Abstract
Legumes account for approximately one third of world primary crop production and are vital sources of protein, oil, carbohydrates, fiber, and minerals for humans, livestock, and industrial processing. Grain nutrient composition varies between legume species as well as between genotypes of the same species. The major metabolic pathways responsible for storage protein, lipid, and starch biosynthesis are well characterized in several plant species, although it remains unclear how partitioning between these pathways and their end products is regulated. Seed development is a complex process that involves coordinated expression and regulation of thousands of genes in different cell and tissue types. The Medicago truncatula Gene Expression Atlas (MtGEA) provides genome-wide expression data for all major organs of M. truncatula, including a rich time series for seed development. This chapter describes how the MtGEA provides a comprehensive view of the genetic and molecular processes of seed development. MtGEA is playing an instrumental role in identifying regulatory and metabolic genes potentially determining seed composition and seed quality. Therefore, MtGEA is a valuable resource for seed biotechnology.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Ariza-Nieto M, Blair MW, Welch RM, Glahn RP (2007) Screening of iron bioavailability patterns in eight bean (Phaseolus vulgaris L.) genotypes using the caco-2 cell in vitro model. J Agric Food Chem 55:7950–7956
Barker DG, Bianchi S, Blondon F, Dattée Y, Duc G, Essad S, Flament P, Gallusci P, Génier G, Guy P, Muel X, Tourneur J, Dénarié J, Huguet T (1990) Medicago truncatula, a model plant for studying the molecular genetics of the Rhizobium-legume symbiosis. Plant Mol Biol Rep 8:40–49
Barnabas AD, Arnott HJ (1990) Calcium oxalate crystal formation in the bean (Phaseolus vulgaris L.) seed coat. Bot Gazette 151:331–341
Baskin CC, Baskin JM (1998) Seeds: ecology, biography, and evolution of dormancy and germination. In: Baskin CC, Baskin JM (eds) . Academic, San Francisco, pp 666
Beddington J (2010) Food security: contributions from science to a new and greener revolution. Philos Trans Royal Soc B: Biol Sci 365:61–71
Benedito VA, Torres-Jerez I, Murray JD, Andriankaja A, Allen S, Kakar K, Wandrey M, Verdier J, Zuber H, Ott T, Moreau S, Niebel A, Frinckey T, Weiller G, He J, Dai X, Zhao PX, Tang Y, Udvardi MK (2008) A gene expression atlas of the model legume, Medicago truncatula. Plant J 55:504–513
Berger F (2003) Endosperm: the crossroad of seed development. Curr Opin Plant Biol 6:42–50
Berger F, Grini PE, Schnittger A (2006) Endosperm: an integrator of seed growth and development. Curr Opin Plant Biol 9:664–670
Broeckling CD, Huhman DV, Farag MA, Smith JT, May GD, Mendes P, Dixon RA, Sumner LW (2005) Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism. J Exp Bot 56:323–336
Campion B, Sparvoli F, Doria E, Tagliabue G, Galasso I, Fileppi M, Bollini R, Nielsen E (2009) Isolation and characterisation of an lpa (low phytic acid) mutant in common bean (Phaseolus vulgaris L.) Theor Appl Genet 118:1211–1221
Cannon SB, May GD, Jackson SA (2009) Three sequenced legume genomes and many crop species: rich opportunities for translational genomics. Plant Physiol 151:970–977
Chabaud M, de Carvalho-Niebel F, Barker DG (2003) Efficient transformation of Medicago truncatula cv. Jemalong using the hypervirulent Agrobacterium tumefaciens strain AGL1. Plant Cell Rep 22:46–51
Choi HK, Mun JH, Kim DJ, Zhu H, Baek JM, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR (2004) Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci U S A 101:15289–15294
Coelho CMM, Benedito VA (2008) Seed development and reserve compound accumulation in common bean (Phaseolus vulgaris L.). Seed Sci Biotechnol 2:42–52
De Sousa Araujo S, Roldao Lopes Amaral Duque AS, Metelo Fernandes Dos Santos DM, Salema Fevereiro MP (2004) An efficient transformation method to regenerate a high number of transgenic plants using a new embryogenic line of Medicago truncatula cv. Jemalong. Plant Cell, Tissue Organ Culture 78:123–131
Dhaubhadel S et al (2003) Isoflavonoid biosynthesis and accumulation in developing soybean seeds. Plant Mol Biol 53:733–743. doi:10.1023/B:PLAN.0000023666.30358.ae
Dixon RA, Pasinetti GM (2010) Flavonoids and isoflavonoids: from plant biology to agriculture and neuroscience. Plant Physiol 154:453–457
Dixon RA, Sumner LW (2003) Legume natural products: understanding and manipulating complex pathways for human and animal health. Plant Physiol 131:878–885
Dixon RA, Xie DY, Sharma SB (2005) Proanthocyanidins—a final frontier in flavonoid research? New Phytol 165:9–28
Djemel N, Guedon D, Lechevalier A, Salon C, Miquel M, Prosperi JM, Rochat C, Boutin JP (2005) Development and composition of the seeds of nine genotypes of the Medicago truncatula species complex. Plant Physiol Biochem 43:557–566
FAO (2009) Declaration of the world summit on food security. (ftp://ftp.fao.org/docrep/fao/meeting/018/k6119e.pdf)
Faria JMR, Buitink J, van Lammeren AAM, Hilhorst HWM (2005) Changes in DNA and microtubules during loss and re-establishment of desiccation tolerance in germinating Medicago truncatula seeds. J Exp Bot 56:2119–2130
Firnhaber C, Pühler A, Küster H (2005) EST sequencing and time course microarray hybridizations identify more than 700 Medicago truncatula genes with developmental expression regulation in flowers and pods. Planta 222:269–283
Gallardo K, Le Signor C, Vandekerckhove J, Thompson RD, Burstin J (2003) Proteomics of Medicago truncatula seed development establishes the time frame of diverse metabolic processes related to reserve accumulation. Plant Physiol 133:664–682
Gallardo K, Kurt C, Thompson R, Ochatt S (2006a) In vitro culture of immature M. truncatula grains under conditions permitting embryo development comparable to that observed in vivo. Plant Sci 170:1052–1058
Gallardo K, Le Signor C, Darmency M, Burstin J, Thompson RD, Rochat C, Boutin J-P, Küster H, Buitink J, Leprince O, Limami A, Grusak MA (2006b) Seed biology of Medicago truncatula. In: The Medicago truncatula handbook. http://www.noble.org/MedicagoHandbook/pdf/SeedBiology.pdf
Gallardo K, Firnhaber C, Zuber H, Hericher D, Belghazi M, Henry C, Kuster H, Thompson RD (2007) A combined proteome and transcriptome analysis of developing Medicago truncatula seeds. Mol Cell Proteomics 6:2165–2179
Gatehouse JA, Evans IM, Bown D, Croy RR, Boulter D (1982) Control of storage-protein synthesis during seed development in pea (Pisum sativum L.). Biochem J 208:119–127
Gatehouse JA, Evans IM, Croy RRD, Boulter D (1986) Differential expression of genes during legume seed development. Phil Trans R Soc Lond B 314:367–384
Gepts P, Beavis WD, Brummer EC, Shoemaker RC, Stalker HT, Weeden NF, Young ND (2005) Legumes as a model plant family. Genomics for food and feed report of the cross-legume advances through genomics conference. Plant Physiol 137:1228–1235
Goffard N, Weiller G (2007a) GeneBins: a database for classifying gene expression data, with application to plant genome arrays. BMC Bioinformatics 8:87
Goffard N, Weiller G (2007b) PathExpress: a web-based tool to identify relevant pathways in gene expression data. Nucl Acids Res 35:176–181
Goldberg RB, de Paiva G, Yadegari R (1994) Plant embryogenesis-zygote to seed. Science 266:605–614
Grela ER, Günter KD (1995) Fatty acid composition and tocopherol content of some legume seeds. Animal Feed Sci Tech 52:325–331
Guillon F, Champ MM-J (2002) Carbohydrate fractions of legumes: uses in human nutrition and potential for health. British J Nutr 88:293–306
Hagerman AE, Butler LG (1981) The specificity of proanthocyanidin-protein interactions. J Biol Chem 256:4494–4497
He J, Benedito VA, Wang M, Murray JD, Zhao PX, Tang Y, Udvardi MK (2009) The Medicago truncatula gene expression atlas web server. BMC Bioinformatics 10:441
Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucl Acids Res 32:D277–D280
Koch K (2004) Sucrose metabolism: regulatory mechanisms and pivotal roles in sugar sensing and plant development. Curr Opin Plant Biol 7:235–246
Le Signor C, Gallardo K, Prosperi JM, Salon C, Quillien L, Thompson R, Duc G (2005) Genetic diversity for seed protein composition in Medicago truncatula. Plant Genet Res 3:59–71
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 Biotech J 7:430–441
Manthey K, Krajinski F, Hohnjec N, Firnhaber C, Pühler A, Perlick AM, Küster H (2004) Transcriptome profiling in root nodules and arbuscular mycorrhiza identifies a collection of novel genes induced during Medicago truncatula root endosymbioses. Mol Plant-Microbe Interact 17:1063–1077
McPhee KE, Zemetra RS, Brown J, Myers JR (2002) Genetic analysis of the raffinose family oligosaccharides in common bean. J Amer Soc Hort Sci 127:376–382
Molvig L, Tabe LM, Eggum BO, Moore AE, Craig S, Spencer D, Higgins TJV (1997) Enhanced methionine levels and increased nutritive value of seeds of transgenic lupins (Lupinus angustifolius L.) expressing a sunflower seed albumin gene. Proc Natl Acad Sci U S A 94:8393–8398
Munier-Jolain NG, Munier-Jolain NM, Roche R, Ney B, Duthion C (1998) Seed growth rate in grain legumes I. Effect of photoassimilate availability on seed growth rate. J Exp Bot 49:1963–1969
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
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
Raboy V (1990) The biochemistry and genetics of phytic acid synthesis in higher plants. In: Inositol Metabolism in Plants (Editors: Morre EJ, Boss WS, Loewus FA). Wiley, New York, pp 55–76
Raboy V (2007) The ABCs of low-phytate crops. Nat Biotechnol 25:874–875
Rajjou L, Gallardo K, Debeaujon I, Vandekerckhove J, Job C, Job D (2004) The effect of α-amanitin on the Arabidopsis seed proteome highlights the distinct roles of stored and neosynthesized mRNAs during germination. Plant Physiol 134:1598–1613
Repetto O, Rogniaux H, Firnhaber C, Zuber H, Küster H, Larré C, Thompson R, Gallardo K (2008) Exploring the nuclear proteome of Medicago truncatula at the switch towards seed filling. Plant J 56:398–410
Rogers C, Wen J, Chen R, Oldroyd G (2009) Deletion-based reverse genetics in Medicago truncatula. Plant Physiol 151:1077–1086
Rushton PJ, Bray CM (1987) Stored and de novo synthesised polyadenylated RNA and loss of vigour and viability in wheat seed. Plant Sci 51:51–59
Santos-Mendoza M, Dubreucq B, Baud S, Parcy F, Caboche M, Lepiniec L (2008) Deciphering gene regulatory networks that control seed development and maturation in Arabidopsis. Plant J 54:608–620
Smeekens S (2000) Sugar-induced signal transduction in plants. Annu Rev Plant Physiol Plant Mol Biol 51:49–81
Tadege M, Wen J, He J, Tu H, Kwak Y, Eschstruth A, Cayrel A, Endre G, Zhao PX, Chabaud M, Ratel P, Mysore SK (2008) Large-scale insertional mutagenesis using the Tnt1 retrotransposon in the model legume Medicago truncatula. Plant J 54:335–347
Thoquet P, Gherardi M, Journet E-P, Kereszt A, Ane J-M, Prosperi J-M, Huguet T (2002) The molecular genetic linkage map of the model legume Medicago truncatula: an essential tool for comparative legume genomics and the isolation of agronomically important genes. BMC Plant Biol 2:1
van der Mensbrugghe D, Osorio Rodarte I, Burns A, Baffes J (2009) How to feed the world in 2050: Macroeconomic environment, commodity markets—a longer term outlook. The World Bank & FAO. http://mpra.ub.uni-muenchen.de/19061/. Accessed 12 Oct 2009
van Dongen JT, Ammerlaan AMH, Wouterlood M, van Aelst AC, Borstlap AC (2003) Structure of the developing pea seed coat and the post‐phloem transport pathway of nutrients. Annals Bot 91:729–737
Veitch NC (2007) Isoflavonoids of the leguminosae. Nat Prod Rep 24:417–464
Verdier J, Kakar K, Gallardo K, Le Signor C, Aubert G, Schlereth A, Town CD, Udvardi MK, Thompson RD (2008) Gene expression profiling of M. truncatula transcription factors identifies putative regulators of grain legume seed filling. Plant Mol Biol 67:567–580
Verdier J et al (2012) MtPAR MYB transcription factor acts as an on switch for proanthocyanidin biosynthesis in Medicago truncatula. Proc Natl Acad Sci U S A 109(5):1766–1771. doi:10.1073/pnas.112091610
Walling L, Drews GN, Goldberg RB (1986) Transcriptional and post-transcriptional regulation of soybean seed protein mRNA levels. Proc Natl Acad Sci U S A 83:2123–2127
Wang HL, Grusak MA (2005) Structure and development of Medicago truncatula pod wall and seed coat. Annals Bot 95:737–747
Watson BS, Asirvatham VS, Wang L, Sumner LW (2003) Mapping the proteome of barrel medic (Medicago truncatula). Plant Physiol 131:1104–1123
Weber H, Borisjuk L, Wobus U (1997) Sugar import and metabolism during seed development. Trends Plant Sci 2:169–174
Weber H, Borisjuk L, Wobus U (2005) Molecular physiology of legume seed development. Annu Rev Plant Biol 56:253–279
Young ND, Cannon SB, Sato S, Kim D, Cook DR, Town CD, Roe BA, Tabata S (2005) Sequencing the genespaces of Medicago truncatula and Lotus japonicus. Plant Physiol 137:1174–1181
Young ND, Udvardi M (2009) Translating Medicago truncatula genomics to crop legumes. Curr Opin Plant Biol 12:193–201
Young ND et al (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480:520–524. doi:10.1038/nature10625
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
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
Verdier, J., Benedito, V.A., Udvardi, M.K. (2012). The Medicago truncatula Gene Expression Atlas (MtGEA): A Tool for Legume Seed Biology and Biotechnology. In: Agrawal, G., Rakwal, R. (eds) Seed Development: OMICS Technologies toward Improvement of Seed Quality and Crop Yield. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-4749-4_7
Download citation
DOI: https://doi.org/10.1007/978-94-007-4749-4_7
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-007-4748-7
Online ISBN: 978-94-007-4749-4
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)