The Effects of Human Selection on Elite Tomato Germplasm and Implications for Genome-based Selection

Human selection to produce tomatoes for distinct market niches, end uses, and environments has had profound effect on the tomato plant, the shape and size of fruit, and diversity of resistance. To assess the distribution of genetic variation and inform future plant breeding, “next generation” sequence data were generated for six tomato varieties and analyzed in a single nucleotide polymorphism (SNP) discovery pipeline. A public SNP array was developed from these analyses using allele frequency data as a principle criterion. To address hypotheses about the effect of human selection and the distribution of variation, a panel of 384 cultivated varieties ranging from land-race and vintage classes to elite parents was assembled.  Contemporary varieties possess greater genetic diversity relative to the gene pool of older cultivated varieties. Analysis of allelic variation, haplotype blocks, and linkage disequilibrium (LD) decay along each chromosome suggest that human selection has not been uniform across the genome.  Breeding for specific market niches has led to selection for groups of unlinked genes. Regions of the genome containing a high frequency of alleles under selection also contain genes affecting fruit size and shape, disease resistance, plant habit, and sugar metabolism, all likely targets for modification through human selection. Knowledge of allele frequency, recombination, and physical position were used to develop optimized sets of SNPs for genome wide selection in different market classes. Gain under selection in contemporary breeding programs now appears to be limited by recombination, ability to collect accurate phenotypic data for large populations, and the lack of multiple trait indices that reflect market value.