Pathogenomics & Disease Resistance

Kostya leads the Pathogenomics & Disease Resistance group at the Crop Science Centre and is Head of Plant Pathology at NIAB where he leads strategic, applied, and commercial research encompassing biology, detection, surveillance, and management of diseases of field crops.

Kostya’s overall research interest is to understand how pathogens cause disease on plants and how plants resist pathogens at the mechanistic and molecular level. The group focuses on understanding the mechanisms of virulence in fungal and oomycete pathogens that cause diseases of global importance in wheat and pulse crops (broad and common beans, peas) such as Septoria tritici blotch, rusts, and downy mildews as well as elucidate the genetic basis of host resistance and leverage this knowledge to developing sustainable solutions for disease control in crops.

Research areas

Role of microbial effectors in plant-pathogen interactions

The ability of pathogens to cause disease in plants is enabled through the secretion of effector proteins. Pathogens deliver effectors either inside plant cells or outside, in the apoplastic space. Depending on the pathogen, the number of effectors produced during infection can be in the hundreds, indicating importance of these proteins in infections. The primary function of effectors is thought to be to disarm the plant through interfering with recognition by the immune system and induction of defence responses, or by affecting other aspects of host plant metabolism and/or development. Some effectors can be recognised by plant disease resistance (R) genes to initiate defence responses, and in these situations, they are termed avirulence (Avr) effectors.

We are interested in identifing and characterising Avr effectors in fungal rust pathogens of cereal and legume crops, as well as in Zymoseptoria tritici – another globally important fungal pathogen of wheat, with the aim of developing a molecular toolbox for monitoring pathogen populations and identification of any new virulent races. We are also interested in understanding what plant cellular processes are manipulated by the effectors and how effectors achieve the various virulence functions. This will help identify new targets for disease control through conventional breeding or genetic engineering/genome editing approaches.

Host plant resistance to diseases

Pathogens, including fungi, oomycetes, bacteria, and viruses pose major threats to crop plant health and global food security. Fungicides are used extensively to control many crop diseases, often due to lack of durable genetic resistance in crops or knowledge on natural plant immunity. There is an urgent need to develop new strategies for durable disease control through improved crop genetics, and this could be achieved through an improved understanding of the different immunity layers and pathways that plants deploy against pathogens. Plants can recognise pathogens via iterations of the widely described immune systems, namely Pattern-triggered Immunity (PTI) and Effector triggered Immunity (ETI). These usually operate in different cellular compartments and have different mechanisms to provide protection.

We are interested in improving the understanding of intracellular nucleotide-binding site leucine-rich repeat immune receptors (NLRs) in common bean and cell surface located wall-associated receptor-like kinases (WAKs) in wheat, and their role in resistance against biotrophic and hemi-biotrophic fungal pathogens, respectively. We are also interested in identifying and characterising genetically new, improved sources of resistance to fungal and viral pathogens of wheat and legume crops, such as common bean and faba bean. This includes exploration of natural and derived genetic resources such as synthetic hexaploid wheat lines, ancestral species introgression lines, and wild interspecies hybrids.

Antimicrobial resistance

Antimicrobial resistance (AMR) is a growing threat to global health, and the excessive use of antimicrobials in agriculture is a major contributor to its development. Plant pathogenic fungi pose a significant problem for food safety and quality, and with fewer fungicides available due to stricter regulations, the risk of AMR development is increasing. Cereals occupy the largest agricultural area in Europe and most developed countries and, due to high fungicide inputs, production of cereals contributes to evolution of AMR in fungal pathogens causing the most important foliar diseases such as Septoria, Ramularia, net blotch, mildews, and rusts. Moreover, fungicide use in agriculture is considered to be a driving factor in the emergence of resistance to azole fungicides in environmental populations of the opportunistic human pathogenic fungi, such as Aspergillus fumigatus.

We are using traditional, as well as aerobiome-based molecular (DNA based) surveys, to monitor AMR and ecological experiments to map and understand the eco-evolutionary processes driving fungicide resistance in populations of fungal wheat pathogens such as Zymoseptoria tritici and yellow rust as well as in A. fumigatus.

About the group leader

Kostya joined NIAB in 2021 from Rothamsted Research where he has led a variety of projects focused on resistance to viral and fungal diseases in barley and wheat that resulted in several principal scientific discoveries and practical solutions. Prior to that, following a PhD in plant virology, he did his postdoctoral study at the Sainsbury Laboratory, Norwich which resulted in the isolation of potato genes Rx and Gpa2 for resistance to viruses and nematodes and equipped Kostya with an-depth knowledge of plant gene silencing. With this background, Kostya extensively utilises both existing and newly developed plant virus-based expression tools, VIGS and VOX, for rapid gene function analysis in plants and associated pathogens.

Led by

Kostya Kanyuka

Kostya Kanyuka

Head of the Pathogenomics & Disease Resistance group

Other research groups

Ian Henderson

Genetic and Epigenetic Inheritance in Plants

Led by Ian Henderson

The Genetic and Epigenetic Inheritance group investigates plant genome structure, function, and evolution. T

Tally Wright

Crop Quantitative Genetics

Led by Tally Wright

The quantitative genetics research group focuses on how genetic variation between different crop accessions can influence their phenotypes, particularly for traits controlled by many genes.

Johannes Kromdijk

Environmental Plant Physiology

Led by Johannes Kromdijk

This group studies the physiology of photosynthesis and its interactions with environmental drivers such as light, water, temperature and CO2 with the ultimate aim to improve crop productivity and water use efficiency.

Stéphanie Swarbreck

Crop Molecular Physiology

Led by Stéphanie Swarbreck

Crop Molecular Physiology group researches nitrogen responsiveness at the gene, the whole plant and the plot level, in order to discover and select crop varieties with a low nitrogen requirement and well adapted to regenerative agriculture practises.

Phil Howell

Crop Genetic Resources

Led by Phil Howell

Our research group carries out the development and characterisation of existing and new crop genetic resources, drawing on NIAB’s experience in genetics, pre-breeding, field testing and tissue culture.

Ji Zhou

Artificial Intelligence and Data sciences

Led by Ji Zhou

This group combines AI, computer vision, and data analytics with expertise in plant phenotyping, breeding, and agronomy to enhance crop production in the UK and developing countries

Natasha Yelina

Crop breeding technologies

Led by Natasha Yelina

Novel breeding technologies in legume crops to enhance the production of new cultivars adapted to changing climatic conditions, as well as having sustainable yields.

Jeongmin Choi

Crop resilience

Led by Jeongmin Choi

As sessile organisms, plants have evolved sophisticated mechanisms to help cope with environmental stress.

Uta Paszkowski

Cereal symbiosis

Led by Uta Paszkowski

The mutually beneficial arbuscular mycorrhizal (AM) symbiosis is the most widespread association between roots of terrestrial plants and fungi of the Glomeromycota.

Lida Derevnina

Crop pathogen immunity

Led by Lida Derevnina

We aim to functionally characterise the NRC network and determine the molecular basis of NLR network mediated immunity.

Giles Oldroyd

Sustainable crop nutrition

Led by Giles Oldroyd

The availability of sources of nitrogen and phosphorus are major limitations to crop productivity. This is primarily addressed through the application of inorganic fertilisers to augment these limiting nutrients.

Sebastian Eves-van den Akker

Plant-parasitic interactions

Led by Sebastian Eves-van den Akker

Combining genomics and molecular biology to understand fundamental questions in host:parasite biology

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