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

Abstract

Tomato, Solanum lycopersicum, is divided into two widely distributed varieties: the cultivated S. lycopersicum var. lycopersicum, and the weedy S. lycopersicum var. cerasiforme. Solanum pimpinellifolium is the most closely related wild species of tomato.The roles of S. pimpinellifolium and S. l. cerasiforme during the domestication of tomato are still under debate. Some authors consider S. l. cerasiforme to be the ancestor, whereas others think that S. l. cerasiforme is an admixture of S. pimpinellifolium and the cultivated S. l. lycopersicum. It is also not clear whether the domestication occurred in the Andean region or in Mesoamerica. We characterized 272 accessions (63 S. pimpinellifolium, 106 S. l. cerasiforme, 95 S. l. lycopersicum 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. Solanum lycopersicum var. cerasiforme and S. l. lycopersicum were also differentiated in the PCA and Structure analyses, which supports maintaining them as different varieties. Solanum pimpinellifolium and the Andean S. l. cerasiforme were more diverse than the non-Andean S. lycopersicum. Solanum lycopersicum var. cerasiforme was morphologically and molecularly intermediate between S. pimpinellifolium and tomato. Solanum lycopersicum var. cerasiforme, 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 S. l. cerasiforme 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.

A cytochrome P450 regulates a domestication trait in cultivated tomato

“…Driven by the selection of alleles from wild relatives and those that arose after the initial domestication events, characters associated with the domestication syndrome such as larger fruit and seed are typically differentiating wild from cultivated forms (4). Genome-wide genetic diversity analyses support the notion that the initial domestication of tomato was situated in Northern Peru and Ecuador (5). Selections from the red-fruited wild relative Solanum pimpinellifolium L. evolved into the semidomesticated Solanum lycopersicum L. var cerasiforme (hereafter referred to as S. l. cerasiforme) bearing fruit of small to medium weight.…”

“…Selections from the red-fruited wild relative Solanum pimpinellifolium L. evolved into the semidomesticated Solanum lycopersicum L. var cerasiforme (hereafter referred to as S. l. cerasiforme) bearing fruit of small to medium weight. S. l. cerasiforme was further domesticated in Mexico giving rise to the large fruited tomato Solanum lycopersicum var lycopersicum (hereafter referred to as S. l. lycopersicum), which to date is cultivated throughout the world (5).…”

Advances in tomato research in the post-genome era

“…It is likely these early populations also transported the plants to central America and Mexico, followed by the Spaniards who brought tomatoes and also potatoes to Europe at the beginning of the 16th century (Blanca et al 2012). At first they were perceived as poisonous and used only for decoration, but they rapidly became staple food in local cuisine, and distributed across the globe as a food crop.…”

Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

“…Over the last two decades, numerous QTLs have been identified for traits such as fresh weight using linkage approaches (Frary et al, 2000;Zhang et al, 2012;Chakrabarti et al, 2013) but also for other fruit-related traits such as fruit ascorbic acid levels (Stevens et al, 2007), sensory and instrumental quality traits (Causse et al, 2002), sugar and organic acids (Fulton et al, 2002), and metabolic components (Schauer et al, 2008). Large tomato germplasm collections have been characterized at the molecular level using simple sequence repeat (Ranc et al, 2008) and single-nucleotide polymorphism (SNP) markers (Blanca et al, 2012;Shirasawa et al, 2013), giving insights into population structure, tomato evolutionary history, and the genetic architecture of traits of agronomic interest. These screens of nucleotide diversity were made possible (for review, see Bauchet and Causse, 2012) in the last couple of years due to the release of the tomato genome sequence (Tomato Genome Consortium, 2012) and derived genomic tools such as a high-density SNP genotyping array .…”