Development of Sequence-Tagged Site Marker Set for Identification of J, J, and St Sub-genomes of in Wheat Background.

(2 = 6 = 42, JJJJStSt) is one of the important resources for the wheat improvement. So far, a few ()-specific molecular markers have been reported, but the number is far from enough to meet the need of identifying alien fragments in wheat- hybrids. In this study, 5,877,409 contigs were assembled using the genotyping-by-sequencing (GBS) data. We obtained 5,452 non-redundant contigs containing mapped -GBS markers with less than 20% similarity to the wheat genome and developed 2,019 sequence-tagged site (STS) molecular markers. Among the markers designed, 745 -specific markers with amplification products in but not in eight wheat landraces were further selected. The distribution of these markers in different homologous groups of varied from 47 (7/12/28 on 6J/6St/6J) to 183 (54/62/67 on 7J/7St/7J). Furthermore, the effectiveness of these -specific markers was verified using wheat- partial amphidiploids, addition lines, substitution lines, and translocation lines. Markers developed in this study provide a convenient, rapid, reliable, and economical method for identifying chromosomes in wheat. In addition, this set of -specific markers can also be used to estimate genetic and physical locations of chromatin in the introgression lines, thus providing valuable information for follow-up studies such as alien gene mining.