Comparative genomic studies among wheat genomes

Wheat is very important crop and has a complex genome; because of its homologeous genes, which locate on homologous chromosomes and belong to homologous genomes. The present study suggested new tools to compare between wheat genomes through its entire expressed sequence tags derived microsatalites (eSSR). This method is easier, cheaper and more effective tool to discover some sequences of the transcriptome through the genomic DNA. Using supported and advanced genetic tools such as; sequencing and bioinformatics analyses helped us to develop this study. Because of the interaction between wheat ancestors, it was necessary to find out whether our genes are orthologous or paralogous .genes. The used samples were belonged to three levels of ploidy (diploid, tetraploid and hexaploid). Eight primers of EST -SSR were used according to different types of motifs (di -, tri- and tetra-) nucleotides. Although our results were detected low percentage of polymorphism (26.7%), this represented in three loci (CFE14, CFE16 and CFE41) of the eSSR primers. This percentage was satisfactory because it is associated with transcribed regions. Through the sequencing and alignment analyses, the eSSR(CFEI4) was alignment with one of the HMW-glutenin genes in geneome A. In respect to the importance of glutetin genes, five specific primers of HMW (HMWDxl,2, HMWSx and HMWy) and LMW (LMW7,8 and LMWS 1) were used to amplify glutenin genes to follow up any differences between the different genomes. Subunit x of HMW -Gs failed to detect differences, while subunit y didnt amplified and also the gene expression had been suppressed in each of; the diploid samples of genome A, and tetraploid individuals while it appeared in diploid samples of genome B and the individuals of hexaploid genome. In contrast, primers LMW7,8 and LMWSI showed variations among the genomes. The glutenin gene of B genome that amplified by primer HMWDxl,2 inserted into vector PMD I 8T, and then sequenced and analyzed by the bioinformatics tools to predict the translated protein. The multiple alignment analysis between the predicted protein and other 18 HMW -GS proved that, the protein prediction is true and the cloned gene is noval one. The qualitative analysis of gene expression of HMW genes was studied by the SDS-PAGE, which was more effective approach to detect variations between species and within species. Due to the absence of y subunits of the HMW glutenin gene in some used wheat species the protein patterns of y subunits also were not expressed at the same species, its expression was silent. Moreover, the results of SDS-PAGE showed that, the absence or presence of GluAl allele was responsible for the clustering of different cultivars between and within species