Assessment of EST- and genomic microsatellite markers for variety discrimination and genetic diversity studies in wheat

It is likely that in the near future sequence information from sequencing programmes and EST libraries will generate an abundance of genic microsatellite markers. This study is focused on the assessment of their likely impact and performance vis-a-vis their genomic counterparts. Microsatellites from two sources were used to assess the genetic diversity in 56 old and new varieties of bread wheat on the UK Recommended List. A set of 12 microsatellite markers generated from genomic libraries and 20 expressed sequence tag (EST)-derived microsatellites were used in the study, and the performance of both marker sets assessed. The EST-derived or genic microsatellites delivered fingerprints of superior quality, amplifying clear products with few stutter bands. Diversity levels as revealed by genic microsatellites are similar to the few published results. The PIC values for the genic markers were generally lower than those calculated for the genomic microsatellites, though advantages of both marker classes for variety identification applications are discussed.