Peach Rootstock Identification by DNA-Fingerprinting with Microsatellite (SSR) Markers

Abstract

Peach ( Prunus persica[L.] Batsch) rootstocks are usually propagated from seed. Seedlings are difficult to distinguish morphologically, and once grafted, no above ground material is available for visual identification. To avoid misidentification and to protect plant varieties and patents, DNA fingerprinting was investigated as a robust rootstock identification tool. The objective of this study was to distinguish progeny from among seven peach seedling rootstocks: Bailey, Halford, Lovell, Nemaguard, Nemared, Guardian ^®(selection 3-17-7) and S-37. We initially screened 102 Prunusmicrosatellite (SSR) markers on Lovell, Nemaguard, Nemared and selection 3-17-7. Seventy-five markers showed polymorphism among these rootstocks. The polymorphic markers were then used to screen Bailey, Halford and S-37. Based on the patterns of amplified DNA fragments (two seedlings from each rootstock were tested), eight SSR-markers reproducibly divided the seven rootstocks into as many as five groups. It was necessary to use a multiplex approach to uniquely identify each rootstock because no single SSR locus evaluated thus far was able to differentiate all seven genotypes. To confirm the identity of the SSR markers, we cloned the polymorphic DNA fragments amplified by one of the eight polymorphic SSR primers, which was developed for an AC-enriched sequence isolated from almond. DNA sequence analysis showed that the amplified fragments shared a common AC-enriched repeat with copy number ranging from 5 to 14. Taken together, these results demonstrate that this microsatellite-based DNA fingerprint system has great potential for peach rootstock identification.