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.
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Acknowledgments
We would like to thank Sean Gordon for providing high and low confidence SNP files. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231. Yin Wang was funded by the China Scholarship Council. Aurélie Lemaire was funded BRAVO (ANR-14-CE19-0012-01). The preliminary data on sequencing were funded by the SILICOTIL project from INRA. The Institut Jean-Pierre Bourgin benefits from the support of the LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS). Work done at the U.S. Department of Agriculture was supported by CRIS project 2030-21000-019.
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Granier, F. et al. (2015). Chemical and Radiation Mutagenesis: Induction and Detection by Whole Genome Sequencing. In: Vogel, J. (eds) Genetics and Genomics of Brachypodium. Plant Genetics and Genomics: Crops and Models, vol 18. Springer, Cham. https://doi.org/10.1007/7397_2015_20
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DOI: https://doi.org/10.1007/7397_2015_20
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