Ancient DNA (aDNA) extraction and amplification from 3500-year-old charred economic crop seeds from Kaymakçı in Western Turkey: comparative sequence analysis using the 26S rDNA gene

Ancient DNA (aDNA) from 3500–4000 years old seeds of Triticum aestivum L. or Triticum durum Dest., Vicia ervillia (L) Willd., Cicer arietinum L. and Vitis vinifera L. excavated from the archaeological site of Kaymakçı was successfully extracted using various isolation methods. The genomic DNA of each species was amplified with respect to the 26S ribosomal DNA (rDNA) gene further using the aDNA of the seeds. The reasons for successful DNA extraction and amplification are likely due to (1) preservation of certain ancient seed specimens in good conditions and (2) use of improved DNA extraction and amplification methods. The results indicate that all seeds were identified correctly by the DNA sequence data from the 26S rDNA gene. Specifically, a morphologically unidentified wheat seed from Kaymakçı was characterized by DNA sequence data as bread wheat (Triticum aestivum). Comparative sequence analysis revealed that specific base positions in the ancient 26S rDNA gene were either lost or substituted with different DNA bases in contemporary seeds, most likely due to continued domestication and breeding activities. Attaining high amounts and a good quality of amplified genomic DNA from ancient seeds will further allow the investigation of the extent of genetic change between ancient seeds and their contemporary species in genetic diversity studies.