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Molecular nature of chemically and physically induced mutants in plants: a review

  • Zarqa Nawaz (a1) (a2) and Qingyao Shu (a1) (a2)


More than 3200 new mutant varieties have been bred and used by millions of farmers, which has significantly contributed to world food security. A lot more mutants have also served as tools for gene discovery and functional analysis. Recent genomic approaches including TILLING (Targeting Induced Local Lesions In Genome) have enabled screening of mutations at the molecular level. This review describes the molecular nature of chemically and physically induced mutations and their repercussions. Analyses of TILLING reports indicate that chemically induced mutations are mostly nucleotide substitutions, but that mutation frequencies fluctuate among plant species ranging from one DNA lesion per 300 kbp in Arabidopsis to one DNA lesion per 30 kbp in bread wheat, which reciprocate with an increase in ploidy levels. The majority (>95%) of chemically induced DNA lesions are silent or missense mutations. Mutations induced by physical mutagens seem to be more diverse, including single-nucleotide substitutions, insertions, inversions and translocations, although short deletions ( < 15 bp) are relatively more predominant. The proportion of complex mutations (translocation, inversions, etc.) may increase with an increase in the linear energy transfer of radiations. In addition, the implications of these findings for the roles of induced mutants in breeding and gene function analysis are briefly discussed.


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Abe, T, Ryuto, H and Fukunishi, N (2012) Ion beam radiation mutagenesis. In: Shu, QY, Forster, BP and Nakagawa, H (eds) Plant Mutation Breeding and Biotechnology. Oxford: CABI, pp. 99108.
Belfield, EJ, Gan, AC, Mithani, A, Brown, C, Jiang, CF, Franklin, K, Alvey, E, Wibowo, A, Jung, M, Bailey, K, Kalwani, S, Ragoussis, J, Mott, R and Harberd, NP (2012) Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana . Genome Research 22: 13061315.
Chawade, A, Sikora, P, Bräutigam, M, Larsson, M, Vivekanad, V, Nakash, MA, Chen, TS and Olsson, O (2010) Development and characterization of an oat TILLING – population and identification of mutations in ligin and β-glucan biosynthesis genes. BMC Plant Biology 10: 86.
Chen, H, Cheng, Z, Ma, X, Wu, H, Liu, Y, Zhou, K, Chen, Y, Ma, W, Bi, J, Zhang, X, Guo, X, Wang, J, Lei, C, Wu, F, Lin, Q, Liu, Y, Liu, L and Jiang, L (2013) A knockdown mutation of yellow-green leaf2 blocks chlorophyll biosynthesis in rice. Plant Cell Reports 32: 18551867.
Cooper, JL, Till, BJ, Laport, RG, Darlow, MC, Kleffner, JM, Jamai, A, El-Mellouki, T, Liu, S, Ritchie, R, Nielsen, N, Bilyeu, KD, Meksem, K, Comai, L and Henikoff, S (2008) Tilling to detect induced mutations in soybean. BMC Plant Biology 8: 9.
Dong, CM, Dalton-Morgan, J, Vicent, K and Sharp, P (2009) A modified TILLING method for wheat breeding. The Plant Genome 2: 3947.
Gottwald, S, Bauer, P, Komatsuda, T, Lundqvist, U and Stein, N (2009) Tilling in the two-rowed barley cultivar ‘Barke’ reveals preferred sites of functional diversity in the gene HvHox1 . BMC Research Notes 2: 114.
Greene, EA, Codomo, CA, Taylor, NE, Henikoff, JG, Till, BJ, Reynolds, SH, Enns, LC, Burtner, C, Johnson, JE, Odden, AR, Comai, L and Henikoff, S (2003) Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis . Genetics 164: 731740.
Harloff, HJ, Lemcke, S, Mittasch, J, Frolov, A, Wu, JG, Dreyer, F, Leckband, G and Jung, C (2012) A mutation screening platform for rapeseed (Brassica napus L.) and the detection of sinpine biosynthesis mutants. Theoretical and Applied Genetics 124: 957969.
Hirano, T, Kazama, Y, Ohbu, S, Shirakawa, Y, Liu, Y, Kambara, T, Fukunishi, N and Abe, T (2012) Molecular nature of mutations induced by high-LET irradiation with argon and carbon ions in Arabidopsis thaliana . Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 735: 1931.
Jankowicz-Cieslak, J, Huynh, OA, Brozynska, M, Nakitandwe, J and Till, BJ (2012) Induction, rapid fixation and retention of mutations in vegetatively propagated banana. Plant Biotechnology Journal 10: 10561066.
Kazama, Y, Hirano, T, Saito, H, Liu, Y, Ohbu, S, Hayashi, Y, Abe, T (2011) Characterization of highly efficient heavy-ion mutagenesis in Arabidopsis thaliana , BMC Plant Biology 11: 161.
Kumar, APK, Boualem, A, Bhattacharya, A, Parikh, S, Desai, N, Zambelli, A, Leon, A, Chatterjee, M and Bendahmane, A (2013) SMART – Sunflower Mutant population And Reverse genetic Tool for crop improvement. BMC Plant Biology 13: 38.
Leitao, JM (2012) Chemical mutagenesis. In: Shu, QY, Forster, BP and Nakagawa, H (eds) Plant Mutation Breeding and Biotechnology. Oxford: CABI, pp. 135158.
Li, X, Song, Y, Century, K, Straight, S, Ronald, P, Dong, X, Lassner, M and Zhang, Y (2001) A fast neutron deletion mutagenesis-based reverse genetics system for plants. Plant Journal 27: 235242.
Li, X and Zhang, Y (2002) Reverse genetics by fast neutron mutagenesis in higher plants. Functional and Integrative Genomics 2: 254258.
Martín, B, Ramiro, M, Martínez-Zapater, JM and Alonso-Blanco, C (2009) A high-density collection of EMS-induced mutations for TILLING in Landsberg erecta genetic background of Arabidopsis . BMC Plant Biology 9: 147.
Mba, C, Afza, R and Shu, QY (2012) Mutagenic radiations: X-rays, ionizing particles and ultraviolet. In: Shu, QY, Forster, BP and Nakagawa, H (eds) Plant Mutation Breeding and Biotechnology. Oxford: CABI, pp. 8390.
McCallum, CM, Comai, L, Greene, EA and Henikoff, S (2000) Targeting induced local lesions in genomes (TILLING) for plant functional genomics. Plant Physiology 123: 439442.
Men, AE, Laniya, ST, Searle, IR, Iturbe-Ormaetxe, I, Gresshoff, I, Jiang, Q, Carroll, BJ and Gresshoff, PM (2002) Fast neutron mutagenesis of soybean (Glycine soja L.) produces a supernodulating mutant containing a large deletion in linkage group H. Genome Letters 1: 147155.
Morita, R, Kusaba, M, Iida, S, Yamaguchi, H, Nishio, T and Nishimura, M (2009) Molecular characterization of mutations induced by gamma irradiation in rice. Genes Genetic Systems 84: 361370.
Pathirana, R (2011) Plant mutation breeding in agriculture. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources. 32: 120.
Rawat, N, Sehgal, SK, Joshi, A, Rothe, N, Wilson, DL, McGraw, N, Vadlani, PV, Li, WL and Gill, BS (2012) A diploid wheat TILLING resource for wheat functional genomics. BMC Plant Biology 12: 205.
Rogers, C, Wen, J, Chen, R and Oldroyd, G (2009) Deletion-based reverse genetics in Medicago truncatula . Plant Physiology 151: 10771086.
Searle, IR, Men, AE, Laniya, TS, Buzas, DM, Iturbe-Ormaetxe, I, Carroll, BJ and Gresshoff, PM (2003) Long-distance signaling in nodulation directed by a CLAVATA1-like receptor kinase. Science 299: 109112.
Shikazono, N, Suzuki, C, Kitamura, S, Watanabe, H, Tano, S and Tanaka, A (2005) Analysis of mutations induced by carbon ions in Arabidopsis thaliana . Journal of Experimental Botany 56: 587596.
Sikora, P, Chawade, A, Larsson, M, Olsson, J and Olsson, O (2011) Mutagenesis as a tool in plant genetics, functional genomics, and breeding. International Journal of Plant Genomics 2011: 314829 doi:10.1155/2011/314829.
Suzuki, T, Eiguchi, M, Kumamaru, T, Satoh, H, Matsusaka, H, Moriguchi, K, Nagato, Y and Kurata, N (2008) MNU-induced mutant pools and high performance TILLING enable finding of any gene mutation in rice. Molecular Genetics and Genomics 279: 213223.
Talamè, V, Bovina, R, Sanguineti, MC, Tuberosa, R, Lundqvist, U and Salvi, S (2008) TILLMORE, a resource for the discovery of chemically induced mutants in barley. Plant Biotechnology Journal 6: 477485.
Till, BJ, Cooper, J, Tai, TH, Colowit, P, Greene, EA, Henikoff, S and Comai, L (2007) Discovery of chemically induced mutations in rice by TILLING. BMC Plant Biology 7: 19.
Uauy, C, Paraiso, F, Colasuonno, P, Tran, RK, Tsai, H, Berardi, S, Comai, L and Dubscovsky, J (2009) A modified TILLING approach to detect induced mutations in tetraploid and hexaploid wheat. BMC Plant Biology 9: 115.
Wang, N, Wang, Y, Tian, F, King, GJ, Zhang, CY, Long, Y, Shi, L and Meng, JL (2008) A functional genomics resources for Brassica napus: development of an EMS mutagenized population and discovery of FAE1 point mutations by TILLING. New Phytologist 180: 751765.
Waugh, R, Leader, DJ, McCallum, N and Caldwell, D (2006) Harvesting the potential of induced biological diversity. Trends in Plant Science 11: 7179.
Zhao, HJ, Cui, HR, Xu, XH, Tan, YY, Fu, JJ, Liu, GZ, Poirier, Y and Shu, QY (2013) Characterization of OsMIK in a rice mutant with reduced phytate content reveals an insertion of a rearranged retrotransposon. Theoretical and Applied Genetics 126: 30093020.


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Molecular nature of chemically and physically induced mutants in plants: a review

  • Zarqa Nawaz (a1) (a2) and Qingyao Shu (a1) (a2)


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