2019 ASHS Annual Conference

Single nucleotide polymorphisms (SNPs) have been commonly used as molecular markers in crop species due to high-throughput genotyping methods. The present study was conducted to identify a core set of SNP markers for identification of commercial tomato cultivars. We collected 48 F₁ cultivars representing four market classes (freshmarket, cherry, grape and rootstock) from 14 private breeding programs. Genotyping by sequencing for this collection generated a total of 90,469 SNPs across 12 chromosomes. Of these, 14,400 SNP were selected based on minor allele frequency (> 5%), missing data rate (< 10%) and minimum depth (5x). These SNPs were further filtered with the polymorphism information content (PIC) values of ≥ 0.3 and genome distribution to identify a core set of 400 SNPs. To validate these core SNPs, a subset of 192 SNPs was used to genotype additional 72 F₁ cultivars (29 freshmarket, 23 cherry, 17 grape and three rootstock) using the Fluidigm dynamic arrays. We found that 152 SNPs (79.16%) showed distinct polymorphisms in the 72 cultivars and these markers were able to differentiate 116 of 120 cultivars (96.67%) using a hierarchical clustering method. Furthermore, a model-based clustering analysis detected four sub-populations in this tomato collection. The 41 of 44 freshmarket cultivars were divided into two subpopulations and seven rootstock cultivars were grouped into one of these subpopulations. The 33 cherry and 36 grape cultivars were not separated into two distinct subpopulations. This sub-population structure was supported by pairwise estimates of F_st. These results suggest that our core set of SNP markers can be a useful resource to develop an effective DNA barcode system for cultivar identification and seed purity test in tomato.