The origins of crop disease: the curious case of kiwifruit canker

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1 The origins of crop disease: the curious case of kiwifruit canker Paul B Rainey New Zealand Institute for Advanced Study & Allan Wilson Centre, Massey University (Auckland, NZ) Max Planck Institute for Evolutionary Biology (Plön, Germany)

2 Nature is rarely nice Ecological opportunity (the fight for limiting resources)

3 Plant pathogens matter Significant human cost ~20% annual loss to food production Irish potato famine ( ) Wheat stem rust (1999-) Psa on kiwifruit (1984-) Telluride Science Research Center

4 Where do pathogens of crop plants come from? Zoonoses and human disease... Emergence of crop pathogens by sampling from pathogens of wild relatives, vs. host shift Domestication likely provides opportunity for the evolution of virulence (e.g., mono-culture, densely planted fields)

5 Kiwifruit - a recently domesticated crop ~70 species of Actinidia native to China and south east Asia Isabel Fraser (1904) brings seeds from China to Whanganui (40 seedlings) Hayward Wright (1925) selects one seedling and establishes the green flesh A. deliciosa Hayward variety (accounts for 99 % of commercial crop plants) Export of Chinese gooseberries begins in 1959 Links between China and NZ initiated in (Dr Li Lairong) underpin A. chinensis Hort 16A with Plant Variety Rights granted in 1995 Kiwifruit grown in NZ, Italy, France, Chile, Japan, Korea, USA

6 The inevitability of disease Disease (fungal and bacterial) noticed from earliest days of commercial plantings Kiwifruit canker disease first recorded in Japan (1980) (and Hunan, China); Korea (1988); Italy (1992); Italy (2008); Rapid global transmission of Psa-V: Te Puke (2010)

7 Our work... The origins of Psa - The source of Psa and capacity for transmission - The nature of the source population Factors shaping Psa evolution - Past and present The bases of disease - Causes of virulence AIMS TO UNDERSTAND To underpin containment, control, and the breeding of Psa resistant kiwifruit Opportunity to understand the emergence of crop disease concomitant with domestication of the host

8 A first chunk recently published...

9 And noticed...

10 What did we do? Collected Psa from NZ and around the world spanning the earliest outbreaks of disease to the latest Isolated chromosomes and sequenced them Developed methods of analysis and performed analyses Examined growth of Psa strains in kiwifruit

11 Independent samplings from a source population 15,329 SNPs and 463,396 invariant sites 1,000 SNPs

12 Recombination & notion of source population

13 SNP analysis of the 2008 global outbreak The genome of Psa-V is comprised of ~6.5 million nucleotides (pieces of information) Strains of Psa-V differ by a very small number of nucleotides, with one exceptional region Because there are so few differences it is impossible to say anything conclusive about who gave Psa-V to whom

14 A star-like phylogeny (uninformative) Divergence within last 10 years Most polymorphism among Italian strains

15 Diversity among Italian and Chinese strains

16 Evolution is extraordinary... China, NZ, Italy China, Italy Chile Evolution doesn t stop: we need to understand the local context of evolutionary change (and you can get involved)

17 Smoking gun C-4 transporter enolase C-4 sugars pyruvate C-4 sugars TCA

18 Summary Source population (south east Asia?) Multiple independent samplings from the source population Implications for present and future control Psa-V: too little diversity to allow drawing of conclusions (most diversity in Italy) Numerous genes -- some implicated in the suppression of innate immunity -- that are the focus of genetic analyses and breeding programmes

19 Rainey Lab contribution to Psa Paul Rainey (NZIAS / MBIE) - Population genomics / genetics Honour McCann (MBIE / NZIAS) - Pathology / genetics / meta-genomics / source population Elena Colombi (Zespri) - Genetics Christina Straub (NZIAS) - Community ecology / population genetics Collaborators (P&FR, MPI, Biocentrum, CAREG, UNC, Arizona, Exeter)

20 Thank you Honour McCann 1,2, Erik H. A. Rikkerink 3, Frederic Bertels 1,4, Mark Fiers 5, Ashley Lu 5, Jonathan Rees-George 3, Mark T. Andersen 3, Andrew P. Gleave 3, Bernhard Haubold 6, Mark W. Wohlers 3, David S. Guttman 2, Pauline W. Wang 2, Christina Straub 1, Joel Vanneste 7, Paul B. Rainey 1,6,*,, Matthew D. Templeton 3,8,*, 1 New Zealand Institute for Advanced Study and Allan Wilson Centre, Massey University, Auckland, New Zealand, 2 Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto Canada, 3 The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand, 4 Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland 5 The New Zealand Institute for Plant & Food Research Limited, Lincoln, New Zealand, 6 Max Planck Institute for Evolutionary Biology, Plön, Germany, The New Zealand Institute for Plant & Food Research Limited, Ruakura, Hamilton, New Zealand, 8 School of Biological Sciences, University of Auckland, Auckland, New Zealand. * Joint senior authors.

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