Abstract
With the completion of the rice genome sequencing project, the next major challenge is the large-scale determination of gene function. A systematic phenotypic profiling of mutant collections will provide major insights into gene functions important for crop growth or production. Thus, detailed phenomics analysis is the key to functional genomics. Currently, the two major types of rice mutant collections are insertional mutants and chemical or irradiation-induced mutants. Here we describe how to manipulate a rice mutant population, including conducting phenomics studies and the subsequent propagation and seed storage. We list the phenotypes screened and also describe how to collect data systematically for a database of the qualitative and quantitative phenotypic traits. Thus, data on mutant lines, phenotypes, and segregation rate for all kinds of mutant populations, as well as integration sites for insertional mutant populations, would be searchable, and the collection would be a good resource for rice functional genomics study.
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References
Hsing, Y. I., Chern, C. G., Fan, M. J., Lu, P. C., Chen, K. T., Lo, S. F., et al. (2007) A rice gene activation/knockout mutant resource for high throughput functional genomics. Plant Mol. Biol. 63, 351–364.
Jeong, D. H., An, S., Kang, H. G., Moon, S., Han, J. J., Park, S., et al. (2002) T-DNA insertional mutagenesis for activation tagging in rice. Plant Physiol. 130, 1636–1644.
Miyao, A., Tanaka, K., Murata, K., Sawaki, H., Takeda, S., Abe, K., et al. (2003) Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell 15, 1771–1780.
He, C., Day, M., Lin, Z., Duan, F., Li, F., and Wu, R. (2007) An efficient method for producing an indexed, insertional-mutant library in rice. Genomics 89, 532–540.
Upadhyaya, N. M., Zhu, Q. H., Zhou, X. R., Eamens, A. L., Hoque, M. S., Ramm, K., et al. (2006) Dissociation (Ds) constructs, mapped Ds launch pads and a transiently-expressed transposase system suitable for localized insertional mutagenesis in rice. Theor. Appl. Genet. 112, 1326–1341.
Kumar, C. S., Wing, R. A., and Sundaresan, V. (2008) Efficient insertional mutagenesis in rice using the maize En/Spm elements. Plant J. 44, 879–892.
Wu, J. L., Wu, C., Lei, C., Baraoidan, M., Bordeos, A., Madamba, M. R., et al. (2005) Chemical- and irradiation-induced mutants of indica rice IR64 for forward and reverse genetics. Plant Mol. Biol. 59, 85–97.
Kurata, N., Miyoshi, K., Nonomura, K. I., Yamazaki, Y., and Ito, Y. (2005) Rice mutants and genes related to organ development, morphogenesis and physiological traits. Plant Cell Physiol. 46, 48–62.
Ma, J. F., Tamai, K., Ichii, M., and Wu, G. F. (2002) A rice mutant defective in Si uptake. Plant Physiol. 130, 2111–2117.
Chern, C. G., Fan, M. J., Yu, S. M., Hour, A. L., Lu, P. C., Lin, Y. C., et al. (2007) A rice phenomics study – phenotype scoring and seed propagation of a T-DNA insertion-induced rice mutant population. Plant Mol. Biol. 65, 427–438.
IRGSP (2005) The map-based sequence of the rice genome. Nature 436, 793–800.
Yu, J., Hu, S., Wang, J., Wong, G. K., Li, S., Liu, B., et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296, 79–92.
Feltus, F. A., Wan, J., Schulze, S. R., Estill, J. C., Jiang, N., and Paterson, A. H. (2004) An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res. 14, 1812–1819.
Hour, A. L., Lin, Y. C., Li, P. F., Chow, T. Y., Lu, W. F., Wei, F. J., et al. (2007) Detection of SNPs between Tainung 67 and Nipponbare rice cultivars. Bot. Stud. 48, 243–253.
Hirochika, H., Guiderdoni, E., An, G., Hsing, Y. I., Eun, M. Y., Upadhyaya, N., et al. (2004) Rice mutant resources for gene discovery. Plant Mol. Biol. 54, 325–334.
An, G., Lee, S., Kim, S. H., and Kim, S. R. (2005). Molecular genetics using T-DNA in rice. Plant Cell Physiol. 46, 14–22.
Suzuki, T., Eiguchi, M., Kumamaru, T., Satoh, H., Matsusaka, H., Moriguchi, K., et al. (2008) MNU-induced mutant pools and high performance TILLING enable finding of any gene mutation in rice. Mol. Genet. Genomics 279, 213–223.
Larmande, P., Gay, C., Lorieux, M., Perin, C., Bouniol, M., Droc, G., et al. (2008) Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library. Nucleic Acids Res. 36, D102–1027.
Zhang, J., Li, C., Wu, C., Xiong, L., Chen, G., Zhang, Q., et al. (2006) RMD: a rice mutant database for functional analysis of the rice genome. Nucleic Acids Res. 34, D745–748.
Ilic, K., Kellogg, E. A., Jaiswal, P., Zapata, F., Stevens, P. F., Vincent L. P., et al. (2007) The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol. 143, 587–599.
Yamazaki, Y., and Jaiswal, P. (2005) Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase. Plant Cell Physiol. 46, 63–68.
Acknowledgments
The authors acknowledge the contributions from Drs. Richard Bruskiewich, International Rice Research Institute, and Chih-Wei Tung, Cornell University, about the phenotype terms of IRRI, PO, PATO, and TO shown in the supplementary table at http://ipmb.sinica.edu.tw/soja/rice/phenomics_comparison/. We also acknowledge Ms. Laura Heraty for critical review of this manuscript. This work was supported by grants from Academia Sinica and the Taiwan National Science Council to CGC, MJF, SCH, SMY, and YICH.
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Chern, CG. et al. (2011). Methods for Rice Phenomics Studies. In: Pereira, A. (eds) Plant Reverse Genetics. Methods in Molecular Biology, vol 678. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-682-5_10
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DOI: https://doi.org/10.1007/978-1-60761-682-5_10
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