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Functional Genomics in Medicago truncatula pp 315–337Cite as

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

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1822))

Abstract

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.

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References

  1. O’Connor SE (2015) Engineering of secondary metabolism. Annu Rev Genet 49:71–94

    Article  PubMed  CAS  Google Scholar 

  2. Tsao R (2010) Chemistry and biochemistry of dietary polyphenols. Forum Nutr 2:1231–1246

    CAS  Google Scholar 

  3. Weng JK, Chapple C (2010) The origin and evolution of lignin biosynthesis. New Phytol 187:273–285

    Article  PubMed  CAS  Google Scholar 

  4. Chang W-C, Song H, Liu H-W, Liu P (2013) Current development in isoprenoid precursor biosynthesis and regulation. Curr Opin Chem Biol 17:571–579

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  5. Bennett RN, Wallsgrove RM (1994) Secondary metabolites in plant defence mechanisms. New Phytol 127:617–633

    Article  CAS  Google Scholar 

  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 35:253–264

    Article  Google Scholar 

  7. Wang Y, Chen R (2013) Regulation of compound leaf development. Plants (Basel) 3:1–17

    Article  PubMed Central  CAS  Google Scholar 

  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 15:231–241

    Google Scholar 

  9. Peng J, Chen R (2011) Auxin efflux transporter MtPIN10 regulates compound leaf and flower development in Medicago truncatula. Plant Signal Behav 6:1537–1544

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  10. Weller JL, Ortega R (2015) Genetic control of flowering time in legumes. Front Plant Sci 6:207

    Article  PubMed  PubMed Central  Google Scholar 

  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 14:2413–2429

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 17:3489–3499

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 4:328–331

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 8:973

    Article  PubMed  PubMed Central  Google Scholar 

  15. Badri M, Chardon F, Huguet T, Aouani ME (2011) Quantitative trait loci associated with drought tolerance in the model legume Medicago truncatula. Euphytica 181:415

    Article  Google Scholar 

  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 14:5240–5251

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 123:50–58

    Article  CAS  Google Scholar 

  18. Dixon RA, Steele CL (1999) Flavonoids and isoflavonoids – a gold mine for metabolic engineering. Trends Plant Sci 4:394–400

    Article  PubMed  CAS  Google Scholar 

  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 35:494–498

    Article  PubMed  CAS  Google Scholar 

  20. Mukne AP, Viswanathan V, Phadatare AG (2011) Structure pre-requisites for isoflavones as effective antibacterial agents. Pharmacogn Rev 5:13–18

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 84:7428–7432

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 117:599–606

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Dixon RA (2004) Phytoestrogens. Annu Rev Plant Biol 55:225–261

    Article  PubMed  CAS  Google Scholar 

  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 59:347–360

    Article  PubMed  CAS  Google Scholar 

  25. Tava A, Scotti C, Avato P (2011) Biosynthesis of saponins in the genus Medicago. Phytochem Rev 10:459–469

    Article  CAS  Google Scholar 

  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 8:1493–1506

    Article  PubMed  CAS  Google Scholar 

  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 170:194–210

    Article  PubMed  CAS  Google Scholar 

  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 102:16573–16578

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 80:469–485

    Article  CAS  Google Scholar 

  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 151:1114–1129

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  31. Liu C, Jun JH, Dixon RA (2014) MYB5 and MYB14 play pivotal roles in seed coat polymer biosynthesis in Medicago truncatula. Plant Physiol 165:1424–1439

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 27:2860–2879

    PubMed  PubMed Central  CAS  Google Scholar 

  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 107:22338–22343

    Article  PubMed  PubMed Central  Google Scholar 

  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 107:14496–14501

    Article  PubMed  PubMed Central  Google Scholar 

  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 107:17803–17808

    Article  PubMed  PubMed Central  Google Scholar 

  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 86:363–375

    Article  PubMed  CAS  Google Scholar 

  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 480:520–524

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  38. Penmetsa RV, Cook DR (2000) Production and characterization of diverse developmental mutants of Medicago truncatula. Plant Physiol 123:1387–1398

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  39. Rogers C, Wen J, Chen R, Oldroyd G (2009) Deletion-based reverse genetics in Medicago truncatula. Plant Physiol 151:1077–1086

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 7:430–441

    Article  PubMed  CAS  Google Scholar 

  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 1069:101–118

    Article  PubMed  CAS  Google Scholar 

  42. Cheng X, Wen J, Tadege M, Ratet P, Mysore KS (2011) Reverse genetics in Medicago truncatula using Tnt1 insertion mutants. Methods Mol Biol 678:179–190

    Article  PubMed  CAS  Google Scholar 

  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 54:335–347

    Article  PubMed  CAS  Google Scholar 

  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 17:141

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  45. Iwashina T (2000) The structure and distribution of the flavonoids in plants. J Plant Res 113:287–299

    Article  CAS  Google Scholar 

  46. Kumar S, Pandey AK (2013) Chemistry and biological activities of flavonoids: an overview. Sci World J 2013:162750

    Google Scholar 

  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 18:1617–1629

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 55:2645–2652

    Article  PubMed  CAS  Google Scholar 

  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 145:601–615

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 47:847–853

    Article  PubMed  CAS  Google Scholar 

  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 27:2210–2226

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 7:735

    PubMed  PubMed Central  Google Scholar 

  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 278:31647–31656

    Article  PubMed  CAS  Google Scholar 

  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 139:652–663

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 13:202–202

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 14:238

    Article  PubMed  PubMed Central  Google Scholar 

  57. Liu C, Wang X, Shulaev V, Dixon RA (2016) A role for leucoanthocyanidin reductase in the extension of proanthocyanidins. Nat Plants 2:16182

    Article  PubMed  CAS  Google Scholar 

  58. Dixon RA, Xie DY, Sharma SB (2005) Proanthocyanidins--a final frontier in flavonoid research? New Phytol 165:9–28

    Article  PubMed  CAS  Google Scholar 

  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 64:499–518

    Article  PubMed  CAS  Google Scholar 

  60. Peel GJ, Pang Y, Modolo LV, Dixon RA (2009) The LAP1 MYB transcription factor orchestrates anthocyanidin biosynthesis and glycosylation in Medicago. Plant J 59:136–149

    Article  PubMed  CAS  Google Scholar 

  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 105:14210–14215

    Article  PubMed  PubMed Central  Google Scholar 

  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 238:139–154

    Article  PubMed  CAS  Google Scholar 

  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 21:2323–2340

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 19:2023–2038

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 23:1536–1555

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  66. Stafford HA, Lester HH (1982) Enzymic and nonenzymic reduction of (+)-dihydroquercetin to its 3,4,-diol. Plant Physiol 70:695–698

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 39:366–380

    Article  PubMed  CAS  Google Scholar 

  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 58:1431–1441

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  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 11:1337–1350

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 8:272–279

    Article  PubMed  CAS  Google Scholar 

  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 12:1863–1878

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 156:1349–1362

    PubMed  PubMed Central  CAS  Google Scholar 

  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 145:736–746

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 130:4859–4869

    Article  PubMed  CAS  Google Scholar 

  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 210:905–921

    Article  PubMed  CAS  Google Scholar 

  76. Xu W, Dubos C, Lepiniec L (2015) Transcriptional control of flavonoid biosynthesis by MYB-bHLH-WDR complexes. Trends Plant Sci 20:176–185

    Article  PubMed  CAS  Google Scholar 

  77. Gonzalez A, Mendenhall J, Huo Y, Lloyd A (2009) TTG1 complex MYBs, MYB5 and TT2, control outer seed coat differentiation. Dev Biol 325:412–421

    Article  PubMed  CAS  Google Scholar 

  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 13:2099–2114

    PubMed  PubMed Central  CAS  Google Scholar 

  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 21:72–89

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 109:1766–1771

    Article  PubMed  PubMed Central  Google Scholar 

  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 28:319–332

    Article  PubMed  CAS  Google Scholar 

  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 62:1189–1200

    Article  PubMed  CAS  Google Scholar 

  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 26:962–980

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 167:693–710

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 2:790–802

    Article  PubMed  CAS  Google Scholar 

  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 128:751–759

    Article  PubMed  CAS  Google Scholar 

  87. Boerjan W, Ralph J, Baucher M (2003) Lignin biosynthesis. Annu Rev Plant Biol 54:519–546

    Article  PubMed  CAS  Google Scholar 

  88. Sun Y, Cheng J (2002) Hydrolysis of lignocellulosic materials for ethanol production: a review. Bioresour Technol 83:1–11

    Article  PubMed  CAS  Google Scholar 

  89. Vanholme R, Demedts B, Morreel K, Ralph J, Boerjan W (2010) Lignin biosynthesis and structure. Plant Physiol 153:895–905

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 10:457–464

    Article  PubMed  CAS  Google Scholar 

  91. Chen F, Dixon RA (2007) Lignin modification improves fermentable sugar yields for biofuel production. Nat Biotechnol 25:759–761

    Article  PubMed  CAS  Google Scholar 

  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 108:3803–3808

    Article  PubMed  PubMed Central  Google Scholar 

  93. Li M, Pu YQ, Ragauskas AJ (2016) Current understanding of the correlation of lignin structure with biomass recalcitrance. Front Chem 4:45

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  94. Gall DL, Ralph J, Donohue TJ, Noguera DR (2017) Biochemical transformation of lignin for deriving valued commodities from lignocellulose. Curr Opin Biotechnol 45:120–126

    Article  PubMed  CAS  Google Scholar 

  95. Fritz JO, Cantrell RP, Lechtenberg VL, Axtell JD, Hertel JM (1981) Brown midrib mutants in sudangrass and grain sorghum. Crop Sci 21:706–709

    Article  CAS  Google Scholar 

  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 26:1055–1059

    Article  CAS  Google Scholar 

  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 170:192–200

    Article  CAS  Google Scholar 

  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 239:230–237

    Article  PubMed  CAS  Google Scholar 

  99. Hisano H, Nandakumar R, Wang ZY (2009) Genetic modification of lignin biosynthesis for improved biofuel production. In Vitro Cell Dev Biol-Plant 45:306–313

    Article  CAS  Google Scholar 

  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 196:978–1000

    Article  PubMed  CAS  Google Scholar 

  101. Eudes A, Liang Y, Mitra P, Loque D (2014) Lignin bioengineering. Curr Opin Biotechnol 26:189–198

    Article  PubMed  CAS  Google Scholar 

  102. Meng XZ, Ragauskas AJ (2014) Recent advances in understanding the role of cellulose accessibility in enzymatic hydrolysis of lignocellulosic substrates. Curr Opin Biotechnol 27:150–158

    Article  PubMed  CAS  Google Scholar 

  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 34:997–1017

    Article  PubMed  CAS  Google Scholar 

  104. Lei L (2017) Lignin evolution: invasion of land. Nat Plants 3:17042

    Article  PubMed  Google Scholar 

  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 2:16050

    Article  PubMed  CAS  Google Scholar 

  106. Bonawitz ND, Chapple C (2010) The genetics of lignin biosynthesis: connecting genotype to phenotype. Annu Rev Genet 44:337–363

    Article  PubMed  CAS  Google Scholar 

  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 341:1103–1106

    Article  PubMed  CAS  Google Scholar 

  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 157:1483–1496

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  109. Committee on Genetically Engineered Crops: Experiences and Prospects (2016) Genetically engineered crops: experiences and prospects. National Academies Press, Washington, DC

    Google Scholar 

  110. Vallet C, Chabbert B, Czaninski Y, Monties B (1996) Histochemistry of lignin deposition during sclerenchyma differentiation in alfalfa stems. Ann Bot 78:625–632

    Article  CAS  Google Scholar 

  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 110:13660–13665

    Article  PubMed  PubMed Central  Google Scholar 

  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 63:100–114

    PubMed  CAS  Google Scholar 

  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) 4:183–195

    Article  CAS  Google Scholar 

  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 11:1268–1273

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  115. Hatfield R, Fukushima RS (2005) Can lignin be accurately measured? Crop Sci 45:832–839

    Article  CAS  Google Scholar 

  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. https://doi.org/10.1371/journal.pone.0110000

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 23–32

    Chapter  Google Scholar 

  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 25:2587–2600

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 57:1187–1195

    Article  PubMed  CAS  Google Scholar 

  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 227:943–956

    Article  PubMed  CAS  Google Scholar 

  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 17:2059–2076

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  122. Zhong R, Ye Z-H (2009) Transcriptional regulation of lignin biosynthesis. Plant Signal Behav 4:1028–1034

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 114:1099–1107

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 6:288

    Article  PubMed  PubMed Central  Google Scholar 

  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 22:3461–3473

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 66:579–590

    Article  PubMed  CAS  Google Scholar 

  127. Augustin JM, Kuzina V, Andersen SB, Bak S (2011) Molecular activities, biosynthesis and evolution of triterpenoid saponins. Phytochemistry 72:435–457

    Article  PubMed  CAS  Google Scholar 

  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 49:439–462

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  129. Thimmappa R, Geisler K, Louveau T, O’Maille P, Osbourn A (2014) Triterpene biosynthesis in plants. Annu Rev Plant Biol 65:225–257

    Article  PubMed  CAS  Google Scholar 

  130. Tava A, Avato P (2006) Chemical and biological activity of triterpene saponins from Medicago species. Nat Prod Commun 1:1159–1180

    CAS  Google Scholar 

  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 23:3070–3081

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 22:850–866

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 504:148–152

    Article  PubMed  CAS  Google Scholar 

  134. Alfred J, Baldwin IT (2015) New opportunities at the wild frontier. elife 4:e06956

    Article  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, USA

    Chenggang Liu, Chan Man Ha & Richard A. Dixon

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  1. Chenggang Liu
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  2. Chan Man Ha
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  3. Richard A. Dixon
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Correspondence to Richard A. Dixon .

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  1. CSIC-UPV, Institute for Plant Cell and Molecular Biology (IBMCP), Valencia, Spain

    Luis A. Cañas

  2. CSIC-UPV, Institute for Plant Cell and Molecular Biology (IBMCP), Valencia, Spain

    José Pío Beltrán

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Liu, C., Ha, C.M., Dixon, R.A. (2018). Functional Genomics in the Study of Metabolic Pathways in Medicago truncatula: An Overview. In: Cañas, L., Beltrán, J. (eds) Functional Genomics in Medicago truncatula. Methods in Molecular Biology, vol 1822. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8633-0_20

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  • DOI: https://doi.org/10.1007/978-1-4939-8633-0_20

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