Mapping of new microsatellite loci derived from ESTs in durum wheat

Use of molecular markers in genome analysis, the systematic mapping of agricultural important traits, and marker-assisted selection have been greatly advanced by the development of reliable PCR-based markers. Over the past decade microsatellites or simple sequence repeats, (SSRs) have attracted considerable attention of researchers. The overall frequency of microsatellites among species was found inversely related to genome size and to the proportion of repetitive DNA but remained constant in the transcribed portion of the genomes. Bioinformatic analysis indicated that the frequency of microsatellites was significantly higher in ESTs than in genomic DNA across all species. Many of the ESTs have been sequenced as an alternative to complete genome sequencing and this creates a formidable resource for microsatellite marker development. The objective of this study was to construct a high density EST- derived SSR chromosome map in durum wheat. A total of 1100 new EST-derived SSRs were screened among two durum wheat cultivars Ciccio and Svevo parents of a RIL mapping population. A total of 124 EST-SSR loci amplified from 100 primer sets were distributed over the 14 chromosomes of A and B genomes. Multiple loci were detected by 19 EST-SSR markers and the highest number of loci was produced by CA594434-462 with 4 loci mapped to the non-homologous groups. The co-localization of separate PCR fragments detected by one couple of primer to the same chromosome region was found and this could be due to duplication of genetic material. Good colinearity was observed among the homoeologous chromosomes. The distribution of microsatellites among seven homologous groups was not random rich gene islands were identified on chromosomes 6A, 6B, 1A and 7B.