Genomic Variation in Vitis Vinifera, from Extant to Contemporary Varieties

Abstract

Ancient DNA (aDNA) of 3500-year-old charred grapevine (Vitis vinifera) seed material excavated from the archaeological site of Kaymak & ccedil;& imath;, G & ouml;lmarmara, T & uuml;rkiye, was subjected to whole genome shotgun sequencing using next-generation sequencing (NGS) technology. After grapevine DNA sequence data was filtered by quality scores and the grapevine DNA file was aligned with the two reference grapevine genomes (Pinot Noir-clone ENTAV115 and PN40024), 44 consensus mapped (CMap) ancient DNA sequences common to both reference genomes were obtained. Majority of these sequences (63.6%) were specific to the nuclear genome while 20.5% and 15.9% were specific to chloroplast and mitochondria genomes, respectively. Thus, 57.1%, 42.8%, and 100% of the CMap DNA sequences were related to previously identified genes in the grapevine nuclear, mitochondria, and chloroplast DNA genomes, respectively. Despite the vegetative propagation of grapevine, substantial base differences between ancient and modern varieties were found; that is, mean SNP (single nucleotide polymorphic) sites per the CMap DNA sequences varied between 1.71 in mitochondria and 2.89 in chloroplast sequences. In general, mean SNPs were low in the CMap DNA sequences annotated to known genes compared to those without any gene assignments. Further analysis of the association of the CMap DNA sequences of nuclear and organelle genomes with the SNP sites pointed out that base changes occurred in modern grapevine varieties compared to ancient grape variety involving genes controlling colour and aroma of grape fruits. To gain further insights about the role of domestication and clonal propagation in grape, future studies dealing with ancient grape DNA need to focus on certain gene regions using whole genome aDNA enrichment as the source of template DNA. The results of this study could provide invaluable reference information for identifying the genes or gene regions in such future studies. However, given the scarcity of ancient grape seeds, the degraded nature of ancient DNA, and measures to prevent contamination and bias, the limited CMap sequences likely represent only a small fraction of the ancient grapevine genome. Accordingly, the findings should be interpreted with these limitations in mind.