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Induced Mutations in Plant Breeding

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Abstract

Many important traits for plant domestication and improvement have resulted from human selection for novel alleles of structural or regulatory genes. In addition to naturally-occurring genetic mutations, novel alleles have been induced in plants by chemical and physical mutagenesis. The goal of mutagenesis is to induce genetic variation in cells that give rise to plants, while minimizing chimeras, sterility and lethality. For several crop species, chemically-mutagenized populations of a few thousand lines were sufficient for finding the desired phenotype. The efficiency of mutation breeding can be improved by screening plants at the genetic level, prior to phenotypic analysis. High-throughput physical methods and, increasingly, next-generation sequencing are being used to identify lines with induced mutations in candidate genes. An alternative approach to increasing the precision of mutation breeding is through gene-specific mutation using engineered nucleases. Allelic diversity in candidate genes, whether induced naturally or experimentally, can be a resource in breeding programs for developing new agricultural traits.

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References

  • Acanda Y, Martínez Ó, Prado MJ et al (2013) EMS mutagenesis and qPCR-HRM prescreening for point mutations in an embryogenic cell suspension of grapevine. Plant Cell Rep 33(471):481

    Google Scholar 

  • Ahloowalia BS, Maluszynski M, Nichterlein K (2004) Global impact of mutation-derived varieties. Euphytica 135:187–204

    Article  Google Scholar 

  • Allen RS, Nakasugi K, Doran RL et al (2013) Facile mutant identification via a single parental backcross method and application of whole genome sequencing based mapping pipelines. Front Plant Sci 4:362

    Article  PubMed Central  PubMed  Google Scholar 

  • Ashikari M, Sasaki A, Ueguchi-Tanaka M et al (2002) Loss-of-function of a rice gibberellin biosynthetic gene, GA20 oxidase (GA20ox-2), led to the rice ‘green revolution’. Breed Sci 52:143–150

    Article  CAS  Google Scholar 

  • Belfield EJ, Gan X, Mithani A et al (2012) Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana. Genome Res 22:1306–1315

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Blomstedt CK, Gleadow RM, O’Donnell N et al (2011) 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

    Article  PubMed  Google Scholar 

  • Boualem A, Fergany M, Fernandez R et al (2008) A conserved mutation in an ethylene biosynthesis enzyme leads to andromonoecy in melons. Science 321:836–838

    Article  CAS  PubMed  Google Scholar 

  • Carlini DB, Stephan W (2003) In vivo introduction of unpreferred synonymous codons into the Drosophila Adh gene results in reduced levels of ADH protein. Genetics 163:239–243

    PubMed Central  CAS  PubMed  Google Scholar 

  • Casella L, Greco R, Bruschi G et al (2013) TILLING in European rice: hunting mutations for crop improvement. Crop Sci 53:2550–2562

    Article  CAS  Google Scholar 

  • Chantreau M, Grec S, Gutierrez L et al (2013) PT-Flax (phenotyping and TILLinG of flax): development of a flax (Linum usitatissimum L.) mutant population and TILLinG platform for forward and reverse genetics. BMC Plant Biol 13:159

    Article  PubMed Central  PubMed  Google Scholar 

  • Colbert T, Till BJ, Tompa R et al (2001) High-throughput screening for induced point mutations. Plant Physiol 126:480–484

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Colbert TG, Hurst SR, Slade AJ (2011) Tomatoes that soften more slowly postharvest due to non-transgenic alterations in an expansin gene. US Patent Application 20110113507

    Google Scholar 

  • Dahmani-Mardas F, Troadec C, Boualem A et al (2010) Engineering melon plants with improved fruit shelf life using the TILLING approach. PLoS One 5, e15776

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Dalmais M, Schmidt J, Le Signor C et al (2008) UTILLdb, a Pisum sativum in silico forward and reverse genetics tool. Genome Biol 9:R43

    Article  PubMed Central  PubMed  Google Scholar 

  • Delker C, Quint M (2011) Expression level polymorphisms: heritable traits shaping natural variation. Trends Plant Sci 16:481–488

    CAS  PubMed  Google Scholar 

  • Dierking E, Bilyeu K (2009) New sources of soybean seed meal and oil composition traits identified through TILLING. BMC Plant Biol 9:89

    Article  PubMed Central  PubMed  Google Scholar 

  • Dong C, Dalton-Morgan J, Vincent K, Sharp P (2009) A modified TILLING method for wheat breeding. Plant Genome 2:39–47

    Article  CAS  Google Scholar 

  • Frerichmann SL, Kirchhoff M, Müller AE et al (2013) EcoTILLING in Beta vulgaris reveals polymorphisms in the FLC-like gene BvFL1 that are associated with annuality and winter hardiness. BMC Plant Biol 13:52

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gady ALF, Hermans FWK, Van de Wal MHBJ et al (2009) Implementation of two high throughput techniques in a novel application: detecting point mutations in large EMS mutated plant populations. Plant Methods 5:13

    Article  PubMed Central  PubMed  Google Scholar 

  • Gady AL, Vriezen WH, Van de Wal MH et al (2012) Induced point mutations in the phytoene synthase 1 gene cause differences in carotenoid content during tomato fruit ripening. Mol Breed 29:801–812

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gilchrist EJ, Sidebottom CHD, Koh CS, MacInnes T et al (2013) A mutant Brassica napus (Canola) population for the identification of new genetic diversity via TILLING and next generation sequencing. PLoS One 8, e84303. doi:10.1371/journal.pone.0084303

    Article  PubMed Central  PubMed  Google Scholar 

  • González M, Xu M, Esteras C et al (2011) Towards a TILLING platform for functional genomics in Piel de Sapo melons. BMC Res Notes 4:289

    Article  PubMed Central  PubMed  Google Scholar 

  • Greene EA, Codomo CA, Taylor NE et al (2003) Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis. Genetics 164:731–740

    PubMed Central  CAS  PubMed  Google Scholar 

  • Hancock CN, Zhang F, Floyd K et al (2011) The rice miniature inverted repeat transposable element mPing is an effective insertional mutagen in soybean. Plant Physiol 157:552–562

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Harloff HJ, Lemcke S, Mittasch J et al (2012) A mutation screening platform for rapeseed (Brassica napus L.) and the detection of sinapine biosynthesis mutants. Theor Appl Genet 124:957–969

    Article  CAS  PubMed  Google Scholar 

  • Hartung F, Schiemann J (2014) Precise plant breeding using new genome editing techniques: opportunities, safety and regulation in the EU. Plant J. doi:10.1111/tpj.12413

    PubMed  Google Scholar 

  • Hwang SG, Hwang JG, Kim DS, Jang CS (2014) Genome-wide DNA polymorphism and transcriptome analysis of an early-maturing rice mutant. Genetica 142:73–85

    Article  CAS  PubMed  Google Scholar 

  • Ibiza VP, Canizares J, Nuez F (2010) EcoTILLING in Capsicum species: searching for new virus resistances. BMC Genomics 11:631

    Article  PubMed Central  PubMed  Google Scholar 

  • Jiang W, Zhou H, Bi H et al (2013) Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res 41, e188. doi:10.1093/nar/gkt780

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Jørgensen JH (1992) Discovery, characterization and exploitation of Mlo powdery mildew resistance in barley. Euphytica 63:141–152

    Article  Google Scholar 

  • Julio E, Laporte F, Reis S et al (2008) Reducing the content of nornicotine in tobacco via targeted mutation breeding. Mol Breed 21:369–381

    Article  CAS  Google Scholar 

  • Kumar AP, Boualem A, Bhattacharya A et al (2013) SMART-sunflower mutant population and reverse genetic tool for crop improvement. BMC Plant Biol 13:38

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Lee LS, Till BJ, Hill H et al (2014) Mutation and mutation screening. In: Henry RJ, Furtado H (eds) Cereal genomics. Humana Press, New York, pp 77–95

    Chapter  Google Scholar 

  • Li X, Lassner M, Zhang Y (2002) Deleteagene: a fast neutron deletion mutagenesis-based gene knockout system for plants. Comp Funct Genomics 3:158–160

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Loeffler DL, Dibya D, Kenseth J et al (2011) TILLING for mutation discovery in rice, wheat, lettuce, tomato and soybean using the advance™ Fs96 high throughput capillary electrophoresis system. In: Abstract of the plant & animal genomes XIX Conference. http://www.intl-pag.org/19/abstracts/P02c_PAGXIX_101.html

  • Lusser M, Davies HV (2013) Comparative regulatory approaches for groups of new plant breeding techniques. New Biotechnol 30:437–446

    Article  CAS  Google Scholar 

  • Mallory AC, Reinhart BJ, Jones-Rhoades MW et al (2004) MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5’region. EMBO J 23:3356–3364

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Maluszynski M (2001) Officially released mutant varieties–the FAO/IAEA database. Plant Cell Tiss Org Cult 65:175–177

    Article  Google Scholar 

  • Marcoz-Ragot C, Gateau I, Koenig J et al (2000) Allelic variation of granule-bound starch synthase proteins in European bread wheat varieties. Plant Breed 119:305–309

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Mba C (2013) Induced mutations unleash the potentials of plant genetic resources for food and agriculture. Agronomy 3:200–231

    Article  Google Scholar 

  • McCallum CM, Comai L, Greene EA, Henikoff S (2000) Targeting induced local lessions in genomes (TILLING) for plant functional genomics. Plant Physiol 123:439–442

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • McCallum CM, Slade AJ, Colbert TG et al (2008) Tomatoes having reduced polygalacturonase activity caused by non-transgenic mutations in the polygalacturonase gene. US Patent 7393996

    Google Scholar 

  • McManus LJ, Sasse J, Blomstedt CK, Bossinger G (2006) Pollen treatment for mutation induction in Eucalyptus globulus ssp. globulus (Myrtaceae). Aust J Bot 54:65–71

    Article  Google Scholar 

  • Muth J, Hartje S, Twyman RM et al (2008) Precision breeding for novel starch variants in potato. Plant Biotechnol J 6:576–584

    Article  CAS  PubMed  Google Scholar 

  • Negrão S, Almadanim MC, Pires IS et al (2012) New allelic variants found in key rice salt-tolerance genes: an association study. Plant Biotechnol J 11:87–100

    Article  PubMed  Google Scholar 

  • Ng PC, Henikoff S (2006) Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet 7:61–80

    Article  CAS  PubMed  Google Scholar 

  • 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 7:34

    Article  PubMed Central  PubMed  Google Scholar 

  • Nordström KJ, Albani MC, James GV et al (2013) Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers. Nat Biotechnol 31:325–330

    Article  PubMed  Google Scholar 

  • Okabe Y, Asamizu E, Saito T et al (2011) Tomato TILLING technology: development of a reverse genetics tool for the efficient isolation of mutants from Micro-Tom mutant libraries. Plant Cell Phys 52:1994–2005

    Article  CAS  Google Scholar 

  • Olsen KM, Wendel JF (2013) A bountiful harvest: genomic insights into crop domestication phenotypes. Annu Rev Plant Biol 64:47–70

    Article  CAS  PubMed  Google Scholar 

  • Pakdeechanuan P, Teoh S, Shoji T, Hashimoto T (2012) Non-functionalization of two CYP82E nicotine N-demethylase genes abolishes nornicotine formation in Nicotiana langsdorffii. Plant Cell Phys 53:2038–2046

    Article  CAS  Google Scholar 

  • Pathirana R (2012) Plant mutation breeding in agriculture. In: Hemming D(ed) Plant sciences reviews. CAB International, Wellingford, England, pp 107–110

    Google Scholar 

  • Piffanelli P, Ramsay L, Waugh R et al (2004) A barley cultivation-associated polymorphism conveys resistance to powdery mildew. Nature 430:887–891

    Article  CAS  PubMed  Google Scholar 

  • Piron F, Nicola M, Mino S et al (2010) An induced mutation in tomato eIF4E leads to immunity to two potyviruses. PLoS One 5, e11313. doi:10.1371/journal.pone.0011313

    Article  PubMed Central  PubMed  Google Scholar 

  • Predieri S (2001) Mutation induction and tissue culture in improving fruits. Plant Cell Tiss Org Cult 64:185–210

    Article  CAS  Google Scholar 

  • Rehm HL (2013) Disease-targeted sequencing: a cornerstone in the clinic. Nat Rev Genet 14:295–300

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Rigola D, van Oeveren J, Janssen A et al (2009) High throughput detection of induced mutations and natural variation using KeyPoint technology. PLoS One 4, e4761

    Article  PubMed Central  PubMed  Google Scholar 

  • Roychowdhury R, Tah J (2013) Mutagenesis- a potential approach for crop improvement. In: Hakeem KR, Ahmad P, Ozturk M (eds) Crop improvement. Springer, New York, pp 149–187

    Chapter  Google Scholar 

  • Ruffel S, Gallois JL, Lesage ML, Caranta C (2005) The recessive potyvirus resistance gene pot-1 is the tomato orthologue of the pepper pvr2-eIF4E gene. Mol Gen Genomics 274:346–353

    Article  CAS  Google Scholar 

  • Saunders R, Deane CM (2010) Synonymous codon usage influences the local protein structure observed. Nucleic Acid Res 38:6719–6728

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Serrat X, Esteban R, Guibourt N et al (2014) EMS mutagenesis in mature seed-derived rice calli as a new method for rapidly obtaining TILLING mutant populations. Plant Meth 10:5

    Article  Google Scholar 

  • Shan Q, Wang Y, Li J et al (2013) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31:686–688

    Article  CAS  PubMed  Google Scholar 

  • Sigurbjörnsson B, Micke A (1974) Philosophy and accomplishments of mutation breeding. In: Polyploidy and induced mutations in plant breeding. IAEA, Vienna, pp 303–343

    Google Scholar 

  • Sikora P, Chawade A, Larsson M et al (2011) Mutagenesis as a tool in plant genetics, functional genomics, and breeding. Int J Plant Genomics. doi:10.1155/2011/314829, ID 31482913

    PubMed Central  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), “green revolution” rice, contains a defective gibberellin 20-oxidase gene. Proc Nat Acad Sci 99:9043–9048

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Stadler LJ (1928) Genetic effects of X-rays in maize. Proc Nat Acad Sci 14:69–72

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Suzuki T, Eiguchi M, Kumamaru T et al (2008) MNU-induced mutant pools and high performance TILLING enable finding of any gene mutation in rice. Mol Genet Genomics 279:213–223

    Article  CAS  PubMed  Google Scholar 

  • Szarejko I, Forster BP (2007) Doubled haploidy and induced mutation. Euphytica 158:359–370

    Article  Google Scholar 

  • Till BJ (2014) Mining genetic resources via Ecotilling. In: Tuberosa R, Graner A, Frison E (eds) Genomics of plant genetic resources. Springer, Dordrecht, pp 349–365

    Chapter  Google Scholar 

  • Till BJ, Reynolds SH, Weil C et al (2004) Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol 4:12

    Article  PubMed Central  PubMed  Google Scholar 

  • 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 51:1116–1125

    Article  CAS  PubMed  Google Scholar 

  • Tsai CJ, Sauna ZE, Kimchi-Sarfaty C et al (2008) Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. J Mol Biol 383:281–291

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Tsai H, Howell T, Nitcher R et al (2011) Discovery of rare mutations in populations: TILLING by sequencing. Plant Physiol 156:1257–1268

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Van Eijk MJT, Van Tunen AJ (2009) High throughput screening of mutagenized populations. US Patent Application 20090170713

    Google Scholar 

  • Vanholme B, Cesarino I, Goeminne G et al (2013) Breeding with rare defective alleles (BRDA): a natural Populus nigra HCT mutant with modified lignin as a case study. New Phytol 198:765–776

    Article  CAS  PubMed  Google Scholar 

  • Voytas DF (2013) Plant genome engineering with sequence-specific nucleases. Annu Rev Plant Biol 64:327–350

    Article  CAS  PubMed  Google Scholar 

  • Wang J, Sun JZ, Liu DC et al (2008a) Analysis of Pina and Pinb alleles in the micro-core collections of Chinese wheat germplasm by ecotilling and identification of a novel Pinb allele. J Cereal Sci 48:836–842

    Article  CAS  Google Scholar 

  • Wang N, Wang Y, Tian F et al (2008b) A functional genomics resource for Brassica napus: development of an EMS mutagenized population and discovery of FAE1 point mutations by TILLING. New Phytol 180:751–765

    Article  CAS  PubMed  Google Scholar 

  • Wang NA, Shi L, Tian F et al (2010) Assessment of FAE1 polymorphisms in three Brassica species using EcoTILLING and their association with differences in seed erucic acid contents. BMC Plant Biol 10:137

    Article  PubMed Central  PubMed  Google Scholar 

  • Wang TL, Uauy C, Robson F, Till B (2012) TILLING in extremis. Plant Biotechnol J 10:761–772

    Article  CAS  PubMed  Google Scholar 

  • Weng J, Li B, Liu C et al (2013) A non-synonymous SNP within the isopentenyl transferase 2 locus is associated with kernel weight in Chinese maize inbreds (Zea mays L.). BMC Plant Biol 13:98

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wu G, Wu Y, Xiao L et al (2008) Zero erucic acid trait of rapeseed (Brassica napus L.) results from a deletion of four base pairs in the fatty acid elongase 1 gene. Theor Appl Genet 116:491–499

    Article  CAS  PubMed  Google Scholar 

  • Wu JL, Wu C, Lei C et al (2005) Chemical-and irradiation-induced mutants of indica rice IR64 for forward and reverse genetics. Plant Mol Biol 59:85–97

    Article  CAS  PubMed  Google Scholar 

  • Xia Y, Li R, Ning Z et al (2013) Single nucleotide polymorphisms in HSP116. 8 and their association with agronomic traits in barley. PLoS One 8, e56816

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Xin Z, Wang ML, Barkley NA 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

    Article  PubMed Central  PubMed  Google Scholar 

  • Yang M, Djukanovic V, Stagg J et al (2009) Targeted mutagenesis in the progeny of maize transgenic plants. Plant Mol Biol 706:669–679

    Article  Google Scholar 

  • Yu S, Liao F, Wang F et al (2012) Identification of rice transcription factors associated with drought tolerance using the ecotilling method. PLoS One 7, e30765

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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Wilde, H.D. (2015). Induced Mutations in Plant Breeding. In: Al-Khayri, J., Jain, S., Johnson, D. (eds) Advances in Plant Breeding Strategies: Breeding, Biotechnology and Molecular Tools. Springer, Cham. https://doi.org/10.1007/978-3-319-22521-0_11

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