Identification of microsatellite loci based on BAC sequencing data and their physical mapping into the soft wheat 5B chromosome

Abstract

The shortage of polymorphic markers for the regions of the wheat chromosomes that encode commercially valuable traits determines the need for studying the wheat microsatellite SSR loci. In this work, SSR markers for individual regions of the short arm of soft wheat chromosome 5B (5BS) were designed based on the sequence data obtained from BAC clones, and regions of the corresponding chromosome were saturated with these markers. Totally, 130 randomly selected BAC clones from 5BS library were sequenced using the IonTorrent platform and assembled in contigs using MIRA software. The assembly characteristics (N50 = 4136 bp) are comparable to the recently obtained data for wheat and related species and are acceptable for the identification of the microsatellite loci. The algorithm utilizing the properties of complex decompositions in the sliding-window mode was used to detect DNA sequences with a repeat unit of 2–4 bp. Analysis of 17770 contigs with a total length of 25879921 bp allowed for the design of 113, 79, and 67 microsatellite SSR loci with a repeat unit of 2, 3, and 4 bp, respectively. SSR markers with a motif of 3 bp were tested using nullitetrasomic lines of Chinese Spring wheat homoeologous group 5. In total, 21 markers specific for chromosome 5B were identified. Eight of these markers were mapped into the distal region of this chromosome (bin 5BS6) using a set of Chinese Spring deletion lines for 5BS. Eight and four markers were mapped to the interstitial region (bins 5BS5 and 5BS4, respectively). One marker was mapped to a pericentromeric bin. Comparative analysis of the distribution of trinucleotide microsatellites over wheat chromosome 5B, and in different cereal species, suggests that the (AAG) n repeat proliferates and is conserved during the evolution of cereals.