Study of ancient north-east Italian grape varieties taking advantage of an optimized aDNA extraction protocol

Grapevine (Vitis vinifera L.) is one of the most extensively cultivated fruit trees in the world. It is cultivated primarily for wine production but also for fruit fresh consumption. Its domestication started in the Near East approximately 11,000 years ago and since then many different varieties evolved through multiple historical pathways. Population genetic studies have been used to infer relatedness and migrations routes, highlighting a key role of Italy in grapevine spreading from Greece to Central and Western Europe.

In this project we have applied a complimentary paleo-genomic approach relying on 146 ancient grape pips from 13 different archaeological sites from North-east in Italy, dated from Bronze age up to middle-age. First of all, we explored the possibility to improve the aDNAextraction step to recover good quality and processable extracts from grapevine pips. We developed the SPE-method exploiting reagents against soil inhibitors coupled with an aDNAsilica binding step. Our optimized method demonstrated a higher yield and more consistent performance across sites compared to previous extraction methods, significantly improving the library production step, particularly in challenging sites. So far, the protocol allowed to get 52 good quality libraries from 10 of the 13 sites. We also conducted target-enriched genome-wide sequencing for 10K SNPs on at least one samples from each archeological site and explored the genetic relationships of the ancient samples with modern grapevine varieties. Tailored analytical approaches were applied according to sequencing coverage gained at each site. The developed pipeline allowed to identify one archaeological sample from XIII century as an identical clone variety to our days. Additional close genetic relationships to varieties still present locally were also highlighted, pointing out migration and local adaptation trajectories of grapevine’s cultivars connected to the territory.