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Protecting Scotland’s crops: disease resistance and pathogen biology

Protecting Scotland’s crops: disease resistance and pathogen biology

  • Plant & Animal Health
  • Plant Disease
  • Crop Improvement
  • 2022-2027
Sustainable Development icon: life on land

Challenges

Scottish agriculture faces significant challenges and opportunities related to changing policy, markets, environment, and technology. More specifically, the agriculture sector needs to maintain and increase profitability by responding to changing market conditions while simultaneously contributing to Scottish Government commitments on greenhouse gas emissions and biodiversity. These objectives must be achieved in an evolving natural environment in which risks, such as increased summer drought, and opportunities, such as increased area of prime agricultural land, are rapidly changing. Underpinning these changes is a need to exploit genetic diversity and accelerate the efficient breeding of crop cultivars adapted to new growing technologies and environments.

The potato and soft fruit industries in Scotland are an economically important part of the agricultural sector. Pathogens and pests, both established and newly emerging, represent major constraints to sustainable crop production. There is a need to develop crops for the future which are more resilient to the changes in climate and require lower high-carbon inputs, such as fertilisers and pesticides. It is important to increase biodiversity by introducing new crops which have increased resilience. Crops with these traits reduce the need for pesticides and thus have a positive environmental impact. Establishing such crops can also extend production seasons, mitigating risk for farmers from sporadic unfavourable growing conditions. Extending the growing season for Scottish soft fruit would also extend the period that fresh locally grown soft fruit would be available for Scottish consumers.

Questions

  • Which existing crops and wild relatives can be utilised to enhance the genetic diversity of crops in Scotland’s land use and biodiversity?
  • What tools and technologies can underpin the genetic improvement of crops relevant to Scotland, including disease resistance and underpinning future farming and land use systems?
  • What are the key interactions of plant pests and pathogens with their hosts for endemic pests and diseases in crops of key relevance for Scotland?

Solutions

This project cuts across the key Scottish crop (potato and soft fruit), to coordinate approaches aimed at mitigating disease threats. Crucial to this research is a detailed molecular understanding of host and pathogen biology and thus the mechanisms that lead to resistance or susceptibility. It is this understanding that will connect germplasm resources with breeding through the development of markers linked to the resistances. We are considering the interactions between microbes, plants, and pathogens in the environment and how these impact disease. Our priorities are the characterisation and mobilisation of durable resistances effective against Potato cyst nematodes (PCN), late blight, and viruses for potatoes, as well as root rot, insects (aphids and two-spotted spider mites) and fungi (botrytis) in soft fruits.

 

Identifying disease resistance in potatoes and soft fruits

We are identifying resistance and tolerance in potatoes and soft fruit crops to a range of key pathogens (Potato: Potato Cyst Nematode (PCN), late blight, and viruses; Soft fruit: root rot causing oomycetes, insects, and fungi) that impact this industry to accelerate resistance breeding. The results are future-proofing potatoes against newly emerging pathogen variations that could potentially threaten deployed resistances.

 

Pathogen biology and effector research in potato and soft fruit

This project is enhancing our understanding of plant resistance mechanisms in potato and soft fruit to develop effective and sustainable control strategies. This covers pathogen biology and effector research. In potatoes, we focus on the penetration of host tissue by late blight and egg hatching in PCN. For raspberries, we are determining the factors that initiate infection from P. Rubi oospores that can be dormant in the soil for many years. This work is relevant to diseases caused by pests and pathogens of other Scottish crops and threats to Scotland’s natural biodiversity and informs disease management strategies.

 

Understanding and enhancing the plant immune system

Sustainable crop production requires attuning the environment (light and light quality, abiotic stresses, and host life cycle) to promote defence are novel aspects. We are exploring how environmental change influences the plant immune system. This includes the identification of beneficial soil microbes for potato protection and the role of beneficial microbes in protecting soft fruit.

 

Disease control options that consider the interaction between crops and the soil

Our previous research revealed that crops grown under sustainably managed soil conditions are less prone to disease compared to those under conventionally managed soils. We are phenotypically assessing disease suppression potential against PCN of microbial antagonists. In raspberry, arbuscular mycorrhizas have been shown to potentially reduce root rot severity. We are examining how these fungi impact disease and other above and below-ground traits.

Project Partners

James Hutton Institute
Underpinning Capacity

Progress

2022 / 2023
2022 / 2023

Identifying disease resistance in potato and soft fruits:

We have screened potato cultivars grown in the UK and have been able to identify the resistance gene complements for several diseases. These findings have already been shared with industry through several stakeholder events. Currently, we are identifying and prioritising novel resistance capacity in the Commonwealth Potato Collection. Ongoing screening of members of a Rubus (more commonly referred to as raspberries and blackberries) association mapping population is taking place to identify members that are tolerant or resistant to naturally occurring pests and diseases. Such a screening is also being undertaken for blueberries with regards to aphids. We have also started to perform hyperspectral imaging on these fruit populations to determine whether there are spectral signatures associated with either resistance or tolerance.

Pathogen biology and effector research in potato and soft fruit:

Progress made with regards to characterising pathogen biology for various microbes include using RNAseq technology on Phytophthora infestans strains deficient in host tissue penetration to identify genes involved during this stage of pathogenesis, determining the conditions required to initiate infection of raspberries by the soil-borne pathogen, Phytophthora rubi and with regards to PCN, we have produce recombinant eggshell annexin protein and are investigating the conditions required for structural analysis. With regards to the effector research aspects, we are mining 'omics' data from P. infestans to identify novel effectors required for infection and then using gene silencing to determine their involvement in infection. At the same time, we are mining 'omics' data of P. rubi and P. fragariae for house-keeping genes, drug targets as well as effectors to design a 'bait' library for enrichment sequencing and have begun the recovery of historic P. rubi isolates from long-term storage. 

Understanding and enhancing the plant immune system:

In the first instance we are trying to ascertain how environmental change influences plant immunity, and to this end have initiated tissue culture of potato plants on which to perform RNAseq for plants that have been treated with white, blue or red light (and that have either been infected with P. infestans or remains uninfected). Secondly, we are studying the effects of plant development and physiology on immune responses. To this end, several genes linked to potato tuber life-cycle phenotypes and abiotic stress resilience that affect plasmodesmatal function, have been identified. Transgenic potato lines focused on abiotic stress resilience are being characterised. We have also set-up Latham and Glen Dee plants to study the role of root architecture on raspberry immunity to root rot. Specifically, we are assessing the role of auxins and inhibitors for their role in plant protection.

Disease control options that consider the interaction between crops and the soil

The first aim of this objective is to identify beneficial soil microbes for potato protection; we have had discussions with colleagues at the James Hutton Institute to identify different soil characteristics that will be used to assess the impact on PCN. The second aim is to determine the role of beneficial microbes in protecting soft fruit; for which we are in discussion with industry with regards to suitable microbes that could confer resistance or tolerance to soft fruit pests or diseases. We have isolated two Trichoderma species to evaluate their effects on three different raspberry cultivars against root rot infection. 

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