Abstract
The modern crop scientist has a large amount of available nucleotide sequence information to identify genes of potential agronomic importance. Using reverse genetic approaches, specific genes can be disrupted, and hypotheses regarding gene function directly tested in vivo. Although a number of reverse genetic methods have been introduced, many are limited in application because they are organism-specific, expensive, transgenic or only transiently disrupt gene function. However, traditional mutagenesis using chemical mutagens has been widely used as a forward genetics strategy to create many new crop plant varieties at relatively low cost. Mutagens such as ethyl methanesulphonate (EMS), cause stable point mutations and thus produce an allelic series of truncation and missense changes that can provide a range of phenotypes. TILLING (Targeting Induced Local Lesions IN Genomes) uses traditional mutagenesis and SNP discovery methods for a reverse genetic strategy that is high in throughput, low in cost, and applicable to most organisms. Over the past six years, TILLING has moved from proof-of-concept to production with the establishment of publicly available services for Arabidopsis, maize, lotus, and barley. Pilot-scale projects have been completed on several other plant species, including wheat. The protocols developed for TILLING have been adapted for the discovery of natural nucleotide diversity, a method termed EcoTILLING. Like TILLING, EcoTILLING is general and has been applied to plants as diverse as Arabidopsis and poplar. We review here current TILLING and EcoTILLING technologies and discuss the progress that has been made in applying these methods to many different plant species.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
An G, Jeong DH, Jung KH, Lee S, (2005) Reverse genetic approaches for functional genomics of rice. Plant Mol Biol 59:111–123
Bradley JT, Reynolds SH, Weil C, Springer N, Burthner C, Young K, Bowers E, Coclomo, CA, Enns LC, Odden AR, Greena EA, Comai L, Henikoff S (2004) Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol 4:12
Burch-Smith TM, Anderson JC, Martin GB, Dinesh-Kumar SP (2004) Applications and advantages of virus-induced gene silencing for gene function studies in plants. Plant J 39:734–746
Caldwell DG, McCallum N, Shaw P, Muehlbauer GJ, Marshall DF, Waugh R (2004) A structured mutant population for forward and reverse genetics in Barley (Hordeum vulgare L.). Plant J 40:143–50
Colbert T, Till BJ, Tompa R, Reynolds S, Steine MN, Yeung AT, McCallum CM, Comai L, Henikoff S, (2001) High-throughput screening for induced point mutations. Plant Physiol 126:480–484
Comai L, Young K, Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Henikoff s (2004) Efficient discovery of DNA polymorphisms in natural populations by EcoTILLING. Plant J 37:778–786
Comai L, Young K, Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Henikoff S (2006) TILLING: practical single-nucleotide mutation discovery. Plant J 45:684–694.
Fuhrmann M, Oertel W, Berthold P, Hegemann P (2005) Removal of mismatched bases from synthetic genes by enzymatic mismatch cleavage. Nucleic Acids Res 33:e58
Gilchrist EJ, Haughn GW, Ying CC, Otto SP, Zhuang J, Cheung D, Hamberger B, Aboutorabi F, Kalynyak T, Johnson L , Bohlmann J, Ellis BE, Douglas CJ, Cronk QC (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
Greene EA, Codomo CA, Taylor NE, Henikoff JG, Till BJ, Reynolds SH, Enns LC, Burtner C, Johnson JE, Odden AR, Comai L, Henikoff S (2003) Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis. Genetics 164:731–740
Henikoff S, Comai L (2003) Single-nucleotide mutations for plant functional genomics. Annu Rev Plant Biol 54:375–401
Hirochika H, Guiderdoni E, Gynheung AN, Hsing Y-I, Moo Young E, Han C-D, Upadhyaya N, Ramachandran S, Qifa Z, Pereira A, Sundaresan V, Hei L, (2004) Rice mutant resources for gene discovery. Plant Mol Biol 54:325–334
Koornneef M, Dellaert LW, van der Veen JH (1982) EMS- and radiation-induced mutation frequencies at individual loci in Arabidopsis thaliana (L.) Heynh. Mutat Res 93:109–123
Kusaba M (2004) RNA interference in crop plants. Curr Opin Biotechnol 15:139–143
Li X, Zhang Y (2002) Reverse genetics by fast neutron mutagenesis in higher plants. Funct Integr Genomics 2:254–258
Maluszynski M, Nichterlein K, Van Zanten L, Ahloowalia BS (2000) Officially released mutant varieties – the FAO/IAEA database. Mutat Breeding 20:1–88
Mashal RD, Koontz J, Sklar J (1995) Detection of mutations by cleavage of DNA heteroduplexes with bacteriophage resolvases. Nat Genet 9:177–183
May BP, Liu H, Vollbrecht E, Senior L, Rabinowicz PD, Roh D, Pan X, Stein L, Freeling M, Alexander D, Martienssen R (2003) Maize-targeted mutagenesis: a knockout resource for maize. Proc Natl Acad Sci USA 100:11541–11546
McCallum CM, Comai L, Greene EA, Henikoff S (2000a) Targeted screening for induced mutations. Nat Biotechnol 18:455–457
McCallum CM, Comai L, Greene EA, Henikoff S (2000b) Targeting induced local lesions IN genomes (TILLING) for plant functional genomics. Plant Physiol 123:439–442
McCarty DR, Settles MA, Suzuki M, Tan B.C., Latshaw S, Porch TG, Robin K, Baier J, Avigne W, Lai J, Messing J, Koch KE, Hannah, LC (2005) Steady-state transposon mutagenesis in inbred maize. Plant J 44:52–61
Ng PC, Henikoff S (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res 31:3812–3814
Oleykowski CA, Bronson Mullins CR, Godwin AK, Yeung AT (1998) Mutation detection using a novel plant endonuclease. Nucleic Acids Res 26:4597–4602
Perry JA, Wang TL, Welham TJ, Gardner S, Pike JM, Yoshida S, Parniske M (2003) A TILLING reverse genetics tool and a web-accessible collection of mutants of the legume Lotus japonicus. Plant Physiol 131:866–871
Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386
Slade AJ, Knauf VC (2005) TILLING moves beyond functional genomics into crop improvement. Transgenic Res 14:109–115
Slade AJ, Fuerstenberg SI, Loeffler D, Steine MN, Facciotti DA (2005) Reverse genetic, nontransgenic approach to wheat crop improvement by TILLING. Nat Biotechnol 23:75–81
Stadler LJ, (1928) Genetic effects of X-rays in maize. Proc Natl Acad Sci USA 14:69–75
Stadler LJ (1929) Chromosome number and the mutation rate in avena and triticum. Proc Natl Acad Sci USA 15:876–881
Taylor NE, Greene EA (2003) PARSESNP: a tool for the analysis of nucleotide polymorphisms. Nucleic Acids Res 31:3808–3811
Till BJ, Burtner C, Comai L, Henikoff S (2004) Mismatch cleavage by single-strand specific nucleases. Nucleic Acids Res 32:2632–2641
Till BJ, Zerr, T, Bowers E, Greene EA, Comai L, Henikoff S (2006) High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling. Nucleic Acids Res 34:e99
Till BJ, Cooper J, Tai TH, Colowit, P, Greene EA, Henikoff S, Comai L (2007) Discovery of chemically induced mutations in rice by TILLING. BMC Plant Biol 7:19
Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Young K, Taylor NE, Henikoff JG, Comai L, Henikoff S (2003) Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res 13:524–530
Wienholds E, Schulte-Merker S, Walderich B, Plasterk RH (2002) Target-selected inactivation of the zebrafish rag1 gene. Science 297:99–102
Youil R, Kemper BW, Cotton RG (1995) Screening for mutations by enzyme mismatch cleavage with T4 endonuclease VII. Proc Natl Acad Sci USA 92:87–91
Zerr T, Henikoff S (2005) Automated band mapping in electrophoretic gel images using background information. Nucleic Acids Res 33:2806–2812
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Springer
About this chapter
Cite this chapter
Till, B.J., Comai, L., Henikoff, S. (2007). Tilling and Ecotilling for Crop Improvement. In: Varshney, R.K., Tuberosa, R. (eds) Genomics-Assisted Crop Improvement. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-6295-7_15
Download citation
DOI: https://doi.org/10.1007/978-1-4020-6295-7_15
Publisher Name: Springer, Dordrecht
Print ISBN: 978-1-4020-6294-0
Online ISBN: 978-1-4020-6295-7
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)