Differential expression of genes in soybean in response to the causal agent of Asian soybean rust (Phakopsora pachyrhizi Sydow) is soybean growth stage-specific

  • Dilip R. Panthee
  • James J. Marois
  • David L. Wright
  • Dario Narváez
  • Joshua S. Yuan
  • C. Neal StewartJr
Original Paper


Understanding plant host response to a pathogen such as Phakopsora pachyrhizi, the causal agent of Asian soybean rust (ASR), under different environmental conditions and growth stages is crucial for developing a resistant plant variety. The main objective of this study was to perform global transcriptome profiling of P. pachyrhizi-exposed soybean (Glycine max) with susceptible reaction to the pathogen from two distinct developmental growth stages using whole genome Affymetrix microarrays of soybean followed by confirmation using a resistant genotype. Soybean cv. 5601T (susceptible to ASR) at the V4 and R1 growth stages and Glycine tomentella (resistant to ASR) plants were inoculated with P. pachyrhizi and leaf samples were collected after 72 h of inoculation for microarray analysis. Upon analyzing the data using Array Assist software at 5% false discovery rate (FDR), a total of 5,056 genes were found significantly differentially expressed at V4 growth stage, of which 2,401 were up-regulated, whereas 579 were found differentially expressed at R1 growth stage, of which 264 were up-regulated. There were 333 differentially expressed common genes between the V4 and R1 growth stages, of which 125 were up-regulated. A large difference in number of differentially expressed genes between the two growth stages indicates that the gene expression is growth-stage-specific. We performed real-time RT-PCR analysis on nine of these genes from both growth stages and both plant species and found results to be congruent with those from the microarray analysis.



This study was supported by Tennessee Soybean Promotion Board and funds from the Tennessee Agricultural Experiment Station. Julia Gouffon at the Affymetrix Core Center of the University of Tennessee, is sincerely acknowledged for her help in conducting the microarray experiment. We appreciate the collaborations and conversations with Vince Pantalone, Kurt Lamour, and Mitra Mazarei. Minimum information about a microarray experiment (MIAME) guidelines were followed in this study.

Supplementary material

122_2008_905_MOESM1_ESM.xls (934 kb)
Table S-1 Differentially expressed genes in soybean in response to Phakopsora pachyrhizi at V4 growth stage (XLS 934 kb)
122_2008_905_MOESM2_ESM.xls (123 kb)
Table S-2 Differentially expressed genes in soybean in response to Phakopsora pachyrhizi at R1 growth stage (XLS 123 kb)
122_2008_905_MOESM3_ESM.xls (174 kb)
Table S-3 Number of transcripts of a gene or a gene family expressed differentially at V4 and R1 growth stage of soybean cv. 5601T in response to Phakopsora pachyrhizi (XLS 173 kb)
122_2008_905_MOESM4_ESM.xls (413 kb)
Table S-4 Differentially expressed unique known genes at V4 growth stage of soybean in response to Phakopsora pachyrhizi (XLS 413 kb)
122_2008_905_MOESM5_ESM.xls (44 kb)
Table S-5 Differentially expressed unique known genes at R1 growth stage of soybean in response to Phakopsora pachyrhizi (XLS 43 kb)
122_2008_905_MOESM6_ESM.xls (78 kb)
Table S-6 Differentially expressed common genes at V4 and R1 growth stages of soybean in response to Phakopsora pachyrhizi (XLS 77 kb)


  1. Akashi T, Aoki T, S Ayabe (1999) Cloning and functional expression of a cytochrome P450 cDNA encoding 2-hydroxyisoflavanone synthase involved in biosynthesis of the isoflavonoid skeleton in licorice. Plant Physiol 121:821–828PubMedCrossRefGoogle Scholar
  2. Bohnert H-J, Ayoubi P, Borchert C, Bressan R-A, Burnap R-L, Cushman J-C, Cushman M-A, Deyholos M, Fischer R, Galbraith D-W, Hasegawa P-M, Jenks M, Kawasaki S, Koiwa H, Kore-eda S, Lee B-H, Michalowski C-B, Misawa E, Nomura M, Ozturk N, Postier B, Prade R, Song C-P, Tanaka Y, Wang H, Zhu J-K (2001) A genomics approach towards salt stress tolerance. Plant Physiol Biochem (Paris) 39:295–311CrossRefGoogle Scholar
  3. Cassab GI, Nieto Sotelo J, Cooper JB (1985) A developmentally regulated hydroxyproline-rich glycoprotein from the cell walls of soybean seed coats. Plant Physiol 77:532–535PubMedCrossRefGoogle Scholar
  4. Chong J, Pierrel M-A, Atanassova R, Werck-Reichhart D, Fritig B, Saindrenan P (2001) Free and conjugated benzoic acid in tobacco plants and cell cultures. Induced accumulation upon elicitation of defense responses and role as salicylic acid precursors. Plant Physiol 125:318–328PubMedCrossRefGoogle Scholar
  5. Coenen C, Bierfreund N, Luthen H (2002) Developmental regulation of H+-ATPase-dependent auxin responses in the diageotropica mutant of tomato (Lycopersicon esculentum). Physiol Plantarum 114:461–471CrossRefGoogle Scholar
  6. Davies C, Boss PK, Robinson SP (1997) Treatment of grape berries, a nonclimacteric fruit with a synthetic auxin, retards ripening and alters the expression of developmentally regulated genes. Plant Physiol 115:1155–1161PubMedGoogle Scholar
  7. DeMortel MV, Recknor JC, Graham MA, Nettleton D, Dittman JD, Nelson RT, Godoy CV, Abdelnoor RV, Almeida ÁMR, Baum TJ, Whitham SA (2007a) Distinct biphasic mRNA changes in response to Asian soybean rust infection. MPMI 20:887–899CrossRefGoogle Scholar
  8. DeMortel MV, Schneider KT, Bancroft T, Nettleton D, Frederick RD, Baum TJ, Whitham SA (2007b) Gene expression in a soybean cultivar containing the Rpp3 gene for resistance to Phakopsora pachyrhizi. Phytopathology 97:S117–S118Google Scholar
  9. 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 143:326–338PubMedCrossRefGoogle Scholar
  10. Dong JZ, Dunstan DI (1996) Characterization of three heat-shock-protein genes and their developmental regulation during somatic embryogenesis in white spruce {Picea glauca (Moench) Voss}. Planta 200:85–91PubMedCrossRefGoogle Scholar
  11. Fehr WR, Caviness CE (1977) Stages of soybean development. Special Report 80, Cooperative Extension Services. Iowa State University, Ames, IA, p 7Google Scholar
  12. Frederick RD, Snyder CL, Peterson GL, Bonde MR (2002) Polymerase chain reaction assays for the detection and discrimination of the soybean rust pathogens Phakopsora pachyrhizi and P. meibomiae. Phytopathology 92:217–227PubMedCrossRefGoogle Scholar
  13. Guenther JF, Chanmanivone N, Galetovic MP, Wallace IS, Cobb JA, Roberts DM (2003) Phosphorylation of soybean nodulin 26 on serine 262 enhances water permeability and is regulated developmentally and by osmotic signals. Plant Cell 15:981–991PubMedCrossRefGoogle Scholar
  14. Gupta GK, Ansari M, Karmakar P, Husain S, Ramteke R (1999) Resurrection of soybean rust (Phakopsora pachyrhizi) in India. In: Kauffman HE (ed) World soybean research conference VI. University of Illinois, Chicago, p 617Google Scholar
  15. Halkier BA, Gershenzon J (2006) Biology and biochemistry of Glucosinolates. Annu Rev Plant Biol 57:303–333PubMedCrossRefGoogle Scholar
  16. Hartman GL, Wang TC, Hymowitz T (1992) Sources of resistance to soybean rust in perennial Glycine species. Plant Dis 76:396–399Google Scholar
  17. Hartman GL, Wang TC, Tschanz AT (1991) Soybean rust development and the quantitative relationship between rust severity and soybean yield. Plant Dis 75:596–600Google Scholar
  18. Higgins CF (1992) ABC transporters: from microorganisms to man. Annu Rev Cell Biol 8:67–113PubMedCrossRefGoogle Scholar
  19. Horiguchi G, Kawakami N, Kusumi K (1998) Developmental regulation of genes for microsome and plastid w-3 fatty acid desaturases in wheat (Triticum aestivum L.). Plant Cell Physiol 39:540–544Google Scholar
  20. Hyten DL, Hartman GL, Nelson RL, Frederick RD, Concibido VC, Narvel JM, Cregan PB (2007) Map location of the Rpp1 locus that confers resistance to soybean rust in soybean. Crop Sci 47:837–840Google Scholar
  21. Jasinski M, Stukkens Y, Degand H, Purnelle B, Marchand-Brynaert J, Boutry M (2001) A plant plasma membrane ATP binding cassette-type transporter is involved in antifungal terpenoid secretion. Plant Cell 13:1095–1108PubMedCrossRefGoogle Scholar
  22. Jung W, Yu O, Lau S-MC, O’Keefe DP, Odell J, Fader G, McGonigle B (2000) Identification and expression of isoflavone synthase, the key enzyme for biosynthesis of isoflavones in legumes. Nat Biotechnol 18:208–212PubMedCrossRefGoogle Scholar
  23. Kawasaki S, Borchert C, Deyholos M, Wang H, Brazille S, Kawai K, Galbraith D, Bohnert H-J (2001) Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 13:889–905PubMedCrossRefGoogle Scholar
  24. Kus JV, Zaton K, Sarkar R, Cameron RK (2002) Age-related resistance in Arabidopsis is a developmentally regulated defense response to Pseudomonas syringae. Plant Cell 14:479–490PubMedCrossRefGoogle Scholar
  25. Lee S, Kim S-Y, Chung E, Joung Y-H, Pai H-B, Hur C-G, Choi D (2004) EST and microarray analyses of pathogen-responsive genes in hot pepper (Capsicum annuum L.) non-host resistance against soybean pustule pathogen (Xanthomonas axonopodis pv. glycines). Funct Integr Genomics 4:196–205PubMedCrossRefGoogle Scholar
  26. León J, Sánchez-Serrano JJ (1999) Molecular biology of jasmonic acid biosynthesis in plants. Plant Physiol Biochem 37:373–380CrossRefGoogle Scholar
  27. Luan S (2003) Protein phosphatases in plants. Annu Rev Plant Biol 54:63–92PubMedCrossRefGoogle Scholar
  28. Luo M, Liang XQ, Dang P, Holbrook CC, Bausher MG, Lee RD, Guo BZ (2005) Microarray-based screening of differentially expressed genes in peanut in response to Aspergillus parasiticus infection and drought stress. Plant Sci 169:695–703CrossRefGoogle Scholar
  29. Martin GB, Bogdanove AJ, Sessa G (2003) Understanding the functions of plant disease resistance proteins. Annu Rev Plant Biol 54:23–61PubMedCrossRefGoogle Scholar
  30. Monteros MJ, Missaoui AM, Phillips DV, Walker DR, Boerma HR (2007) Mapping and confirmation of the ‘Hyuuga’ red-brown lesion resistance gene for Asian soybean rust. Crop Sci 47:829–836Google Scholar
  31. Moy P, Qutob D, Chapman BP, Atkinson I, Gijzen M (2004) Patterns of gene expression upon infection of soybean plants by Phytophthora sojae. MPMI 17:1051–1062PubMedCrossRefGoogle Scholar
  32. Panthee DR, Yuan JS, Wright DL, Marois JJ, Mailhot D Jr, NS C (2007) Gene expression analysis in soybean in response to the causal agent of Asian soybean rust (Phakopsora pachyrhizi Sydow) in an early growth stage. Funct Integr Genomics 7:291–301PubMedCrossRefGoogle Scholar
  33. Pasquer F, Isidore E, Zarn J, Keller B (2005) Specific patterns of changes in wheat gene expression after treatment with three antifungal compounds. Plant Mol Biol 57:693–707PubMedCrossRefGoogle Scholar
  34. Puthoff D-P, Nettleton D, Rodermel S-R, Baum T-J (2003) Arabidopsis gene expression changes during cyst nematode parasitism revealed by statistical analyses of microarray expression profiles. Plant J 33:911–921PubMedCrossRefGoogle Scholar
  35. Rahangdale SR, Raut VM (2003) Evaluation of soybean germplasm lines for rust (Phakopsora pachyrhizi) resistance. Indian J Agric Sci 73:120–121Google Scholar
  36. Ramteke R, Karmakar PG, Gupta GK, Singh RK, Khan IR (2003) Resistance genes for rust and yellow mosaic diseases in soybean—a review. J Oilseeds Res 20:195–203Google Scholar
  37. Rea PA (2007) Plant ATP-binding cassette transporters. Annu Rev Plant Biol 58:347–375PubMedCrossRefGoogle Scholar
  38. Ribnicky DM, Shulaev V, Raskin I (1998) Intermediates of salicylic acid biosynthesis in tobacco. Plant Physiol 118:565–572PubMedCrossRefGoogle Scholar
  39. Rojas A, Almoguera C, Carranco R (2002) Selective activation of the developmentally regulated Ha hsp17.6 G1 promoter by heat stress transcription factors. Plant Physiol 129:1207–1215PubMedCrossRefGoogle Scholar
  40. Schenk PM, Kazan K, Wilson I, Anderson JP, Richmond T, Somerville SC, Manners JM (2000) Coordinated plant defense responses in Arabidopsis revealed by microarray analysis. PNAS 97:11655–11660PubMedCrossRefGoogle Scholar
  41. Schilmiller AL, Koo AJK, Howe GA (2007) Functional diversification of acyl-coenzyme A oxidases in jasmonic acid biosynthesis and action. Plant Physiol 143:812–824PubMedCrossRefGoogle Scholar
  42. Schneider KT, DeMortel MV, Nettleton D, Frederick RD, Baum TJ, Whitham SA (2006) Microarray analysis of Rpp3-mediated resistance to soybean rust infection. In: National soybean rust symposium, The American Phytopathological Society, 3340 Pilot Knob Road, St. Paul, MN, 5512, St. Loius, MOGoogle Scholar
  43. Schoen DJ, Burdon JJ, Brown AHD (1992) Resistance of Glycine tomentella to soybean leaf rust Phakopsora pachyrhizi in relation to ploidy level and geographic distribution. Theor Appl Genet 83:827–832CrossRefGoogle Scholar
  44. Schuler MA, Werck-Reichhart D (2003) Functional genomics of P450s. Annu Rev Plant Biol 54:629–667PubMedCrossRefGoogle Scholar
  45. Shen H, Chen J, Wang Z, Yang C, Sasaki T, Yamamoto Y, Matsumoto H, Yan X (2006) Root plasma membrane H+-ATPase is involved in the adaptation of soybean to phosphorus starvation. J Exp Bot 57:1353–1362PubMedCrossRefGoogle Scholar
  46. Shimada N, Akashi T, Aoki T, S Ayabe (2000) Induction of isoflavonoid pathway in the model legume Lotus japonicus: molecular characterization of enzymes involved in phytoalexin biosynthesis. Plant Sci 160:37–47PubMedCrossRefGoogle Scholar
  47. Soytech Inc. (2006) Oilseed statistics. 2006 Soy and oilseed blue book: the annual directory of the world oilseed directory. Soytech Inc., Bar Harbor, pp 314–358Google Scholar
  48. Stewart CN Jr, Via LE (1993) A rapid CTAB DNA isolation technique useful for RAPD fingerprinting and other PCR applications. Biotechniques 14:748–751PubMedGoogle Scholar
  49. Subramanian S, Graham MY, Yu O, Graham TL (2005) RNA interference of soybean isoflavone synthase genes leads to silencing in tissues distal to the transformation site and to enhanced susceptibility to Phytophthora sojae. Plant Physiol 137:1345–1353PubMedCrossRefGoogle Scholar
  50. Tian L, Wang J, Fong MP (2003) Genetic control of developmental changes induced by disruption of Arabidopsis histone deacetylase 1 (AtHD1) expression. Genetics 165:399–409PubMedGoogle Scholar
  51. Tian ZD, Liu J, Wang BL, Xie CH (2006) Screening and expression analysis of Phytophthora infestans induced genes in potato leaves with horizontal resistance. Plant Cell Rep 25:1094–1103PubMedCrossRefGoogle Scholar
  52. Tschanz A, Shanmugasundaram S (1984) Soybean rust. In: Shibles R (ed) World soybean research conference III. Westview Press Inc., London, pp 562–567Google Scholar
  53. Wasternack C, Miersch O, Kramell R, Hause B, Ward J, Beale M, Boland W, Parthier B, Feussner I (1998) Jasmonic acid: biosynthesis, signal transduction, gene expression. Fett/Lipid 100:139–146CrossRefGoogle Scholar
  54. Wildermuth MC, Dewdney J, Wu G, Ausubel FM (2001) Isochorismate synthase is required to synthesize salicylic acid for plant defence. Nature 414:562–565PubMedCrossRefGoogle Scholar
  55. Winkel-Shirley B (2001) Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology. Plant Physiol 126:485–493PubMedCrossRefGoogle Scholar
  56. Wu Z, Irizarry R, Gentleman R, Martinez Murillo F, Spencer F (2004) A model based background adjustment for oligonucleotide expression arrays. J Am Stat Assoc 99:909–917CrossRefGoogle Scholar
  57. Yen S-K, Chung M-C, Chen P-C, Yen HE (2001) Environmental and developmental regulation of the wound-induced cell wall protein WI12 in the halophyte ice plant. Plant Physiol 127:517–528PubMedCrossRefGoogle Scholar
  58. Yu O, Shi J, Hession AO, Maxwell CA, McGonigle B, Odell JT (2003) Metabolic engineering to increase isoflavone concentration in soybean seeds. Phytochemistry 63:753–763PubMedCrossRefGoogle Scholar
  59. Yuan JS, Reed A, Chen F Jr, NS C (2006) Statistical analysis of real-time PCR data. BMC Bioinformatics I7:85CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Dilip R. Panthee
    • 1
    • 3
  • James J. Marois
    • 2
  • David L. Wright
    • 2
  • Dario Narváez
    • 2
  • Joshua S. Yuan
    • 1
  • C. Neal StewartJr
    • 1
  1. 1.Department of Plant Sciences, 252 Ellington Plant SciencesThe University of TennesseeKnoxvilleUSA
  2. 2.North Florida Agriculture Research and Education CenterThe University of FloridaQuincyUSA
  3. 3.Department of Horticultural Science, Mountain Horticultural Crops Research and Extension CenterNorth Carolina State UniversityMills RiverUSA

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