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

Abstract

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.

Notes

Acknowledgments

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)

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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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