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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.

journal of the american society for horticultural science

Feasibility of Genome-wide Association Analysis Using a Small Single Nucleotide Polymorphism Panel in an Apple Breeding Population Segregating for Fruit Skin Color