NIAB - National Institute of Agricultural Botany

Home > Research > BBSRC Doctoral Training Programme

BBSRC Doctoral Training Programme

Projects available at NIAB

The Chocolate spot toolbox

Chocolate spot (Botrytis fabae) is an important disease of the emerging legume crop faba bean (Vicia faba). It causes severe crop losses and there are currently no fully resistant commercial cultivars or resistance genes available. NIAB has assembled a large collection (>900 accessions and inbred lines) of V. faba, including lines partially resistant to chocolate spot, as well as >200 isolates of B. fabae from around the UK. This 10-week DTP rotation project provides an exciting opportunity to initiate parallel research into resistance sources and pathogen dynamics, providing the basis for future breeding towards resistance. This will be achieved through:

  1. Identification of sources of resistance to chocolate spot: faba bean lines will be inoculated with B. fabae in a controlled environment to determine the range of natural exploitable resistance available.
  2. Exploration of the genetic diversity within NIAB’s collection of B. fabae isolates: the sequenced genome of the extensively characterised and closely related pathogen B. cinerea will be used to develop molecular markers for validation in B. fabae.

Supervisor: Dr Anne Webb (

Developing new plant-breeding tools for the long-chain, omega-3 oil crop Buglossoidies arvensis

The inclusion of fish oils containing long chain omega-3 poly-unsaturated fatty acids (PUFAs) has been shown to have been associated with reduced rates of cardio-vascular disease. Buglossoides arvensis (Corn Gromwell), a previous weed of cereal crops, is a new spring crop for the U.K. which provides a sustainable, non-GM source of stearidonic acid (SDA). SDA is (one) precursor in the biosynthesis of the LC-PUFAs eicosatetraenoic acid (ETA 20:4 n-3), eicosapentaenoic acid (EPA, 20:5 n-3) and docosahexaenoic acid (DHA, 22:6 n-3), commonly found in fish oils (Ruiz-Lopez et al., 2014 Plant J 77: 198-208).

NIAB, in collaboration with Tech Crops International (TCI), is developing* new B. arvensis varieties for commercial production of SDA. Although a relatively diverse collection of B. arvensis germplasm is available (to the breeder), current genetic resources are limited and breeding must rely on classical methods to develop new, improved varieties. This project aims to develop a series of inter-simple sequence repeat (ISSR) markers (Korpelainen et al., 2007 BioTechniques 42: 479-486) to screen the B. arvensis collection held at NIAB. Using a series of generic ISSR primers, PCR products will be directly sequenced to obtain information adjacent to SSR sites to develop new molecular markers. New markers will then be used to establish any phylogenetic relationships and possible population structure between accessions. The development of new molecular tools will facilitate the selection of improved B. arvensis lines and also aid in the identifying genes controlling keys traits such as oil yield or profile. The DTP placement will provide the candidate with the opportunity to experience practical development of breeding tools with potential for direct application to a new U.K. crop.

Supervisors: Dr Thomas Wood (, Dr Steven Bentley (

Ergot susceptibility in hexaploid wheat: analysis of transcriptome timecourse

The Ergot fungus infects wheat via its’ floral tissue and within days colonises the whole flower to become a mycotoxin-rich fungal mass called an ergot. There is no known full resistance to this fungus and as such we have completed a detailed transcriptome study covering the first 7 days in a susceptible interaction. We are aiming to understand how the fungus invades and what the key moments are that determine the success of infection, and to understand what the plant resistance responses are. The initial analysis of the transcriptome data suggests that there are a large set of Auxin responsive genes that are induced by 3 days after inoculation, implying that perturbation of the plants auxin homeostasis could be the target of the pathogen in order to facilitate a successful colonisation.

This 10-week DTP project will use a set of bioinformatic tools to analyse our vast dataset to answer relevant biological questions about the progression of disease. There is scope for carrying out RT-PCR to confirm changes in gene expression patterns. The student will also have a chance to clone a fragment of an auxin responsive gene into an RNAi entry vector destined for plant transformation and to genotype GM wheat plants already in production.

Supervisor: Dr Anna Gordon (

Capturing Photosynthetic Efficiency Traits from Tetraploid Wheat

Ancestral wheat species harbour novel genetic variation that we hope to capture in wheat improvement efforts. At NIAB we are intercrossing a range of tetraploid wheats (Triticum durum, T. dicoccum, and T. dicoccoides) with modern hexaploid bread wheat (T. aestivum), through resynthesis and direct crossing, as part of WISP, the BBSRC public-good wheat pre-breeding program.   Diversity in photosynthetic and water use efficiency (WUE) traits was observed in our collection of tetraploid wheats, extending above and below the values obtained for elite bread wheats.  This PhD will interrogate the tetraploid gene pool with the ambition of improving the photosynthetic capacity of bread wheat in future varieties.

The research will involve:

  1. development of novel mapping populations from reciprocal crosses between parents which contrast for key traits
  2. phenotyping of these populations with gas exchange techniques to establish the heritability of photosynthesis and WUE traits
  3. identification of quantitative trait loci (QTL) using high density molecular markers and bioinformatic tools to begin trait dissection
  4. investigation of the influence of influence of the cytoplasm in the expression of photosynthesis / WUE phenotypes

Dr Fiona Leigh (

Developing genetic markers for wheat domestication traits

NIAB is providing the ‘synthetics pillar’ of WISP, a BBSRC public-good wheat pre-breeding programme, which involves developing two parallel streams of wheat pre-breeding material.  The first is based upon resynthesis (a recreation of the rare hybridisation event that led to the emergence of hexaploid wheat 10 000 years ago, see NIAB Synthetic Hexaploid Wheat), and the second involves direct crossing between tetraploids and hexaploids. Through this work, we are introducing diversity from a range of wild and cultivated diploid (Aegilops tauschii, DD genome) and tetraploid (Triticum durum, T. dicoccoides, T. dicoccum, all AABB) species into elite hexaploid wheat varieties (T. aestivum, AABBDD).

Many of the lines we produce will display many undesirable “weedy” characteristics, such as shattering seed heads or adhering glumes. Shattering is caused by the homoeologous Br loci (Watanabe et al., 2006. J Appl Genet 47: 93-98), whilst tenacious glumes are controlled by the Sog and Tg loci (Sood et al., 2009. Theor Appl Genet 119: 341-351). The most important domestication gene, the Q locus, has been cloned and appears to belong to the AP2 family of transcription factors (Simons et al., 2006. Genetics 172: 547-555). Genetic markers for these characters 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.

Diploid, tetraploid and hexaploid materials from our WISP programme can be characterised for threshability and then screened with published markers linked to these major domestication loci, together with additional SNP-based markers developed by WISP genotyping partners.  Existing segregating populations will be used to develop co-dominant markers suitable for high-throughput genotyping. This is likely to require 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 these loci in order to better understand the underlying mechanism of each character and how they interact. As well as making the pool of non-domesticated wheat relatives more accessible to breeders, this may give some new indications on how to optimise the balance between desirable threshability and undesirable grain shedding.

Supervisor: Dr Phil Howell (

Grain cadmium levels in tetraploid and hexaploid wheat

The NIAB pre-breeding group are intercrossing tetraploid wheats (Triticum durum, T. dicoccum and T. dicoccoides) with hexaploid bread wheat (T. aestivum), as part of WISP, the BBSRC public-good wheat pre-breeding programme. Grain samples of tetraploid wheat have consistently shown higher levels of the toxic heavy metal cadmium (Cd) than hexaploid wheat, and low-Cd accumulation is now a trait of major importance to durum wheat breeders. However, a significant proportion of recent UK bread wheat varieties have tetraploid parentage in their pedigrees, largely coming from T. dicoccoides, which has unknown Cd status. In addition, our WISP pre-breeding work may be inadvertently transferring high-Cd alleles from tetraploid wheat into low-Cd hexaploid wheat.

Recent work has identified a locus (Cdu1) which explained 82% of the phenotypic variation in Cd accumulation in a segregating durum wheat population, and which has been mapped to a 0.7cM interval on chromosome 5BL (Wiebe et al., 2010. Theor Appl Genet 121:1047-1058). Flanking markers can be used to screen a large range of tetraploid and hexaploid accessions from our WISP crossing work. Wholegrain flour samples, originating from field trials of these accessions, can be prepared for ICP-MS analysis (in conjunction with the Department of Earth Sciences) to determine Cd levels.

This screening approach will allow a detailed genetic analysis of cadmium uptake in our WISP material. The durum Cdu1 interval corresponds to a relatively small region (approx. 285 kbp) in both rice and brachypodium (Wiebe et al., 2010), so the development of diagnostic genetic markers suitable for high-throughput genotyping in wheat should be possible. These can then be used for routine selection against high-Cd alleles in segregating WISP populations, and transferred to commercial breeding programmes as necessary.

Cadmium accumulation may also be a suitable phenotype for exploring changes in gene expression following polyploidisation. For example, would a hexaploid derived from a high-Cd tetraploid through re-synthesis necessarily accumulate the same Cd levels as its tetraploid progenitor? What is the role of the (presumably non-functional) Cdu1 homoeologues on the A- and D-genomes?

Supervisor: Dr Phil Howell (

Improved root traits in wheat

We would like to offer a PhD project to study potential improved root traits in wheat, extending published work from other species. The aim is to increase wheat root length, and thus improve water use efficiency, to improve P, N & K uptake and measure the effect on yield. We have transformed wheat with constructs to constitutively express wheat homologues of genes involved in these root traits, or to reduce their expression by RNAi-silencing. The 10 week DTP project will include genotyping and phenotyping of these materials and identify homozygous plants for further characterisation.

Supervisor: Dr Emma Wallington (

Deploying next-generation biological resources and dense SNP chips for the genetic dissection of brown rust resistance in wheat

This project will deploy the NIAB 8 founder elite wheat MAGIC population and the dense 90k genotype dataset to investigate the genetic basis of brown rust resistance, a major wheat pathogen in the UK and worldwide. Brown rust is caused by the fungal pathogen Puccina recondita, and can reduce yields by up to 50%. As leaders of the UK Cereal Pathogen Virulence Survey, NIAB possesses the national brown rust isolate collection. Using the expertise and resources available, this project will undertake replicated phenotypic tests for seedling resistance to specific brown rust isolates under controlled environment conditions. Subsequently, the phenotypic data generated will be combined with the existing 90k SNP data to identify genetic components of brown rust resistance. The genomic context of these markers will be investigated using emerging wheat physical and sequence resources and comparative genomic approaches, and breeder-friendly genetic markers generated, as time permits. Previous screens for yellow rust resistance in the MAGIC population have identified highly significantly associated genetic markers, and interestingly, transgressive segregation for resistance.

This workpackage forms part of a wider objective of utilising wheat MAGIC for the efficient application of genomics-assisted plant breeding for sustainable wheat production, targeting (but not limited to) disease resistance and yield components within a unified genetic mapping platform.

Supervisors: Dr I Mackay (, Dr J Cockram (

Rapid Bulk Inbreeding as an alternative to single seed descent

Single seed descent (SSD) is a commonly used method for the creation of recombinant inbred lines in plant breeding and crop genetics. For each line of descent, it involves a single selfed individual from a parent being taken forward to the next generation. Over several generations, and following multiple independent lines of decent, a new set of recombinant inbred lines is derived from a cross. In cereals, this process is fast (2-3 generations of selfing per year) but is labour intensive since plants must be harvested individually with a single seed from each parent plant sown for the next generation. Rapid Bulk Inbreeding (RaBId) is an alternative in which plants are harvested and seed threshed as a bulk. Sowing seed for the next generation can then be automated. RaBId eliminates much labour, but genetic variation will be lost since lines of descent are no longer independent. However, computer simulations of bi-parental crosses suggest that a small number of genetic markers can be used after bulk inbreeding is complete to select a subset of lines which are at least as independent as lines developed by SSD. This project will extend these simulations to more complex crossing schemes, such as MAGIC, and also test RaBId empirically using marker data from a French multi-founder population.

Supervisor: Dr I Mackay (

A comparison of genomic selection and marker assisted selection in a bi-parental cross

Genomic selection is a method of breeding in which large numbers of markers are used to predict traits without recourse to identifying individual QTL through linkage or association mapping. In marker-assisted selection, linkage and association mapping must first identify individual markers with statistically significant effects on target traits. Selection then takes place on a score based on these markers alone. Using cross-validation approaches this project will compare genomic selection and marker assisted selection in bi-parental crosses and in association mapping panels of winter wheat.

Supervisors: Dr K Gardner (, Dr I Mackay (

Comparison of genetic and pedigree based relationships in the UK winter wheat pedigree

We have catalogued the common pedigree of contemporary UK winter wheat lines stretching back over 50 years. High density marker data are available on many of the contemporary and ancestral lines. This project will compare relationships among lines computed from markers and from the pedigree. Results will be used to test the accuracy of the pedigree, to compare the use of pedigree and marker based relationship matrices in association mapping and to search for regions of the genome from ancestral lines which appear overrepresented in their descendents.

Supervisors: Dr K Gardner (, Dr I Mackay (

The effect of Ppd on stress tolerance at germination and establishment in wheat

Ppd is a locus in cereals characterised primarily by its major effect on flowering time and height. However, it is also known to influence frost tolerance and winter kill. This project will use a set of near isogenic lines in wheat to assess if an effect of Ppd-D1 can be detected on germination and coleoptile emergence rates in laboratory tests. The tests will then be extended to impose water logging, drought and freezing tests on seeds and seedlings. The work will be extended to survey variation across parents of mapping population and representatives of adapted UK germplasm prior to initiating linkage and association mapping experiments.

Supervisors: Dr A Bentley (, Dr I Mackay (

The use of historical trials data to track genetic and environmental trends in UK crops

Published work (Mackay et al. 2010) in which historical data from variety trials was reanalysed, demonstrated that from 1982 to 2007 the most important component of yield increase in the major UK arable crops was genetic rather than environmental (arising from either climate change or changes in crop agronomy). These analyses can be updated with the addition of a further seven years’ data. In addition to historical trials data, there are also several datasets available in which old varieties have been compared with new varieties in the same trial series. These trials can be analysed separately and also combined with the historical trials series to assess bias in the reanalysis of historical data and the extent to which varieties have been bred not only for increased yield but also for adaptation to the prevalent environment. The original analyses indicated that annual weather records could be used to identify drivers of variety instability over years. There are more data available on variation between trial locations within years and the extension of the analyses to incorporate these should give a more accurate assessment of the causes of variety instability.

Mackay, I., A. Horwell, J. Garner, J. White, J. McKee, and H. Philpott. "Reanalyses of the historical series of UK variety trials to quantify the contributions of genetic and environmental factors to trends and variability in yield over time." Theoretical and Applied Genetics 122, no. 1 (2011): 225-238.

Supervisor: Dr I Mackay (


PhD opportunities in Statistical and Quantitative Genetics

Covering the application of methods from statistical, population and quantitative genetics to improve the efficiency of plant breeding, NIAB can offer projects ranging from the development of novel methods and algorithms for trait mapping to more practical lab & field based experimentation including:

  • Association mapping in wheat and barley
  • Development and application of methods for genomic selection in autogamous species.
  • Processes for improving the speed and efficiency of inbreeding in crop breeding.
  • The Multiparent Advanced Generation Intercross (MAGIC)
  • The design of breeding programmes

Dr Ian Mackay (

Further information on the DTP programme
Details on how to apply

If you would like more information about studying for a PhD at NIAB and potential projects please contact Andy Greenland (; +441223 342349)