Genome-wide SNP Variation in Cultivated Tomato (Solanum lycopersicum L.)

Cultivated tomato (Solanum lycopersicum L.) is a major vegetable crop with high economic value and is an important source of provitamin A and vitamin C to human diet. Recently, a high-throughput genotyping array was developed using genome-wide single nucleotide polymorphisms (SNPs) in tomato. In this study, we genotyped a collection of 48 Korean elite tomato varieties (26 fresh market and 22 cherry) using 7,720 SNPs of this array. Among 6,652 polymorphic SNPs (86.1%) in the entire collection, there were 6,589 SNPs with < 10% missing data. The 4,733 (61.3%) and 6,087 (78.8%) SNPs were polymorphic in the fresh market and cherry varieties, respectively. In order to investigate genetic variation, the SNP genotypes of the Korean tomato germplasm were analyzed along with the previously reported data on SNPs of the 277 Solanaceae Agricultural Coordinated Project (SolCAP) varieties (109 fresh market, 27 cherry, and 141 processing). Principal component analysis, pairwise F_st, and Nei’s standard genetic distance revealed genetic differentiation between these five sub-populations. A further division was found within the Korean cherry varieties using the unweighted pair group mean algorithm (UPGMA). The fresh market and cherry sub-populations in the Korean tomato germplasm showed similar levels of genetic diversity as the corresponding SolCAP sub-populations. We detected genomic regions that may be responsible for genetic differentiation between two sub-populations in the Korean germplasm by visualizing the polymorphic information content values of SNPs. These results suggest that breeding practices for market niches and environmental adaptation could lead to allelic variation in cultivated tomatoes in Korea.