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Title: Genome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen

Author
item COOKE, DAVID - The James Hutton Institute
item CANO, LILIANA - Sainsbury Laboratory
item RAFFAELE, SYLVAIN - Sainsbury Laboratory
item BAIN, RUAIRIDH - Scottish Agricultural College
item COOKE, LOUISE - Agri-Food And Biosciences Institute
item THERINGTON, GRAHAM - Sainsbury Laboratory
item Deahl, Kenneth
item FARRER, RHYS - Sainsbury Laboratory
item GILROY, ELEANOR - The James Hutton Institute
item Goss, Erica
item Grunwald, Niklaus - Nik
item HEIN, INGO - The James Hutton Institute
item MACLEAN, DANIEL - Sainsbury Laboratory
item MCNICOL, JIM - The James Hutton Institute
item RANDALL, EVA - The James Hutton Institute
item OLIVA, RICARDO - The Army Polytechnic School
item PEL, MATHIEU - Wageningen Agricultural University
item SHAW, DAVID - Sarvari Research Trust
item SQUIRES, JULIE - The James Hutton Institute
item TAYLOR, MORAY - The Food And Environment Research Agency
item VLEESHOUWERS, VIVIANNE - Wageningen Agricultural University
item BIRCH, PAUL - University Of Dundee
item LEES, ALISON - The James Hutton Institute
item KAMOUN, SOPHIEN - Sainsbury Laboratory

Submitted to: PLoS Pathogens
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/17/2012
Publication Date: N/A
Citation: N/A

Interpretive Summary: Late blight remains the most destructive disease to affect the potato worldwide and causes significant financial damage to the industry in terms of crop loss and chemical control costs. Joint research in the US and Europe has demonstrated the value of using markers and disease attributes to monitor pathogen diversity. This research has revealed a significant change in the pathogen population in Ireland and the UK. This manuscript describes the findings that populations of the potato late blight pathogen have changed dramatically in recent decades owing to pathogen migration that has occurred on a global scale and the ability of the pathogen to overcome previously effective forms of plant host resistance. Continued work in this area will greatly benefit the consumer and the potato farmer.

Technical Abstract: Pest and pathogen losses pose a serious threat to global food security and ever since the 19th century Irish famine, potato late blight has exemplified this threat1,2. The causal oomycete pathogen, Phytophthora infestans, undergoes major population shifts in agricultural systems via the successive emergence and migration of asexual lineages3. The phenotypic and genotypic bases of these selective sweeps are largely unknown but management strategies need to adapt to reflect the changing pathogen population. Here, we used molecular markers4 to document the emergence of a lineage, termed 13_A2, in the European P. infestans population, and its rapid displacement of other lineages to exceed 75% of the pathogen population across Great Britain in less than three years. We show that isolates of the 13_A2 lineage are among the most aggressive on cultivated potatoes, outcompete other aggressive lineages in the field, and overcome previously effective forms of plant host resistance. Genome analyses of a 13_A2 isolate revealed extensive genetic and expression polymorphisms particularly in effector genes. Copy number variations, gene gains and losses, amino-acid replacements and changes in expression patterns of disease effector genes within the 13_A2 isolate likely contribute to enhanced virulence and aggressiveness to drive this population displacement. Importantly, 13_A2 isolates carry intact and in planta induced Avrblb1, Avrblb2 and Avrvnt1 effector genes that induce resistance in potato lines carrying the corresponding R immune receptor genes Rpi-blb1, Rpi-blb2, and Rpi-vnt1.1. These findings facilitate a strategy for deploying genetic resistance to mitigate the impact of the 13_A2 lineage and illustrate how pathogen population monitoring combined with genome analysis informs the management of devastating disease epidemics.