Functional Genomics in the Study of Metabolic Pathways in Medicago truncatula: An Overview

  • Chenggang Liu
  • Chan Man Ha
  • Richard A. DixonEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1822)


In addition to its value as a model system for studies on symbiotic nitrogen fixation, Medicago truncatula has recently become an organism of choice for dissection of complex pathways of secondary metabolism. This work has been driven by two main reasons, both with practical implications. First Medicago species possess a wide range of flavonoid and terpenoid natural products, many of which, for example, the isoflavonoids and triterpene saponins, have important biological activities impacting both plant and animal (including human) health. Second, M. truncatula serves as an excellent model for alfalfa, the world’s major forage legume, and forage quality is determined in large part by the concentrations of products of secondary metabolism, particularly lignin and condensed tannins. We here review recent progress in understanding the pathways leading to flavonoids, lignin, and triterpene saponins through utilization of genetic resources in M. truncatula.


Flavonoid Lignin Metabolite transport Proanthocyanidin Saponin Transcriptional regulation Transposon insertion mutant Triterpene 


  1. 1.
    O’Connor SE (2015) Engineering of secondary metabolism. Annu Rev Genet 49:71–94PubMedCrossRefGoogle Scholar
  2. 2.
    Tsao R (2010) Chemistry and biochemistry of dietary polyphenols. Forum Nutr 2:1231–1246Google Scholar
  3. 3.
    Weng JK, Chapple C (2010) The origin and evolution of lignin biosynthesis. New Phytol 187:273–285PubMedCrossRefGoogle Scholar
  4. 4.
    Chang W-C, Song H, Liu H-W, Liu P (2013) Current development in isoprenoid precursor biosynthesis and regulation. Curr Opin Chem Biol 17:571–579PubMedPubMedCentralCrossRefGoogle Scholar
  5. 5.
    Bennett RN, Wallsgrove RM (1994) Secondary metabolites in plant defence mechanisms. New Phytol 127:617–633CrossRefGoogle Scholar
  6. 6.
    Rose RJ (2008) Medicago truncatula as a model for understanding plant interactions with other organisms, plant development and stress biology: past, present and future. Funct Plant Biol 35:253–264CrossRefGoogle Scholar
  7. 7.
    Wang Y, Chen R (2013) Regulation of compound leaf development. Plants (Basel) 3:1–17PubMedCentralCrossRefGoogle Scholar
  8. 8.
    Benlloch R, Navarro C, Beltrán J, Cañas LA (2003) Floral development of the model legume Medicago truncatula: ontogeny studies as a tool to better characterize homeotic mutations. Sex Plant Reprod 15:231–241Google Scholar
  9. 9.
    Peng J, Chen R (2011) Auxin efflux transporter MtPIN10 regulates compound leaf and flower development in Medicago truncatula. Plant Signal Behav 6:1537–1544PubMedPubMedCentralCrossRefGoogle Scholar
  10. 10.
    Weller JL, Ortega R (2015) Genetic control of flowering time in legumes. Front Plant Sci 6:207PubMedPubMedCentralCrossRefGoogle Scholar
  11. 11.
    Harrison MJ, Dewbre GR, Liu J (2002) A phosphate transporter from Medicago truncatula involved in the acquisition of phosphate released by arbuscular mycorrhizal fungi. Plant Cell 14:2413–2429PubMedPubMedCentralCrossRefGoogle Scholar
  12. 12.
    Genre A, Chabaud M, Timmers T, Bonfante P, Barker DG (2005) Arbuscular mycorrhizal fungi elicit a novel intracellular apparatus in Medicago truncatula root epidermal cells before infection. Plant Cell 17:3489–3499PubMedPubMedCentralCrossRefGoogle Scholar
  13. 13.
    Guo S, Kamphuis LG, Gao L, Edwards OR, Singh KB (2009) Two independent resistance genes in the Medicago truncatula cultivar jester confer resistance to two different aphid species of the genus Acyrthosiphon. Plant Signal Behav 4:328–331PubMedPubMedCentralCrossRefGoogle Scholar
  14. 14.
    Chen T, Duan L, Zhou B, Yu H, Zhu H, Cao Y, Zhang Z (2017) Interplay of pathogen-induced defense responses and symbiotic establishment in Medicago truncatula. Front Microbiol 8:973PubMedPubMedCentralCrossRefGoogle Scholar
  15. 15.
    Badri M, Chardon F, Huguet T, Aouani ME (2011) Quantitative trait loci associated with drought tolerance in the model legume Medicago truncatula. Euphytica 181:415CrossRefGoogle Scholar
  16. 16.
    Gil-Quintana E, Lyon D, Staudinger C, Wienkoop S, González EM (2015) Medicago truncatula and Glycine max: different drought tolerance and similar local response of the root nodule proteome. J Proteome Res 14:5240–5251PubMedPubMedCentralCrossRefGoogle Scholar
  17. 17.
    Liu L, Zhang Z, Dong J, Wang T (2016) Overexpression of MtWRKY76 increases both salt and drought tolerance in Medicago truncatula. Environ Exp Bot 123:50–58CrossRefGoogle Scholar
  18. 18.
    Dixon RA, Steele CL (1999) Flavonoids and isoflavonoids – a gold mine for metabolic engineering. Trends Plant Sci 4:394–400PubMedCrossRefGoogle Scholar
  19. 19.
    Tanaka H, Sato M, Fujiwara S, Hirata M, Etoh H, Takeuchi H (2002) Antibacterial activity of isoflavonoids isolated from Erythrina variegata against methicillin-resistant Staphylococcus aureus. Lett Appl Microbiol 35:494–498PubMedCrossRefGoogle Scholar
  20. 20.
    Mukne AP, Viswanathan V, Phadatare AG (2011) Structure pre-requisites for isoflavones as effective antibacterial agents. Pharmacogn Rev 5:13–18PubMedPubMedCentralCrossRefGoogle Scholar
  21. 21.
    Kosslak RM, Bookland R, Barkei J, Paaren HE, Appelbaum ER (1987) Induction of Bradyrhizobium japonicum common nod genes by isoflavones isolated from Glycine max. Proc Natl Acad Sci U S A 84:7428–7432PubMedPubMedCentralCrossRefGoogle Scholar
  22. 22.
    Pueppke SG, Bolaños-Vásquez MC, Werner D, Bec-Ferté M-P, Promé J-C, Krishnan HB (1998) Release of flavonoids by the soybean cultivars McCall and Peking and their perception as signals by the nitrogen-fixing symbiont Sinorhizobium fredii. Plant Physiol 117:599–606PubMedPubMedCentralCrossRefGoogle Scholar
  23. 23.
    Dixon RA (2004) Phytoestrogens. Annu Rev Plant Biol 55:225–261PubMedCrossRefGoogle Scholar
  24. 24.
    Huhman DV, Sumner LW (2002) Metabolic profiling of saponins in Medicago sativa and Medicago truncatula using HPLC coupled to an electrospray ion-trap mass spectrometer. Phytochemistry 59:347–360PubMedCrossRefGoogle Scholar
  25. 25.
    Tava A, Scotti C, Avato P (2011) Biosynthesis of saponins in the genus Medicago. Phytochem Rev 10:459–469CrossRefGoogle Scholar
  26. 26.
    Biazzi E, Carelli M, Tava A, Abbruscato P, Losini I, Avato P, Scotti C, Calderini O (2015) CYP72A67 catalyzes a key oxidative step in Medicago truncatula hemolytic saponin biosynthesis. Mol Plant 8:1493–1506PubMedCrossRefGoogle Scholar
  27. 27.
    Mertens J, Pollier J, Vanden Bossche R, Lopez-Vidriero I, Franco-Zorrilla JM, Goossens A (2016) The bHLH transcription factors TSAR1 and TSAR2 regulate triterpene saponin biosynthesis in Medicago truncatula. Plant Physiol 170:194–210PubMedCrossRefGoogle Scholar
  28. 28.
    Reddy MSS, Chen F, Shadle G, Jackson L, Aljoe H, Dixon RA (2005) Targeted down-regulation of cytochrome P450 enzymes for forage quality improvement in alfalfa (Medicago sativa L.). Proc Natl Acad Sci U S A 102:16573–16578PubMedPubMedCentralCrossRefGoogle Scholar
  29. 29.
    McMahon LR, McAllister T, Berg BP, Majak W, Acharya SN, Popp JD, Coulman BE, Wang Y, Cheng KJ (2000) A review of the effect of forage condensed tannins on ruminal fermentation and bloat in grazing cattle. Can J Plant Sci 80:469–485CrossRefGoogle Scholar
  30. 30.
    Pang Y, Wenger JP, Saathoff K, Peel GJ, Wen J, Huhman D, Allen SN, Tang Y, Cheng X, Tadege M, Ratet P, Mysore KS, Sumner LW, Marks MD, Dixon RA (2009) A WD40 repeat protein from Medicago truncatula is necessary for tissue-specific anthocyanin and proanthocyanidin biosynthesis but not for trichome development. Plant Physiol 151:1114–1129PubMedPubMedCentralCrossRefGoogle Scholar
  31. 31.
    Liu C, Jun JH, Dixon RA (2014) MYB5 and MYB14 play pivotal roles in seed coat polymer biosynthesis in Medicago truncatula. Plant Physiol 165:1424–1439PubMedPubMedCentralCrossRefGoogle Scholar
  32. 32.
    Jun JH, Liu C, Xiao X, Dixon RA (2015) The transcriptional repressor MYB2 regulates both spatial and temporal patterns of proanthocyandin and anthocyanin pigmentation in Medicago truncatula. Plant Cell 27:2860–2879PubMedPubMedCentralGoogle Scholar
  33. 33.
    Wang H, Avci U, Nakashima J, Hahn MG, Chen F, Dixon RA (2010) Mutation of WRKY transcription factors initiates pith secondary wall formation and increases stem biomass in dicotyledonous plants. Proc Natl Acad Sci U S A 107:22338–22343PubMedPubMedCentralCrossRefGoogle Scholar
  34. 34.
    Zhao Q, Wang H, Yin Y, Xu Y, Chen F, Dixon RA (2010) Syringyl lignin biosynthesis is directly regulated by a secondary cell wall master switch. Proc Natl Acad Sci U S A 107:14496–14501PubMedPubMedCentralCrossRefGoogle Scholar
  35. 35.
    Zhou R, Jackson L, Shadle G, Nakashima J, Temple S, Chen F, Dixon RA (2010) Distinct cinnamoyl CoA reductases involved in parallel routes to lignin in Medicago truncatula. Proc Natl Acad Sci U S A 107:17803–17808PubMedPubMedCentralCrossRefGoogle Scholar
  36. 36.
    Ha CM, Escamilla-Trevino L, Yarce JC, Kim H, Ralph J, Chen F, Dixon RA (2016) An essential role of caffeoyl shikimate esterase in monolignol biosynthesis in Medicago truncatula. Plant J 86:363–375PubMedCrossRefGoogle Scholar
  37. 37.
    Young ND, Debelle F, Oldroyd GED, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KFX, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KAT, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Berges H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Dai X, Doyle JJ, Dudez A-M, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, Goldstein S, Gonzalez AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray SJ, Jeong D-H, Jing Y, Jocker A, Kenton SM, Kim D-J, Klee K, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun J-H, Najar FZ, Nicholson C, Noirot C, O’Bleness M, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli C, Schiex T, Segurens B, Severin AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang B-B, Wang K, Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Denarie J, Dixon RA, May GD, Schwartz DC, Rogers J, Quetier F, Town CD, Roe BA (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480:520–524PubMedPubMedCentralCrossRefGoogle Scholar
  38. 38.
    Penmetsa RV, Cook DR (2000) Production and characterization of diverse developmental mutants of Medicago truncatula. Plant Physiol 123:1387–1398PubMedPubMedCentralCrossRefGoogle Scholar
  39. 39.
    Rogers C, Wen J, Chen R, Oldroyd G (2009) Deletion-based reverse genetics in Medicago truncatula. Plant Physiol 151:1077–1086PubMedPubMedCentralCrossRefGoogle Scholar
  40. 40.
    Le Signor C, Savois V, Aubert G, Verdier J, Nicolas M, Pagny G, Moussy F, Sanchez M, Baker D, Clarke J, Thompson R (2009) Optimizing TILLING populations for reverse genetics in Medicago truncatula. Plant Biotechnol J 7:430–441PubMedCrossRefGoogle Scholar
  41. 41.
    Carelli M, Calderini O, Panara F, Porceddu A, Losini I, Piffanelli P, Arcioni S, Scotti C (2013) Reverse genetics in Medicago truncatula using a TILLING mutant collection. Methods Mol Biol 1069:101–118PubMedCrossRefGoogle Scholar
  42. 42.
    Cheng X, Wen J, Tadege M, Ratet P, Mysore KS (2011) Reverse genetics in Medicago truncatula using Tnt1 insertion mutants. Methods Mol Biol 678:179–190PubMedCrossRefGoogle Scholar
  43. 43.
    Tadege M, Wen J, He J, Tu H, Kwak Y, Eschstruth A, Cayrel A, Endre G, Zhao PX, Chabaud M, Ratet P, Mysore KS (2008) Large-scale insertional mutagenesis using the Tnt1 retrotransposon in the model legume Medicago truncatula. Plant J 54:335–347PubMedCrossRefGoogle Scholar
  44. 44.
    Veerappan V, Jani M, Kadel K, Troiani T, Gale R, Mayes T, Shulaev E, Wen J, Mysore KS, Azad RK, Dickstein R (2016) Rapid identification of causative insertions underlying Medicago truncatula Tnt1 mutants defective in symbiotic nitrogen fixation from a forward genetic screen by whole genome sequencing. BMC Genomics 17:141PubMedPubMedCentralCrossRefGoogle Scholar
  45. 45.
    Iwashina T (2000) The structure and distribution of the flavonoids in plants. J Plant Res 113:287–299CrossRefGoogle Scholar
  46. 46.
    Kumar S, Pandey AK (2013) Chemistry and biological activities of flavonoids: an overview. Sci World J 2013:162750Google Scholar
  47. 47.
    Wasson AP, Pellerone FI, Mathesius U (2006) Silencing the flavonoid pathway in Medicago truncatula inhibits root nodule formation and prevents auxin transport. Regulation by rhizobia. Plant Cell 18:1617–1629PubMedPubMedCentralCrossRefGoogle Scholar
  48. 48.
    Kowalska I, Stochmal A, Kapusta I, Janda B, Pizza C, Piacente S, Oleszek W (2007) Flavonoids from barrel medic (Medicago truncatula) aerial parts. J Agric Food Chem 55:2645–2652PubMedCrossRefGoogle Scholar
  49. 49.
    Pang Y, Peel GJ, Wright E, Wang Z, Dixon RA (2007) Early steps in proanthocyanidin biosynthesis in the model legume Medicago truncatula. Plant Physiol 145:601–615PubMedPubMedCentralCrossRefGoogle Scholar
  50. 50.
    Jasiński M, Kachlicki P, Rodziewicz P, Figlerowicz M, Stobiecki M (2009) Changes in the profile of flavonoid accumulation in Medicago truncatula leaves during infection with fungal pathogen Phoma medicaginis. Plant Physiol Biochem 47:847–853PubMedCrossRefGoogle Scholar
  51. 51.
    Ng JL, Hassan S, Truong TT, Hocart CH, Laffont C, Frugier F, Mathesius U (2015) Flavonoids and auxin transport inhibitors rescue symbiotic nodulation in the Medicago truncatula cytokinin perception mutant cre1. Plant Cell 27:2210–2226PubMedPubMedCentralCrossRefGoogle Scholar
  52. 52.
    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 7:735PubMedPubMedCentralGoogle Scholar
  53. 53.
    Tanner GJ, Francki KT, Abrahams S, Watson JM, Larkin PJ, Ashton AR (2003) Proanthocyanidin biosynthesis in plants. Purification of legume leucoanthocyanidin reductase and molecular cloning of its cDNA. J Biol Chem 278:31647–31656PubMedCrossRefGoogle Scholar
  54. 54.
    Bogs J, Downey MO, Harvey JS, Ashton AR, Tanner GJ, Robinson SP (2005) Proanthocyanidin synthesis and expression of genes encoding leucoanthocyanidin reductase and anthocyanidin reductase in developing grape berries and grapevine leaves. Plant Physiol 139:652–663PubMedPubMedCentralCrossRefGoogle Scholar
  55. 55.
    Liu Y, Shi Z, Maximova S, Payne MJ, Guiltinan MJ (2013) Proanthocyanidin synthesis in Theobroma cacao: genes encoding anthocyanidin synthase, anthocyanidin reductase, and leucoanthocyanidin reductase. BMC Plant Biol 13:202–202PubMedPubMedCentralCrossRefGoogle Scholar
  56. 56.
    Ferraro K, Jin AL, Nguyen T-D, Reinecke DM, Ozga JA, Ro D-K (2014) Characterization of proanthocyanidin metabolism in pea (Pisum sativum) seeds. BMC Plant Biol 14:238PubMedPubMedCentralCrossRefGoogle Scholar
  57. 57.
    Liu C, Wang X, Shulaev V, Dixon RA (2016) A role for leucoanthocyanidin reductase in the extension of proanthocyanidins. Nat Plants 2:16182PubMedCrossRefGoogle Scholar
  58. 58.
    Dixon RA, Xie DY, Sharma SB (2005) Proanthocyanidins--a final frontier in flavonoid research? New Phytol 165:9–28PubMedCrossRefGoogle Scholar
  59. 59.
    Modolo LV, Blount JW, Achnine L, Naoumkina MA, Wang X, Dixon RA (2007) A functional genomics approach to (iso)flavonoid glycosylation in the model legume Medicago truncatula. Plant Mol Biol 64:499–518PubMedCrossRefGoogle Scholar
  60. 60.
    Peel GJ, Pang Y, Modolo LV, Dixon RA (2009) The LAP1 MYB transcription factor orchestrates anthocyanidin biosynthesis and glycosylation in Medicago. Plant J 59:136–149PubMedCrossRefGoogle Scholar
  61. 61.
    Pang Y, Peel GJ, Sharma SB, Tang Y, Dixon RA (2008) A transcript profiling approach reveals an epicatechin-specific glucosyltransferase expressed in the seed coat of Medicago truncatula. Proc Natl Acad Sci U S A 105:14210–14215PubMedPubMedCentralCrossRefGoogle Scholar
  62. 62.
    Pang Y, Cheng X, Huhman DV, Ma J, Peel GJ, Yonekura-Sakakibara K, Saito K, Shen G, Sumner LW, Tang Y, Wen J, Yun J, Dixon RA (2013) Medicago glucosyltransferase UGT72L1: potential roles in proanthocyanidin biosynthesis. Planta 238:139–154PubMedCrossRefGoogle Scholar
  63. 63.
    Zhao J, Dixon RA (2009) MATE transporters facilitate vacuolar uptake of epicatechin 3′-O-glucoside for proanthocyanidin biosynthesis in Medicago truncatula and Arabidopsis. Plant Cell 21:2323–2340PubMedPubMedCentralCrossRefGoogle Scholar
  64. 64.
    Marinova K, Pourcel L, Weder B, Schwarz M, Barron D, Routaboul JM, Debeaujon I, Klein M (2007) The Arabidopsis MATE transporter TT12 acts as a vacuolar flavonoid/H+ -antiporter active in proanthocyanidin-accumulating cells of the seed coat. Plant Cell 19:2023–2038PubMedPubMedCentralCrossRefGoogle Scholar
  65. 65.
    Zhao J, Huhman D, Shadle G, He X-Z, Sumner LW, Tang Y, Dixon RA (2011) MATE2 mediates vacuolar sequestration of flavonoid glycosides and glycoside malonates in Medicago truncatula. Plant Cell 23:1536–1555PubMedPubMedCentralCrossRefGoogle Scholar
  66. 66.
    Stafford HA, Lester HH (1982) Enzymic and nonenzymic reduction of (+)-dihydroquercetin to its 3,4,-diol. Plant Physiol 70:695–698PubMedPubMedCentralCrossRefGoogle Scholar
  67. 67.
    Baudry A, Heim MA, Dubreucq B, Caboche M, Weisshaar B, Lepiniec L (2004) TT2, TT8, and TTG1 synergistically specify the expression of BANYULS and proanthocyanidin biosynthesis in Arabidopsis thaliana. Plant J 39:366–380PubMedCrossRefGoogle Scholar
  68. 68.
    Lloyd A, Brockman A, Aguirre L, Campbell A, Bean A, Cantero A, Gonzalez A (2017) Advances in the MYB-BHLH-WD repeat (MBW) pigment regulatory model: addition of a WRKY factor and co-option of an anthocyanin MYB for betalain regulation. Plant Cell Physiol 58:1431–1441PubMedCrossRefPubMedCentralGoogle Scholar
  69. 69.
    Walker AR, Davison PA, Bolognesi-Winfield AC, James CM, Srinivasan N, Blundell TL, Esch JJ, Marks MD, Gray JC (1999) The TRANSPARENT TESTA GLABRA1 locus, which regulates trichome differentiation and anthocyanin biosynthesis in Arabidopsis, encodes a WD40 repeat protein. Plant Cell 11:1337–1350PubMedPubMedCentralCrossRefGoogle Scholar
  70. 70.
    Broun P (2005) Transcriptional control of flavonoid biosynthesis: a complex network of conserved regulators involved in multiple aspects of differentiation in Arabidopsis. Curr Opin Plant Biol 8:272–279PubMedCrossRefGoogle Scholar
  71. 71.
    Nesi N, Debeaujon I, Jond C, Pelletier G, Caboche M, Lepiniec L (2000) The TT8 gene encodes a basic helix-loop-helix domain protein required for expression of DFR and BAN genes in Arabidopsis siliques. Plant Cell 12:1863–1878PubMedPubMedCentralCrossRefGoogle Scholar
  72. 72.
    Payne CT, Zhang F, Lloyd AM (2000) GL3 encodes a bHLH protein that regulates trichome development in arabidopsis through interaction with GL1 and TTG1. Genetics 156:1349–1362PubMedPubMedCentralGoogle Scholar
  73. 73.
    Morohashi K, Zhao M, Yang M, Read B, Lloyd A, Lamb R, Grotewold E (2007) Participation of the Arabidopsis bHLH factor GL3 in trichome initiation regulatory events. Plant Physiol 145:736–746PubMedPubMedCentralCrossRefGoogle Scholar
  74. 74.
    Zhang F, Gonzalez A, Zhao M, Payne CT, Lloyd A (2003) A network of redundant bHLH proteins functions in all TTG1-dependent pathways of Arabidopsis. Development 130:4859–4869PubMedCrossRefGoogle Scholar
  75. 75.
    Li P, Chen B, Zhang G, Chen L, Dong Q, Wen J, Mysore KS, Zhao J (2016) Regulation of anthocyanin and proanthocyanidin biosynthesis by Medicago truncatula bHLH transcription factor MtTT8. New Phytol 210:905–921PubMedCrossRefGoogle Scholar
  76. 76.
    Xu W, Dubos C, Lepiniec L (2015) Transcriptional control of flavonoid biosynthesis by MYB-bHLH-WDR complexes. Trends Plant Sci 20:176–185PubMedCrossRefGoogle Scholar
  77. 77.
    Gonzalez A, Mendenhall J, Huo Y, Lloyd A (2009) TTG1 complex MYBs, MYB5 and TT2, control outer seed coat differentiation. Dev Biol 325:412–421PubMedCrossRefGoogle Scholar
  78. 78.
    Nesi N, Jond C, Debeaujon I, Caboche M, Lepiniec L (2001) The arabidopsis TT2 gene encodes an R2R3 MYB domain protein that acts as a key determinant for proanthocyanidin accumulation in developing seed. Plant Cell 13:2099–2114PubMedPubMedCentralGoogle Scholar
  79. 79.
    Li SF, Milliken ON, Pham H, Seyit R, Napoli R, Preston J, Koltunow AM, Parish RW (2009) The Arabidopsis MYB5 transcription factor regulates mucilage synthesis, seed coat development, and trichome morphogenesis. Plant Cell 21:72–89PubMedPubMedCentralCrossRefGoogle Scholar
  80. 80.
    Verdier J, Zhao J, Torres-Jerez I, Ge S, Liu C, He X, Mysore KS, Dixon RA, Udvardi MK (2012) MtPAR MYB transcription factor acts as an on switch for proanthocyanidin biosynthesis in Medicago truncatula. Proc Natl Acad Sci U S A 109:1766–1771PubMedPubMedCentralCrossRefGoogle Scholar
  81. 81.
    Aharoni A, De Vos CH, Wein M, Sun Z, Greco R, Kroon A, Mol JN, O’Connell AP (2001) The strawberry FaMYB1 transcription factor suppresses anthocyanin and flavonol accumulation in transgenic tobacco. Plant J 28:319–332PubMedCrossRefGoogle Scholar
  82. 82.
    Paolocci F, Robbins MP, Passeri V, Hauck B, Morris P, Rubini A, Arcioni S, Damiani F (2011) The strawberry transcription factor FaMYB1 inhibits the biosynthesis of proanthocyanidins in Lotus corniculatus leaves. J Exp Bot 62:1189–1200PubMedCrossRefGoogle Scholar
  83. 83.
    Albert NW, Davies KM, Lewis DH, Zhang H, Montefiori M, Brendolise C, Boase MR, Ngo H, Jameson PE, Schwinn KE (2014) A conserved network of transcriptional activators and repressors regulates anthocyanin pigmentation in eudicots. Plant Cell 26:962–980PubMedPubMedCentralCrossRefGoogle Scholar
  84. 84.
    Yoshida K, Ma D, Constabel CP (2015) The MYB182 protein down-regulates proanthocyanidin and anthocyanin biosynthesis in poplar by repressing both structural and regulatory flavonoid genes. Plant Physiol 167:693–710PubMedPubMedCentralCrossRefGoogle Scholar
  85. 85.
    Zhu H-F, Fitzsimmons K, Khandelwal A, Kranz RG (2009) CPC, a single-repeat R3 MYB, is a negative regulator of anthocyanin biosynthesis in Arabidopsis. Mol Plant 2:790–802PubMedCrossRefGoogle Scholar
  86. 86.
    Bhalla A, Bansal N, Kumar S, Bischoff KM, Sani RK (2013) Improved lignocellulose conversion to biofuels with thermophilic bacteria and thermostable enzymes. Bioresour Technol 128:751–759PubMedCrossRefGoogle Scholar
  87. 87.
    Boerjan W, Ralph J, Baucher M (2003) Lignin biosynthesis. Annu Rev Plant Biol 54:519–546PubMedCrossRefGoogle Scholar
  88. 88.
    Sun Y, Cheng J (2002) Hydrolysis of lignocellulosic materials for ethanol production: a review. Bioresour Technol 83:1–11PubMedCrossRefGoogle Scholar
  89. 89.
    Vanholme R, Demedts B, Morreel K, Ralph J, Boerjan W (2010) Lignin biosynthesis and structure. Plant Physiol 153:895–905PubMedPubMedCentralCrossRefGoogle Scholar
  90. 90.
    Guo D, Chen F, Wheeler J, Winder J, Selman S, Peterson M, Dixon RA (2001) Improvement of in-rumen digestibility of alfalfa forage by genetic manipulation of lignin O-methyltransferases. Transgenic Res 10:457–464PubMedCrossRefGoogle Scholar
  91. 91.
    Chen F, Dixon RA (2007) Lignin modification improves fermentable sugar yields for biofuel production. Nat Biotechnol 25:759–761PubMedCrossRefGoogle Scholar
  92. 92.
    Fu C, Mielenz JR, Xiao X, Ge Y, Hamilton CY, Rodriguez M Jr, Chen F, Foston M, Ragauskas A, Bouton J, Dixon RA, Wang ZY (2011) Genetic manipulation of lignin reduces recalcitrance and improves ethanol production from switchgrass. Proc Natl Acad Sci U S A 108:3803–3808PubMedPubMedCentralCrossRefGoogle Scholar
  93. 93.
    Li M, Pu YQ, Ragauskas AJ (2016) Current understanding of the correlation of lignin structure with biomass recalcitrance. Front Chem 4:45PubMedPubMedCentralCrossRefGoogle Scholar
  94. 94.
    Gall DL, Ralph J, Donohue TJ, Noguera DR (2017) Biochemical transformation of lignin for deriving valued commodities from lignocellulose. Curr Opin Biotechnol 45:120–126PubMedCrossRefGoogle Scholar
  95. 95.
    Fritz JO, Cantrell RP, Lechtenberg VL, Axtell JD, Hertel JM (1981) Brown midrib mutants in sudangrass and grain sorghum. Crop Sci 21:706–709CrossRefGoogle Scholar
  96. 96.
    Cherney JH, Moore KJ, Volenec JJ, Axtell JD (1986) Rate and extent of digestion of cell wall components of brown-midrib sorghum species. Crop Sci 26:1055–1059CrossRefGoogle Scholar
  97. 97.
    Getachew G, Ibanez 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 170:192–200CrossRefGoogle Scholar
  98. 98.
    Tong ZY, Li H, Zhang RX, Ma L, Dong JL, Wang T (2015) Co-downregulation of the hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase and coumarate 3-hydroxylase significantly increases cellulose content in transgenic alfalfa (Medicago sativa L.). Plant Sci 239:230–237PubMedCrossRefGoogle Scholar
  99. 99.
    Hisano H, Nandakumar R, Wang ZY (2009) Genetic modification of lignin biosynthesis for improved biofuel production. In Vitro Cell Dev Biol-Plant 45:306–313CrossRefGoogle Scholar
  100. 100.
    Vanholme R, Morreel K, Darrah C, Oyarce P, Grabber JH, Ralph J, Boerjan W (2012) Metabolic engineering of novel lignin in biomass crops. New Phytol 196:978–1000PubMedCrossRefGoogle Scholar
  101. 101.
    Eudes A, Liang Y, Mitra P, Loque D (2014) Lignin bioengineering. Curr Opin Biotechnol 26:189–198PubMedCrossRefGoogle Scholar
  102. 102.
    Meng XZ, Ragauskas AJ (2014) Recent advances in understanding the role of cellulose accessibility in enzymatic hydrolysis of lignocellulosic substrates. Curr Opin Biotechnol 27:150–158PubMedCrossRefGoogle Scholar
  103. 103.
    Wang Y, Fan C, Hu H, Li Y, Sun D, Wang Y, Peng L (2016) Genetic modification of plant cell walls to enhance biomass yield and biofuel production in bioenergy crops. Biotechnol Adv 34:997–1017PubMedCrossRefGoogle Scholar
  104. 104.
    Lei L (2017) Lignin evolution: invasion of land. Nat Plants 3:17042PubMedCrossRefGoogle Scholar
  105. 105.
    Barros J, Serrani-Yarce JC, Chen F, Baxter D, Venables BJ, Dixon RA (2016) Role of bifunctional ammonia-lyase in grass cell wall biosynthesis. Nat Plants 2:16050PubMedCrossRefGoogle Scholar
  106. 106.
    Bonawitz ND, Chapple C (2010) The genetics of lignin biosynthesis: connecting genotype to phenotype. Annu Rev Genet 44:337–363PubMedCrossRefGoogle Scholar
  107. 107.
    Vanholme R, Cesarino I, Rataj K, Xiao Y, Sundin L, Goeminne G, Kim H, Cross J, Morreel K, Araujo P, Welsh L, Haustraete J, McClellan C, Vanholme B, Ralph J, Simpson GG, Halpin C, Boerjan W (2013) Caffeoyl shikimate esterase (CSE) is an enzyme in the lignin biosynthetic pathway in Arabidopsis. Science 341:1103–1106PubMedCrossRefGoogle Scholar
  108. 108.
    Zhou CE, Han L, Pislariu C, Nakashima J, Fu CX, Jiang QZ, Quan L, Blancaflor EB, Tang YH, Bouton JH, Udvardi M, Xia GM, Wang ZY (2011) From model to crop: functional analysis of a stay-green gene in the model legume Medicago truncatula and effective use of the gene for alfalfa improvement. Plant Physiol 157:1483–1496PubMedPubMedCentralCrossRefGoogle Scholar
  109. 109.
    Committee on Genetically Engineered Crops: Experiences and Prospects (2016) Genetically engineered crops: experiences and prospects. National Academies Press, Washington, DCGoogle Scholar
  110. 110.
    Vallet C, Chabbert B, Czaninski Y, Monties B (1996) Histochemistry of lignin deposition during sclerenchyma differentiation in alfalfa stems. Ann Bot 78:625–632CrossRefGoogle Scholar
  111. 111.
    Zhao Q, Tobimatsu Y, Zhou R, Pattathil S, Gallego-Giraldo L, Fu C, Jackson LA, Hahn MG, Kim H, Chen F, Ralph J, Dixon RA (2013) Loss of function of cinnamyl alcohol dehydrogenase 1 leads to unconventional lignin and a temperature-sensitive growth defect in Medicago truncatula. Proc Natl Acad Sci U S A 110:13660–13665PubMedPubMedCentralCrossRefGoogle Scholar
  112. 112.
    Zhao Q, Gallego-Giraldo L, Wang H, Zeng Y, Ding SY, Chen F, Dixon RA (2010) An NAC transcription factor orchestrates multiple features of cell wall development in Medicago truncatula. Plant J 63:100–114PubMedGoogle Scholar
  113. 113.
    Fagerstedt KV, Saranpaa P, Tapanila T, Immanen J, Serra JA, Nieminen K (2015) Determining the composition of lignins in different tissues of silver birch. Plants (Basel) 4:183–195CrossRefGoogle Scholar
  114. 114.
    Harman-Ware AE, Foster C, Happs RM, Doeppke C, Meunier K, Gehan J, Yue FX, Lu FC, Davis MF (2016) A thioacidolysis method tailored for higher-throughput quantitative analysis of lignin monomers. Biotechnol J 11:1268–1273PubMedPubMedCentralCrossRefGoogle Scholar
  115. 115.
    Hatfield R, Fukushima RS (2005) Can lignin be accurately measured? Crop Sci 45:832–839CrossRefGoogle Scholar
  116. 116.
    Moreira-Vilar FC, Siqueira-Soares RD, Finger-Teixeira A, de Oliveira DM, Ferro AP, da Rocha GJ, Ferrarese MDL, dos Santos WD, Ferrarese O (2014) The acetyl bromide method is faster, simpler and presents best recovery of lignin in different herbaceous tissues than klason and thioglycolic acid methods. PLoS One 9(10):e110000. CrossRefPubMedPubMedCentralGoogle Scholar
  117. 117.
    Nakano J, Meshitsuka G (1992) The detection of lignin. In: Lin SY, Dence CW (eds) Methods in lignin chemistry. Springer Berlin Heidelberg, Berlin, Heidelberg, pp 23–32CrossRefGoogle Scholar
  118. 118.
    Tobimatsu Y, Chen F, Nakashima J, Escamilla-Trevino LL, Jackson L, Dixon RA, Ralph J (2013) Coexistence but independent biosynthesis of catechyl and guaiacyl/syringyl lignin polymers in seed coats. Plant Cell 25:2587–2600PubMedPubMedCentralCrossRefGoogle Scholar
  119. 119.
    Lauvergeat V, Lacomme C, Lacombe E, Lasserre E, Roby D, Grima-Pettenati J (2001) Two cinnamoyl-CoA reductase (CCR) genes from Arabidopsis thaliana are differentially expressed during development and in response to infection with pathogenic bacteria. Phytochemistry 57:1187–1195PubMedCrossRefGoogle Scholar
  120. 120.
    Mir Derikvand M, Sierra JB, Ruel K, Pollet B, Do CT, Thevenin 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 227:943–956PubMedCrossRefGoogle Scholar
  121. 121.
    Sibout R, Eudes A, Mouille G, Pollet B, Lapierre C, Jouanin L, Seguin A (2005) CINNAMYL ALCOHOL DEHYDROGENASE-C and -D are the primary genes involved in lignin biosynthesis in the floral stem of Arabidopsis. Plant Cell 17:2059–2076PubMedPubMedCentralCrossRefGoogle Scholar
  122. 122.
    Zhong R, Ye Z-H (2009) Transcriptional regulation of lignin biosynthesis. Plant Signal Behav 4:1028–1034PubMedPubMedCentralCrossRefGoogle Scholar
  123. 123.
    Ko JH, Jeon HW, Kim WC, Kim JY, Han KH (2014) The MYB46/MYB83-mediated transcriptional regulatory programme is a gatekeeper of secondary wall biosynthesis. Ann Bot 114:1099–1107PubMedPubMedCentralCrossRefGoogle Scholar
  124. 124.
    Nakano Y, Yamaguchiz M, Endo H, Rejab NA, Ohtani M (2015) NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants. Front Plant Sci 6:288PubMedPubMedCentralCrossRefGoogle Scholar
  125. 125.
    Ohashi-Ito K, Oda Y, Fukuda H (2010) Arabidopsis vascular-related NAC-DOMAIN6 directly regulates the genes that govern programmed cell death and secondary wall formation during xylem differentiation. Plant Cell 22:3461–3473PubMedPubMedCentralCrossRefGoogle Scholar
  126. 126.
    Yamaguchi M, Mitsuda N, Ohtani M, Ohme-Takagi M, Kato K, Demura T (2011) VASCULAR-RELATED NAC-DOMAIN7 directly regulates the expression of a broad range of genes for xylem vessel formation. Plant J 66:579–590PubMedCrossRefGoogle Scholar
  127. 127.
    Augustin JM, Kuzina V, Andersen SB, Bak S (2011) Molecular activities, biosynthesis and evolution of triterpenoid saponins. Phytochemistry 72:435–457PubMedCrossRefGoogle Scholar
  128. 128.
    Moses T, Papadopoulou KK, Osbourn A (2014) Metabolic and functional diversity of saponins, biosynthetic intermediates and semi-synthetic derivatives. Crit Rev Biochem Mol Biol 49:439–462PubMedPubMedCentralCrossRefGoogle Scholar
  129. 129.
    Thimmappa R, Geisler K, Louveau T, O’Maille P, Osbourn A (2014) Triterpene biosynthesis in plants. Annu Rev Plant Biol 65:225–257PubMedCrossRefGoogle Scholar
  130. 130.
    Tava A, Avato P (2006) Chemical and biological activity of triterpene saponins from Medicago species. Nat Prod Commun 1:1159–1180Google Scholar
  131. 131.
    Carelli M, Biazzi E, Panara F, Tava A, Scaramelli L, Porceddu A, Graham N, Odoardi M, Piano E, Arcioni S, May S, Scotti C, Calderini O (2011) Medicago truncatula CYP716A12 is a multifunctional oxidase involved in the biosynthesis of hemolytic saponins. Plant Cell 23:3070–3081PubMedPubMedCentralCrossRefGoogle Scholar
  132. 132.
    Naoumkina MA, Modolo LV, Huhman DV, Urbanczyk-Wochniak E, Tang YH, Sumner LW, Dixon RA (2010) Genomic and coexpression analyses predict multiple genes involved in triterpene saponin biosynthesis in Medicago truncatula. Plant Cell 22:850–866PubMedPubMedCentralCrossRefGoogle Scholar
  133. 133.
    Pollier J, Moses T, Gonzalez-Guzman M, De Geyter N, Lippens S, Vanden Bossche R, Marhavy P, Kremer A, Morreel K, Guerin CJ, Tava A, Oleszek W, Thevelein JM, Campos N, Goormachtig S, Goossens A (2013) The protein quality control system manages plant defence compound synthesis. Nature 504:148–152PubMedCrossRefGoogle Scholar
  134. 134.
    Alfred J, Baldwin IT (2015) New opportunities at the wild frontier. elife 4:e06956PubMedCentralCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Chenggang Liu
    • 1
  • Chan Man Ha
    • 1
  • Richard A. Dixon
    • 1
    Email author
  1. 1.BioDiscovery Institute and Department of Biological SciencesUniversity of North TexasDentonUSA

Personalised recommendations