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

PLoS Pathogens

Louise R. Cooke¹  Eva Randall²  Niklaus J. Grünwald³  David S. Shaw⁴  Paul R. J. Birch⁵  Ingo Hein⁶  Erica M. Goss⁶  Ruairidh A. Bain⁷  Eleanor M. Gilroy⁸  Ricardo F. Oliva⁸  Sophien Kamoun⁸  David E. L. Cooke⁸  Daniel MacLean⁸  Vivianne G. A. A. Vleeshouwers⁸  James W. McNicol⁹  Mathieu A. Pel⁹  Graham J. Etherington⁹  Rhys A. Farrer⁹  Liliana M. Cano⁹  Sylvain Raffaele⁹  Moray C. Taylor^1,10  Kenneth L. Deahl^1,11  Julie N. Squires^1,12  Alison K. Lees^1,12 

[1] Agri-Food and Biosciences Institute, Belfast, United Kingdom;Biomathematics and Statistics Scotland, The James Hutton Institute, Invergowrie, Dundee, United Kingdom;Emerging Pathogens Institute & Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America;Escuela Politecnica del Ejercito, Sangolquí, Ecuador;Food and Environment Research Agency, Sand Hutton, York, United Kingdom;Horticultural Crops Research Laboratory, USDA ARS, Corvallis, Oregon, United States of America;SAC, Edinburgh, United Kingdom;The James Hutton Institute, Invergowrie, Dundee, United Kingdom;The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom;The Sarvari Research Trust, Henfaes Research Centre, Abergwyngregyn, Llanfairfechan, United Kingdom;USDA-ARS/PSI-GIFVL, BARC-West, Beltsville, Maryland, United States of America;Wageningen UR Plant Breeding, Wageningen, The Netherlands

关键词: Potato;    Genomics;    Pathogens;    Plant pathogens;    United Kingdom;    Copy number variation;    Sequence alignment;    Vegetable crops;   

DOI  :  10.1371/journal.ppat.1002940

学科分类：生物科学（综合）

来源: Public Library of Science

【 摘 要 】

Pest and pathogen losses jeopardise global food security and ever since the 19th 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.

【 授权许可】

CC BY