. We demonstrate that harvest time and fruit size can be predicted with relatively high accuracies (r > 0.46) using genomic prediction. Rapid decay of linkage disequilibrium (LD) in apples means whole-genome sequencing may be required for well-powered GWAS. However, rapid LD decay also promises to enable extremely high resolution mapping of causal variants, which holds great potential for advancing MAS and genome editing.