Abstract
Molecular techniques have created the opportunity for great advances in plant mutation genetics and the science of mutation breeding. The powerful targeted induced local lesions in genomes (TILLING) technique has introduced the possibility of reverse genetics—the ability to screen for mutations at the DNA level prior to assessing phenotype. Fundamental to TILLING is the induction of mutant populations (or alternatively, the identification of mutants in the environment); and mutation induction requires an understanding and assessment of the appropriate mutagen dose required. The techniques of mutation induction, dose optimization, and TILLING are explained.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Muller HJ (1927) Artificial transmutation of the gene. Science 66:84–87
Stadler LJ (1928) Mutations in barley induced by x-rays and radium. Science 68:186–187
Ahloowalia BS, Maluszynski M, Nichterlein K (2004) Global impact of mutation-derived varieties. Euphytica 135:187–204
Wang ZY, Zheng F, Shen G et al (1995) The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy gene. Plant J 7:613–622
Bradbury LMT, Fitzgerald TL, Henry RJ et al (2005) The gene for fragrance in rice. Plant Biotechnol J 3:363–370
Juwattanasomran R, Somta P, Chankaew S et al (2011) A SNP in GmBADH2gene associates with fragrance in vegetable soybean variety "Kaori" and SNAP marker development for the fragrance. Theor Appl Genet 122:533–541
Monna L, Kitazawa N, Yoshino R et al (2002) Positional cloning of rice semidwarfing gene, sd-1: rice "Green revolution gene" encodes a mutant enzyme involved in gibberellin synthesis. DNA Res 9:11–17
Konishi S, Izawa T, Lin SY et al (2006) An SNP caused loss of seed shattering during rice domestication. Science 312:1392–1396
van Harten AM (1998) Mutation Breeding: theory and practical applications. Cambridge University Press, Cambridge, p 113ff
McCallum CM, Comai L, Greene EA et al (2000) Targeted screening for induced mutations. Nat Biotechnol 18:455–457
Wienholds E, van Eeden F, Kosters M et al (2003) Efficient target-selected mutagenesis in zebrafish. Genome Res 13:2700–2707
Greene E, Codomo C, Taylor N et al (2003) Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis. Genet 164:731–740
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
Bruggemann E, Handwerger K, Essex C et al (1996) Analysis of fast neutron-generated mutants at the Arabidopsis thaliana HY4 locus. Plant J 10:755–760
Shirley BW, Hanley S, Goodman HM (1992) Effects of ionizing radiation on a plant genome: analysis of two arabidopsis transparent testa mutations. Plant Cell 4:333–347
Shikazono N, Suzuki C, Watanabe H et al (2005) Analysis of mutations induced by carbon ions in Arabidopsis thaliana. J Exp Bot 56:587–596
Kazama Y, Hirano T, Saito H et al (2011) Characterization of highly efficient heavy-ion mutagenesis in Arabidopsis thaliana. BMC Plant Biol 11:161–170
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. Genet 169:881–889
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
Harding SS, Mohamad O (2009) Radiosensitivity test on two varieties of Terengganu and Arab used in mutation breeding of roselle (Hibiscus sabdariffa L.). Afr J Plant Sci 3:181–183
Plewa MJ, Dowd PA, Wagner ED (1984) Calibration of the maize yg2 assay using gamma radiation and ethylmethanesulfonate. Environ Mutagen 6:781–795
Sarduie-Nasab S, Sharifi-Sirchi GR, Torabi-Sirchi MH (2010) Assessment of dissimilar gamma irradiations on barley (Hordeum vulgare spp.). J Plant Breed Crop Sci 2:59–63
Lundqvist U (1992) Mutation Research in Barley. PhD Thesis. Swedish University of Agricultural Sciences, Svalov
Koornneeff M, Dellaert LWM, van der Veen JH (1982) EMS- and relation-induced mutation frequencies at individual loci in Arabidopsis thaliana (L.) Heynh. Mutat Res 93:109–123
Lee LS, Izquierdo L, Rice N et al (2004) Modifying sorghum starch/protein structure for human consumption. 54th Cereal Chemistry Division Conference of the Royal Australian Chemical Institute. Canberra, pp 308–310
Schy WE, Plewa MJ (1989) Molecular dosimetry studies of forward mutation induced at the yg2 locus in maize by ethyl methanesulfonate. Mutat Res 211:231–241
van Zeeland AA (1996) Molecular dosimetry of chemical mutagens. Relationship between DNA adduct formation and genetic changes analyzed at the molecular level. Mutat Res 353:123–150
Henikoff S, Comai L (2003) Single-nucleotide mutations for plant functional genomics. Annu Rev Plant Biol 54:375–401
Laurie DA, Pratchett N, Allen RL et al (1996) RFLP mapping of the barley homeotic mutant lax-a. Theor Appl Genet 93:81–85
Voylokov AV, Korzun V, Borner A (1998) Mapping of three self-fertility mutations in rye (Secale cereale L.) using RFLP, isozyme and morphological markers. Theor Appl Genet 97:147–153
Williams KJ, Fisher JM, Langridge P (1996) Development of a PCR-based allele-specific assay from an RFLP probe linked to resistance to cereal cyst nematode in wheat. Genome 39:798–801
Godwin ID, Sangduen N, Kunanuvatchaidach R et al (1997) RAPD polymorphisms among variant and phenotypically normal rice (Oryza sativa var indica) somaclonal progenies. Plant Cell Rep 16:320–324
Osipova ES, Koveza OV, Troitskij AV et al (2003) Analysis of specific RAPD and ISSR fragments in maize (Zea mays L.) somaclones and development of SCAR markers on their basis. Russ J Genet 39:1412–1419
Suo GL, Huang ZJ, He CF et al (2001) Identification of the molecular markers linked to the salt-resistance locus in the wheat using RAPD-BSA technique. Acta Botanica Sinica 43:598–602
Fu H-W, Li Y-F, Shu Q-Y (2008) A revisit of mutation induction by gamma rays in rice (Oryza sativa L.): implications of microsatellite markers for quality control. Mol Breed 22:281–288
Lu JY, Zhang WL, Xue H et al (2010) Changes in AFLP and SSR DNA polymorphisms induced by short-term space flight of rice seeds. Biol Plantarum 54:112–116
Salina E, Borner A, Leonova I et al (2000) Microsatellite mapping of the induced sphaerococcoid mutation genes in Triticum aestivum. Theor Appl Genet 100:686–689
Schmidt AL, Mitter V (2004) Microsatellite mutation directed by an external stimulus. Mutat Res 568:233–243
Castiglioni P, Pozzi C, Heun M et al (1998) An AFLP-based procedure for the efficient mapping of mutations and DNA probes in barley. Genet 149:2039–2056
Komatsuda T, Maxim P, Senthil N et al (2004) High-density AFLP map of nonbrittle rachis 1 (btr1) and 2 (btr2) genes in barley (Hordeum vulgare L.). Theor Appl Genet 109:986–995
Pasini L, Stile MR, Puja E et al (2008) The integration of mutant loci affecting maize endosperm development in a dense genetic map using an AFLP-based procedure. Mol Breed 22:527–541
Rashid M, Liu R-H, Jin W et al (2009) Genomic diversity among Basmati rice (Oryza sativa L) mutants obtained through Co-60 gamma radiations using AFLP markers. Afr J Biotechnol 8:6777–6783
Wienholds E, Schulte-Merker S, Walderich B et al (2002) Target-selected inactivation of the zebrafish rag1 gene. Science 297:99–102
Oleykowski CA, Mullins CRB, Godwin AK et al (1998) Mutation detection using a novel plant endonuclease. Nucleic Acids Res 26:4597–4602
McCallum CM, Comai L, Greene EA et al (2000) Targeting Induced Local Lesions IN Genomes (TILLING) for plant functional genomics. Plant Physiol 123:439–442
Caldwell D, 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
Slade AJ, Knauf VC (2005) TILLING moves beyond functional genomics into crop improvement. Transgenic Res 14:109–115
Till B, Reynolds S, Weil C et al (2004) Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol 4:1471–2229
Xin Z, Li Wang M, Barkley N et al (2008) Applying genotyping (TILLING) and phenotyping analyses to elucidate gene function in a chemically induced sorghum mutant population. BMC Plant Biol 8:103. doi:10.1186/1471-2229-8-103
Cordeiro G, Eliott FG, Henry RJ (2006) An optimized ecotilling protocol for polyploids or pooled samples using a capillary electrophoresis system. Anal Biochem 355:145–147
Domon E, Saito A, Takeda K (2002) Comparison of the waxy locus sequence from a non-waxy strain and two waxy mutants of spontaneous and artificial origins in barley. Genes Genet Syst 77:351–359
Szantai E, Ronai Z, Szilagyi A et al (2005) Haplotyping by capillary electrophoresis. J Chromatogr A 1079:41–49
Tsai H, Howell T, Nitcher R et al (2011) Discovery of rare mutations in populations: TILLING by sequencing. Plant Physiol 156:1257–1268. doi:10.1104/pp. 110.169748
Till BJ, Zerr T, Comai L et al (2006) A protocol for TILLING and Ecotilling in plants and animals. Nat Protoc 1:2465–2477. doi:10.1038/nprot.2006.329
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. doi:10.1101/gr.977903
Jankowicz-Cieslak J, Huynh OA, Bado S et al (2011) Reverse-genetics by TILLING expands through the plant kingdom. Emir J Food Agric 23:290–300
Till BJ, Burtner C, Comai L et al (2004) Mismatch cleavage by single-strand specific nucleases. Nucleic Acids Res 32:2632–2641, 32/8/2632 [pii]10.1093/nar/gkh599
Triques K, Piednoir E, Dalmais M et al (2008) Mutation detection using ENDO1: application to disease diagnostics in humans and TILLING and Eco-TILLING in plants. BMC Mol Biol 9:42. doi:10.1186/1471-2199-9-42
Stephenson P, Baker D, Girin T et al (2010) A rich TILLING resource for studying gene function in Brassica rapa. BMC Plant Biol 10:62. doi:10.1186/1471-2229-10-62
Ramos ML, Huntley JJ, Maleki SJ et al (2009) Identification and characterization of a hypoallergenic ortholog of Ara h 2.01. Plant Mol Biol 69:325–335. doi:10.1007/s11103-008-9428-z
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. doi:10.1038/nbt1043
Blomstedt CK, Gleadow RM, O'Donnell N et al (2012) A combined biochemical screen and TILLING approach identifies mutations in Sorghum bicolor L. Moench resulting in acyanogenic forage production. Plant Biotechnol J 10:54–66. doi:10.1111/j.1467-7652.2011.00646.x
Till BJ, Reynolds SH, Weil C et al (2004) Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol 4:12. doi:10.1186/1471-2229-4-12
Cooper JL, Till BJ, Laport RG et al (2008) TILLING to detect induced mutations in soybean. BMC Plant Biol 8:9. doi:10.1186/1471-2229-8-9
Till BJ, Cooper J, Tai TH et al (2007) Discovery of chemically induced mutations in rice by TILLING. BMC Plant Biol 7:19. doi:10.1186/1471-2229-7-19
Marroni F, Pinosio S, Di Centa E et al (2011) Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation Ecotilling. Plant J 67:736–745. doi:10.1111/j.1365-313X.2011.04627.x
Till BJ, Zerr T, Bowers E et al (2006) High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling. Nucleic Acids Res 34:e99, 34/13/e99 [pii]10.1093/nar/gkl479
Till BJ, Jankowicz-Cieslak J, Sagi L et al (2010) Discovery of nucleotide polymorphisms in the Musa gene pool by Ecotilling. Theor Appl Genet 121:1381–1389. doi:10.1007/s00122-010-1395-5
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. doi:10.1186/1471-2229-11-156
Vriet C, Welham T, Brachmann A et al (2010) A suite of Lotus japonicus starch mutants reveals both conserved and novel features of starch metabolism. Plant Physiol 154:643–655. doi:10.1104/pp. 110.161844
Cross MJ, Waters DL, Lee LS et al (2008) Endonucleolytic mutation analysis by internal labeling (EMAIL). Electrophoresis 29:1291–1301. doi:10.1002/elps.200700452
Wang TL, Uauy C, Robson F et al (2012) TILLING in extremis. Plant Biotechnol J 10:761–772. doi:10.1111/j.1467-7652.2012.00708.x
Zerr T, Henikoff S (2005) Automated band mapping in electrophoretic gel images using background information. Nucleic Acids Res 33(9):2806–2812, 33/9/2806 [pii]10.1093/nar/gki580
Abramoff MD, Magalhael PJ, Ram SJ (2004) Image processing with ImageJ. Biophotonics International 11:36–42
Acknowledgments
Authors B.J.T., O.A.H., and J.J-C. wish to thank Kamila Kozak-Stankiewicz for supplying lupine samples used for making Fig. 2c. Funding for the work on low-cost TILLING and EcoTILLING was provided by 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.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media New York
About this protocol
Cite this protocol
Lee, L.S., Till, B.J., Hill, H., Huynh, O.A., Jankowicz-Cieslak, J. (2014). Mutation and Mutation Screening. In: Henry, R., Furtado, A. (eds) Cereal Genomics. Methods in Molecular Biology, vol 1099. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-715-0_8
Download citation
DOI: https://doi.org/10.1007/978-1-62703-715-0_8
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-714-3
Online ISBN: 978-1-62703-715-0
eBook Packages: Springer Protocols