Evolution of linked avirulence effectors in Leptosphaeria maculans is affected by genomic environment and exposure to resistance genes in host plants.

Angela P. Van de Wouw,Bruce A. McDonald,Patrick C. Brunner,James K. Hane,Richard P. Oliver,Anton J. Cozijnsen,Barbara J. Howlett

doi:10.1371/journal.ppat.1001180

Angela P. Van de Wouw, Bruce A. McDonald + Show 5 more

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https://doi.org/10.1371/journal.ppat.1001180

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Abstract

Brassica napus (canola) cultivars and isolates of the blackleg fungus, Leptosphaeria maculans interact in a ‘gene for gene’ manner whereby plant resistance (R) genes are complementary to pathogen avirulence (Avr) genes. Avirulence genes encode proteins that belong to a class of pathogen molecules known as effectors, which includes small secreted proteins that play a role in disease. In Australia in 2003 canola cultivars with the Rlm1 resistance gene suffered a breakdown of disease resistance, resulting in severe yield losses. This was associated with a large increase in the frequency of virulence alleles of the complementary avirulence gene, AvrLm1, in fungal populations. Surprisingly, the frequency of virulence alleles of AvrLm6 (complementary to Rlm6) also increased dramatically, even though the cultivars did not contain Rlm6. In the L. maculans genome, AvrLm1 and AvrLm6 are linked along with five other genes in a region interspersed with transposable elements that have been degenerated by Repeat-Induced Point (RIP) mutations. Analyses of 295 Australian isolates showed deletions, RIP mutations and/or non-RIP derived amino acid substitutions in the predicted proteins encoded by these seven genes. The degree of RIP mutations within single copy sequences in this region was proportional to their proximity to the degenerated transposable elements. The RIP alleles were monophyletic and were present only in isolates collected after resistance conferred by Rlm1 broke down, whereas deletion alleles belonged to several polyphyletic lineages and were present before and after the resistance breakdown. Thus, genomic environment and exposure to resistance genes in B. napus has affected the evolution of these linked avirulence genes in L. maculans.

Highlights

The fungus Leptosphaeria maculans causes blackleg and is the major disease of Brassica napus worldwide [1]
The fungus Leptosphaeria maculans causes blackleg, the major disease of canola worldwide. Populations of this fungus rapidly adapt to selection pressures such as the extensive sowing of canola with particular disease resistance genes
In 2000, cultivars with major gene resistance, termed ‘sylvestris’ resistance, were released commercially and grown extensively in some areas of Australia. These cultivars were derived from a synthetic B. napus line produced by crossing the two progenitor species, B. oleracea subsp. alboglabra and an accession of B. rapa subsp. sylvestris that had a high level of resistance to L. maculans [14]

Summary

Introduction

The fungus Leptosphaeria maculans causes blackleg (phoma stem canker) and is the major disease of Brassica napus (canola) worldwide [1]. The major source of inoculum is wind-borne ascospores, which are released from sexual fruiting bodies on infected stubble (crop residue) of previous crops and can be transmitted several kilometres. This fungus has a ‘gene for gene’ interaction with its host (canola) such that pathogen avirulence alleles render the pathogen unable to attack host genotypes with the corresponding resistance genes [2]. Twelve genes conferring resistance to L. maculans (Rlm, LepR1-3) have been identified from Brassica species [3,4] Nine of these genes have been mapped but none have yet been cloned [5,6]. AvrLm6 and AvrLm4-7 encode SSPs with six and eight cysteine residues, respectively, whilst the AvrLm1 protein, which is a SSP, has only one cysteine [8,9,10]

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