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Title: Efficient genome-wide detection and cataloging of EMS-induced mutations using exome capture and next-generation sequencing

Author
item HENRY, ISABELLE - University Of California
item NAGALAKSHMI, UGRAPPA - University Of California
item LIEBERMAN, MERIC - University Of California
item NGO, KATHIE - University Of California
item KRASILEVA, KSENIA - University Of California
item VASQUEZ-GROSS, HANS - University Of California
item AKHUNOVA, ALINA - Kansas State University
item AKHUNOVA, EDUARD - Kansas State University
item DUBCOVSKY, JORGE - University Of California
item Tai, Thomas
item COMAI, LUCA - University Of California

Submitted to: The Plant Cell
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/19/2014
Publication Date: 4/11/2014
Publication URL: http://www.plantcell.org/content/26/4/1382.abstract?sid=0256eb0a-81a1-458f-94ce-a9c358174ee2
Citation: Henry, I.M., Nagalakshmi, U., Lieberman, M.C., Ngo, K.J., Krasileva, K.V., Vasquez-Gross, H., Akhunova, A., Akhunova, E., Dubcovsky, J., Tai, T., Comai, L. 2014. Efficient genome-wide detection and cataloging of EMS-induced mutations using exome capture and next-generation sequencing. The Plant Cell. 26:1-17.

Interpretive Summary:

Technical Abstract: Chemical mutagenesis efficiently generates phenotypic variation in otherwise homogeneous genetic backgrounds, enabling functional analysis of genes. Advances in mutation detection have brought the utility of induced mutant populations on par with those produced by insertional mutagenesis, but systematic cataloguing of mutations would further increase their utility. We examined the suitability of multiplexed global exome capture and sequencing coupled with custom-developed bioinformatics tools to identify mutations in well-characterized mutant populations of rice (Oryza sativa) and wheat (Triticum aestivum). In rice, we identified ~18,000 induced mutations from 72 independent M2 individuals. Functional evaluation indicated the recovery of potentially deleterious mutations for >2600 genes. We further observed that specific sequence and cytosine methylation patterns surrounding the targeted guanine residues strongly affect their probability to be alkylated by ethyl methanesulfonate. Application of these methods to six independent M2 lines of tetraploid wheat demonstrated that our bioinformatics pipeline is applicable to polyploids. In conclusion, we provide a method for developing large-scale induced mutation resources with relatively small investments that is applicable to resource-poor organisms. Furthermore, our results demonstrate that large libraries of sequenced mutations can be readily generated, providing enhanced opportunities to study gene function and assess the effect of sequence and chromatin context on mutations.