Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens


Soybean (Glycine max (L.) Merr.) is an important crop that provides a sustainable source of protein and oil worldwide. Soybean cyst nematode (Heterodera glycines Ichinohe) is a microscopic roundworm that feeds on the roots of soybean and is a major constraint to soybean production. This nematode causes more than US$1 billion in yield losses annually in the United States alone1, making it the most economically important pathogen on soybean. Although planting of resistant cultivars forms the core management strategy for this pathogen, nothing is known about the nature of resistance. Moreover, the increase in virulent populations of this parasite on most known resistance sources necessitates the development of novel approaches for control. Here we report the map-based cloning of a gene at the Rhg4 (for resistance to Heterodera glycines 4) locus, a major quantitative trait locus contributing to resistance to this pathogen. Mutation analysis, gene silencing and transgenic complementation confirm that the gene confers resistance. The gene encodes a serine hydroxymethyltransferase, an enzyme that is ubiquitous in nature and structurally conserved across kingdoms. The enzyme is responsible for interconversion of serine and glycine and is essential for cellular one-carbon metabolism. Alleles of Rhg4 conferring resistance or susceptibility differ by two genetic polymorphisms that alter a key regulatory property of the enzyme. Our discovery reveals an unprecedented plant resistance mechanism against a pathogen. The mechanistic knowledge of the resistance gene can be readily exploited to improve nematode resistance of soybean, an increasingly important global crop.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type



Prices may be subject to local taxes which are calculated during checkout

Figure 1: Rhg4 positional cloning and functional validation of SHMT by TILLING.
Figure 2: Haplotypes identified at SHMT in 28 soybean lines.
Figure 3: Functional validation of SHMT by VIGS, RNAi and complementation.
Figure 4: Modelled structure and biochemical analysis of SHMT.

Accession codes

Primary accessions


Data deposits

All sequences have been deposited in GenBank/EMBL/DDBJ under the following accession numbers: Forrest SHMT full-length genomic DNA, JQ714083; Essex SHMT full-length genomic DNA, JQ714084; Forrest SHMT cDNA sequence, JQ714080; Essex SHMT cDNA sequence, JQ714079; Forrest SHMT TILLING mutant F6266 sequence, JQ714081; Forrest SHMT TILLING mutant F6756 sequence, JQ714082; Forrest SUB1 cDNA sequence, JQ762395; Essex SUB1 cDNA sequence, JQ62396; Forrest SUB1 promoter sequence, JQ762397; Essex SUB1 promoter sequence, JQ904711.


  1. Koenning, S. R. & Wrather, J. A. Suppression of soybean yield potential in the continental United States from plant diseases estimated from 2006 to 2009. Plant Health Prog. (2010)

  2. Caldwell, B. E., Brim, C. A. & Ross, J. P. Inheritance of resistance of soybeans to the cyst nematode, Heterodera glycines. Agron. J. 52, 635–636 (1960)

    Article  Google Scholar 

  3. Matson, A. L. & Williams, L. F. Evidence of a fourth gene for resistance to the soybean cyst nematode. Crop Sci. 5, 477 (1965)

    Article  Google Scholar 

  4. Concibido, V. C., Diers, B. W. & Arelli, P. R. A decade of QTL mapping for cyst nematode resistance in soybean. Crop Sci. 44, 1121–1131 (2004)

    Article  CAS  Google Scholar 

  5. Meksem, K. et al. ‘Forrest’ resistance to the soybean cyst nematode is bigenic: saturation mapping of the Rhg1 and Rhg4 loci. Theor. Appl. Genet. 103, 710–717 (2001)

    Article  CAS  Google Scholar 

  6. Endo, B. Y. Histological responses of resistant and susceptible soybean varieties, and backcross progeny to entry development of Heterodera glycines. Phytopathology 55, 375–381 (1965)

    CAS  Google Scholar 

  7. Dong, K. & Opperman, C. H. Genetic analysis of parasitism in soybean cyst nematode Heterodera glycines. Genetics 146, 1311–1318 (1997)

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Niblack, T. L., Colgrove, A. L., Colgrove, K. & Bond, J. P. Shift in virulence of soybean cyst nematode is associated with use of resistance from PI 88788. Online. Plant Health Prog. (2008)

  9. Melito, S. et al. A nematode demographics assay in transgenic roots reveals no significant impacts of the Rhg1 locus LRR-Kinase on soybean cyst nematode resistance. BMC Plant Biol. 10, 104 (2010)

    Article  Google Scholar 

  10. Liu, X. et al. Soybean cyst nematode resistance in soybean is independent of the Rhg4 locus LRR-RLK gene. Func. Integr. Gen. 11, 539–549 (2011)

    Article  CAS  Google Scholar 

  11. Cooper, J. L. et al. TILLING to detect induced mutations in soybean. BMC Plant Biol. 8, 9 (2008)

    Article  Google Scholar 

  12. Meksem, K. et al. TILLING: A reverse genetics and a functional genomics tool in soybean. In The handbook of Plant Functional Genomics: Concepts and Protocols (eds Kahl, G. & Meksem, K. ) 251–265 (Wiley, 2008)

    Chapter  Google Scholar 

  13. Hyten, D. et al. Impacts of genetic bottlenecks on soybean genome diversity. Proc. Natl Acad. Sci. USA 103, 16666–16671 (2007)

    Article  ADS  Google Scholar 

  14. Zhang, C. Q., Bradshaw, J. D., Whitham, S. A. & Hill, J. H. The development of an efficient multipurpose Bean pod mottle virus viral vector set for foreign gene expression and RNA silencing. Plant Physiol. 153, 52–65 (2010)

    Article  CAS  Google Scholar 

  15. Kandoth, P. K. et al. The soybean Rhg1 locus for resistance to the soybean cyst nematode Heterodera glycines regulates expression of a large number of stress- and defense-related genes in degenerating feeding cells. Plant Physiol. 155, 1960–1975 (2011)

    Article  CAS  Google Scholar 

  16. Alfadhli, S. & Rathod, P. K. Gene organization of a Plasmodium falciparum serine hydroxymethyltransferase and its functional expression in Escherichia coli. Mol. Biochem. Parasitol. 110, 283–291 (2000)

    Article  CAS  Google Scholar 

  17. Reed, M. C., Lieb, A. & Nijhout, H. F. The biological significance of substrate inhibition: A mechanism with diverse functions. Bioessays 32, 422–429 (2010)

    Article  CAS  Google Scholar 

  18. Skibola, C. F. et al. Polymorphisms in the thymidylate synthase and serine hydroxymethyltransferase genes and risk of adult acute lymphocytic leukemia. Blood 99, 3786–3791 (2002)

    Article  CAS  Google Scholar 

  19. Lim, U. et al. Polymorphisms in cytoplasmic serine hydroxymethyltransferase and methylenetetrahydrofolate reductase affect the risk of cardiovascular disease in men. J. Nutr. 135, 1989–1994 (2005)

    Article  CAS  Google Scholar 

  20. Heil, S. G. et al. Is mutated serine hydroxymethyltransferase (SHMT) involved in the etiology of neural tube defects? Mol. Genet. Metab. 73, 164–172 (2001)

    Article  CAS  Google Scholar 

  21. Kim, Y. I. Role of folate in colon cancer development and progression. J. Nutr. 133, 3731S–3739S (2003)

    Article  CAS  Google Scholar 

  22. Ithal, N. et al. Developmental transcript profiling of cyst nematode feeding cells in soybean roots. Mol. Plant Microbe Interact. 20, 510–525 (2007)

    Article  CAS  Google Scholar 

  23. Hofmann, J. et al. Metabolic profiling reveal local and systemic responses of host plants to nematode parasitism. Plant J. 62, 1058–1071 (2010)

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  24. Novakovic, P., Stempak, J. M., Sohn, K.-J. & Kim, J.-I. Effects of folate deficiency on gene expression in the apoptosis and cancer pathways in colon cancer cells. Carcinogenesis 27, 916–924 (2006)

    Article  CAS  Google Scholar 

  25. Bagnyukova, T. V. et al. Induction of oxidative stress and DNA damage in rat brain by a folate/methyl-deficient diet. Brain Res. 1237, 44–51 (2008)

    Article  CAS  Google Scholar 

  26. Šali, A. & Blundell, T. L. Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779–815 (1993)

    Article  Google Scholar 

  27. Zhang, Y., Sun, K. & Roje, S. An HPLC-based fluorometric assay for serine hydroxymetyltransferase. Anal. Biochem. 375, 367–369 (2008)

    Article  CAS  Google Scholar 

  28. Niblack, T. L., Heinz, R. D., Smith, G. S. & Donald, P. A. Distribution, density, and diversity of Heterodera glycines in Missouri. J. Nematol. 25, 880–886 (1993)

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Hartwig, E. F. & Epps, J. M. Registration of ‘Forrest’ soybeans. Crop Sci. 13, 287 (1973)

    Article  Google Scholar 

  30. Smith, T. J. & Camper, H. M. Registration of Essex soybean. Crop Sci. 13, 495 (1973)

    Article  Google Scholar 

  31. Bernard, R. L. & Cremeens, C. R. Registration of ‘Williams 82’ soybean. Crop Sci. 28, 1027–1028 (1988)

    Google Scholar 

  32. Brown, S. et al. A high-throughput automated technique for counting females of Heterodera glycines using a fluorescence-based imaging system. J. Nematol. 42, 201–206 (2010)

    PubMed  PubMed Central  Google Scholar 

  33. Hwang, T. Y. et al. High density integrated linkage map based on SSR markers in soybean. DNA Res. 16, 213–225 (2009)

    Article  CAS  Google Scholar 

  34. Meksem, K. et al. Two large-inset soybean genomic libraries constructed in a binary vector: Applications in chromosome walking and genome wide physical mapping. Theor. Appl. Genet. 101, 747–755 (2000)

    Article  CAS  Google Scholar 

  35. Wang, J. et al. Dual roles for the variable domain in protein trafficking and host-specific recognition of Heterodera glycines CLE effector proteins. New Phytol. 187, 1003–1017 (2010)

    Article  CAS  Google Scholar 

  36. Kumar, P., Henikoff, S. & Ng, P. C. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nature Protocols 4, 1073–1081 (2009)

    Article  CAS  Google Scholar 

  37. Xiao, Y.-L. et al. Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variants. Plant Physiol. 139, 1323–1337 (2005)

    Article  CAS  Google Scholar 

  38. Jefferson, R. A. Assaying chimeric genes in plants: the GUS gene fusion system. Plant Mol. Biol. Rep. 5, 387–405 (1987)

    Article  CAS  Google Scholar 

  39. Stauffer, G. V., Plamann, M. D. & Stauffer, L. T. Construction and expression of hybrid plasmids containing the Escherichia coli glyA gene. Gene 14, 63–72 (1981)

    Article  CAS  Google Scholar 

Download references


We thank X. Yang for technical assistance with soybean hairy root propagation and M. Kroll for proofreading the manuscript. We thank R. Hussey, W. Gassmann, P. Gresshoff, A. Bendahmane, D. Xu and B. McClure for critical reading of the manuscript. We thank K. Sharma and S. Puthur for use of the HPLC facility and technical help. This work was supported by the Illinois-Missouri Biotechnology Alliance (project 2005-3 to M.G.M. and K.M.), United Soybean Board (project 0253 to K.M., S.C. and M.G.M.; project 3253 to K.M. and S.C.; project 2268 to K.M. and M.G.M; project 1251 to J.H. and S.A.W.), USDA-NIFA (grant 2006-35300-17195 to K.M.), the National Science Foundation Plant Genome Research Program (grant 0820642 to S.A.W., J.H., M.G.M. and T.J.B.), the National Science Foundation CAREER Program (DBI-0845196 to D.K.), Missouri Soybean Merchandising Council (project 258 to M.G.M.), Illinois Soybean Association, North Central Soybean Research Program, Iowa Soybean Association, and a Department of Education Graduate Assistance in Areas of National Need (GAANN) Fellowship (to S.D.W.).

Author information

Authors and Affiliations



S.L. and P.K.K. contributed equally as first authors. K.M. and M.G.M. contributed equally as senior authors. S.L. carried out mapping and haplotyping studies. S.L., A.J. and T.E.-M. developed the TILLING population used in this study. S.C. developed two of the RIL populations used in this study. S.L. identified the TILLING mutants and conducted the haplotyping analysis. G.Y. and R.H. carried out SCN phenotyping of all RILs, TILLING mutants, and soybean lines. G.Y. collected leaf tissues for RIL and TILLING studies. P.K.K. collected leaf tissues haplotyping analyses. P.K.K. and S.L. confirmed the mutations, cloned the genes, and conducted sequence analyses. P.K.K., C.Y., R.H. and P.S.J. developed and carried out VIGS assays. P.K.K. conducted RNAi experiments. P.K.K. carried out the promoter analysis. P.K.K. and J.A. carried out the complementation analysis. S.D.W. and D.K. performed the computational analysis. P.K.K. performed the biochemical studies. J.H., S.A.W. and T.J.B. provided materials and advice for VIGS analysis. K.M., M.G.M. and D.K. designed the research, and together with S.L., P.K.K. and S.D.W. wrote the manuscript. All authors reviewed and commented on the manuscript.

Corresponding authors

Correspondence to Melissa G. Mitchum or Khalid Meksem.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Figures

This file contains Supplementary Figures 1–4. (PDF 900 kb)

Supplementary Table 1

This file contains the haplotyping of soybean Pls at the Rhg4 and rhg1 locl. (XLSX 17 kb)

Supplementary Table 2

This file contains details of the primers used in this study. (XLSX 15 kb)

Supplementary Data 1

This file contains data relevant to this study. (TXT 569 kb)

A homology model of the Essex GmSHMT homodimer showing functional annotation of the Forrest polymorphisms.

Shown are each of the GmSHMT monomers with the ligand binding sites and Forrest mutations mapped onto their surface (we note that the contributing parts of the ligand binding sites are not identical between the two monomers). When two ligand binding sites overlap only the colored surface for one of the sites is shown. (MOV 27613 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Liu, S., Kandoth, P., Warren, S. et al. A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens. Nature 492, 256–260 (2012).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing