Genetic variations of F1 tomato cultivars revealed by a core set of SSR and InDel markers

- The core set of SSRs and InDels detected genetic variations in the 62F1 tomato cultivars.
- Fresh market, grape, and cherry cultivars represented distinct sub-populations.
- High levels of genetic diversity were observed in the three sub-populations.

Tomato (Solanum lycopersicum L.) is a major vegetable cultivated worldwide and has been used as a model plant for basic research. Since tomato genome sequences were uncovered in 2012, genome-wide molecular markers have been developed. However, these markers have not been often used to explore genetic variations in commercial tomato cultivars. In this study, we collected 62 F1 tomato cultivars from 16 private seed companies to investigate genetic relationships using SSR and InDel markers. A total of 242 SSR and 76 InDel primer sets were tested for polymorphism using a subset of eight cultivars representing diverse morphological characteristics. Based on the clear polymorphism and simple banding pattern, 6 SSR and 35 InDel markers were selected for further analysis. The polymorphic information content (PIC) values of the 41 markers ranged from 0.243 to 0.375 with an average of 0.350. Principal component analysis revealed that the 62 cultivars were separated into three clusters representing fresh market, grape, and cherry tomatoes. We found two major clusters consisting of fresh market (cluster I) and both grape and cherry (cluster II) in the unweighted pair group mean algorithm (UPGMA) dendrogram. In cluster II, the grape and cherry cultivars were divided into two sub-clusters. This genetic differentiation was validated by pairwise estimates of Fst and Nei's standard genetic distance. In addition, the estimates of allelic richness (A) and expected heterozygosity (He) suggest high levels of genetic diversity in each of the three sub-populations. These results will benefit the tomato research community in developing new elite cultivars. The core set of SSR and InDel markers will also be a useful tool for cultivar identification and seed purity test.