Abstract
The recent availability of large-scale genomic data has allowed researchers to begin deciphering plant gene function. Plant mutagenesis is a powerful tool for the identification and characterization of the function of specific genes linked to phenotypes. TILLING (Targeting Induced Local Lesions IN Genomes) is a general reverse-genetics tool that combines traditional mutagenesis with high-throughput methods of mutation discovery among mutagenized populations. The aim of TILLING is to identify mutagenized genotypes that affect specific phenotypes. Securing genetic diversity and selecting efficient progeny are the most important factors in plant breeding. During the evolutionary process, the gene pool has skewed towards a direction that is favorable to humans and some essential alleles may have been lost during the selection processes. Genome editing using an engineered nuclease is a target-directed, controlled, and predictable approach that can provide a genetically diverse gene pool and shorten cultivar development time. Depending on engineered nucleases and plant species types, the mutagenesis rate and outcomes show significant differences, indicating that nuclease types and characteristics, efficient target mutagenesis, construction and delivery of the nuclease, selection and verification of the mutants, and off-target mutagenesis need to be considered. Genomic sequence variations generated by chemical and/or physical mutagenesis can be strongly related to changes in phenotype. Haplotype analysis allows plant breeding knowledge to be expanded and can help improve understanding of diversity at the genomic sequence level. Experiments using SNP haplotypes can provide insights into plant evolution, and can contribute to phenotypic analysis, and expectation and characterization of mutagenized plant phenotypes.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Alonso JM, Stepanova AN, Solano R et al (2003) Five components of the ethylene-response pathway identified in a screen for weak ethylene-insensitive mutants in Arabidopsis. Proc Natl Acad Sci USA 100:2992–2997
Botticella E, Sestili F, Hernandez-Lopez A et al (2011) High resolution melting analysis for the detection of EMS induced mutations in wheat SbeIIa genes. BMC Plant Biol 11:156
Cai CQ, Doyon Y, Ainley WM et al (2013) Targeted transgene integration in plant cells using designed zinc finger nucleases. Plant Mol Biol 69:699–709
Caldwell DG, McCallum N, Shaw P et al (2004) A structured mutant population for forward and reverse genetics in Barley (Hordeum vulgare L.). Plant J 40:143–150
Carroll D, Morton JJ, Beumer KJ et al (2006) Design, construction and in vitro testing of zinc finger nucleases. Nat Protoc 1:1329–1341
Cermak T, Doyle EL, Christian M et al (2011) Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res 39:e82
Chun JB, Ha BK, Jang DS et al (2012) Identification of mutations in OASA1 gene from a gamma-irradiated rice mutant population. Plant Breed 131:276–281
Colbert T, Till BJ, Tompa R et al (2001) High-throughput screening for induced point mutations. Plant Physiol 126:480–484
Comai L, Young K, Till BJ et al (2004) Efficient discovery of DNA polymorphisms in natural populations by Ecotilling. Plant J 37:778–786
Cooper JL, Till BJ, Laport RG et al (2008) TILLING to detect induced mutations in soybean. BMC Plant Biol 8:9
Cornu TI, Thibodeau-Beganny S, Guhl E et al (2008) DNA-binding specificity is a major determinant of the activity and toxicity of zinc-finger nucleases. Mol Ther 16:352–358
Curtin SJ, Zhang F, Sander JD et al (2011) Targeted mutagenesis of duplicated genes in soybean with zinc-finger nucleases breakthrough technologies. Plant Physiol 156:466–473
de Pater S, Neuteboom LW, Pinas JE et al (2009) ZFN-induced mutagenesis and gene-targeting in Arabidopsis through Agrobacterium-mediated floral dip transformation. Plant Biotechnol J 7:821–835
Dong C, Dalton-Morgan J, Vincent K et al (2009) A modified TILLING method for wheat breeding. Plant Gen 2:39–47
Even-Faitelson L, Samach A, Melamed-Bessudo C et al (2011) Localized egg-cell expression of effector proteins for targeted modification of the Arabidopsis genome. Plant J 68:929–937
Gady AL, Hermans FW, Van de Wal MH et al (2009) Implementation of two high through-put techniques in a novel application: detecting point mutations in large EMS mutated plant populations. Plant Methods 5:13
Galeano CH, Gomez M, Rodriguez LM et al (2009) CEL I nuclease digestion for SNP discovery and marker development in common bean (L.). Crop Sci 49:381–394
Gasiunas G, Siksynys V (2013) RNA-dependent DNA endonuclease Cas9 of the CRISPR system: Holy Grail of genome editing? Trends Microbiol 21:562–567
Gilchrist EJ, Haughn GW, Ying CC et al (2006) Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa. Mol Ecol 15:1367–1378
Gore MA, Chia J-M, Elshire RJ et al (2009) A first-generation haplotype map of maize. Science 326:1115–1117
Hegyi J, Schwartz RA, Hegyi V (2004) Pellagra: dermatitis, dementia, and diarrhea. Int J Dermatol 43:1–5
Hoffmann D, Jiang Q, Men A et al (2007) Nodulation deficiency caused by fast neutron mutagenesis of the model legume Lotus japonicus. J Plant Physiol 164:460–469
Hoshaw JP, Unger-Wallace E, Zhang F et al (2010) A transient assay for monitoring zinc finger nuclease activity at endogenous plant gene targets. Methods Mol Biol 649:299–313
Huang X, Wei X, Sang T et al (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–967
Huang X, Zhao Y, Wei X et al (2012) Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet 44:32–39
Hurt JA, Thibodeau SA, Hirsh AS et al (2003) Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection. Proc Natl Acad Sci USA 100:12271–12276
Kadaru SB, Yadav AS, Fjellstrom RG et al (2006) Alternative Ecotilling protocol for rapid, cost-effective single-nucleotide polymorphism discovery and genotyping in rice (Oryza sativa L.). Plant Mol Biol Rep 24:3–22
Keim P, Olson TC, Shoemaker RC (1988) A rapid protocol for isolating soybean DNA. Soybean Genet Newslett 15:150–152
Kim DS, Lee IS, Jang CS et al (2004) Development of AFLP-derived STS markers for the selection of 5-methyltryptophan-resistant rice mutants. Plant Cell Rep 23:71–80
Kim HJ, Um EJ, Cho SR et al (2011) Surrogate reporters for enrichment of cells with nuclease-induced mutations. Nat Methods 11:941–943
Kisaka H, Kisaka M, Kameya T (1996) Characterization of interfamilial somatic hybrids between 5-methyltryptophan resistant rice (Oryza sativa L.) and 5MT-sensitive carrot (Daucuscarota L.); expression of resistance to 5MT by the somatic hybrids. Breed Sci 46:221–226
Krattinger S, Wicker T, Keller B (2009) Map-based cloning of genes in Triticeae (wheat and barley). In: Muehlbauer GJ, Feuillet C (eds) Genetics and genomics of the Triticeae. Springer, New York, pp 337–357
Kurowska M, Daszkowska-Golec A, Gruszka D et al (2011) TILLING – a shortcut in functional genomics. J Appl Genet 52:371–390
Li X, Song Y, Century K et al (2001) A fast neutron deletion mutagenesis‐based reverse genetics system for plants. Plant J 27:235–242
Li X, Lassner M, Zhang Y (2002) Deleteagene: a fast neutron deletion mutagenesis-based gene knockout system for plants. Comp Funct Genomics 3:158–160
Li T, Liu B, Spalding MH et al (2012) High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat Biotechnol 30:390–392
Lloyd A, Plaisier CL, Carroll D et al (2005) Targeted mutagenesis using zinc-finger nucleases in Arabidopsis. Proc Natl Acad Sci USA 102:2232–2237
Lochlainn SÓ, Amoah S, Graham NS et al (2011) High Resolution Melt (HRM) analysis is an efficient tool to genotype EMS mutants in complex crop genomes. Plant Methods 7:1–9
Lucki I (1998) The spectrum of behaviors influenced by serotonin. Biol Psychiatry 44:151–162
Mahfouz MM, Li L (2011) TALE nucleases and next generation GM crops. GM Crops 2:99–103
Mahfouz MM, Li L, Shamimuzzaman M et al (2011) De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks. Proc Natl Acad Sci USA 108:2623–2628
Mandell JG, Barbas CF (2006) Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases. Nucleic Acids Res 34:W516–W523
Marton I, Zuker A, Shklarman E et al (2010) Non-transgenic genome modification in plant cells. Plant Physiol 154:1079–1087
McCallum CM, Comai L, Greene EA et al (2000) Targeted screening for induced mutations. Nat Biotechnol 18:455–457
Men AE, Laniya TS, Searle IR et al (2002) Fast neutron mutagenesis of soybean (Glycine soja L.) produces a supernodulating mutant containing a large deletion in linkage group H. Genome Lett 1:147–155
Nieto C, Piron F, Dalmais M et al (2007) EcoTILLING for the identification of allelic variants of melon eIF4E, a factor that controls virus susceptibility. BMC Plant Biol 7:34
Oldroyd GE, Long SR (2003) Identification and characterization of nodulation-signaling pathway 2, a gene of Medicago truncatula involved in nod factor signaling. Plant Physiol 131:1027–1032
Oleykowski CA, Mullins CRB, Godwin AK et al (1998) Mutation detection using a novel plant endonuclease. Nucleic Acids Res 26:4597–4602
Osakabe K, Osakabe Y, Toki S (2010) Site-directed mutagenesis in Arabidopsis using custom-designed zinc finger nucleases. Proc Natl Acad Sci USA 107:12034–12039
Perry JA, Wang TL, Welham TJ et al (2003) A TILLING reverse genetics tool and a web-accessible collection of mutants of the legume Lotus japonicus. Plant Physiol 131:866–871
Petolino JF, Worden A, Curlee K et al (2010) Zinc finger nuclease-mediated transgene deletion. Plant Mol Biol 73:617–628
Pruett-Miller SM, Reading DW, Porter SN et al (2009) Attenuation of zinc finger nuclease toxicity by small-molecule regulation of protein levels. PLoS Genet 5:e1000376
Rafalski JA (2010) Association genetics in crop improvement. Curr Opin Plant Biol 13:174–180
Rogers C, Wen J, Chen R et al (2009) Deletion-based reverse genetics in Medicago truncatula. Plant Physiol 151:1077–1086
Saika H, Oikawa A, Matsuda F et al (2011) Application of gene targeting to designed mutation breeding of high-tryptophan rice. Plant Physiol 156:1269–1277
Sander JD, Dahlborg EJ, Goodwin MJ et al (2011) Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Methods 8:67–69
Sato Y, Shirasawa K, Takahashi Y et al (2006) Mutant selection from progeny of gamma-ray-irradiated rice by DNA heteroduplex cleavage using Brassica petiole extract. Breed Sci 56:179–183
Searle IR, Men AE, Laniya TS et al (2003) Long-distance signaling in nodulation directed by a CLAVATA1-like receptor kinase. Science 299:109–112
Shan Q, Wang Y, Chen K et al (2013) Rapid and efficient gene modification in rice and brachypodium using TALENs. Mol Plant 6:1365–1368. doi:10.1093/mp/sss162
Shukla VK, Doyon Y, Miller JC et al (2009) Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature 459:437–441
Slade AJ, Fuerstenberg SI, Loeffler D et al (2004) A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING. Nat Biotechnol 23:75–81
Takano-Kai N, Jiang H, Kubo T et al (2009) Evolutionary history of GS3, a gene conferring grain length in rice. Genetics 182:1323–1334
Till BJ, Reynolds SH, Greene EA et al (2003) Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res 13:524–530
Till BJ, Burtner C, Comai L et al (2004a) Mismatch cleavage by single-strand specific nuclease. Nucleic Acids Res 32:2632–2641
Till BJ, Reynolds SH, Weil C et al (2004b) Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol 4:12
Till BJ, Zerr T, Comai L et al (2006) A protocol for TILLING and Ecotilling in plants and animals. Nat Protoc 1:2465–2477
Till BJ, Cooper J, Tai TH et al (2007) Discovery of chemically induced mutations in rice by TILLING. BMC Plant Biol 7:19
Tovkach A, Zeevi V, Tzfira T (2009) A toolbox and procedural notes for characterizing novel zinc finger nucleases for genome editing in plant cells. Plant J 57:747–757
Townsend JA, Wright DA, Winfrey RJ et al (2009) High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature 459:442–445
Tsai H, Howell T, Nitcher R et al (2011) Discovery of rare mutations in populations: TILLING by sequencing. Plant Physiol 156:1257–1268
Tzfira T, Weinthal D, Marton I et al (2012) Genome modifications in plant cells by custom-made restriction enzymes. Plant Biotechnol J 10:373–389
Urnov FD, Rebar EJ, Holmes MC et al (2010) Genome editing with engineered zinc finger nucleases. Nat Rev Genet 11:636–646
Wang J, Sun J, Liu D et al (2008) Analysis of Pina and Pinb alleles in the micro-core collections of Chinese wheat germplasm by Ecotilling and identification of a novel Pinb allele. J Cereal Sci 48:836–842
Wang TL, Uauy C, Robson F et al (2012) TILLING in extremis. Plant Biotechnol J 10:761–772
Wright DA, Townsend JA, Winfrey RJ Jr et al (2005) High-frequency homologous recombination in plants mediated by zinc-finger nucleases. Plant J 44:693–705
Zhang L, Fetch T, Nirmala J et al (2006) Rpr1, a gene required for Rpg1-dependent resistance to stem rust in barley. Theor Appl Genet 113:847–855
Zhang J, Lu Y, Yuan Y et al (2009) Map-based cloning and characterization of a gene controlling hairiness and seed coat color traits in Brassica rapa. Plant Mol Biol 69:553–563
Zhang F, Maeder ML, Unger-Wallace E et al (2010) High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proc Natl Acad Sci USA 107:12028–12033
Zinc finger consortium. www.zincfingers.org
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
Lee, GJ., Kim, DG., Kwon, SJ., Choi, HI., Kim, D.S. (2015). Identification of Mutagenized Plant Populations. In: Koh, HJ., Kwon, SY., Thomson, M. (eds) Current Technologies in Plant Molecular Breeding. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9996-6_7
Download citation
DOI: https://doi.org/10.1007/978-94-017-9996-6_7
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-017-9995-9
Online ISBN: 978-94-017-9996-6
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)