Genetic diversity, variety identification and gene detection in some Egyptian grape varieties by SSR and SCoT markers

Abstract

Leaves of seven Egyptian grape varieties represent different range of agronomic and morphological traits were genotyped using Start-codon Targeted (SCoT) and Simple Sequence Repeats (SSR). The 24 SCoT primers generated 362 total fragments with 77.10% of polymorphism and 0.04 of average PIC. Dice coefficient that shows the genetic similarity and relationship was also used between the seven varieties. On one hand, SCoT analysis successfully characterized 73 unique positive and negative markers differentiating between the rootstock varieties especially those with green and red fruits. On the other hand, the seven SSR primers produced 73 fragments with 86.30% total polymorphism and 0.14 of average PIC. It also provided 19 unique positive and negative markers differentiating between the rootstock varieties. SO4 variety was identified by the highest number of positive unique markers (5). Both Scot and SSR analysis had covered 0.02% (0.10 Mbp) of V.vinifera genome. The SCoT covered 0.96 Mbp and SSR covered 846 bp. Together, the covered region encompassed about 22 genes of grape genome. Further, eight SCoT polymorphic bands were purified, cloned and sequenced. Of which, four SCoT sequences (SCoT3600, SCoT4450, SCoT6200 and SCoT12550) showed high similarity to some potential genes.