Journal Article

Genome Analyses of an Aggressive and Invasive Lineage of the Irish Potato Famine Pathogen

Cano, Liliana M., Gilroy, Eleanor M., Birch, Paul R. J., Farrer, Rhys A., Hein, Ingo, Shaw, David S., Raffaele, Sylvain, Lees, Alison K., Goss, Erica M., Vleeshouwers, Vivianne G. A. A., Cooke, Louise R., Kamoun, Sophien, Taylor, Moray C., Etherington, Graham J., Grünwald, Niklaus J., Randall, Eva, McNicol, James W., Oliva, Ricardo F., Cooke, David E. L., Deahl, Kenneth L., Pel, Mathieu A., Squires, Julie N., Bain, Ruairidh A., MacLean, Daniel

2012

Overview

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.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Agricultural sciences / Biology / clonal lineages / Crop diseases / Crops, Agricultural - microbiology / Development and progression / disease outbreaks / Diseases and pests / DNA Copy Number Variations / expression / Famine / Farming systems / Flowers & plants / Food security / Gene Expression Profiling / genes / Genes, Plant / Genetic aspects / genetic markers / genetic resistance / Genome, Fungal / Genomics / genotypic diversity / Great Britain / Health aspects / host plants / Host-parasite relationships / Host-Pathogen Interactions / Immunity, Innate / immunologic receptors / late blight / Life Sciences / Microbial genetics / microsatellite markers / monitoring / Pathogens / pests / phenotype / Physiological aspects / Phytophthora diseases / Phytophthora infestans / Phytophthora infestans - genetics / Phytophthora infestans - pathogenicity / phytophthora-infestans populations / plant / Plant Diseases - microbiology / Plant genetics / Plant Proteins - genetics / Polymorphism, Genetic / Potatoes / resistance / rxlr effectors / sequence analysis / Sequence Analysis, DNA / Solanum tuberosum - microbiology / Solanum tuberosum subsp. tuberosum / Vegetables / virulence