DNA polymorphism among 18 species of Triticum-Aegilops complex using wheat EST-SSRs

Abstract

PCR primers were designed for 78 expressed sequence tag-simple sequence repeats (EST-SSRs), which represented a subset of over 800 SSRs that were located by us in wheat EST database. When tested for functionality on several varieties of common wheat (Triticum aestivum) including Chinese Spring, 64 of these 78 primer pairs were found to be functional. These 64 functional primer pairs were used for a study of transferability and polymorphism among 18 Triticeae species belonging to Triticum-Aegilops complex. These species had as many as seven genomes in their constitution and represented three ploidy levels (2x, 4x, 6x). The primer pairs each gave amplified products not only in progenitor species containing A, B (including S and G) and D genomes, but also in alien species that contained other genomes (M, N, C and U). The cross-species transferability was as high as 84%, and the fragments of expected size were available with 92% EST-SSR primers in one or more species. This suggested a high level of conservation of DNA sequences belonging to the transcribed portion of the genome, and also indicated that each wheat EST-SSR is perhaps derived from an SSR in an ancestral genome of Triticeae. A very high proportion (88%) of the above 92% EST-SSRs, which gave amplified fragments of expected size, detected polymorphism. The number of alleles ranged from 2 to 14 with an average of 6.8 alleles per locus. A number of EST-SSR primers also proved useful in discriminating different genera, species within a particular genus and the different genomes of the tribe Triticeae. Therefore, EST-SSRs may be used in studies on polymorphism, genetic diversity, gene mapping and synteny conservation across different species of Triticeae. This is in sharp contrast to the situation with genomic SSRs, which are more locus specific.