Comprehensive Genotyping of the Peach Collection at the National Clonal Germplasm Repository in Davis

We used genotyping by sequencing (GBS), a low-cost, high-throughput sequencing technology to genotype 333 Prunus accessions, preserved at the Prunus collection of the National Clonal Germplasm Repository (NCGR) in Davis, California. The Prunus collection is the second largest in this genebank with more than 90 taxa and in excess of 1600 accessions of Prunus spp that includes almonds, apricots, cherries, peaches and plums. The accessions genotyped here consist of heirlooms (old cultivars never patented, or off patent), landraces, breeder’s lines, and wild relatives of the peach from all over the world. Majority of accessions belonged to Prunus persica (84%), with 10% of them being wild relatives (P. mira, P. davidiana, and P. ferganensis) and 6% categorized as hybrids between peach and other related species and Prunus spp. The method produced on average 1 million sequence reads per accession, with majority of the accessions having more than 500,000 reads. We identified 18,008 single-nucleotide polymorphism (SNP) markers, present in at least ≥ 80% of analyzed accessions distributed across the entire genome. These genomic data will serve as a resource for breeders seeking to develop peach cultivars that will meet the challenge of changing climates, markets, and horticultural practices. The use of these SNP markers for conservation, management and utilization of the NCGR collection as well as for genome-wide association studies (GWAS) in combination with phenotypic data available through Germplasm Resources Information Network (GRIN) will be discussed.