Marker-Assisted Selection in Tomato Breeding

Abstract

The cultivated tomato, Solanum lycopersicum L., is the second most consumed vegetable crop after potato and unquestionably the most popular garden crop in the world. There are more varieties of tomato sold worldwide than any other vegetable crop. Most of the commercial cultivars of tomato have been developed through phenotypic selection and traditional breeding. However, with the advent of molecular markers and marker-assisted selection (MAS) technology, tomato genetics and breeding research has entered into a new and exciting era. Molecular markers have been used extensively for genetic mapping as well as identification and characterization of genes and QTLs for many agriculturally important traits in tomato, including disease and insect resistance, abiotic stress tolerance, and flower- and fruit-related characteristics. The technology also has been utilized for marker-assisted breeding for several economically important traits, in particular disease resistance. However, the extent to which MAS has been employed in public and private tomato breeding programs has not been clearly determined. The objectives of this study were to review the publically-available molecular markers for major disease resistance traits in tomato and assess their current and potential use in public and private tomato breeding programs. A review of the literature indicated that although markers have been identified for most disease resistance traits in tomato, not all of them have been verified or are readily applicable in breeding programs. For example, many markers are not validated across tomato genotypes or are not polymorphic within tomato breeding populations, thus greatly reducing their utility in crop improvement programs. However, there seems to be a considerable use of markers, particularly in the private sector, for various purposes, including testing hybrid purity, screening breeding populations for disease resistance, and marker assisted backcross breeding. Here we provide a summary of molecular markers available for major disease resistance traits in tomato and discuss their actual use in tomato breeding programs. It appears that many of the available markers may need to be further refined or examined for trait association and presence of polymorphism in breeding populations. However, with the recent advances in tomato genome and transcriptome sequencing, it is becoming increasingly possible to develop new and more informative PCR-based markers, including single nucleotide polymorphisms (SNPs), to further facilitate the use of markers in tomato breeding. It is also expected that more markers will become available via the emerging technology of genotyping by sequencing (GBS).