Long tomato microsatellites are predominantly associated with centromeric regions

Area of Science:

• Plant genetics
• Molecular biology
• Genomics

Background:

• Microsatellites are crucial genetic markers in crop plants, requiring high polymorphism and even genome distribution.
• Previous research indicated GATA microsatellites in tomato are concentrated near centromeres.

Purpose of the Study:

• To isolate and characterize tomato microsatellites with long arrays of GA, GT, AT, and GATA motifs.
• To assess the variability of these microsatellites within *Lycopersicon esculentum* varieties.
• To map these microsatellites onto the tomato genetic map to understand their distribution.

Main Methods:

• Isolation of tomato microsatellites with long arrays (>20 repeats) of specific dinucleotide and tetranucleotide motifs.
• Assessment of microsatellite polymorphism (allele number) across diverse *Lycopersicon esculentum* lines.
• Genetic mapping of isolated microsatellites onto the established tomato genetic map.

Main Results:

• Microsatellite markers showed 1-5 alleles in tested *L. esculentum* varieties.
• Mapping confirmed GATA microsatellites are clustered around tomato centromeres.
• Long dinucleotide microsatellites (GA, GT, AT) were also found to be highly clustered in centromeric regions.

Conclusions:

• The centromeric clustering of long dinucleotide and GATA microsatellites complicates their use for whole-genome genetic mapping in tomato.
• Microsatellites with shorter repeat arrays may be more appropriate for broad genetic mapping despite lower polymorphism.
• The identified microsatellite markers could be valuable for studying tomato centromeric regions and for cultivar identification.