A multidisciplinary study of archaeological grape seeds

Abstract

We report here the first integrated investigation of both ancient DNA and proteins in archaeobotanical samples: medieval grape (Vitis vinifera L.) seeds, preserved by anoxic waterlogging, from an early medieval (seventh–eighth century A.D.) Byzantine rural settlement in the Salento area (Lecce, Italy) and a late (fourteenth–fifteenth century A.D.) medieval site in York (England). Pyrolysis gas chromatography mass spectrometry documented good carbohydrate preservation, whilst amino acid analysis revealed approximately 90% loss of the original protein content. In the York sample, mass spectrometry-based sequencing identified several degraded ancient peptides. Nuclear microsatellite locus (VVS2, VVMD5, VVMD7, ZAG62 and ZAG79) analysis permitted a tentative comparison of the genetic profiles of both the ancient samples with the modern varieties. The ability to recover microsatellite DNA has potential to improve biomolecular analysis on ancient grape seeds from archaeological contexts. Although the investigation of five microsatellite loci cannot assign the ancient samples to any geographic region or modern cultivar, the results allow speculation that the material from York was not grown locally, whilst the remains from Supersano could represent a trace of contacts with the eastern Mediterranean.Electronic supplementary materialThe online version of this article (doi:10.1007/s00114-009-0629-3) contains supplementary material, which is available to authorized users.

Multidisciplinary investigation of identity of the “Areni” grape variety

“…The successful amplification of 5 SSR markers from an ancient DNA extracted early and late medieval grape seeds was reported by Cappellini et al (2010). In our investigation we used steam to extract DNA instead of the seeds, because though V. vinifera is a hermaphrodite the crosses cannot be excluded, and consequently, analyses of ancient wood remains would also be useful to characterize old cultivars and compare their DNA profiles with those from modern ones [17,18]. The expected and observed heterozygosity values were relatively high, with average at 0.632 and 0.690 accordingly.…”

“…In general from 6 to 22 microsatellites are required to fully resolve the cultivar for modern grape samples [14][15][16]. The successful amplification of 5 SSR markers from an ancient DNA extracted early and late medieval grape seeds was reported by Cappellini et al (2010). In our investigation we used steam to extract DNA instead of the seeds, because though V. vinifera is a hermaphrodite the crosses cannot be excluded, and consequently, analyses of ancient wood remains would also be useful to characterize old cultivars and compare their DNA profiles with those from modern ones [17,18].…”

The limits and potential of paleogenomic techniques for reconstructing grapevine domestication

“…Sediment and other contaminants were removed from branches by removing the external bark with a sterile scalpel. All samples were extracted using a method which had previously been used on archaeological grape pips (Cappellini et al, 2010), and has been validated across a wide range of non-carbonized archaeobotanical remains (Wales et al, 2014). In addition to the standard extraction technique, portions of the two oldest vines were extracted using an enzymatic technique in an attempt to more thoroughly disrupt cell walls and release DNA (Manen et al, 2005).…”

“…To date, few published studies have utilized grape aDNA, either for methodological studies (Wales et al, 2014, Wales et al, 2012, or in conventional PCR-based approaches (Cappellini et al, 2010;Foley et al, 2012;Hansson and Foley, 2008;Manen et al, 2003). Here, we circumvent the limitations of PCR-based studies (discussed by Knapp and Hofreiter, 2010;Rizzi et al, 2012) and attempt to characterize plastomes from 27 archaeological grape samples using a target-enrichment methodology and high-throughput DNA sequencing.…”

Validation of a Non-Targeted LC-MS Approach for Identifying Ancient Proteins: Method Development on Bone to Improve Artifact Residue Analysis

“…Mass spectrometry approaches that provide a general scan of archaeological protein residues from cooking pottery, on the other hand, may not pinpoint original residues because exogenous proteins can overwhelm their signal (but see Cappellini et al 2010;Heaton et al 2009;Nielsen-Marsh 2005;Solazzo et al 2008). Put simply, when using mass spectrometry, a morass of exogenous protein from soil bacteria can overwhelm the signals of more archaeologically meaningful residues leaving them undetected.…”