Highly Parallel SNP Genotyping Reveals Patterns of Human Selection in Elite Tomato Germplasm and Suggests Strategies for Genome-Wide Selection

Tomatoes have been selected for distinct market uses and environments. This selection has affected the architecture of the plant, the shape and size of fruit, and increased the diversity of resistance loci. Sequence data were generated for six tomato varieties using a “next generation” sequencing by synthesis strategy, and analyzed for single nucleotide polymorphism (SNP) using allele frequency data and genome position as principle criterion. A public SNP array was developed from these analyses. Genotyping was performed on a panel of 384 cultivated varieties including land-race, vintage (heirloom), and elite parents. The contemporary varieties possessed greater genetic diversity relative to the gene pool of older cultivated varieties. Analysis of allele frequencies, FST outliers, and linkage disequilibrium (LD) decay revealed regions of the genome that appear to be under selection. Regions of the genome containing a high frequency of alleles under selection also contain genes affecting fruit size and shape, disease resistance, and plant habit all likely targets for modification through human selection. Subsequent analysis of an optimized subset of 384 SNPs in a nested population of recombinant inbred lines is revealing regions of the genome that contribute to plant size, yield, and fruit quality characteristics within the context of breeding programs. Translating these results into increased gain under selection appears to be limited by recombination and our ability to collect accurate phenotypic data for large populations.