Advertisement

TILLING for Mutations in Model Plants and Crops

  • Zerihun Tadele
  • Chikelu MBA
  • Bradley J. Till
Chapter

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.

Keywords

Background Mutation Missense Change Tilling Population Mutation Discovery Traditional Sanger Sequencing 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

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.

References

  1. Ahloowalia BS, Maluszynski M, Nichterlein K (2004) Global impact of mutation derived varieties. Euphytica 135:187–204CrossRefGoogle Scholar
  2. Albert TJ, Molla MN, Muzny DM et al. (2007) Direct selection of human genomic loci by microarray hybridization. Nat Methods 4:903–905CrossRefPubMedGoogle Scholar
  3. Bauer R (1957) The induction of vegetative mutations in Ribes nigrum. Hereditas 43:323–337CrossRefGoogle Scholar
  4. Bentley A, MacLennan B, Calvo J et al. (2000) Targeted recovery of mutations in Drosophila. Genetics 156:1169–1173PubMedGoogle Scholar
  5. 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. 40:143–150CrossRefPubMedGoogle Scholar
  6. Ceballos H, Iglesias CA, Pérez JC et al. (2004) Cassava breeding: opportunities and challenges. Plant Mol Biol 56:503–516CrossRefPubMedGoogle Scholar
  7. CNAP, Centre for Novel Agricultural Products (2006) CNAP Artemisia Project. Press pack. The University of York, UKGoogle Scholar
  8. Colbert T, Till BJ, Tompa R et al. (2001) High-throughput screening for induced point mutations Plant Physiol 126:480–484CrossRefPubMedGoogle Scholar
  9. Comai L Young K, Reynolds SH et al. (2004) Efficient discovery of DNA polymorphisms in natural populations by ecotilling. Plant J 37:778–86CrossRefGoogle Scholar
  10. Conway G, Toenniessen G (1999) Feeding the world in the twenty-first century. Nature 402:C55–C58CrossRefGoogle Scholar
  11. Cooper JL, Till BJ, Laport RG et al. (2008) TILLING to detect induced mutations in soybean. BMC Plant Biol 8:9CrossRefPubMedGoogle Scholar
  12. Enserink M (2007) Malaria treatments: ACT two. Science 318:560–563CrossRefPubMedGoogle Scholar
  13. FAO, Food and Agricultural Organization (2002) World agriculture: towards 2015/2030. FAO, RomeGoogle Scholar
  14. Forster BP, Heberle-Bors E, Kasha KJ et al. (2007) The resurgence of haploids in higher plants. Trends Plant Sci 12:368–375CrossRefPubMedGoogle Scholar
  15. 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, RomeGoogle Scholar
  16. Garvin MR, Gharrett AJ (2007) DEco-TILLING: an inexpensive method for single nucleotide polymorphism discovery that reduces ascertainment bias. Mol Ecol Notes 7:735–746CrossRefGoogle Scholar
  17. Gaul H (1958) Present aspects of induced mutations in plant breeding. Euphytica 7:275–289Google Scholar
  18. Getahun H, Lambein F, Vanhoorne M et al. (2003) Food-aid cereals to reduce neurolathyrism related to grasspea preparations during famine. Lancet 362:1808–1810CrossRefPubMedGoogle Scholar
  19. Gilchrist EJ, O’Neil NJ, Rose AM et al. (2006a) TILLING is an effective reverse genetics technique for Caenorhabditis elegans. BMC Genomics 7:262CrossRefPubMedGoogle Scholar
  20. 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 15:1367–1378CrossRefPubMedGoogle Scholar
  21. Greene EA, Codomo CA, Taylor NE et al. (2003) Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis. Genetics 164:731–740PubMedGoogle Scholar
  22. Hall N (2007) Advanced sequencing technologies and their wider impact in microbiology. J Expt Biol 209:1518–1525CrossRefGoogle Scholar
  23. Henikoff S, Comai L (2003) Single-nucleotide mutations for plant functional genomics. Annu Rev Plant Biol 54:375–401CrossRefPubMedGoogle Scholar
  24. Hough LF, Weaver GM (1959) Irradiation as an aid in fruit variety improvement: I. Mutations in the Peach. J Hered 50:59–62Google Scholar
  25. IFPRI, International Food Policy Research Institute (2002) Green Revolution: curse or blessing? IFPRI, Washington DCGoogle Scholar
  26. 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 ppGoogle Scholar
  27. Konzak CF (1957) Genetic effects of radiation on higher plants. Q Rev Biol 32:27–45CrossRefPubMedGoogle Scholar
  28. Li X, Song Y, Century K et al. (2001) A fast neutron deletion mutagenesis-based reverse genetics system for plants. Plant J 27:235–242CrossRefPubMedGoogle Scholar
  29. Mac-Key J (1956) Mutation Breeding in Europe. Brookhaven Symp Biol 9:141–156Google Scholar
  30. Maluszynski M, Nichterlein K, van Zanten L et al. (2000) Officially released mutant varieties – the FAO/IAEA Database. Mut Breed Rev 12:1–84Google Scholar
  31. 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 309–335Google Scholar
  32. McCallum CM, Comai L, Greene EA et al. (2000a) Targeted screening for induced mutations. Nat Biotechnol 18:455–457CrossRefPubMedGoogle Scholar
  33. McCallum CM, Comai L, Greene EA et al. (2000b) Targeting induced local lesions IN genomes (TILLING) for plant functional genomics. Plant Physiol 123:439–442CrossRefPubMedGoogle Scholar
  34. 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 52–62Google Scholar
  35. 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, NYGoogle Scholar
  36. Muller HJ (1928) The measurement of gene mutation rate in Drosophila, its high variability, and its dependence upon temperature. Genetics 13:279–357PubMedGoogle Scholar
  37. 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 302:81–84CrossRefPubMedGoogle Scholar
  38. 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 169:881–889CrossRefPubMedGoogle Scholar
  39. Naylor RL, Falcon WP, Goodman RM et al. (2004) Biotechnology in the developing world: a case for increased investments in orphan crops. Food Policy 29:15–44CrossRefGoogle Scholar
  40. Nelson RJ, Rosamond L, Naylor RL et al. (2004) The role of genomics research in improvement of “orphan” crops. Crop Sci 44:1901–1904CrossRefGoogle Scholar
  41. Nickell LG (1956) The continuous submerged cultivation of plant tissue as single cells. Proc Nat Acad Sci U S A 42:848–850CrossRefGoogle Scholar
  42. 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 7:34CrossRefPubMedGoogle Scholar
  43. Ng PC, Henikoff S (2003) SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 31:3812–3814CrossRefPubMedGoogle Scholar
  44. 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):21–28Google Scholar
  45. 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, 2008Google Scholar
  46. Peng J, Richards DE, Hartley NM et al. (1999) Green revolution genes encode mutant gibberellin response modulators. Nature 400:258–261Google Scholar
  47. 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. 131:866–871CrossRefPubMedGoogle Scholar
  48. 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 23–32Google Scholar
  49. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386PubMedGoogle Scholar
  50. Sasaki A, Ashikari M, Ueguchi-Tanaka M et al. (2002) Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416:701–702CrossRefPubMedGoogle Scholar
  51. 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 56:179–183CrossRefGoogle Scholar
  52. Shendure JA, Porreca GJ, Church GM (2008) Overview of DNA sequencing strategies. Curr Protoc Mol Biol Chapter 7:Unit 7.1Google Scholar
  53. Singleton WR (1955) The contribution of radiation genetics to agriculture. Agronomy J 47:113–117CrossRefGoogle Scholar
  54. Slade AJ, Fuerstenberg SI, Loeffler D et al. (2005) A reverse genetic, Nontransgenic approach to wheat crop improvement by TILLING. Nat Biotechnol. 23:75–81CrossRefPubMedGoogle Scholar
  55. Smith HH (1958) Radiation in the production of useful mutations. Bot Rev 24:1–24CrossRefGoogle Scholar
  56. Spaenij-Dekking L, KooyWinkelaar Y, Koning F (2005) The Ethiopian cereal tef in celiac disease. New Engl J Med 353:1748–1749CrossRefPubMedGoogle Scholar
  57. 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 76–113Google Scholar
  58. 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 99:9043–9048CrossRefGoogle Scholar
  59. 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 279:213–223CrossRefPubMedGoogle Scholar
  60. Szarejko I, Forster BP (2007) Doubled haploidy and induced mutation. Euphytica158:359–370CrossRefGoogle Scholar
  61. Taylor NE, Greene EA (2003) PARSESNP: A tool for the analysis of nucleotide polymorphisms. Nucleic Acids Res 31:3808–3811CrossRefPubMedGoogle Scholar
  62. Till BJ, Reynolds SH, Greene EA et al. (2003) Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res 13:524–530CrossRefPubMedGoogle Scholar
  63. Till BJ, Reynolds SH, Weil C et al. (2004a) Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol 4:12CrossRefPubMedGoogle Scholar
  64. Till BJ, Burtner C, Comai L et al. (2004b) Mismatch cleavage by single-strand specific nucleases. Nucleic Acids Res 32:2632–2641CrossRefPubMedGoogle Scholar
  65. Till BJ, Zerr T, Bowers E et al. (2006a) High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling. Nucleic Acids Res 34:e99CrossRefGoogle Scholar
  66. Till BJ, Zerr T, Comai L et al. (2006b) A protocol for TILLING and Ecotilling in plants and animals. Nat Protoc 1:2465–2477CrossRefPubMedGoogle Scholar
  67. Till BJ, Cooper J, Tai TH et al. (2007) Discovery of chemically induced mutations in rice by TILLING. BMC Plant Biol 7:19CrossRefPubMedGoogle Scholar
  68. 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 51:1116–1125CrossRefPubMedGoogle Scholar
  69. United Nations (2007) World population prospects, the 2006 revision. United Nations Department of Economic and Social Affairs, New YorkGoogle Scholar
  70. Van Harten AM (1998) Mutation Breeding: Theory and Practical Applications. Cambridge University Press, Cambridge, UK, pp 353Google Scholar
  71. Vetter J (2000) Plant cyanogenic glycosides. Toxocon 38:11–36CrossRefGoogle Scholar
  72. von Braun J, Pachauri RK (2006) The Promises and Challenges of Biofuels for the Poor in Developing Countries. International Food Policy Institute, Washington DCGoogle Scholar
  73. Wang Y, Li J (2006) Genes controlling plant architecture. Curr Opin Biotechnol 17:123–129CrossRefPubMedGoogle Scholar
  74. Wienholds E, Schulte-Merker S et al. (2002) Target-selected inactivation of the zebrafish rag1 gene. Science 297:99–102CrossRefPubMedGoogle Scholar
  75. Wienholds E, van Eeden F, Kosters M et al. (2003) Efficient target-selected mutagenesis in zebrafish. Genome Res 13:2700–2707CrossRefPubMedGoogle Scholar
  76. Williams JT, Haq N (2002) Global research on underutilized crops. An assessment of current activities and proposals for enhanced cooperation. ICUC, Southampton, UKGoogle Scholar
  77. Winkler S, Schwabedissen A, Backasch D et al. (2005) Target-selected mutant screen by TILLING in Drosophila. Genome Res15:718–723CrossRefPubMedGoogle Scholar
  78. Ye X, Al-Babili S, Klöti A et al. (2000) Engineering the provitamin A (beta-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. Science 287:303–305CrossRefPubMedGoogle Scholar
  79. Zerr T, Henikoff S (2005) Automated band mapping in electrophoretic gel images using background information. Nucleic Acids Res 33:2806–2812CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.Institute of Plant Sciences, University of BernBernSwitzerland
  2. 2.Plant Breeding Unit, FAO/IAEA Agricultural and Biotechnology LaboratorySeibersdorfAustria

Personalised recommendations