Analysis of microsatellites in major crops assessed by computational and experimental approaches

Over 85Mb publicly available expressed sequence tags (ESTs) from four agronomically important crops were used to search for the types and frequencies of simple sequence repeats (SSRs) with motif length of 1-6bp. The frequency of EST-SSRs was one in 11.81kb in rice, 17.42kb in wheat, 23.80kb in soybean, and 28.32kb in maize, respectively. Trinucleotide repeats were the most abundant SSR types with up to 47 trinucleotide repeat units in 100kb ESTs. Compared with dicots, monocots contained GC-rich tri- and hexa-motifs, especially rice where 23.6 CCG motif occurred in 100kb ESTs. 597 EST-SSR primer pairs were designed for wheat, of which, 478 primer pairs had successful PCR amplifications. The percentage of polymorphism was up to 41.8% among wheat varieties, that could be used to construct a transcriptional map of wheat. Cross-species amplification was detected. Among the 478 functional primers from wheat, 255 EST-SSRs amplified fragments in rice, maize and soybean way, indicating high degree of transferability between species, that facilitate comparative mapping and homologous gene cloning.