Tomato microsatellite marker development: allelic diversity and genetic map position

Tatiana Areshchenkova and Martin W. Ganal

Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany

Genetic linkage maps and their associated technologies have been used successfully for a number of applications in plant breeding and genetics including characterization of genetic variation in germplasm collections, gene tagging, map-based gene cloning, and analysis of quantitative traits. Microsatellites or simple sequence repeats based on repeating units of 2-4 bp are the DNA markers of choice in mammalian systems, and are becoming more important in plant systems. The advantages for their usability as molecular markers are that they are codominant and as a PCR-based technique amenable to automatization. Most importantly, microsatellites markers are a multiallelic system that detects a much higher level of DNA polymorphism that any other marker system. Cultivated tomato is well known for its low level of DNA polymorphism. Because of this, highly polymorphic markers are required for mapping and genome analysis within Lycopersicon esculentum. Tomato microsatellites containing long arrays (>20 repeating units) of GA, GT, TA and GATA motives isolated from tomato genomic libraries were assessed for their variability within L. esculentum varieties and mapped onto a genetic map of tomato. The investigated microsatellite markers exhibited up to 5 alleles in a diverse set of L. esculentum lines. Mapping of the microsatellites onto the genetic map of tomato demonstrates that, as previously shown, GATA microsatellites are highly clustered in the region of the tomato centromeres. Interestingly, the same centromeric location was now found for long dinucleotide microsatellite markers. Because of this uneven distribution, genetic mapping of the entire tomato genome using long microsatellites will be very difficult to achieve but some microsatellite markers might provide a useful tool to study the molecular structure of tomato centromeres and for variety identification.