Nuclear SSR-based Genetic diversity and STRUCTURE analysis of Greek Tomato ecotypes and the Greek Tomato Database (GTD) 

Tomato is cultivated in Greece for more than 200 years, even though is not native. Along with a favorable environment for the crop all the year round, Greece has become a major competitor in tomato production around Europe. However, there is an increasing demand to improve tomato crop. People have devoted a significant effort for crop improvement via phenotypic screening resulting in a large number of tomato ecotypes. An increasing demand to clarify the relationships among local tomato genotypes utilizing the most preferred molecular markers the Simple Sequence Repeats (SSR-markers) is the main objective of this study. Twenty-nine tomato ecotypes cultivated in Crete, Greece were genotyped utilizing eleven simple sequence repeat (SSR) along with the Structure analysis of the germplasm. A neighbor-joining dendrogram of the 29 ecotypes was produced. The statistical analysis proved that 58% of the genetic variation (p < 0.0001) resided among populations and 42% (p < 0.0001) resided within populations. The Structure analysis indicated that nine ancestral populations are hidden inside the group of ecotypes tested, using Evanno’s method. The final objective was make these data publicly available through the first Greek relational database (GreekTomatoDatabase-GTD). GTD was developed making publicly available all the methodology around the analysis performed, the first molecular fingerprint of 29 tomato ecotypes grown in Crete, Greece, as well as phenotypic and viral information.