Construction of High Density Radiation Hybrid Map of Bread Wheat Chromosome 4A

Bread wheat (Triticum aestivum) has large (17 Gb) and complex allohexaploid genome with high proportion (80%) of repetitive sequences. The complex nature prevents assembly of reference genome sequence from shot-gun sequence reads. To facilitate this work, genome complexity needs to be decreased and additional information regarding its structural organization is necessary. Construction of chromosome-specific physical maps has been an important step to decrease genome complexity and allowed division of labor among different laboratories (www.wheatgenome.org). Subsequent steps involve orientation and anchoring of physical maps along the chromosomes using suitable markers. However, classical recombination maps provide insufficient resolution, including massive marker clustering due to uneven crossover distribution along chromosomes. In contrast, genome maps developed using radiation hybrid (RH) panels do not rely on natural recombination and offer high and uniform resolution. We have constructed endosperm RH panel of 1,100 lines for wheat chromosome 4A. 119 most informative RH lines along with chromosome 4A deletion lines and a set of controls were genotyped using wheat 90k-SNP-Infinium chip.  81,587 reliable marker calls, out of which 2,698 were specific for chromosome 4A, were acquired and used for RH map construction. 2,683 markers were mapped to the deletion lines and identified 19 bins, out of them two identified for the first time. The chromosome deletion and RH maps will be used to anchor physical map of chromosome 4A. This work has been supported by the Czech Science Foundation (GA14-07164S), Czech Ministry of Education (LO1204) and Internal Grant Agency of Palacky University (PrF-2014-001).