RosBREED Deploys Genome-Wide Scans In Peach, Apple, and Cherry

SNP-based genome scans are in development for peach, apple and cherry as public genomics resources for the international Rosaceae research community. The USDA-funded multi-institutional and trans-disciplinary project “RosBREED” is creating crop-specific SNP genome scan platforms at a targeted resolution of at least one polymorphic SNP marker every 5 cM in any random cross. Within RosBREED, these genome scans will be used with Pedigree-Based Analysis to identify and validate many marker-locus-trait associations for application in breeding. SNP detection, validation, and final content decisions were completed in 2010. For SNP detection, 27 founders of apple, cherry, and peach re-sequenced mostly with Illumina GA-IIx were chosen based on representation of worldwide breeding germplasm. Re-sequencing of apple genomic DNA was coordinated among the U.S., the Agricultural Research Council of South Africa, and New Zealand’s Plant & Food Research. In peach, genomic DNA was re-sequenced from 58 accessions coordinated between the U.S., Europe’s FruitBreedomics project, and the International Peach Genome Initiative. Sequences were also generated from 16 sweet and eight tart cherry accessions. A SOAP/SOAPSNP-based pipeline was developed to identify SNPs after alignment to the ‘Golden Delicious’ genome sequence for apple and the double haploid ‘Lovell’ peach genome sequence for peach and cherry. The GoldenGate assay was used to validate subsets of these SNPs and to investigate haplotypic diversity at the planned resolution of the final SNP arrays (one SNP per 70 Kb). These “fine-mapped regions” of the genome targeted particular loci responsible for important breeding traits. In apple, 20 of the 144 apple SNPs were located within a 1.4 Mb region at the Malic acid (Ma) locus on Malus linkage group (LG) 16.  For cherry, a 0.86 Mb region spanning a fruit size locus on Prunus LG 2 was targeted with 24 SNPs, while for peach, 0.77 Mb around the Freestone-Melting flesh (F-M) locus was spanned with 14 SNPs. Considerable haplotypic diversity was detected in these regions. SNP filtering parameters were revised based on SNP conversion in the GoldenGate assay and resulted in ordering a 9K Infinium array for apple, a 9K Infinium array for peach, and a 6K Infinium array for cherry. Genome-wide scans using this high-throughput Infinium SNP technology are underway for 472 individuals representing important breeding parents for each of these crops. These genomics resources will enable new marker-locus-trait association discovery as well as validation of associations in breeding germplasm for major Rosaceae crops and across this economically important plant family.