Functional & Integrative Genomics

, Volume 10, Issue 4, pp 447–462 | Cite as

Functional genomics of soybean for improvement of productivity in adverse conditions



Global soybean production is frequently impacted by various stresses, including both abiotic and biotic stresses. To develop soybean plants with enhanced tolerance to different stressors, functional genomics of soybean and a comprehensive understanding of available biotechnological resources and approaches are essential. In this review, we will discuss recent advances in soybean functional genomics which provide unprecedented opportunities to understand global patterns of gene expression, gene regulatory networks, various physiological, biochemical, and metabolic pathways as well as their association with the development of specific phenotypes. Soybean functional genomics, therefore, will ultimately enable us to develop new soybean varieties with improved productivity under adverse conditions by genetic engineering.


Soybean Stress Functional genomics Comparative genomics 



Expressed sequence tag


Full-length cDNA


Gene ontology


Linkage group


Marker-assisted selection


Mass spectrometry


Quantitative trait locus


Recombinant inbred lines


Soybean cyst nematode


Soybean rust


Transcription factor



Research in Tran’s lab is supported by Grants-in-Aid (Start-up) for Scientific Research (No. 21870046) from Ministry of Education, Culture, Sports, Science and Technology of Japan, and by Start-up Support grant (No. M36-57000) from Yokohama Institute Director Discretionary Funds.


  1. Abel GH (1969) Inheritance of the capacity for chloride inclusion and chloride exclusion by soybeans. Crop Sci 9:697–698Google Scholar
  2. Afzal AJ, Natarajan A, Saini N, Iqbal MJ, Geisler M, El Shemy HA, Mungur R, Willmitzer L, Lightfoot DA (2009) The nematode resistance allele at the rhg1 locus alters the proteome and primary metabolism of soybean roots. Plant Physiol 151:1264–1280PubMedGoogle Scholar
  3. Agrawal GK, Hajduch M, Graham K, Thelen JJ (2008) In-depth investigation of the soybean seed-filling proteome and comparison with a parallel study of rapeseed. Plant Physiol 148:504–518PubMedGoogle Scholar
  4. Ahsan N, Komatsu S (2009) Comparative analyses of the proteomes of leaves and flowers at various stages of development reveal organ-specific functional differentiation of proteins in soybean. Proteomics 9:4889–4907PubMedGoogle Scholar
  5. An S, Park S, Jeong DH et al (2003) Generation and analysis of end sequence database for T-DNA tagging lines in rice. Plant Physiol 133:2040–2047PubMedGoogle Scholar
  6. Anai T, Yamada T, Kinoshita T, Rahman SM, Takagi Y (2005) Identification of corresponding genes for three low-alpha-linolenic acid mutants and elucidation of their contribution to fatty acid biosynthesis in soybean seed. Plant Science 168:1615–1623Google Scholar
  7. Ashfield T, Ong LE, Nobuta K, Schneider CM, Innes RW (2004) Convergent evolution of disease resistance gene specificity in two flowering plant families. Plant Cell 16:309–318PubMedGoogle Scholar
  8. Benkeblia N, Shinano T, Osaki M (2007) Metabolite profiling and assessment of metabolome compartmentation of soybean leaves using non-aqueous fractionation and GC-MS analysis. Metabolomics 3:297–305Google Scholar
  9. Bhattacharyya MK, Narayanan NN, Gao H et al (2005) Identification of a large cluster of coiled coil-nucleotide binding site—leucine rich repeat-type genes from the Rps1 region containing Phytophthora resistance genes in soybean. Theor Appl Genet 111:75–86PubMedGoogle Scholar
  10. Brechenmacher L, Lee J, Sachdev S, Song Z, Nguyen TH, Joshi T, Oehrle N, Libault M, Mooney B, Xu D, Cooper B, Stacey G (2009) Establishment of a protein reference map for soybean root hair cells. Plant Physiol 149:670–682PubMedGoogle Scholar
  11. Burch-Smith TM, Anderson JC, Martin GB, Dinesh-Kumar SP (2004) Applications and advantages of virus-induced gene silencing for gene function studies in plants. Plant J 39:734–746PubMedGoogle Scholar
  12. Chen M, Wang QY, Cheng XG et al (2007) GmDREB2, a soybean DRE-binding transcription factor, conferred drought and high-salt tolerance in transgenic plants. Biochem Biophy Res Comm 353:299–305Google Scholar
  13. Cheng L, Huan S, Sheng Y et al (2009) GMCHI, cloned from soybean (Glycine max (L.) Merr.) enhances survival in transgenic Arabidopsis under abiotic stress. Plant Cell Rep 28:145–153PubMedGoogle Scholar
  14. Choi HK, Mun JH, Kim DJ et al (2004) Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci USA 101:15289–15294PubMedGoogle Scholar
  15. Concibido VC, Diers BW, Arelli PR (2004) A decade of QTL mapping for cyst nematode resistance in soybean. Crop Sci 44:1121–1131Google Scholar
  16. Cooper J, Till BJ, Laport RG et al (2008) TILLING to detect induced mutations in soybean. BMC Plant Biol 8:9PubMedGoogle Scholar
  17. Cornelious B, Chen P, Chen Y, de Leon N, Shannon JG, Wan D (2005) Identification of QTLs underlying water-logging tolerance in soybean. Mol Breeding 16:103–112Google Scholar
  18. Cowperthwaite M, Park W, Xu Z, Yan X, Maurais S, Dooner H (2002) Use of the transposon Ac as a gene-searching engine in the maize genome. Plant Cell 14:713–726PubMedGoogle Scholar
  19. Cregan PB, Mudge J, Fickus EW, Danesh D, Denny R, Young ND (1999) Two simple sequence repeat markers to select for soybean cyst nematode resistance conditioned by the rhg1 locus. Theor Appl Genet 99:811–818Google Scholar
  20. Czechowski T, Bari RP, Stitt M, Scheible WR, Udvardi MK (2004) Real-time RT-PCR profiling of over 1,400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. Plant J 38:366–379PubMedGoogle Scholar
  21. Danson J, Wasano K, Nose A (2000) Infection of rice plants with the sheath blight fungus causes an activation of pentose phosphate and glycolytic pathways. Eur J Plant Pathol 106:555–561Google Scholar
  22. de Ronde JA, Cress WA, Krüger GHJ, Strasser RJ, Van Staden J (2004a) Photosynthetic response of transgenic soybean plants, containing an Arabidopsis P5CR gene during heat and drought stress. J Plant Physiol 161:1211–1224PubMedGoogle Scholar
  23. de Ronde JA, Laurie RN, Caetano T, Greyling MM, Kerepesi I (2004b) Comparative study between transgenic and non-transgenic soybean lines proved transgenic lines to be more drought tolerant. Euphytica 158:123–132Google Scholar
  24. Du W, Wang M, Fu S, Yu D (2009) Mapping QTLs for seed yield and drought susceptibility index in soybean (Glycine max L.) across different environments. J Genet Genomics 36:721–731PubMedGoogle Scholar
  25. Duranti M (2006) Grain legume proteins and nutraceutical properties. Fitoterapia 77:67–82PubMedGoogle Scholar
  26. Funatsuki H, Kawaguchi K, Matsuba S, Sato Y, Ishimoto M (2005) Mapping of QTL associated with chilling tolerance during reproductive growth in soybean. Theor Appl Genet 111:851–861PubMedGoogle Scholar
  27. Gao H, Bhattacharyya MK (2008) The soybean-Phytophthora resistance locus Rps1-k encompasses coiled coil-nucleotide binding-leucine rich repeat-like genes and repetitive sequences. BMC Plant Biol 8:29PubMedGoogle Scholar
  28. Gao H, Narayanan NN, Ellison L, Bhattacharyya MK (2005) Two classes of highly similar coiled coil-nucleotide binding-leucine rich repeat genes isolated from the Rps1-k locus encode Phytophthora resistance in soybean. Mol Plant Microbe Interact 18:1035–1045PubMedGoogle Scholar
  29. Garcia A, Calvo ES, de Souza Kiihl RA, Harada A, Hiromoto DM, Vieira LG (2008) Molecular mapping of soybean rust (Phakopsora pachyrhizi) resistance genes: discovery of a novel locus and alleles. Theor Appl Genet 117:545–553PubMedGoogle Scholar
  30. 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 137:1228–1235PubMedGoogle Scholar
  31. Githiri SM, Watanabe S, Harada K, Takahashi R (2006) QTL analysis of flooding tolerance in soybean at an early vegetative growth stage. Plant Breed 125:613–618Google Scholar
  32. Gonzales MD, Gajendran K, Farmer AD, Archuleta E, Beavis WD (2007) Leveraging model legume information to find candidate genes for soybean sudden death syndrome using the legume information system. Methods Mol Biol 406:245–259PubMedGoogle Scholar
  33. Gore MA, Hayes AJ, Jeong SC, Yue YG, Buss GR, Maroof S (2002) Mapping tightly linked genes controlling potyvirus infection at the Rsv1 and Rpv1 region in soybean. Genome 5:592–599Google Scholar
  34. Grant D, Nelson RT, Cannon SB, Shoemaker RC (2010) SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res 38:D843–D846PubMedGoogle Scholar
  35. Guo B, Sleper DA, Arelli PR, Shannon JG, Nguyen HT (2005) Identification of QTLs associated with resistance to soybean cyst nematode races 2, 3 and 5 in soybean PI 90763. Theor Appl Genet 111:965–971PubMedGoogle Scholar
  36. Guo B, Sleper DA, Nguyen HT, Arelli PR, Shannon JG (2006) Quantitative trait loci underlying resistance to three soybean cyst nematode populations in soybean PI404198A. Crop Sci 46:224–233Google Scholar
  37. Gutierrez-Gonzalez JJ, Guttikonda SK, Tran LS, Aldrich DL, Zhong R, Yu O, Nguyen HT, Sleper DA (2010) Differential expression of isoflavone biosynthetic genes in soybean during water deficits. Plant Cell Physiol PMID:20430761Google Scholar
  38. Hamwieh A, Xu DH (2008) Conserved salt tolerance quantitative trait locus (QTL) in wild and cultivated soybeans. Breed Sci 58:355–359Google Scholar
  39. Hartmann S, Lu D, Phillips J, Vision TJ (2006) Phytome: a platform for plant comparative genomics. Nucleic Acids Res 34:D724–D730PubMedGoogle Scholar
  40. Hartwig EE (1986) Identification of a fourth major gene conferring resistance to soybean rust. Crop Sci 26:1135–1136Google Scholar
  41. Hashiguchi A, Sakata K, Komatsu S (2009) Proteome analysis of early-stage soybean seedlings under flooding stress. J Proteome Res 8:2058–2069PubMedGoogle Scholar
  42. Hayes AJ, Ma G, Buss GR, Saghai Maroof MA (2000) Molecular marker mapping of Rsv4, a gene conferring resistance to all known strains of soybean mosaic virus. Crop Sci 40:1434–1437Google Scholar
  43. Hayes AJ, Jeong SC, Gore MA, Yu YG, Buss GR, Tolin SA, Maroof MA (2004) Recombination within a nucleotide-binding-site/leucine-rich-repeat gene cluster produces new variants conditioning resistance to soybean mosaic virus in soybeans. Genetics 166:493–503PubMedGoogle Scholar
  44. Hermsmeier D, Hart JK, Byzova M, Rodermel SR, Baum TJ (2000) Changes in mRNA abundances within Heterodera schachtiiinfected roots of Arabidopsis thaliana. Mol Plant-Microbe Interact 13:309–315PubMedGoogle Scholar
  45. Hill J, Nelson E, Tilman D, Polasky S, Tiffany D (2006) Environmental, economic, and energetic costs and benefits of biodiesel and ethanol biofuels. Proc Natl Acad Sci USA 103:11206–11210PubMedGoogle Scholar
  46. Hoefle C, Loehrer M, Schaffrath U, Frank M, Schultheiss H, Hückelhoven R (2009) Transgenic suppression of cell death limits penetration success of the soybean rust fungus Phakopsora pachyrhizi into epidermal cells of barley. Phytopathology 99:220–226PubMedGoogle Scholar
  47. Hu H, Dai M, Yao J, Xiao B, Li X, Zhang Q, Xiong L (2006) Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proc Natl Acad Sci USA 103:12987–12992PubMedGoogle Scholar
  48. Hu H, You J, Fang Y, Zhu X, Qi Z, Xiong L (2008) Characterization of transcription factor gene SNAC2 conferring cold and salt tolerance in rice. Plant Mol Biol 67:169–181PubMedGoogle Scholar
  49. Hwang TY, Moon JK, Yu S, Yang K, Mohankumar S, Yu YH, Lee YH, Kim HS, Kim HM, Maroof MA, Jeong SC (2006) Application of comparative genomics in developing molecular markers tightly linked to the virus resistance gene Rsv4 in soybean. Genome 49:380–388PubMedGoogle Scholar
  50. Hyten DL, Choi IY, Song Q, Shoemaker RC, Nelson RL, Costa JM, Specht JE, Cregan PB (2007) Highly variable patterns of linkage disequilibrium in multiple soybean populations. Genetics 175:1937–1944PubMedGoogle Scholar
  51. Ikeda T, Ohnishi S, Senda M, Miyoshi T, Ishimoto M, Kitamura K, Funatsuki H (2009) A novel major quantitative trait locus controlling seed development at low temperature in soybean (Glycine max). Theor Appl Genet 118:1477–1488PubMedGoogle Scholar
  52. Iqbal MJ, Ahsan R, Afzal AJ, Jamai A, Meksem K, El Shemy H, Lightfoot DA (2009) Analysis of the activity of the soybean laccase encoded within the Rfs2/rhg1 locus. Curr Issues Mol Biol 11:11–19Google Scholar
  53. Ithal N, Recknor J, Nettleton D, Hearne L, Maier T, Baum TJ, Mitchum MG (2007) Parallel genome-wide expression profiling of host and pathogen during soybean cyst nematode infection of soybean. Mol Plant Microbe Interact 20:293–305PubMedGoogle Scholar
  54. Jeong SC, Maroof MAS (2004) Detection and genotyping of SNPs tightly linked to two disease resistance loci, Rsv1 and Rsv3, of soybean. Plant Breeding 123:305–310Google Scholar
  55. Jeong SC, Kristipati S, Hayes AJ, Maughan PJ, Noffsinger SL, Gunduz I, Buss GR, Maroof MA (2002) Genetic and sequence analysis of markers tightly linked to the soybean mosaic virus resistance gene, Rsv3. Crop Sci 42:265–270PubMedGoogle Scholar
  56. Kasuga T, Salimath SS, Shi J, Gijzen M, Buzzell RI, Bhattacharyya MK (1997) High resolution genetic and physical mapping of molecular markers linked to the Phytophthora resistance gene Rps1-k in soybean. Mol Plant-Microbe Interact 10:1035–1044Google Scholar
  57. Kasuga M, Liu Q, Miura S, Yamaguchi-Shinozaki K, Shinozaki K (1999) Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor. Nat Biotechnol 17:287–291PubMedGoogle Scholar
  58. Katerji N, van Horn JW, Hamdy A, Mastrorilli M (2004) Comparison of corn yield response to plant water stress caused by salinity and drought. Agric Water Manage 65:95–101Google Scholar
  59. Kazi S, Shultz J, Afzal J, Hashmi R, Jasim M, Bond J, Arelli PR, Lightfoot DA (2010) Iso-lines and inbred-lines confirmed loci that underlie resistance from cultivar 'Hartwig' to three soybean cyst nematode populations. Theor Appl Genet 120:633–644PubMedGoogle Scholar
  60. Keerio IM, Chang YS, Mirjat MA, Lakho MH, Bhatti IP (2001) The rate of nitrogen fixation in soybean root nodules after heat stress and recovery period. Inter J Agri Biol 3:512–514Google Scholar
  61. Kim KS, Bellendir S, Hudson KA, Hill CB, Hartman GL, Hyten DL, Hudson ME, Diers BW (2010) Fine mapping the soybean aphid resistance gene Rag1 in soybean. Theor Appl Genet 120:1063–1071PubMedGoogle Scholar
  62. Klink VP, Matthews BF (2009) Emerging approaches to broaden resistance of soybean to soybean cyst nematode as supported by gene expression studies. Plant Physiol 2009(151):1017–1022Google Scholar
  63. Klink VP, Overall CC, Alkharouf NW, Macdonald MH, Matthews BF (2007) A time-course comparative microarray analysis of an incompatible and compatible response by Glycine max (soybean) to Heterodera glycines (soybean cyst nematode) infection. Planta 226:1423–1447PubMedGoogle Scholar
  64. Klink VP, Hosseini P, MacDonald MH, Alkharouf NW, Matthews BF (2009) Population-specific gene expression in the plant pathogenic nematode Heterodera glycines exists prior to infection and during the onset of a resistant or susceptible reaction in the roots of the Glycine max genotype Peking. BMC Genomics 10:111PubMedGoogle Scholar
  65. Ko TS, Korban SS, Somers DA (2006) Soybean (Glycine max) transformation using immature cotyledon explants. Methods Mol Biol 343:397–405PubMedGoogle Scholar
  66. Kocsy G, Laurie R, Szalai G et al (2005) Genetic manipulation of proline levels affects antioxidants in soybean subjected to simultaneous drought and heat stresses. Physiol Plant 124:227–235Google Scholar
  67. Komatsu S, Yamamoto R, Nanjo Y, Mikami Y, Yunokawa H, Sakata KA (2009) Comprehensive analysis of the soybean genes and proteins expressed under flooding stress using transcriptome and proteome techniques. J Proteome Res 8:4766–4778PubMedGoogle Scholar
  68. Ladrera R, Marino D, Larrainzar E, González EM, Arrese-Igor C (2007) Reduced carbon availability to bacteroids and elevated ureides in nodules, but not in shoots, are involved in the nitrogen fixation response to early drought in soybean. Plant Physiol 145:539–546PubMedGoogle Scholar
  69. Le BH, Wagmaister JA, Kawashima T, Bui AQ, Harada JJ, Goldberg RB (2007) Using genomics to study legume seed development. Plant Physiol 144:562–574PubMedGoogle Scholar
  70. Lee GJ, Boerma HR, Villagarcia MR, Zhou X, Carter TE Jr, Li Z, Gibbs MO (2004) A major QTL conditioning salt tolerance in S-100 soybean and descendent cultivars. Theor Appl Genet 109:1610–1619PubMedGoogle Scholar
  71. Lee GJ, Wu X, Shannon JG, Sleper DA, Nguyen HT (2006) Genome mapping and molecular breeding in plants: soybean. In: Kole C (ed) Genome mapping and molecular breeding in plants, vol 2, oilseeds. Springer, USA, pp 1–45Google Scholar
  72. Liao Y, Zhang JS, Chen SY, Zhang WK (2008a) Role of GmbZIP132 under abscisic acid and salt stresses. J Integ Plant Biol 50:221–230Google Scholar
  73. Liao Y, Zou HF, Wei W et al (2008b) Soybean GmbZIP144, GmbZIP162 and GmbZIP178 genes function as negative regulator of ABA signaling and confer salt and freezing tolerance in transgenic Arabidopsis. Planta 228:225–240PubMedGoogle Scholar
  74. Libault M, Joshi T, Benedito VA, Xu D, Udvardi MK, Stacey G (2009) Legume transcription factor genes: what makes legumes so special? Plant Physiol 151:991–1001PubMedGoogle Scholar
  75. Lightfoot DA, Meksem K (1999) Novel polynucleotides and polypeptides relating to loci underlying resistance to soybean cyst nematode and methods of use thereof. Patent pending. #11/009,154Google Scholar
  76. Luo Q, Yu B, Liu Y (2005) Differential sensitivity of chloride and sodium ions in seedling of Glycine max and G. soja under NaCl stress. J Plant Physiol 162:1003–1012PubMedGoogle Scholar
  77. Manavalan LP, Guttikonda SK, Tran LS, Nguyen HT (2009) Physiological and molecular approaches to improve drought resistance in soybean. Plant Cell Physiol 50:1260–1276PubMedGoogle Scholar
  78. Marino D, Frendo P, Ladrera R, Zabalza A, Puppo A, Arrese-Igor C, González EM (2007) Nitrogen fixation control under drought stress. Localized or systemic? Plant Physiol 143:1968–1974PubMedGoogle Scholar
  79. Mathieu M, Winters EK, Kong F et al (2009) Establishment of a soybean (Glycine max (L.) Merr.) transposon-based mutagenesis repository. Planta 229:279–289PubMedGoogle Scholar
  80. Matsuda F, Hirai MY, Sasaki E et al (2010) AtMetExpress development: a phytochemical atlas of Arabidopsis development. Plant Physiol 152:566–578PubMedGoogle Scholar
  81. Mazarei M, Elling AA, Maier TR, Puthoff DP, Baum TJ (2007) GmEREBP1 is a transcription factor activating defense genes in soybean and Arabidopsis. Mol Plant Microbe Interact 20:107–119PubMedGoogle Scholar
  82. McLean RJ, Byth DE (1980) Inheritance of resistance to rust (Phakopsora pachyrhizi) in soybean. Aust J Agric Res 31:951–956Google Scholar
  83. Meksem K, Ruben E, Hyten D, Triwitayakorn K, Lightfoot DA (2001) Conversion of AFLP bands into high-throughput DNA markers. Mol Genet Genomics 265:207–214PubMedGoogle Scholar
  84. Men EA, Laniya ST, Searle RI et al (2002) Fast neutron mutagenesis of soybean (Glycine soja L.) produces a supernodulating mutant containing a large deletion. Genome Lett 3:147–155Google Scholar
  85. Meyer JD, Silva DC, Yang C, Pedley KF, Zhang C, van de Mortel M, Hill JH, Shoemaker RC, Abdelnoor RV, Whitham SA, Graham MA (2009) Identification and analyses of candidate genes for rpp 4-mediated resistance to Asian soybean rust in soybean. Plant Physiol 150:295–307PubMedGoogle Scholar
  86. Mian MAR, Mailey MA, Ashley DA et al (1996) Molecular markers associated with water use efficiency and leaf ash in soybean. Crop Sci 36:1252–1257Google Scholar
  87. Mian MAR, Ashley DA, Boerma HR (1998) An additional QTL for water use efficiency in soybean. Crop Sci 38:390–393Google Scholar
  88. Mochida K, Yoshida T, Sakurai T, Yamaguchi-Shinozaki K, Shinozaki K, Tran LS (2009) In silico analysis of transcription factor repertoire and prediction of stress responsive transcription factors in soybean. DNA Res 16:353–356PubMedGoogle Scholar
  89. 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 26:290–291PubMedGoogle Scholar
  90. Monteros MJ, Missaoui A, Phillips DV, Walker DR, Boerma HR (2007) Mapping and confirmation of the Hyuuga-red-brown lesion resistance gene for Asian soybean rust. Crop Science 47:829–836Google Scholar
  91. Nakashima K, Tran L-SP, Nguyen VD, Fujita M, Maruyama K, Todaka D, Ito Y, Hayashi N, Shinozaki K, Yamaguchi-Shinozaki K (2007) Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. Plant J 51:617–630PubMedGoogle Scholar
  92. O'Brian MR, Vance CP (2007) Legume biology: sequence to seeds. Plant Physiol 144:537PubMedGoogle Scholar
  93. Olhoft PM, Donovan CM, Somers DA (2006) Soybean (Glycine max) transformation using mature cotyledonary node explants. Methods Mol Biol 343:385–396PubMedGoogle Scholar
  94. Pathan MS, Lee JD, Shannon JG, Nguyen HT (2007) Recent advances in breeding for drought and salt stress tolerance in soybean. In: Jenks MA, Hasegawa PM, Jain SM (eds) Advances in molecular-breeding toward drought and salt tolerant crops. Springer, USA, pp 739–773Google Scholar
  95. Phang TH, Shao G, Lam HM (2008) Salt tolerance in soybean. J Integr Plant Biol 50:1196–1212PubMedGoogle Scholar
  96. Pinheiro GL, Marques CS, Costa MD et al (2009) Complete inventory of soybean NAC transcription factors: sequence conservation and expression analysis uncover their distinct roles in stress response. Gene 444:10–23PubMedGoogle Scholar
  97. Ray JD, Morel W, Smith JR, Frederick RD, Miles MR (2009) Genetics and mapping of adult plant rust resistance in soybean PI 587886 and PI 587880A. Theor Appl Genet 119:271–280PubMedGoogle Scholar
  98. Reyna N, Cornelious B, Shannon JG, Sneller CH (2003) Evaluation of a QTL for waterlogging tolerance in southern soybean germplasm. Crop Sci 43:2077–2082Google Scholar
  99. Riechmann JL, Ratcliffe OJ (2000) A genomic perspective on plant transcription factors. Curr Opin Plant Biol 3:423–434PubMedGoogle Scholar
  100. Ruben E, Aziz J, Afzal J, Njiti VN, Triwitayakorn K, Iqbal MJ, Yaegashi S, Arelli PR, Town CD, Ishihara H, Meksem K, Lightfoot DA (2006) Genomic analysis of the ‘Peking’ rhg1 locus: candidate genes that underlie soybean resistance to the cyst nematode. Mol Genet Genome 276:320–330Google Scholar
  101. Sakata K, Ohyanagi H, Nobori H, Nakamura T, Hashiguchi A, Nanjo Y, Mikami Y, Yunokawa H, Komatsu S (2009) Soybean proteome database: a data resource for plant differential omics. J Proteome Res 8:3539–3548PubMedGoogle Scholar
  102. Sakuma Y, Maruyama K, Osakabe Y, Qin F, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2006) Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression. Plant Cell 18:1292–1309PubMedGoogle Scholar
  103. Sato S, Tabata S (2006) Lotus japonicus as a platform for legume research. Curr Opin Plant Biol 9:128–132PubMedGoogle Scholar
  104. Sayama T, Nakazaki T, Ishikawa G et al (2009) QTL analysis of seed-flooding tolerance in soybean (Glycine max (L.) Merr.). Plant Sci 176:514–521Google Scholar
  105. Schmutz J, Cannon SB, Schlueter J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183PubMedGoogle Scholar
  106. Seki M, Narusaka M, Kamiya A et al (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science 296:141–145PubMedGoogle Scholar
  107. Senda M, Kasai A, Yumoto S, Akada S, Ishikawa R, Harada T, Niizeki M (2002) Sequence divergence at chalcone synthase gene in pigmented seed coat soybean mutants of the inhibitor locus. Genes Genet Syst 77:341–350PubMedGoogle Scholar
  108. Shoemaker RC, Cregan PB, Vodkin LO (2004) Soybean genomics. In: Shibles RM, Herper JA, Wilson RF, Shoemaker RC (eds) Soybeans: improvement, production, and uses. ASA-CSSA-SSSA, Madison, pp 235–255Google Scholar
  109. Shoemaker RC, Schlueter J, Doyle JJ (2006) Paleopolyploidy and gene duplication in soybean and other legumes. Curr Opin Plant Biol 9:104–109PubMedGoogle Scholar
  110. Shultz JL, Kazi S, Afzal JA, Bashir R, Lightfoot DA (2007a) The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. Theor Appl Genet 114:1081–1090PubMedGoogle Scholar
  111. Shultz JL, Ray JD, Smith JR, Mengistu A (2007b) A soybean mapping population specific to the early soybean production system. DNA Seq 18:104–111PubMedGoogle Scholar
  112. Silva DCG, Yamanaka N, Brogin RL et al (2008) Molecular mapping of two loci that confer resistance to Asian rust in soybean. Theor Appl Genet 117:57–63PubMedGoogle Scholar
  113. Song QJ, Marek LF, Shoemaker RC, Lark KG, Concibido VC, Delannay X, Specht JE, Cregan PB (2004) A new integrated genetic linkage map of the soybean. Theor Appl Genet 109:122–128PubMedGoogle Scholar
  114. Soria-Guerra RE, Rosales-Mendoza S, Chang S et al (2010) Transcriptome analysis of resistant and susceptible genotypes of Glycine tomentella during Phakopsora pachyrhizi infection reveals novel rust resistance genes. Theor Appl Genet 120:1315–1333PubMedGoogle Scholar
  115. Stacey G, Libault M, Brechenmacher L, Wan J, May GD (2006) Genetics and functional genomics of legume nodulation. Curr Opin Plant Biol 9:110–121PubMedGoogle Scholar
  116. Stracke S, Sato S, Sandal N, Koyama M, Kaneko T, Tabata S, Parniske M (2004) Exploitation of colinear relationships between the genomes of Lotus japonicus, Pisum sativum and Arabidopsis thaliana, for positional cloning of a legume symbiosis gene. Theor Appl Genet 108:442–449PubMedGoogle Scholar
  117. Tadege M, Ratet P, Mysore KS (2005) Insertional mutagenesis: a swiss army knife for functional genomics of Medicago truncatula. Trends Plant Sci 10:229–235PubMedGoogle Scholar
  118. Toorchi M, Yukawa K, Nouri MZ, Komatsu S (2009) Proteomics approach for identifying osmotic-stress-related proteins in soybean roots. Peptides 30:2108–2117PubMedGoogle Scholar
  119. Tran LS, Mochida K (2010a) Identification and prediction of abiotic stress responsive transcription factors involved in abiotic stress signaling in soybean. Plant Sig Behav 5:255–257Google Scholar
  120. Tran LS, Mochida K (2010b) A platform for functional prediction and comparative analyses of transcription factors of legumes and beyond. Plant Signal Behav PMID:20023425Google Scholar
  121. Tran LS, Nguyen HT (2009) Future Biotechnology of Legumes. In: Emerich WD, Krishnan H (eds) Nitrogen fixation in crop production. ASA-CSA-SSSA, Madison, pp 265–308Google Scholar
  122. Tran LS, Nakashima K, Sakuma Y, Simpson SD, Fujita Y, Maruyama K, Fujita M, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2004) Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter. Plant Cell 16:2481–2498PubMedGoogle Scholar
  123. Tran LS, Nakashima K, Shinozaki K, Yamaguchi-Shinozaki K (2007a) Plant gene networks in osmotic stress response: from genes to regulatory networks. Methods Enzymol 428:109–128PubMedGoogle Scholar
  124. Tran LS, Nakashima K, Sakuma Y, Osakabe Y, Qin F, Simpson SD, Maruyama K, Fujita Y, Shinozaki K, Yamaguchi-Shinozaki K (2007b) Co-expression of the stress-inducible zinc finger homeodomain ZFHD1 and NAC transcription factors enhances expression of the ERD1 gene in Arabidopsis. Plant J 49:46–63PubMedGoogle Scholar
  125. Tran LS, Quach TN, Guttikonda SK, Aldrich DL, Kumar R, Neelakandan A, Valliyodan B, Nguyen HT (2009) Molecular characterization of stress-inducible GmNAC genes in soybean. Mol Genet Genomics 281:647–664PubMedGoogle Scholar
  126. Tran LS, Nishiyama R, Shinozaki K, Yamaguchi-Shinozaki K (2010) Potential utilization of NAC transcription factors to enhance abiotic stress tolerance in plants by biotechnological approach. GM Crops 1:32–39Google Scholar
  127. Tuyen DD, Lal SK, Xu DH (2010) Identification of a major QTL allele from wild soybean (Glycine soja Sieb. & Zucc.) for increasing alkaline salt tolerance in soybean. Theor Appl Genet PMID:20204319Google Scholar
  128. Udvardi MK, Kakar K, Wandrey M, Montanari O, Murray J, Andriankaja A, Zhang JY, Benedito V, Hofer JM, Chueng F, Town CD (2007) Legume transcription factors: global regulators of plant development and response to the environment. Plant Physiol 144:538–549PubMedGoogle Scholar
  129. Umezawa T, Sakurai T, Totoki Y et al (2008) Sequencing and analysis of approximately 40000 soybean cDNA clones from a full-length-enriched cDNA library. DNA Res 15:333–346PubMedGoogle Scholar
  130. Urano K, Kurihara Y, Seki M, Shinozaki K (2010) 'Omics' analyses of regulatory networks in plant abiotic stress responses. Curr Opin Plant Biol 13:132–138PubMedGoogle Scholar
  131. VanToai TT, Martin SK, Chase K, Boru G, Schnipke V, Schmitthenner AF, Lark KG (2001) Identification of a QTL associated with tolerance of soybean to soil waterlogging. Crop Sci 41:1247–1252Google Scholar
  132. Vodkin LO, Khanna A, Shealy R et al (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 5:73PubMedGoogle Scholar
  133. Vuong T, Wu X, Pathan MS, Valliyodan B, Nguyen HT (2007) Genomics approaches to soybean improvement. In: Varshney PK, Tuberosa R (eds) Genomics-assisted crop improvement, vol 2, Genomics applications in crops. Springer, USA, pp 243–279Google Scholar
  134. 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 10:14Google Scholar
  135. Wei W, Huang J, Hao YJ et al (2009) Soybean GmPHD-type transcription regulators improve stress tolerance in transgenic Arabidopsis plants. PLoS One 4:e7209PubMedGoogle Scholar
  136. Wrather JA, Koenning SR (2006) Estimates of disease effects on soybean yields in the United States 2003 to 2005. J Nematol 38:173–180PubMedGoogle Scholar
  137. Wrather JA, Anderson TR, Arsyad DM et al (2001a) Soybean disease loss estimates for the top ten soybean-producing countries in 1998. Can J Plant Pathol 23:115–121Google Scholar
  138. Wrather JA, Stienstra WC, Koenning SR (2001b) Soybean disease loss estimates for the United States from 1996 to 1998. Can J Plant Pathol 23:122–131Google Scholar
  139. Wu W, Zhang Q, Zhu Y, Lam HM, Cai Z, Guo D (2008) Comparative metabolic profiling reveals secondary metabolites correlated with soybean salt tolerance. J Agric Food Chem 56:11132–11138PubMedGoogle Scholar
  140. Wu X, Blake S, Sleper D, Shannon G, Cregan P, Nguyen H (2009) QTL, additive and epistatic effects for SCN resistance in PI 437654. Theor Appl Genet 118:1093–1105PubMedGoogle Scholar
  141. Xu CP, Garrett WM, Sullivan J, Caperna TJ, Natarajan S (2006) Separation and identification of soybean leaf proteins by two-dimensional gel electrophoresis and mass spectrometry. Phytochemistry 67:2431–2440PubMedGoogle Scholar
  142. Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391–407Google Scholar
  143. Yamagishi N, Yoshikawa N (2009) Virus-induced gene silencing in soybean seeds and the emergence stage of soybean plants with Apple latent spherical virus vectors. Plant Mol Biol 71:15–24PubMedGoogle Scholar
  144. Yamaguchi M, Valliyodan B, Zhang J, Lenoble ME, Yu O, Rogers EE, Nguyen HT, Sharp RE (2010) Regulation of growth response to water stress in the soybean primary root. I. Proteomic analysis reveals region-specific regulation of phenylpropanoid metabolism and control of free iron in the elongation zone. Plant Cell Environ 33:223–243PubMedGoogle Scholar
  145. Yamamoto YY, Yoshitsugu T, Sakurai T, Seki M, Shinozaki K, Obokata J (2009) Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis. Plant J 60:350–362PubMedGoogle Scholar
  146. Young ND, Shoemaker RC (2006) Genome studies and molecular genetics. Part 1: model legumes. Exploring the structure, function and evolution of legume genomes. Curr Opin Plant Biol 9:95–98PubMedGoogle Scholar
  147. Yu YG, Buss GR, Maroof MA (1996) Isolation of a superfamily of candidate disease-resistance genes in soybean based on a conserved nucleotide-binding site. Proc Natl Acad Sci USA 93:11751–11756PubMedGoogle Scholar
  148. Zhang G, Chen M, Chen X et al (2008) Phylogeny, gene structures, and expression patterns of the ERF gene family in soybean (Glycine max L.). J Exp Bot 59:4905–4917Google Scholar
  149. Zhang C, Yang C, Whitham SA, Hill JH (2009) Development and use of an efficient DNA-based viral gene silencing vector for soybean. Mol Plant Microbe Interact 22:123–131PubMedGoogle Scholar
  150. Zhang C, Bradshaw JD, Whitham SA, Hill JH (2010) The development of an efficient multi-purpose BPMV viral vector set for foreign gene expression and RNA silencing. Plant Physiol 153:52–65PubMedGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  1. 1.RIKEN Plant Science CenterYokohamaJapan

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