Variation Revealed by SNP Genotyping and Morphology Provides Insight into the Origin of the Tomato

<div><p>Tomato, <em>Solanum lycopersicum</em>, is divided into two widely distributed varieties: the cultivated <em>S. lycopersicum</em> var. <em>lycopersicum</em>, and the weedy <em>S. lycopersicum</em> var. <em>cerasiforme</em>. <em>Solanum pimpinellifolium</em> is the most closely related wild species of tomato.</p> <p>The roles of <em>S. pimpinellifolium</em> and <em>S. l. cerasiforme</em> during the domestication of tomato are still under debate. Some authors consider <em>S. l. cerasiforme</em> to be the ancestor, whereas others think that <em>S. l. cerasiforme</em> is an admixture of <em>S. pimpinellifolium</em> and the cultivated <em>S. l. lycopersicum</em>. It is also not clear whether the domestication occurred in the Andean region or in Mesoamerica. We characterized 272 accessions (63 <em>S. pimpinellifolium</em>, 106 <em>S. l. cerasiforme</em>, 95 <em>S. l. lycopersicum</em> and 8 derived from hybridization processes) were morphologically and genetically using the SolCap platform (7,414 SNPs). The two species were distinguished in a PCA analysis and displayed a rich geographic structure. <em>Solanum lycopersicum</em> var. <em>cerasiforme</em> and <em>S. l. lycopersicum</em> were also differentiated in the PCA and Structure analyses, which supports maintaining them as different varieties. <em>Solanum pimpinellifolium</em> and the Andean <em>S. l. cerasiforme</em> were more diverse than the non-Andean <em>S. lycopersicum</em>. <em>Solanum lycopersicum</em> var. <em>cerasiforme</em> was morphologically and molecularly intermediate between <em>S. pimpinellifolium</em> and tomato. <em>Solanum lycopersicum</em> var. <em>cerasiforme</em>, with the exception of several Ecuadorian and Mexican accessions, is composed of the products of admixture processes according to the Structure analysis. The non-admixtured <em>S. l. cerasiforme</em> might be similar to the ancestral cultivars from which the cultivated tomato originated, and presents remarkable morphological diversity, including fruits of up to 6 cm in diameter. The data obtained would fit a model in which a pre-domestication took place in the Andean region, with the domestication being completed in Mesoamerica. Subsequently, the Spaniards took plants from Mesoamerica to Spain and from there they were exported to the rest of the world.</p>