**2. Diversity of the tomato clade species**

Tomato belongs to the large and diverse *Solanaceae* family also called Nightshades which includes more than three thousand species. Among them, major crops arose from Old world (Eggplant from Asia) and New world (pepper, potato, tobacco, tomato from South America). The *Lycopersicon* clade contains the domesticated tomato (*Solanum lycopersicum*) and its 12 closest wild relatives (Peralta and Spooner 2005). The radiation of tomato clade has been estimated to 7.8 (Nesbitt and Tanksley 2002) and to 2.7 Million years between *S. lycopersicum* and *S. pennellii*(Kamenetzky et al. 2010). First detailed studies on this group of wild relatives were made by Charles Rick and colleagues since the 40's. Tomato clade species are originated from the Andean region, including Peru, Bolivia, Ecuador, Colombia and Chile (Figure 1). On Figure 1, *lycopersicon* species distributions are defined according to geographic data from the Tomato Genetics Resource Center, UC Davis http://tgrc. ucdavis.edu/Data/Acc/dataframe.aspx? start=GIS\_ dataoption. aspx&navstart=nav.html. Their growing environments range from near sea level to 3,300 m altitude, from arid to rainy climate and from Andeans Highlands to the coast of Galapagos Islands (*S. cheesmaniae; S. galapagense*). Their habitats are often narrow and isolated valleys where they were adapted to particular microclimates and various soil types. Their very large range of ecological conditions contributed to the diversity of the wild species. This broad variation is also expressed at the morphological, physiological, sexual and molecular levels (Peralta and Spooner 2005). Over times, several phylogenetic classifications have been proposed and several adjustments occurred. Being first classified in the *Solanum* genus, the group turned to a specific genus, *Lycopersicum* (Miller, 1731). It recently got renamed *Solanum* within an updated classification (Peralta and Spooner 2001). Taxonomic, ecological, reproductive, breeding specificities for each member of the clade are listed in Table 1 and reviewed by Peralta and colleagues (Peralta, Spooner et al. 2007). The first classification was morphology based (Luckwill 1943). Later molecular data confirmed tomato membership of Linnaeus classification, but also improved subtaxa classification (Spooner 2008). The tomato clade is an interesting example for research on plant biodiversity, notably, on evolution, adaptation, human domestication and nutrition perspectives (Peralta and Spooner 2007). Nowadays, across South America, populations of wild tomatoes are being severely reduced. Their natural habitats are shrinking due to urban development and intensive agriculture as well as goat herding in the highlands, as recently documented by a botanical expedition in Peru. (Grandillo, Chetelat et al. 2011).

These technologies and related data analysis allow a complete and combined reading of genomes and related levels of expression (transcriptome, proteome, metabolome) in a high throughput way. Among the new approaches, QTL mapping techniques in natural populations or genome wide association studies will facilitate the genetic characterization of

In this chapter we will first show how tomato diversity evolved from its early domestication until today. We will discuss how valuable tomato genetic resources are, and that investigating natural variation not only highlights existing diversity -which is of critical use for cultivated tomato improvement- but can also provide insights into the evolution and genetic bases of complex traits. In the last part, we will present how molecular markers have

Tomato belongs to the large and diverse *Solanaceae* family also called Nightshades which includes more than three thousand species. Among them, major crops arose from Old world (Eggplant from Asia) and New world (pepper, potato, tobacco, tomato from South America). The *Lycopersicon* clade contains the domesticated tomato (*Solanum lycopersicum*) and its 12 closest wild relatives (Peralta and Spooner 2005). The radiation of tomato clade has been estimated to 7.8 (Nesbitt and Tanksley 2002) and to 2.7 Million years between *S. lycopersicum* and *S. pennellii*(Kamenetzky et al. 2010). First detailed studies on this group of wild relatives were made by Charles Rick and colleagues since the 40's. Tomato clade species are originated from the Andean region, including Peru, Bolivia, Ecuador, Colombia and Chile (Figure 1). On Figure 1, *lycopersicon* species distributions are defined according to geographic data from the Tomato Genetics Resource Center, UC Davis http://tgrc. ucdavis.edu/Data/Acc/dataframe.aspx? start=GIS\_ dataoption. aspx&navstart=nav.html. Their growing environments range from near sea level to 3,300 m altitude, from arid to rainy climate and from Andeans Highlands to the coast of Galapagos Islands (*S. cheesmaniae; S. galapagense*). Their habitats are often narrow and isolated valleys where they were adapted to particular microclimates and various soil types. Their very large range of ecological conditions contributed to the diversity of the wild species. This broad variation is also expressed at the morphological, physiological, sexual and molecular levels (Peralta and Spooner 2005). Over times, several phylogenetic classifications have been proposed and several adjustments occurred. Being first classified in the *Solanum* genus, the group turned to a specific genus, *Lycopersicum* (Miller, 1731). It recently got renamed *Solanum* within an updated classification (Peralta and Spooner 2001). Taxonomic, ecological, reproductive, breeding specificities for each member of the clade are listed in Table 1 and reviewed by Peralta and colleagues (Peralta, Spooner et al. 2007). The first classification was morphology based (Luckwill 1943). Later molecular data confirmed tomato membership of Linnaeus classification, but also improved subtaxa classification (Spooner 2008). The tomato clade is an interesting example for research on plant biodiversity, notably, on evolution, adaptation, human domestication and nutrition perspectives (Peralta and Spooner 2007). Nowadays, across South America, populations of wild tomatoes are being severely reduced. Their natural habitats are shrinking due to urban development and intensive agriculture as well as goat herding in the highlands, as recently documented by a botanical expedition in Peru.

complex traits and germplasm management of both wild and cultivated tomatoes.

completed our view.

(Grandillo, Chetelat et al. 2011).

**2. Diversity of the tomato clade species** 

Fig. 1. Geographic distribution of wild species in *Solanum* section *lycopersicon.* 

Many studies were conducted on evolutionary aspects of the lycopersicon clade. The mating system was extensively studied, using the clade as a model to study its effects on species variation (Bedinger, Chetelat et al. 2011). Mating system has played a key role in evolution of wild tomatoes, varying from allogamous self-incompatible, to facultative allogamous, to autogamous and self-compatible (Table 1). Flower stigma exertion and gametophytic incompatibility system contribute in greater outcrossing and genetic diversity. All the species of the clade are intercrossable (Table 1), but with a variable success rate (Rick, Fobes et al. 1977a; Rick, Fobes et al. 1979). Fruit color discriminate the wild relative species. Most of the latter carry green fruits, with the exception of the two species from the Galapagos (with yellow and orange fruits) and *S. pimpinellifolium*, which is the only wild relative species with red fruits. *S. pimpinellifolium* fruits are round, small, weighing only few grams. These fruits are edible and the species referred as the currant tomato. The plant presents a reduced apical dominance and prostrate growth habit resulting in a large shrub with inflorescence carrying many flowers and fruits (Paran and van der Knaap 2007). *S. pimpinellifolium* undergone bottleneck only recently with a drastic reduction of its natural habitats and is now an endangered species (Biodiversity-International 2006). *S. lycopersicum* var *cerasiforme* fruit is larger than *S. pimpinellifolium*  and is commonly round and red. This subspecies of tomato is referred to as the "cherry tomato". It has been proposed as the direct ancestor of cultivated tomato because of its diversity, its wide spread occurrence in central America and its close genetic relationship with cultivated tomato (Rick and Chetelat 1995). The modern cultivated tomato, *S. lycopersicum*, is cosmopolite. It has spread all around the world and is now cultivated under a broad range of environments and conditions.

#### **3. Tomato domestication in South America**

Domestication is a special type of species diversification, distinct from species divergence through natural selection in the wild (Darwin and Wallace 1858). Domesticated species differ from wild and relative species for a set of traits known as the domestication syndrome (Doebley, Gaut et al. 2006). Domestication is often controlled by a limited number of chromosomal regions with major phenotypic effect (Purugganan and Fuller 2009). In tomato, edible fruits, attractive red color and fruit size increase are characterizing this process.

The domestication time of tomato is unclear. It is supposed to be due to a recent divergence from S. *pimpinellifolium.* The first hypothesis supports Peru as the center of origin and domestication (de Candolle 1882). This hypothesis gives emphasis on botanical evidences and has been complemented by botanical, linguistic and historical aspects. It was further supported by other colleagues (Müller 1940a; Müller 1940b; Luckwill 1943) and recent molecular studies (Nesbitt and Tanksley 2002). Nevertheless, very little and unclear archeological evidences are available to clearly support this hypothesis (McMeekin 1992). The second hypothesis supports that domestication occurred primarily in Mexico in the Vera Cruz Puebla area (Jenkins 1948), as there is no evidence for pre-Colombian cultivation of tomato in South America but good evidences in Mexico. Referring to Guilandini (1572), Jenkins also argued that tomato name comes most probably from the Mexican Nahua people word "Tomatl" that described "plants bearing globous and juicy fruit" (Sahagún 1988). Based on its


Table 1. Principal features of the *lycopersicon* subsection (*Solanum* sect. *Lycopersicon*) Data are compiled from Peralta *et al*. 2007, Moyle *et al*. 2008, Grandillo *et al*. 2011

136 Genetic Diversity in Plants

Many studies were conducted on evolutionary aspects of the lycopersicon clade. The mating system was extensively studied, using the clade as a model to study its effects on species variation (Bedinger, Chetelat et al. 2011). Mating system has played a key role in evolution of wild tomatoes, varying from allogamous self-incompatible, to facultative allogamous, to autogamous and self-compatible (Table 1). Flower stigma exertion and gametophytic incompatibility system contribute in greater outcrossing and genetic diversity. All the species of the clade are intercrossable (Table 1), but with a variable success rate (Rick, Fobes et al. 1977a; Rick, Fobes et al. 1979). Fruit color discriminate the wild relative species. Most of the latter carry green fruits, with the exception of the two species from the Galapagos (with yellow and orange fruits) and *S. pimpinellifolium*, which is the only wild relative species with red fruits. *S. pimpinellifolium* fruits are round, small, weighing only few grams. These fruits are edible and the species referred as the currant tomato. The plant presents a reduced apical dominance and prostrate growth habit resulting in a large shrub with inflorescence carrying many flowers and fruits (Paran and van der Knaap 2007). *S. pimpinellifolium* undergone bottleneck only recently with a drastic reduction of its natural habitats and is now an endangered species (Biodiversity-International 2006). *S. lycopersicum* var *cerasiforme* fruit is larger than *S. pimpinellifolium*  and is commonly round and red. This subspecies of tomato is referred to as the "cherry tomato". It has been proposed as the direct ancestor of cultivated tomato because of its diversity, its wide spread occurrence in central America and its close genetic relationship with cultivated tomato (Rick and Chetelat 1995). The modern cultivated tomato, *S. lycopersicum*, is cosmopolite. It has spread all around the world and is now cultivated

Domestication is a special type of species diversification, distinct from species divergence through natural selection in the wild (Darwin and Wallace 1858). Domesticated species differ from wild and relative species for a set of traits known as the domestication syndrome (Doebley, Gaut et al. 2006). Domestication is often controlled by a limited number of chromosomal regions with major phenotypic effect (Purugganan and Fuller 2009). In tomato, edible fruits, attractive red color and fruit size increase are characterizing this

The domestication time of tomato is unclear. It is supposed to be due to a recent divergence from S. *pimpinellifolium.* The first hypothesis supports Peru as the center of origin and domestication (de Candolle 1882). This hypothesis gives emphasis on botanical evidences and has been complemented by botanical, linguistic and historical aspects. It was further supported by other colleagues (Müller 1940a; Müller 1940b; Luckwill 1943) and recent molecular studies (Nesbitt and Tanksley 2002). Nevertheless, very little and unclear archeological evidences are available to clearly support this hypothesis (McMeekin 1992). The second hypothesis supports that domestication occurred primarily in Mexico in the Vera Cruz Puebla area (Jenkins 1948), as there is no evidence for pre-Colombian cultivation of tomato in South America but good evidences in Mexico. Referring to Guilandini (1572), Jenkins also argued that tomato name comes most probably from the Mexican Nahua people word "Tomatl" that described "plants bearing globous and juicy fruit" (Sahagún 1988). Based on its

under a broad range of environments and conditions.

**3. Tomato domestication in South America** 

process.

center theory, Harlan suggested that biloculed domesticated forms found in south Mexico and Guatemala are the oldest cultivated types (Harlan 1971). Quoting Sahagun, Diez argued that tomato was totally "integrated" in the Aztec civilization food consumption in XVI century, contrary to South American Incas (Diez and Nuez 2008). Nevertheless, two authors identified Quechua names possibly referring to tomato: "pirca" (Horkheimer 1973) and "pesco-tomate" (Yakovleff 1935). However, botanists consider the origins of tomato domestication as unsolved (Peralta and Spooner 2007b). These authors mention recent evidences showing that the Mexican hypothesis is not supported by comparative data, as South American and Mexican tomato accessions share similar isozymes (Rick and Fobes 1975) as well as molecular markers (Villand, Skroch et al. 1998). So far, no evidence appears to be enough conclusive and tomatoes may have been domesticated independently in both areas. To go further a more extensive analysis of molecular polymorphism in the wild and cultivated tomatoes is needed. This would allow investigating demographic scenarios and estimating the parameters of these scenarios (bottleneck intensity, ancestral population size, migration rates) using Markovian model implemented in tools such as IM\* program (Hey and Nielsen 2004) or ABC1 methodology (Beaumont, Zhang et al. 2002; Lopes and Beaumont 2010). Very recently, this approach has been implemented to infer past demography and ecological parameters of two tomato wild relatives, *S. chilense* and *S. peruvianum* (Tellier, Laurent et al. 2011).

Many authors consider *S. lycopersicum* var. *cerasiforme* as ancestral form of the cultivated tomato. It is present in both Mexico and Peru, on the contrary to *S. pimpinellifolium* which is absent from Mexico. If we assume that *S.l. cerasiforme* results from direct domestication from *S. pimpinellifolium*, a consequence of this domestication is that *S.l. cerasiforme* suffered a decrease of its population effective size during domestication (Bai and Lindhout 2007). Subsequent changes occurred for domestication traits such as growth habit, mating system, gigantism and fruit morphological diversity. Notably a change from exerted to inserted stigmas is responsible for the change from partial allogamy to strict autogamy. Selection for self-pollinating as well as shortening of the stigma compared to close wild relatives such as *S. pimpinellifolium* has allowed a yield increase (Rick 1977b). This "selfing syndrome" (Sicard and Lenhard 2011) is striking in tomato where a mutation in gene controlling stigma length has been identified in cultivated germplasm (Chen, Cong et al. 2007).
