Genome-wide Survey of Genetic Diversity in Apple Using Genotyping-by-Sequencing

With the advent of next-generation sequencing technologies it is now possible to generate large numbers of genetic markers without the need to rely on costly microarray platforms. Genotyping-by-Sequencing (GBS) enables the simultaneous identification and genotyping of single nucleotide polymorphisms (SNPs) in a highly multiplexed sample of multiple individuals. To investigate the domestication and breeding history of apples and to provide a foundation for marker-assisted breeding, we have used GBS to genotype ~2000 wild and cultivated apples from the USDA apple germplasm collection. From ~700 Gbp of sequence data generated from 42 lanes of the Illumina Hi-Seq platform, we have identified over 1,000,000 SNPs in the apple genome. Using these data, we demonstrate that patterns of population structure are in agreement with known relationships among apple species and cultivars. In addition, we present results of a preliminary genome scan for selection to identify the loci targeted during apple domestication and breeding.