EST ‐ SSR markers from five sequenced cDNA libraries of common bean ( P haseolus vulgaris L.) comparing three bioinformatic algorithms

Expressed sequence tags ( EST s) are a rich source of SSR sequences, but the proportion of long Class I microsatellites with many repeats vs. short Class II microsatellites with few repeats is an important factor to consider. Class I microsatellites, with more than 20 bp of repeats, tend to make better markers with higher polymorphism. The goal of this study was to determine the frequency of Class I and Class II microsatellites in a collection of over 21 000 EST s from a single study of five different tissues of common bean: two types of leaves, nodules, pods and roots. For this objective, we used three different bioinformatics pipelines: Automated Microsatellite Marker Development ( AMMD ), Batchprimer3 and SSRL ocator. In addition, we determined the frequency of single or multiple SSR s in the assembled EST s, the frequency of perfect and compound repeats and whether Class I microsatellites were mainly di‐nucleotide or tri‐nucleotide motifs with each of the search engines. Primers were designed for a total of 175 microsatellites concentrating on class I microsatellites identified with SSR locator. A few other microsatellites were included from the other search engines, AMMD and Batchprimer3 programs so as to have a representative set of class II markers for comparison sake. The comparison of 95 class I vs. 80 class II markers confirmed that the Class I were more polymorphic and therefore more useful.