ARABLE: Monitoring for emerging threats to UK OSR crops posed by novel variants and fungicide resistant strains of fungal pathogens
Lead Research Organisation:
Rothamsted Research
Department Name: Protecting Crops and the Environment
Abstract
Oilseed rape (OSR) crops in the UK are threatened by two main fungal diseases: light leaf spot (LLS) caused by Pyrenopeziza brassicae (lineage 1) and Phoma caused by Plenodomus lingam / Plenodomus biglobosus. In the UK, Phoma and LLS each cause >£100M in crop losses despite costly fungicide applications (primarily DeMethylation Inhibitors (DMIs)). New variants and fungicide resistant strains of these pathogens have been reported recently from other geographic regions and may threaten UK OSR crops should they emerge there.
The first P. brassicae risk relates to decreased fungicide sensitivity, where DMI resistance was found in European P. brassicae populations including the UK. Decreased DMI sensitivity is mediated by alterations in the CYP51 gene, including point mutations in the coding region (G460S or S508T) and inserts in the upstream control (promoter) region. Fungal isolates from Ireland with a G460S+S508T genotype had a much reduced DMI sensitivity. Therefore, work is required to monitor for changes in the fungicide sensitivity status of UK P. brassicae populations and screen for the G460S+S508T genotype.
An additional risk from P. brassicae has recently identified a lineage 2 variant responsible for chlorotic leaf spot outbreaks in the US Pacific northwest. There lineage 2 appears to be a recent introduction that has undergone rapid invasive spread. This damaging variant now threatens adjacent Canadian OSR production and could affect European OSR production, particularly given the unknown implications of lineages 1 and 2 coming into contact and increasing use of brassica cover crop seed produced in the US Pacific northwest. Research is thus required to monitor the lineages currently present in UK pathogen populations.
For Phoma, one threat to UK OSR comes from fungicide resistant P. lingam / P. biglobosus. Until 2015, in vitro testing had shown both pathogens to be sensitive to DMIs. However, recent work has shown DMI resistance in 15-24% of the P. lingam population in Australia and the Czech Republic. Such resistance is associated with inserts in the CYP51 promoter region. Whether DMI resistance has also emerged in P. lingam, and also P. biglobosus, pathogen populations in the UK requires investigation. A further Phoma threat relates to the recent discovery in Europe of the P. biglobosus 'canadensis' subclade. Prior to this only the P. biglobosus 'brassicae' subclade had been reported in Europe. There is increasing evidence that the P. biglobosus subclade variants pose different risks to OSR health, that may require distinct disease management strategies. Data is thus required on the pathogen population structure of subclades present in the UK OSR crops.
In the proposed project, we will work with our collaborator, BASF who will collect OSR leaves from field trials showing Phoma (Jan 23) and LLS (Mar 23) symptoms. At least ten trials will be sampled from the UK and potentially some additional EU locations. Samples will be sent to RRes for fungal isolation, with the aim of collecting 50-100 isolates each of P. brassicae, P. lingam, and P. biglobosus . These isolates will be deposited into the RRes and OREGIN culture collections. Isolate DNA will be extracted, and P. brassicae strains lineage typed via lineage-specific amplification. Plenodomus isolates will be typed using species-specific DNA primers specific for P. lingam / P. biglobosus. For P. biglobosus isolates, the internal transcribed spacer (ITS) region will be sequenced to determine subclade (subgroup) identities. Isolates of all three species will be screened in vitro for sensitivity to fungicides, including DMIs (prothioconazole-desthio, mefentrifluconazole) and a QoI (pyraclostrobin), and for the least DMI sensitive isolates, CYP51 will be examined molecularly to explore possible resistance mechanisms.
The first P. brassicae risk relates to decreased fungicide sensitivity, where DMI resistance was found in European P. brassicae populations including the UK. Decreased DMI sensitivity is mediated by alterations in the CYP51 gene, including point mutations in the coding region (G460S or S508T) and inserts in the upstream control (promoter) region. Fungal isolates from Ireland with a G460S+S508T genotype had a much reduced DMI sensitivity. Therefore, work is required to monitor for changes in the fungicide sensitivity status of UK P. brassicae populations and screen for the G460S+S508T genotype.
An additional risk from P. brassicae has recently identified a lineage 2 variant responsible for chlorotic leaf spot outbreaks in the US Pacific northwest. There lineage 2 appears to be a recent introduction that has undergone rapid invasive spread. This damaging variant now threatens adjacent Canadian OSR production and could affect European OSR production, particularly given the unknown implications of lineages 1 and 2 coming into contact and increasing use of brassica cover crop seed produced in the US Pacific northwest. Research is thus required to monitor the lineages currently present in UK pathogen populations.
For Phoma, one threat to UK OSR comes from fungicide resistant P. lingam / P. biglobosus. Until 2015, in vitro testing had shown both pathogens to be sensitive to DMIs. However, recent work has shown DMI resistance in 15-24% of the P. lingam population in Australia and the Czech Republic. Such resistance is associated with inserts in the CYP51 promoter region. Whether DMI resistance has also emerged in P. lingam, and also P. biglobosus, pathogen populations in the UK requires investigation. A further Phoma threat relates to the recent discovery in Europe of the P. biglobosus 'canadensis' subclade. Prior to this only the P. biglobosus 'brassicae' subclade had been reported in Europe. There is increasing evidence that the P. biglobosus subclade variants pose different risks to OSR health, that may require distinct disease management strategies. Data is thus required on the pathogen population structure of subclades present in the UK OSR crops.
In the proposed project, we will work with our collaborator, BASF who will collect OSR leaves from field trials showing Phoma (Jan 23) and LLS (Mar 23) symptoms. At least ten trials will be sampled from the UK and potentially some additional EU locations. Samples will be sent to RRes for fungal isolation, with the aim of collecting 50-100 isolates each of P. brassicae, P. lingam, and P. biglobosus . These isolates will be deposited into the RRes and OREGIN culture collections. Isolate DNA will be extracted, and P. brassicae strains lineage typed via lineage-specific amplification. Plenodomus isolates will be typed using species-specific DNA primers specific for P. lingam / P. biglobosus. For P. biglobosus isolates, the internal transcribed spacer (ITS) region will be sequenced to determine subclade (subgroup) identities. Isolates of all three species will be screened in vitro for sensitivity to fungicides, including DMIs (prothioconazole-desthio, mefentrifluconazole) and a QoI (pyraclostrobin), and for the least DMI sensitive isolates, CYP51 will be examined molecularly to explore possible resistance mechanisms.
Technical Summary
Oilseed rape (OSR) and vegetable brassicas are economically important crops grown for food and energy throughout the world. UK OSR yields are under constant pressure from abiotic and biotic threats, the latter including fungal pathogens responsible for Light Leaf Spot (Pyrenopeziza brassicae) and Phoma (Plenodomus lingam and Plenodomus biglobosus). In the UK, each disease causes >£100M in crop losses despite costly fungicides applications (mainly DeMethylation Inhibitors (DMIs)). Novel genetic variants and fungicide resistant strains of these pathogens are emerging in different geographic regions of the world and should they emerge in other regions could threaten international (and UK) OSR crops. For P. brassicae, threats include increasingly fungicide resistant strains particularly to DMIs, plus the recently described lineage 2 variant responsible for disease outbreaks in the USA. For Plenodomus spp., threats include the emergence of strains resistant to DMI fungicides such as has recently been reported in Australian and Czech Republic P. lingam populations, and also from the new P. biglobosus subclade 'canadensis' variant recently identified in Europe (in the UK). In the proposed project, OSR samples with LLS and Phoma will be collected by the industrial partner (BASF) from trials mainly throughout the UK, but also from Ireland and Denmark. New collections of all three pathogens will be established at Rres. DNA will be extracted from isolates and screened via PCR and/or sequencing to monitor for new pathogen variants. Isolates will also be tested for sensitivity to fungicides including DMIs to investigate possible emergence of fungicide resistance, with representative isolates examined molecularly to characterise any underpinning resistance mechanisms. This project will enable early detection of emerging pathogen threats that will inform both disease and resistance management strategies to contribute towards UK and international OSR security.
