Combining Radiation Hybrids and 45K NimbleGen array to develop High Density Marker Scaffold for D-genome of Chinese Spring and Aegilops tauschii accession AL8/78

Radiation hybrid (RH) mapping, has proven to provide a much higher and more uniform resolution across the whole length of the chromosome as compared to the genetic mapping. In order to construct high-resolution RH-based physical maps of the wheat D-genome chromosomes that integrate the BAC based contigs, we developed D-Genome RH (DGRH₁) panels for Aegilops tauschii accession AL8/78 (1,510 DGRH_1s) and reference hexaploid wheat “Chinese Spring” (2,565 DGRH_1s). The mapping resolution of these RH panels estimated with markers covering known distances was found to be <140kb. Using a set of molecular markers evenly spanning the entire D-genome, a set of most informative lines was selected from both Ae. tauschii-DGRH_1s (423 lines) and Chinese Spring DGRH_1s (430 lines). First generation RH maps based on 178 RH lines and 676 markers (641 DArT and 35 SSR) showed a map ratio of 17:1 (cR/cM) when compared with the genetic maps. A NimbleGen array with ~ 30,000 retro-junction markers and ~15, 000 gene based markers specific to D-genome, was designed. Initially, the array was used to physically map the markers onto individual D-genome chromosomes and 41 deletion bin lines, using available cytogenetic stocks. Now, we have genotyped ~850 RH lines with 45K NimbleGen array and the data has been used to develop a dense marker scaffold for wheat D-genome assembly. This research will also provide valuable resources for wheat map based cloning studies of genes present on the D- genome along with an unprecedented view into the evolution of grass genomes.