Home > Science > PhDs at NIAB > BBSRC Doctoral Training Programme BBSRC Doctoral Training Programme
Projects available at NIAB
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Domestication of the African vine Cryptolepis sanguinolenta for cultivation by smallholder African farmers
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Supervisors: Drs Keith Gardner and Alison Bentley
Rotation project: Identifying genes underlying complex traits in crop plants is critical to modern plant breeding. A significant advance in this field has been the generation of multiparent mapping populations, in which NIAB has taken a leading role with development of an eight-founder multiparent advanced generation inter-cross (MAGIC) population for wheat. Surprisingly, about 15% of markers in this population were found to exhibit segregation distortion (SD), despite an absence of intentional selection (Gardner et al. in review). We have mapped about 40 significantly distorted linkage blocks to a range of locations across the genome. Some of the most strongly distorted blocks are long and associated with high marker density. These most likely represent introgression fragments from other grass species which have been incorporated into the wheat gene pool by breeders to broaden the genetic base of the crop and improve specific traits such as disease resistance and yield. We have confirmed this to be the case for two prominent SD linkage blocks. The student will continue this work with other possible introgression fragments and strongly SD blocks. They will investigate the occurrence of each block in the ultra-high density 820K wheat SNP array dataset and in association mapping panels of European wheat at NIAB. The sources of potential introgressions will be tracked using a pedigree of contemporary UK wheat lines developed by NIAB. The student will then develop and validate KASP markers for linkage blocks of interest, to aid wheat breeders in tracking the blocks during breeding.
PhD project: Linkage blocks showing SD in the MAGIC population are possibly subject to viability or fertility selection and negative interactions between linkage blocks from different genetic backgrounds may be of considerable importance. For all SD blocks, including introgressions, plant breeders need to be able to disentangle the loci causing desirable and undesirable phenotypic effects, and hence reduce “linkage drag”. We are currently developing Near Isogenic Lines (NILs) varying only in the presence/absence of the most prominent introgression fragments. These will enable investigation of the phenotypic effects of these linkage blocks in the field and glasshouse. To identify potential causative genetic differences, a targeted exome-sequencing approach will be used. The student will first interrogate both recently published wheat genome sequences (http://www.wheatgenome.org/, http://www.genomebiology.com/2015/16/1/26) using bioinformatics methods to identify all potential genes in the regions of the introgression fragments. This information can then be used to efficiently sequence the NILs and other lines to identify variants unique to the introgression fragments and potentially underlying phenotypic variation. Overall, the project will develop powerful tools for the ongoing exploitation of favourable introgressions in wheat breeding. The student will receive a thorough training in modern crop genetics, from field phenotyping to state-of-the-art bioinformatics and creation of novel genomics resources.
Supervisor: Mario Caccamo, Head of Crop Bioinformatics
Rotation project: Access to genetic diversity information is one of the pillars underpinning modern crop breeding technologies. The challenge to breed higher-yielding better-quality eco-efficient crops in the context of changing climate conditions will only be met by utilising all available tools and the informed use of genetic diversity will be a crucial one.
This project will be focused on the design and implementation of a computational framework to represent diversity data for several varieties of cereal crops. The work will be initially conducted to effectively call and represent single-nucleotide polymorphisms (SNPs) for rice varieties native to Vietnam. This initial prototype will, however, set the basis to work with other more complex grasses. At 430Mb rice has a smaller and better-characterised genome than other crops such as wheat, which at 17Gb ranks as one of the largest genomes sequenced to date.
During the initial phase (rotation programme) the PhD student will work with current variant calling algorithms. The student will analyse data from whole-genome sequencing reads already generated for ~100 rice lines. This dataset includes a number of samples that have been sequenced deep enough to support first-pass assemblies to capture novel genomic features. These rice varieties have been selected by our collaborators at the Agricultural Genetics Institutes (Hanoi, Vietnam) to study phenotypes relevant to Vietnamese conditions including salt-tolerance and disease resistance. One of the greatest threats to rice production in Vietnam is incursion of sea water, climate change also brings increased threats of flooding, periods of drought and newly emergent pests and pathogens.
PhD project: This work is part of a larger programme to develop novel computational approaches for the representation and access of crop diversity data to enable modern breeding technologies. In particular, as more diversity datasets are generated by the scientific community we will look into the integration of data from other technologies such as optical mapping, and from different sources such as RNA-Seq. The PhD student will have a unique opportunity to work with advanced computing resources in a high-performance environment and be embedded in a team of other students working in crop genomics.
Areas of interest:
- Assembly approaches for variation analysis.
- Complex crops – genomics and bioinformatics.
- Data representation (in the context of large datasets).
- Data presentation tools for modern breeding strategies.
Literature
Huang et al. (2010). Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genetics.
Iqbal, Z., Caccamo, M., Turner, I., Flicek, P., & McVean, G. (2012). De novo assembly and genotyping of variants using colored de Bruijn graphs. Nature Genetics.
The 3,000 rice genomes project GigaScience. doi:10.1186/2047-217X-3-7
Supervisor: Mario Caccamo, Head of Crop Bioinformatics
Rotation project: A genomic sequence is of little use unless we can identify features such as genes and regulatory elements that are encoded within the long string of nucleotides. A number of sophisticated software tools have been developed over the years to support the annotation and functional characterisation of gene structures. These tools assume a relatively high quality reference genome that is used as the backbone upon which to annotate genes. As more genomes are available, however, the single-genome approach will be substituted by a pangenomics one that can capture the whole-spectrum of genomic diversity within a species. Representing crop diversity data in this way will play a key role in the identification of useful novel diversity for use in modern breeding technologies.
This project will develop a novel strategy for the annotation of gene structures in the context of the pangenome. We will not assume a single linear genome rather a graph-based data structure representing the genomic diversity from a large number of individuals. We will focus attention on areas that are especially relevant to crop genomes such as high-repeat content, the presence of homeologous genes (polyploidy) and integration with genetic information (i.e.markers).
During the initial phase (rotation) the PhD student will work with a high-level representation of the data (e.g Cortex coloured-graph approach). We will first develop a prototype for an RNA-Seq alignment tool that will work directly on the underlying graph structure.
PhD project: Following this we will explore a number of areas that will require the development of novel algorithms:
- Repeat annotation directly on the graph based on k-mer frequency and known repetitive elements.
- Projection of gene structures from annotation performed in a canonical reference.
- The application of hidden- Markov models directly to the coloured graph structure. A priori this is not a computationally tractable problem therefore it will require the development of a strategy to reduced the search space.
- The implementation of splice-aware alignment tools to deal with long RNA-Seq reads. As longer reads are generated by the current sequencing technologies the demand for suitable alignment tools for cDNA sequences will increase.
This work is part of a larger programme to develop novel computational approaches for the representation and access of crop diversity data to support modern breeding technologies. The PhD student will have a unique opportunity to work with advanced computing resources in a high-performance environment and be embedded in a team of other postdocs and students working in crop genomics.
Literature
1 “De novo assembly and genotyping of variants using colored de Bruijn graphs”. Iqbal Z, Caccamo M, et al. Nature Genetics doi 10.1038/ng.1028.
Supervisors: Drs Anna Gordon, Alison Bentley and Lesley Boyd
Infection of grain by fungal pathogens results in yield loss and toxin contamination in cereal crops worldwide. Two important diseases of UK cereal production are caused by fungi with contrasting modes of ear/grain infection. The fungus Claviceps purpurea (Cp) infects wheat ovules, replacing the seed with fungal sclerotia and causing Ergot. Ergot sclerotia are full of a toxic cocktail that in humans causes the medieval disease St Antony’s Fire. The more opportunistic Fusarium pathogen complex (causing Fusarium Head Blight; FHB) infects all parts of the wheat ear, leading to production of harmful mycotoxins within the developing grain.
Ground-breaking research at NIAB indicates that Cp co-opts the plant’s Gibberellic Acid (GA) pathways to establish infection and reproduce. Partial resistance to Ergot has been found to co-locate with the wheat dwarfing genes, Rht-1Bb and Rht-1Db (Gordon et al 2015; TAG in press). These DELLA protein mutants are non-responsive to GA, resulting in growth retardation (Peng et al 1999; Nature 40: 256). Preliminary results in wheat transgenic lines expressing a bean GA2 oxidase1 specifically in ovules indicates that lowering GA levels results in reduced Cp infection and smaller sclerotia. Resistance to FHB, which can be classified by infection type, has also been shown to be linked to the wheat dwarfing genes (Srinivasachary et al 2009; TAG 118: 695), GA being hypothesised to play a role in the ability of the fungus to spread within the ear.
Rotation project: The student will confirm the effect of expressing bean GA2 oxidase1 on Cp resistance and extend these tests to look at resistance to Fusarium spp in the FHB complex. The correlation between ergot and FHB resistance phenotypes with bean GA2 oxidase1 expression levels will be studied using qRT-PCR. The student will undertake bioinformatics analyses to identify the wheat homologues of bean GA2 oxidase1, clone and sequence the homoeologues (3 genomes in hexaploid wheat) from the wheat cv. Fielder (transgenic genotype), and develop primers to determine the background expression of the wheat endogenous GA2 oxidase 1 in wild-type and transgenic lines.
PhD project: Additional work would involve measuring GA levels in wild-type and transgenic wheat lines, correlating GA levels with Cp and FHB infection/resistance. GA assays would be carried out at Rothamsted Research in collaboration with Andy Phillip’s group. If GA levels do prove a significant factor in Cp and FHB infection of wheat the project could explore how GA levels in ovules and ears are manipulated by the pathogen, the effects of the Rht-1Bb/1Db dwarfing alleles on GA levels and how this results in reduced infection. The FHB/GA interaction could be extended to include the use of transgenic Fusarium isolates expressing fluorescent tags (GFP, dsRed) to further elucidate the specificity of the relationship between plant and pathogen.
We have recently sequenced the Cp genome and have identified a partial GA biosynthesis gene cluster, similar to the GA biosynthesis gene cluster in Fusarium fujikori. Transcriptomics analyses shows that this Cp gene cluster is expressed during the first 7 days of infection, so the ability of the pathogens to synthesise GA needs to be further explored.
Additional traits of interest, including reduced grain size also appears to be linked to GA depletion, and given that there is very little known about the ovule GA status in our most important UK crop, there is scope here for the project to deliver exciting new knowledge.
The student will receive training in functional gene analysis, bioinformatics, qRT-PCR and gene expression analysis, GA biochemistry, plant pathology, wheat genetics and genomic characterisation.
Supervisors: Dr Tom Wood and Dr Anne Webb
Rotation project: Chocolate spot, caused by Botrytis fabae, is an important disease of faba bean (Vicia faba) which can cause severe crop losses. Currently there are no resistant commercial cultivars available. Resistant faba bean lines have been identified, but in many cases, replicated trials in different locations failed to reproduce these findings. One explanation could be the existence of strains with different virulence profiles. The genetic diversity of B. fabae and also variation for virulence within the B. fabae population, are currently unknown. The rotation project will explore the genetic diversity within B. fabae, assess for population structure, and ascertain if differences in virulence exist within UK B. fabae isolates.
At NIAB we hold a collection of approx. 200 isolates of B. fabae as well as >900 accessions of Vicia faba of which approx. 125 lines are inbred through at least 6 generations. Within the 10 week DTP rotation project the student will conduct a virulence test of several B. fabae isolates on selected lines of faba bean as well as screening a selection of UK isolates with molecular markers to get an overview of the genetic diversity within the collection. Based on these results isolates will be selected and sequenced using NGS technology. A reference genome for B. fabae will then be assembled and annotated, for use in subsequent comparative genomics studies during the full PhD project.
PhD project: Genetic diversity and virulence patterns in Botrytis fabae, the pathogen causing chocolate spot of faba bean (Vicia faba). The PhD project will focus on investigating for variation in virulence between strains and the genetic diversity between and within populations of Botrytis fabae. Efforts to breed fully resistant cultivars have been unsuccessful to date. Trials at NIAB have previously identified several sources of promising partial resistance to chocolate spot from which we have developed mapping populations with the aim of identifying QTLs conferring partial resistance. The PhD student’s work will be complementary to this work, identifying virulence genes and investigating variation in pathogenicity within B. fabae. This will involve using the B. fabae reference genome as a basis for expression analyses to identify potential virulence genes. Throughout the project the student will acquire a wide range of skills in the areas of microbiology, genetics, molecular biology and bioinformatics. This will allow the student to test fundamental hypotheses whilst also contributing to an applied plant breeding programme to help improve food security.
Supervisor: Dr Phil Howell
NIAB’s pre-breeding programme introduces diversity into elite varieties of hexaploid wheat (T. aestivum, AABBDD) from a range of wild and cultivated diploid and tetraploid relatives (Aegilops tauschii, DD genome; Triticum durum, T. dicoccoides, T. dicoccum, all AABB). This platform of wide crossing and re-synthesis provides the ‘synthetics pillar’ of WISP, the BBSRC’s public-good wheat pre-breeding programme.
A proportion of our pre-breeding recombinant lines display undesirable “weedy” characteristics inherited from these relatives, such as shattering seed heads or adhering glumes. These were bred out long ago during the domestication of wheat, and their presence in pre-breeding lines can inhibit the exploitation of otherwise promising material by commercial breeders. Diploid, tetraploid and hexaploid parental and recombinant materials can be phenotypically characterised for threshability and then screened with published markers linked to the major domestication loci Q, Br, Sog and Tg. Additional SNP-based markers developed specifically for WISP germplasm can also be used to characterise the material. Genetic markers for these domestication traits will greatly aid the selection of improved pre-breeding material and help widen the pool of diversity available to commercial wheat breeders, ultimately leading to improvements in yield stability, pest and disease resistance, and the tolerance of abiotic stresses.
References:
Dvorak et al., 2012. J Hered 103:426-441
Simons et al., 2006. Genetics 172: 547-555
PhD projects: NIAB’s Cereal Pre-Breeding group aims to capture novel diversity and transfer it into the backgrounds of elite UK-adapted varieties for phenotypic evaluation, with the best lines passing into commercial breeding programmes for exploitation. We are developing thousands of recombinant pre-breeding lines which represent a large germplasm resource for subsequent research.
PhD projects would typically involve the dissection of important phenotypes such as domestication traits and yield components. The number, significance and location of genes controlling these characters would be determined through QTL mapping, and validated across different germplasm. Recombinant pre-breeding lines will be used to develop high-resolution maps around the QTLs, including co-dominant markers suitable for high-throughput genotyping. This is likely to involve a bio-informatics approach exploiting synteny with rice, maize and brachypodium. Once very close linkage is established, it should be possible to develop near-isogenic lines for the target loci in order to better understand the underlying mechanisms of each character and how they interact. Where possible, candidate genes will be identified and hypotheses tested through the use of TILLING populations, transformation or genome editing.
Supervisor: Dr Phil Howell
Grain size, often expressed as Thousand Grain Weight (TGW), is a key yield component in wheat, and many QTLs for TGW have been detected in mapping populations. Digital grain imaging equipment enables the high-throughput analysis of grain shape parameters, revealing that seed size and shape are largely independent traits. Candidate genes for grain length and grain width have been identified in rice, and one of the orthologues, TaGW2, has been associated with grain weight in wheat.
Previous studies have shown that Synthetic Hexaploid Wheat lines (SHWs) can carry alleles for high TGW, and physically large and heavy grains are a common feature of many of the higher-yielding SHW-derived lines selected from NIAB’s pre-breeding work. It is likely that these are novel alleles not already present in the elite germplasm pool commonly used by breeders. Grain samples taken from multiple trials will be screened at NIAB using digital imaging to generate phenotype data. This will then be combined with existing genotype data to detect QTLs for grain size and shape, and look for co-segregation with candidate genes. The role of TGW in absolute yield will be explored, together with trade-offs between grain size and other yield components such as grain number.
References:
Yu et al., 2014. J Integr Agric 13:1835-44
Simmonds et al., BMC Plant Biol 14:191
PhD projects: NIAB’s Cereal Pre-Breeding group aims to capture novel diversity and transfer it into the backgrounds of elite UK-adapted varieties for phenotypic evaluation, with the best lines passing into commercial breeding programmes for exploitation. We are developing thousands of recombinant pre-breeding lines which represent a large germplasm resource for subsequent research.
PhD projects would typically involve the dissection of important phenotypes such as domestication traits and yield components. The number, significance and location of genes controlling these characters would be determined through QTL mapping, and validated across different germplasm. Recombinant pre-breeding lines will be used to develop high-resolution maps around the QTLs, including co-dominant markers suitable for high-throughput genotyping. This is likely to involve a bio-informatics approach exploiting synteny with rice, maize and brachypodium. Once very close linkage is established, it should be possible to develop near-isogenic lines for the target loci in order to better understand the underlying mechanisms of each character and how they interact. Where possible, candidate genes will be identified and hypotheses tested through the use of TILLING populations, transformation or genome editing.
Supervisors: James Cockram and Ian Mackay
Wheat is the UK’s most important crop. Grain, flour and breadmaking quality are critical traits for suitability of wheat harvests for intended end use. Genetic improvement is the most sustainable approach towards improving wheat quality. Recent advances in wheat genomics, mapping-population design and statistical analyses provide a timely opportunity to perform UK-relevant, high-resolution genetic analyses of wheat quality traits.
Methodology: This project will use a unique wheat resources generated at NIAB: a multi-parent advanced generation inter-cross (MAGIC) population, generated from eight UK varieties via multiple rounds of intercrossing, resulting in 1,000 progeny (Mackay et al. 2014). Parents include four classified as NABIM quality group 2 or above (Hereward, Xi19, Rialto, Robigus). The population has been genotyped with a high-density 90k SNP array. Along with facilities for quality testing and molecular labs at NIAB, these resources will be used to undertake fine-scale dissection of the genetic regions controlling multiple wheat quality traits.
Project aims are to generate:
- Fine-scale genetic analysis of multiple grain quality characters within a single high-resolution mapping platform.
- Breeder friendly genetic markers tagging these traits, and ultimately, map-based cloning of selected QTL.
- Tools and approaches with which to try to predict quality, and the ability to test these hypotheses via test bakes.
This project represents the first time a UK-relevant MAGIC population has been used to investigate wheat grain quality characteristics. The project is well aligned with industrial and grower interests, and ultimately aims to provide genomics-informed strategies for the development of new varieties with improved quality parameters.
References
Mackay I, Bansept-Basler P, Barber T, Bentley AR, Cockram J, Elderfield J, Gosman N, Greenland AJ, Horsnell R, Howells R, O’Sullivan DM, Rose GA, Howell P (2014). An eight-parent multiparent advanced generation intercross population for winter-sown wheat: creation, properties and validation. G3: Genes Genomes Genetics, 4: 1603-1610.
Supervisor: Dr Alison Bentley
Rotation project: Wheat is Europe’s main crop, essential for food security. With no evidence for decreasing demand, current production must be accelerated, but cannot do so through expanded agricultural area. This priority process of sustainable intensification requires novel approaches to drive increased yield potential. Proposed is the adoption of new genomics tools offering potential for accelerating selection, thereby reducing time, and ultimately, cost. Although yet to be fully validated for its cost versus benefit in commercial plant breeding, genomic selection (GS) is a front-runner: it removes the burden of phenotyping selection candidates, replacing phenotype with genotype to predict breeding value based on a trained model.
The economic and time cost of phenotyping is a current bottleneck to the genetic dissection of complex traits and accurate implementation of GS. For example, physiological and development traits are rarely phenotyped in routine trialling because of their complexity. As a result there is little information describing the genetic basis or predictive potential of physiological traits and many remain elusive beyond empirical breeder selection.
In this project, the student will employ a suite of complementary resources leveraging emerging genomics approaches on physiological targets directly relevant to driving wheat yield and its components. High-density genotypes have already been generated on an elite UK population, and the student will interrogate these using bioinformatic and quantitative genetic approaches. Field data is also available to support the dissection of the genetic control of physiological trait variation for the application of GS.
There is huge potential to use advanced physiological understanding, linked with genomics, to develop resource-efficient tools for wheat breeding.
PhD project: The rotation project can be rapidly scaled to encompass a suite of complementary and commercially relevant wheat populations available at NIAB. These populations are linked by a common parent, and also have contrasting parents with no significant pedigree overlap. Previous evidence supports their contrasting nature for creation of commercially relevant segregating populations. The student will use these populations, alone and in combination to optimise methods for phenotyping physiological development targeted to the application of GS. Descriptive high-density phenotypes will be combined with high density genotypes (and accompanying bioinformatic analyses) for mapping and GS. Extending outwards, the developed tools will be validated and then used in larger, more complex populations. Such populations have an inherent phenotyping bottleneck due to their large size, with mapping precision ultimately limited by accuracy of the phenotype.
The ability to make accurate predictions on traits influencing yield or its components will be tested via the initiation of a GS-led rapid recurrent selection scheme.
The student will gain experience in a number of key areas, including wheat breeding, field phenotyping, molecular biology, bioinformatics and quantitative genetics. They will have the opportunity to collaborate with a number of industrial and academic partners in an exciting and emerging field of research and application.
Three recent relevant references
Abberton M, Batley J, Bentley A et al. (2015) Global agricultural intensification during climate change: a role for genomics. Plant Biotechnology Journal [in press].
Kole C, Muthamilarasan M, Henry R, Edwards D, Sharma R, Abberton M, Batley J, Bentley A et al. (2015) Application of genomics for generation of climate resilient crops: Progress and prospects. Frontiers in Plant Science [in press].
Bentley A et al. (2014) Applying association mapping and genomic selection to the dissection of key traits in elite European wheat. Theoretical and Applied Genetics 127: 2619-2633.
If you would like more information about the projects or studying for a PhD at NIAB, please contact the project supervisor(s).
PhD students
Rowena Downie
BBSRC DTP Targeted Studentship, Cambridge University
Deploying effector and genomic approaches for the genetic dissection of pathogen-host interactions betweentwo necrotic pathogens (Pyrenophora tritici-repentis and Parastagonorum nodorum) and the UK’s most important crop, wheat.

Rowena is investigating pathogen-host interactions between Parastagonospora nodorum, Pyrenophora tritici-repentis and wheat (Triticum aestivum L.), using the recently developed Multiparent Advanced Generation InterCross (MAGIC) population (8-parent, 1,000 progeny).
P. nodorum and P. tritici-repentis are necrotrophic fungi and are important pathogens of one of the world’s most economically important cereal crops, wheat. Both pathogens secrete necrotrophic protein effectors that mediate host cell death, providing nutrients for continued infection. Pathogen effectors are a recent discovery that has revolutionised disease resistance breeding for necrotrophic disease in crop species, allowing often more complex genetic resistance mechanisms to be broken down into constituent parts. To date, three necrotrophic effectors have been identified and cloned from P. nodorum and P. tritici-repentis: ToxA, Tox1 and Tox3.
Rowena started her four year project in October 2015. She studied for her MSci in Biology at the University of Bristol, completing her thesis at the cereal genomics laboratory with Prof. K Edwards as supervisor. Here, Rowena carried out QTL analysis of an F5 Triticum aestivum Apogee x Paragon population, investigating plant and ear structure along with grain traits.
Supervisors: Dr James Cockram; Prof. Richard Oliver
Advisors: Dr Kar-Chun Tan; Dr Huyen Phan
Tally Wright
BBSRC DTP, University of Cambridge
Capturing Photosynthetic Traits from Ancestral Wheat Species.

Tally is researching photosynthetic variation in wild ancestral relatives of bread wheat. Furthermore, he will be mapping genes controlling desirable photosynthetic efficiency and capacity traits in novel tetraploid material. Tally’s overall goal is to identify genes controlling beneficial photosynthetic traits in wild ancestors that could be introgressed into modern varieties.
The human population is expected to exceed 9 billion by 2050, therefore the emphasis on global food security has reached critical importance. Raising photosynthetic capacity in wheat is a major bottleneck in increasing yield to feed a hungry world. Wild ancestors of bread wheat may still offer an untapped genetic reserve which could be the key to breaking this bottleneck.
Tally is part of the Cambridge University DTP program and started his three year PhD project in June 2015. He will partly spend his time at NIAB and the Department of Plant Sciences. Tally studied for his BSc in Marine Biology at the University of Portsmouth. After graduating, he started working at NIAB as a research assistant in the Pre-Breeding department. After being assigned onto the BBSRC DTP Programme, Tally completed his MRes at the University of Cambridge with projects that involved research at NIAB and the Department of Plant Sciences. On top of the project that Tally took forwards as his PhD, he completed a 10 week rotation with Dr Phil Howell investigating cadmium accumulation in tetraploid wheat. Since starting his PhD project Tally has completed a three month Professional Internship for PhD Students (PIPS) at KWS UK Ltd working on commercial research wheat projects.
Supervisors: Dr Fiona Leigh and Professor Howard Griffiths.
Franziska Fischer
BBSRC DTP, University of Cambridge
Silent wars: Characterising the interaction between wheat and Fusarium Head Blight
Affiliations: Department of Plant Sciences, University of Cambridge; Cambridge Commonwealth, European and International Trust
Research Interests
Fusarium head blight (FHB) is a disease caused by a group of fungi in cereals which affects all major cereal growing regions worldwide. It not only causes substantial yield loss, but also jeopardises animal and human health, because the fungi involved produce toxins.
In the UK, the disease can have substantial impact on local farms during epidemic years, while losses on a global scale run into millions of pounds annually. Since agronomic counter measures are still only partially effective, resistance towards FHB in crops is all the more valuable. However, to date we do not know of a fully resistant variety.
Franziska’s research project is investigating potential resistance mechanisms in modern UK wheat varieties using NIAB’s eight-parent MAGIC population. Furthermore, in terms of knowing your foe, she is adopting a set of new methods in molecular biology to provide a better picture of Fusarium populations in the UK and beyond.
Take part in the NIAB Fusarium Survey
Biography:
Franziska completed research projects with Disease Resistance and Diagnostics at NIAB and with Ottoline Leyser’s Group at the Sainsbury Laboratory, University of Cambridge, before returning to NIAB for her PhD research in October 2014. She is originally from Germany and holds an MSc in Crop Improvement (University of Nottingham), as well as an M.Sc. with a major in Agribusiness and Agricultural Economics (Technische Universität München TUM). Franziska has pursued her interest in both these areas during placements with the Food and Agriculture Organization of the United Nations and KWS UK Ltd. Her interest in plant-pathogen interaction was sparked by an MSc project on Ganoderma in oil palm, conducted in Semenyih, Malaysia.
Supervisor: Dr Alison Bentley
Tobias Barber
iCASE BBSRC DTP Cambridge University and RAGT Seeds Ltd
Testing new genomic methods to accelerate genetic gain for UK wheat improvement

Toby’s project is an Industrial CASE partnership with RAGT Seeds Ltd. to optimise the application of quantitative methods including genomic selection (GS) in wheat breeding.
Toby is working on a series of nested mapping populations and derivatives from the NIAB Elite MAGIC population. He is assessing a number of agronomically significant target traits in key European wheat environments, with a focus on yield components and nitrogen-use-efficiency. This is coupled with molecular and genetic analysis using next-generation sequencing. Toby will also develop and validate algorithms for GS to test extension of trait prediction into larger, more complex experimental populations of relevance to UK wheat to create a platform for scaling this project‘s impact for the future of wheat improvement.
Toby started his PhD project at NIAB in January 2017 after completing a 10 week rotation project at the Sainsbury Laboratory in the Ottoline Leyser group looking at the effect of differing nitrate concentrations on root plasticity in Brachypodium Distachyon. Toby graduated from the University of Plymouth with a degree in Geography and after travelling for an extended period he found work at NIAB. Toby has worked in the trials and farm team, working with a variety of arable and vegetable crops, in the ornamentals department, with new varieties for DUS testing and for several years in the research department, running and planning field trials and collecting high-quality phenotypic data.
Emily Marr
BBSRC DTP, University of Cambridge
Dissecting the genetic control of root system architecture in crops
Emily is investigating the genetic regulation of root system architecture (RSA) in bread wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), oat (Avena sativa L.) and chemically mutagenized Targeting Induced Local Lesions In Genomes (TILLING) populations of cvs. Kronos and Cadenza.
The projected increase in drought incidence requires the development of crops that are capable of withstanding extreme weather events. Furthermore, the current inefficiency of nutrient use represents environmental and economic losses. Although root system architecture, the spatial configuration of roots in the soil, is fundamental for nutrient and water uptake, it has often been overlooked in crop breeding due to the challenge of phenotyping organs below ground. However, RSA has a direct impact on grain yield and improved root systems can ensure that a higher proportion of applied fertiliser is taken up by the crop.
Emily is undertaking forward genetic screening to fine-map loci controlling RSA in wheat, barley and oat mapping populations. She aims to identify and characterise major-effect genes located within the mapped loci. She is also undertaking reverse genetic screening to characterise putative wheat RSA genes in TILLING populations containing artificially induced mutations. As part of a collaboration between NIAB and the Institute of Manufacturing at the University of Cambridge, Emily is involved in a laser ablation tomography project to study wheat root cortical aerenchyma.
Emily started her four-year PhD in October 2016 as part of the BBSRC DTP programme. She gained a BA (Hons) Cantab. in Natural Sciences from the University of Cambridge with a specialisation in Plant Sciences. She has previously completed projects at the Jodrell Laboratory in the Royal Botanic Gardens, Kew, the Sainsbury Laboratory Cambridge University (SLCU), and in the Department of Plant Sciences at the University of Cambridge.
Eleni Tente
BBSRC DTP, University of Cambridge
Project title: “How does Claviceps purpurea interact with the Gibberellic acid pathways in developing wheat ovules, and what are the implications for resistance and yield”
Eleni is investigating host-pathogen interactions between wheat (Triticum aestivum L.) and Claviceps purpurea.
Claviceps purpurea is a biotrophic fungal pathogen of a range of cereals and grasses, being the causative agent of ergot disease. While little is known about the molecular interactions that take place during infection, the Gibberellic acid (GA) hormone was recently found to play a role in the successful infection of wheat by the C. purpurea (Gordon et al., 2015). Understanding the role of plant hormones in influencing and facilitating the fungus’s development, and the C. purpurea genes responsible for infection has the potential to significantly expand our knowledge of the mechanisms governing this host-fungus relationship.
Eleni started her four year project in October 2016. She studied for her MSc in Plant Genetic Manipulation at the University of Nottingham, UK. After graduating she worked for a year at the University of California, San Diego, under the supervision of Dr. Jose Pruneda-Paz, where she examined the transcriptional networks that operate during the circadian regulation of plant pathogen-induced defence responses.
Tom Reynolds
BBSRC iCASE, University of Cambridge and Senova Ltd
Chocolate spot: Pathogenicity dynamics, population diversity and host resistance to Botrytis fabae
Tom is researching the interaction between the pathogen Botrytis fabae and its host Vicia faba in the UK. He is looking for quantitative trait loci (QTLs) defining resistance loci in V. faba, and examining the geographic and temporal distribution of B. fabae genetic variation.
Chocolate spot, caused by the fungus Botrytis fabae, can cause crop loss during wet seasons. However, little resistance to B. fabae exists within commercial V. faba lines. Delimiting new resistance QTLs will allow selection of more resistant V. faba varieties, reducing the necessity for fungicides and improving productivity of this valuable legume crop. Exploring the genetic diversity of this fungus will advise on which isolates are most virulent in the UK, and the rate of change of this pathogen in the UK.
Tom started his four year project in October 2016. He studied for his Bachelor’s degree at Durham University, reading Biological Sciences. Tom also holds a Master of Science in Plant Genetics and Crop Improvement from the University of East Anglia. He completed his masters research project in the lab of Cyril Zipfel at The Sainsbury Laboratory Norwich, under the supervision of Jacqueline Monaghan. There he worked on mapping a gene implicated in basal immunity in Arabidopsis thaliana. Between degrees Tom worked on hardware programming and prototype development with Sarum Hydraulics, Wiltshire.
Supervisor: Tom Wood