Page Banner

United States Department of Agriculture

Agricultural Research Service

Research Project: Generation and Characterization of Novel Genetic Variation in Rice for the Enhancement of Grain Quality and Agronomic Performance

Location: Crops Pathology and Genetics Research

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

Authors
item Henry, Isabelle -
item Nagalakshmi, Ugrappa -
item Lieberman, Meric -
item Ngo, Kathie -
item Krasileva, Ksenia -
item Vasquez-Gross, Hans -
item Akhunova, Alina -
item Akhunova, Eduard -
item Dubcovsky, Jorge -
item Tai, Thomas
item Comai, Luca -

Submitted to: The Plant Cell
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 19, 2014
Publication Date: April 11, 2014
Repository 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.

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.

Last Modified: 12/21/2014
Footer Content Back to Top of Page