Host Genetic Resistance in : A Valuable Tool for the Integrated Management of the Fungal Pathogen .

Management of plant disease in agro-ecosystems ideally relies on a combination of host genetic resistance, chemical control, and cultural practices. Growers increasingly rely on chemical and genetic options, but their relative benefits in disease control, yield, and economic outcomes are rarely quantified. We explore this relationship for blackleg crown canker disease (caused by ), a major biotic constraint limiting canola production globally.

The ilv2 gene, encoding acetolactate synthase for branched chain amino acid biosynthesis, is required for plant pathogenicity by Leptosphaeria maculans.

Background: Control of blackleg disease of canola caused by the fungus Leptosphaeria maculans relies on strategies such as the inhibition of growth with fungicides. However, other chemicals are used during canola cultivation, including fertilizers and herbicides. There is widespread use of herbicides that target the acetolactate synthase (ALS) enzyme involved in branched chain amino acid synthesis and low levels of these amino acids within leaves of Brassica species.

Deep amplicon sequencing reveals extensive allelic diversity in the erg11/CYP51 promoter and allows multi-population DMI fungicide resistance monitoring in the canola pathogen Leptosphaeria maculans.

Continued use of fungicides provides a strong selection pressure towards strains with mutations to render these chemicals less effective. Previous research has shown that resistance to the demethylation inhibitor (DMI) fungicides, which target ergosterol synthesis, in the canola pathogen Leptosphaeria maculans has emerged in Australia and Europe. The change in fungicide sensitivity of individual isolates was found to be due to DNA insertions into the promoter of the erg11/CYP51 DMI target gene.

Identification of candidate genes for resistance against in .

Utilising resistance () genes, such as , against , the causal agent of blackleg in canola (), could help manage the disease in the field and increase crop yield. Here we present a genome wide association study (GWAS) in to identify candidate genes. Disease phenotyping of 104 genotypes revealed 30 resistant and 74 susceptible lines.

Molecular Interactions Between and Species.

Canola is an important oilseed crop, providing food, feed, and fuel around the world. However, blackleg disease, caused by the ascomycete , causes significant yield losses annually. With the recent advances in genomic technologies, the understanding of the interaction has rapidly increased, with numerous and genes cloned, setting this system up as a model organism for studying plant-pathogen associations.

Independent breakdown events of the Brassica napus Rlm7 resistance gene including via the off-target impact of a dual-specificity avirulence interaction.

Protection of many crops is achieved through the use of genetic resistance. Leptosphaeria maculans, the causal agent of blackleg disease of Brassica napus, has emerged as a model for understanding gene-for-gene interactions that occur between plants and pathogens. Whilst many of the characterized avirulence effector genes interact with a single resistance gene in the host, the AvrLm4-7 avirulence gene is recognized by two resistance genes, Rlm4 and Rlm7.

A conserved ZnCys transcription factor, identified in a spontaneous mutant from in vitro passaging, is involved in pathogenicity of the blackleg fungus Leptosphaeria maculans.

Continuous passaging in vitro can lead to the accumulation of changes in DNA sequence that potentially affect the properties of microbes, making them different from the original isolates. The identification of such genetic alterations is rare in fungi. A set of insertional mutants in the plant pathogenic fungus Leptosphaeria maculans, all derived from the same transformation experiment, had independent Agrobacterium T-DNA insertions and reduced pathogenicity on canola (Brassica napus).

Sterol Demethylation Inhibitor Fungicide Resistance in is Caused by Modifications in the Regulatory Region of .

Blackleg is a worldwide disease of canola (), caused by a complex of fungal species in the genus , that impacts canola production and seed quality. Demethylation inhibitor (DMI) fungicides that target sterol 14α-demethylase are an integral part of disease control. Here, we report six DMI-resistant isolates of and two different types of genetic modification related to the resistance.

Biotechnological potential of engineering pathogen effector proteins for use in plant disease management.

A key component in the management of many diseases of crops is the use of plant disease resistance genes. However, the discovery and then sequence identification of these plant genes is challenging, whereas the characterization of the molecules that they recognize, the effector/avirulence products in pathogens, is often considerably more straight forward. Effectors are small proteins secreted by pathogens that can play major roles in modulating a plant's defense against attack.

A New Subclade of Identified from .

Blackleg (Phoma stem canker) of crucifers is a globally important disease caused by the ascomycete species complex comprising of and . Six blackleg isolates recovered from cv. Mizspoona in the Willamette Valley of Oregon were characterized as based on standard pathogenicity tests and molecular phylogenetic analysis.

Analysis of Repeat Induced Point (RIP) Mutations in Indicates Variability in the RIP Process Between Fungal Species.

Gene duplication contributes to evolutionary potential, yet many duplications in a genome arise from the activity of "selfish" genetic elements such as transposable elements. Fungi have a number of mechanisms by which they limit the expansion of transposons, including Repeat Induced Point mutation (RIP). RIP has been best characterized in the Sordariomycete , wherein duplicated DNA regions are recognized after cell fusion, but before nuclear fusion during the sexual cycle, and then mutated.

Spontaneous and CRISPR/Cas9-induced mutation of the osmosensor histidine kinase of the canola pathogen .

Background: The dicarboximide fungicide iprodione has been used to combat blackleg disease of canola (), caused by the fungus . For example, in Australia the fungicide was used in the late 1990s but is no longer registered for use against blackleg disease, and therefore the impact of iprodione on has not been investigated.

Results: Resistance to iprodione emerged spontaneously under in vitro conditions at high frequency.

Identification of isolates of the plant pathogen Leptosphaeria maculans with resistance to the triazole fungicide fluquinconazole using a novel In Planta assay.

Leptosphaeria maculans is the major pathogen of canola (oilseed rape, Brassica napus) worldwide. In Australia, the use of azole fungicides has contributed to the 50-fold increase in canola production in the last 25 years. However, extensive application of fungicides sets the stage for the selection of fungal populations with resistance.

One gene-one name: the AvrLmJ1 avirulence gene of Leptosphaeria maculans is AvrLm5.

Leptosphaeria maculans, the causal agent of blackleg disease, interacts with Brassica napus (oilseed rape, canola) and other Brassica hosts in a gene-for-gene manner. The avirulence gene AvrLmJ1 has been cloned previously and shown to interact with an unidentified Brassica juncea resistance gene. In this study, we show that the AvrLmJ1 gene maps to the same position as the AvrLm5 locus.

A Large Family of AvrLm6-like Genes in the Apple and Pear Scab Pathogens, Venturia inaequalis and Venturia pirina.

Venturia inaequalis and V. pirina are Dothideomycete fungi that cause apple scab and pear scab disease, respectively. Whole genome sequencing of V.

Evolution of virulence in fungal plant pathogens: exploiting fungal genomics to control plant disease.

The propensity of a fungal pathogen to evolve virulence depends on features of its biology (e.g. mode of reproduction) and of its genome (e.

Next-generation genome sequencing can be used to rapidly characterise sequences flanking T-DNA insertions in random insertional mutants of .

Background: Banks of mutants with random insertions of T-DNA from are often used in forward genetics approaches to identify phenotypes of interest. Upon identification of mutants of interest, the flanking sequences of the inserted T-DNA must be identified so that the mutated gene can be characterised. However, for many fungi, this task is not trivial as widely used PCR-based methods such as thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR) are not successful.

Gene loss in the fungal canola pathogen Leptosphaeria maculans.

Recent comparisons of the increasing number of genome sequences have revealed that variation in gene content is considerably more prevalent than previously thought. This variation is likely to have a pronounced effect on phenotypic diversity and represents a crucial target for the assessment of genomic diversity. Leptosphaeria maculans, a causative agent of phoma stem canker, is the most devastating fungal pathogen of Brassica napus (oilseed rape/canola).

Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens.

Background: Many plant-pathogenic fungi have a tendency towards genome size expansion, mostly driven by increasing content of transposable elements (TEs). Through comparative and evolutionary genomics, five members of the Leptosphaeria maculans-Leptosphaeria biglobosa species complex (class Dothideomycetes, order Pleosporales), having different host ranges and pathogenic abilities towards cruciferous plants, were studied to infer the role of TEs on genome shaping, speciation, and on the rise of better adapted pathogens.

Results: L.

Mitochondrial microsatellite markers for the Australian ectomycorrhizal fungus Laccaria sp. A (Hydnangiaceae).

Premise Of The Study: Microsatellite loci were developed for the ectomycorrhizal fungus Laccaria sp. A to investigate the population genetic structure of this fungal symbiont across its fragmented distribution in southeastern Australia. •

Methods And Results: A partial genome sequence from an individual collection of Laccaria sp.

Genomes and transcriptomes of partners in plant-fungal-interactions between canola (Brassica napus) and two Leptosphaeria species.

Leptosphaeria maculans 'brassicae' is a damaging fungal pathogen of canola (Brassica napus), causing lesions on cotyledons and leaves, and cankers on the lower stem. A related species, L. biglobosa 'canadensis', colonises cotyledons but causes few stem cankers.

An avirulence gene, AvrLmJ1, from the blackleg fungus, Leptosphaeria maculans, confers avirulence to Brassica juncea cultivars.

The fungus Leptosphaeria maculans causes blackleg of Brassica species. Here, we report the mapping and subsequent cloning of an avirulence gene from L. maculans.

Multigene sequence data reveal morphologically cryptic phylogenetic species within the genus Laccaria in southern Australia.

Laccaria (Hydnangiaceae, Agaricales, Basidiomycota) is one of the more intensively studied ectomycorrhizal genera; however, species boundaries within Laccaria and the closely related Hydnangium and Podohydnangium in Australia have not yet been examined with molecular sequence data. Based on morphological characters, eight native species of Laccaria are currently recognized in Australia, as well as three Hydnangium species and the monotypic Podohydnangium australe. Sequences of the internal transcribed spacer region of nuclear rDNA (ITS), RNA polymerase beta subunit II (rpb2) and translation elongation factor 1 alpha (tef-1α) were generated from 77 collections of Laccaria, Hydnangium and Podohydnangium from Australia.

Fungal pathogenicity genes in the age of 'omics'.

The identification of the fungal genes essential for disease underpins the development of disease control strategies. Improved technologies for gene identification and functional analyses, as well as a plethora of sequenced fungal genomes, have led to the characterization of hundreds of genes, denoted as pathogenicity genes, which are required by fungi to cause disease. We describe recent technologies applied to characterize the fungal genes involved in disease and focus on some genes that are likely to attract continuing research activity.

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations.

Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi are pathogens or mutualists and are model systems to analyse effector genes and their mechanisms of diversification.