Skip to main content

Abstract

Grain legumes are the crop plants belonging to family Leguminosae that are cultivated for their seed yield for the purpose of human food or animal feed. They possess high metabolic activity and fluxes in seeds and are an important source of protein in vegetarian diet or when the intake from animal or fish source is not available. Soybean (Glycine max) L. Merr. is the world’s most widely grown grain legume. In addition to a high seed protein content (approximately 40 %), soybean seeds are also a major source of vegetable oil (approximately 20 %) and many beneficial plant natural compounds, such as isoflavonoids. Recently, soybean has gained considerable attention as a major crop for biodiesel production. It has a complex genome with a large genome size (~ 1115 Mb) that has undergone at least two genome duplication events within the last 60 million years (Gill et al. Plant Physiol, 151: 1167–1174, 2009; Schlueter et al. Genome, 47: 868–876, 2004; Shoemaker et al. Genetics, 144: 329–338,1996). The research efforts in the past decades in soybean in the area of genome mapping, molecular breeding, genomics, and whole genome sequencing have generated a vast amount of data and knowledge, providing unique opportunities to the legume community to conduct both basic and applied research in soybean and its close relatives.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Baldi G, Salamini F (1973) Variability of essential amino acid content in seeds of 22 Phaseolus species. Theor Appl Genet 43:75–78

    Article  Google Scholar 

  • Bolon YT, Joseph B, Cannon S, Graham M, Diers B, Farmer A, May G, Muehlbauer G, Specht J, Tu Z, Weeks N, Xu W, Shoemaker R, Vance C (2010) Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean. BMC Plant Biol 10:41

    Article  PubMed  Google Scholar 

  • Broughton WJ, Hernandez G, Blair M, Beebe S, Gepts P, Vanderleyden J (2003) Beans (Phaseolus spp.)—model food legumes. Plant Soil 252:55–128

    Article  CAS  Google Scholar 

  • Copeland LO, McDonald MB (2001) Seed formation and development. In: Copeland LO, McDonald MB (eds) Principles of seed science and technology, 4th edition. Kluwer Academic, Massachusetts, pp 17–38

    Chapter  Google Scholar 

  • Corner EJH (1951) The leguminous seed. Phytomorphology 1:117–150

    Google Scholar 

  • Das S, Ehlers J, Close T, Roberts P (2010) Transcriptional profiling of root-knot nematode induced feeding sites in cowpea (Vigna unguiculata L. Walp.) using a soybean genome array. BMC Genomics 11:480

    Article  PubMed  Google Scholar 

  • Dhaubhadel S, Gijzen M, Moy P, Farhangkhoee M (2007) Transcriptome analysis reveals a critical role of CHS7 and CHS8 genes for isoflavonoid synthesis in soybean seeds. Plant Physiol 143:326–338

    Article  PubMed  CAS  Google Scholar 

  • Ehlers JD, Hall AE (1997) Cowpea (Vigna unguiculata L. Walp.). Field Crops Res 53:187–204

    Article  Google Scholar 

  • Gehring M, Choi Y, Fischer RL (2004) Imprinting and seed development. Plant Cell 16:S203–S213

    Article  PubMed  CAS  Google Scholar 

  • Gill N, Findley S, Wallling JG, Hans C, Ma J, Doyle J, Stacey G, Jackson SA (2009) Molecular and chromosomal evidence for allopolyploidy in soybean. Plant Physiol 151:1167–1174

    Article  PubMed  CAS  Google Scholar 

  • Goel S, Raina SN, Ogihara Y (2002) Molecular evolution and phylogenetic implications of internal transcribed spacer sequences of nuclear ribosomal DNA in the Phaseolus-Vigna complex. Mol Phylogenet Evol 22:1–19

    Article  PubMed  CAS  Google Scholar 

  • Goldberg RB, Hoschek G, Ditta GS, Breidenback RW (1981a) Developmental regulation of cloned superabundant embryo mRNAs in soybean seeds. Dev Biol 83:218–231

    Article  CAS  Google Scholar 

  • Goldberg RB, Hoschek G, Tam SH, Ditta GS, Breidenback RW (1981b) Abundance, diversity, and regulation of mRNA sequence sets in soybean embryogenesis. Dev Biol 83:201–217

    Article  CAS  Google Scholar 

  • Goldberg RB, Barker SJ, Perez-Grau L (1989) Regulation of gene expression during plant embryogenesis. Cell 56:149–160

    Article  PubMed  CAS  Google Scholar 

  • Goldberg RB, Depaiva G, Yadegari R (1994) Plant embryogenesis-zygote to seed. Science 266:605–614

    Google Scholar 

  • Jones SI, Gonzalez DO, Vodkin LO (2010) Flux of transcript patterns during soybean seed development. BMC Genomics 11:136

    Article  PubMed  Google Scholar 

  • Joshi T, Yan Z, Libault M, Jeong D-H, Park S, Green P, Sherrier DJ, Farmer A, May G, Meyers B, Xu D, Stacey G (2010) Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics 11:S14

    Article  Google Scholar 

  • Kawashima T, Wang X, Henry KF, Bi Y, Weterings K, Goldberg RB (2009) Identification of cis-regulatory sequences that activate transcription in the suspensor of plant embryos. Proc Natl Acad Sci U S A 106:3627–3632

    Article  PubMed  CAS  Google Scholar 

  • Kim HK, Choi YH, Verpoorte R (2010) NMR-based metabolomic analysis of plants. Nat Protoc 5:536–549

    Article  PubMed  CAS  Google Scholar 

  • Lavin M, Herendeen PS, Wojciechowski MF (2005) Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary. Syst Biol 54:575–594

    Article  PubMed  Google Scholar 

  • Le BH, Wagmaister JA, Kawashima T, Bui AQ, Harada JJ, Goldberg RB (2007) Using genomics to study legume seed development. Plant Physiol 144:562–574

    Article  PubMed  CAS  Google Scholar 

  • Lightfoot DA (2008) Soybean genomics: developments through the use of cultivar “Forrest”. Int J Plant Genomics 2008:793158

    Google Scholar 

  • Marioni JC, Mason CE, Mane SM, AStephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18:1509–1517

    Article  PubMed  CAS  Google Scholar 

  • Marsolais F, Pajak A, Yin F, Taylor M, Gabriel M, Merino DM, Ma V, Kameka A, Vijayan P, Pham H, Huang S, Rivoal J, Bett K, Hernández-Sebastià C, Liu Q, Bertrand A, Chapman R (2010) Proteomic analysis of common bean seed with storage protein deficiency reveals up-regulation of sulfur-rich proteins and starch and raffinose metabolic enzymes, and down-regulation of the secretory pathway. J Proteomics 73:1587–1600

    Article  PubMed  CAS  Google Scholar 

  • McClean P, Gepts P, Jackson S, Lavin M (2008) Phaseolus vulgaris: a diploid model for soybean. In: Stacey G (ed) Genetics and genomics of soybean. Springer, New York, pp 55–78

    Chapter  Google Scholar 

  • McClean P, Kami J, Gepts P (2004) Genomics and genetic diversity in common bean. In: Wilson RF, Stalker HT, Brummer EC (eds) Legume crop genomics. AOCS, Illinois, pp 60–82

    Google Scholar 

  • McClean PE, Mamidi S, McConnell M, Chikara S, Lee R (2010) Synteny mapping between common bean and soybean reveals extensive blocks of shared loci. BMC Genomics 11:184

    Article  PubMed  Google Scholar 

  • Mensack MM, Fitzgerald VK, Ryan EP, Lewis MR, Thompson HJ, Brick MA (2010) Evaluation of diversity among common beans (Phaseolus vulgaris L.) from two centers of domestication using ‘omics’ technologies. BMC Genomics 11:686

    Article  PubMed  CAS  Google Scholar 

  • Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11:31–46

    Article  PubMed  CAS  Google Scholar 

  • Miller SS, Bowman LA, Gijzen M, Miki BLA (1999) Early development of the seed coat of soybean (Glycine max). Ann Bot 84:297–304

    Article  Google Scholar 

  • Mochida K, Yoshida T, Sakurai T, Yamaguchi-Shinozaki K, Shinozaki K, Tran LS (2010) LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors. Bioinformatics 26:290–291

    Article  PubMed  CAS  Google Scholar 

  • Muchero W, Diop NN, Bhat PR, Fenton RD, Wanamaker S, Pottorff M, Hearne S, Cisse N, Fatokun C, Ehlers JD, Roberts PA, Close TJ (2009) A consensus genetic map of cowpea [Vigna unguiculata (L.) Walp.] and synteny based on EST-derived SNPs. Proc Natl Acad Sci U S A 106:18159–18164

    Article  PubMed  CAS  Google Scholar 

  • Otoul E, Maréchal R, Dardenne G, Desmedt F (1975) Des dipeptides soufrés différencient nettement Vigna radiata de Vigna mungo. Phytochemistry 14:173–179

    Article  CAS  Google Scholar 

  • Padovese R, Kina SM, Barros RMC, Borelli P, Marquez UML (2001) Biological importance of gamma-glutamyl-S-methylcysteine of kidney bean (Phaseolus vulgaris L.). Food Chem 73:291–297

    Article  CAS  Google Scholar 

  • Panthee DR, Pantalone VR, Sams CE, Saxton AM, West DR, Orf JH, Killam AS (2006) Quantitative trait loci controlling sulfur containing amino acids, methionine and cysteine, in soybean seeds. Theor Appl Genet 112:546–553

    Article  PubMed  CAS  Google Scholar 

  • Ranathunge K, Shao S, Qutob D, Gijzen M, Peterson CA, Bernards MA (2010) Properties of the soybean seed coat cuticle change during development. Planta 31:1171–1188

    Article  Google Scholar 

  • Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray. Science 270:467–470

    Article  PubMed  CAS  Google Scholar 

  • Schlueter JA, Dixon P, Granger C, Grant D, Clark L, Doyle JJ, Shoemaker RC (2004) Mining EST databases to resolve evolutionary events in major crop species. Genome 47:868–876

    Article  PubMed  CAS  Google Scholar 

  • Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183

    Article  PubMed  CAS  Google Scholar 

  • Severin A, Woody J, Bolon YT, Joseph B, Diers B, Farmer A, Muehlbauer G, Nelson R, Grant D, Specht J, Graham M, Cannon S, May G, Vance C, Shoemaker R (2010) RNA-seq atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biol 10:160

    Article  PubMed  Google Scholar 

  • Shoemaker RC, Polzin K, Labate J, Specht J, Brummer EC, Olson T, Young N, Concibido V, Wilcox J, Tamulonis JP, Kochert G, Boerma HR (1996) Genome duplication in soybean (Glycine subgenus soja). Genetics 144:329–338

    PubMed  CAS  Google Scholar 

  • Shoemaker R, Keim P, Vodkin LO, Retzel E, Clifton SW, Waterson R, Smoller D, Coryell V, Khanna A, Erpelding J, Gai X, Brendel V, Raph-Schmidt C, Shoop EG, Vielweber CJ, Schmatz M, Pape D, Bowers Y, Theising B, Martin J, Dante M, Wylie T, Granger C (2002) A compilation of soybean ESTs: generation and analysis. Genome 45:329–338

    Article  PubMed  Google Scholar 

  • Stears RL, Martinsky T, Schena M (2003) Trends in microarray analysis. Nat Med 9:140–145

    Article  PubMed  CAS  Google Scholar 

  • Stefanovic S, Pfeil BE, Palmer JD, Doyle JJ (2009) Relationships among Phaseoloid legumes based on sequences from eight chloroplast regions. Syst Botany 34:115–128

    Article  Google Scholar 

  • Taylor M, Chapman R, Beyaert R, Hernández-Sebastià C, Marsolais F (2008) Seed storage protein deficiency improves sulfur amino acid content in common bean (Phaseolus vulgaris L.): redirection of sulfur from gamma-glutamyl-S-methyl-cysteine. J Agric Food Chem 56:5647–5654.

    Article  PubMed  CAS  Google Scholar 

  • Thibaud-Nissen F, Shealy RT, Khanna A, Vodkin LO (2003) Clustering of microarray data reveals transcript patterns associated with somatic embryogenesis in soybean. Plant Physiol 132:118–136

    Article  PubMed  CAS  Google Scholar 

  • Tomooka N, Vaughan DA, Maxted N, Moss H (2002) The Asian Vigna: Genus Vigna subgenus Ceratotropis genetic resources. Academic, Dordrecht

    Google Scholar 

  • Varshney RK, Penmetsa RV, Dutta S, Kulwal PL, Saxena RK, Datta S, Sharma TR, Rosen B, Carrasquilla-Garcia N, Farmer AD, Dubey A, Saxena KB, Gao J, Fakrudin B, Singh MN, Singh BP, Wanjari KB, Yuan M, Srivastava RK, Kilian A, Upadhyaya HD, Mallikarjuna N, Town CD, Bruening GE, He G, May GD, McCombie R, Jackson SA, Singh NK, Cook DR (2009) Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.). Mol Breed 1–16

    Google Scholar 

  • Vodkin LO, Khanna A, Shealy R, Clough SJ, Gonzalez DO, Philip R, Zabala G, Thibuad-Nissen F, Sidarous M, Stromvik MV, Shoop E, Schmidt C, Retzel E, Erpelding J, Shoemaker RC, Rodriguez-Huete AM, Polacco JC, Coryell V, Keim P, Gong G, Liu L, Pardinas J, Schweitzer P (2004) Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant. BMC Genomics 5:73

    Article  PubMed  Google Scholar 

  • Walbot V (1978) Control mechanisms for plant embryogeny. In: Clutter M (ed) Dormancy and developmental arrest. Academic, New York, pp 113–166

    Google Scholar 

  • Wang ML, Barkley NA, Gillaspie GA, Pederson GA (2008) Phylogenetic relationships and genetic diversity of the USDA Vigna germplasm collection revealed by gene-derived markers and sequencing. Genetics Res 90:467–480

    Article  CAS  Google Scholar 

  • Wang Z, Libault M, Joshi T, Valliyodan B, Nguyen HT, Xu D, Stacey G, Cheng J (2010) SoyDB: A knowledge database of soybean transcription factors. BMC Plant Biol 10:14

    Article  PubMed  Google Scholar 

  • Weber H, Borisjuk L, Wobus U (2005) Molecular physiology of legume seed development. Annu Rev Plant Biol 56:253–279

    Article  PubMed  CAS  Google Scholar 

  • Weterings K, Apuya NR, Bi Y, Fischer RL, Harada JJ, Goldberg RB (2001) Regional localization of suspensor mRNAs during early embryo development. Plant Cell 13:2409–2425

    PubMed  CAS  Google Scholar 

  • Wobus U, Weber H (1999) Seed maturation: Genetic programs and control signals. Curr. Opin. Plant Biol 2:33–38

    CAS  Google Scholar 

  • Yang SS, Valdes-Lopez O, Xu WW, Bucciarelli B, Gronwald JW, Hernandez G, Vance CP (2010) Transcript profiling of common bean (Phaseolus vulgaris L.) using the GeneChip soybean genome array: Optimizing analysis by masking biased probes. BMC Plant Biol 10:85

    Article  PubMed  Google Scholar 

  • Yi H, Ravilious GE, Galant A, Krishnan HB, Jez JM (2010a) From sulfur to homoglutathione: thiol metabolism in soybean. Amino Acids 39:963–978

    Article  CAS  Google Scholar 

  • Yi J, Derynck MR, Chen L, Dhaubhadel S (2010b) Differential expression of CHS7 and CHS8 genes in soybean. Planta 231:741–753

    Article  CAS  Google Scholar 

  • Yi J, Derynck MR, Li X, Telmer P, Marsolais F, Dhaubhadel S (2010c) A single repeat MYB transcription factor, GmMYB176, regulates CHS8 gene expression and affects isoflavonoid biosynthesis in soybean. Plant J 62:1019–1034

    CAS  Google Scholar 

  • Yin F, Pajak A, Chapman R, Sharpe A, Huang S, Marsolais F (2011) Analysis of common bean expressed sequence tags identifies sulfur metabolic pathways active in seed and sulfur-rich proteins highly expressed in the absence of phaseolin and major lectins. BMC Genomics 12:268

    Article  PubMed  CAS  Google Scholar 

  • Zhang Z, Yu J, Li D, Liu F, Zhou X, Wang T, Ling Y, Su Z (2010) PMRD: plant microRNA database. Nucl Acids Res 38:D806–D813

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Sangeeta Dhaubhadel .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Dhaubhadel, S., Marsolais, F. (2012). Transcriptomics of Legume Seed: Soybean a Model Grain Legume. 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_8

Download citation

Publish with us

Policies and ethics