Unlocking Genetic Potential of the Peach Collection at the National Clonal Germplasm Repository in Davis, California

Genotyping by sequencing (GBS), a low-cost, high-throughput sequencing technology, has been used to analyze diversity in 510 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 were catalogued as Prunus persica (85%), with 8% of them considered wild relatives (P. mira, P. davidiana, P. kansuensis and P. ferganensis) and 7% categorized as hybrids between peach and other related species and Prunus spp (unknown). The method produced on average 1.2 million sequence reads per accession, with majority of the accessions having more than 500,000 reads. We identified 23,402 single-nucleotide polymorphism (SNP) markers, with allele frequency > 0.05, present in at least ≥ 90% of all analyzed accessions distributed across the entire genome. Population structure revealed 5 groups. Prunus persica population was structured in three groups and remaining two groups constituted of P. davidiana and P. mira individuals, respectively. Population structure uncovered origin of accessions catalogued as P. kansuensis (1) and P. ferganensis (2) to be P. davidiana and P. persica, respectively. In addition, accessions catalogued as Prunus spp. were assigned to the related group, mostly P. persica, or remained unstructured together with other interspecific hybrids. 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 for water use efficiency and data available through Germplasm Resources Information Network (GRIN), will be discussed.