In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species

Abstract

During the last decade microsatellites or SSRs (simple sequence repeats) have been proven to be the markers of choice in plant genetics research and for breeding purposes because of their hypervariability and ease of detection. However, development of these markers is expensive, labour intensive and time consuming, in particular, if they are being developed from genomic libraries. In the context of large-scale sequencing and genomics programmes in various cereal species at different laboratories, a large set of expressed sequence tags (ESTs) is being generated, which can be used to search for microsatellites. Keeping in view the importance of such type of SSRs, available ESTs of some cereal species like barley, maize, oats, rice, rye and wheat were investigated for a study of abundance, frequency and distribution of various types of microsatellites. SSRs were present in about 7% to 10% of the total ESTs in the investigated cereal genomes. On the basis of surveying EST sequences amounting to 75.2 Mb in barley, 54.7 Mb in maize, 43.9 Mb in rice, 3.7 Mb in rye, 41.6 Mb in sorghum and 37.5 Mb in wheat, the frequency of SSRs was 1/7.5 kb in barley, 1/7.5 kb in maize, 1/6.2 kb in wheat, 1/5.5 kb in rye and sorghum and 1/3.9 kb in rice. The overall average SSR frequency for these species is 1/6.0 kb. Trimeric repeats are the most abundant (54% to 78%) class of microsatellites followed by dimeric repeats (17% to 40%). Among the trimeric repeats the motifs CCG are the most common in all the cases ranging from 32% in wheat to 49% in sorghum. When all these SSRs were analysed for assessing their potential to develop new markers, unique primer pairs could be designed for 30% to 70% of the total non-redundant microsatellites which are up to 3% of total ESTs in the studied species.