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Lupins to be fortified for disease resistance

Dr Elaine Gough has joined an established team working on priority lupin diseases to investigate new means of improving efficiencies to deliver disease resistance screening to breeders.
Photo: Evan Collis

Key points

  • A cross-institutional skill set is being brought together to fast-track disease screening and tool development for narrow-leafed lupins
  • New expertise is being added to the team
  • Four priority diseases are to be the focus of this project – phomopsis, anthracnose, cucumber mosaic virus and sclerotinia

The ‘coming of age’ of technologies – together with new recruits – will see a step change in disease resistance screening and development of breeding tools for narrow-leafed lupins.

An ambitious new project is underway drawing together a team of experts in a concerted effort to fortify the resistance of narrow-leafed lupins (NLL) to a suite of diseases.

Historically, good levels of resistance to diseases have been bred into NLL in Western Australia. However, circumstances are driving increased need to invest in NLL development. Given the increased requirement for biological fixed nitrogen in cropping systems, growing markets for plant-based protein and continuing threats from fungal and viral diseases, it is timely to review achievements and deploy new technology to improve the yield stability of NLLs.

To address these issues for NLL, GRDC has invested together with the WA Agricultural Research Collaboration (WAARC) in a major project. It brings together established and new lupin experts from the Western Australia Department of Primary Industries and Regional Development (DPIRD), Murdoch University, Curtin University and Australian Grain Technologies (AGT).

The five-year project will screen and genotype selected recombinant inbred line (RIL) populations and a core set of germplasm selected from cultivars, breeding lines and wild introductions to identify resistance genes to four high priority NLL diseases: phomopsis, cucumber mosaic virus (CMV), anthracnose and sclerotinia.

Dr Darshan Sharma, DPIRD portfolio manager for genetic improvement, says the project is uniquely placed to combine years of NLL germplasm development and disease know-how with new enabling technologies and personnel to provide a step-change in performance for the crop.

“Not only will we be addressing significant industry challenges for NLL, this project also provides the opportunity to build capacity for Western Australia,” Dr Sharma says.

Sharon Westcott is filling the pivotal role of project coordinator liaising between the institutions, while Dr Elaine Gough has joined the team as a plant pathologist from the University of Southern Queensland.

“Elaine brings years of international commercial pathology experience, together with a recently completed PhD focusing on the interactions of nematodes, mycorrhizae and rhizobium in mungbeans.”

They both will be working with teams from the partner organisations that have years of experience with researching pathology and genetics of resistance in NLL and other legume crops. Teams are led by Dr Lars Kamphius at the Centre for Crop and Disease Management and Professor Chengdao Li at Murdoch University.

Dr Gough says she is keen to learn from experienced pathologists while also investigating new techniques and processes to improve efficiencies in disease breeding for NLL.

“It is exciting to join such a strong technical crew to ultimately deliver new NLL varieties to growers faster through developing new phenotyping processes, which will improve the speed and accuracy of disease screening,” she says.

Research approach

The project will develop higher-throughput phenotyping methods, deploying traditional methodologies, artificial intelligence and molecular techniques to provide effective and robust screening tools for breeding companies and researchers.

Genomic selection, modelling tools and genomic data will be used to select resistant lines and develop genetic markers for marker-assisted selection to be able to pyramid resistance genes into elite cultivars.

The outputs from the project will be shared with prebreeders and breeders to reduce the impacts of these diseases on the NLL industry.

New team members Sharon Westcott (centre) and Dr Elaine Gough stand to benefit from years of Geoff Thomas’ NLL pathology experience. Photo: Evan Collis

DPIRD plant pathologist Geoff Thomas says the project is undertaking a stocktake on the progress for developing resistance to four key NLL diseases – phomopsis, anthracnose, CMV and sclerotinia (see BOX).

Phomopsis resistance has been a key target for the breeding program and many varieties currently available have useful levels of resistance in stems or pods. Resistance in stems and pods can be independent and so work in this disease will have to focus on both traits separately.

Improved screening techniques and identification of new sources of resistance will be the focus for stem phomopsis. Developing molecular markers for current resistance genes and looking for new sources of resistance through more efficient screening techniques is the target for phomopsis pod resistance.

“For anthracnose, we have good levels of resistance and it is a matter of identifying new sources and refining resistance for anthracnose in the pods of NLL,” Mr Thomas says.

“CMV, however, is seed-borne and has a wide host range. It takes longer to assess for resistance to this disease as, at present, we need to progress through a complete plant cycle. We also don’t have molecular markers for resistance and do not fully understand the genetics of resistance to the disease.”

Sclerotinia research for disease resistance in NLL is at a very early stage as it is an emerging disease for NLL, so the knowledge base needs to be established.

The project will draw on a diversity set for NLL comprising 500 lines with a core set of 300 drawn from germplasm resources from several regions, such as Russia, Spain and Morocco, together with lines developed in various programs in Australia over the years. Added to this resource will be knowledge from the recently sequenced NLL genome, work supported by GRDC with significant research effort contributed by researchers from Murdoch University.

“The project will be capitalising on the ‘coming of age’ of technology, accessing artificial technology such as drone imaging and new molecular approaches,” Mr Thomas says.

“It will also have synergies with major new GRDC investments such as the National Virology Project (‘Effective virus management in grain crops’) and maintain a working relationship with the Australian NLL breeding company, Australian Grain Technologies.”

“Ultimately, we will be cementing and improving selection and screening processes for NLL disease to deliver improved resistance and tools to breeders to deliver improved NLL varieties to growers faster.”

Status of significant narrow-leafed lupin diseases


The causal agent of phomopsis is the fungus Diaporthe toxica, which produces a mycotoxin as it grows in mature lupin plant stems. The fungus is found in all lupin growing regions. This toxin causes lupinosis in grazing livestock and may even cause animal death (as seen in WA in 2023). Phomopsis can also cause a reduction in crop yield, if infection occurs early in plant growth leading to lodging. Pod infection results in discoloured seeds and shrivelled seeds that can also contain low levels of mycotoxin. Seed discolouration and production of the mycotoxin phomopsin in seeds can significantly impact grain quality and marketability (stock and human food implications).

Cucumber Mosaic Virus

Cucumber mosaic virus (CMV) is a serious disease ofNLL worldwide. CMV is seed-transmitted in NLL with secondary spread by natural aphid transmission. Plants that grow from infected seed are the primary source of inoculum for field epidemics in WA. Recent favourable seasons have seen an increase in CMV infection in lupin seed stocks, particularly in eastern Australia.

Yield losses can reach 60 per cent when all plants in a crop become infected. Losses from CMV infection are greatest when seed with greater than one per cent infection is sown, aphids arrive early and widespread plant infection occurs. The outcome of sowing seed infected with different levels of CMV varies greatly from year to year and site to site.


The causal agent of anthracnose is the fungus Colletotrichum lupini. Anthracnose lesions can form on any part of the plant above ground; however, the characterising symptom is lesions causing twisting and severing of stems, branches and pods. Even improved tolerance varieties can succumb to yield losses of 25 per cent under very high disease pressure, with resistance more effective in stems than pods. In susceptible varieties losses of greater than 50 per cent have been recorded in favourable environments (complete crop loss is possible in worst case situations).


Sclerotinia is an emerging threat to NLL; it infects a range of broadleaf crops, particularly canola. More than 50 per cent of lupin crops surveyed in 2021 and 2022 were infected with sclerotinia across all surveyed port zones in WA, with greatest impact in high and medium-rainfall zones. Greatest within-paddock incidence occurred in the Geraldton and Kwinana North zones. Approximately 50 per cent of field trials in 2021 and 2022 showed a statistically significant yield increase from fungicide application, usually when more than 30 per cent of plants were infected. Yield loss caused by lupin sclerotinia was variable and ranged from four to 23 per cent (average 11 per cent).

Source: DPIRD

More information: Sharon Westcott

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