University of Dundee

Dr Ingo Hein

Plant Pathogen Co-evolution
Position: 
Principal Investigator
Affiliation: 
Address: 
University of Dundee at JHI, Errol Road, Invergowrie, Dundee
Full Telephone: 
+44 (0) 01382 568869, int ext
Email: 

Research

My work connects the disciplines of plant pathology and potato genetics. My research is aimed at the fundamental and applied aspects of crop and pathogen genomics as well as genetics to deliver crop protection against biotic threats. I have developed genomic tools to effectively harness and study the naturally occurring diversity of co-evolving plant and pathogen components that determine the outcome of the infection process. This fundamental knowledge is utilised, often with commercial partners, to identify and develop complementary pathogen control mechanisms. My current research is focused on the Solanaceae crop potato and the oomycete pathogen Phytophthora infestans. I am exploring the diversity within the Commonwealth Potato Collection (CPC) held at the James Hutton Institute to identify novel receptors and plant genes targeted by pathogens. The diversity within the interacting potato and P. infestans genes is utilised to address key biological questions including elucidating the function of pathogen effectors and the mechanisms that lead to resistance.

Teaching

2015 – Present   BS42005 Advanced Plant Sciences

2017 – Present   BS32008 Plant Sciences 

2010 – 2013       MRes course: Crops for the future. Modules: Genetics of resistance; Resistance to oomycete pathogens

Publications

  1. Baker K, Stephen G, Strachan S, Armstrong M, Hein I*.(2018) BLASTmap: A Shiny-Based Application to Visualize BLAST Results as Interactive Heat Maps and a Tool to Design Gene-Specific Baits for Bespoke Target Enrichment Sequencing.Methods Mol Biol. 2018;1848:199-206.
  2. Armstrong M.R., Vossen J., Lim T.Y., Hutten R.C.B., Xu J., Strachan S.M., Harrower B., Champouret N., Gilroy E.M. and Hein I.*(2018) Tracking disease resistance deployment in potato breeding by enrichment sequencing. Plant Biotechnol J.doi: 10.1111/pbi.12997. 
  3. Thilliez G.J.A., Armstrong M.R., Lim T.Y., Baker K., Jouet A., Ward B., van Oosterhout C., Jones J.D.G, Huitema E., Birch P.R.J, and Hein I* (2018). Pathogen enrichment sequencing (PenSeq) enables population genomic studies in oomycetes. New Phytologist.DOI:10.1111/nph.15441 
  4. Jouet A., Saunders D.G.O., McMullan M., Ward B., Furzer O., Jupe F., Cevik V., Hein I., Thilliez G.J.A., Holub E., van Oosterhout C., Jones J.D.G(2018) Albugo candida race diversity, ploidy, and host-associated microbes revealed using DNA sequence capture on diseased plants in the field. New Phytologist. DOI:10.1111/nph.15417
  5. He Q., Naqvi S., McLellan H.,  Boevink P.C., Champouret N., Hein I.,  Birch P.R.J. (2018)Plant pathogen effector utilizes host susceptibility factor NRL1 to degrade the immune regulator SWAP70. Proceedings of the National Academy of Sciences. 115 E7834-E7843
  6. Chen X., LewandowskaD., Armstrong M.R., Baker K., Lim T.Y, Bayer M., Harrower B., McLean K., Jupe F., Witek K., Lees A., Jones J.D., Bryan G.J. and Hein I.*(2018)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
  7. Jiang R., Li J., Tian Z., Du J., Armstrong M., Baker K., Lim T.Y, Vossen J., He H., Portal L., Zhou J., Bonierbale M., Hein I*,Lindqvist-Kreuze H., Xie C.(2018)Potato late blight field resistance from QTL dPI09c is conferred by the NB-LRR gene R8. J Exp Bot. 24; 69:1545-1555
  8. Giolai M, Paajanen P, Verweij W, Percival-Alwyn L, Baker D, Witek K, Jupe F, Bryan G, HeinI, JonesJD, Clark MD. (2016)Targeted capture and sequencing of gene-sized DNA molecules. Biotechniques; 1;61:315-322.
  9. Van Weymers, P., Baker K., Chen. X., Harrower B., Cooke D.E.L., Gilroy, E.M., Birch P.R.J., Thilliez G., Lees A.K., Lynott J.S., Armstrong M.R., McKenzie G., Bryan G.J. and Hein I.*(2016) Utilizing ‘Omic’ technologies to identify and prioritize novel sources of resistance to the oomycete pathogen Phytophthora infestans in potato germplasm collections. Front in Plant Science; 7:672. 
  10. Boevink P.C, Wang X., McLellan H., He Q., Naqvi S., Armstrong M.R., Zhang W., Hein I., Gilroy E.M., Tian Z. and Birch P.R.J. (2016)A Phytophthora infestans RXLR effector targets plant PP1c isoforms that promote late blight disease. Nature Communication; 29;7 10311 
  11. Wiesel L., Davis J.L, Milne L., Fernandez V.R., Herold M.B., Middlefell Williams J., Morris J., Hedley P.E., Harrower B., Newton A.C., Birch P.R., Gilroy E.M. and Hein I.*(2015)A transcriptional reference map of defence hormone responses in potato. Scientific Reports;19;5 15229
  12. Destefanis M., Nagy I., Bryan G., McLean K., Hein I., Rigney B., Jones W.J., Griffin D. and Milbourne D. (2015)A disease resistance locus on potato and tomato chromosome 4 exhibits a conserved multipartite structure displaying different rates of evolution in different lineages. BMC Plant Biology;15:255 
  13. Wiesel L., Newton A.C., Elliott I., Booty D., Gilroy E.M., Birch P.R. and Hein I.*(2014) Molecular effects of resistance elicitors from biological origin and their potential for crop protection. Frontiers Plant Science;5:655. doi:10.3389/fpls.2014.00655
  14. Chapman S., Stevens L.J,  Boevink P.C., Engelhardt S., Alexander C.J., Harrower B., Champouret N., McGeachy K., Pauline S M Van Weymers P.S.M, Chen X., Birch P.R.J and Hein I.*(2014) Detection of the virulent form of AVR3a from Phytophthora infestans following artificial evolution of potato resistance gene R3a, PLoS ONE; Vol. 9, No. 10, e110158, 23.10.2014.
  15. Tomcynska I., Jupe F., Hein I., Marczewski W. and Sliwka J. (2014) Hypersensitive response to Potato virus Y in potato cultivar Sarpo Mira is conferred by the Ny-Smira gene located on the long arm of chromosome IX. Molecular Breeding; DOI 10.1007/s11032-014-0050-2
  16. Jupe F., Chen X., Verweij W., Witek K., Jones J.D.G. and Hein I.*(2014) Genomic DNA library preparation for resistance gene enrichment and sequencing (RenSeq) in plants.Methods in Molecular Biology
  17. Jupe F., Witek K., Verweij W., Sliwka J., Pritchard L., Etherington G.J., Maclean D., Cock P.J., Leggett R.M., Bryan G.J., Milne L., Hein I.* and Jones D.J.* (2013)Resistance gene enrichment sequencing (RenSeq) enables re-annotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. The Plant Journal;76, 530-544
  18. Engelhardt S., Boevink C.P., Armstrong M.R., Hein I.and Birch P.R.J(2012) Re-localisation of late blight resistance protein R3a to endosomal compartments is associated with effector recognition and required for the immune response. The Plant Cell 24, 5142-5158
  19. Birch, P.R.J., Bryan, G.J., Fenton, B., Gilroy, E.M., Hein, I., Jones, J.T., Prashar, A., Taylor, M.A., Torrance, L. & Toth, I.K. (2012)Crops that feed the world 8: potato: Are the trends of increased global production sustainable?  Food Security;4, 477-508.
  20. Cooke D.E., Cano L.M., Raffaele S., Bain R.A., Cooke L.R., Etherington G.J., Deahl K.L., Farrer R.A., Gilroy E.M., Goss E.M., Grünwald N.J., Hein I., Maclean D., McNicol J.W., Randall E., Oliva R.F., Pel M.A., Shaw D.S., Squires J.N., Taylor M.C., Vleeshouwers V.G., Birch P.R., Lees A.K. and Kamoun S. (2012) Genome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen. PLoS Pathogen;8:e1002940
  21. Saunders, D., Breen, S., Win., J., Shornack, S., Hein I., Bozkurt, T.O., Champouret, N., Birch, P.R.J., Gilroy, E.Mand Kamoun, S(2012) Host protein BSL1 associates with Phytophthora infestansRXLR effector PiAVR2 and the immune receptor R2 to mediate disease resistance. The Plant Cell;24: 3420-3434.
  22. Jupe F., Pritchard L., Etherington G.J., Mackenzie K., Cock P.J., Wright F., Kumar Sharma, S., Bolser D., Bryan G.J., Jones J.D., and Hein I.* (2012) Identification and localisation of the NB-LRR gene family within the potato genome. BMC Genomics;13:75doi:10.1186/1471-2164-13-75.
  23. Whisson S.C., Avrova A.O., Boevink C.P., Armstrong M.R., Seman Z.A., Hein I., and Birch P.R.J. (2011).Exploiting Knowledge of Pathogen Effectors to Enhance Late Blight Resistance in Potato. Potato Research;54: 325-340. 
  24. Sun X., Gilroy E.M., Chini A., Nurmberg P.L., Hein I., Lacomme C., Birch P.R.J, Hussain A., Yun B.W. and Loake G.J.(2011) ADS1 encodes a MATE-transporter that negatively regulates plant disease resistance. New Phytologist;192:471-82.
  25. Gilroy E.M., Breen S., Whisson S.C., Squires J., Hein I., Kaczmarek M., Turnbull D., Boevink P.C., Lokossou A., Cano L.M., Morales J., Avrova A.O., Pritchard L., Randall E., Lees A., Govers F., van West P., Kamoun S., Vleeshouwers V.G., Cooke D.E., Birch P.R. (2011) Presence/absence, differential expression and sequence polymorphisms between PiAVR2 and PiAVR2-like in Phytophthora infestans determine virulence on R2 plants. New Phytologist;191: 763-776.
  26. Gilroy E.M., Taylor R.M., Hein I., Boevink P., Sadanandom A., Birch P.R (2011) CMPG1-dependent cell death follows perception of diverse pathogen elicitors at the host plasma membrane and is suppressed by Phytophthora infestansRXLR effector AVR3a. New Phytologist;190: 653-666.
  27. Rietman H., Champouret N., Hein I., Niks R. E., Vleeshouwers V. G. A. A. (2010)Plants and oomycetes, an intimate relationship: co-evolutionary principles and impact on agricultural practice. CAB Reviews;58: 1-17.
  28. Bos J.I., Armstrong M.R., Gilroy E.M., Boevink P.C, Hein I.,Taylor R.M, Zhendong T., Engelhardt S., Vetukuri R.R, Harrower B., Dixelius C., Bryan G., Sadanandom A., Whisson S.C., Kamoun S., Birch P.R.(2010)Phytophthora infestans effector AVR3ais essential for virulence and manipulates plant immunity by stabilizing host E3 ligase CMPG1.Proceedings of the National Academy of Sciences; 25:9909-9914.
  29. Hein I., Gilroy E.M., Armstrong M.R. and Birch P.R.J.(2009) The zig-zag-zig in oomycete-plant interactions. Molecular Plant Pathology;10:547-62.
  30. Hein I., Birch P.R.J., Danan S., Lefebvre V., Odeny D.A., Gebhardt C., Trognitz F. and Bryan G.J. (2009) Progress in mapping and cloning qualitative and quantitative resistance againstPhytophthora infestans in potato and its wild relatives. Potato Research;DOI 10.1007/s11540-009-9129-2.
  31. Crampton G.B. Hein I.and Berger K.D. (2009)Salicylic acid confers resistance to a biotrophic rust pathogen, Puccinia substriata in pearl millet, Pennisetum glaucumMolecular Plant Pathology;10:291-304.
  32. Graham J.Hackett C.A., Smith K., Woodhead M., Hein I.and McCallum S.(2009) Mapping QTLs for developmental traits in raspberry from bud break to ripe fruit. Theoretical and Applied Genetics;118:1143-1155.
  33. Bryan G. andHein I.,(2008) Genomic Resources and Tools for Gene Function Analysis in Potato. International Journal of Plant Genomics;2008:216513.
  34. Birch P.R.J., Boevink P.C., Gilroy E.M., Hein I., Pritchard L. and Whisson S.C.(2008) Oomycete RXLReffectors: delivery, functional redundancy, and durable disease resistance. Current Opinion in Plant Biology;11, 373-379.
  35. Song B-K., Hein I., Waugh R., MarshallD., Nadarajah K., Yap S.-J. and Ratnam W.(2008)The 172-kb genomic DNA region of the O. rufipogon yld1.1 locus: comparative sequence analysis with O. sativassp. japonica and O. sativa ssp. indicaFunctional & Integrative Genomics;9, 97-108.
  36. Sharma S.K, Millam S., Hein I., and Bryan G.J. (2008)Cloning and molecular characterisation of a potato SERK gene transcriptionally induced during initiation of somatic embryogenesis.Planta;228, 319-330.
  37. Hein I., McLean K., Chalhoub B., and Bryan G.J (2007)Generation and Screening of a BAC library from a diploid potato clone to unravel durable late blight resistance on linkage group IV.International Journal of Plant Genomics;(2007:51421).
  38. Whisson S.C., Boevink P.C., Moleleki L., Avrova A.O., Morales J.G., Gilroy E.M., Armstrong M.R.,  Grouffaud S., van West P., Chapman S., Hein I., Toth I.K., Pritchard L. and Birch P.R.J. (2007)A translocation signal for delivery of oomycete effector proteins into host plant cells.Nature;450, 115-118.
  39. Gilroy E.M., Hein I.,van der Hoorn R., Boevink P.C., Venter E., McLellan H., Kaffarnik F., Hrubikova K., Shaw J., Holeva M., Lopez E.C., Borras-Hidalgo O., Pritchard L., Loake G.J., Lacomme C. and Birch P.R.J (2007)Involvement of cathepsin B in the plant disease resistance hypersensitive response.The Plant Journal;52, 1-13.
  40. van den Berg N.,  Berger D., Hein I., Birch P., Wingfield and  M., Viljoen A.(2007) Tolerance in banana to Fusarium wilt is associated with early up-regulation of cell wall-strengthening genes in the roots. Molecular Plant Pathology;37, 818-824.
  41. Berger D.K, Crampton B.G., Hein I., Vos W. (2007) Screening of cDNA libraries on glass slide microarrays. Methods in Molecular Biology;382, 177-203.
  42. Avrova A.O., Whisson S.C., Venter E., De Luca S., Hein I., Pritchard L. and Birch P.R.J. (2007) A novel, non-protein coding infection-specific gene family is clustered throughout the genome of Phytophthora infestansMicrobiology;153: 747-759.
  43. van Nugteren I., Hein I.and Berger D.K.(2007)  Development of a virus-induced gene silencing system in pearl millet.  South African Journal of Botany;73: 339-339.
  44. Collazo C., Ramos P.L., Chacón O., Borroto C.J., López Y., Pujol M., Thomma B.P.H.J., Hein I.and Borras O.(2006) Phenotypical and molecular characterization of the Tomato mottle Taino virus - Nicotiana megalosiphon interaction. Physiological and Molecular Plant Pathology;67: 231-236.
  45. Hein I., Barciszewska-Pacak M., Hrubikova K., Williamson S., Dinesen M., Soenderby I.E., Sundar S., Jarmolowski A., Shirasu K. and Lacomme C.(2005) Virus-Induced Gene Silencing-Based Functional Characterization of Genes Associated with Powdery Mildew Resistance in Barley. Plant Physiology;138:2155-2164.
  46. Liu H., Hedley P., Cardle L., Wright K.M., Hein I., Marshall D. and Waugh R.(2005) Characterisation and functional analysis of two barley caleosins expressed during barley caryopsis development. Planta;221:513-522.
  47. Hein I., Williamson S., Russell J. and Powell W.(2005) Isolation of high molecular weight DNA suitable for BAC library construction from woody perennial soft-fruit species. BioTechniques; 38:69-71.
  48. Faivre-Rampant O., Gilroy E.M., Hrubikova K., Hein I., Millam S., Loake G.J., Birch P.R.J. and Taylor M., Lacomme C. (2004) Potato Virus X-Induced Gene Silencing in Leaves and Tubers of Potato. Plant Physiology;134:1308-1316.
  49. van den Berg N., Crampton B.G., Hein I., Birch P.R.J. and Berger D.K.(2004) High-throughput screening of suppression subtractive hybridization cDNA libraries using DNA microarray analysis. BioTechniques;37:818-824.
  50. Hein I., Campbell E.I., Woodhead M., Hedley P.E., Young V., Morris W.L., Ramsay L., Stockhaus J., Lyon G.D., Newton A.C. and Birch P.R.J.(2004) Characterisation of early transcriptional changes involving multiple signalling pathways in the Mla13barley interaction with powdery mildew (Blumeria graminis f. sp. hordei).Planta;218:803-813.
  51. Avrova A.O., Taleb N., Rokka V.-M., Heilbronn J., Campbell E., Hein I.,Gilroy E.M., Cardle L., Bradshaw J.E., Stewart H.E., Jaufeerally-Fakim Y., Loake G. and Birch P.R.J.(2004) Potato oxysterol binding protein and cathepsin B are rapidly up‐regulated in independent defence pathways that distinguish R gene‐mediated and field resistances to Phytophthora infestans. Molecular Plant Pathology;5: 45-56.
  52. Lacomme C., Hrubikova K. and Hein I.  (2003) Enhancement of virus-induced gene silencing through viral-based production of inverted-repeats.The Plant Journal;34:543-553.
  53. Windhovel A., Hein I., Dabrowa R. and Stockhaus J.(2001) Characterization of a novel class of plant homeodomain proteins that bind to the C4 phosphoenolpyruvate carboxylase gene of Flaveria trinerviaPlant Molecular Biology; 45:201-214