AUTHOR=Qiao Linyi , Liu Shujuan , Li Jianbo , Li Shijiao , Yu Zhihui , Liu Cheng , Li Xin , Liu Jing , Ren Yongkang , Zhang Peng , Zhang Xiaojun , Yang Zujun , Chang Zhijian 

TITLE=Development of Sequence-Tagged Site Marker Set for Identification of J, JS, and St Sub-genomes of Thinopyrum intermedium in Wheat Background

JOURNAL=Frontiers in Plant Science

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2021.685216

DOI=10.3389/fpls.2021.685216

ISSN=1664-462X

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