Development of new SSR markers for homoeologous WFZP gene loci based on the study of the structure and location of microsatellites in gene-rich regions of chromosomes 2AS, 2BS, and 2DS in bread wheat

Abstract

Microsatellites, or simple sequence repeats, are widely distributed in eukaryotic genomes, including plant genomes. The peculiarities of the structure and location of the microsatellite loci determine their potential as molecular genetic markers and can influence the assumed function of microsatellites in important biological processes. The identification and study of the distribution of microsatellite loci in gene-rich genome regions of the bread wheat and the development (based on them) of new microsatellite markers are of practical interest and are important for the study of the organization of the bread wheat genome. The sequences of BAC clones that contain the homoeologous WFZP genes of the bread wheat (Triticum aestivum L.) controlling the development of the ear were the basis for the identification and localization of microsatellite loci in gene-rich regions of the 2AS, 2BS, and 2DS chromosomes. Diand trinucleotide microsatellite repeats are the most widespread in the studied sequences. The AG and GA/TC motifs prevail among the dinucleotide motifs; the dinucleotide repeats are found in noncoding gene regions, mobile elements, and nonannotated DNA sequences. Most of the trinucleotide repeats are associated with mobile genetic elements. It was found that homoeologous microsatellite loci are located either in the genes or in the nonannotated DNA sequences. The comparison of the structure of homoeologous loci demonstrated that the divergence in them is associated both with a change in the number of repeats and with nucleotide substitutions. The new microsatellite markers, which are colocalized in the genetic maps with the WFZP-A-B-D genes and can be used for marking these genes in molecular genetic studies and in breeding controlled by markers, were developed.