We describe the physical and genetic analysis of two gene-rich recombination hot spots that lie on homoeologous regions of chromosomes 5A and 5B in wheat. Chromosome group 5 deletion lines were used to physically map markers within the targeted intervals. The targeted deletion interval on 5A accounts for less than 1% of the long arm and contains the Q gene. The targeted interval on 5B accounts for 4% of the long arm. DNA markers were targeted to the 5B segment using comparative mapping of anonymous RFLP clones and to the 5A segment using comparative mapping, mRNA differential display, and AFLP analysis. Genetic linkage maps of the regions were constructed using segregating populations derived from Triticum dicoccoides disomic substitutions of chromosomes 5A and 5B into Chinese Spring wheat. The level of recombination within the deletion intervals on chromosomes 5A and 5B was 18- and 22-fold greater, respectively, than that estimated for the whole genome. Estimates of physical to genetic distances were 250 kb/cM and 200 kb/cM for the regions of 5A and 5B, respectively. These data suggest that a unique level of chromatin organization exists within the hot spot regions, and the characteristics of the regions appear to be conserved throughout the evolution of the Triticeae. The Q gene is one of the most important genes involved in the domestication of bread wheat because it controls the squareheaded phenotype and free-threshing characteristics. The strategy of using AFLPs and differential display on the 5A deletion lines for targeting markers to the Q locus proved to be effective. The Q locus is flanked by an AFLP-derived DNA marker linked 2.4 cM on the proximal side and the deletion breakpoint on the distal side. Strategies and implications for cloning the Q gene are discussed.
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