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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » Research » Publications at this Location » Publication #327765
Title: Chemical and radiation mutagenesis: Induction and detection by whole genome sequencing

Author
item GRANIER, FABIENE - Institut National De La Recherche Agronomique (INRA)
item LEMAIRE, AURELIE - Institut National De La Recherche Agronomique (INRA)
item WANG, YIN - Institut National De La Recherche Agronomique (INRA)
item LEBRIS, PHILIPPE - Institut National De La Recherche Agronomique (INRA)
item ANTELME, SEBASTIENE - Institut National De La Recherche Agronomique (INRA)
item VOGEL, JOHN - Joint Genome Institute
item L Chingcuanco, Debbie
item SIBOUT, RICHARD - Institut National De La Recherche Agronomique (INRA)

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 11/6/2016
Publication Date: 1/4/2016
Citation: Granier, F., Lemaire, A., Wang, Y., Lebris, P., Antelme, S., Vogel, J., Chingcuanco, D.L., Sibout, R. 2016. Chemical and radiation mutagenesis: Induction and detection by whole genome sequencing. In:Vogel, J., editor. Genetics and Genomics of Brachypodium. Cham, Switzerland:Springer International Publishing. p. 155-170. doi: 10.1007/7397.2015.12.

Interpretive Summary: Brachypodium distachyon has emerged as a powerful model system to address fundamental questions in grass biology. Gaining insights into the function of more than 34,000 genes identified in its sequenced genome will further expand its utility for basic research. To this end, we generated three Brachypodium mutagenized populations using ethyl methanesulfonate (EMS), sodium azide (NaN3) and fast-neutron radiation (FNR). Targeting Induced Local Lesions in Genomes (TILLING) was initially applied to identify mutations in genes of interest. With the decreasing cost of DNA sequencing, we plan to utilize whole genome sequencing (WGS) to establish a genome-wide sequence-indexed library of mutations. This genetic resource will facilitate the elucidation of the molecular basis of important traits in cereal crops and bioenergy feedstocks.

Technical Abstract: Brachypodium distachyon has emerged as an effective model system to address fundamental questions in grass biology. With its small sequenced genome, short generation time and rapidly expanding array of genetic tools B. distachyon is an ideal system to elucidate the molecular basis of important traits in crops and bioenergy feedstocks. Induced mutations are one of the pillars of modern molecular genetics and are particularly useful for assigning function to individual genes. Due to their ease of use and low cost, mutagenic chemicals and ionizing radiation have been widely used to create mutant populations of many different organisms. The major limitations for these mutagens are the difficulty of identifying the specific mutation responsible for an observed phenotype and the difficulty of identifying mutations in a gene of interest. As a step toward addressing these limitations, Targeting Induced Local Lesions in Genomes (TILLING) has been developed as an efficient method to rapidly identify mutations in genes of interest. Recently, the decreasing cost of DNA sequencing has made it feasible to detect mutations throughout the genome using whole genome sequencing. This promises to revolutionize the use of chemical and radiation mutants in research. In this chapter we describe the status of B. distachyon mutagenesis including the methods, mutagens, TILLING populations and initial results using whole genome sequencing to identify induced genetic variation.