Genetic Diversity Analysis in a Collection of Tomato Germplasm Using Indel Markers

Cultivated tomato (Solanum lycopersium L) is an economically important vegetable crop all around the world. The two reference genome sequences of tomato, which were published in 2012, have leveraged marker development. Recently, a large number of Indels were identified through in silico analysis using the reference genome sequences. In this study, we investigated genetic diversity in a collection of 187 tomato accessions using the Indel markers. The tomato collection consisted of 174 cultivated varieties and 13 wild species (4 S. habrochaites, 1 S. arcanum, 4 S. chilense, 1 S. pimpinellifolium, and 3 S. peruvianum). The 174 cultivated varieties were derived from 11 countries representing Russia (55 varieties), China (51 varieties), South Korea (33 varieties), Uzbekistan (20 varieties), and others (15 varieties). This germplasm collection was genotyped using the 31 Indel markers that were selected based on polymorphism and clear banding pattern. Principal component analysis (PCA) revealed that a high level of genetic variation was present in the cultivated tomato varieties. We also found two major clusters and that the tomato varieties from China, South Korea, Russia, and Uzbekistan were divided into these clusters. In addition, there was a minor cluster consisting of mainly the Chinese varieties. The wild species were distinct from all of these clusters. This genetic clustering was shown in the UPGMA dendrogram. These results suggest that our collection of cultivated tomatoes is a useful resource to develop a core collection for genetics and breeding in tomato.

^*Corresponding author E-mail: sungchur@sejong.ac.kr