Assessing the genetic variation in cultivated tomatoes (Solanum lycopersicum L.) using genome-wide single nucleotide polymorphisms

Abstract

Tomato (Solanum lycopersicum L.) is an economically important vegetable crop worldwide. Recently, a high-density single nucleotide polymorphism (SNP) array was developed based on genome-wide SNPs in tomato. In this study, we genotyped a collection of 48 Korean elite tomato varieties (26 fresh market and 22 cultivated cherry) using 7,720 SNPs of this array. Out of 6,652 polymorphic SNPs (86.1%) in the entire collection, there were 6,589 SNPs with < 10% missing data. The number of polymorphic SNPs in the fresh market and cultivated cherry subpopulations were 4,733 (61.3%) and 6,087 (78.8%), respectively. To examine the genetic variation between sub-populations, 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 cultivated cherry, and 141 processing). Principal component analysis, pairwise F (st), and Nei's standard genetic distance revealed genetic differentiation between these five sub-populations. Moreover, we validated another division within the Korean cherry varieties using the unweighted pair group mean algorithm (UPGMA). The genetic diversity of each sub-population was estimated based on allelic richness and expected heterozygosity. The fresh market and cultivated cherry sub-populations in the Korean tomato germplasm showed similar levels of genetic diversity as the corresponding SolCAP sub-populations. Visualization of the polymorphic information revealed genomic regions that differed between the two sub-populations in the Korean tomato germplasm. These results suggest that diversifying selection for market niches and environmental adaptation has led to allelic variation in cultivated tomatoes in Korea.