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A pigeonpea gene confers resistance to Asian soybean rust in soybean


Asian soybean rust (ASR), caused by the fungus Phakopsora pachyrhizi, is one of the most economically important crop diseases, but is only treatable with fungicides, which are becoming less effective owing to the emergence of fungicide resistance. There are no commercial soybean cultivars with durable resistance to P. pachyrhizi, and although soybean resistance loci have been mapped, no resistance genes have been cloned. We report the cloning of a P. pachyrhizi resistance gene CcRpp1 (Cajanus cajan Resistance against Phakopsora pachyrhizi 1) from pigeonpea (Cajanus cajan) and show that CcRpp1 confers full resistance to P. pachyrhizi in soybean. Our findings show that legume species related to soybean such as pigeonpea, cowpea, common bean and others could provide a valuable and diverse pool of resistance traits for crop improvement.

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Figure 1: C.cajan accessions display different reactions to P. pachyrhizi field isolates from Brazil.
Figure 2: Characterization of the CcRpp1 locus in four accessions of C. cajan.
Figure 3: Characterization of soybean plants heterologously expressing CcRpp1.

Accession codes

Primary accessions

European Nucleotide Archive


  1. Goellner, K. et al. Phakopsora pachyrhizi, the causal agent of Asian soybean rust. Mol. Plant Pathol. 11, 169–177 (2010).

    Article  CAS  Google Scholar 

  2. Yorinori, J.T. et al. Epidemics of soybean rust (Phakopsora pachyrhizi) in Brazil and Paraguay from 2001 to 2003. Plant Dis. 89, 675–677 (2005).

    Article  CAS  Google Scholar 

  3. Scherm, H., Christianoa, R.S.C., Eskerb, P.D., Del Pontec, E.M. & Godoy, C.V. Quantitative review of fungicide efficacy trials for managing soybean rust in Brazil. Crop Prot. 28, 774–782 (2009).

    Article  CAS  Google Scholar 

  4. Kelly, H.Y. et al. From select agent to an established pathogen: the response to Phakopsora pachyrhizi (soybean rust) in North America. Phytopathology 105, 905–916 (2015).

    Article  Google Scholar 

  5. Reis, E.M., Deuner, E. & Zanatta, M. In vivo sensitivity of Phakopsora pachyrhizi to DMI and QoI fungicides. Summa Phytopathol. 41, 21–24 (2015).

    Article  Google Scholar 

  6. Hyten, D.L. et al. Map location of the Rpp1 locus that confers resistance to soybean rust in soybean. Crop Sci. 47, 837–838 (2007).

    Article  CAS  Google Scholar 

  7. Yu, N. et al. Fine mapping of the Asian soybean rust resistance gene Rpp2 from soybean PI 230970. Theor. Appl. Genet. 128, 387–396 (2015).

    Article  CAS  Google Scholar 

  8. Hyten, D.L. et al. Bulked segregant analysis using the GoldenGate assay to locate the Rpp3 locus that confers resistance to soybean rust in soybean. Crop Sci. 49, 265–271 (2009).

    Article  CAS  Google Scholar 

  9. Silva, D.C.G. et al. Molecular mapping of two loci that confer resistance to Asian rust in soybean. Theor. Appl. Genet. 117, 57–63 (2008).

    Article  CAS  Google Scholar 

  10. Li, S., Smith, J.R., Ray, J.D. & Frederick, R.D. Identification of a new soybean rust resistance gene in PI 567102B. Theor. Appl. Genet. 125, 133–142 (2012).

    Article  CAS  Google Scholar 

  11. Garcia, A. et al. Molecular mapping of soybean rust (Phakopsora pachyrhizi) resistance genes: discovery of a novel locus and alleles. Theor. Appl. Genet. 117, 545–553 (2008).

    Article  CAS  Google Scholar 

  12. Kim, K.S. et al. Molecular mapping of soybean rust resistance in soybean accession PI 561356 and SNP haplotype analysis of the Rpp1 region in diverse germplasm. Theor. Appl. Genet. 125, 1339–1352 (2012).

    Article  CAS  Google Scholar 

  13. Monteros, M.J., Missaoui, A.M., Phillips, D.V., Walker, D.R. & Boerma, H.R. Mapping and confirmation of the 'Hyuuga' red-brown lesion resistance gene for Asian soybean rust. Crop Sci. 47, 829–834 (2007).

    Article  CAS  Google Scholar 

  14. Meyer, J.D. et al. Identification and analyses of candidate genes for rpp4-mediated resistance to Asian soybean rust in soybean. Plant Physiol. 150, 295–307 (2009).

    Article  CAS  Google Scholar 

  15. Akamatsu, H. et al. Pathogenic diversity of soybean rust in Argentina, Brazil, and Paraguay. J. Gen. Plant Pathol. 79, 28–40 (2013).

    Article  Google Scholar 

  16. Paul, C., Hartman, G.L., Marois, J.J., Wright, D.L. & Walker, D.R. First report of Phakopsora pachyrhizi adapting to Soybean genotypes with Rpp1 or Rpp6 rust resistance genes in field plots in the United States. Plant Dis. 97, 1379 (2013).

    Article  CAS  Google Scholar 

  17. Miles, M.R., Frederick, R.D. & Hartman, G.L. Evaluation of soybean germplasm for resistance to Phakopsora pachyrhizi. Plant Health Prog. http://dx.doi:10.1094/PHP-2006-0104-01-RS. (2006).

    Article  Google Scholar 

  18. Langenbach, C. et al. Interspecies gene transfer provides soybean resistance to a fungal pathogen. Plant Biotechnol. J. http://dx.doi.10.1111/pbi.12418 (2015).

  19. Ellis, J. Insights into nonhost disease resistance: can they assist disease control in agriculture? Plant Cell 18, 523–528 (2006).

    Article  CAS  Google Scholar 

  20. Slaminko, T.L., Miles, M.R., Frederick, R.D., Bonde, M.R. & Hartman, G.L. New legume hosts of Phakopsora pachyrhizi based on greenhouse evaluations. Plant Dis. 92, 767–771 (2008).

    Article  CAS  Google Scholar 

  21. Bonde, M.R. et al. Comparative susceptibilities of legume species to infection by Phakopsora pachyrhizi. Plant Dis. 92, 30–36 (2008).

    Article  CAS  Google Scholar 

  22. Ono, Y., Buritica, U.P. & Hennen, J.F. Delimitation of Phakopsora, Physopella and Cerotelium and their species on Leguminosae. Mycol. Res. 96, 825–850 (1992).

    Article  Google Scholar 

  23. Provazi, M., Camargo, L.H.G., Santos, P.M. & Godoy, R. Descrição botânica de linhagens puras selecionadas de guandu. Rev. Bras. Zootec. 36, 328–334 (2007).

    Article  Google Scholar 

  24. Jones, J.D.G. & Dangl, J.L. The plant immune system. Nature 444, 323–329 (2006).

    Article  CAS  Google Scholar 

  25. Dodds, P.N. & Rathjen, J.P. Plant immunity: towards an integrated view of plant-pathogen interactions. Nat. Rev. Genet. 11, 539–548 (2010).

    Article  CAS  Google Scholar 

  26. Allen, R.L. et al. Natural variation reveals key amino acids in a downy mildew effector that alters recognition specificity by an Arabidopsis resistance gene. Mol. Plant Pathol. 9, 511–523 (2008).

    Article  CAS  Google Scholar 

  27. Ravensdale, M., Nemri, A., Thrall, P.H., Ellis, J.G. & Dodds, P.N. Co-evolutionary interactions between host resistance and pathogen effector genes in flax rust disease. Mol. Plant Pathol. 12, 93–102 (2011).

    Article  CAS  Google Scholar 

  28. Gurr, S.J. & Rushton, P.J. Engineering plants with increased disease resistance: what are we going to express? Trends Biotechnol. 23, 275–282 (2005).

    Article  CAS  Google Scholar 

  29. Doyle, J.J. & Luckow, M.A. The rest of the iceberg. Legume diversity and evolution in a phylogenetic context. Plant Physiol. 131, 900–910 (2003).

    Article  CAS  Google Scholar 

  30. Jones, J.D.G. et al. Elevating crop disease resistance with cloned genes. Phil. Trans. R. Soc. B 369, 20130087 (2014).

    Article  Google Scholar 

  31. Meyers, B.C., Kozik, A., Griego, A., Kuang, H. & Michelmore, R.W. Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15, 809–834 (2003).

    Article  CAS  Google Scholar 

  32. Ameline-Torregrosa, C. et al. Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula. Plant Physiol. 146, 5–21 (2008).

    Article  CAS  Google Scholar 

  33. Zhang, Z., Schwartz, S., Wagner, L. & Miller, W. A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 7, 203–214 (2000).

    Article  CAS  Google Scholar 

  34. Simpson, J.T. et al. ABySS: a parallel assembler for short read sequence data. Genome Res. 19, 1117–1123 (2009).

    Article  CAS  Google Scholar 

  35. Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851–1858 (2008).

    Article  CAS  Google Scholar 

  36. Neff, M.M., Turk, E. & Kalishman, M. Web-based primer design for single nucleotide polymorphism analysis. Trends Genet. 18, 613–615 (2002).

    Article  CAS  Google Scholar 

  37. Schmutz, J. et al. Genome sequence of the palaeopolyploid soybean. Nature 463, 178–183 (2010).

    Article  CAS  Google Scholar 

  38. Varshney, R.K. et al. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat. Biotechnol. 30, 83–89 (2012).

    Article  CAS  Google Scholar 

  39. Varshney, R.K. et al. Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.). Mol. Breed. 26, 393–408 (2010).

    Article  CAS  Google Scholar 

  40. Gordon, D. Viewing and editing assembled sequences using consed. Curr. Protoc. Bioinformatics 2, 11.2 (2004).

    Google Scholar 

  41. Gordon, D., Desmarais, C. & Green, P. Automated finishing with autofinish. Genome Res. 11, 614–625 (2001).

    Article  CAS  Google Scholar 

  42. Gordon, D., Abajian, C. & Green, P. Consed: a graphical tool for sequence finishing. Genome Res. 8, 195–202 (1998).

    Article  CAS  Google Scholar 

  43. Koren, S. et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat. Biotechnol. 30, 693–700 (2012).

    Article  CAS  Google Scholar 

  44. Chin, C.-S. et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563–569 (2013).

    Article  CAS  Google Scholar 

  45. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    Article  CAS  Google Scholar 

  46. Milne, I. et al. Using Tablet for visual exploration of second-generation sequencing data. Brief. Bioinform. 14, 193–202 (2013).

    Article  CAS  Google Scholar 

  47. Kearse, M. et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649 (2012).

    Article  Google Scholar 

  48. Langenbach, C., Campe, R., Schaffrath, U., Goellner, K. & Conrath, U. UDP-glucosyltransferase UGT84A2/BRT1 is required for Arabidopsis nonhost resistance to the Asian soybean rust pathogen Phakopsora pachyrhizi. New Phytol. 198, 536–545 (2013).

    Article  CAS  Google Scholar 

  49. Xia, B.S. et al. Nucleotide sequence of a soybean (Glycine max L. Merr.) ubiquitin gene. Plant Physiol. 104, 805–806 (1994).

    Article  CAS  Google Scholar 

  50. Li, Z. et al. Site-specific integration of transgenes in soybean via recombinase-mediated DNA cassette exchange. Plant Physiol. 151, 1087–1095 (2009).

    Article  CAS  Google Scholar 

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This research was supported by grants from the 2Blades Foundation to The Sainsbury Laboratory and the Universidade Federal de Viçosa. 2Blades support was funded in part by DuPont-Pioneer. We wish to thank R. Godoy for providing the seeds of the C. cajan accessions used in this work. Work performed by D.R.C. and J.B. was supported by NSF award DBI 0605251. Next-generation and BAC sequencing was financed by the 2Blades Foundation. We thank G. Etherington and C. Schudoma for bioinformatics support, J. Pike for assisting in the preparation of the Solexa sequencing libraries, S. Perkins and the JIC horticultural team for excellent plant care, and the TSL support team for media preparation. We thank the DuPont Pioneer Soybean Transformation group for generating CcRpp1 transgenic events and the Controlled Environment group for growth, maintenance and seed advancement of transgenic material. We thank N. Penido, E. Feitosa Araújo and T. Castro Silva for excellent technical support during the high-resolution genotyping screenings and E.S. Mizubuti for helping with drawing Figure 1b. We thank D. Da Silva Toledo and L. Carlos Costa for plant care at UFV. We thank J. Pacheco Badel for implanting and curating a searchable seed database to support our genetic studies. We thank Y. Yamaoka for kindly providing the Japanese isolate T1-4. We acknowledge D. Horvath, M. Moscou and B. Staskawicz for many helpful discussions.

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Authors and Affiliations



C.G.K., G.A.G., S.R.N., B.d.V.A.M., G.T., J.C.d.O., G.R., S.M., L.P., K.B., E.J., G.I., G.T. and S.H.B. performed research. D.R.C., J.B., C.B., B.S. and D.M. contributed bioinformatic tools. C.G.K., S.H.B., B.S., G.R., G.J.R., K.E.B., D.R.C., B.B.H.W., J.D.G.J., H.P.v.E. and E.W. analyzed the data. E.W., J.D.G.J., S.H.B., K.E.B., B.B.H.W., B.S., D.R.C., G.J.R., G.R., C.B. and G.W. edited the manuscript. C.G.K. and H.P.v.E. wrote the paper. K.E.B., G.W., E.W., B.B.H.W., H.P.v.E., J.D.G.J. and S.H.B. directed aspects of the project.

Corresponding author

Correspondence to H Peter van Esse.

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Competing interests

A patent application covering this work has been filed. 2Blades Foundation support was funded in part by DuPont-Pioneer.

Integrated supplementary information

Supplementary Figure 1 Fine-mapping of the CcRpp1 locus in the Cajanus cajan accession G119-99

(a) Physical and genetic map interval for the CcRpp1 locus based on the C. cajan reference genome scaffold (variety “Asha”). (b) Gain and loss of functions key recombinants closing the CcRpp1 genetic interval.

Supplementary Figure 2 Southern blot analyses to verify BAC clone integrity and NB-LRR copy number

(a) Southern blot of BglII- and HindIII-digested DNA of BAC 6G on the identified NB-LRR genes (NB 1-4) and, as a control, digested genomic DNA from the resistant parent G119-99. (b) Southern blot of HindIII- digested DNA of BACs 3F, 6G and the BAC clone obtained from DNA isolated from the resistant parent G59-95. The biotin labelled probe was designed on the region coding for the so-called “P-loop”, a highly variable structural feature present in NB-LRR proteins. The gene coding for CcRpp1 is indicated in bold.

Supplementary Figure 3 Visualization of RNAseq reads aligned to the four NB-LRR candidate genes NB-1, -2, -3 and -4.

(a) RNAseq reads from the resistant parent G119-99 aligned against the CcRpp1 locus sequence of 205,344 bp. (b) Close-up of the NB-LRR genes -1 to -4 paired-end read coverage.

Supplementary Figure 4 CcRpp1 expressing plants are not more resistant against another fungal plant pathogen

Disease score on CcRpp1 expressing plants homozygous for the transgene compared with segregating null plants when challenged with Fusarium virguliforme. Each dot represents a technical replicate consisting of 4-5 plants; different colours indicate different biological replicates; different symbols indicate technical replicates. Blue error bars indicate non-parametric (bootstrapped) limited 95% confidence interval of the mean. (see Supplementary Files 8-10 for details on the statistic analyses and figure generation).

Supplementary Figure 5 Expression of CcRpp1 does not impact basic agronomic traits

(a) Null segregants compared to plants expressing CcRpp1 at 8 weeks after germination. (b) Canopy area*of null segregants and plants homozygous for the CcRpp1 transgene (event CcRpp1 7.1) (c) Germination rate plotted against the expected germination rate. Numbers below zero indicate a lower than expected germination rate. Blue error bars indicate non-parametric (bootstrapped) limited 95% confidence interval of the mean. (see Supplementary Files 11-16 for details on the statistic analyses and figure generation). *Surface area determined with ImageJ 1.48a.

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Supplementary Figures 1–5 and Supplementary Tables 1–6 (PDF 1215 kb)

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Kawashima, C., Guimarães, G., Nogueira, S. et al. A pigeonpea gene confers resistance to Asian soybean rust in soybean. Nat Biotechnol 34, 661–665 (2016).

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