Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2007;2007:64358.
doi: 10.1155/2007/64358.

Genome Mapping and Molecular Breeding of Tomato

Free PMC article

Genome Mapping and Molecular Breeding of Tomato

Majid R Foolad. Int J Plant Genomics. .
Free PMC article


The cultivated tomato, Lycopersicon esculentum, is the second most consumed vegetable worldwide and a well-studied crop species in terms of genetics, genomics, and breeding. It is one of the earliest crop plants for which a genetic linkage map was constructed, and currently there are several molecular maps based on crosses between the cultivated and various wild species of tomato. The high-density molecular map, developed based on an L. esculentum x L. pennellii cross, includes more than 2200 markers with an average marker distance of less than 1 cM and an average of 750 kbp per cM. Different types of molecular markers such as RFLPs, AFLPs, SSRs, CAPS, RGAs, ESTs, and COSs have been developed and mapped onto the 12 tomato chromosomes. Markers have been used extensively for identification and mapping of genes and QTLs for many biologically and agriculturally important traits and occasionally for germplasm screening, fingerprinting, and marker-assisted breeding. The utility of MAS in tomato breeding has been restricted largely due to limited marker polymorphism within the cultivated species and economical reasons. Also, when used, MAS has been employed mainly for improving simply-inherited traits and not much for improving complex traits. The latter has been due to unavailability of reliable PCR-based markers and problems with linkage drag. Efforts are being made to develop high-throughput markers with greater resolution, including SNPs. The expanding tomato EST database, which currently includes approximately 214 000 sequences, the new microarray DNA chips, and the ongoing sequencing project are expected to aid development of more practical markers. Several BAC libraries have been developed that facilitate map-based cloning of genes and QTLs. Sequencing of the euchromatic portions of the tomato genome is paving the way for comparative and functional analysis of important genes and QTLs.


Figure 1
Figure 1
A linkage map of the 12 tomato chromosomes constructed based on a BC1 population of a cross between L. esculentum breeding line NC84173 and L. hirsutum accession PI126445; the framework map was adapted from [217], however, recently more markers were added to the map. The names of the markers and map distances between them are shown at the right of the chromosomes. The map includes 141 RFLP markers (black color) and 73 resistance gene analogs (RGAs; blue color). The LOD plots at the left of the chromosomes indicate the most likely positions of QTLs for early blight resistance as identified in the BC1 (black curves), BC1S1-1999 (red curves) and BC1S1-2000 (blue curves) populations, as adapted from [242]. The dotted black vertical lines indicates a LOD value of 2.4, a threshold value that the LOD score must cross to allow the presence of a QTL to be inferred. The highest LOD score obtained for each chromosome is shown on the Y-axis. Markers denoted in boxes indicate the approximate locations of QTLs detected for early blight resistance in a selective genotyping study [243]. The approximate locations of disease-resistance genes (R genes) and QTLs (Q), as inferred from published research, are shown at the right of the chromosomes. Descriptions of the R genes and QTLs are as diplayed in Table 2.

Similar articles

See all similar articles

Cited by 58 articles

See all "Cited by" articles


    1. Willcox JK, Catignani GL, Lazarus S. Tomatoes and cardiovascular health. Critical Reviews in Food Science and Nutrition. 2003;43(1):1–18. - PubMed
    1. Rick CM. Hybridization of Crop Plants. Madison, Wis, USA: American Society of Agronomy/Crop Science Society of America; 1980. Tomato; pp. 669–680.
    1. Vinson JA, Hao Y, Su X, Zubik L. Phenol antioxidant quantity and quality in foods: vegetables. Journal of Agricultural and Food Chemistry. 1998;46(9):3630–3634.
    1. Nguyen ML, Schwartz SJ. Lycopene: chemical chemical and biological properties. Food Technology. 1999;53(2):38–45.
    1. Giovannucci E. Tomatoes, tomato-based products, lycopene, and cancer: review of the epidemiologic literature. Journal of the National Cancer Institute. 1999;91(4):317–331. - PubMed

LinkOut - more resources