Late blight caused by Phytophthora infestans greatly constrains potato production. Many Resistance (R) genes were cloned from wild Solanum species and/or introduced into potato cultivars by breeding. However, individual R genes have been overcome by P. infestans evolution; durable resistance remains elusive. We positionally cloned a new R gene, Rpi-amr1, from Solanum americanum, that encodes an NRC helper-dependent CC-NLR protein. Rpi-amr1 confers resistance in potato to all 19 P. infestans isolates tested. Using association genomics and long-read RenSeq, we defined eight additional Rpi-amr1 alleles from different S. americanum and related species. Despite only ~90% identity between Rpi-amr1 proteins, all confer late blight resistance but differentially recognize Avramr1 orthologues and paralogues. We propose that Rpi-amr1 gene family diversity assists detection of diverse paralogues and alleles of the recognized effector, facilitating durable resistance against P. infestans.
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Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors
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Supporting raw reads were deposited in European Nucleotide Archive under project number PRJEB38240. BAC and Rpi-amr1 allele sequences were deposited in GenBank under accession numbers MW345286-95 and MW348763. Detailed accession information is shown in Supplementary Table 7. All the materials in this study are available upon request.
World Food and Agriculture: Statistical Pocketbook 2019 (FAO, 2019).
Saville, A. et al. Fungicide sensitivity of U.S. genotypes of Phytophthora infestans to six oomycete-targeted compounds. Plant Dis. 99, 659–666 (2015).
Malcolmson, J. F. & Black, W. New R genes in Solanum demissum lindl. And their complementary races of Phytophthora infestans (Mont.) de Bary. Euphytica 15, 199–203 (1966).
Park, T.-H. et al. The late blight resistance locus Rpi-bib3 from Solanum bulbocastanum belongs to a major late blight R gene cluster on chromosome 4 of potato. Mol. Plant Microbe Interact. 18, 722–729 (2005).
Huang, S. et al. Comparative genomics enabled the isolation of the R3a late blight resistance gene in potato. Plant J. 42, 251–261 (2005).
Vossen, J. H. et al. The Solanum demissum R8 late blight resistance gene is an Sw-5 homologue that has been deployed worldwide in late blight resistant varieties. Theor. Appl. Genet. 129, 1785–1796 (2016).
Song, J. et al. Gene RB cloned from Solanum bulbocastanum confers broad spectrum resistance to potato late blight. Proc. Natl Acad. Sci. USA 100, 9128–9133 (2003).
van der Vossen, E. A. G. et al. The Rpi-blb2 gene from Solanum bulbocastanum is an Mi-1 gene homologue conferring broad-spectrum late blight resistance in potato. Plant J. 44, 208–222 (2005).
Pel, M. A. et al. Mapping and cloning of late blight resistance genes from Solanum venturii using an interspecific candidate gene approach. Mol. Plant Microbe Interact. 22, 601–615 (2009).
Foster, S. J. et al. Rpi-vnt1.1, a Tm-22 homologue from Solanum venturii, confers resistance to potato late blight. Mol. Plant Microbe Interact. 22, 589–600 (2009).
Jones, J. D. G., Vance, R. E. & Dangl, J. L. Intracellular innate immune surveillance devices in plants and animals. Science 354, aaf6395 (2016).
Wu, C.-H. et al. NLR network mediates immunity to diverse plant pathogens. Proc. Natl Acad. Sci. USA 114, 8113–8118 (2017).
Fry, W. Phytophthora infestans: the plant (and R gene) destroyer. Mol. Plant Pathol. 9, 385–402 (2008).
Jones, J. D. G. & Dangl, J. L. The plant immune system. Nature 444, 323–329 (2006).
Rehmany, A. P. et al. Differential recognition of highly divergent downy mildew avirulence gene alleles by RPP1 resistance genes from two Arabidopsis lines. Plant Cell 17, 1839–1850 (2005).
Vleeshouwers, V. G. A. A. et al. Effector genomics accelerates discovery and functional profiling of potato disease resistance and Phytophthora infestans avirulence genes. PLoS ONE 3, e2875 (2008).
Haas, B. J. et al. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461, 393–398 (2009).
Armstrong, M. R. et al. An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm. Proc. Natl Acad. Sci. USA 102, 7766–7771 (2005).
Stam, R., Silva Arias, G. A. & Tellier, A. Subsets of NLR genes show differential signatures of adaptation during colonization of new habitats. New Phytol. 224, 367–379 (2019).
Van de Weyer, A.-L. et al. A species-wide inventory of NLR genes and alleles in Arabidopsis thaliana. Cell 178, 1260–1272 (2019).
McDowell, J. M. et al. Intragenic recombination and diversifying selection contribute to the evolution of downy mildew resistance at the RPP8 locus of Arabidopsis. Plant Cell 10, 1861–1874 (1998).
Liu, J. et al. Genetic variation and evolution of the Pi9 blast resistance locus in the AA genome Oryza species. J. Plant Biol. 54, 294–302 (2011).
Ellis, J. G., Lawrence, G. J., Luck, J. E. & Dodds, P. N. Identification of regions in alleles of the flax rust resistance gene L that determine differences in gene-for-gene specificity. Plant Cell 11, 495–506 (1999).
Seeholzer, S. et al. Diversity at the Mla powdery mildew resistance locus from cultivated barley reveals sites of positive selection. Mol. Plant Microbe Interact. 23, 497–509 (2010).
Saur, I. M. et al. Multiple pairs of allelic MLA immune receptor-powdery mildew AVRA effectors argue for a direct recognition mechanism. eLife 8, 1957 (2019).
Anderson, C. et al. Genome analysis and avirulence gene cloning using a high-density RADseq linkage map of the flax rust fungus, Melampsora lini. BMC Genomics 17, 667 (2016).
Jupe, F. et al. Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. Plant J. 76, 530–544 (2013).
Thilliez, G. J. A. et al. Pathogen enrichment sequencing (PenSeq) enables population genomic studies in oomycetes. New Phytol. 4, 903 (2018).
Jouet, A. et al. Albugo candida race diversity, ploidy and host-associated microbes revealed using DNA sequence capture on diseased plants in the field. New Phytol. 93, 959 (2018).
Witek, K. et al. Accelerated cloning of a potato late blight-resistance gene using RenSeq and SMRT sequencing. Nat. Biotechnol. 34, 656–660 (2016).
Lin, X. et al. Identification of Avramr1 from Phytophthora infestans using long read and cDNA pathogen-enrichment sequencing (PenSeq). Mol. Plant Pathol. 21, 1502–1512 (2020).
Kamoun, S., van West, P., Vleeshouwers, V. G. A. A., de Groot, K. E. & Govers, F. Resistance of Nicotiana benthamiana to Phytophthora infestans is mediated by the recognition of the elicitor protein INF1. Plant Cell 10, 1413–1425 (1998).
Grund, E., Tremousaygue, D. & Deslandes, L. Plant NLRs with integrated domains: unity makes strength. Plant Physiol. 179, 1227–1235 (2019).
Chen, X. et al. Identification and rapid mapping of a gene conferring broad-spectrum late blight resistance in the diploid potato species Solanum verrucosum through DNA capture technologies. Theor. Appl. Genet. 131, 1287–1297 (2018).
Xu, X. et al. Genome sequence and analysis of the tuber crop potato. Nature 475, 189–195 (2011).
Wu, C.-H. et al. NRC4 gene cluster is not essential for bacterial flagellin-triggered immunity. Plant Physiol. 182, 455–459 (2020).
Adachi, H. et al. An N-terminal motif in NLR immune receptors is functionally conserved across distantly related plant species. eLife 8, 121 (2019).
Colon, L. T. et al. Resistance to potato late blight (Phytophthora infestans (Mont.) de Bary) in Solanum nigrum, S. villosum and their sexual hybrids with S. tuberosum and S. demissum. Euphytica 66, 55–64 (1992).
Lebecka, R. Host–pathogen interaction between Phytophthora infestans and Solanum nigrum, S. villosum, and S. scabrum. Eur. J. Plant Pathol. 120, 233–240 (2007).
Poczai, P. & Hyvönen, J. On the origin of Solanum nigrum: can networks help? Mol. Biol. Rep. 38, 1171–1185 (2010).
Ward, B. J. & van Oosterhout, C. HYBRIDCHECK: software for the rapid detection, visualization and dating of recombinant regions in genome sequence data. Mol. Ecol. Resour. 16, 534–539 (2016).
Vleeshouwers, V. G. A. A. et al. Understanding and exploiting late blight resistance in the age of effectors. Annu. Rev. Phytopathol. 49, 507–531 (2011).
Vleeshouwers, V. G. A. A., van Dooijeweert, W., Govers, F., Kamoun, S. & Colon, L. T. The hypersensitive response is associated with host and nonhost resistance to Phytophthora infestans. Planta 210, 853–864 (2000).
Jones, J. D. G. et al. Elevating crop disease resistance with cloned genes. Philos. Trans. R. Soc. Lond. B 369, 20130087 (2014).
Dodds, P. N. et al. Direct protein interaction underlies gene-for-gene specificity and coevolution of the flax resistance genes and flax rust avirulence genes. Proc. Natl Acad. Sci. USA 103, 8888–8893 (2006).
Jouet, A., McMullan, M. & van Oosterhout, C. The effects of recombination, mutation and selection on the evolution of the Rp1 resistance genes in grasses. Mol. Ecol. 24, 3077–3092 (2015).
Ohta, T. Gene conversion vs point mutation in generating variability at the antigen recognition site of major histocompatibility complex loci. J. Mol. Evol. 41, 115–119 (1995).
Spurgin, L. G. et al. Gene conversion rapidly generates major histocompatibility complex diversity in recently founded bird populations. Mol. Ecol. 20, 5213–5225 (2011).
Huang, J. et al. Phytophthora effectors modulate genome-wide alternative splicing of host mRNAs to reprogram plant immunity. Mol. Plant 13, 1470–1484 (2020).
Sato, S. et al. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485, 635–641 (2012).
Steuernagel, B. et al. NLR-parser: rapid annotation of plant NLR complements. Bioinformatics 10, 1665–1667 (2015).
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).
Stanke, M. & Morgenstern, B. AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res. 33, W465–W467 (2005).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Li, H. et al. The sequence alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Koboldt, D. C. et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22, 568–576 (2012).
Fiume, M., Williams, V., Brook, A. & Bioinformatics, M. B. Savant: genome browser for high-throughput sequencing data. Bioinformatics 25, 1938–1944 (2010).
Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-seq. Bioinformatics 25, 1105–1111 (2009).
Kumar, A., Taylor, M. A., Arif, S. A. M. & Davies, H. V. Potato plants expressing antisense and sense S-adenosylmethionine decarboxylase (SAMDC) transgenes show altered levels of polyamines and ethylene: antisense plants display abnormal phenotypes. Plant J. 9, 147–158 (1996).
Castel, B. et al. Diverse NLR immune receptors activate defence via the RPW8- NLR NRG1. New Phytol. 222, 966–980 (2019).
Thompson, J. D., Higgins, D. G., Gibson, T. J. & CLUSTAL, W. Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680 (1994).
Kumar, S., Nei, M., Dudley, J. & Tamura, K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief. Bioinform. 9, 299–306 (2008).
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).
Gouy, M., Guindon, S. & Gascuel, O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 27, 221–224 (2009).
Rozas, J. & Sánchez-DelBarrio, J. C. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496–2497 (2009).
Xia, X. DAMBE: a comprehensive software package for data analysis in molecular biology and evolution. Mol. Biol. Evol. 30, 1720–1728 (2013).
Ratmann, O., Lam, H. M. & Boni, M. F. Improved algorithmic complexity for the 3SEQ recombination detection algorithm. Mol. Biol. Evol. 35, 247–251 (2017).
Kent, W. J. BLAT—the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002).
Phanstiel D. H. Sushi: Tools for visualizing genomics data. R package version 1.26.0 (2020).
Champouret, N. et al. Phytophthora infestans isolates lacking class I ipiO variants are virulent on Rpi-blb1 potato. Mol. Plant Microbe Interact. 22, 1535–1545 (2009).
Cooke, D. E. L. et al. Genome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen. PLoS Pathog. 8, e1002940 (2012).
This research was financed from BBSRC grant no. BB/P021646/1 and the Gatsby Charitable Foundation. This research was supported in part by the NBI Computing infrastructure for Science (CiS) group through the provision of a High-Performance Computing Cluster. We would like to thank TSL bioinformatics team, transformation team and horticultural team for their support. We thank Experimental Garden and Genebank of Radboud University (Nijmegen, the Netherlands), IPK Gatersleben (Germany) and S. Knapp (Natural History Museum, London, United Kingdom) for access to S. americanum, S. nigrescens and S. nigrum genetic diversity and G. Kessel, F. Govers and P. Birch for providing P. infestans isolates.
K.W., H.S.K., F.G.J. and J.D.G.J. are named inventors on a patent application (PCT/US2017/066691) pertaining to Rpi-amr1 that was filed by the 2Blades Foundation on behalf of the Sainsbury Laboratory. The other authors declare no competing interests.
Peer review information Nature Plants thanks Erik Andreasson, Marc Ghislain and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Figs. 1–8 and Tables 1–4.
Table 5. Population genetics summary statistics calculated for Rpi-amr1 and Avramr1 homologues. Table 6. Evidence of sequence exchange between Rpi-amr1 orthologues and paralogues from SP2273 using 3SEQ. An exact non-parametric mosaicism statistic algorithm was implemented in 3SEQ; we found statistical evidence of recombination (the null hypothesis of clonal evolution was rejected). Table 7. Accession numbers of all sequencing data in this study.
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Witek, K., Lin, X., Karki, H.S. et al. A complex resistance locus in Solanum americanum recognizes a conserved Phytophthora effector. Nat. Plants 7, 198–208 (2021). https://doi.org/10.1038/s41477-021-00854-9
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