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Development of Flax (Linum usitatissimum L.) Mutant Populations for Forward and Reverse Genetics

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Genetics and Genomics of Linum

Abstract

Mutagenesis has long been used to increase genetic diversity in different crop species including cultivated flax. In particular, ethyl methane sulfonate (EMS) has been used to create large mutant populations that can be screened using TILLING to identify mutations in specific genes via a reverse genetics approach. Additionally, forward genetics can be used to identify mutants showing interesting phenotypes. Such approaches have been used to identify flax mutants showing modifications in fiber cell wall structure and seed metabolism. The creation and characterization of flax mutant populations is a powerful strategy for gene discovery and for introducing genetic variability in this species that has a narrow genetic base.

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References

  • Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H et al (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol 30(2):174

    Article  CAS  PubMed  Google Scholar 

  • Allaby RG, Peterson GW, Merriwether DA, Fu YB (2005) Evidence of the domestication history of flax (Linum usitatissimum L.) from genetic diversity of the sad2 locus. Theor Appl Genet 112(1):58–65

    Article  CAS  PubMed  Google Scholar 

  • Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P et al (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301(5633):653–657

    Article  PubMed  Google Scholar 

  • An G, Lee S, Kim SH, Kim SR (2005) Molecular genetics using T-DNA in rice. Plant Cell Physiol 46(1):14–22

    Article  CAS  PubMed  Google Scholar 

  • Bacelis K (2001) Experimental mutagenesis in fiber flax breeding. Biologia 1:40–43

    Google Scholar 

  • Baucher M, Chabbert B, Pilate G, Doorsselaere JV, Tollier MT, Petit-Conil M, Cornu D, Monties B, Montagu MV, Inze D, Jouanin L, Boerjan W (1996) Red xylem and higher lignin extractability by down-regulating a cinnamyl alcohol dehydrogenase in poplar. Plant Physiol 112:1479–1490

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bendahmane A, Triques K, Sturbois B, Aubourg S, Caboche M (2004) Method for producing highly sensitive endonucleases, novel preparations of endonucleases and uses thereof. PCT/EP2005/009220

    Google Scholar 

  • Bendahmane A, Marcel F, Dalmais M, Beaumont G, Mania B (2016) SENTINEL, SOFTWARE dedicated to TILLING by NGS Analysis. Certifier par l’Agence pour la Protection des programmes. Inter Deposit Digital Number.FR001.240004.000.R.P.2016.000.10000

    Google Scholar 

  • Bhat IA, Pandit UJ, Sheikh IA, Hassan ZU (2017) Physical and chemical mutagenesis in Linum usitatissimum L. to induce variability in seed germination, survival and growth rate traits. Curr Bot 7:28–32

    Article  CAS  Google Scholar 

  • Chantreau M, Grec S, Gutierrez L, Dalmais M, Pineau C, Demailly H 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(1):159

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chantreau M, Portelette A, Dauwe R, Kiyoto S, Crônier D, Morreel K et al (2014) Ectopic lignification in the flax lignified bast fiber1 mutant stem is associated with tissue-specific modifications in gene expression and cell wall composition. Plant Cell 26(11):4462–4482

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Choi Y, Sims GE, Murphy S, Miller JR, Chan AP (2012) Predicting the functional effect of amino acid substitutions and indels. PLoS One 7(10):e46688

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cloutier S, Ragupathy R, Miranda E, Radovanovic N, Reimer E, Walichnowski A et al (2012) Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.). Theor Appl Genet 125(8):1783–1795

    Article  PubMed  PubMed Central  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(2):R43. https://doi.org/10.1186/gb-2008-9-2-r43

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dalmais M, Antelme S, Ho-Yue-Kuang S, Wang Y, Darracq O, d’Yvoire MB et al (2013) A TILLING platform for functional genomics in Brachypodium distachyon. PLoS One 8(6):e65503

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dash PK, Cao Y, Jailani AK, Gupta P, Venglat P, Xiang D et al (2014) Genome-wide analysis of drought induced gene expression changes in flax (Linum usitatissimum). GM Crops Food 5(2):106–119

    Article  PubMed  PubMed Central  Google Scholar 

  • Day A, Neutelings G, Nolin F, Grec S, Habrant A, Crônier D, Maher B, Rolando C, David H, Chabbert B, Hawkins S (2009) Caffeoyl coenzyme A O-methyltransferase down-regulation is associated with modifications in lignin and cell-wall architecture in flax secondary xylem. Plant Physiol Biochem PPB Société Française Physiol Végétale 47:9–19

    CAS  Google Scholar 

  • Fekih R, Takagi H, Tamiru M, Abe A, Natsume S, Yaegashi H et al (2013) MutMap+: genetic mapping and mutant identification without crossing in rice. PLoS One 8(7):e68529

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fenart S, Ndong YPA, Duarte J, Rivière N, Wilmer J, van Wuytswinkel O et al (2010) Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray. BMC Genomics 11(1):592

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ferguson LR, Denny WA (1990) Frameshift mutagenesis by acridines and other reversibly-binding DNA ligands. Mutagenesis 5(6):529–540

    Article  CAS  PubMed  Google Scholar 

  • Fofana B, Ghose K, Somalraju A, McCallum J, Main D, Deyholos MK et al (2017a) Induced mutagenesis in UGT74S1 gene leads to stable new flax lines with altered secoisolariciresinol diglucoside (SDG) profiles. Front Plant Sci 8:1638

    Article  PubMed  PubMed Central  Google Scholar 

  • Fofana B, Ghose K, McCallum J, You FM, Cloutier S (2017b) UGT74S1 is the key player in controlling secoisolariciresinol diglucoside (SDG) formation in flax. BMC Plant Biol 17(1):35

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Galindo-González L, Deyholos MK (2016) RNA-seq transcriptome response of flax (Linum usitatissimum L.) to the pathogenic fungus Fusarium oxysporum f. sp. lini. Front Plant Sci 7:1766

    Article  PubMed  PubMed Central  Google Scholar 

  • Galindo-González L, Pinzón-Latorre D, Bergen EA, Jensen DC, Deyholos MK (2015) Ion torrent sequencing as a tool for mutation discovery in the flax (Linum usitatissimum L.) genome. Plant Methods 11(1):19

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Green AG, Marshall DR (1984) Isolation of induced mutants in linseed (Linum usitatissimum) having reduced linolenic acid content. Euphytica 33(2):321–328

    Article  CAS  Google Scholar 

  • Griffiths AJ, Wessler SR, Lewontin RC, Gelbart WM, Suzuki DT, Miller JH (2005) An introduction to genetic analysis. Macmillan, New York

    Google Scholar 

  • Guo Y, Abernathy B, Zeng Y, Ozias-Akins P (2015) TILLING by sequencing to identify induced mutations in stress resistance genes of peanut (Arachis hypogaea). BMC Genomics 16(1):157. https://doi.org/10.1186/s12864-015-1348-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Henikoff S, Till BJ, Comai L (2004) TILLING. Traditional mutagenesis meets functional genomics. Plant Physiol 135(2):630–636

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Henry IM, Nagalakshmi U, Lieberman MC, Ngo KJ, Krasileva KV, Vasquez-Gross H et al (2014) Efficient genome-wide detection and cataloging of EMS-induced mutations using exome capture and next-generation sequencing. Plant Cell 26(4):1382–1397

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hsia MM, O’Malley R, Cartwright A, Nieu R, Gordon SP, Kelly S et al (2017) Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection. Plant J 91:361

    Article  CAS  PubMed  Google Scholar 

  • Huis R, Morreel K, Fliniaux O, Lucau-Danila A, Fénart S, Grec S et al (2012) Natural hypolignification is associated with extensive oligolignol accumulation in flax stems. Plant Physiol 158:1893

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jander G, Norris SR, Rounsley SD, Bush DF, Levin IM, Last RL (2002) Arabidopsis map-based cloning in the post-genome era. Plant Physiol 129(2):440–450

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kulmi MRM, Mogali SC, Patil KS, Leelavathi TM (2017) Isolation of high-yielding mutants through EMS-induced mutagenesis in linseed (Linum usitatissimum L.). Int J Curr Microbiol App Sci 6(8):278–285

    Article  CAS  Google Scholar 

  • Kumar P, Henikoff S, Ng PC (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4(7):1073–1081

    Article  CAS  PubMed  Google Scholar 

  • Kumar AP, McKeown PC, Boualem A, Ryder P, Brychkova G, Bendahmane A et al (2017) TILLING by sequencing (TbyS) for targeted genome mutagenesis in crops. Mol Breed 37(2):14

    Article  CAS  Google Scholar 

  • Le Roy J, Huss B, Creach A, Hawkins S, Neutelings G (2016) Glycosylation is a major regulator of phenylpropanoid availability and biological activity in plants. Front Plant Sci 7:735

    PubMed  PubMed Central  Google Scholar 

  • Le Roy J, Blervacq AS, Créach A, Huss B, Hawkins S, Neutelings G (2017) Spatial regulation of monolignol biosynthesis and laccase genes control developmental and stress-related lignin in flax. BMC Plant Biol 17(1):124

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mo Y, Howell T, Vasquez-Gross H, de Haro LA, Dubcovsky J, Pearce S (2017) Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study. Mol Genet Genomics:293(2):463–477

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mokshina N, Gorshkova T, Deyholos MK (2014) Chitinase-like (CTL) and cellulose synthase (CESA) gene expression in gelatinous-type cellulosic walls of flax (Linum usitatissimum L.) bast fibers. PLoS One 9(6):e97949

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nordström KJ, Albani MC, James GV, Gutjahr C, Hartwig B, Turck F 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(4):325

    Article  PubMed  CAS  Google Scholar 

  • Ntiamoah C, Rowland GG (1997) Inheritance and characterization of two low linolenic acid EMS-induced McGregor mutant flax (Linum usitatissimum). Can J Plant Sci 77(3):353–358

    Article  Google Scholar 

  • Pinzon-Latorre D, Deyholos MK (2014) Pectinmethylesterases (PME) and pectinmethylesterase inhibitors (PMEI) enriched during phloem fiber development in flax (Linum usitatissimum). PLoS One 9:e105386

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Puyo S, Montaudon D, Pourquier P (2014) From old alkylating agents to new minor groove binders. Crit Rev Oncol Hematol 89(1):43–61

    Article  PubMed  Google Scholar 

  • Roach MJ, Deyholos MK (2007) Microarray analysis of flax (Linum usitatissimum L.) stems identifies transcripts enriched in fibre-bearing phloem tissues. Mol Genet Genomics 278(2):149–165

    Article  CAS  PubMed  Google Scholar 

  • Roach MJ, Mokshina NY, Badhan A, Snegireva AV, Hobson N, Deyholos MK, Gorshkova TA (2011) Development of cellulosic secondary walls in flax fibers requires B-galactosidase. Plant Physiol 156:1351–1363

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rowland GG, Bhatty RS (1990) Ethyl methanesulphonate induced fatty acid mutations in flax. J Am Oil Chem Soc 67(4):213–214

    Article  CAS  Google Scholar 

  • Sandmann S, de Graaf AO, van der Reijden BA, Jansen JH, Dugas M (2017) GLM-based optimization of NGS data analysis: a case study of Roche 454, ion torrent PGM and Illumina NextSeq sequencing data. PLoS One 12(2):e0171983

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sauer NJ, Narváez-Vásquez J, Mozoruk J, Miller RB, Warburg ZJ, Woodward MJ et al (2016) Oligonucleotide-mediated genome editing provides precision and function to engineered nucleases and antibiotics in plants. Plant Physiol 170(4):1917–1928

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schneeberger K (2014) Using next-generation sequencing to isolate mutant genes from forward genetic screens. Nat Rev Genet 15(10):662

    Article  CAS  PubMed  Google Scholar 

  • Sibout R, Eudes A, Mouille G, Pollet B, Lapierre C, Jouanin L, Séguin A (2005) Cinnamyl alcohol dehydrogenase-C and -D are the primary genes involved in lignin biosynthesis in the floral stem of Arabidopsis. Plant Cell Online 17:2059–2076

    Article  CAS  Google Scholar 

  • Sikora P, Chawade A, Larsson M, Olsson J, Olsson O (2011) Mutagenesis as a tool in plant genetics, functional genomics, and breeding. Int J Plant Genom 2011:1

    Article  CAS  Google Scholar 

  • Srinivasachar D, Malik RS (1971) Gamma-ray induced variability in the iodine value of linseed oil. Curr Sci 11:298–299

    Google Scholar 

  • Sudarshan GP, Kulkarni M, Akhov L, Ashe P, Shaterian H, Cloutier S et al (2017) QTL mapping and molecular characterization of the classical D locus controlling seed and flower color in Linum usitatissimum (flax). Sci Rep 7(1):15751

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sun H, Schneeberger K (2015) SHOREmap v3. 0: fast and accurate identification of causal mutations from forward genetic screens. In Plant Functional Genomics (pp. 381–395). Humana Press, New York, NY

    Google Scholar 

  • Sveinsson S, McDill J, Wong GK, Li J, Li X, Deyholos MK, Cronk QC (2013) Phylogenetic pinpointing of a paleopolyploidy event within the flax genus (Linum) using transcriptomics. Ann Bot 113(5):753–761

    Article  PubMed  PubMed Central  Google Scholar 

  • Tejklová E (2002) Curly stem-an induced mutation in flax (Linum usitatissimum L.). Czech J Genet Plant Breed 38(3/4):125–128

    Google Scholar 

  • Till BJ, Burtner C, Comai L, Henikoff S (2004) Mismatch cleavage by single-strand specific nucleases. Nucleic Acids Res 32(8):2632–2641. https://doi.org/10.1093/nar/gkh599

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Triques K, Sturbois B, Gallais S, Dalmais M, Chauvin S, Clepet C, Aubourg S, Rameau C, Caboche M, Bendahmane A (2007 Sep) Characterization of Arabidopsis thaliana mismatch specific endonucleases: application to mutation discovery by TILLING in pea. Plant J 51(6):1116–1125

    Article  CAS  PubMed  Google Scholar 

  • Tsai H, Howell T, Nitcher R, Missirian V, Watson B, Ngo KJ, Lieberman M, Fass J, Uauy C, Tran RK, Khan AA, Filkov V, Tai TH, Dubcovsky J, Comai L (2011) Discovery of rare mutations in populations: TILLING by sequencing. Plant Physiol 156:1257–1268

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vereshchagin AG (1973) The variability of individual flax seeds in fatty acid composition. Biokhimiya 38:573–582

    CAS  Google Scholar 

  • Vrinten P, Hu Z, Munchinsky MA, Rowland G, Qiu X (2005) Two FAD3 desaturase genes control the level of linolenic acid in flax seed. Plant Physiol 139(1):79–87

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J et al (2012a) The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant J 72(3):461–473

    Article  PubMed  CAS  Google Scholar 

  • Wang TL, Uauy C, Robson F, Till B (2012b) TILLING in extremis. Plant Biotechnol J 10(7):761–772

    Article  CAS  PubMed  Google Scholar 

  • Wróbel-Kwiatkowska M, Starzycki M, Zebrowski J, Oszmianski J, Szopa J (2007) Lignin deficiency in transgenic flax resulted in plants with improved mechanical properties. J Biotechnol 128:919–934

    Article  PubMed  CAS  Google Scholar 

  • You FM, Xiao J, Li P, Yao Z, Jia G, He L, ...Cloutier S (2018) Chromosome‐scale pseudomolecules refined by optical, physical and genetic maps in flax. The Plant Journal, 95(2), 371–384

    Article  CAS  PubMed  Google Scholar 

  • Zhang N, Deyholos MK (2016) RNASeq analysis of the shoot apex of flax (Linum usitatissimum) to identify phloem fiber specification genes. Front Plant Sci 7:950

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

SH and SG gratefully acknowledge the support of the University of Lille, the Research Federation (Université de Lille, CNRS FR 3688, FRABio, Biochimie Structurale et Fonctionnelle des Assemblages Biomoléculaires), the Region “Hauts-de-France” (project ALIBIOTECH), and the French National Research Agency (ANR, project PT-Flax).

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Grec, S., Dalmais, M., Chatterjee, M., Bendahmane, A., Hawkins, S. (2019). Development of Flax (Linum usitatissimum L.) Mutant Populations for Forward and Reverse Genetics. In: Cullis, C. (eds) Genetics and Genomics of Linum. Plant Genetics and Genomics: Crops and Models, vol 23. Springer, Cham. https://doi.org/10.1007/978-3-030-23964-0_10

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