Final Report Summary - TIME CAPSULE (Biomolecular investigation on archaeological grape seeds: a genetic time capsule from the past)
Project context
The TIME CAPSULE project was initially intended to investigate functional aspects related to environmental adaptation and genetic variability of grapes cultivated in antiquity, through biomolecular analysis of ancient nucleic acid residues preserved in grape seeds and other archaeo-botanical findings recovered in archaeological excavations. The same approach was also planned to be used to characterise one phenotypic trait, the colour of grape berries, which determines the colour of the wine produced from those berries. Altogether, this approach would have allowed for a comparison of genetic information from ancient samples with data previously acquired from modern samples. However, as soon as the researcher joined the host institution he realised that the methodology the project was based on, i.e. PCR-based investigation of single loci, would soon become outdated for strategic research into ancient DNA. For this reason, the scientist in charge and the researcher decided to double their efforts in developing the researcher's skills in high-throughput DNA sequencing, learning wet-laboratory techniques first and then bioinformatic methodologies to process the generated data.
A previously unplanned phase of methodological design and optimisation was introduced to enable a comparison of large-scale solution-based DNA capture-enrichment methods on ancient plant DNA (Avila Arcos et al., 2011) and to define an assay to prescreen ancient plant remains destined for shotgun sequencing (Wales et al., 2012). A state-of-the-art procedure for target enrichment was set up, optimised and applied to several samples (approximately 20) from several archaeological excavations in the Mediterranean and Caucasus areas, dating from 3rd millennium BC to the late medieval period. All the experience accumulated in this phase was developed and presented in a book chapter about the possibilities and limitations associated with the investigation of ancient biomolecules from archaeo-botanical remains (Wales, Andersen, Cappellini, in press). Once this new expertise was acquired, the researcher collaborated in other plant aDNA research projects active at the host institution; in particular he was involved a sister project on ancient maize and another project on aDNA infestation from potato blight.
Project outcomes
At the time the project concluded, bioinformatics analysis of all acquired data was in progress. This will soon allow for the characterisation of the genetic variability of the ancient grape seeds investigated and a comparison with the variability among modern cultivars. This could potentially have important implications for the reconstruction of grape domestication processes and possibly help to identify ancestors of modern grape varieties and the derived wines. This desirable perspective would represent a strong selling point in favour of the European winemaking agro-industrial sector in global wine trading competition.
The other main project objectives, namely the investigation of functional aspects through trascriptomics investigation and the assay to determine berry colour (red/white) will be addressed in future research at the host institution, where the researcher is continuing to work as a postdoc research assistant within a broader research area focused on biomolecular investigation on archaeo-botanical remains. Although from a preliminary observation it may appear that the objectives originally defined in the project were only partially achieved and in a timeframe that does not respect the milestones initially defined, the scientist in charge and the researcher believe the strategy they chose to adopt will pay back in the mid to long term.
The TIME CAPSULE project was initially intended to investigate functional aspects related to environmental adaptation and genetic variability of grapes cultivated in antiquity, through biomolecular analysis of ancient nucleic acid residues preserved in grape seeds and other archaeo-botanical findings recovered in archaeological excavations. The same approach was also planned to be used to characterise one phenotypic trait, the colour of grape berries, which determines the colour of the wine produced from those berries. Altogether, this approach would have allowed for a comparison of genetic information from ancient samples with data previously acquired from modern samples. However, as soon as the researcher joined the host institution he realised that the methodology the project was based on, i.e. PCR-based investigation of single loci, would soon become outdated for strategic research into ancient DNA. For this reason, the scientist in charge and the researcher decided to double their efforts in developing the researcher's skills in high-throughput DNA sequencing, learning wet-laboratory techniques first and then bioinformatic methodologies to process the generated data.
A previously unplanned phase of methodological design and optimisation was introduced to enable a comparison of large-scale solution-based DNA capture-enrichment methods on ancient plant DNA (Avila Arcos et al., 2011) and to define an assay to prescreen ancient plant remains destined for shotgun sequencing (Wales et al., 2012). A state-of-the-art procedure for target enrichment was set up, optimised and applied to several samples (approximately 20) from several archaeological excavations in the Mediterranean and Caucasus areas, dating from 3rd millennium BC to the late medieval period. All the experience accumulated in this phase was developed and presented in a book chapter about the possibilities and limitations associated with the investigation of ancient biomolecules from archaeo-botanical remains (Wales, Andersen, Cappellini, in press). Once this new expertise was acquired, the researcher collaborated in other plant aDNA research projects active at the host institution; in particular he was involved a sister project on ancient maize and another project on aDNA infestation from potato blight.
Project outcomes
At the time the project concluded, bioinformatics analysis of all acquired data was in progress. This will soon allow for the characterisation of the genetic variability of the ancient grape seeds investigated and a comparison with the variability among modern cultivars. This could potentially have important implications for the reconstruction of grape domestication processes and possibly help to identify ancestors of modern grape varieties and the derived wines. This desirable perspective would represent a strong selling point in favour of the European winemaking agro-industrial sector in global wine trading competition.
The other main project objectives, namely the investigation of functional aspects through trascriptomics investigation and the assay to determine berry colour (red/white) will be addressed in future research at the host institution, where the researcher is continuing to work as a postdoc research assistant within a broader research area focused on biomolecular investigation on archaeo-botanical remains. Although from a preliminary observation it may appear that the objectives originally defined in the project were only partially achieved and in a timeframe that does not respect the milestones initially defined, the scientist in charge and the researcher believe the strategy they chose to adopt will pay back in the mid to long term.