PLS221: TOMATO (2nd part)


Besides morphological markers, many of which are available in tomato and have been quite useful in the past, isozyme and DNA-based markers are extensively developed in this crop. Among DNA-based markers, we have practically all the existing assortment of these, including RFLPs, RAPDs, microsatellites, AFLPs, SCAR, COS, CAPs and SNPs among few others. I will describe each of these briefly as a review.

Allozyme markers:

These emerged at least 35 years ago as a set of extremely useful markers. Work on this area was initiated by Rick and his group in 1973. The original objective of the program was to study the genetic relationships among the cultivated tomato and its wild species, in order to provide information on possible centers of domestication of this crop.

RFLP markers:

This technique have been available for approximately 25 years, picked from the tool box of molecular geneticists. In brief, it consist in extracting total DNA from a plant, shearing it with a set of specialized enzymes called restriction endonucleases, and separating the DNA fragments by electrophoresis.

Probes have been developed from genomic and cDNA libraries.

PCR based markers:





COS markers (Conserved orthologs set, based on A. thaliana)

CAP (cleveage amplified polymorphism)

Current tomato maps markers and other resources available at the (Solanacea Genomics Network) ; International Tomato Sequencing Project; Lycopersicon Genomic Resources

Application of molecular markers in the tomato:

I will mention just a few applications:

1) Tagging useful genes for marker assisted selection:

Nematode resistance, Mi

Tobacco mosaic virus,

Other disease resistance genes tagged with markers include, cladosporium (Cf-2 to 9, Some of these genes have been cloned), Verticillium (Ve), Fusarium (loci I1 and I3), tomato spotted wilt virus (Sw5), Pseudomonas resistance gene (Pto), that has also been cloned, Xanthomonas resistance and powdery mildew resistance (Lv) and a few others.

Other useful linkages are markers to male sterility. Prx-2 and the male sterility gene ms-10 on chromosome 2 are at 1.5cM.  In hybrid seed production operations.

Markers have been developed for sucrose accumulation based on primers of the invertase gene, responsible for this process in L. hirsutum and other green fruited species (Hadas et al. 1995).

Markers and QTL have been identified for fruit shape, seed weight and ripening, resistance to late blight (Doganlar et al. 2000a & b, Ku et al. 1999).

2) Seed purity determinations.

It is important to seed companies to be able to detect parental plants that may be contaminating F1 hybrid seed due to accidental selfings. The enzyme Adh is particularly useful for this application. Also it is possible to perform this test with some RFLP and PCR-based markers, including RAPD markers (Paran et al. 1995, Rom et al. 1995).

Related to this activity is fingerprinting or variety identification. This can be accomplished readily with GACA microsatellites and a few other PCR- based markers.

3) Speeding up introgression of useful genes from exotic germplasm:

4) Detection of genes controlling quantitative traits:(see Tanksley et al. 1982, Heredity 49:11).

Molecular markers can be used to estimate how many genes control a quantitative trait and their organization and distribution on the chromosomes. This procedure has been used in tomato for traits such as cold tolerance, fruit weight, stigma exertion, content of 2-tri-decadone, an antibiotic compound responsible for insect resistance and soluble solids, among others.

5) Map-based gene cloning: Recent efforts have been focused to map-based or positional cloning of genes of importance such as disease resistance genes among others, such as QTL for fruit size and sugar content.

The role of wild relatives in tomato improvement

Tomato Genetics Stock Center

Classically, the Lycopersicon species are divided into two major complexes according to fruit color: subgenus Eulycopersicon for red-fruited and Eriopersicon for green fruited ssp. These are also classified by their hybridization affinity to cultivated tomato into two main complexes, esculentum and peruvianum complex. You can learn more about each species by clicking these two sites.

The Lycopersicon species:

A) RED FRUITED SPECIES: (Eulycopersicon) Self-compatibility reaction.

L.esculentum SC (S. lycopersicon)

L. esculentum var cerasiforme (Red Cherry) SC

L. pimpinellifolium SC (S. pimpinellifolium)

L. cheesmanii form typicum SC (S. chessmaniae)

L. cheesmanii form minor SC (S. galapagence)


L. peruvianum , races glandulosum, dentatum, humifusum SI* (S.corneliomullerii, S. arcanum, S. huaylasense, S. peruvianum)

L. chilense SI ( S. chilense)

L. hirsutum form typicum SI (S. habrochaites)

L. hirsutum form glabratum SC

L. parviflorum SC (S. neorickii)

L. chmielewskii SC ( S. chemieleskii)

L. pennellii SI/SC (S. pennellii)

Solanum species related to Lycopersicon:

S. lycopersicoides SI

S. ochrantum SI

S. sitiens SI

*one SC accession found for these species

Muller 1940 published one of the first modern taxonomic treatments of Lycopersicon. This work was revised by Luckwill three years later. At that time six species and six subspecies were recognized. Based on crossing relationships, Rick established a total of nine species. The center of distribution of the genus is in the Andes, which spreads from Ecuador to the North, Chile to the South, the Galapagos Islands to the West and to the Eastern side of the Andes to the East.

Recently the taxonomic genus have been totally revised by Spooner and reclassified it as Solanum recognizing 13 species based on chloroplast and nuclear molecular markers to lump them to Solanum and morphological descriptors to name the species. Some of the species names have been changed and a few botanical forms or varieties have been elevated to species in spite of not being reproductively isolated. For example the two forms of L. hirsutum, typicum and glabratum, in spite of having insipient reproductive barriers including unilateral incompatibility, are not distinguished in the new system as forms or subspecies. On the other hand, the two forms of L. cheesmanii, which differ only morphologically for a few traits and are fully interfertile, are recognized in the new system as two different species.

With very few exceptions, most of the wild species are outcrossers, in contrast to the cultivated tomato, which is a selfer. There are many species of wild bees which are responsible for the pollination of the tomato species in their native habitat.

 The range of the cultivated tomato L. esculentum is the widest of all the species, discounting modern cultivars and later introductions. For example primitive cultivars including the cherry tomato , var. cerasiforme are found in a wide distribution range, from Peru to Mexico.


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L. peruvianum (old classification) include more than one species. This species has been now separated into four species, S.corneliomullerii, S. arcanum, S. huaylasense, S. peruvianum. L. chilense, which is found in northern Chile. This species might be a good source of drought resistance because of its extensive root system able to reach very deep into the water table. L. peruvianum is an important source of virus and nematode resistance.

Level of DNA polymorphism within accessions and species is highly correlated with mating system. The self incompatible (SI) species are 10 fold more variable than the SC species.

Zuriaga et al (2009) has reported the most recent phylogenetic treatment of the species in the section Lycopersicon based on AFLP and nuclear sequences CT179 and CT66. They failed to distinguish S. corneliomulleri from S. peruvianum. Otherwise the species relationships is very similar to that reported by Nesbitt and Tanksley (2002).

Cytogenetics of species hybrids

Hybrids between tomato and the colored fruited species classified under the subgenus Eulycopersicon behave like intraspecific tomato hybrids (Rick and Butler 1956). No evidence of chromosomal differentiation has been observed among these species.

Rick (1969) pioneered the use of controlled introgression to create chromosome substitution lines between L. pennellii and L. esculentum. This work has been now extended using molecular markers.

Hybrids between tomato and L. peruvianum are difficult to obtain due to breakdown of the endosperm. Embryo rescue and culture in vitro is necessary to obtain these hybrids. When tetraploid L. esculentum is crossed to diploid L. peruvianum, normal endosperm development takes place, resulting in fertile seeds able to germinate without special aids. The resulting hybrids are sesquidiploids, having two chromosome sets of L. esculentum and one of L. peruvianum.

Intergeneric hybrids: Rick (1951) was the first to obtain L. esculentum x S. lycopersicoides hybrids, which required embryo rescue from 30 day old fruits. Chromosome pairs in the diploid hybrid ranged from 8 to 24 with an average of 14.8.

Recent work by Ji and Chetelat (TAG 106:979-89, 2003) working with addition and substitution lines demonstrate that S. lycopersicoides chromosomes are homoeologous to Lycopersicon chromosomes. This was based on observation of preferential chromosome pairing and reduced recombination. Chromosome arm 10L in S. lycopersicoides differs by its tomato counterpart by an inversion, which is also present in potato.

The EEL sesquidiploid served also as a bridge by crossing it to S. sitiens for producing esc x sitiens hybrids.

Somatic hybridization:

In contrast to the progress attained in tomato by interspecific and intergeneric sexual hybridizations, little progress has been made through somatic hybridization. 

Transformation techniques

Available in tomatoes, by leaf disk and cotyledon co-cultivation with Agrobacterium. Several research groups have developed transgenic tomato plants carrying potentially useful genes, such as herbicide and insect resistance. For insect resistance, plants were transformed with a gene synthesizing a lepidopteran specific insect control protein from Bacillus thurigensis (Bt gene). In field tests plants were resistant to tobacco hornworm, fruitworm (Heliothis) and pin worm (Keiferia).

The antisense technology is quite developed in tomato for longer fruit shelve life. This was the basis for developing Calgene's Flavr-Savr tomatoes.

Mechanisms for controlling pollination

Most current tomato varieties are F1 hybrids, all are produced by hand emasculation and pollination. However, there is the potential to use natural control mechanisms for pollination in hybrid seed production. These are male sterility and self-incompatibility.

Male sterility:

There are over 50 male sterile spontaneous mutants in tomato. They are all determined by nuclear genes, therefore, there is no cytoplasmic male sterility (cms) in tomato. 

Self-incompatibility (SI) and unilateral incompatibility (UI).

Autogamy and allogamy are both found among the tomato species. Autogamous species a have inserted stigmata, which is most extreme in modern tomato varieties, whereas in allogamous species, most of which are self-incompatible, have exerted stigmata. Chen and Tanksley (2005) found that level of stigma exertion is determined by a single QTL which consists of 5 closely linked genes determining anther and stigma length.

Self-incompatibility (SI): It is an strategy developed by some plant species to prevent self-fertilization. The operating system of self-incompatibility in Lycopersicon is the gametophytic system. In this case, tube growth is arrested in the style in incompatible reactions. The specificity of the reaction is due to S-RNAses expressed in the style degrading incompatible pollen tubes.

Types of S alleles in Lycopersicon: Self incompatible S1 to  n, self compatible: SP and Se
Allelic interactions: SP> S1=S2....=Sn>Se

Thus self compatibility can be dominant (SP) or recessive (Se) to SI.

The table below summarizes the crosses that succeed and those than fail depending on which species is used as female parent.

Successful cross

Unsuccessful cross

SeSe (female) x S1S2(male)

S1S2 (female) x  SeSe(male) 

SeSe(female) x SPSP(male)

SPSP(female) x SeSe (male)

SPSP (female) x S1S2 (male)


S1S2 (female) x SPSP (male)


Thus, when analyzing expected phenotypes and genotypes from SI x SC crosses, UI must be also considered.
Unilateral incompatibility (UI) genes for L. pennellii has been mapped on chromosomes 1, 6 and 10. On chromosome 1, the gene is quite close to or on the S locus. This confirms the presumption that SI and UI are associated. UI seems controlled by an interaction between expression at the S locus and other genes (Chetelat et al. 1991).

Research Perspectives

The future for tomato research is bright, considering that its genome will be sequenced to completion soon. It has now extensive genomic resources, such as well mapped chromosomes, markers, ESTs, microarrays, cytogenetic stocks and many others. The advent of recombinant DNA and its application to the tomato has resulted in important developments, which will have implications in the future of tomato breeding.

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Last Modified: April 1, 2010
Carlos F Quiros, 1998