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Title: DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum

Author
item KUMAR, AJAY - North Dakota State University
item BASSI, FILIPPO - North Dakota State University
item Gu, Yong
item Dogramaci, Munevver
item Kianian, Shahryar

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/11/2012
Publication Date: 7/27/2012
Citation: Kumar, A., Bassi, F.M., Gu, Y.Q., Dogramaci, M., Kianian, S. 2012. DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum. Biomed Central (BMC) Genomics. doi 10.1186/1471-2164-13-339.

Interpretive Summary: Polyploid bread wheat is one of the most important staple crop worldwide. However, due to its large and complex genome, genetic mapping and map-based cloning of genes controlling agronomically important traits in polyploid wheat remains a challenge for crop improvement. In this work, a novel mapping technology, radiation hybrid (RH) mapping, was developed to generate a high resolution map for the wheat genome. Our results show that RH map provides higher and more uniform resolution than conventional genetic maps. The technique can be applied to other important crops with complex genomes.

Technical Abstract: The uneven distribution of recombination across the length of chromosomes results in inaccurate estimates of genetic to physical distances. In wheat (Triticum aestivum L.) chromosome 3B, it has been estimated that 90% of the cross over occurs in distal sub-telomeric regions representing 40% of the chromosome. Radiation hybrid (RH) mapping which does not relyon recombination is a strategy to map genomes and has been widely employed in animal species and more recently in some plants. RH maps have been proposed to provide i) higher and ii) more uniform resolution than genetic maps, and iii) to be independent of the distribution patterns observed for meiotic recombination. An in vivo RH panel was generated for mapping chromosome 3B of wheat in an attempt to provide a complete physical scaffold for this ~1 Gb segment of the genome and compare the resolution to previous genetic maps. A high density RH map with 541 markers anchored to chromosome 3B spanning a total distance of 1871.9 cR was generated. Detailed comparisons with a genetic map of similar quality confirmed that i) the overall resolution of the RH map was 10.5 folds higher and ii) six folds more uniform. A significant interaction (r=0.879 at p=0.01) was observed between the DNA repair mechanism and the distribution of crossing-over events. This observation could be explained by accepting the possibility that the DNA repair mechanism in somatic cells is affected by the chromatin state in a way similar to the effect that chromatin state has on recombination frequencies in gametic cells. The RH data presented here support for the first time in vivo the hypothesis of noncasual interaction between recombination hot-spots and DNA repair. Further, two major hypotheses are presented on how chromatin compactness could effect the DNA repair mechanism. Since the initial RH application 37 years ago, we were able to show for the first time that the iii) third hypothesis of RH mapping might not be entirely correct.