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A time-course comparative microarray analysis of an incompatible and compatible response by Glycine max (soybean) to Heterodera glycines (soybean cyst nematode) infection

Planta volume 226, pages 1423–1447 (2007)Cite this article

Abstract

The development of an infection in soybean [Glycine max L. cultivar (cv.) Peking] roots by incompatible (I) and compatible (C) populations of soybean cyst nematode (SCN) (Heterodera glycines) was assayed using an Affymetrix® soybean GeneChip®. This time-course microarray analysis, using 37,744 probe sets, measured transcript abundance during I and C. These analyses reveal that infection by individual I and C H. glycines populations influence the transcription of G. max genes differently. A substantial difference in gene expression is present between I and C at 12 h post infection. Thus, G. max can differentiate between I and C nematode populations even before they have begun to select their feeding sites. The microarray analysis identified genes induced earlier in infection during I than C. MA also identified amplitude differences in transcript abundance between I and C reactions. Some of the probe sets measuring increased transcript levels during I represented no apical meristem (NAM) and WRKY transcription factors as well as NBS-LRR kinases. Later during I, heat shock protein (HSPs) probe sets (i.e. HSP90, HSP70, ClpB/HSP101) measured increased transcript abundance. These results demonstrate that G. max roots respond very differently to the different H. glycines races even before their feeding site selection has occurred. The ability of G. max to engage an I reaction, thus, appears to be dependent on the ability of root cells to recognize the different races of H. glycines because these experiments were conducted in the identical G. max genetic background.

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Abbreviations

EST:

Expressed sequence tag

hpi:

Hours post inoculation

dpi:

Days post inoculation

SCN:

Soybean cyst nematode

J2:

Second stage juvenile

cv.:

Cultivar

I:

Incompatible

C:

Compatible

NAM:

No apical meristem

MA:

Microarray analysis

CUC:

CUP-SHAPED COTYLEDON

NAC:

NAM-ATAF-CUC

HSP:

Heat shock protein

MRS:

Moisture replacement system

KTI:

Kunitz trypsin inhibitor

OPR:

12-Oxophytodienoate reductase

EDS1:

Enhanced disease susceptibility 1

SAG101:

SENESCENCE-ASSOCIATED GENE101

LOX:

Lipoxygenase

NPR1:

Non expressor of PR genes 1

LTP:

Lipid transfer protein

PAD4:

PHYTOALEXIN-DEFICIENT4

PIP1C:

Plasma membrane intrinsic protein 1C

GER:

Germin-like protein

HEL:

Hevein-like protein

FLA6:

Fasciclin-like arabinogalactan-protein

MPA:

Median polish algorithm

RCC1:

Regulator of chromosome condensation

PRR:

Pattern recognition receptors

PAMP:

Pathogen-associated molecular pattern

RKN:

Root knot nematode

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Acknowledgments

The authors thank Dr. David Munroe and Nicole Lum at the Laboratory of Molecular Technology, SAIC-Frederick, National Cancer Institute at Frederick, Frederick, MD 21701, USA for the Affymetrix® array hybridizations and data acquisition. All data, raw and normalized, are stored in the Soybean Genomics and Microarray Database (Alkharouf et al. 2004), available through the web site (http://www.towson.edu/nalkharo/SGMD/SupplementalSites/GmWholeRootIC/). The authors greatly appreciate the continued support provided by the United Soybean Board under grant 5214. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the United States Department of Agriculture. The authors greatly appreciate careful reading and critical comments of the manuscript provided by Dr. Leslie Wanner, United States Department of Agriculture. The authors thank Veronica Martins for careful editing of the manuscript.

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Authors and Affiliations

  1. United States Department of Agriculture, Soybean Genomics and Improvement Laboratory, 10300 Baltimore Ave. Bldg 006, Beltsville, MD, 20705, USA

    Vincent P. Klink, Christopher C. Overall, Margaret H. MacDonald & Benjamin F. Matthews

  2. Department of Bioinformatics and Computational Biology, George Mason University, Manassas, VA, 20110, USA

    Christopher C. Overall

  3. Jess and Mildred Fisher College of Science and Mathematics, Department of Computer and Information Sciences, Towson University, 7800 York Road, Towson, MD, 21252, USA

    Nadim W. Alkharouf

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  1. Vincent P. Klink
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  2. Christopher C. Overall
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  3. Nadim W. Alkharouf
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Correspondence to Vincent P. Klink.

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Vincent P. Klink and Christopher C. Overall have contributed equally to this work.

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Klink, V.P., Overall, C.C., Alkharouf, N.W. et al. 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, 1423–1447 (2007). https://doi.org/10.1007/s00425-007-0581-4

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Keywords

  • Soybean
  • Glycine max
  • Soybean cyst nematode (SCN)
  • Heterodera glycines
  • Microarray
  • Gene expression
  • Plant pathogen
  • Parasite
  • Affymetrix®
  • Microarray