Evaluating DNA Extraction and Analysis of Ancient Seeds: A Study in Peach

Abstract

The peach (Prunus persica) is one of the most widely grown stone fruit in the world but its origin and domestication is still being debated. Genetic research has focused on identifying desirable genes for agricultural purposes, suitable genetic targets for species identification, the development of a genetic linkage map for the peach, and ultimately the publication of the whole genome by the International Peach Genome Initiative. However, there has been no genetic research applied to ancient peach stones. In the present study DNA was extracted from modern peach samples collected from the Zhejiang Province in China to assess the most effective methods to extract DNA from seeds. These methods were then applied to an archaeological peach stone collected from the Maoshan archaeological site in China dated to the Liangzhu Culture Period. A search for previously sequenced genetic targets from P. persica and its wild species P. ferganensis, P. mira, P. kansuensis, and P. davidiana was performed to search for suitable genes for genetic and phylogenetic analysis. Phylogenetic analysis was used to evaluate the genetic targets for species identification. A Type II chlorophyll a/b-binding protein gene (Lhcb2) was identified as an ideal marker for species identification for ancient peach specimens due to its small amplicon size and ability to amplify DNA from low quantities. Chloroplast DNA and microsatellite markers were assessed for their ability to distinguish between peach and its various wild species. Several chloroplast genes successfully amplified DNA in the modern peach samples (rbcL, psbM-trnD, clpP), but were not successful when applied to ancient samples. GC-MS analysis was performed on the ancient peach stones to determine whether miscoding lesions were present in the DNA sequence which may have led to amplification failure. Damage due to oxidation and hydrolysis are consistent with the location in which the stone was collected and suggest the possibility of exposure to water and burning. Both sources of damage may explain the lack of amplification of these archeological samples.