High-Density SNP Analysis of Cultivated Tomato (Solanum lycopersicum L.)

Next generation sequencing has generated extensive sequence data in many plant species. These resources have facilitated genome-wide discovery of single nucleotide polymorphisms (SNPs) and development of high-throughput genotyping platforms. We designed a high density Infinium array with 8,784 SNPs identified by using Illumina GAII transcriptome sequences of six tomato accessions (four cultivated varieties and two wild accessions). Of these, 7,720 SNPs passed production quality check and were used to genotype a tomato germplasm panel (n=489) representing cultivated varieties (processing, fresh market, and vintage) and wild species. We obtained high quality genotype data (< 10% missing data) from 7,375 SNPs across the panel. The polymorphism rates of these SNPs were 63.3% for processing varieties, 86.8% for fresh market varieties, 81.4% for vintage varieties, and 96.9% for wild species. Graphing minor allele frequency (MAF) relative to genetic and physical positions revealed differences in haplotype blocks between cultivated groups. The extent of linkage disequilibrium (LD) was examined across each chromosome with LD decay ranging between 1.3-12.2 cM within processing varieties, 3.4-12.2 cM within fresh market varieties, and 0.6-21.7 cM within vintage varieties. The highest level of LD was detected on chromosome 4 while chromosome 7 showed more rapid LD decay, regardless of market class. Chromosomes 4, 5 and 11 were among the most variable based on polymorphic marker number and MAF. Principle component analysis demonstrated genetic differentiation between and within market classes. Our results indicate that SNP resources can be leveraged for tomato improvement within cultivated populations typical of breeding programs.