Methodology article

Discovery of chemically induced mutations in rice by TILLING

Bradley J Till^{* 1,2} , Jennifer Cooper^{* 1} , Thomas H Tai³ , Peter Colowit³ , Elizabeth A Greene¹ , Steven Henikoff¹ and Luca Comai^2,4

¹Fred Hutchinson Cancer Research Center, Seattle, WA 98107, USA

²Department of Biology, University of Washington, Box 355325, Seattle, WA 98195, USA

³USDA-ARS, Crops Pathology and Genetics Research Unit, Department of Plant Sciences, Davis, CA 95616, USA

⁴Section of Plant Biology and Genome Center, UC Davis, Davis, CA 95616, USA

author email corresponding author email* Contributed equally

BMC Plant Biology 2007, 7:19doi:10.1186/1471-2229-7-19

Published:	11 April 2007

Abstract

Background

Rice is both a food source for a majority of the world's population and an important model system. Available functional genomics resources include targeted insertion mutagenesis and transgenic tools. While these can be powerful, a non-transgenic, unbiased targeted mutagenesis method that can generate a range of allele types would add considerably to the analysis of the rice genome. TILLING (Targeting Induced Local Lesions in Genomes), a general reverse genetic technique that combines traditional mutagenesis with high throughput methods for mutation discovery, is such a method.

Results

To apply TILLING to rice, we developed two mutagenized rice populations. One population was developed by treatment with the chemical mutagen ethyl methanesulphonate (EMS), and the other with a combination of sodium azide plus methyl-nitrosourea (Az-MNU). To find induced mutations, target regions of 0.7–1.5 kilobases were PCR amplified using gene specific primers labeled with fluorescent dyes. Heteroduplexes were formed through denaturation and annealing of PCR products, mismatches digested with a crude preparation of CEL I nuclease and cleaved fragments visualized using denaturing polyacrylamide gel electrophoresis. In 10 target genes screened, we identified 27 nucleotide changes in the EMS-treated population and 30 in the Az-MNU population.

Conclusion

We estimate that the density of induced mutations is two- to threefold higher than previously reported rice populations (about 1/300 kb). By comparison to other plants used in public TILLING services, we conclude that the populations described here would be suitable for use in a large scale TILLING project.