Abstract
Brachypodium distachyon (Brachypodium) is a novel model plant for structural and functional genomic studies of Poaceae. Brachypodium has many favorable features, such as small size, small genome, short life cycle, and easy handling. Bioethanol, as renewable resource, has been widely studied as a replacement for fossil fuels. Lignin is involved with the efficiency of energy feedstock. It is generally accepted that bioethanol production is negatively affected by lignin content. Brachypodium was irradiated with gamma irradiation, at doses of 50, 100, 150, 200, and 250 Gy, and 25 M2 plants that showed the least staining with phloroglucinol were selected. Nucleotide alteration within genes that contribute to the lignin biosynthesis pathway was analyzed. In total, 4 INDELs and 249 SNPs which included 2 additional nonsense mutations, a mutation at the start codon, and a mutation at the 3′ splicing site were identified in the M2 lines. The transition/transversion rate was 7.59, and single nucleotide substitutions were found every 1,143 bp. As biological resources, the M2 populations generated in this work will contribute to functional genomics of Brachypodium and to the breeding of grass crops.
Similar content being viewed by others
References
Bouvier D’Yvoire M, Boucjabke-Coussa O, Voorend W, Antelme S, Cézard L et al (2013) Disrupting the cinnamyl alcohol dehydrogenase 1 gene (BdCAD1) leads to altered lignification and improved saccharification in Brachypodium distachyon. Plant J 73:496–508
Chapple C, Ladisch M, Melian R (2007) Loosening lignin’s grip on biofuel production. Nat Biotechnol 25:746–747
Chen F, Dixon RA (2007) Lignin modification improves fermentable sugar yields for biofuel production. Nat Biotechnol 25:759–761
Cheng L, Yang H, Lin B, Wang Y, Li W, Wang D, Chang F (2010) Effect of gamma-ray radiation on physiological, morphological characters and chromosome aberrations of minitubers in Solanum tuberosum L. Int J Radiat Biol 86:791–799
Chun JB, Ha BK, Jang DS, Song MR, Lee KJ, Kim JB, Kim SH, Kang SY, Lee GJ, Seo YW, Kim DS (2012) Identification of mutations in OASA1 gene from a gamma-irradiated rice mutant population. Plant Breed 131:276–281
Do CT, Pollet B, Thévenin J, Sibout R, Denoue D, Barrière Y, Lapierre C, Jouanin L (2007) Both caffeoyl coenzyme A 3-O-methyltransferase 1 and caffeic acid O-methyltransferase 1 are involved in redundant functions for lignin, flavonoids and sinapoyl malate biosynthesis in Arabidopsis. Planta 226:1117–1129
DOE (2006) Breaking the biological barriers to cellulosic ethanol. A Research Roadmap Resulting from the Biomass to Biofuels Workshop Sponsored by the U.S. Department of Energy, 2005, MD, USA, pp 181–184
Donini P, Sonnino A (1998) Induced mutation in plant breeding: current status and future outlook. In: Jain SM (ed) Somaclonal variation and induced mutation in crop improvement. Kluwer Academic, London, pp 255–291
Draper J, Mur LAJ, Jenkins G, Ghosh-Biswas GC, Bablak P, Hasterok R, Routledge APM (2001) Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiol 127:1539–1555
Elkind Y, Edwards R, Mavandad M, Hedrick SA, Ribak O, Dixon RA, Lamb CJ (1990) Abnormal plant development and down-regulation of phenylpropanoid biosynthesis in transgenic tobacco containing a heterologous phenylalanine ammonia-lyase gene. Proc Natl Acad Sci USA 87:9057–9061
Fu HW, Li YF, Shu QY (2008) A revisit of mutation induction by gamma rays in rice (Oryza sativa L.) implications of microsatellite markers for quality control. Mol Breed 22:281–288
Fu C, Mielenz JR, Xiao X, Ge Y, Hamilton CY et al (2011) Genetic manipulation of lignin reduces recalcitrance and improves ethanol production from switchgrass. Proc Natl Acad Sci USA 108:3803–3808
Getachewa G, Ibáñez AM, Pittroff W, Dandekar AM, McCaslin M, Goyal S, Reisen P, DePeters EJ, Putnam DH (2011) A comparative study between lignin down regulated alfalfa lines and their respective unmodified controls on the nutritional characteristics of hay. Anim Feed Sci Technol 170:192–200
Giussani LM, Sánchez JH, Zuloaga FO, Kellogg EA (2001) A molecular phylogeny of the grass subfamily Panicoideae (Poaceae) shows multiple origins of C4 photosynthesis. Am J Bot 88:1993–2012
Gray KA, Zhao L, Emptage M (2006) Bioethanol. Curr Opin Chem Biol 10:141–146
Henikoff S, Comai L (2003) Single-nucleotide mutations for plant functional genomics. Annu Rev Plant Biol 54:375–401
Keating JD, Panganiban C, Mansfield SD (2006) Tolerance and adaptation of ethanologenic yeasts to lignocellulosic inhibitory compounds. Biotechnol Bioeng 93:1196–1206
Kellogg EA (2001) Evolutionary history of the grasses. Plant Physiol 125:1198–1205
Korbie DJ, Mattick JS (2008) Touchdown PCR for increased specificity and sensitivity in PCR amplification. Nat Protoc 3:1452–1456
Lai J, Li R, Xu X, Jin W, XU M et al (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42:1027–1031
Leplé JC, Dauwe R, Morreel K, Storme V, Lapierre C et al (2007) Downregulation of cinnamoyl-coenzyme A reductase in poplar: multiple-level phenotyping reveals effects on cell wall polymer metabolism and structure. Plant Cell 19:3669–3691
Lorenz AJ, Anex RP, Isci A, Coors JG, de Leon N, Weimer PJ (2009) Forage quality and composition measurements as predictors of ethanol yield from maize (Zea mays L.) stover. Biotechnol Biofuels 2:5
Martínez JMF, Mancha M, Osorio J, Garcés R (1997) Sunflower mutant containing high levels of palmitic acid in high oleic background. Euphytica 97:113–116
Matsukura C, Yamaguchi I, Inamura M, Ban Y, Kobayashi Y, Yin YG, Saito T, Kuwata C, Imanishi S, Nishimura S (2007) Generation of gamma irradiation-induced mutant lines of the miniature tomato (Solanum lycopersicum L.) cultivar ‘Micro-Tom’. Plant Biotechnol NAR 24:39–44
McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K et al (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci USA 106:12273–12278
Mir Derikvand M, Sierra JB, Ruel K, Pollet B, Do CT, Thévenin J, Buffard D, Jouanin L, Lapierre C (2008) Redirection of the phenylpropanoid pathway to feruloyl malate in Arabidopsis mutants deficient for cinnamoyl-CoA reductase 1. Planta 227:943–956
Monties B (1989) Lignins. In: Harborne JB (ed) Methods in plant biochemistry. Academic Press, London, pp 113–157
Pinçon G, Maury S, Hoffmann L, Geoffroy P, Lapierre C, Pollet B, Legrand M (2001) Repression of O-methyltransferase genes in transgenic tobacco affects lignin synthesis and plant growth. Phytochemistry 57:1167–1176
Pomar F, Merino F, Ros Barceló A (2002) O-4-Linked coniferyl and sinapyl aldehydes in lignifying cell walls are the main targets of the Wiesner (phloroglucinol-HCl) reaction. Protoplasma 220:17–28
Ragauskas AJ, Williams CK, Davison BH, Britovsek G, Cairney J, Eckert CA, Frederick WJ, Hallett JP, Leak DJ, Liotta CL, Mielenz JR, Murphy R, Templer R, Tschaplinski T (2006) The path forward for biofuels and biomaterials. Science 311:484–489
Ralph J, Akiyama T, Kim H, Lu F, Schatz PF, Marita JM, Ralph SA, Reddy MSS, Chen F, Dixon RA (2006) Effects of coumarate 3-hydroxylase down-regulation on lignin structure. J Biol Chem 281:8843–8853
Sato Y, Shirasawa K, Takahashi Y, Nishimura M, Nishio T (2006) Mutant selection from progeny of gamma-ray-irradiated rice by DNA heteroduplex cleavage using Brassica petiole extract. Breed Sci 56:179–183
Schilmiller AL, Stout J, Weng JK, Humphreys J, Ruegger MO, Chapple C (2009) Mutations in the cinnamate 4-hydroxylase gene impact metabolism, growth and development in Arabidopsis. Plant J 60:771–782
Speer EO (1987) A method of retaining phloroglucinol proof lignin. Stain Technol 62:279–280
Suzuki T, Eiguchi M, Kumamaru T, Satoh H, Matsusaka H, Moriguchi K, Nagato Y, Kurata N (2008) MNU-induced mutant pools and high performance TILLING enable finding of any gene mutation in rice. Mol Genet Genomics 279:213–223
Tanaka A, Shikazono N, Hase Y (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. Radiat Res 51:223–233
Torney F, Moeller L, Scarpa A, Wang K (2007) Genetic engineering approaches to improve bioethanol production from maize. Curr Opin Biotechnol 18:193–199
Van Acker R, Vanholme R, Storme V, Mortimer JC, Dupree P, Boerjan W (2013) Lignin biosynthesis perturbations affect secondary cell wall composition and saccharification yield in Arabidopsis thaliana. Biotechnol Biofuels 6:46
Wang Y, Wang F, Zhai H, Liu Q (2007) Production of a useful mutant by chronic irradiation in sweet potato. Sci Hortic Amsterdam 111:173–178
Wu JL, Wu C, Lei C, Baraoidan M, Bordeos A et al (2005) Chemical- and irradiation-induced mutants of indica rice IR64 for forward and reverse genetics. Plant Mol Biol 59:85–97
Yuan JS, Tiller KH, Al-Ahmad H, Stewart NR, Stewart NC (2008) Plants to power: bioenergy to fuel the future. Trends Plant Sci 13:421–429
Acknowledgments
This research was supported by Radiation Technology R&D Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Sciense, ICT and Future Planning (NRF-2012M2A2A6035566). This work was supported by a Grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No. PJ0080312013), Rural Development Administration, Republic of Korea.
Conflict of interest
The authors declare no conflict of interest.
Author information
Authors and Affiliations
Corresponding author
Additional information
Man Bo Lee and Dae Yeon Kim contributed equally to this paper.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Lee, M.B., Kim, D.Y., Hong, M.J. et al. Identification of gamma irradiated Brachypodium mutants with altered genes responsible for lignin biosynthesis. Genes Genom 36, 65–76 (2014). https://doi.org/10.1007/s13258-013-0142-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13258-013-0142-0