**10. References**

Albrecht, E., M. Escobar, et al. (2010). "Genetic diversity and population structure in the tomato-like nightshades Solanum lycopersicoides and S. sitiens." *Annals of Botany* 105(4): 535-554.

Crossing wild and cultivated species can reveal alleles left behind during the domestication process. Molecular markers strongly helped to reinforce the use of wild relatives (Zamir 2008). Interfacing genetic resources management and plant breeding, pre-breeding is now recognized as an important adjunct to plant breeding, as a way to introduce new traits from non-adapted populations and wild relatives, notably for abiotic stress (FAO 2010). Nevertheless, the extensive use of this genetic richness contained in seed banks and germplasm collection faces limits. The difficulty to introgress accurately the targeted allele (with favorable effect) without unfavorable ones, carried on by "linkage drag", remains.

With the emergence of bioinformatics and nanotechnologies -so called "post-genomics" erathe last decade has opened high throughput sequencing era. Now, conducting large intraspecific studies becomes a reality in tomato, allowing a better characterization of its genetic diversity. With the completion of its genome sequence (Mueller, Lankhorst et al. 2009) and rich annotation as well as a large number of tools available via SGN (SOL Genome Network; http://solgenomics.net/organism/solanum\_lycopersicum/genome) platform (Bombarely, Menda et al. 2010), tomato and its relatives is the most advanced vegetable crop. A draft of the genome sequence of *S. pimpinellifolium* LA1589 is also released by D. Ware, W. R. McCombie, and Z. B. Lippman at Cold Spring Harbor Laboratory allowing a detailed comparison of both species. The genome sequences of tomato provide clues for understanding the Solanum clade

Progress in sequencing technologies has reached the point where genotyping by sequencing (GBS) is now possible (Davey, Hohenlohe et al. 2011; Elshire, Glaubitz et al. 2011). This opens new perspectives in terms of genetic diversity management, notably toward conservation and survey of large populations. In a near future, techniques such as GBS may allow breeders and scientists of the tomato community to determine population characteristics prior concretely establishing genome or nucleotide diversity. GBS opens ways to a global and quantitative management of diversity, and let foresee an *a priori* genetic resource management. It also opens perspectives in allele based breeding called genomic

If *ex situ* germplasm conservation is well developed and will benefit of these developments, *in situ* conservation of tomato and its wild relatives is becoming critical due to major ecological changes in its area origin. Efforts on *in situ* conservation and participatory approaches as proposed by Jarvis, Brown et al (2008) and (Thomas, Dawson et al. 2011) could be very useful to maintain the adaptive potential of tomato genetic resources. Nuez and colleagues proposed to use *S. cheesmanii* accessions now stored in germplasm banks to reinstate some extinct populations in Galapagos Islands (Nuez et al. 2004). This could help avoiding the present paradox: the more knowledge we gain on tomato diversity and its

evolutive history, the less available those genetic resources are available in the wild.

Albrecht, E., M. Escobar, et al. (2010). "Genetic diversity and population structure in the

tomato-like nightshades Solanum lycopersicoides and S. sitiens." *Annals of Botany*

evolutive history and identify genes involved in fleshy fruit development.

selection (Hamblin, Buckler et al. 2011).

**10. References** 

105(4): 535-554.

**9. Conclusion: Toward a change in the way to manage and use diversity** 


 http://www.scientificamerican.com/article.cfm?id=case-against-heirloomtomatoes


Caicedo, A. L. and B. A. Schaal (2004). "Population structure and phylogeography of

Canady, M. A., V. Meglic, et al. (2005). "A library of *Solanum lycopersicoides* introgression

Casals, J., L. Pascual, et al. (2011). "The risks of success in quality vegetable markets: Possible

Causse, M. Duffe, P. et al (2004). "A genetic map of candidate genes and QTLs involved in

Causse, M., C. Friguet, et al. (2010). "Consumer Preferences for Fresh Tomato at the

Causse, M., V. Saliba-Colombani, et al. (2002). "QTL analysis of fruit quality in fresh market

Chunwongse, J. C., L. Black, et al. (2002). Molecular mapping of the Ph-3 gene for late blight resistance in tomato. *Journal of Horticultural science and Technology* 77(3): 281-286. Comai, L. and S. Henikoff (2006). "TILLING: practical single-nucleotide mutation

Cong, B., L. S. Barrero, et al. (2008). "Regulatory change in YABBY-like transcription factor

Darwin, C. (1859). *On the Origin of Species by Means of Natural Selection*. London, J. Murray. Darwin, C. and A. Wallace (1858). "On the Tendency of Species to form Varieties; and on the

Darwin, S. C., S. Knapp, et al. (2003). "Taxonomy of tomatoes in the Galpagos Islands:

Davey, J. W., P. A. Hohenlohe, et al. (2011). "Genome-wide genetic marker discovery and

de Vos, R. C. H., R. D. Hall, et al. (2011). Metabolomics of a Model Fruit: Tomato. *Annual* 

Diez M.-.J. and Nuez, F. (2008). Tomato. *Vegetables II Fabaceae, Liliaceae, Solanaceae, and* 

Dixon, M. S., D. A. Jones, et al. (1996). "The Tomato Cf-2 Disease Resistance Locus

Comprises Two Functional Genes Encoding Leucine-Rich Repeat Proteins." *Cell*

*Proceedings of the Linnean Society of London. Zoology* 3(9): 45-62.

led to evolution of extreme fruit size during tomato domestication." *Nature Genetics*

Perpetuation of Varieties and Species by natural means of selection." *Journal of the* 

native and introduced species of *Solanum* section *Lycopersicon* (Solanaceae) "

genotyping using next-generation sequencing." *Nature Reviews Genetics* 12(7): 499-

instrumental traits." *Journal of Experimental Botany* 53(377): 2089-2098. Chen, K. Y., B. Cong, et al. (2007). "Changes in Regulation of a Transcription Factor Lead to

Autogamy in Cultivated Tomatoes." *Science* 318(5850): 643-645.

discovery." *The Plant Journal* 45(4): 684-694.

*Systematics and Biodiversity* 1(1): 29-53.

de Candolle, A. P. (1882). *L'origine des plantes cultivées*. Paris.

*Umbelliferae*. Prohens J. and Nuez, F.: 249-323.

lines in cultivated tomato." *Genome* 48(4): 685-697.

dissatisfaction." *Scientia Horticulturae* 130(1): 78-84.

1871-1882.

1685.

*Science* 75(9): S531-S541.

40(6): 800-804.

510.

*Plant Reviews* 109-155.

84(3): 451-459.

*Solanum pimpinellifolium* inferred from a nuclear gene." *Molecular Ecology* 13(7):

genetic erosion in Marmande tomatoes (*Solanum lycopersicum* L.) and consumer

tomato fruit size and composition." *Journal of Experimental Botany* 55(403): 1671-

European Scale: A Common Segmentation on Taste and Firmness." *Journal of Food* 

tomato: a few chromosome regions control the variation of sensory and


Grandillo, S., H. M. Ku, et al. (1999). "Identifying the loci responsible for natural variation in fruit size and shape in tomato." *Theoretical and Applied Genetics* 99(6): 978-987. Gur, A., S. Osorio, et al. (2010). "*hi2-1*, A QTL which improves harvest index, earliness and

Gur, A., Y. Semel, et al. (2011). "Yield quantitative trait loci from wild tomato are

Hamblin, M. T., E. S. Buckler, et al. (2011). "Population genetics of genomics-based crop

Harlan, J. R. (1971). "Agricultural Origins: Centers and Noncenters." *Science* 174(4008): 468-

He, C., V. Poysa, et al. (2003). "Development and characterization of simple sequence repeat

Hey, J. and R. Nielsen (2004). "Multilocus methods for estimating population sizes,

Itkin, M., H. Seybold, et al. (2009). "TOMATO AGAMOUS-LIKE 1 is a component of the fruit ripening regulatory network." *The Plant Journal* 60(6): 1081-1095. Jarvis, D. I., A. H. D. Brown, et al. (2008). "From the Cover: A global perspective of the

Jimenez-Gomez, J. and J. Maloof (2009). "Sequence diversity in three tomato species: SNPs,

Kamenetzky, L., R. Asís, et al. (2010). "Genomic analysis of wild tomato introgressions

Keurentjes, J. J. B. (2009). "Genetical metabolomics: closing in on phenotypes." *Current* 

Kramer, M. G. and K. Redenbaugh (1994). "Commercialization of a tomato with an antisense

Krieger, U., Z. B. Lippman, et al. (2010). "The flowering gene SINGLE FLOWER TRUSS

drives heterosis for yield in tomato." *Nature Genetics* 42(5): 459-463.

*esculentum* cultivars." *Theoretical and Applied Genetics* 106(2): 363-373. Hemming, M. N., S. Basuki, et al. (2004). "Fine mapping of the tomato gene for fusarium wilt

candidate for *I-3*." *Theoretical and Applied Genetics* 109(2): 409-418.

*Drosophila pseudoobscura* and *D. persimilis*." *Genetics* 167(2): 747-760. Horkheimer, H. (1973). *Alimentación y obtención de alimentos en el Perú prehispánico.* Lima. Isaacson, T., G. Ronen, et al. (2002). "Cloning of tangerine from tomato reveals a carotenoid

Jenkins, J. (1948). "The origin of the cultivated tomato." *Economic Botany* 2(4): 379-392.

markers, and molecular evolution." *BMC Plant Biology* 9(1): 85.

improvement methods." *Trends in Genetics* 27(3): 98-106.

*Genetics* 121(8): 1587-1599.

*The Plant Cell Online* 14(2): 333-342.

*Opinion in Plant Biology* 12(2): 223-230.

420.

474.

1786.

297.

alters metabolite accumulation of processing tomatoes." *Theoretical and Applied* 

predominately expressed by the shoot." *Theoretical and Applied Genetics* 122(2): 405-

(SSR) markers and their use in determining relationships among *Lycopersicon* 

resistance and elimination of a co-segregating resistance gene analogue as a

migration rates and divergence time, with applications to the divergence of

isomerase essential for the production of β-carotene and xanthophylls in plants."

richness and evenness of traditional crop-variety diversity maintained by farming communities." *Proceedings of the National Academy of Sciences* 105(14): 5326-5331.

determining metabolism- and yield-associated traits." *Plant Physiology* 152(4): 1772-

polygalacturonase gene: The FLAVR SAVR™ tomato story." *Euphytica* 79(3): 293-


Lopes, J. S. and M. A. Beaumont (2010). "ABC: A useful Bayesian tool for the analysis of

Luckwill, L. C. (1943). "The genus *Lycopersicon*: an historical, biological, and taxonomical

Manning, K., M. Tör, et al. (2006). "A naturally occurring epigenetic mutation in a gene

Martin, G., S. Brommonschenkel, et al. (1993). "Map-based cloning of a protein kinase gene conferring disease resistance in tomato." *Science* 262(5138): 1432-1436. Mazzucato, A., R. Papa, et al. (2008). "Genetic diversity, structure and marker-trait

McCue, G. A. (1952). "The history of the use of the tomato: an annotated bibliography."

McKhann, H. I., C. Camilleri, et al. (2004). "Nested core collections maximizing genetic

McMeekin, D. (1992). "Representations on pre-columbian spindle whorls of the floral and

Menda, N., Y. Semel, et al. (2004). "In silico screening of a saturated mutation library of

Mendel, G. (1866). Experiments in plant hybridization : original traduction from *Versuche* 

Miller, J. C. and S. D. Tanksley (1990). "RFLP analysis of phylogenetic relationships and

Minoia, S., A. Petrozza, et al. (2010). "A new mutant genetic resource for tomato crop improvement by TILLING technology." *BMC Research Notes* 3(1): 69. Monforte, A. J. and S. D. Tanksley (2000). "Development of a set of near isogenic and

Moreau, P., P. Thoquet, et al. (1998). "Genetic Mapping of Ph-2, a Single Locus Controlling

Mounet, F., A. Moing, et al. (2009). " Gene and metabolite regulatory network of early

Müller, C. H. (1940a). "A revision of the genus *Lycopersicon*. ." *U.S.D.A. Miscellanous* 

Müller, C. H. (1940b). "The taxonomy and distribution of the genus *Lycopersicon*." *National* 

fruit composition and development." *Plant Physiology* 149(3): 1505-1528. Mueller, L. A., R. K. Lankhorst, et al. (2009). "A Snapshot of the emerging tomato genome

*über Plflanzenhybriden* by W. Bateson completed by R. Blumberg, Electronic

genetic variation in the genus *Lycopersicon*." *Theoretical and Applied Genetics* 80(4):

backcross recombinant inbred lines containing most of the *Lycopersicon hirsutum* genome in a *L. esculentum* genetic background: A tool for gene mapping and gene

Partial Resistance to Phytophthora infestans in Tomato." *Molecular Plant-Microbe* 

developing fruit tissues highlights new candidate genes for the control of tomato

diversity in *Arabidopsis thaliana*." *The Plant Journal* 38(1): 193-202.

fruit structure of economic plants." *Economic Botany* 46(2): 171-180.

survey of the wild and cultivated tomatoes. ." *Aberdeen University Studies*(120): 1–44.

encoding an SBP-box transcription factor inhibits tomato fruit ripening." *Nature* 

associations in a collection of Italian tomato (Solanum lycopersicum L.) landraces."

population data." *Infection, Genetics and Evolution* 10(6): 825-832.

*Theoretical and Applied Genetics* 116(5): 657-669.

tomato." *The Plant Journal* 38(5): 861-872.

Scholarly Publishing Project.

discovery." *Genome* 43(5): 803-813.

sequence." *Plant Gen.* 2(1): 78-92.

*Horticulture Magazine*(19): 157–160.

*Interactions* 11(4): 259-269.

*Publications*(382): 1–28.

437-448.

*Annals of the Missouri Botanical Garden* 39(4): 289-348.

*Genetics* 38(8): 948-952.


Peralta, I. E. and D. M. Spooner (2001). "Granule-bound starch synthase (GBSSI) gene

Pertuzé, R. A., Y. Ji, et al. (2002). "Comparative linkage map of the *Solanum lycopersicoides*

Piron, F., M. Nicolaï, et al. (2010). "An Induced Mutation in Tomato eIF4E Leads to

Price, A. L., N. A. Zaitlen, et al. (2010). "New approaches to population stratification in genome-wide association studies." *Nature Reviews Genetics* 11(7): 459-463. Pritchard, J. K., M. Stephens, et al. (2000). "Inference of population structure ssing multilocus

Purugganan, M. D. and D. Q. Fuller (2009). "The nature of selection during plant

Quinet, M., J.-M. Kinet, et al. (2011). "Flowering response of the uniflora:blind:self-pruning

Ramsay, L., J. Comadran, et al. (2011). "INTERMEDIUM-C, a modifier of lateral spikelet

Ranc, N. (2010). Analyse du polymorphisme de gènes de composantes de la qualité des

d'association gènes/QTL. Montpellier, SupAgro. Thèse de doctorat: 348. Ranc, N., S. Muños, et al. (2008). "A clarified position for *Solanum lycopersicum* var.

Rick (1977). "Conservation of tomato species germplasm. ." *California Agriculture* 31((9)): 32-

Rick, C. M. (1991). "Tomato Paste: A concentrated review of genetic highlights from the

Rick, C. M. and R. T. Chetelat (1995). "Utilization of related wild species for tomato

Rick , C. M. and F. Fobes (1975). "Allozyme variation in the cultivated tomato and closely

Rick, C. M., J. F. Fobes, et al. (1977). "Genetic variation in *Lycopersicon pimpinellifolium*:

Rick, C. M., J. F. Fobes, et al. (1979). "Evolution of mating systems in *Lycopersicon hirsutum* as

Evidence of evolutionary change in mating systems." *Plant Systematics and Evolution*

deduced from genetic variation in electrophoretic and morphological characters."

related species." *Bulletin of the Torrey Botanical Club* 102(6): 376-384.

beginnings to the advent of molecular." *Genetics* 128(1): 1-5.

and jointless:uniflora:self-pruning tomato (*Solanum lycopersicum*) triple mutants."

fertility in barley, is an ortholog of the maize domestication gene TEOSINTE

fruits dans les ressources génétiques sauvages et cultivées de tomate ; recherche

cerasiforme in the evolutionary history of tomatoes (*Solanaceae*)." *BMC Plant Biology*

Immunity to Two potyviruses." *PLoS ONE* 5(6): e11313.

genotype data." *Genetics* 155(2): 945-959.

domestication." *Nature* 457(7231): 843-848.

BRANCHED 1." *Nature Genetics* 43(2): 169-172.

improvement." *Acta Horticulturae* 412: 21-38.

*Plant Systematics and Evolution* 132(4): 279-298.

*Physiologia Plantarum* 141(2): 166-176.

subsection *Lycopersicon*)." *American Journal of botany* 88(10): 1888-1902. Peralta, I. E. and D. M. Spooner (2005). Morphological characterization and relationships of

104: 227-257.

1012.

8(1): 130.

127(2): 139-170.

33

phylogeny of wild tomatoes (*Solanum* L. section *Lycopersicon* [Mill.] Wettst.

wild tomatoes (*Solanum L.* Section *Lycopersicon*). *A Festschrift for William G. D'Arcy*. T. B. Croat, V. C. Hollowell and R. C. Keating, Missouri Botanical Garden Press.

and *S. sitiens* genomes and their differentiation from tomato." *Genome* 45(6): 1003-


SolCAP (2008). USDA-CSREES awards \$5.4 million to SolCAP *SolCAP News .* Michigan State

Stadler, T., A. M. Florez-Rueda, et al. (2012). "Testing for "Snowballing" hybrid

Stevens, M. A. and C. M. Rick. (1986 ). Genetics and breeding. *The Tomato Crop: A Scientific Basis for Improvement.* J. G. A. a. J. Rudich. London, Chapman and Hall: 35-109. Stevens, R., M. Buret, et al. (2007). "Candidate genes and quantitative trait loci affecting fruit

Szymkowiak, E. J. and E. E. Irish (2005). "JOINTLESS suppresses sympodial identity in

Tadmor, Y., E. Fridman, et al. (2002). "Identification of malodorous, a wild species allele

Tam, S. M., C. Mhiri, et al. (2005). "Comparative analyses of genetic diversities within

Tanksley, D., H. Medina-Filho, et al. (1981). "The effect of isozyme selection on metric

Tanksley, S. D., M. W. Ganal, et al. (1992). "High density molecular linkage maps of the

Tanksley, S. D., S. Grandillo, et al. (1996). "Advanced backcross QTL analysis in a cross

Tanksley, S. D. and G. S. Khush (2002). Charles Madera Rick. *Bibliographical Memoirs* 84: 307-

Tellier, A., I. Fischer, et al. (2011). "Fitness effects of derived deleterious mutations in four

Tellier, A., S. J. Y. Laurent, et al. (2011). "Inference of seed bank parameters in two wild

Thomas, M., J. Dawson, et al. (2011). "Seed exchanges, a key to analyze crop diversity

Tieman, D., M. Taylor, et al. (2006). "Tomato aromatic amino acid decarboxylases participate

Tikunov, Y. A. Lommen , et al. (2005). "A Novel Approach for Nontargeted Data Analysis

*Proceedings of the National Academy of Sciences* 103(21): 8287-8292.

estimates*." Molecular Biology and Evolution.* 29(1): 31-34

inflorescence meristems of tomato." *Planta* 223(4): 646-658.

*Agricultural and Food Chemistry* 50(7): 2005-2009.

SSR." *Theoretical and Applied Genetics* 110(5): 819-831.

procedure." *Theoretical and Applied Genetics* 60(5): 291-296.

tomato and potato genomes." *Genetics* 132(4): 1141-1160.

*Theoretical and Applied Genetics* 92(2): 213-224.

*Academy of Sciences* 108(41): 17052-17057.

Physiology 139(3): 1125-1137.

incompatibilities in *Solanum*: impact of ancestral polymorphism and divergence

ascorbic acid content in three tomato populations." *Plant Physiology* 143(4): 1943-

affecting tomato aroma that was selected against during domestication." *Journal of* 

tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and

characters in an interspecific backcross of tomato — basis of an early screening

between an elite processing line of tomato and its wild relative *L. pimpinellifolium*."

closely related wild tomato species with spatial structure." *Heredity* 107(3): 189-

tomato species using ecological and genetic data." *Proceedings of the National* 

dynamics in farmer-led on-farm conservation." *Genetic Resources and Crop Evolution*

in synthesis of the flavor volatiles 2-phenylethanol and 2-phenylacetaldehyde."

for Metabolomics. Large-Scale Profiling of Tomato Fruit Volatiles." Plant

University, East Lansing.

1953.

319.

199.

58(3): 321-338.

