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Open Access Research article

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

Ajay Kumar1, Filippo M Bassi1, Etienne Paux2, Omar Al-Azzam3, Monika Michalak de Jimenez1, Anne M Denton3, Yong Q Gu4, Eric Huttner5, Andrzej Kilian5, Sachin Kumar6, Aakash Goyal6, Muhammad J Iqbal1, Vijay K Tiwari7, Munevver Dogramaci8, Harindra S Balyan6, Harcharan S Dhaliwal9, Pushpendra K Gupta6, Gursharn S Randhawa10, Catherine Feuillet2, Wojciech P Pawlowski11 and Shahryar F Kianian1*

Author Affiliations

1 Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA

2 INRA-UBP 1095, Genetics Diversity and Ecophysiology of Cereals, Clermont-Ferrand, 63100, France

3 Department of Computer Science, North Dakota State University, Fargo, ND, 58102, USA

4 USDA-ARS, Western Regional Research Center, Albany, CA, 94710, USA

5 Diversity Arrays Technology Pty Ltd, Yarralumla, ACT, 2600, Australia

6 Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 25004, India

7 Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA

8 USDA-ARS, Biosciences Research Laboratory, Fargo, ND, 58102, USA

9 Akal School of Biotechnology, Eternal University, Baru Sahib, 173101, India

10 Department of Biotechnology, Indian Institute of Technology, Roorkee, 247667, India

11 Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA

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BMC Genomics 2012, 13:339  doi:10.1186/1471-2164-13-339

Published: 24 July 2012

Abstract

Background

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 events occur in distal sub-telomeric regions representing 40% of the chromosome. Radiation hybrid (RH) mapping which does not rely on 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 scaffold for this ~1 Gb segment of the genome and compare the resolution to previous genetic maps.

Results

A high density RH map with 541 marker loci 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 fold higher and ii) six fold 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.

Conclusions

The RH data presented here support for the first time in vivo the hypothesis of non-casual interaction between recombination hot-spots and DNA repair. Further, two major hypotheses are presented on how chromatin compactness could affect 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.

Keywords:
Non homologous end joining; Physical mapping; Gamma radiation; Deletion mutant; Chromatin; Wheat chromosome 3B; Radiation hybrid