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Timecourse microarray analyses reveal global changes in gene expression of susceptible Glycine max (soybean) roots during infection by Heterodera glycines (soybean cyst nematode)

Planta volume 224, pages 838–852 (2006)Cite this article

Abstract

Changes in gene expression within roots of Glycine max (soybean), cv. Kent, susceptible to infection by Heterodera glycines (the soybean cyst nematode [SCN]), at 6, 12, and 24 h, and 2, 4, 6, and 8 days post-inoculation were monitored using microarrays containing more than 6,000 cDNA inserts. Replicate, independent biological samples were examined at each time point. Gene expression was analyzed statistically using T-tests, ANOVA, clustering algorithms, and online analytical processing (OLAP). These analyses allow the user to query the data in several ways without importing the data into third-party software. RT-PCR confirmed that WRKY6 transcription factor, trehalose phosphate synthase, EIF4a, Skp1, and CLB1 were differentially induced across most time-points. Other genes induced across most timepoints included lipoxygenase, calmodulin, phospholipase C, metallothionein-like protein, and chalcone reductase. RT-PCR demonstrated enhanced expression during the first 12 h of infection for Kunitz trypsin inhibitor and sucrose synthase. The stress-related gene, SAM-22, phospholipase D and 12-oxophytodienoate reductase were also induced at the early time-points. At 6 and 8 dpi there was an abundance of transcripts expressed that encoded genes involved in transcription and protein synthesis. Some of those genes included ribosomal proteins, and initiation and elongation factors. Several genes involved in carbon metabolism and transport were also more abundant. Those genes included glyceraldehyde 3-phosphate dehydrogenase, fructose-bisphosphate aldolase and sucrose synthase. These results identified specific changes in gene transcript levels triggered by infection of susceptible soybean roots by SCN.

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Abbreviations

EST:

Expressed sequence tag

hpi:

Hours post-infection

dpi:

Days post-infection

LCM:

Laser capture microdissection

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Acknowledgements

The authors thank Kris Pilitt and Ann Deiter for their technical support. The authors would also like to thank Nathan Uhlmann, Antoni J. Rafalski, Julie M. Vogel, Feng Han, Carl Simmons, and Guihua Lu from Dupont Inc. for their amplification and identification of the Dupont clones mentioned in this study. All data, raw and normalized, are stored in the Soybean Genomics and Microarray Database (Alkharouf and Matthews 2004) and are available through the web site [http://www.bldg6.arsusda.gov/benlab/]. This work was supported by the United Soybean Board under grant 3214 and USDA CSREES National Research Initiative grant 99-35302-8189. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the United States Department of Agriculture.

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Author notes

  1. Nadim W. Alkharouf

    Present address: Genome Sciences Centre, BC Cancer Agency, Suite 100, 570 West 7th Avenue, Vancouver, BC, Canada, V5Z 4S6

Authors and Affiliations

  1. USDA-ARS-PSI-SGIL, Bldg.006, Rm 118, 10300 Baltimore Avenue, Beltsville, MD, 20705, USA

    Nadim W. Alkharouf, Vincent P. Klink, Imed B. Chouikha, Hunter S. Beard, Margaret H. MacDonald & Benjamin F. Matthews

  2. School of Computational Sciences, George Mason University, Manassas, VA, 20110, USA

    Nadim W. Alkharouf & Imed B. Chouikha

  3. Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA

    Nadim W. Alkharouf

  4. United States Department of Agriculture, Nematology Laboratory, Beltsville, MD, 20705, USA

    Susan Meyer

  5. Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA

    Halina T. Knap

  6. Graduate School Biotechnology Studies, University of Maryland University College, College Park, MD, 20742, USA

    Rana Khan

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Alkharouf, N.W., Klink, V.P., Chouikha, I.B. et al. Timecourse microarray analyses reveal global changes in gene expression of susceptible Glycine max (soybean) roots during infection by Heterodera glycines (soybean cyst nematode). Planta 224, 838–852 (2006). https://doi.org/10.1007/s00425-006-0270-8

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Keywords

  • Glycine max
  • Heterodera glycines
  • Microarray
  • Gene expression
  • OLAP
  • Soybean cyst nematode
  • Laser capture microdissection (LCM)