Abstract
IR64, the most widely grown indicarice in South and Southeast Asia, possesses many positive agronomic characteristics (e.g., wide adaptability, high yield potential, tolerance to multiple diseases and pests, and good eating quality,) that make it an ideal genotype for identifying mutational changes in traits of agronomic importance. We have produced a large collection of chemical and irradiation-induced IR64 mutants with different genetic lesions that are amenable to both forward and reverse genetics. About 60,000 IR64 mutants have been generated by mutagenesis using chemicals (diepoxybutane and ethylmethanesulfonate) and irradiation (fast neutron and gamma ray). More than 38,000 independent lines have been advanced to M4 generation enabling evaluation of quantitative traits by replicated trials. Morphological variations at vegetative and reproductive stages, including plant architecture, growth habit, pigmentation and various physiological characters, are commonly observed in the four mutagenized populations. Conditional mutants such as gain or loss of resistance to blast, bacterial blight, and tungro disease have been identified at frequencies ranging from 0.01% to 0.1%. Results from pilot experiments indicate that the mutant collections are suitable for reverse genetics through PCR-detection of deletions and TILLING. Furthermore, deletions can be detected using oligomer chips suggesting a general technique to pinpoint deletions when genome-wide oligomer chips are broadly available. M4 mutant seeds are available for users for screening of altered response to multiple stresses. So far, more than 15,000 mutant lines have been distributed. To facilitate broad usage of the mutants, a mutant database has been constructed in the International Rice Information System (IRIS; http: //www.iris.irri.org) to document the phenotypes and gene function discovered by users.
Article PDF
Similar content being viewed by others
References
T. Altmann G. Felix A. Jessop A. Kauschmann U. Uwer H. Pena-Cortes L. Willmitzer (1995) ArticleTitleAc/Ds transposon mutagenesis in Arabidopsis thaliana: mutant spectrum and frequency of Ds insertion mutants Mol. Gen. Genet 247 646–652 Occurrence Handle10.1007/BF00290357 Occurrence Handle7603445
M. Ashikari J. Wu M. Yano T. Sasaki A. Yoshimura (1999) ArticleTitleRice gibberellin-insensitive dwarf mutant gene Dwarf 1 encodes the alpha-subunit of GTP-binding protein Proc. Natl. Acad. Sci. USA 96 10284–10289 Occurrence Handle10.1073/pnas.96.18.10284 Occurrence Handle10468600
J. Borevitz D. Liang D. Plouffe H. Chang T. Zhu D. Weigel C. Berry E. Winzeler J. Chory (2003) ArticleTitleLarge-scale identification of single-feature polymorphisms in complex genomes Genome Res 13 513–523 Occurrence Handle10.1101/gr.541303 Occurrence Handle12618383
E. Bruggemann K. Handwerger C. Essex G. Storz (1996) ArticleTitleAnalysis of fast neutron-generated mutants at the Arabidopsis thaliana HY4 locus Plant J 10 755–760 Occurrence Handle10.1046/j.1365-313X.1996.10040755.x Occurrence Handle8893551
Chang H.S., Wu C., Zeng L., Dunn M., Wang G.L., Leung H., Goff S., Wang X., Zhu T. and Leach J.E. (2003). Detection of deleted genes in rice mutants using the Rice GeneChip genome array. Abstracts of Plant and Animal Genome XI. 11–15 January 2003, San Diego, California. p. 100.
Q. Feng Y. Zhang P. Hao S. Wang G. Fu Y. Huang Y. Li J. Zhu Y. Liu X. Hu P. Jia Y. Zhang Q. Zhao K. Ying S. Yu Y. Tang Q. Weng L. Zhang Y. Lu J. Mu Y. Lu L. Zhang Z. Yu D. Fan X. Liu T. Lu C. Li Y. Wu T. Sun H. Lei T. Li H. Hu J. Guan M. Wu R. Zhang B. Zhou Z. Chen L. Chen Z. Jin R. Wang H. Yin Z. Cai S. Ren G. Lv W. Gu G. Zhu Y. Tu J. Jia Y. Zhang J. Chen H. Kang X. Chen C. Shao Y. Sun Q. Hu X. Zhang W. Zhang L. Wang C. Ding H. Sheng J. Gu S. Chen L. Ni F. Zhu W. Chen L. Lan Y. Lai Z. Cheng M. Gu J. Jiang J. Li G. Hong Y. Xue B. Han (2002) ArticleTitleSequence and analysis of rice chromosome 4 Nature 420 316–320 Occurrence Handle10.1038/nature01183 Occurrence Handle12447439
S. Goff D. Ricke T. Lan G. Presting R. Wang M. Dunn J. Glazebrook A. Sessions P. Oeller H. Varma D. Hadley D. Hutchison C. Martin F. Katagiri B. Lange T. Moughamer Y. Xia P. Budworth J. Zhong T. Miguel U. Paszkowski S. Zhang T. Colbert W. Sun L. Chen B. Cooper S. Park T. Wood L. Mao P. Quail R. Wing R. Dean Y. Yu A. Zharkikh R. Shen S. Sahasrabudhe A. Thomas R. Cannings A. Gutin D. Pruss J. Reid S. Tavtigian J. Mitchell G. Eldredge T. Scholl R. Miller S. Bhatnager N. Adey T. Rubano N. Tusneem R. Robinson J. Feldhaus T. Macalma A. Oliphant S. Briggs (2002) ArticleTitleA draft seqeunce of the rice genomes (Oryza sativa L. ssp. japonica) Science 296 92–100 Occurrence Handle10.1126/science.1068275 Occurrence Handle11935018
R. Greco P.B.F. Ouwerkerk R.J. Kam Particlede C. Sallaud C. Favalli L. Colombo E. Guiderdoni A.H. Meijer J.H.C. Hoge A. Pereira (2003) ArticleTitleTranspositional behaviour of an Ac/Ds system for reverse genetics in rice Theor. Appl. Genet 108 10–24 Occurrence Handle10.1007/s00122-003-1416-8 Occurrence Handle14513217
S. Henikoff L. Comai (2003) ArticleTitleSingle-nucleotide mutations for plant functional genomics Annu. Rev. Plant Biol 54 375–401 Occurrence Handle10.1146/annurev.arplant.54.031902.135009 Occurrence Handle14502996
H. Hirochika (2001) ArticleTitleContribution of the Tos17 retrotransposon to rice functional genomics Curr. Opin. Plant. Biol 4 118–22 Occurrence Handle10.1016/S1369-5266(00)00146-1 Occurrence Handle11228433
H. Hirochika E. Guiderdoni G. An Y. Hsing M.Y. Eun C.D. Han N. Upadhyaya S. Ramachandran Q. Zhang A. Pereira V. Sundaresan H. Leung (2004) ArticleTitleRice mutant resources for gene discovery Plant Mol. Biol 54 325–334 Occurrence Handle10.1023/B:PLAN.0000036368.74758.66 Occurrence Handle15284490
J. Jeon S. Lee K. Jung S. Jun D. Jeong J. Lee C. Kim S. Jang K. Yang J. Nam K. An M. Han R. Sung H. Choi J. Yu J. Choi S. Cho S. Cha S. Kim G. An (2000) ArticleTitleT-DNA insertional mutagenesis for functional genomics in rice Plant J 22 561–570 Occurrence Handle10.1046/j.1365-313x.2000.00767.x Occurrence Handle10886776
D. Jeong S. An H. Kang S. Moon J. Han S. Park H. Lee K. An G. An (2002) ArticleTitleT-DNA insertional mutagenesis for activation tagging in rice Plant Physiol 130 1636–1644 Occurrence Handle10.1104/pp.014357 Occurrence Handle12481047
P. Krysan J. Young M. Sussman (1999) ArticleTitleT-DNA as an insertional mutagen in Arabidopsis Plant Cell 11 2283–2290 Occurrence Handle10.1105/tpc.11.12.2283 Occurrence Handle10590158
M. Koornneef L. Dellaert J. Veen Particlevan der (1982) ArticleTitleEMS- and radiation-induce mutation frequencies at individual loci in Arabidopsis thaliana(L.) heynh Mutation Res 93 109–123 Occurrence Handle7062928
D. Lee T. Kim S. Lee H. Kim S. Rhee B. Yoon G. Pfeifer C. Lee (2002) ArticleTitleMutations induced by 1,3-butadiene metabolites, butadiene diolepoxide and 1,2,3,4-dipoxybutane at the Hprtlocus in CHO-K1 cells Mol. Cells 31 411–419
Leung H., Wu C., Baraoidan M., Bordeos A., Ramos M., Madamba S., Cabauatan P., Vera Cruz C., Portugal A., Reves G., Bruskiewich R., McLaren G., Gregorio G., Bennett J., Brar D., Khush G., Schnable P., Wang G. and Leach J. (2001). Deletion mutants for functional genomics: progress in phenotyping, sequence assignment, and database development. In: Khush G., Brar D., Hardy B. (ed.) Rice Genetics IV.Science Publishers Inc., New Delhi, pp. 239–251
H. Leung G. An (2004) ArticleTitleRice functional genomics: large scale gene discovery and applications for crop improvement Adv. Agron 82 55–111
X. Li Y. Song K. Century S. Straight P. Ronald X. Dong M. Lassner Y. Zhang (2001) ArticleTitleA fast neutron deletion mutagenesis-based reverse genetics system for plants Plant J 27 235–242 Occurrence Handle10.1046/j.1365-313x.2001.01084.x Occurrence Handle11532169
L. Liu J. Spoerke E. Mulligan J. Chen B. Reardon B. Westlund L. Sun K. Abel B. Armstrong G. Hardiman J. King L. McCague M. Basson R. Clover C. Johnson (1999) ArticleTitleHigh-throughput isolation of Caenorhabditis elegans deletion mutants Genome Res 9 859–867 Occurrence Handle10.1101/gr.9.9.859 Occurrence Handle10508845
G. Liu L. Wang Z. Zhou H. Leung G.L. Wang C. He (2004) ArticleTitlePhysical mapping of a rice lesion mimic gene, Spl1, to a 70-kb segment of rice chromosome 12 Mol. Genet. Genom 272 108–115
M. Maluszynski K. Nichterlein L. Zanten Particlevan B. Ahloowalia (2000) ArticleTitleOfficial released mutant varieties- the FAO/IAEA database Mutation Breed 12 1–88
P. Manosalva M. Ryba-White C. Wu C. Lei M. Baraoidan H. Leung J. Leach (2003) ArticleTitleA PCR-based screening strategy for detecting deletions in defense response genes in rice Phytopathology 93 S57
C. McCallum L. Comai E. Greene S. Henikoff (2000) ArticleTitleTargeted screening for induced mutations Nature Biotech 18 455–457 Occurrence Handle10.1038/74542
C. McCallum L. Comai E. Greene S. Henikoff (2000) ArticleTitleTargeting induced local lesions in genomes (TILLING) for plant functional genomics Plant Physiol 123 439–442 Occurrence Handle10.1104/pp.123.2.439 Occurrence Handle10859174
A. Miyao K. Tanaka K. Murata H. Sawaki S. Takeda K. Abe Y. Shinozuka K. Onosato H. Hirochika (2003) ArticleTitleTarget 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 Occurrence Handle10.1105/tpc.012559 Occurrence Handle12897251
J.H. Nadeau W.N. Frankel (2000) ArticleTitleThe roads from phenotypic variation to gene discovery: mutagenesis versus QTLs Nature Genet 25 381–384 Occurrence Handle10.1038/78051 Occurrence Handle10932178
P. Okubara P. Anderson O. Ochoa R. Michelmore (1994) ArticleTitleMutants of downy mildew resistance in Lactuca sativa (lettuce) Genetics 137 867–874 Occurrence Handle8088530
G. Rao (1977) ArticleTitleEfficiency and effectiveness of gamma rays and EMS in rice Cytologia 42 443–450
L. Recio A. Steen L. Pluta K. Meyer C. Saranko (2001) ArticleTitleMutational spectrum of 1,3-butadiene and metabolites 1,2-epoxybutene and 1,2,3,4-diepoxybutane to assess mutagenic mechanisms Chem. Biol. Interct 135 IssueID136 325–341 Occurrence Handle10.1016/S0009-2797(01)00220-4
B. Shirley S. Hanley H. Goodman (1992) ArticleTitleEffects of ionizing radiation on a plant genome: analysis of two Arabidopsis transparent testa mutations Plant Cell 4 333–347 Occurrence Handle10.1105/tpc.4.3.333 Occurrence Handle1354004
T. Sasaki T. Matsumoto K. Yamamoto K. Sakata T. Baba Y. Katayose J. Wu Y. Niimura Z. Cheng Y. Nagamura B. Antonio H. Kanamori S. Hosokawa M. Masukawa K. Arikawa Y. Chiden M. Hayashi M. Okamoto T. Ando H. Aoki K. Arita M. Hamada C. Harada S. Hijishita M. Honda Y. Ichikawa A. Idonuma M. Iijima M. Ikeda M. Ikeno S. Ito T. Ito Y. Ito Y. Ito K. IwabuchiA. Kamiya W. Karasawa S. Katagiri A. Kikuta N. Kobayashi I. Kono K. Machita T. Maehara H. Mizuno T. Mizubayashi Y. Mukai H. Nagasaki M. Nakashima Y. Nakama Y. Nakamichi M. Nakamura N. Namiki M. Negishi I. Ohta N. Ono S. Saji K. Sakai M. Shibata T. Shimokawa A. Shomura J. Song Y. Takazaki K. Terasawa K. Tsuji K. Waki H. Yamagata H. Yamane S. Yoshiki R. Yoshihara K. Yukawa H. Zhong H. Iwama T. Endo H. Ito J. Hahn H.I. Kim M.Y. Eun M. Yano J. Jiang T. Gojobori (2002) ArticleTitleThe genome sequence and structure of rice chromosome 1 Nature 420 312–316 Occurrence Handle10.1038/nature01184 Occurrence Handle12447438
B. Till S. Reynolds E. Greene C. Codomo L. Enns J. Johnson C. Burtner A. Odden K. Young N. Taylor J. Henikoff L. Comai S. Henikoff (2003) ArticleTitleLarge-scale discovery of induced point mutations with high-throughput TILLING Genome Res 13 524–530 Occurrence Handle10.1101/gr.977903 Occurrence Handle12618384
N.M. Upadhyaya X.-R. Zhou Q.-H. Zhu K. Ramm L. Wu A. Eamens R. Sivakumar T. Kato D.-W. Yun C. Santhoshkumar K.K. Narayanan J.W. Peacock E.S. Dennis (2002) ArticleTitleAn iAc/Ds gene and enhancer trapping system for insertional mutagenesis in rice Funct Plant Biol 29 547–559
Wang G.L., Wu C., Zeng L., He C., Baraoidan M., Goaes da Silva F., Williams C.E., Ronald P. and Leung H. (2004). Isolation and characterization of rice mutants susceptible to Xanthomonas oryzae pv oryzae. Theor Appl Genet. 379-384
E. Winzeler C. Castillo-Davis G. Oshiro D. Liang D. Richards Y. Zhou D. Hartl (2003) ArticleTitleGenetic diversity in yeast assessed with whole-genome oligonucleotide arrays Genetics 163 79–89 Occurrence Handle12586698
C. Wu X. Li W. Yuan G. Chen A. Kilian J. Li C. Xu X. Li D.-X. Zhou S. Wang Q. Zhang (2003) ArticleTitleDevelopment of enhancer trap lines for functional analysis of the rice genome Plant J 35 418–427 Occurrence Handle10.1046/j.1365-313X.2003.01808.x Occurrence Handle12887592
J. Yu S. Hu J. Wang G. Wong S. Li B. Liu Y. Deng L. Dai Y. Zhou X. Zhang M. Cao J. Liu J. Sun J. Tang Y. Chen X. Huang W. Lin C. Ye W. Tong L. Cong J. Geng Y. Han L. Li W. Li G. Hu X. Huang W. Li J. Li Z. Liu L. Li J. Liu Q. Qi J. Liu L. Li T. Li X. Wang H. Lu T. Wu M. Zhu P. Ni H. Han W. Dong X. Ren X. Feng P. Cui X. Li H. Wang X. Xu W. Zhai Z. Xu J. Zhang S. He J. Zhang J. Xu K. Zhang X. Zheng J. Dong W. Zeng L. Tao J. Ye J. Tan X. Ren X. Chen J. He D. Liu W. Tian C. Tian H. Xia Q. Bao G. Li H. Gao T. Cao J. Wang W. Zhao P. Li W. Chen X. Wang Y. Zhang J. Hu J. Wang S. Liu J. Yang G. Zhang Y. Xiong Z. Li L. Mao C. Zhou Z. Zhu R. Chen B. Hao W. Zheng S. Chen W. Guo G. Li S. Liu M. Tao J. Wang L. Zhu L. Yuan H. Yang (2002) ArticleTitleA draft sequence of the rice genome (Oryza sativa L. ssp. indica) Science 296 79–92 Occurrence Handle10.1126/science.1068037 Occurrence Handle11935017
L. Zeng S. Qu A. Bordeos C. Yang M. Baraoidan H. Yan Q. Xie B.H. Nahm H. Leung G.L. Wang (2004) ArticleTitleSpl11, a negative regulator of plant cell death and defense, encodes a U-Box/ARM repeat protein endowed with E3 ubiquitin ligase activity Plant Cell 16 2795–2808 Occurrence Handle10.1105/tpc.104.025171 Occurrence Handle15377756
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Wu, JL., Wu, C., Lei, C. et al. Chemical- and Irradiation-induced Mutants of Indica Rice IR64 for Forward and Reverse Genetics. Plant Mol Biol 59, 85–97 (2005). https://doi.org/10.1007/s11103-004-5112-0
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/s11103-004-5112-0