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

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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.

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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.

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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. 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. http://dx.doi.org/10.1094/PHP-2010-1122-01-RS (2010)

  2. 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)

  3. 3

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

  4. 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)

  5. 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)

  6. 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)

  7. 7

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

  8. 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. http://dx.doi.org/10.1094/PHP-2008-0118-01-RS (2008)

  9. 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)

  10. 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)

  11. 11

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

  12. 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)

  13. 13

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

  14. 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)

  15. 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)

  16. 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)

  17. 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)

  18. 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)

  19. 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)

  20. 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)

  21. 21

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

  22. 22

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

  23. 23

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

  24. 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)

  25. 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)

  26. 26

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

  27. 27

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

  28. 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)

  29. 29

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

  30. 30

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

  31. 31

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

  32. 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)

  33. 33

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

  34. 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)

  35. 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)

  36. 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)

  37. 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)

  38. 38

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

  39. 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)

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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

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.

Correspondence to Melissa G. Mitchum or Khalid Meksem.

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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)

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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) doi:10.1038/nature11651

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