Sequencing and High-Density SNP Genotyping Reveals the Signature of Crop Wild Relatives on the Genome of Cultivated Tomato.

The history of tomato (Solanum lycopersicum L.) improvement includes wild species introgressions. Since the early 1900s, wild relatives have been used to introgress new alleles into cultivated tomato. Crop wild relatives, accessed from the C. M. Rick Tomato Genetics Resource Center (TGRC) and the National Plant Germplasm System (NPGS) have been essential donors of disease resistance, fruit quality traits and genes responsible for differentiating fresh-market and processing tomatoes. Genome resequencing of >400 accessions and high-density SNP genotyping of 1,000 accessions demonstrates that cultivated germplasm is divided into distinct sub-populations based on market class, adaptation, and/or breeding history. The contemporary processing and fresh-market varieties are also distinct from vintage (Heirloom) germplasm. The population structure observed reflects a genetic signature of selection within cultivated tomato. Genetic diversity within the contemporary cultivated sub-populations as measured using allelic richness, expected heterozygosity, and polymorphic information content now exceeds levels found in the vintage sub-population.  Genomic data therefore provides evidence that variation is increased in contemporary varieties relative to vintage varieties, suggesting that introgression and selection is beginning to reverse the effects of genetic bottlenecks which occurred during domestication and introduction of the crop into Europe.