Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat

In hexaploid wheat (Triticum aestivum L.) (AABBDD, C = 17000 Mb), repeat DNA accounts for ∼90% of the genome, of which transposable elements (TEs) constitute 60%-80%. Despite the dynamic evolution of TEs, our previous study indicated that the majority of TEs are conserved and collinear between the homologous wheat genomes, based on identical insertion patterns. In this study, we exploited the unique and abundant TE insertion junction regions identified from diploid Aegilops tauschii to develop genome-specific repeat DNA junction markers (RJM) for use in hexaploid wheat. In this study, both BAC end and random shotgun sequences were used to search for RJM. Of the 300 RJM primer pairs tested, 269 (90%) amplified single bands from diploid Ae. tauschii. Of these 269 primer pairs, 260 (97%) amplified hexaploid wheat and 9 (3%) amplified Ae. tauschii only. Among the RJM primers that amplified hexaploid wheat, 88% were successfully assigned to individual chromosomes of the hexaploid D genome. Among the 38 RJM primers mapped on chromosome 6D, 31 (82%) were unambiguously mapped to delineated bins of the chromosome using various wheat deletion lines. Our results suggest that the unique RJM derived from the diploid D genome could facilitate genetic, physical, and radiation mapping of the hexaploid wheat D genome.