Development of a saturated linkage map for apple using a high-throughput GoldenGate™ SNP platform

Single Nucleotide Polymorphisms (SNPs) are becoming the markers of choice in pursuing linkage studies due to their abundance at high frequencies within genomes and availability of high-throughput and cost-effective genotyping platforms. Among the different genotyping platforms, the Illumina GoldenGate™ SNP genotyping assay has proven to be efficient for many plant species.  However, incidence of high levels of nucleotide polymorphisms, combined with complex genomes, could also negatively influence the utility of the GoldenGate™ assay.  In this study, SNPs from a publicly available apple EST database were identified using bioinformatics tools and an Oligo Pool Assay (OPA) for 1536 SNPs was custom-synthesized. These SNPs were used to construct a well-saturated linkage map for an apple mapping population consisting of 90 F1 individuals derived from Co-op 16 × Co-op 17 cross.   All 1536 SNPs were genotyped using the Illumina GoldenGate™ technology.  A total of 583 SNPs segregated in the mapping population, and were used to construct a combined genetic map for both parents using the Haldane’s mapping function.  The genetic map consisted of 17 linkage groups corresponding to 17 haploid sets of apple chromosomes.  On average, there were 34 ± 6 markers per linkage group with 25 minimum and 45 maximum markers per linkage group.  The average interval between markers was 2 ± 4 cM with a maximum interval of 23 cM on linkage group 16.  The total length of the map was 1288 cM with an average length of 76 ± 14 cM per linkage group.  This newly revised apple genetic linkage map, predominantly saturated with genic SNP-based markers, was constructed in a relatively short period of time. These genic SNPs will also serve as valuable resources to the apple research community for pursuing marker-trait associations, comparative genomics studies, and population genetic efforts.