Genetic Diversity of Grape Based on Chloroplast DNA Sequence Analysis

In our previous work we investigated DNA sequence diversity at two non-coding plastid DNA regions in a geographically diverse group of 113 Vitis vinifera cultivars. Four plastid haplotypes were evident in these samples and they were designated by their character-states at each of the 3 polymorphic positions (ATA, ATT, GTA and AAA haplotypes) (Beridze et al., 2011). In the present investigation the eight Georgian ('Rkatsiteli', 'Saperavi', 'Ckhaveri', 'Meskhuri Mtsvane', 'Aladasturi', 'Krakhuna', 'Tsitska', 'Tsolikouri') and three French ('Chardonnay', 'Gouais Blanc', 'Chasselas') grape cultivars from different haplogroups of Vitis vinifera along with the two American species Vitis rupestris and Vitis champinii were performed. The comparison of sequenced chloroplast DNA of Vitis vinifera cultivars revealed high level of identity among the members of same haplogroup. 100% identity were detected between 'Chardonnay' and 'Gouais Blanc', differing from 'Meskhuri Mtsvane' by 2 indels (all ATA haplogroup). The difference between 'Chasselas' and 'Saperavi' was a single insertion (ATT haplogroup), while 'Maxxa', 'Chkhaveri', 'Aladasturi', 'Krakhuna', 'Tsitska' and 'Tsolikouri' were all identical to each other (GTA haplogroup). Short and long indels were detected in the chloroplast DNA of all grape cultivars. 47 identical SNPs were detected in AAA, ATA, ATT haplotypes and 119 identical SNPs in Vitis rupestris and Vitis champinii in comparison to the GTA haplotype. Additionally 18 SNPs were detected in 'Saperavi'; 4 for 'Rkatsiteli', 6 for 'Meskhuri Mtsvane' and 11 SNPs for both 'Rkatsiteli' and 'Meskhuri Mtsvane'. A 54-bp deletion in the trnC-GCA - petN intergenic spacer and 33-bp duplication in rps16 - trnQ-UUG intergenic region was observed in AAA, ATT and ATA haplotypes suggesting, that compared to GTA haplotype, these haplotypes are more closely related to each other. The phylogenetic scheme based on indel priority of grape chloroplast DNA are presented.