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

Ajay Kumar, Filippo M. Bassi, Etienne Paux, Omar Al-Azzam, Monika M. de Jimenez, Anne M. Denton, Yong Q. Gu, Eric Huttner, Andrzej Kilian, Sachin Kumar, Aakash Goyal, Muhammad J. Iqbal, Vijay K. Tiwari, Munevver Dogramaci, Harindra S. Balyan, Harcharan S. Dhaliwal, Pushpendra K. Gupta, Gursharn S. Randhawa, Catherine Feuillet, Wojciech P. PawlowskiShahryar F. Kianian

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18 Scopus citations

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.

Original languageEnglish (US)
Article number339
JournalBMC Genomics
Volume13
Issue number1
DOIs
StatePublished - Jul 24 2012

Bibliographical note

Funding Information:
The authors wish to thank Justin Hegstad and Allen Peckrul for assistance in the development of RH panel and capable technical support throughout the research; Dr. Matthew Hayden (VABC, Melbourne, AUS) for precious contributions in designing the DEASY control marker; Dr. Nellye Cubizolles (INRA, Clermont Ferrand, FR) for technical support in the use of cfp markers; Dr. Cyrille Saintenac (INRA, Clermont Ferrand, FR) and his collaborators for making publicly available their excellent work. This work was supported by funding from the National Science Foundation, Plant Genome Research Program (NSF-PGRP) grant No. IOS-0822100 to SFK. Additional support from the NSF-PGRP Developing Country Collaboration aided the assistance of student interns A.Kumar, S.K., A.G., and V.T.; F.M.B was partially supported by Program Master and Back Regione Autonoma della Sardegna and Monsanto Beachell-Borlaug International Scholarship.

Keywords

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

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