Diversity and Population Structure in a Geographic Sample of Tomato Accessions

ABSTRACT Domesticated tomato (Solanum lycopersicum L.) dispersed out of Latin America nearly 500 yr ago, but little is known about its global patterns of genetic diversity. To gain insight into these patterns we assembled a panel of 30 accessions that sampled five major geographic regions. All accessions were evaluated for highly heritable horticultural traits and nutritional content. Lycopene (mean = 10.41 ug g−1), total soluble solids (mean Brix = 6.03%), and vitamin C (mean = 50.77 ug ml−1) varied two‐ to three‐fold among accessions. Lycopene was somewhat low while Brix was typical of tomato varieties. Amplicons from 49 genes (22.9 kbp in total) were sequenced in two plants per accession. Nucleotide diversity (π = 0.00112) was slightly lower than a panel of landraces but higher than a set of fresh‐market and processing varieties. South America was the only region with a significantly higher mean π relative to the other geographic regions. An analysis of molecular variance (AMOVA) of gene frequencies showed that large fractions of the total variation were partitioned into accessions within regions (36%) and individuals within accessions (61%). Therefore, targeted sampling of accessions and individual plants, irrespective of geographic source, is an optimal strategy to obtain diverse genotypes. Population structure analysis defined two clusters that were not associated with a priori groups. South American germplasm is promising as a source of new alleles but no geographic region should be viewed as a poor source of tomato genetic variation.