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TILLING for Mutations in Model Plants and Crops

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Molecular Techniques in Crop Improvement

Abstract

A growing world population, changing climate and limiting fossil fuels will provide new pressures on human production of food, medicine, fuels and feed stock in the twenty-first century. Enhanced crop production promises to ameliorate these pressures. Crops can be bred for increased yields of calories, starch, nutrients, natural medicinal compounds, and other important products. Enhanced resistance to biotic and abiotic stresses can be introduced, toxins removed, and industrial qualities such as fibre strength and biofuel per mass can be increased. Induced and natural mutations provide a powerful method for the generation of heritable enhanced traits. While mainly exploited in forward, phenotype driven, approaches, the rapid accumulation of plant genomic sequence information and hypotheses regarding gene function allows the use of mutations in reverse genetic approaches to identify lesions in specific target genes. Such gene-driven approaches promise to speed up the process of creating novel phenotypes, and can enable the generation of phenotypes unobtainable by traditional forward methods. TILLING (Targeting Induced Local Lesions IN Genome) is a high-throughput and low cost reverse genetic method for the discovery of induced mutations. The method has been modified for the identification of natural nucleotide polymorphisms, a process called Ecotilling. The methods are general and have been applied to many species, including a variety of different crops. In this chapter the current status of the TILLING and Ecotilling methods and provide an overview of progress in applying these methods to different plant species, with a focus on work related to food production for developing nations.

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References

  • Ahloowalia BS, Maluszynski M, Nichterlein K (2004) Global impact of mutation derived varieties. Euphytica 135:187–204

    Article  Google Scholar 

  • Albert TJ, Molla MN, Muzny DM et al. (2007) Direct selection of human genomic loci by microarray hybridization. Nat Methods 4:903–905

    Article  CAS  PubMed  Google Scholar 

  • Bauer R (1957) The induction of vegetative mutations in Ribes nigrum. Hereditas 43:323–337

    Article  Google Scholar 

  • Bentley A, MacLennan B, Calvo J et al. (2000) Targeted recovery of mutations in Drosophila. Genetics 156:1169–1173

    CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Ceballos H, Iglesias CA, Pérez JC et al. (2004) Cassava breeding: opportunities and challenges. Plant Mol Biol 56:503–516

    Article  CAS  PubMed  Google Scholar 

  • CNAP, Centre for Novel Agricultural Products (2006) CNAP Artemisia Project. Press pack. The University of York, UK

    Google Scholar 

  • Colbert T, Till BJ, Tompa R et al. (2001) High-throughput screening for induced point mutations Plant Physiol 126:480–484

    Article  CAS  PubMed  Google Scholar 

  • Comai L Young K, Reynolds SH et al. (2004) Efficient discovery of DNA polymorphisms in natural populations by ecotilling. Plant J 37:778–86

    Article  Google Scholar 

  • Conway G, Toenniessen G (1999) Feeding the world in the twenty-first century. Nature 402:C55–C58

    Article  Google Scholar 

  • Cooper JL, Till BJ, Laport RG et al. (2008) TILLING to detect induced mutations in soybean. BMC Plant Biol 8:9

    Article  PubMed  Google Scholar 

  • Enserink M (2007) Malaria treatments: ACT two. Science 318:560–563

    Article  CAS  PubMed  Google Scholar 

  • FAO, Food and Agricultural Organization (2002) World agriculture: towards 2015/2030. FAO, Rome

    Google Scholar 

  • Forster BP, Heberle-Bors E, Kasha KJ et al. (2007) The resurgence of haploids in higher plants. Trends Plant Sci 12:368–375

    Article  CAS  PubMed  Google Scholar 

  • Gale M (2002) Applications of molecular biology and genomics to geneticenhancement of crop tolerance to abiotic stress – a discussion document. Food and Agriculture Organization of the United Nations, Rome

    Google Scholar 

  • Garvin MR, Gharrett AJ (2007) DEco-TILLING: an inexpensive method for single nucleotide polymorphism discovery that reduces ascertainment bias. Mol Ecol Notes 7:735–746

    Article  CAS  Google Scholar 

  • Gaul H (1958) Present aspects of induced mutations in plant breeding. Euphytica 7:275–289

    Google Scholar 

  • Getahun H, Lambein F, Vanhoorne M et al. (2003) Food-aid cereals to reduce neurolathyrism related to grasspea preparations during famine. Lancet 362:1808–1810

    Article  PubMed  Google Scholar 

  • Gilchrist EJ, O’Neil NJ, Rose AM et al. (2006a) TILLING is an effective reverse genetics technique for Caenorhabditis elegans. BMC Genomics 7:262

    Article  PubMed  Google Scholar 

  • Gilchrist EJ, Haughn GW, Ying CC et al. (2006b) Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa. Mol Ecol 15:1367–1378

    Article  CAS  PubMed  Google Scholar 

  • Greene EA, Codomo CA, Taylor NE et al. (2003) Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis. Genetics 164:731–740

    CAS  PubMed  Google Scholar 

  • Hall N (2007) Advanced sequencing technologies and their wider impact in microbiology. J Expt Biol 209:1518–1525

    Article  Google Scholar 

  • Henikoff S, Comai L (2003) Single-nucleotide mutations for plant functional genomics. Annu Rev Plant Biol 54:375–401

    Article  CAS  PubMed  Google Scholar 

  • Hough LF, Weaver GM (1959) Irradiation as an aid in fruit variety improvement: I. Mutations in the Peach. J Hered 50:59–62

    Google Scholar 

  • IFPRI, International Food Policy Research Institute (2002) Green Revolution: curse or blessing? IFPRI, Washington DC

    Google Scholar 

  • Ketema S (1997) Tef [(Eragrostis tef (Zucc.)Trotter]. Promoting the conservation and use of underutilized and neglected crops. 12. Institute of Plant Genetics and Crop Plant Research, Gatersleben/International Plant Genetic Resources institute, Rome, Italy. 50 pp

    Google Scholar 

  • Konzak CF (1957) Genetic effects of radiation on higher plants. Q Rev Biol 32:27–45

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Mac-Key J (1956) Mutation Breeding in Europe. Brookhaven Symp Biol 9:141–156

    Google Scholar 

  • Maluszynski M, Nichterlein K, van Zanten L et al. (2000) Officially released mutant varieties – the FAO/IAEA Database. Mut Breed Rev 12:1–84

    Google Scholar 

  • Maluszynski M, Kasha KJ, Szarejko I (2003) Published doubled haploid protocols in plant species. In: Maluszynski M, Kasha KJ, Forster BP, Szarejko I (eds) Doubled hapolid production in crop plants: a manual. Kluwer Academic, Dordrecht, The Netherlands, pp 309–335

    Google Scholar 

  • McCallum CM, Comai L, Greene EA et al. (2000a) Targeted screening for induced mutations. Nat Biotechnol 18:455–457

    Article  CAS  PubMed  Google Scholar 

  • McCallum CM, Comai L, Greene EA et al. (2000b) Targeting induced local lesions IN genomes (TILLING) for plant functional genomics. Plant Physiol 123:439–442

    Article  CAS  PubMed  Google Scholar 

  • Micke A, Donini B (1993) Induced Mutations. In: Hayward MD, Bosemark NO, Romagosa I (eds) Plant Breeding, Principles and Prospects. Chapman and Hall, London, UK, pp 52–62

    Google Scholar 

  • Miksche JP, Shapiro S (1963) Use of neutron irradiations in the Brookhaven Mutations Program. Technical Report. From International Atomic Energy Agency Symposium on the Biological Effects of Neutron Irradiations, Upton, NY

    Google Scholar 

  • Muller HJ (1928) The measurement of gene mutation rate in Drosophila, its high variability, and its dependence upon temperature. Genetics 13:279–357

    CAS  PubMed  Google Scholar 

  • Multani DBS, Briggs SP, Chamberlin MA et al. (2003) Loss of an MDR Transporter in Compact Stalks of Maize br2 and Sorghum dw3 Mutants. Science 302:81–84

    Article  CAS  PubMed  Google Scholar 

  • Naito K, Kusaba M, Shikazono N et al. (2005) Transmissible and nontransmissible mutations induced by irradiating Arabidopsis thaliana pollen with gamma-rays and carbon ions. Genetics 169:881–889

    Article  CAS  PubMed  Google Scholar 

  • Naylor RL, Falcon WP, Goodman RM et al. (2004) Biotechnology in the developing world: a case for increased investments in orphan crops. Food Policy 29:15–44

    Article  Google Scholar 

  • Nelson RJ, Rosamond L, Naylor RL et al. (2004) The role of genomics research in improvement of “orphan” crops. Crop Sci 44:1901–1904

    Article  Google Scholar 

  • Nickell LG (1956) The continuous submerged cultivation of plant tissue as single cells. Proc Nat Acad Sci U S A 42:848–850

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • Ng PC, Henikoff S (2003) SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 31:3812–3814

    Article  CAS  PubMed  Google Scholar 

  • Novak FJ, Afza R, Van Duren M et al. (1990) Mutation induction by gamma irradiation of in vitro cultured shoot-tips of banana and plantain (Musa cvs). Top Agric (Trinidad) 60(1):21–28

    Google Scholar 

  • NRC (National Research Council) (1996) Tef. In: Lost crops of Africa.Vol. I.: Grains. National Academy of Press, Washington DC. Nutrient Data Laboratory, United States Department of Agriculture pp 215–235. http://www.nutritiondata.com/facts-C00001-01c20cX.html#nutrients-per-serving. Accessed May 20, 2008

    Google Scholar 

  • Peng J, Richards DE, Hartley NM et al. (1999) Green revolution genes encode mutant gibberellin response modulators. Nature 400:258–261

    Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Roux NS (2004) Mutation Induction in Musa. In: Jain SM, Swennen, R (eds) Banana improvement: cellular, molecular biology and induced mutations. Science Publishers Inc., Enfield, NH, USA, pp 23–32

    Google Scholar 

  • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386

    CAS  PubMed  Google Scholar 

  • Sasaki A, Ashikari M, Ueguchi-Tanaka M et al. (2002) Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416:701–702

    Article  CAS  PubMed  Google Scholar 

  • Sato Y, Shirasawa K, Takahashi Y, Nishimura M, Nishio T (2006) Mutant selection from progeny of gamma-ray-irradiated rice by DNA heteroduplex cleavage using Brassica Petiole extract. Breed Science 56:179–183

    Article  CAS  Google Scholar 

  • Shendure JA, Porreca GJ, Church GM (2008) Overview of DNA sequencing strategies. Curr Protoc Mol Biol Chapter 7:Unit 7.1

    Google Scholar 

  • Singleton WR (1955) The contribution of radiation genetics to agriculture. Agronomy J 47:113–117

    Article  Google Scholar 

  • Slade AJ, Fuerstenberg SI, Loeffler D et al. (2005) A reverse genetic, Nontransgenic approach to wheat crop improvement by TILLING. Nat Biotechnol. 23:75–81

    Article  CAS  PubMed  Google Scholar 

  • Smith HH (1958) Radiation in the production of useful mutations. Bot Rev 24:1–24

    Article  Google Scholar 

  • Spaenij-Dekking L, KooyWinkelaar Y, Koning F (2005) The Ethiopian cereal tef in celiac disease. New Engl J Med 353:1748–1749

    Article  CAS  PubMed  Google Scholar 

  • Sparrow AH (1956) Cytological changes induced by ionizing radiations and their possible relation to the production of useful mutations in plants. Work Conference on Radiation Induced Mutations. Biology Department, Brookhaven National Laboratory, Upton, New York, pp 76–113

    Google Scholar 

  • Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), “green revolution”rice, contains a defective gibberellin 20-oxidase gene. Proc Nat Acad Sci U S A 99:9043–9048

    Article  CAS  Google Scholar 

  • Suzuki T, Eiguchi M, Kumamaru T, Satoh H, Matsusaka H, Moriguchi K, Nagato Y, Kurata N (2008) MNU-induced mutant pools and high performance TILLING enable finding of any gene mutation in rice. Mol Genet Genomics 279:213–223

    Article  CAS  PubMed  Google Scholar 

  • Szarejko I, Forster BP (2007) Doubled haploidy and induced mutation. Euphytica158:359–370

    Article  Google Scholar 

  • Taylor NE, Greene EA (2003) PARSESNP: A tool for the analysis of nucleotide polymorphisms. Nucleic Acids Res 31:3808–3811

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Till BJ, Reynolds SH, Weil C et al. (2004a) Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol 4:12

    Article  PubMed  Google Scholar 

  • Till BJ, Burtner C, Comai L et al. (2004b) Mismatch cleavage by single-strand specific nucleases. Nucleic Acids Res 32:2632–2641

    Article  CAS  PubMed  Google Scholar 

  • Till BJ, Zerr T, Bowers E et al. (2006a) High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling. Nucleic Acids Res 34:e99

    Article  Google Scholar 

  • Till BJ, Zerr T, Comai L et al. (2006b) A protocol for TILLING and Ecotilling in plants and animals. Nat Protoc 1:2465–2477

    Article  CAS  PubMed  Google Scholar 

  • Till BJ, Cooper J, Tai TH et al. (2007) Discovery of chemically induced mutations in rice by TILLING. BMC Plant Biol 7:19

    Article  PubMed  Google Scholar 

  • Triques K, Sturbois B, Gallais S et al. (2007) Characterization of Arabidopsis thaliana mismatch specific endonucleases: application to mutation discovery by TILLING in pea. Plant J 51:1116–1125

    Article  CAS  PubMed  Google Scholar 

  • United Nations (2007) World population prospects, the 2006 revision. United Nations Department of Economic and Social Affairs, New York

    Google Scholar 

  • Van Harten AM (1998) Mutation Breeding: Theory and Practical Applications. Cambridge University Press, Cambridge, UK, pp 353

    Google Scholar 

  • Vetter J (2000) Plant cyanogenic glycosides. Toxocon 38:11–36

    Article  CAS  Google Scholar 

  • von Braun J, Pachauri RK (2006) The Promises and Challenges of Biofuels for the Poor in Developing Countries. International Food Policy Institute, Washington DC

    Google Scholar 

  • Wang Y, Li J (2006) Genes controlling plant architecture. Curr Opin Biotechnol 17:123–129

    Article  CAS  PubMed  Google Scholar 

  • Wienholds E, Schulte-Merker S et al. (2002) Target-selected inactivation of the zebrafish rag1 gene. Science 297:99–102

    Article  CAS  PubMed  Google Scholar 

  • Wienholds E, van Eeden F, Kosters M et al. (2003) Efficient target-selected mutagenesis in zebrafish. Genome Res 13:2700–2707

    Article  CAS  PubMed  Google Scholar 

  • Williams JT, Haq N (2002) Global research on underutilized crops. An assessment of current activities and proposals for enhanced cooperation. ICUC, Southampton, UK

    Google Scholar 

  • Winkler S, Schwabedissen A, Backasch D et al. (2005) Target-selected mutant screen by TILLING in Drosophila. Genome Res15:718–723

    Article  CAS  PubMed  Google Scholar 

  • Ye X, Al-Babili S, Klöti A et al. (2000) Engineering the provitamin A (beta-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. Science 287:303–305

    Article  CAS  PubMed  Google Scholar 

  • Zerr T, Henikoff S (2005) Automated band mapping in electrophoretic gel images using background information. Nucleic Acids Res 33:2806–2812

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

ZT is grateful to Syngenta Foundation for Sustainable Agriculture and University of Bern for financial support to the Tef Biotechnology Project. The Food and Agriculture Organization of the United Nations and the International Atomic Energy Agency through their Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture provide generous support for induced crop mutagenesis activities; this makes the work of BT and CM possible at the Agency’s laboratories in Seibersdorf, Austria.

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Authors and Affiliations

  1. Institute of Plant Sciences, University of Bern, Bern, Switzerland

    Zerihun Tadele

  2. Plant Breeding Unit, FAO/IAEA Agricultural and Biotechnology Laboratory, Seibersdorf, Austria

    Chikelu MBA & Bradley J. Till

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  1. Zerihun Tadele
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  2. Chikelu MBA
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  3. Bradley J. Till
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Correspondence to Bradley J. Till .

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Editors and Affiliations

  1. Department of Applied Biology, University of Helsinki, Helsinki, Finland

    S. Mohan Jain

  2. Institute (IRRI), Social Sciences Division, International Rice Research, Metro Manila, Philippines

    D.S. Brar

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Tadele, Z., MBA, C., Till, B.J. (2010). TILLING for Mutations in Model Plants and Crops. In: Jain, S., Brar, D. (eds) Molecular Techniques in Crop Improvement. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-2967-6_13

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