BLACKLEG AND SOFT ROT OF POTATO IN FINLAND: MORE THAN A DECADE OF MONITORING AND CHARACTERIZATIONS OF THE ETIOLOGY AND DISEASE OUTBREAKS

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Elmer Curtis Lee
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Docent in Plant Pathology, University of Helsinki Senior Research Scientist,

1 BLACKLEG AND SOFT ROT OF POTATO IN FINLAND: MORE THAN A DECADE OF MONITORING AND CHARACTERIZATIONS OF THE ETIOLOGY AND DISEASE OUTBREAKS Yeshitila Degefu Docent in Plant Pathology, University of Helsinki Senior Research Scientist, Natural Resources Institute Finland (Luke), Green Technology Unit 1 Yeshitila Degefu

2 Outline o Blackleg and soft rot of potato in Finland- past and present o Dickeya and Pectobacterium species- old and new o Research enabled by tools and resources of genomics (the genomic era) o Characterization of disease outbreaks o Diagnosis and detection, opportunities and challenges o Achievements, prospects and Conclusions 2 Yeshitila Degefu

3 Blackleg and soft rot of potato Symptoms and damage 3 Yeshitila Degefu

4 Disease could occur on field, during transit and in storage Field outbreak Packing,Transit and storage Shop 4 Yeshitila Degefu

5 Blackleg and soft rot bacteria in Finland- A brief HISTORY o Present since many decades under different names o Problem increased rapidly in o A decreased in the 1970s due to developments in disease certification schemes o Once again the disease has become a considerable threat since early Yeshitila Degefu

6 The focus of the work during the last decade o Monitoring and survelance o In seed health testing method 6 Yeshitila Degefu

7 Blackleg Aetiology in Finland Shift from a serotype one species (Pectobacterium atrosepticum) (Harju & Kankila, 1993 to multiple taxa ( Degefu et al. 2009, 2013, Laurila et al. 2010).. Methodological issues!!! 7 Yeshitila Degefu

8 Advances in Methodolgy: Diagnostics in the genomic era Progress in the availabilty of genomic data made in the past decade (genomic era) contributed to wide spread transformation into research enabled by tools and resources of genomics Molecular diagnostics 8 Yeshitila Degefu

9 Pathogen Detection and diagnosis : Empowered by advances in Molecular Biology Blackleg and soft rot identification and diagnosis until 2004 was based on visual inspection and serological methods. Degefu Y. Unpublished 9 Yeshitila Degefu

10 Blackleg Aetiology- Current knowledge A serotype of one species P. atrosepticum (Harju & Kankila, 1993) Current list Pectobacterium atrosepticum Pectobacterium brasiliensis Pectobacterium carotovorum Pectobacterium wasabiae Dickeya solani. Perhaps some unknowns??? Degefu et al., 2009, 2013, Laurila et al. 2010) -Emerging & re.-emerging -(pathogen dynamics) 10 Yeshitila Degefu

Percentage of positive samples Incidence of Dickeya and Pectobacterium i in Finnish seed potato o Dickeya solani was first detected from the autonomous island, Åland, in the South West region between

11 Percentage of positive samples Incidence of Dickeya and Pectobacterium i in Finnish seed potato o Dickeya solani was first detected from the autonomous island, Åland, in the South West region between Finland and Sweden where most of the production of industrial potato and potato chips manufacturing is concentrated. 80,0 70,0 60,0 50,0 40,0 30,0 P. atrosepticum P. carotovorum Dickeya spp o Soon spread to other potato and seed potato growing regions including the High Grade (HG) zone. 20,0 10,0 0, o Became the predominant species causing blackleg during warm seasons (Degefu et al. 2013, Annals of Applied Biology) (Degefu et al J. Phytopathology 157: ) Oulu region Åland 11 Yeshitila Degefu

12 Implification of diversity of causal agents o Blackleg /soft rot - a diseases complex o Diagnostic costs and complexity o Disease occurence, a likely phenomenon (Irrespective of the type of summer warm or cool ) o Blackleg and soft rot- consistent threats o Possible complications in disease management 12 Yeshitila Degefu

13 Dickeya solani: the game changer Severity of blackleg outbreak, direct loss of harvest and losses from down grading of seed lots have increased significantly since the introduction and establishment of Dickeya solani 13 Yeshitila Degefu

temperatures of about 25ᴼC resulted in heavy infection from symptom free

14 Dickeya solani is aggressive and spread rapidly within potato fields The lesson from the Finnish summer of 2015 indicated that 5-7 days with temperatures of about 25ᴼC resulted in heavy infection from symptom free condition, thereby rejection of the fields. (Degefu Y. Unpublished) 14 Yeshitila Degefu

15 Weather determines the species prevalence- species of the year! Degefu et al Ann. Appl. Biol. 162: Yeshitila Degefu

16 Advances in disease diagnostic technology and species characterizations o Methods for parallel detection of patato pathogens MICROARRAYS in theory a method with unlimited multiplexing capability 16 Yeshitila Degefu

17 DETECTION MICROARRAY Degefu et al. (2016). Evaluation of microarray in the detection of major bacterial pathogens of potato from tubers. EPPO Bulletin 46: Yeshitila Degefu

18 For investigations on Specificy and sensitivity of the Microaarays! Degefu et al. (2016). Evaluation of microarrays in the detection of major bacterial pathogens of potato from tubers. EPPO Bulletin 46: Yeshitila Degefu

Species Characterization- Genome Comparison Degefu et al. 2013. Ann Appl Biol 162:231-241 Fig.5.

Patterns of Dickeya reference species and selected strains of a new clade of Dickeya isolated in

Method of cluster analysis: UPGMA, Branch quality: Cophenetic correlation Figure 6.

19 Species Characterization- Genome Comparison Degefu et al Ann Appl Biol 162: Fig.5. REP-PCR analysis. Patterns of Dickeya reference species and selected strains of a new clade of Dickeya isolated in Finland (A). Phylogenetic analysis based on REP-PCR electophoregram made in BioNumerics Software, (B). Method of cluster analysis: UPGMA, Branch quality: Cophenetic correlation Figure 6. Comparison of the PFGE patterns of six strains of Dickeya spp. and tested Dickeya strains isolated in Finland. As a standard Salmonella enterica serotype Braenderup (strain H9812, ATCC) was used. 19 Yeshitila Degefu

20 A decade of monitoring Dickeya and Pectobacterium species in the HG area SUMMARY 1. A functional end user diagnostic laboratory in place for effective monitoring 2. Methods for specific and sensitive detection of Dickeya and Pectobacterium spp. optimized and validated 3. Diagnostic services to seed companies, producers etc at home and abroad provided 4. A cheklist of old and new Dickeya and Pectobacterium species found in Finland made available 5. Characterization of outbreaks, role and incidence of the different species conducted, large collection of Finnish strains maintained and genome comparisons and species characterization of Finnish collections of D. solani carried out 6. Dissemination of knowledge through publications in international journals, professional news letters, lectures, both in national and international workshops and conferences, field days, etc. And consultations to producers and agricultural advisory services (ProAgria) etc. 7. Increased Dickeya and Pectobacterium awareness among producers, risk evaluation and informed decision support system created. 8. Active participation in European joint partneships 9. Problem areas for future investigations identified. 20 Yeshitila Degefu

21 Take home message o Start Healthy- Test for latent infection and use Disease free seeds o Remain Healthy (Vigilant)- monitoring and disease survelance 21 Yeshitila Degefu

22 Acknowledgements Special thanks to Ewa Lojkowska, Marta Potrykus, Małgorzata Golanowska, University of Gdansk and my own Team at the Natural Resources Institute Finland ( Luke) Oulu 22 Yeshitila Degefu

23 Why potato matters? MANY REASONS TO POTATOES More potassium than three bananas!!! Blue congo 100 g Three glasses of red wine 400 g of strawberries 23 Yeshitila Degefu

24 Thank you for your attention 24 Yeshitila Degefu

Volume XII, Number 17 September 18, Silver Scurf and Black Dot Development on Fresh Marketed Russet Norkotah Tubers in Storage

Research & Extension for the Potato Industry of Idaho, Oregon, & Washington Andrew Jensen, Editor. ajensen@potatoes.com; 509-760-4859 www.nwpotatoresearch.com Volume XII, Number 17 September 18, 2012 Silver