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BBSRC Doctoral Training Programme

Applications are now open for the BBSRC DTP Programme beginning October 2013


Examples of projects available at NIAB


Competitive inhibition between Fusarium species in maize


Background

The fungal pathogens F. graminearum and F. culmorum have major impacts on yield and quality in the UK’s major arable crops, wheat and barley, as well as in maize, which is increasingly cultivated as a forage crop. An increase in maize production in the UK could alter F. graminearum and F. culmorum profiles in wheat and barley, potentially leading to increases in strain aggressiveness and mycotoxin production.

Fusarium populations collected from naturally infected maize fields in the UK show evidence of F. culmorum inhibition in the presence of F. graminearum.  In this project, genetic modification of F. culmorum and F. graminearum isolates with fluorescent labels will be undertaken in order to investigate (via fluorescence microscopy) interaction and competitive inhibition between these two important pathogenic species. 

Overall aim
Maize production in the UK is increasing. As a result, it is crucial to identify host-pathogen interactions with key pathogens, including F. graminearum and F. culmorum, which also have potential impacts on other major arable UK crops.  Exploration of maize infection patterns with F. graminearum and F. culmorum will be facilitated via transformation of UK isolates of each species with green fluorescence protein (GFP) and dsRed fluorescence, respectively. This modification will allow for the study of the species interaction, clarifying the occurrence of   inhibition between the species, and the individual aggressiveness of each species within the maize system.

Supervisors
Ryan Basler, Dr. Alison Bentley and Dr. Jane Thomas
 

Wheat genome dynamics

The next challenge facing wheat breeders is to increase yields to secure food supplies as the climate changes and as pressure mounts to reduce chemical inputs. Synthetic hexaploid wheats (SHW) have the potential to introduce novel traits to the wheat crop, but little is known about the changes in gene content, expression and regulation that accompany the polyploidisation phenomenon. This project will use next generation sequencing and transcriptomics technologies to investigate the dynamic nature of genomic rearrangements and gene expression following polyploidization.

Co-supervisors: Fiona Leigh,  Nick Gosman, Phil Howell

 

Fine mapping  of host sensitivity to Stagonospora nodorum effectors in wheat

Necrotrophic wheat leaf spot pathogens, Stagonospora nodorum (SNB), Septoria tritici (STB) and tan spot (Pyrenophora tritici-repentis, or Pt-r) cause significant wheat yield losses globally. The discovery that a host of proteinacious molecules (effectors) mediate host-microbe interaction and disease symptom development represents a paradigm shift within the field of phytopathology. Pathogen genome sequencing to discover new effectors can now be used to identify the corresponding host resistance loci. In collaboration with the Australian Centre for Necrotrophic Fungal Pathogens (ACNFP) at Curtin University in Western Australia, we are using powerful complementary genetic tools to discover genes controlling host sensitivity to a range of effectors.

Co-Supervisors: Nick Gosman, Alison Bentley & Gemma Rose

 

Developing genetic markers for wheat domestication traits

Many of the lines we produce through our pre-breeding work will still display “weedy” characteristics which may be advantageous in the wild but are undesirable in crop species. For example, most wild grasses bear seeds on a spike which readily shatters at maturity and produce grains with tenacious glumes that firmly adhere to the surface of the seed, in contrast to the non-shattering, free-threshing ears of cultivated wheat. Genetic markers for domestication traits such as these will greatly aid the selection of improved pre-breeding material and help widen the pool of diversity available to wheat breeders, ultimately leading to improvements in yield stability, pest and disease resistance, and the tolerance of abiotic stresses.

Co-supervisors: Phil Howell, Nick Gosman, Alison Bentley and Fiona Leigh

 

A few good genes: the flowering time network

Genes controlling floral initiation and plant height are critical factors in a plant’s response to the environment and for environmental adaptation. Work on model species like Arabidopsis thaliana suggests that there are great number of genes interacting to control flowering and stature; however, variation at only a few critical loci has been shown to have a large effect. In wheat, these ‘few good genes’ include photoperiod response (Ppd), Vernalization (Vrn) and height reduction (Rht). Based on these genes, we have created an allelic series of near iso-genic lines in wheat (the FT Network). The aim of this project is to utilize the FT Network to dissect the effect on crop development of gene variants in isolation and in combination. The work will address questions of crop responses to climate change and inform improvements to crop based modelling in wheat.

Co-supervisors: Nick Gosman, Alison Bentley, James Cockram

For more information please contact: Andy Greenland, Ian Mackay, Donal O' Sullivan, Jane Thomas

 

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

Background: Wheat (Triticum aestivum L.) is the world’s most widely cultivated crop, and plays a critical role in global food security and sustainability. Breeding strategies which incorporate information on wheat genetic variation (genome-assisted strategies) are a critical component towards securing sustainable production. Concerted efforts are underway to obtain the reference wheat genome sequence, a cornerstone of genome-assisted breeding (www.wheatgenome.org). However, it is the ability to apply sequence data using appropriate wheat biological resources and statistical methods that will ultimately deliver the yield increases required. Towards this goal, NIAB have developed Europe’s only publicly available wheat Multiparent Advanced Generation Inter-Cross (MAGIC) population, generated by systematically crossing multiple parental lines over many generations (BBSRC grant BB/E007260/1). The resulting population of 1,000 progeny represents a unique platform for the genetic dissection of agronomic traits (Mackay & Powell, Trend Plant Sci 12:57-63; Cavanagh et al, Curr Opin Plant Biol 11:1-7). NIAB’s MAGIC population has recently been genotyped with the state-of-the-art 90,000 Illumina iSelect wheat SNP chip.

Project aims: This 12 week rotation project will deploy the 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 Ian Mackay, Dr James Cockram

 

Coupling next-generation sequencing with next-generation germplasm resources: utilizing the Multiparent Advanced Generation Inter-Cross (MAGIC) population for trait dissection in wheat.

Background: Advances in Next-Generation Sequencing (NGS) have not been matched by concomitant advances in wheat genetic mapping germplasm resources. Until this happens, the true power of NGS for wheat improvement will not be fully realised. The development of Europe’s only publicly available wheat MAGIC populations at NIAB means that this impasse has now been bridged (BBSRC grant BB/E007260/1). MAGIC populations are constructed by crossing multiple founder lines over multiple generations, resulting in high-resolution (high recombination, high allelic input) platforms for detailed dissection of the genetic basis of trait inheritance, as well as epistatic and QTL x environment interactions (Mackay & Powell, Trend Plant Sci 12:57-63; Cavanagh et al, Curr Opin Plant Biol 11:1-7). Before the MAGIC population can be widely utilised, it must first be validated. As a component of this process, this 12 week rotation project will utilise the following resources to identify genes and genetic polymorphisms associated with a target morphological trait in wheat:

  1. A Nimblegene sequence-capture wheat chip (150Mbp, est 95% of all wheat genes)
  2. NGS sequencing using the Illumina HiSeq2000
  3. Bulked pools of DNA selected from the 1,000 MAGIC progeny lines


Project aims:
Prior to project start, we will send 2 bulk DNA samples for hybridisation to the exome-capture chip and subsequent deep sequencing using NGS. One bulk will consist of lines which contain awns (spike-like structures on the wheat ear), while the second will contain lines which lack awns. The project will analyse the sequencing data to identify genes and genetic markers closely linked to the phenotype, based on a comparison of the depth of sequence and composition of gene variants in each pool. These results will be contrasted with our 90,000 iSelect SNP dataset on the MAGIC population, in which we have identified genetic markers closely linked to awn presence/absence. Identification of the set of linked genes will allow:

  1. Determination of the physical context of linked genes using emerging wheat genomics resources (physical map and genome sequence) and comparative genomics.
  2. Identification of candidate genes
  3. Development of molecular markers for genotyping across MAGIC and additional validation populations.


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 Ian Mackay, Dr James Cockram

 

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

 

For further information on the DTP programme please visit the Cambridge University site at http://bbsrcdtp.lifesci.cam.ac.uk. For details on how to apply and closing dates click on http://bbsrcdtp.lifesci.cam.ac.uk/prospective.

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