Assessing the potential for polymorphism detection across different cereals using EST-SSR primer pairs developed from sorghum and pearl millet

Abstract

An expressed sequence tag (EST) is a short sub-sequence of a transcribed nucleotide sequence. ESTs represent portions of expressed genes. They may be used to identify gene transcripts, which lead to prediction of their protein product, and eventually to determination of their function. Thus ESTs are instrumental in gene discovery and gene sequence determination. ESTs from several species can be used in the analysis of both structural and functional relationships in these genomes. Simple sequence repeats (SSRs) or microsatellites are ubiquitous in eukaryotic genomes. SSRs are composed of tandernly repeated 1-6 bp units. SSRs are valued because of their abundance, variation, wide distribution within the genome, multi-allelic nature and co-dominant inheritance. The presence of SSRs in the transcripts of genes suggests that they may have a role in gene expression or function. SSR markers extended to the transcribed part of the genome are called Expressed Sequence Tag derived SSRs. Since a putative function based on their corresponding ESTs can be deduced for such EST-SSRs, they represent a class of functional markers. These sequences can be used to provide an estimate of diversity in the expressed portion of the genome and may be useful for comparative mapping, for tagging important traits of interest, and for additional map-based cloning of important genes. Because these are from the transcribed part of the genome ESTSSRs are often conserved across species and also across related genera in Poaceae. Thus once primers for EST-SSR markers have been developed, these may be used across a number of-related species and may actually prove superior to SSR markers extracted from genomic libraries for diversity estimation, transferability, and comparative mapping. Even though the polymorphism between the species is less using the ESTSSR primer pairs, once developed they can be used across the species for gene diversity, and comparative mapping studies with fewer inputs