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Journal of Experimental Botany 2007 58(12):3407-3418; doi:10.1093/jxb/erm211
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© 2007 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. This paper is available online free of all access charges (see http://jxb.oxfordjournals.org/open_access.html for further details)

RESEARCH PAPER

GeneChip profiling of transcriptional responses to soybean cyst nematode, Heterodera glycines, colonization of soybean roots

David P. Puthoff1, Mindy L. Ehrenfried1, Bryan T. Vinyard2 and Mark L. Tucker1,*

1Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, BARC-West, Beltsville, MD 20705, USA
2Biometrical Consulting Service, Agricultural Research Service, United States Department of Agriculture, BARC-West, Beltsville, MD 20705, USA

* To whom correspondence should be addressed. E-mail: mark.tucker{at}ars.usda.gov

Soybean cyst nematode (SCN) is currently the most devastating pathogen of soybean. SCN penetrates the root and migrates toward the central vascular bundle where it establishes a complex multinucleated feeding structure that provides plant-derived nutrients to support the development and growth of the nematode. To identify host genes that play significant roles in SCN development in susceptible roots, RNA from SCN-inoculated and non-inoculated root pieces were hybridized to the Affymetrix soybean genome GeneChips. RNA was collected at 8, 12, and 16 d post-inoculation from root pieces that displayed multiple swollen female SCN and similar root pieces from non-inoculated roots. Branch roots and root tips were trimmed from the root pieces to minimize the amount of RNA contributed by these organs. Of the 35 593 transcripts represented on the GeneChip, approximately 26 500 were expressed in the SCN-colonized root pieces. ANOVA followed by False Discovery Rate analysis indicated that the expression levels of 4616 transcripts changed significantly (Q-value ≤0.05) in response to SCN. In this set of 4616 transcripts, 1404 transcripts increased >2-fold and 739 decreased >2-fold. Of the transcripts to which a function could be assigned, a large proportion was associated with cell wall structure. Other functional categories that included a large number of up-regulated transcripts were defence, metabolism, and histones, and a smaller group of transcripts associated with signal transduction and transcription.

Key words: Affymetrix, cell wall, cyst nematode, False Discovery Rate, GeneChip, Glycine max, Heterodera glycines, histones, plant defence, soybean

Received 23 May 2007; Revised 18 July 2007 Accepted 30 July 2007


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