Advertisement

Functional Genomics and Genetic Control of Flower and Fruit Development in Medicago truncatula: An Overview

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

Abstract

A-, B-, and C-class genes code for MADS-box transcription factors required for floral organ identity in angiosperms. Other members of the family are also crucial to ensure proper carpel and fruit development. Development of genetic and genomic tools for Medicago truncatula has allowed its use as model system to study the genetic control of flower and fruit development in legumes. M. truncatula contains a single A-class gene, four B-function genes, and three C-class genes in its genome. This has made possible to do extensive functional characterization of these MADS-box transcription factors using gene expression analyses, protein-protein interactions, and forward and reverse genetic approaches. We have demonstrated the functions of these MADS-box transcription factors and the respective contributions of paralogous gene pairs to M. truncatula floral development. We have also defined the evolutionary outcomes of each duplicated pairs thus testing theoretical framework of several models about the evolution by gene duplication. Moreover, we have also studied the function of MADS-box fruit genes and how they may have contributed to the diversification of pod morphology within the Medicago genus. Our findings not only have contributed to increase knowledge in the field of the genetic control of flower and fruit development but also have provided a more complete understanding of the complexity of evolution by gene duplication and protein sequence diversification.

Keywords

Medicago truncatula Floral development MADS-box genes Gene duplication Paralog genes evolution 

Notes

Acknowledgments

We gratefully acknowledge funding from the Spanish Ministry of Economy and Competitiveness (http://www.idi.mineco.gob.es/portal/site/MICINN) grant BIO2016-75485-R and BIO2015-64531-R.

References

  1. 1.
    Bowman JL, Smyth DR, Meyerowitz EM (2012) The ABC model of flower development: then and now. Development 139:4095–4098CrossRefPubMedGoogle Scholar
  2. 2.
    Coen ES, Carpenter R, Martin C (1986) Transposable elements generate novel spatial patterns of gene expression in Antirrhinum majus. Cell 47:285–296CrossRefPubMedGoogle Scholar
  3. 3.
    Sommer H, Bonas U, Saedler H (1988) Transposon-induced alterations in the promoter region affect transcription of the chalcone synthase gene of Antirrhinum majus. Mol Gen Genet 211:49–55CrossRefPubMedGoogle Scholar
  4. 4.
    Carpenter R, Coen ES (1990) Floral homeotic mutations produced by transposon-mutagenesis in Antirrhinum majus. Genes Dev 4:1483–1493CrossRefPubMedGoogle Scholar
  5. 5.
    Sommer H, Beltran JP, Huijser P, Pape H, Lonnig WE, Saedler H, Schwarz-Sommer Z (1990) Deficiens, a homeotic gene involved in the control of flower morphogenesis in Antirrhinum majus: the protein shows homology to transcription factors. EMBO J 9:605–613PubMedPubMedCentralCrossRefGoogle Scholar
  6. 6.
    Bowman JL, Smyth DR, Meyerowitz EM (1991) Genetic interactions among floral homeotic genes of Arabidopsis. Development 112:1–20PubMedGoogle Scholar
  7. 7.
    Schwarz-Sommer Z, Huijser P, Nacken W, Saedler H, Sommer H (1990) Genetic control of flower development by homeotic genes in Antirrhinum majus. Science 250:931–936CrossRefPubMedGoogle Scholar
  8. 8.
    Coen ES, Meyerowitz EM (1991) The war of the whorls: genetic interactions controlling flower development. Nature 353:31–37CrossRefGoogle Scholar
  9. 9.
    Ditta G, Pinyopich A, Robles P, Pelaz S, Yanofsky MF (2004) The SEP4 gene of Arabidopsis thaliana functions in floral organ and meristem identity. Curr Biol 14:1935–1940CrossRefPubMedGoogle Scholar
  10. 10.
    Pelaz S, Ditta GS, Baumann E, Wisman E, Yanofsky MF (2000) B and C floral organ identity functions require SEPALLATA MADS-box genes. Nature 405:200–203CrossRefPubMedGoogle Scholar
  11. 11.
    Aukerman MJ, Sakai H (2003) Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 15:2730–2741CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Chen X (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303:2022–2025CrossRefPubMedGoogle Scholar
  13. 13.
    Prunet N, Jack TP (2014) Flower development in Arabidopsis: there is more to it than learning your ABCs. Methods Mol Biol 1110:3–33CrossRefPubMedGoogle Scholar
  14. 14.
    Smaczniak C, Immink RG, Muino JM, Blanvillain R, Busscher M, Busscher-Lange J, Dinh QD, Liu S, Westphal AH, Boeren S et al (2012) Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development. Proc Natl Acad Sci U S A 109:1560–1565CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Weigel D, Meyerowitz EM (1994) The ABCs of floral homeotic genes. Cell 78:203–209CrossRefPubMedGoogle Scholar
  16. 16.
    Melzer R, Theissen G (2009) Reconstitution of ‘floral quartets’ in vitro involving class B and class E floral homeotic proteins. Nucleic Acids Res 37:2723–2736CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Egea-Cortines M, Saedler H, Sommer H (1999) Ternary complex formation between the MADS-box proteins SQUAMOSA, DEFICIENS and GLOBOSA is involved in the control of floral architecture in Antirrhinum majus. EMBO J 18:5370–5379CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Melzer R, Verelst W, Theissen G (2009) The class E floral homeotic protein SEPALLATA3 is sufficient to loop DNA in ‘floral quartet’-like complexes in vitro. Nucleic Acids Res 37:144–157CrossRefPubMedGoogle Scholar
  19. 19.
    Becker A, Lange M (2010) VIGS--genomics goes functional. Trends Plant Sci 15:1–4CrossRefPubMedGoogle Scholar
  20. 20.
    Tucker SC (2003) Floral development in legumes. Plant Physiol 131:911–926CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    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
  22. 22.
    Ferrandiz C, Navarro C, Gomez MD, Canas LA, Beltran JP (1999) Flower development in pisum sativum: from the war of the whorls to the battle of the common primordia. Dev Genet 25:280–290CrossRefPubMedGoogle Scholar
  23. 23.
    Benlloch R, d'Erfurth I, Ferrandiz C, Cosson V, Beltran JP, Canas LA, Kondorosi A, Madueno F, Ratet P (2006) Isolation of mtpim proves Tnt1 a useful reverse genetics tool in Medicago truncatula and uncovers new aspects of AP1-like functions in legumes. Plant Physiol 142:972–983CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Benlloch R, Roque E, Ferrandiz C, Cosson V, Caballero T, Penmetsa RV, Beltran JP, Canas LA, Ratet P, Madueno F (2009) Analysis of B function in legumes: PISTILLATA proteins do not require the PI motif for floral organ development in Medicago truncatula. Plant J 60:102–111CrossRefPubMedGoogle Scholar
  25. 25.
    Hecht V, Foucher F, Ferrandiz C, Macknight R, Navarro C, Morin J, Vardy ME, Ellis N, Beltran JP, Rameau C et al (2005) Conservation of Arabidopsis flowering genes in model legumes. Plant Physiol 137:1420–1434CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Roque E, Serwatowska J, Cruz Rochina M, Wen J, Mysore KS, Yenush L, Beltran JP, Canas LA (2013) Functional specialization of duplicated AP3-like genes in Medicago truncatula. Plant J 73:663–675CrossRefPubMedGoogle Scholar
  27. 27.
    Serwatowska J, Roque E, Gomez-Mena C, Constantin GD, Wen J, Mysore KS, Lund OS, Johansen E, Beltran JP, Canas LA (2014) Two euAGAMOUS genes control C-function in Medicago truncatula. PLoS One 9:e103770CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Roque E, Fares MA, Yenush L, Rochina MC, Wen J, Mysore KS, Gomez-Mena C, Beltran JP, Canas LA (2016) Evolution by gene duplication of Medicago truncatula PISTILLATA-like transcription factors. J Exp Bot 67:1805–1817CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Irish VF, Sussex IM (1990) Function of the apetala-1 gene during Arabidopsis floral development. Plant Cell 2:741–753CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Jofuku KD, den Boer BG, Van Montagu M, Okamuro JK (1994) Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Plant Cell 6:1211–1225CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Mandel MA, Gustafson-Brown C, Savidge B, Yanofsky MF (1992) Molecular characterization of the Arabidopsis floral homeotic gene APETALA1. Nature 360:273–277CrossRefPubMedGoogle Scholar
  32. 32.
    Keck E, McSteen P, Carpenter R, Coen E (2003) Separation of genetic functions controlling organ identity in flowers. EMBO J 22:1058–1066CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Bowman JL, Alvarez J, Weigel D, Meyerowitz EM, Smyth DR (1993) Control of flower development in Arabidopsis thaliana by APETALA1 and interacting genes. Development 119:721–743Google Scholar
  34. 34.
    Causier B, Schwarz-Sommer Z, Davies B (2010) Floral organ identity: 20 years of ABCs. Semin Cell Dev Biol 21:73–79CrossRefPubMedGoogle Scholar
  35. 35.
    Cheng X, Wen J, Tadege M, Ratet P, Mysore KS (2011) Reverse genetics in Medicago truncatula using Tnt1 insertion mutants. Methods Mol Biol 678:179–190CrossRefPubMedGoogle Scholar
  36. 36.
    d’Erfurth I, Cosson V, Eschstruth A, Lucas H, Kondorosi A, Ratet P (2003) Efficient transposition of the Tnt1 tobacco retrotransposon in the model legume Medicago truncatula. Plant J 34:95–106CrossRefPubMedGoogle Scholar
  37. 37.
    Tadege M, Ratet P, Mysore KS (2005) Insertional mutagenesis: a Swiss Army knife for functional genomics of Medicago truncatula. Trends Plant Sci 10:229–235CrossRefPubMedGoogle Scholar
  38. 38.
    Tadege M, Wen J, He J, Tu H, Kwak Y, Eschstruth A, Cayrel A, Endre G, Zhao PX, Chabaud M et al (2008) Large-scale insertional mutagenesis using the Tnt1 retrotransposon in the model legume Medicago truncatula. Plant J 54:335–347CrossRefPubMedGoogle Scholar
  39. 39.
    Huijser P, Klein J, Lonnig WE, Meijer H, Saedler H, Sommer H (1992) Bracteomania, an inflorescence anomaly, is caused by the loss of function of the MADS-box gene squamosa in Antirrhinum majus. EMBO J 11:1239–1249PubMedPubMedCentralCrossRefGoogle Scholar
  40. 40.
    Taylor SA, Hofer JM, Murfet IC, Sollinger JD, Singer SR, Knox MR, Ellis TH (2002) PROLIFERATING INFLORESCENCE MERISTEM, a MADS-box gene that regulates floral meristem identity in pea. Plant Physiol 129:1150–1159CrossRefPubMedPubMedCentralGoogle Scholar
  41. 41.
    Berbel A, Navarro C, Ferrandiz C, Canas LA, Madueno F, Beltran JP (2001) Analysis of PEAM4, the pea AP1 functional homologue, supports a model for AP1-like genes controlling both floral meristem and floral organ identity in different plant species. Plant J 25:441–451CrossRefPubMedGoogle Scholar
  42. 42.
    Litt A, Kramer EM (2010) The ABC model and the diversification of floral organ identity. Semin Cell Dev Biol 21:129–137CrossRefPubMedGoogle Scholar
  43. 43.
    Bowman JL, Smyth DR, Meyerowitz EM (1989) Genes directing flower development in Arabidopsis. Plant Cell 1:37–52CrossRefPubMedPubMedCentralGoogle Scholar
  44. 44.
    Jack T, Brockman LL, Meyerowitz EM (1992) The homeotic gene APETALA3 of Arabidopsis thaliana encodes a MADS box and is expressed in petals and stamens. Cell 68:683–697CrossRefPubMedGoogle Scholar
  45. 45.
    Goto K, Meyerowitz EM (1994) Function and regulation of the Arabidopsis floral homeotic gene PISTILLATA. Genes Dev 8:1548–1560CrossRefPubMedGoogle Scholar
  46. 46.
    Jack T, Fox GL, Meyerowitz EM (1994) Arabidopsis homeotic gene APETALA3 ectopic expression: transcriptional and posttranscriptional regulation determine floral organ identity. Cell 76:703–716CrossRefPubMedGoogle Scholar
  47. 47.
    Schwarz-Sommer Z, Hue I, Huijser P, Flor PJ, Hansen R, Tetens F, Lonnig WE, Saedler H, Sommer H (1992) Characterization of the Antirrhinum floral homeotic MADS-box gene deficiens: evidence for DNA binding and autoregulation of its persistent expression throughout flower development. EMBO J 11:251–263PubMedPubMedCentralCrossRefGoogle Scholar
  48. 48.
    Trobner W, Ramirez L, Motte P, Hue I, Huijser P, Lonnig WE, Saedler H, Sommer H, Schwarz-Sommer Z (1992) GLOBOSA: a homeotic gene which interacts with DEFICIENS in the control of Antirrhinum floral organogenesis. EMBO J 11:4693–4704PubMedPubMedCentralCrossRefGoogle Scholar
  49. 49.
    Kim S, Yoo MJ, Albert VA, Farris JS, Soltis PS, Soltis DE (2004) Phylogeny and diversification of B-function MADS-box genes in angiosperms: evolutionary and functional implications of a 260-million-year-old duplication. Am J Bot 91:2102–2118CrossRefPubMedGoogle Scholar
  50. 50.
    Kramer E, Di Stilio VS, Schlulter PM (2003) Complex patterns of gene duplication in the APETALA3 and PISTILLATA lineages of the Ranunculaceae. Int J Plant Sci 164:1–11CrossRefGoogle Scholar
  51. 51.
    Kramer EM, Dorit RL, Irish VF (1998) Molecular evolution of genes controlling petal and stamen development: duplication and divergence within the APETALA3 and PISTILLATA MADS-box gene lineages. Genetics 149:765–783PubMedPubMedCentralGoogle Scholar
  52. 52.
    Kramer EM, Irish VF (2000) Evolution of the petal and stamen developmental programs: evidence from comparative studies of the lower eudicots and basal angiosperms. Int J Plant Sci 161:S29–S40CrossRefGoogle Scholar
  53. 53.
    Stellari GM, Jaramillo MA, Kramer EM (2004) Evolution of the APETALA3 and PISTILLATA lineages of MADS-box-containing genes in the basal angiosperms. Mol Biol Evol 21:506–519CrossRefPubMedGoogle Scholar
  54. 54.
    Viaene T, Vekemans D, Irish VF, Geeraerts A, Huysmans S, Janssens S, Smets E, Geuten K (2009) Pistillata--duplications as a mode for floral diversification in (basal) asterids. Mol Biol Evol 26:2627–2645CrossRefPubMedGoogle Scholar
  55. 55.
    Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Schiex T et al (2006) Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci U S A 103:14959–14964CrossRefPubMedPubMedCentralGoogle Scholar
  56. 56.
    Cheng X, Wang M, Lee HK, Tadege M, Ratet P, Udvardi M, Mysore KS, Wen J (2014) An efficient reverse genetics platform in the model legume Medicago truncatula. New Phytol 201:1065–1076CrossRefPubMedGoogle Scholar
  57. 57.
    Penmetsa RV, Cook DR (2000) Production and characterization of diverse developmental mutants of Medicago truncatula. Plant Physiol 123:1387–1398CrossRefPubMedPubMedCentralGoogle Scholar
  58. 58.
    Bradley D, Carpenter R, Sommer H, Hartley N, Coen E (1993) Complementary floral homeotic phenotypes result from opposite orientations of a transposon at the plena locus of Antirrhinum. Cell 72:85–95CrossRefPubMedGoogle Scholar
  59. 59.
    Liljegren SJ, Ditta GS, Eshed Y, Savidge B, Bowman JL, Yanofsky MF (2000) SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis. Nature 404:766–770CrossRefPubMedGoogle Scholar
  60. 60.
    Pinyopich A, Ditta GS, Savidge B, Liljegren SJ, Baumann E, Wisman E, Yanofsky MF (2003) Assessing the redundancy of MADS-box genes during carpel and ovule development. Nature 424:85–88CrossRefPubMedGoogle Scholar
  61. 61.
    Davies B, Motte P, Keck E, Saedler H, Sommer H, Schwarz-Sommer Z (1999) PLENA and FARINELLI: redundancy and regulatory interactions between two Antirrhinum MADS-box factors controlling flower development. EMBO J 18:4023–4034CrossRefPubMedPubMedCentralGoogle Scholar
  62. 62.
    Becker A, Theissen G (2003) The major clades of MADS-box genes and their role in the development and evolution of flowering plants. Mol Phylogenet Evol 29:464–489CrossRefPubMedGoogle Scholar
  63. 63.
    Causier B, Castillo R, Zhou J, Ingram R, Xue Y, Schwarz-Sommer Z, Davies B (2005) Evolution in action: following function in duplicated floral homeotic genes. Curr Biol 15:1508–1512CrossRefPubMedGoogle Scholar
  64. 64.
    Irish VF (2003) The evolution of floral homeotic gene function. BioEssays 25:637–646CrossRefPubMedGoogle Scholar
  65. 65.
    Kramer EM, Jaramillo MA, Di Stilio VS (2004) Patterns of gene duplication and functional evolution during the diversification of the AGAMOUS subfamily of MADS box genes in angiosperms. Genetics 166:1011–1023CrossRefPubMedPubMedCentralGoogle Scholar
  66. 66.
    Zahn LM, Leebens-Mack JH, Arrington JM, Hu Y, Landherr LL, dePamphilis CW, Becker A, Theissen G, Ma H (2006) Conservation and divergence in the AGAMOUS subfamily of MADS-box genes: evidence of independent sub- and neofunctionalization events. Evol Dev 8:30–45CrossRefPubMedGoogle Scholar
  67. 67.
    Fourquin C, del Cerro C, Victoria FC, Vialette-Guiraud A, de Oliveira AC, Ferrandiz C (2013) A change in SHATTERPROOF protein lies at the origin of a fruit morphological novelty and a new strategy for seed dispersal in Medicago genus. Plant Physiol 162:907–917CrossRefPubMedPubMedCentralGoogle Scholar
  68. 68.
    Birchler JA, Veitia RA (2007) The gene balance hypothesis: from classical genetics to modern genomics. Plant Cell 19:395–402CrossRefPubMedPubMedCentralGoogle Scholar
  69. 69.
    Edger PP, Pires JC (2009) Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes. Chromosom Res 17:699–717CrossRefGoogle Scholar
  70. 70.
    Freeling M, Thomas BC (2006) Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res 16:805–814CrossRefPubMedGoogle Scholar
  71. 71.
    Polhill RM (1994) Classification of the Leguminosae and complete synopsis of legume genera. In: Bisby FA, Buckingham J, Harborne JB (eds) Phytochemical dictionary of the Leguminosae, vol 1. Chapman & Hall, LondonGoogle Scholar
  72. 72.
    Lewis GP, Schrire B, Mackinder B, Lock M (2005) Legumes of the world. Kew Publishing, Richmond, UKGoogle Scholar
  73. 73.
    Small E, Jomphe M (1989) A synopsis of the genus Medicago (Leguminosae). Can J Bot 67:3260–3294Google Scholar
  74. 74.
    Small E, Brookes B (1984) Coiling of alfalfa pods in relation to resistance against seed chalcids: additional observations. Canad J Plant Sci 64:659–665CrossRefGoogle Scholar
  75. 75.
    Ballester P, Ferrándiz C (2017) Shattering fruits: variations in a dehiscent theme. Curr Opin Plant Biol 35:68–75CrossRefPubMedGoogle Scholar
  76. 76.
    Liljegren SJ, Roeder AHK, Kempin SA, Gremski K, Østergaard L, Guimil S, Reyes DK, Yanofsky MF (2004) Control of fruit patterning in Arabidopsis by INDEHISCENT. Cell 116:843–853CrossRefPubMedGoogle Scholar
  77. 77.
    Rajani S, Sundaresan V (2001) The Arabidopsis myc/bHLH gene ALCATRAZ enables cell separation in fruit dehiscence. Curr Biol 11:1914–1922CrossRefPubMedGoogle Scholar
  78. 78.
    Ferrandiz C, Liljegren SJ, Yanofsky MF (2000) Negative regulation of the SHATTERPROOF genes by FRUITFULL during Arabidopsis fruit development. Science 289:436–438CrossRefPubMedGoogle Scholar
  79. 79.
    Ferrandiz C, Fourquin C (2014) Role of the FUL-SHP network in the evolution of fruit morphology and function. J Exp Bot 65:4505–4513CrossRefPubMedGoogle Scholar

Copyright information

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

Authors and Affiliations

  1. 1.Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV)Ciudad Politécnica de la Innovación Edf. 8EValenciaSpain
  2. 2.CSIC-UPVInstitute for Plant Cell and Molecular Biology(IBMCP)ValenciaSpain

Personalised recommendations