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

David E L Cooke (1) , Liliana M Cano (2) , Sylvain Raffaele (2) , Ruairidh A Bain (3) , Louise R Cooke (4) , Graham J Etherington (2) , Kenneth L Deahl (5) , Rhys A Farrer (2) , Eleanor M Gilroy (1) , Erica M Goss (6, 7) , Niklaus J Grünwald (6) , Ingo Hein (1) , Daniel Maclean (2) , James W Mcnicol (8) , Eva Randall (1) , Ricardo F Oliva (2, 9) , Mathieu A Pel (10) , David S Shaw (11) , Julie N Squires (1) , Moray C Taylor (12) , Vivianne G a A Vleeshouwers (10) , Paul R J Birch (1, 13) , Alison K Lees (1) , Sophien Kamoun (2)

1 The James Hutton Institute
2 TSL - The Sainsbury Laboratory [Norwich]
3 SAC
4 Agri-Food and Biosciences Institute
5 PSI-GIFVL, BARC-West
6 Horticultural Crops Research Laboratory
7 Emerging Pathogens Institute & Department of Plant Pathology
8 Biomathematics and Statistics Scotland
9 Escuela Politecnica del Ejercito
10 Plant Breeding
11 The Sarvari Research Trust
12 The Food and Environment Research Agency Sand Hutton
13 Sustainable Livestock Systems, SAC

Pest and pathogen losses jeopardise global food security and ever since the 19(th) century Irish famine, potato late blight has exemplified this threat. The causal oomycete pathogen, Phytophthora infestans, undergoes major population shifts in agricultural systems via the successive emergence and migration of asexual lineages. 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 markers 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 trigger resistance in potato lines carrying the corresponding R immune receptor genes Rpi-blb1, Rpi-blb2, and Rpi-vnt1.1. These findings point towards 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.

Mots clés: potato

Mots clés: analyse génomique; pomme de terre; maladie des plantes

Domaines: Sciences agricoles

David E L Cooke, Liliana M Cano, Sylvain Raffaele, Ruairidh A Bain, Louise R Cooke, et al.. Genome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen. PLoS Pathogens, 2012, 8 (10), ⟨10.1371/journal.ppat.1002940⟩. ⟨hal-01607590⟩