a placeholder

Early Stage Researcher Opportunities

Across the CerealPath network, we have 15 Early Stage Researcher opportunities. At this point, applicants are closed and we are in the process or selecting and recruiting candidates. Details of the recruited candidates can be found here.

ESR1: Characterisation of a European stem rust race and identification of its effector complement by mutational genomics GB flag

John Innes Centre

Applications for this position are now closed

Overview

Within the gene discovery and breeding research area, the approach is to identify candidate genes and determine their potential to enhance cereal disease resistance. By the end of the training period, each Early Stage Researcher associated with the research area will have learned how to identify and assess the potential of candidate disease resistance genes.

Objectives

The overarching long-term objective for this project is to identify and exploit PGT effectors as tools in wheat disease resistance breeding. Specifically, the successful candidate will use a novel mutational genomics approach to isolate and characterise PGT effectors.

Research Affiliation and Supervision

This position will be based at the John Innes Centre in the UK and the researcher will be a registered doctoral candidate at the University of East Anglia.

The research project will be carried out under the under the principal supervision of Dr Brande Wulff and Dr Cristobal Uauy.

Secondment Details

Details of the secondment will be posted shortly.

Eligibility

This position is based in the UK, which means that any potential candidates for this position cannot have lived in the UK for more than 12 months out of the 36 months up to the CerealPath Reference Date.

Background

The wheat stem rust fungus Puccinia graminis f.sp. tritici (PGT) is a devastating disease of wheat which has been associated with multiple crop failures and famine. A key to stabilising wheat yields during the Green Revolution was the development of stem rust resistant wheat varieties. In recent years, new supervirulent races have emerged in Africa causing widespread crop failure. Their spread out of Africa is a concern for global food security.

We are pursuing a transgenic approach to control the disease based on pyramiding cloned stem rust resistance (Sr) genes from wild grasses in combination at a single locus in wheat. However, we need to identify the corresponding protein molecules (effectors) in PGT recognised by these Sr genes. Effectors are proteins secreted by the pathogen to subvert the host. In certain host genotypes, plant resistance proteins can recognize these effectors as signatures of invasion, triggering disease resistance and leading to localised host cell death. Therefore, effectors can be used as probes to confirm the individual function of each Sr gene in a stack.

The overarching long-term objective for this project is to identify and exploit PGT effectors as tools in wheat disease resistance breeding. Specifically, the successful candidate will use a novel mutational genomics approach to isolate and characterise PGT effectors.

This PhD will be jointly supervised by scientists in the John Innes Centre and The Genome Analysis Centre (Norwich Research Park), and colleagues at the National Institute of Agricultural Botany (Cambridge). The PhD will provide excellent training in phytopathology, molecular plant biology, genomics, and bioinformatics in a world-renowned environment for academic and research excellence.

ESR2: Genomic prediction of Fusarium head blight resistance in adapted bread/durum wheat germplasm AT flag

Universitaet fuer Bodenkultur Wien

Applications for this position are now closed.

Overview

Resistance to Fusarium head blight (FHB) in wheat is governed by multiple loci, many of which have small individual effects. Within the gene discovery and breeding research area, the approach on the one hand is to identify candidate genes and determine their potential to enhance cereal disease resistance, and on the other hand to develop tools for use in breeding. With the advent of modern molecular fingerprinting tools it became feasible to derive genome-wide predictions for complex phenotypes, such as FHB resistance.Each Early Stage Researcher associated with this research area will learn how assess the potential of candidate disease resistance genes. ESR2 will learn in addition how to develop and refine genome-wide prediction tools for polygenic FHB resistance in wheat. ESR2 will combine high-level expertise in statistical genetics with phytopathology and breeding. ESR2 is expected to show a strong interest in statistical genetics, plant breeding and disease resistance. Pre-knowledge in biometrical data analysis of large data sets particularly using the R statistical language is of advantage.

Objectives

The principal objective of this project is to train ESR2 to determine the genetic architecture of Fusarium resistance using genome-wide high-density DNA markers and field-based phenotypic data obtained on advanced wheat breeding lines. The work involves: field testing and field phenotyping of several 100 wheat lines during three seasons, statistical analysis of field observation data, DNA preparation from all lines, DNA fingerprinting of all lines using SNP markers, data management of field data and genetic fingerprinting data, bio-statistical analysis of phenotypic and genomic data for development, refinement and validation of genome wide predictions of Fusarium resistance.

Research Affiliation and Supervision

This position will be based at Universitaet fuer Bodenkultur Wien and the candidate will be a registered doctoral candidate at Universitaet fuer Bodenkultur Wien.

Potential candidates should familiarise themselves with the admissions criteria for doctoral studies at BOKU.

The research project will be carried out under the under the principal supervision of Professor Hermann Burstmayr, with input from Dr Ewen Mullins, Dr Olivier Robert and Professor Beat Keller.

Secondment Details

This project will involve a research secondment of 2 months at Florimond-Desprez, the purpose of which is to provide training on practical wheat breeding activities, training on implementation of genomic data in a real breeding project, training on wheat breeding.

Eligibility Criteria

This position is based in Austria, which means that any potential candidates for this position cannot have lived in the Austria for more than 12 months out of the 36 months up to the CerealPath Reference Date.

Background

Hermann Buerstmayr (BOKU) has previously worked extensively to identify genetic loci that contribute to wheat resistance to Fusarium head blight disease. The fine mapping of these to shorter intervals would reduce any negative effects of genetic linkage and, under his direction, this is the goal of ESR2. ESR2 will use a combination of crossing and molecular marker analysis and the expertise and facilities of BOKU, Florimond-Desprez and Teagasc. Using the experience gained in this process, ESR2 will develop genomic predictive functions for selection in wheat and consequently assess the economic value of genomic selection and genomic prediction.

ESR3: Development of molecular markers for Fusarium head blight resistance breeding IE flag

University College Dublin

Applications for this position are now closed

Overview

Within the gene discover and breeding research area, the approach is to identify candidate genes and determine their potential to enhance cereal disease resistance. By the end of the training period, each Early Stage Researcher associated with the research area will have learned how to identify and assess the potential of candidate disease resistance genes.

Objectives

The principal objectives of this project are to train ESR3 in the skills necessary to expedite the deployment of FHB disease resistance in wheat and barley.

Research Affiliation and Supervision

This position will be based in University College Dublin and the candidate will be a registered doctoral candidate at University College Dublin.

Candidates interested in this position should look at the materials regarding entry into doctoral programmes at University College Dublin.

The research project will be carried out under the under the principal supervision of Professor Fiona Doohan, with input from Dr Sebastian Praud, Dr Simon Berry and Professor Beat Keller.

Secondment Details

This project will involve a research secondment of 11 months at Biogemma, the purpose of which is to identify polymorphisms and markers for candidate resistance genes in wheat breeding and elite germplasms.

Eligibility Criteria

This position is based in the Republic of Ireland, which means that any potential candidates for this position cannot have lived in the Republic of Ireland for more than 12 months out of the 36 months up to the CerealPath Reference Date.

Background

ESR3 will explore the field potential of a cohort of previously identified candidate disease resistance genes (note that all also assess trade-off effects of genes and thus link to the trade off and pathogen evolution research area).

Fiona Doohan (UCD) previously identified genes that positively contribute to resistance to Fusarium head blight disease. Directed by Prof. Doohan, in collaboration with BGA and using a combination of molecular biology, bioinformatics and marker-assisted selection expertise in-house and at UCD, ESR3 will determine if natural allelic variation within these candidate genes/gene promoters contributes to wheat resistance to this disease. Concurrently, using a combination of genetic engineering technology and plant pathology studies, they will determine if candidate genes have negative trade-off effects on either other diseases or plant vigour when overexpressed in wheat/the model monocot Brachypodium. Brachypodium is frequently used a model monocot for wheat because of its small sequenced genome and its relatively short generation time.

ESR4: Identification of resistance genes to take-all and Fusarium root rot in wheat GB flag

John Innes Centre

Applications for this position are now closed

Overview

Within the gene discover and breeding research area, the approach is to identify candidate genes and determine their potential to enhance cereal disease resistance. By the end of the training period, each Early Stage Researcher associated with the research area will have learned how to identify and assess the potential of candidate disease resistance genes.

Objectives

The principal objective of this project is to train ESR4 in the skills necessary to identify take-all and root rot disease resistance genes for the wheat breeding industry and bioactive products that can be used as seed treatments for the control of root diseases.

Research Supervision and Affiliation

This project will be based at the John Innes Centre and the candidate will be a registered doctoral candidate at the University of East Anglia.

The project will be undertaken under the principal supervision of Dr Paul Nicholson, Dr Patrick Ward, , Dr Angela Feechan and Professor Beat Keller.

Secondment Details

This position will involve a research secondment of 2 months in Envirotech, the purpose of which is to test the bioactive products against root diseases of wheat.

Eligibility Criteria

This position is based in the UK, which means that any potential candidates for this position cannot have lived in the UK for more than 12 months out of the 36 months up to the CerealPath Reference Date.

Background

ESR4 will explore the field potential of a cohort of previously identified candidate disease resistance genes (note that all also assess trade-off effects of genes and thus link to WP10).

Paul Nicholson (JIC) has used Brachypodium as a model for cereal diseases, and by screening a library of T-DNA insertion mutants, he has recently identified candidate genes that contribute to take-all and Fusarium root rot resistance. Directed by Paul Nicholson, and benefiting from expertise and resources at JIC, ESR4 will use a bioinformatics approach to identify wheat TILLING lines carrying mutations in the homologs of these candidate disease resistance genes. By studying the disease response and phenotype of these mutants and their backcrossed derivatives (backcrossed to parents to reduce background mutations), they will determine the potential of the genes to enhance resistance to Fusarium root rot and will study their effect, if any, on plant phenotype. ESR4 will also benefit from the industrial supervision and experience of Envirotech, where they will determine if their products have potential for the control of these root diseases (thus ESR4 also links to WP9 on assessing bioactives for disease control).

ESR5: Genetic diversity and functional analysis of adult wheat leaf rust resistance genes CH flag

Universitaet Zuerich

Applications for this position are now closed

Overview

Within the gene discover and breeding research area, the approach is to identify candidate genes and determine their potential to enhance cereal disease resistance. By the end of the training period, each Early Stage Researcher associated with the research area will have learned how to identify and assess the potential of candidate disease resistance genes.

Objectives

The principal objective of this project is to train ESR5 in the skills necessary to determine allelic diversity, molecular function and genetic interactions of adult plant leaf rust disease resistance QTL from wheat.

Research Supervision and Affiliation

This project will be based at Universitaet Zuerich and the candidate will be a registered doctoral candidate at Universitaet Zuerich.

The project will be undertaken under the principal supervision of Professor Keller, with input from Dr Viktor Korzun, Dr Ewen Mullins and Dr Cristobal Uauy.

Secondment Details

This position will involve a research secondment of 3 months in KWS Lochow GmbH, the purpose of which is to perform high throughput marker analysis of haplotype in diverse germplasm, training in marker integration in wheat breeding and possibly wheat transformation.

Eligibility Criteria

This position is based in the Switzerland, which means that any potential candidates for this position cannot have lived in Switzerland for more than 12 months out of the 36 months up to the CerealPath Reference Date.

Background

ESR5 will explore the field potential of a cohort of previously identified candidate disease resistance genes (note that all also assess trade-off effects of genes and thus link to WP10).

ESR5 will analyse the allelic diversity and function of rust resistance QTL 1B. Under the direction of Beat Keller (UZH) and with the aid of KWS, they will analyse the haplotypes and characterise candidate genes of interest.

ESR6: Integrated control of wheat foliar diseases using biocontrol agents and silicon DK flag

Københavns Universitet

Applications for this position are now closed

Overview

There are immediate areas of research and training which will be critical in determining the usefulness of these and other endophytes as inoculants for field crops. This includes investigations into how best to develop a commercial product, the maintenance or loss of fungal competence over time, the most effective inoculant delivery methods, and determination if they can offer a safe and viable economic alternative or supplement to traditional chemical crop treatments.

Objectives

The main objectives of this project will be to train ESR6 to determine the efficacy and mechanisms elicited by beneficial microorganisms and bioactive Si compounds in the control of key foliar diseases in wheat exhibiting different pathogenic lifestyles.

Research Affiliation and Supervision

This project will be based at Københavns Universitet and the researcher will be a registered doctoral candidate at Københavns Universitet.

Interested applicants should view the documents pertaining to doctoral studies at Københavns Universitet.

The project will be conducted under the principal supervision of Dr Hans Jørgensen and Dr Birgit Jensen with input from Dr Tina Henriksson, Professor Paul Nicholson, Professor Fiona Doohan and Professor David Collinge.

Secondment Details

This project will involve a research secondment of 2 months at University College Dublin, the purpose of which is to learn to isolate cereal endophytes and a further 2 months at Lantmännen, the purpose of which will be to optimise field inoculation and assess the field effect of biocontrol agents on a range of diseases.

Eligibility Criteria

his position is based in Denmark, which means that any potential candidates for this position cannot have lived in the Denmark for more than 12 months out of the 36 months up to the CerealPath Reference Date.

Background

Using microbiological, molecular, pathology and field expertise at UCPH, UCD and Lantmännen, ESR6 will isolate a range of wheat endophytes and determine their mode of action and potential for control of cereal diseases. Towards further improving field application and efficacy, in collaboration with UCPH and Lantmännen, ESR6 will determine if endophytes can be used in combination with other bioactive products to obtain additive synergistic effects for disease control.

ESR7: The effect of host genotype on the efficacy of beneficial microorganisms in controlling foliar cereal disease DK flag

Københavns Universitet

Applications for this position are now closed

Overview

There are immediate areas of research and training which will be critical in determining the usefulness of these and other endophytes as inoculants for field crops. This includes investigations into how best to develop a commercial product, the maintenance or loss of fungal competence over time, the most effective inoculant delivery methods, and determination if they can offer a safe and viable economic alternative or supplement to traditional chemical crop treatments.

Objectives

The main objectives of this project will be to train ESR7 with the skills necessary to determine the practical applicability of biocontrol fungi, including novel endophytes, with specific reference to the influence of effect of host genotype and causal disease organism on their efficacy.

Research Affiliation and Supervision

This project will be based at the Københavns Universitet and the researcher will be a registered doctoral candidate at the Københavns Universitet.

Interested applicants should view the documents pertaining to doctoral studies at Københavns Universitet.

The project will be carried out under the principal supervision of Professor David Collinge and Dr. Birgit Jensen with input from Dr Annette Olesen, Dr Angela Feechan and dr Hans Jørgensen.

Secondment Details

This project will involve a research secondment of 3 months to Lantmännen, the purpose of which will be to optimise field inoculation and assess the field effect of biocontrol agents on FHB-inoculated wheat heads.

Eligibility Criteria

This position is based in Denmark, which means that any potential candidates for this position cannot have lived in the Denmark for more than 12 months out of the 36 months up to the CerealPath Reference Date.

Background

Using microbiological, molecular, pathology and field expertise at UCPH, UCD and Lantmännen, ESR6 will isolate a range of wheat endophytes and determine their mode of action and potential for control of cereal diseases. Building on recent work at UCPH, ESR7 will further explore the potential of the endophyte Clonostachys rosea to control cereal diseases, with specific focus on the optimisation of product formulation for field application. Using expertise at Københavns Universitet and Lantmännen, ESR7 will explore the effect of host genotype on endophyte efficacy, as this could significantly influence field performance.

ESR8: Isolation and characterisation of novel fungal root endophytes from wild relatives of barley and wheat for resistance to Fusarium and Gaeumannomyces IE flag

Trinity College Dublin

Applications for this position are now closed

Overview

There are immediate areas of research and training which will be critical in determining the usefulness of these and other endophytes as inoculants for field crops. This includes investigations into how best to develop a commercial product, the maintenance or loss of fungal competence over time, the most effective inoculant delivery methods, and determination if they can offer a safe and viable economic alternative or supplement to traditional chemical crop treatments.

Objectives

The objective of this project will be To train ESR8 to screen wild relatives of barley and wheat in NW Europe (partner countries) for novel endophytes and to evaluate their impact on disease resistance, mode of action and potential for commercial application.

Research Affiliation and Supervision

This project will be based at Trinity College Dublin and the researcher will be a registered Doctoral candidate at Trinity College Dublin.

The project will be carried out under the principal supervision of Professor Trevor Hodkinson, with input from Mr Donal Fitzgerald (Goldcrop), Professor James Brown and Dr Hans Jorgensen (UCPH), Dr Birgit Jensen, Professor David Collinge and Mr Brian Murphy (Trinity College Dublin).

Secondment Details

This project will involve a research secondment of 2 months at University College Dublin , to examine endophyte isolation, a further 2 months at Kobenhavns Universitet, to work with ESR6 to determine endophyte mode of action, and finally 3 months with Goldcrop to investigate commercial application of endophytes as a seed treatment.

Eligibility Criteria

This position is based in Ireland, which means that any potential candidates for this position cannot have lived in the Ireland for more than 12 months out of the 36 months up to the CerealPath Reference Date.

Background

ESR8 benefits from the grass phylogenetic experience of Trevor Hodkinson (Trinity College Dublin); under his direction and in collaboration with UCD and Goldcrop, he will train ESR8 in the taxonomic skills needed to identify wild grasses growing in areas of high root disease pressure. At UCD, ESR8 will receive training in the microbiological and molecular skills to characterise endophytes isolated from the wild grasses and determine their mode of action and potential to control cereal diseases. Using the resources and expertise at Goldcrop, ESR8 will determine the field potential of select endophytes that show promise for disease control.

ESR9: Evaluation and development of a citrus-derived bioactive for the control of root and head diseases of cereals IE flag

Envirotech Innovative Products Ltd

Applications for this position are now closed

Overview

There are immediate areas of research and training which will be critical in determining the usefulness of these and other endophytes as inoculants for field crops. This includes investigations into how best to develop a commercial product, the maintenance or loss of fungal competence over time, the most effective inoculant delivery methods, and determination if they can offer a safe and viable economic alternative or supplement to traditional chemical crop treatments.

Objectives

The principal objective of this project is to train ESR9 to test the broad applicability of citrus bioactives as a pre-harvest treatment to enhance wheat and barley grain quality and safety.

Research Affiliation and Supervision

This project will be based at Envirotech and the candidate will be a registered Doctoral candidate at University College Dublin.

The project will be conducted under the principal supervision of Dr Patrick Ward, with input from Dr. Algela Feechan, Dr Cristobal Uauy and Dr Hans Jorgensen.

Secondment Details

This project will involve a research secondment of 5 months with University College Dublin to train in the methods needed to test the mode of action of bioactives. And a further 5 months split between Agricultural Magnetics and University College Dublin to test the field biocontrol activity of the product.

Eligibility Criteria

This position is based in Ireland, which means that any potential candidates for this position cannot have lived in the Ireland for more than 12 months out of the 36 months up to the CerealPath Reference Date.

Background

Envirotech have developed a bioactive citrus derivative that is used for prevention of post-harvest spoilage. Recently, this product has also shown potential for the control of plant diseases, including those of wheat (unpubl. data). Using microbiological, pathology, molecular and product application expertise at Envirotech, UCD and Agricultural Magnetics, ESR9 will explore the potential of this product to control cereal diseases. They will determine the mode of action of the product using gene expression, microscopy and culturing techniques. They will determine the field potential of their product, as compared to that of chemicals currently used for disease control.

ESR10: RNA-based control of fungal root diseases of cereals DE flag

Justus-Liebig Universitaet, Giessen

Applications for this position are now closed

Overview

RNA interference (RNAi) is a natural phenomenon in plants, whereby plants silence various genes in response to an external stimulus. This host-induced gene silencing (HIGS) can be used to silence specific pathogen or plant genes and thus control plant diseases and it can be achieved via both GM and non-GM approaches. One approach is the in planta expression of pathogen-lethal RNAi signals via a GM approach. Alternatively, lethal RNAi signals can be applied to the plant as a treatment, or an agent such as a virus can be used to induce natural RNAi plant signals that target specific genes.

Objectives

The principal objective of this project is to train ESR10 to determine the potential of host-induced gene silencing (HIGS) as both a biotechnological and naturally occurring resistance strategy.

Research Affiliation and Supervision

This project will be based at Justus-Liebig Universitaet, Giessen and the candidate will be a registered Doctoral Candidate at Justus-Liebig Universitaet, Giessen.

The project will be carried out under the principal supervision of Professor Karl-Heinz Kogel, with input from Dr Jean-Marie Desailly, Dr Angela Feechan and Dr Hans Jorgensen.

Secondment Details

This project will involve a research secondment of 2 months with Phytoauxilium, in order to gain experience in an SME environment where natural product development for disease control is a key priority; there will be a further 1 month at University College Dublin to collaborate with ESR11 in RNAi technology.

Eligibility Criteria

This position is based in Germany, which means that any potential candidates for this position cannot have lived in the Germany for more than 12 months out of the 36 months up to the CerealPath Reference Date.

Background

Under the direction of Karl Kogel and using a combination of pathology and molecular technologies, ESR10 will investigate the potential disease range that can be targeted via RNAi-based inhibition of the essential fungal protein CYP51. They will work with Phytoauxilium to determine if RNAi can be integrated into their bioactive disease control products and thereby gain experience in industry and commercial product development.

ESR11: Host-induced gene silencing (HIGS) as a biotechnological and natural tool for controlling barley diseases. DE flag

Leibniz-Institut fuer Pflanzengenetik und Kulturpflanzenforschung

Applications for this position are now closed

Overview

RNA interference (RNAi) is a natural phenomenon in plants, whereby plants silence various genes in response to developmental signals or external stimuli. The host-induced gene silencing (HIGS) can be used to silence specific pathogen genes and thus control diseases and it can be achieved via both GM- and non-GM approaches. One approach is the in planta expression of pathogen-lethal RNAi signals via a GM approach. Alternatively, lethal RNAi signals can be applied to the plant as a treatment, or an agent such as a virus can be used to induce natural RNAi plant signals that target specific genes. Proof of concept for HIGS as a GM approach has been obtained in recent years whereas the question of HIGS as naturally occurring — and selectable — phenomenon in plants is still open.

Objectives

The principal objective of this project is to train ESR11 in RNAi-based disease control of cereal pathogens.

Research Affiliation and Supervision

This project will be based at Leibniz-Institut fuer Pflanzengenetik und Kulturpflanzenforschung and the candidate will be a registered Doctoral Candidate at Halle University.

The project will be completed under the principal supervision of Dr Patrick Schweizer with input from Professor Fiona Doohan, Dr Viktor Korzun and Dr Hans Jorgensen.

Candidates interested in this project should consult the details of the IPK Graduate Programme.

Secondment Details

This project will involve a research secondment of 3 months with KWS Lochow, the purpose of which will be to conduct field trials for FHB resistance QTL/GWAS mapping including gene-silencing genes as markers.

Eligibility Criteria

This position is based in Germany, which means that any potential candidates for this position cannot have lived in the Germany for more than 12 months out of the 36 months up to the CerealPath Reference Date.

Background

Under the direction of Patrick Schweizer, ESR11 will explore the potential of both GM and non-GM-based HIGS for disease control. They will use transient HIGS assays to determine potential strong HIGS targets in Fusarium for the generation of HIGS transgenic plants. They will also determine the nature of host genetic loci that influence the efficacy of HIGS . Working with KWS, ESR11 will map the wheat loci that affect HIGS and develop molecular markers to expedite the breeding of these genes into commercial wheat varieties.

ESR12: Assessing trade-off effects of durable resistance to biotrophic diseases of cereals GB flag

John Innes Centre

Applications for this position are now closed

Overview

The fitness of a plant in terms of yield and environmental adaptation can be altered due to the introgression of disease resistance genes, particularly those that affect fundamental plant regulatory networks. Over millennia, farmers and breeders have selected for disease resistance genes that minimise the economic cost of defence. Research on plant disease control adds greatly to our knowledge of fundamental plant processes and plant-microbe interactions, but it is often dissociated from the field situation where the most important parameter is to obtain consistently high yields from season to season. Having identified new control methods (e.g. genes, new targets for marker-assisted selection, non-GM RNAi/HIGs or new biological and bioactive compounds for disease control), it is important that a cereal pathology training programme underlines the importance of determining if there are trade-off effects with respect to either plant development, susceptibility to other diseases, or pathogen adaptability.

Objectives

Within this project, the ESR will be trained to research trade-offs between responses of cereals to biotrophic and necrotrophic fungal diseases, and the potential for mitigating these trade-offs in order to produce high-yielding cereal varieties.

Research Affiliation and Supervision

This position will be based at the John Innes Centre in the UK and the researcher will be a registered doctoral candidate at the University of East Anglia.

The project will be conducted under the principal supervision of Professor James Brown, with input from Dr Ewen Mullins, Professor David Collinge and Dr Paul Nicholson.

Secondment Details

This project will involve a 3-month secondment in order to conduct collaborative experiments on disease resistance and epidemiology in field trials.

Eligibility

This position is based in the UK, which means that any potential candidates for this position cannot have lived in the UK for more than 12 months out of the 36 months up to the CerealPath Reference Date.

Background

The goal of this project is to understand trade-offs between the responses of wheat to biotrophic fungal diseases, such as rusts and mildew, and necrotrophic diseases such as Septoria tritici blotch, blast and Ramularia leaf spot. This trade-off has been demonstrated experimentally at JIC but its significance for breeding elite cereal varieties is unclear at present. Directed by James Brown and in collaboration with others, ESR12 will investigate the relevance of the biotroph/ necrotroph trade-off for the breeding of elite cereal varieties. ESR12 will study the extent to which the trade-off operates in field conditions and whether it can be mitigated by reassorting genes through the process of plant breeding. This will include QTL analysis of susceptibility to necrotrophic pathogens and quantitative analysis of the relationship between responses to biotrophs and necrotrophs. It will also include study of biological and genetic mechanisms underpinning the bio/necro trade-off and the consequences for yield and yield components.

ESR13: Assessing the epidemiological and agronomic impact of germplasm genetically enhanced to resist Septoria tritici blotch IE flag

Teagasc

Applications for this position are now closed

Overview

The fitness of a plant in terms of yield and environmental adaptation can be altered due to the introgression of disease resistance genes, particularly those that affect fundamental plant regulatory networks. Over millennia, farmers and breeders have selected for disease resistance genes that minimise the economic cost of defence. Research on plant disease control adds greatly to our knowledge of fundamental plant processes and plant-microbe interactions, but it is often dissociated from the field situation where the most important parameter is to obtain consistently high yields from season to season. Having identified new control methods (e.g. genes, new targets for marker-assisted selection, non-GM RNAi/HIGs or new biological and bioactive compounds for disease control), it is important that a cereal pathology training programme underlines the importance of determining if there are trade-off effects with respect to either plant development, susceptibility to other diseases, or pathogen adaptability.

Objectives

The principal objectives of this Project will be To train ESR13 with the skills needed to evaluate the impact of deploying Septoria tritici blotch disease resistance loci in the field on broad-spectrum disease resistance, pathogen epidemiology, chemical inputs and crop agronomy.

Research Affiliation and Supervision

This position will be based at the Teagasc in the Ireland and the researcher will be a registered doctoral candidate at University College Dublin.

Candidates interested in this position should look at the materials regarding entry into doctoral programmes at University College Dublin.

The project will be conducted under the principal supervision of Dr Ewen Mullins, with input from Dr Simon Berry, Mr John Spink, Professor Fiona Doohan Doohan and Professor James Brown.

Secondment Details

This project will involve a 2 month secondment to Limagrain UK Ltd and the John Innes Centre, the purpose of which is to conduct field evaluations of resistance.

Eligibility

This position is based in Ireland, which means that any potential candidates for this position cannot have lived in Ireland for more than 12 months out of the 36 months up to the CerealPath Reference Date.

Background

Under the direction of Ewen Mullins (Teagasc) and in collaboration with John Spink (Teagasc), JIC and LVH UK, ESR13 will assess and monitor the epidemiological and agronomic impact of germplasm genetically enhanced to resist Septoria tritici blotch disease. Using a combination of agronomy, pathology and modeling skills, ESR13 will produce the prerequisite datasets to bridge the critical step between generating novel germplasm and ensuring its potential under field conditions is maximised. This includes determining the trade-off effects between host resistance and fungicide application. These studies will use a population of the causal pathogen, Zymoseptoria tritici (formerly known as Septoria tritici), collected across both a temporal and geographic spread, in order to gain insight into the effect of the relatively rapid rate of pathogen evolution on trade-off and crop production.

ESR13 directly links to ESR14.

ESR 14: Identification and characterisation of Zymoseptoria tritici fungal effectors IE flag

University College Dublin

Applications for this position are now closed

Overview

The fitness of a plant in terms of yield and environmental adaptation can be altered due to the introgression of disease resistance genes, particularly those that affect fundamental plant regulatory networks. Over millennia, farmers and breeders have selected for disease resistance genes that minimise the economic cost of defence. Research on plant disease control adds greatly to our knowledge of fundamental plant processes and plant-microbe interactions, but it is often dissociated from the field situation where the most important parameter is to obtain consistently high yields from season to season. Having identified new control methods (e.g. genes, new targets for marker-assisted selection, non-GM RNAi/HIGs or new biological and bioactive compounds for disease control), it is important that a cereal pathology training programme underlines the importance of determining if there are trade-off effects with respect to either plant development, susceptibility to other diseases, or pathogen adaptability.

Objectives

The principal objectives of this Project will be to train ESR14 to decipher the nature and role of fungal effectors in Septoria tritici blotch disease of wheat.

Research Affiliation and Supervision

This position will be based at University College Dublin in the Ireland and the researcher will be a registered doctoral candidate at University College Dublin.

Candidates interested in this position should look at the materials regarding entry into doctoral programmes at University College Dublin.

The project will be conducted under the principal supervision of Dr Angela Feechan, with input from Mr Donal Fitzgerald, Professor Karl-Heinz Kogel, Dr Hans Jorgensen and Prof. Brown.

Secondment Details

This project will involve a 1 month secondment at Justus-Liebig Universitaet, Giessen, the purpose of which is to learn application of RNA-based technologies in the wheat — Zymoseptoria tritici system, with a further 2 months at Goldcrop, to collect Z. tritici isolates and gain experience in industry.

Eligibility

This position is based in Ireland, which means that any potential candidates for this position cannot have lived in Ireland for more than 12 months out of the 36 months up to the CerealPath Reference Date.

Background

The goal of this project is to determine the evolutionary nature of Z. tritici. Effectors are molecules that play an important role in host colonisation and many of them suppress the plant immune system, allowing disease to flourish. Directed by Angela Feechan, and in collaboration with JLU and Goldcrop, ESR14 will use a combination of bioinformatics and molecular biology to identify and analyse the evolutionary diversity of Z. tritici effectors. In collaboration with Justus-Liebig Universitaet, ESR14 will be trained in RNAi and will use this technology to determine if specific effectors play a role in disease development.

ESR15: Identification of broad-spectrum resistance genes IE flag

University College Dublin

Applications for this position are now closed

Overview

By analysing and exploiting cereal evolution, we can identify a new cohort of hitherto uncharacterised disease resistance genes, so-called lineage-specific or "orphan" genes. A role for these genes in lineage-specific adaptations is now supported by a growing number of examples from a spectrum of diverse organisms. Recently Fiona Doohan (UCD) lodged a patent application on the use of a wheat lineage-specific gene that enhances resistance to disease (application no. EP14177179.0). Using a more comprehensive bioinformatics analysis preliminary assessment has confirmed that it is possible to select orphan genes that are responsive to multiple diseases and these are thus interesting candidates for broad rather than disease-specific responses.

Objectives

The principal objectives of this Project will be To train ESR15 to identify and characterise lineage-specific genes that show potential for broad-spectrum disease resistance.

Research Affiliation and Supervision

This position will be based at the University College Dublin in Ireland and the researcher will be a registered doctoral candidate at University College Dublin.

Candidates interested in this position should look at the materials regarding entry into doctoral programmes at University College Dublin.

The project will be conducted under the principal supervision of Professor Fiona Doohan, with input from Dr Simon Berry, Dr Patrick Schweizer and Professor James Brown.

Secondment Details

This project will involve a research secondment of 1 month to Leibniz-Institut fuer Pflanzengenetik und Kulturpflanzenforschung, the purpose of which is to collaborate on wheat transformation experiments and a further 2 months with Limagrain UK Ltd, to collect germplasm and conduct allelic diversity studies for select lineage-specific genes.

Eligibility

This position is based in Ireland, which means that any potential candidates for this position cannot have lived in Ireland for more than 12 months out of the 36 months up to the CerealPath Reference Date

Background

Directed by Fiona Doohan, ESR15 will use a more comprehensive bioinformatics approach to analyse an array of both in-house and public transcriptome data in order to identify and delineate lineage-specific genes that are responsive to a broad array of diseases. They will use virus-induced gene silencing to determine if these contribute to resistance to an array of pathogens. The most promising gene will be overexpressed in Brachypodium and, time permitting, in wheat (in collaboration with IPK). The responsiveness of the GM wheat and Brachypodium to an array of pathogens under glasshouse conditions will confirm the potential of genes for broad-spectrum resistance. In collaboration with LVH UK, they will analyse allelic variation across lineage-specific genes of interest and will develop markers to track variants of interest, facilitating their rapid integration into breeding programmes.

This page was last updated on 14th September 2017