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Lidia Lozano, Ignasi Iglesias, Diego Micheletti, Michela Troggio, Satish Kumar, Richard K. Volz, Andrew C. Allan, David Chagné and Susan E. Gardiner

Single-nucleotide polymorphisms (SNPs) have been used for a range of genetic studies and are now starting to be applied for marker-assisted selection in plant breeding programs. To identify SNP markers associated with red fruit skin color, we conducted a genome-wide association (GWA) analysis in an apple (Malus ×domestica Borkh.) breeding population comprising 94 phenotyped individuals using a 384-plex SNP assay. Linkage disequilibrium (LD) analysis indicated that LD extends over a long physical distance in the population (17 Mbp), indicating that a small number of generations separates the individuals. No significant association of anthocyanin content, overcolor, and colorimetric measures (a*, b*, L*, a/b*, and hue angle) with a marker was identified, although the apple fruit skin color locus has been previously located on apple linkage group 9. Our trial of a small SNP panel for GWA in apple breeding material has demonstrated the limitation of this approach for marker trait association.