Development and Application of EST-STS Markers Specific to Chromosome 1RS of Secale cereale

Molecular markers are important tools that have been used to identify the short arm of rye chromosome 1R (1RS) which contains many useful genes introgressed into wheat background. Wheat expressed sequence tag (EST) sequences are valuable for developing molecular markers since ESTs are derived from gene transcripts and more likely to be conserved between wheat and its relative species. In the present study, 35 sequence-tagged site (STS) primers were designed based on EST sequences distributed on homology group 1 chromosomes of Triticum aestivum and used to screen specific markers for chromosome 1RS of Secale cereale. Two primer pairs different from the early studies, STS WE3, which amplified a 1680-bp and a 1750-bp fragment, and STS WE126, which produced a 850-bp fragment from rye genome, were proved to be specific to chromosome 1RS since the corresponding fragments were only amplified from 1R chromosome addition line and wheat-rye lines with chromosome 1RS, but not from wheat-rye 2R-7R chromosome addition lines and the other lines lacking chromosome 1RS. Eleven wheat-rye lines derived from ‘Xiaoyan 6’ and ‘German White’ were used to test the presence of specific markers for 1RS. The specific fragments of 1RS were amplified in 4 wheat-rye lines, but not in the other lines. The testing results using EST-STS markers of 1RS were consistent with those obtained from fluorescence in situ hybridization (FISH), suggesting that these markers specific to 1RS could be used in marker-assisted selection (MAS) for incorporating 1RS into wheat cultivars in breeding.