Solving the Puzzle of Barley Genomic Sequences By Radiation Hybrid Mapping.

The large genome size (5.1 Gb) and high portion of the repetitive sequences (84%) complicate the assembly of barley genome sequence. To completely assemble the genome, a high resolution map is required for anchoring the repetitive sequences to the chromosomal regions. However, available barley genetic maps do not provide much information for almost half of the genome that is located in the recombination-poor regions. An alternative to the conventional genetic maps is radiation hybrid (RH) mapping. In this method radiation is used to induce random chromosomal deletions along the chromosomes. The irradiated genome is then rescued by infusing it into a host cell. Subsequently, the developed population (RH panel) is genotyped and markers are mapped based on co-retention frequency in the panel. In this study, we irradiated ~1000 seeds of ‘Chinese Spring’ (CS) wheat (Triticum aestivum) addition lines carrying barley (Hordeum vulgare L.) chromosome 3H. About 300 of the irradiated lines survived and were crossed to CS to develop ~1000 RH lines. We tested the RH panel by genotyping ~400 lines with 35 EST markers. We subsequently, generated an RH map and were able to anchor several contigs to the map. To utilize the developed RH panel in a high throughput genotyping system, 68,451 repeat junction markers (RJMs) were designed using 1.82 Gb of the barley chromosome 3H survey sequencing data. These markers are ~92% barley-specific and are not interfered by the background wheat genome. The map generated in this study is the first RH of barley and indicates the potential use of RH maps in assembly of the sequences and developing a complete sequence of the barley genome.