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The Brachypodium distachyon Root System: A Tractable Model to Investigate Grass Roots

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Genetics and Genomics of Brachypodium

Part of the book series: Plant Genetics and Genomics: Crops and Models ((PGG,volume 18))

Abstract

The root systems of land plants mine the soil for water and essential edaphic nutrients that are needed for the vegetative and reproductive phases of shoot growth. Different root system architectures exist across the angiosperms, and while there are many variants, two principal layouts are associated with the monocotyledon-dicotyledon divide: whereas a primary taproot and its branch roots typically dominate dicotyledon root systems, monocotyledon root systems appear overall more complex and are typically dominated by post-embryonic shoot-borne roots. Brachypodium distachyon (Brachypodium) displays all the characteristics of a monocotyledon root system; however its complexity is minimal as compared to many other monocotyledon species, notably crops. Together with its relatively small size, this makes the Brachypodium root system a tractable model for monocotyledon root development that can be easily investigated in tissue culture but also in soil. First molecular genetic and physiological studies already point to distinct regulatory mechanisms and environmental responses in Brachypodium as compared to well-characterized dicotyledon model species. These results highlight the worthwhileness of studying the Brachypodium root system and its value as a credible model to decipher major evolutionary-developmental facets of angiosperm root system diversity. Moreover, the fact that Brachypodium is a wild plant that has not undergone human selection contrasts with the crops that serve as key monocotyledon models so far. Therefore, analysis of Brachypodium can be instructive with respect to root traits that have been modified or lost during crop domestication, especially in the closely related temperate cereals, barley, rye and wheat. Combined with natural germplasm collections, Brachypodium is thus an ideal model to investigate ecological, evolutionary and developmental aspects of monocotyledon root systems and their relation to crop performance.

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References

  • AGI. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000;408(6814):796–815.

    Article  Google Scholar 

  • Alves SC, Worland B, Thole V, Snape JW, Bevan MW, Vain P. A protocol for Agrobacterium-mediated transformation of Brachypodium distachyon community standard line Bd21. Nat Protoc. 2009;4(5):638–49.

    Article  CAS  PubMed  Google Scholar 

  • Baltes NJ, Voytas DF. Enabling plant synthetic biology through genome engineering. Trends Biotechnol. 2014;33(2):120–31.

    Article  PubMed  Google Scholar 

  • Beuchat J, Li S, Ragni L, Shindo C, Kohn MH, Hardtke CS. A hyperactive quantitative trait locus allele of Arabidopsis BRX contributes to natural variation in root growth vigor. Proc Natl Acad Sci U S A. 2010;107(18):8475–80.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Bragg JN, Wu J, Gordon SP, Guttman ME, Thilmony R, Lazo GR, et al. Generation and characterization of the Western Regional Research Center Brachypodium T-DNA insertional mutant collection. PLoS One. 2012;7(9):e41916.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Brenner S. In the beginning was the worm. Genetics. 2009;182(2):413–5.

    Article  PubMed Central  PubMed  Google Scholar 

  • Catalan P, Chalhoub B, Chochois V, Garvin DF, Hasterok R, Manzaneda AJ, et al. Update on the genomics and basic biology of Brachypodium: International Brachypodium Initiative (IBI). Trends Plant Sci. 2014;19(7):414–8.

    Article  CAS  PubMed  Google Scholar 

  • Cho H, Ryu H, Rho S, Hill K, Smith S, Audenaert D, et al. A secreted peptide acts on BIN2-mediated phosphorylation of ARFs to potentiate auxin response during lateral root development. Nat Cell Biol. 2014;16(1):66–76.

    Article  CAS  PubMed  Google Scholar 

  • Chochois V, Vogel JP, Watt M. Application of Brachypodium to the genetic improvement of wheat roots. J Exp Bot. 2012;63(9):3467–74.

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • de Lange O, Binder A, Lahaye T. From dead leaf, to new life: TAL effectors as tools for synthetic biology. Plant J. 2014;78(5):753–71.

    Article  PubMed  Google Scholar 

  • De Rybel B, Audenaert D, Vert G, Rozhon W, Mayerhofer J, Peelman F, et al. Chemical inhibition of a subset of Arabidopsis thaliana GSK3-like kinases activates brassinosteroid signaling. Chem Biol. 2009;16(6):594–604.

    Article  PubMed  Google Scholar 

  • Depuydt S, Hardtke CS. Hormone signalling crosstalk in plant growth regulation. Curr Biol. 2011;21(9):R365–73.

    Article  CAS  PubMed  Google Scholar 

  • Draper J, Mur LA, Jenkins G, Ghosh-Biswas GC, Bablak P, Hasterok R, et al. Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiol. 2001;127(4):1539–55.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Girin T, David LC, Chardin C, Sibout R, Krapp A, Ferrario-Mery S, et al. Brachypodium: a promising hub between model species and cereals. J Exp Bot. 2014;65(19):5683–96.

    Article  PubMed  Google Scholar 

  • Goddard R, Peraldi A, Ridout C, Nicholson P. Enhanced disease resistance caused by BRI1 mutation is conserved between Brachypodium distachyon and barley (Hordeum vulgare). Mol Plant-Microbe Interact. 2014;27(10):1095–106.

    Article  CAS  PubMed  Google Scholar 

  • Gordon SP, Priest H, Des Marais DL, Schackwitz W, Figueroa M, Martin J, et al. Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines. Plant J. 2014;79(3):361–74.

    Article  CAS  PubMed  Google Scholar 

  • Grierson C, Schiefelbein J. Root hairs. Arabidopsis Book. 2002;1:e0060.

    Article  PubMed Central  PubMed  Google Scholar 

  • Helariutta Y, Fukaki H, Wysocka-Diller J, Nakajima K, Jung J, Sena G, et al. The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling. Cell. 2000;101(5):555–67.

    Article  CAS  PubMed  Google Scholar 

  • Hong JJ, Park YS, Bravo A, Bhattarai KK, Daniels DA, Harrison MJ. Diversity of morphology and function in arbuscular mycorrhizal symbioses in Brachypodium distachyon. Planta. 2012;236(3):851–65.

    Article  CAS  PubMed  Google Scholar 

  • Ingram PA, Zhu J, Shariff A, Davis IW, Benfey PN, Elich T. High-throughput imaging and analysis of root system architecture in Brachypodium distachyon under differential nutrient availability. Philos Trans R Soc Lond B Biol Sci. 2012;367(1595):1559–69.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 2010;463(7282):763–8.

    Article  Google Scholar 

  • Kerk NM, Feldman LJ. A biochemical-model for the initiation and maintenance of the quiescent center - implications for organization of root-meristems. Development. 1995;121(9):2825–33.

    CAS  Google Scholar 

  • Kim CM, Dolan L. Root hair development involves asymmetric cell division in Brachypodium distachyon and symmetric division in Oryza sativa. New Phytol. 2011;192(3):601–10.

    Article  CAS  PubMed  Google Scholar 

  • Liang X, Wang H, Mao L, Hu Y, Dong T, Zhang Y, et al. Involvement of COP1 in ethylene- and light-regulated hypocotyl elongation. Planta. 2012;236(6):1791–802.

    Article  CAS  PubMed  Google Scholar 

  • Lopez-Bucio J, Cruz-Ramirez A, Herrera-Estrella L. The role of nutrient availability in regulating root architecture. Curr Opin Plant Biol. 2003;6(3):280–7.

    Article  CAS  PubMed  Google Scholar 

  • Makarevitch I, Thompson A, Muehlbauer GJ, Springer NM. Brd1 gene in maize encodes a brassinosteroid C-6 oxidase. PLoS One. 2012;7(1):e30798.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Marzec M, Melzer M, Szarejko I. The evolutionary context of root epidermis cell patterning in grasses (Poaceae). Plant Signal Behav. 2014;9(1), e27972.

    Article  PubMed Central  PubMed  Google Scholar 

  • McCourt P, Benning C. Arabidopsis: a rich harvest 10 years after completion of the genome sequence. Plant J. 2010;61(6):905–8.

    Article  CAS  PubMed  Google Scholar 

  • Meyerowitz EM. Arabidopsis, a useful weed. Cell. 1989;56(2):263–9.

    Article  CAS  PubMed  Google Scholar 

  • Mori M, Nomura T, Ooka H, Ishizaka M, Yokota T, Sugimoto K, et al. Isolation and characterization of a rice dwarf mutant with a defect in brassinosteroid biosynthesis. Plant Physiol. 2002;130(3):1152–61.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mouchel CF, Briggs GC, Hardtke CS. Natural genetic variation in Arabidopsis identifies BREVIS RADIX, a novel regulator of cell proliferation and elongation in the root. Genes Dev. 2004;18(6):700–14.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Nakajima K, Sena G, Nawy T, Benfey PN. Intercellular movement of the putative transcription factor SHR in root patterning. Nature. 2001;413(6853):307–11.

    Article  CAS  PubMed  Google Scholar 

  • Nomura T, Kushiro T, Yokota T, Kamiya Y, Bishop GJ, Yamaguchi S. The last reaction producing brassinolide is catalyzed by cytochrome P-450s, CYP85A3 in tomato and CYP85A2 in Arabidopsis. J Biol Chem. 2005;280(18):17873–9.

    Article  CAS  PubMed  Google Scholar 

  • Osmont KS, Sibout R, Hardtke CS. Hidden branches: developments in root system architecture. Annu Rev Plant Biol. 2007;58:93–113.

    Article  CAS  PubMed  Google Scholar 

  • Pacheco-Villalobos D, Hardtke CS. Natural genetic variation of root system architecture from Arabidopsis to Brachypodium: towards adaptive value. Philos Trans R Soc Lond B Biol Sci. 2012;367(1595):1552–8.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Pacheco-Villalobos D, Sankar M, Ljung K, Hardtke CS. Disturbed local auxin homeostasis enhances cellular anisotropy and reveals alternative wiring of auxin-ethylene crosstalk in Brachypodium distachyon seminal roots. PLoS Genet. 2013;9(6):e1003564.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Parker D, Beckmann M, Enot DP, Overy DP, Rios ZC, Gilbert M, et al. Rice blast infection of Brachypodium distachyon as a model system to study dynamic host/pathogen interactions. Nat Protoc. 2008;3(3):435–45.

    Article  CAS  PubMed  Google Scholar 

  • Poire R, Chochois V, Sirault XR, Vogel JP, Watt M, Furbank RT. Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Brachypodium distachyon. J Integr Plant Biol. 2014;56(8):781–96.

    Article  CAS  PubMed  Google Scholar 

  • Routledge AP, Shelley G, Smith JV, Talbot NJ, Draper J, Mur LA. Magnaporthe grisea interactions with the model grass Brachypodium distachyon closely resemble those with rice (Oryza sativa). Mol Plant Pathol. 2004;5(4):253–65.

    Article  CAS  PubMed  Google Scholar 

  • Stepanova AN, Robertson-Hoyt J, Yun J, Benavente LM, Xie DY, Dolezal K, et al. TAA1-mediated auxin biosynthesis is essential for hormone crosstalk and plant development. Cell. 2008;133(1):177–91.

    Article  CAS  PubMed  Google Scholar 

  • Stepanova AN, Yun J, Robles LM, Novak O, He W, Guo H, et al. The Arabidopsis YUCCA1 flavin monooxygenase functions in the indole-3-pyruvic acid branch of auxin biosynthesis. Plant Cell. 2011;23(11):3961–73.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Svistoonoff S, Creff A, Reymond M, Sigoillot-Claude C, Ricaud L, Blanchet A, et al. Root tip contact with low-phosphate media reprograms plant root architecture. Nat Genet. 2007;39(6):792–6.

    Article  CAS  PubMed  Google Scholar 

  • Tao Y, Ferrer JL, Ljung K, Pojer F, Hong F, Long JA, et al. Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants. Cell. 2008;133(1):164–76.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Thole V, Vain P. Agrobacterium-mediated transformation of Brachypodium distachyon. Methods Mol Biol. 2012;847:137–49.

    Article  CAS  PubMed  Google Scholar 

  • Thole V, Worland B, Wright J, Bevan MW, Vain P. Distribution and characterization of more than 1000 T-DNA tags in the genome of Brachypodium distachyon community standard line Bd21. Plant Biotechnol J. 2010;8(6):734–47.

    Article  CAS  PubMed  Google Scholar 

  • Thole V, Peraldi A, Worland B, Nicholson P, Doonan JH, Vain P. T-DNA mutagenesis in Brachypodium distachyon. J Exp Bot. 2012;63(2):567–76.

    Article  CAS  PubMed  Google Scholar 

  • Vain P, Worland B, Thole V, McKenzie N, Alves SC, Opanowicz M, et al. Agrobacterium-mediated transformation of the temperate grass Brachypodium distachyon (genotype Bd21) for T-DNA insertional mutagenesis. Plant Biotechnol J. 2008;6(3):236–45.

    Article  CAS  PubMed  Google Scholar 

  • Watt M, Schneebeli K, Dong P, Wilson IW. The shoot and root growth of Brachypodium and its potential as a model for wheat and other cereal crops. Funct Plant Biol. 2009;36(10-11):960–9.

    Article  Google Scholar 

  • Won C, Shen X, Mashiguchi K, Zheng Z, Dai X, Cheng Y, et al. Conversion of tryptophan to indole-3-acetic acid by TRYPTOPHAN AMINOTRANSFERASES OF ARABIDOPSIS and YUCCAs in Arabidopsis. Proc Natl Acad Sci U S A. 2011;108(45):18518–23.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wu S, Lee CM, Hayashi T, Price S, Divol F, Henry S, et al. A plausible mechanism, based upon Short-Root movement, for regulating the number of cortex cell layers in roots. Proc Natl Acad Sci U S A. 2014;111(45):16184–9.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Xu Y, Zhang X, Li Q, Cheng Z, Lou H, Ge L, et al. BdBRD1, a brassinosteroid C-6 oxidase homolog in Brachypodium distachyon L., is required for multiple organ development. Plant Physiol Biochem. 2015;86:91–9.

    Article  CAS  PubMed  Google Scholar 

  • Zheng Z, Guo Y, Novak O, Dai X, Zhao Y, Ljung K, et al. Coordination of auxin and ethylene biosynthesis by the aminotransferase VAS1. Nat Chem Biol. 2013;9(4):244–6.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland

    Christian S. Hardtke & David Pacheco-Villalobos

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  1. Christian S. Hardtke
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  2. David Pacheco-Villalobos
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Correspondence to Christian S. Hardtke .

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Editors and Affiliations

  1. DOE Joint Genome Institute, Walnut Creek, California, USA

    John P. Vogel

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Hardtke, C.S., Pacheco-Villalobos, D. (2015). The Brachypodium distachyon Root System: A Tractable Model to Investigate Grass Roots. In: Vogel, J. (eds) Genetics and Genomics of Brachypodium. Plant Genetics and Genomics: Crops and Models, vol 18. Springer, Cham. https://doi.org/10.1007/7397_2015_6

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