Genome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen.
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.
The James Hutton Institute, Invergowrie, Dundee, United Kingdom. david.cooke@hutton.ac.uk
David E L
DE
Cooke
Liliana M
LM
Cano
Sylvain
S
Raffaele
Ruairidh A
RA
Bain
Louise R
LR
Cooke
Graham J
GJ
Etherington
Kenneth L
KL
Deahl
Rhys A
RA
Farrer
Eleanor M
EM
Gilroy
Erica M
EM
Goss
Niklaus J
NJ
Grünwald
Ingo
I
Hein
Daniel
D
MacLean
James W
JW
McNicol
Eva
E
Randall
Ricardo F
RF
Oliva
Mathieu A
MA
Pel
David S
DS
Shaw
Julie N
JN
Squires
Moray C
MC
Taylor
Vivianne G A A
VG
Vleeshouwers
Paul R J
PR
Birch
Alison K
AK
Lees
Sophien
S
Kamoun
D018556:Crops, Agricultural / Q000382:microbiology; D056915:DNA Copy Number Variations; D020869:Gene Expression Profiling; D017343:Genes, Plant; D016681:Genome, Fungal; D054884:Host-Pathogen Interactions; D007113:Immunity, Innate; D055750:Phytophthora infestans / Q000235:genetics* / Q000472:pathogenicity*; D010935:Plant Diseases / Q000382:microbiology*; D010940:Plant Proteins / Q000235:genetics; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D011198:Solanum tuberosum / Q000382:microbiology*
D010940:Plant Proteins