Mutant Resources and Mutagenomics in crop plants

  • Suprasanna Prasanna Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
  • S. Mohan Jain Department of Agricultural Sciences, University of Helsinki, PL-27, Helsinki, Finland


Agricultural sustainability and food security are major challenges facing continued population growth. Integration of existing and new technologies for the induction and exploitation of genetic diversity towards developing healthier, nutritious and productive crops is the need of the hour. Mutagenesis is a proven technology for the development of improved or novel varieties with desirable traits. Several mutant genes have been successfully explored, either directly or indirectly, to complement crop productivity. The advent of genomics approaches and plant genome sequencing has benefitted mutation discovery and mutant characterization. Plant mutant repositories are being established to serve as platforms for basic and applied research in crop improvement. This review briefly outlines the impact and molecular/genomic characterization of induced mutations in crop improvement.

Keywords: Induced mutations, mutants, mutagenomics, plants


Abe, A., S. Kosugi., K.Yoshida., S. Natsume., H. Takagi., H. Kanzaki., H. Matsumura., K. Yoshida., C. Mitsuoka., M. Tamiru., H. Innan., L. Cano., S. Kamoun. and R. Terauchi. (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol 30: 174–178
Ahloowalia, B.S., Maluszynski, M. and K. Nichterlein. 2004. Global impact of mutation-derived varieties. Euphytica 135:187–204
Belfield, E.J., C. Brown, X. Gan, C. Jiang, D. Baban, A. Mithani, R. Mott, J. Ragoussis, and N.P. Harberd. 2014. Microarray-based ultra-high resolution discovery of genomic deletion mutations. BMC Genom. 15:224.
Bradshaw, J.E. 2016. Mutation Breeding Plant Breeding: Past, Present and Future, Springer Int. Publ. Switzerland, DOI 10.1007/978-3-319-23285-0_16
Dong, C., J. Dalton-Morgan., K. Vincent. and P. Sharp. 2009. A modified TILLING method for wheat breeding. Plant Genome 2:39–47.
Fekih, R., H. Takagi., M. Tamiru.,A. Abe.,S. Natsume.,H. Yaegashi., S.Sharma., S. Sharma., H. Kanzaki., H. Matsumura., H. Saitoh., C. Mitsuoka. , H. Utsushi. , A. Uemura. , E. Kanzaki. , S. Kosugi. , K. Yoshida. , L. Cano. , S. Kamoun. , R. Terauchi (2013) MutMap+: Genetic Mapping and Mutant Identification without crossing in Rice. PLoS ONE 8(7): e68529. doi:10.1371/journal.pone.0068529
Gady, A.L.F., W.H. Vriezen., M.H.B.J. Van de Wal., P. Huang., A.G. Bovy., R.G.F. Visser, and C.W.B. Bachem. 2011. Induced point mutations in the phytoene synthase 1 gene cause differences in carotenoid content during tomato fruit ripening. Mol. Breeding 29(3): 801–812.
Guo, H., Yan, Z., Li, X., Xie, Y., Xiong, H., Liu, Y., Zhao, L., Gu, J., Zhao, S. and Liu, L. (2017). Development of a High-Efficient Mutation Resource with Phenotypic Variation in Hexaploid Winter Wheat and Identification of Novel Alleles in the TaAGP.L-B1 Gene. Frontiers in Plant Science, 8, 1404.
Hallerman, E. and E. Grabau. 2016. Crop biotechnology: a pivotal moment for global acceptance. Food and Energy Security 5(1): 3–17.
Henry, I.M., U. Nagalakshmi., M.C. Lieberman., K.J. Ngo., K.V. Krasileva., H. Vasquez-Gross., A. Alina., E. Akhunov., J. Dubcovsky., T.H. Tai., and L. Comai. 2014. Efficient Genome-Wide Detection and Cataloguing of EMS-Induced Mutations Using Exome Capture and Next-Generation Sequencing. The Plant Cell, 26(4): 1382–1397.
Hirano, T., Y. Kazama., K. Ishii., S. Ohbu., Y. Shirakawa. and T. Abe T. 2015. Comprehensive identification of mutations induced by heavy-ion beam irradiation in Arabidopsis thaliana. Plant J. 82(1):93-104
Jain, S.M. 2005. Major mutation-assisted plant breeding programmes supported by FAO/IAEA. Plant Cell Tissue Organ Cult. 82:113–121.
Jain, S.M. 2010. Mutagenesis in crop improvement under the climate change. Rom Biotechnol. Lett. 15(2):88–106.
Jain, S.M. and P. Suprasanna. 2011. Induced mutations for enhancing nutrition and food production. Gene Conserve 40:201–215.
Jain, S.M, N. Roux., Suprasanna. Penna., and B. Till. 2011. Mutations and Cultivar Development of Banana. In: M. Pillay and A. Tenkouano, (eds.), Banana Breeding: Progress and Challenges, CRC Press, Taylor & Francis, pp 201-215.
Kazama, Y., Hirano, T., Saito, H., Liu, Y., Ohbu, S., Hayashi, Y. and T. Abe 2011. Characterization of highly efficient heavy-ion mutagenesis in Arabidopsis thaliana. BMC Plant Biology 2011:161.
Kharkwal, M.C., and Q.Y. Shu. 2009. The role of induced mutations in world food security. In: Induced plant mutations in the genomics era. Proceedings of the International Joint FAO/IAEA Symp IAEA, Vienna, pp 33–38.
King, R., Bird, N., Ramirez-Gonzalez, R., Coghill, J.A., Patil, A., Hassani-Pak, K., U. Cristobal., A.L. Phillips. 2015. Mutation Scanning in Wheat by Exon Capture and Next-Generation Sequencing. PLoS ONE 10(9): e0137549. doi:10.1371/journal.pone.0137549
Kumar, A.P.K., P. C. McKeown., B. Adnane., P. Ryder., G. Brychkova., A. Bendahmane., A. Sarkar., M. Chatterjee. and C. Spillane. 2017. TILLING by Sequencing (TbyS) for targeted genome mutagenesis in crops. Mol Breeding 37:14 DOI 10.1007/s11032-017-0620-1
Lawrenson, T., S. Oluwaseyi., N. Stacey., C. Li., L. Østergaard., N. Patron., C. Uauy. and W. Harwood. (2015) Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease. Genome Biology (2015) 16:258, DOI 10.1186/s13059-015-0826-7
Li, Y. D., Z. Z. Chu., X. G. Liu., H. C. Jing., Y. G. Liu. and D. Y. Hao. 2010. A cost-effective high-resolution melting approach using the EvaGreen dye for DNA polymorphism detection and genotyping in plants. J. Integr. Plant Biol. 52:1036–1042.
Li, G., Jain, R., Chern, M., Pham, N.T., Martin, J.A., Wei, T., Schackwitz, W.S., Lipzen, A.M., Duong, P.Q., Jones, K.C., Jiang, L, Ruan, D, Bauer, D., Peng, Y., Barry, K.W., Schmutz, J., Ronald, P.C. (2017) The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies. Plant Cell. 29(6):1218-1231
Liu, L.X., Guo, H., Zhao, L, Gu, J. and S. Zhao. 2007. Achievements in the past twenty years and perspective outlook of crop space breeding in China. Jour. Nucl. Agric. Sci. 21(6): 589–592.
Lundqvist, U. 2009. Eighty Years of Scandinavian Barley Mutation Genetics and Breeding. In: Q.Y. Shu (ed.), Induced Plant Mutations in the Genomics Era. Food and Agriculture Organization of the United Nations, Rome, 2009, pp 39-43.
Lusser, M. and C. Parisi., D. Plan D. and E. Rodríguez-Cerezo. 2012. Deployment of new biotechnologies in plant breeding. Nature Biotechnology 30:231-239.
Mba, C. 2013. Induced Mutations Unleash the Potentials of Plant Genetic Resources for Food and Agriculture. Agronomy 3:200-231.
Mirajkar, S.J., Suprasanna, P. and Vaidya, E.R., 2016. Spatial distribution and dynamics of sucrose metabolising enzymes in radiation induced mutants of sugarcane. Plant Physiol. Biochem. 100: 85–93.
Morita, R., Kusaba, M., Iida, S., Yamaguchi, H., Nishio, T., Nishimura, M. 2009. Molecular characterization of mutations induced by gamma irradiation in rice. Genes & Genetic Systems 84: 361-370.
Nadeau, J.H. 2000. Muta-genetics or muta-genomics: the feasibility of large-scale mutagenesis and phenotyping programs. Mammalian Genome 11: 603–607.
Nakagawa, H. 2009. Induced mutations in plant breeding and biological researches in Japan. In: Q.Y. Shu (ed.), Induced Plant Mutations in the Genomics Era. Food and Agriculture Organization of the United Nations, Rome, pp 51-58.
Nawaz, Z. and Q. Shu. 2014. Molecular nature of chemically and physically induced mutants in plants: a review. Plant Genetic Resources 12:S74-S78.
Negi, P., A.N. Rai. and P. Suprasanna. 2016. Moving through the stressed genome: emerging regulatory roles for transposons in plant stress response. Front. Plant Sci. 7:1448. doi: 10.3389/fpls.2016.01448.
Nogué, F., K. Mara, C. Collonnier, and J.M. Casacuberta. 2016. Genome engineering and plant breeding: impact on trait discovery and development. Plant Cell Reports, 35, 1475–1486.
O’Rourke, J.A., L.P. Iniguez, B. Bucciarelli, J. Roessler., J. Schmutz., P.E. McClean., S.A. Jackson., G. Hernandez., M.A. Graham., R.M. Stupar. and C.P. Vance. 2013. A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar. Front. Plant Sci. 4: 210.
Parry, M.A.J., P.J. Madgwick., C. Bayon., K. Tearall., A. Hernandez-Lopez., M. Baudo., M. Rakszegi., W. Hamada., A. Al-Yassin., H. Ouabbou., M. Labhilili. and A.L. Phillips. 2009. Mutation discovery for crop improvement. Jour Exp Bot, Vol. 60, No. 10, pp. 2817–2825.
Phillips, R.L. and H.W. Rines. 2009. Expanding the Boundaries of Gene Variation for Crop Improvement. In: Q.Y. Shu (ed.), Induced Plant Mutations in the Genomics Era. Food and Agriculture Organization of the United Nations, Rome, pp, 21-26.
Pretty, J. 2008. Agricultural sustainability: concepts, principles and evidence. Philosophical Transactions of the Royal Society B: Biological Sciences, 363(1491), 447–465.
Rahaman, M.M., D. Chen., Z. Gillani., C. Klukas. and M. Chen. 2015. Advanced phenotyping and phenotype data analysis for the study of plant growth and development. Front. Plant Sci. 6:619. doi: 10.3389/fpls.2015.00619
Ryuto, H., N.Fukunishi., Y. Hayashi., H. Ichida., T. Abe., M. Kase. and Y. Yano. 2008. Heavy-ion beam irradiation facility for biological samples in RIKEN. Plant Biotechnology 25: 119–12
Saika, H., A. Oikawa., F. Matsuda., H. Onodera., K. Saito. and S.Toki. 2011. Application of Gene Targeting to Designed Mutation Breeding of High-Tryptophan Rice. Plant Physiology, 156(3), 1269–1277.
Sato, Y., Shirasawa, K, Takahashi, Y., Nishimura, M. and T. Nishio. 2006. Mutant selection from progeny of gamma-rayirradiated rice by DNA heteroduplex cleavage using Brassica petiole extract. Breed Sci 56:179–183.
Shikata, M., K. Hoshikawa., T. Ariizumi., N. Fukuda., Y. Yamazaki. and H. Ezura. 2015. TOMATOMA Update: Phenotypic and Metabolite Information in the Micro-Tom Mutant Resource. Plant Cell Physiol 57 (1): e11. doi: 10.1093/pcp/pcv194.
Shirasawa, K., H. Hirakawa., T. Nunome., S. Tabata. and S. Isobe. 2016. Genome‐wide survey of artificial mutations induced by ethyl methanesulfonate and gamma rays in tomato. Plant Biotechnology Journal, 14(1), 51–60.
Shukla, V.K., Y. Doyon., J.C. Miller., R.C. DeKelver, E.A. Moehle, S.E. Worden., J.C. Mitchell., N.L. Arnold, S. Gopalan., X. Meng., V.M. Choi., J.M. Rock., Y.Y. Wu., G.E. Katibah, G. Zhifang., D. McCaskill., M.A. Simpson., B. Blakeslee., S.A. Greenwalt., H.J. Butler., S.J. Hinkley., L. Zhang., E.J. Rebar., P.D. Gregory. and F.D. Urnov. 2009. Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature 459: 437–441.
Sikora, P., A. Chawade., M. Larsson., J. Olsson. and O. Olsson. 2011. Mutagenesis as a Tool in Plant Genetics, Functional Genomics, and Breeding. International Journal of Plant Genomics, ID 314829, 13 pages, doi:10.1155/2011/314829
Slota, M., M. Maluszynski. and I. Szarejko. 2017. Bioinformatics-based assessment of the relevance of candidate genes for mutation discovery. J. Jankowicz-Cieslak et al. (eds.), Biotechnologies for Plant Mutation Breeding. Springer International. pp 263-280
Song, G., M. Jia., K. Chen., X. Kong., B. Khattak., C. Xie., A. Li. and L. Mao. 2016. CRISPR/Cas9: A powerful tool for crop genome editing. The Crop Journal 4: 75–82.
Sun, Y., G. Jiao., Z. Liu., X. Zhang., J. Li., X. Guo., W. Du., J. Du., F. Francis., Y. Zhao. and L. Xia. 2017. Generation of high-amylose rice through CRISPR/Cas9-mediated targeted mutagenesis of starch branching enzymes. Front. Plant Sci. 8:298. doi: 10.3389/fpls.2017.00298
Suprasanna, P., Jain, S.M., Ochatt, S.J., Kulkarni, V.M. and S. Predieri. 2012. Applications of in vitro techniques in mutation breeding of vegetatively propagated crops. In: Shu QY, Forster BP, Nakagawa H (eds) Plant mutation breeding and biotechnology. CABI Publishing, Wallingford, pp 371–385.
Suprasanna, P., S.J. Mirajkar., V.Y. Patade. and S.M. Jain. 2014. Induced mutagenesis for improving plant abiotic stress tolerance. In: Tomlekova NB, Kozgar MI and Wani MR (eds), Mutagenesis: exploring novel genes and pathways, Wageningen Academic Publishers, pp 347-376.
Suprasanna, P., S.J. Mirajkar. and S.G. Bhagwat. 2015. Induced mutations and crop improvement. In: Bahadur B, Venkat Rajam M, Sahijram L and Krishnamurthy KV (eds.), Plant Biology and Biotechnology, Volume I: Plant Diversity, Organization, Function and Improvement, Springer India, pp 593-617.
Suprasanna, P., T.R. Ganapathi, S. G. Ghag, S. M. Jain. 2017. Genetic modifications of horticultural plants by induced mutations and transgenic approach-Acta Hort (in press)
Tanaka, A., N. Shikazono., and Y. Hase. 2010. Studies on Biological Effects of Ion Beams on Lethality, Molecular Nature of Mutation, Mutation Rate, and Spectrum of Mutation Phenotype for Mutation Breeding in Higher Plants. J. Radiat. Res., 51: 223–233.
Till, B.J., J. Cooper., T.H. Tai., P. Colowit., E.A. Greene., S. Henikoff. and L. Comai. 2007. Discovery of chemically induced mutations in rice by TILLING. BMC Plant Biol 7:1–12.
Tsai, H., T. Howell., R. Nitcher., V. Missirian., B. Watson., K.J. Ngo., M. Lieberman., J. Fass., C. Uauy., R.K. Tran., A.A. Khan., V. Filkov., T.H. Tai., J. Dubcovsky. and L. Comai. 2011. Discovery of rare mutations in populations: TILLING by sequencing. Plant Physiol 156(3):1257–1268.
Tsuda, M., A. Kaga., T. Anai., T. Shimizu., T. Sayama., K. Takagi., K. Machita., S. Watanabe., M. Nishimura., N. Yamada., S. Mori., H. Sasaki., H. Kanamori., Y. Katayose. and M. Ishimoto. 2015. Construction of a high-density mutant library in soybean and development of a mutant retrieval method using amplicon sequencing. MC Genomics, 16:1014.
Uchida, N., T. Sakamoto., T. Kurata. and M. Tasaka. 2011. Identification of EMS-induced causal mutations in a non-reference Arabidopsis thaliana accession by whole genome sequencing. Plant Cell Physiol. 52:716 –722.
UNFPA (2012) The state of the world population report. By choice, not by chance: family planning, human rights and development. United Nations Population Fund, New York
Voytas, D.F. 2013. Plant genome engineering with sequence-specific nucleases. Annu Rev Plant Biol 64: 327–350.
Voytas, D.F. and G.C. Gao. 2014. Precision Genome Engineering and Agriculture: Opportunities and Regulatory Challenges. PLoS Biol 12(6): e1001877.
Wilde, H.W., C.Yihua., J. Peng. and A. Bhattacharya. 2012. Targeted mutation breeding of horticultural plants. Emir. J. Food Agric. 24 (1): 31-41.
Wu, Y., Y. Zhang., W. Yu., M. Song and Z.L. Yu. 2005. The Progress of the Research and Application of Ion Implantation Biotechnology in China. Solid State Phenomena Vol. 107: 37-42.
Yan, W., Z. Chen., J. Lu., C. Xu., G. Xie., Y., Y. Li., X.W. Deng., H. He., X. Tang. 2016. Simultaneous Identification of Multiple Causal Mutations in Rice. Frontiers in Plant Science, 7, 2055.
589 Views | 539 Downloads
How to Cite
Prasanna, S., and S. M. Jain. “Mutant Resources and Mutagenomics in Crop Plants”. Emirates Journal of Food and Agriculture, Vol. 29, no. 9, Oct. 2017, pp. 651-7, doi: Accessed 27 June 2022.
Review Article