My research is designed to exploit genomics based technologies to identify, map, isolate, manipulate and express different alleles controlling traits of importance for improved performance, in wheat.
Three areas of research are of particular importance to my group:
This five-year project began in February 2007 with funding supplied by BBSRC under the Bioinformatics and Biological Resources (BBR) program. The aim is to provide a one-stop shop for wheat functional genomics providing UK researchers with authenticated data and biological resources, which are freely available without restriction. The first step in this program was to upgrade the monogram network website to provide an up-to-date hub from which to disseminate information.
The second phase of the program is to update the resources held at Bristol including images, sequence and microarray data and make these available under the Monogram network umbrella. We hope that in future, other research groups will add their own datasets to the Monogram network site and search facilities. We report on progress made with Bristol based resources and comment on the future activities including plans to incorporate forthcoming 454 sequence data for wheat. We will also show how we have been streamlining the search for resources at the Monogram network Website so that users can get at the data they need without needing to check, or indeed be aware of, multiple databases based in different institutes. Finally we invite interested parties to email us at the above address to suggest tools and/or resources that they can contribute to the Monogram network or are an unmet need by the UK wheat and cereals research community.
i. Varietal SNPs
Possibly the groups biggest target is the generation of molecular markers (SNPs) which can be used by the wheat breeders. We have approached this task in two ways; first, we have utilized over 3.5 million expressed sequence tags from the major cereal taxa to electronically mine over 176 000 putative single nucleotide polymorphisms (SNPs). Secondly, we have instigated a £1.7 million project, in collaboration with Neil and Anthony Hall (Liverpool) and Mike Bevan (JIC) to generate a large amount of wheat genome sequence information with the aim of mining the data for new SNPs in UK germplasm.
ii. Homoeologous SNPs
The large and complex wheat genome creates experimental challenges, for instance, complications of single locus marker development, but also opportunities: the development of cytogenetic stocks and the study of gene expression in polyploids where anywhere between zero and three homoeologous gene copies may be expressed in a tissue at any time. Our recent studies have highlighted the limitations of measuring global gene expression in polyploid species using current micro-array technologies, due to the inability of current arrays to discriminate between related sequences (homoeologs and paralogs). The confirmation of such array studies can be particularly problematic where the probe sets on the array detect different homoeologs to primers subsequently designed for confirmatory RT-PCR. Here we describe a custom microarray (244,000 features) consisting of various homoeologous and paralogous specific feature s and representing nearly eleven thousand wheat loci. Results show the array is capable of discriminating between genomes of wheat, and we report on the levels of gene expression in newly formed synthetic hexaploids compared to their diploid and tetraploid parents.
The long term goal of this project is to generate wheat plants with elevated levels of genetic diversity and/or recombination. To produce such plants we have generated various transgenic lines designed to interfere with the expression of key genes (PMS2, Msh2 and Msh6/7) known to be involved in mismatch repair. We hypothesise that such plants will have two interesting characteristics; firstly, they will be unable to repair damage to their DNA and therefore they will carry an increased genetic load, and secondly, as mismatch repair is thought to be involved in homologous and homoeologous recombination, they will show elevated levels of recombination between related, but divergent sequences, for instance on homoeologous chromosomes.
Our initial results suggest that while lines designed to interfere with Msh2 expression do have reduced mismatch repair activity, lines designed to interfere with PMS2 and Msh6/7 expression do not.
To provide the project with a focus, initially we intend to use the Msh2 RNAi lines to generate novel combinations of HMW-glutenin alleles; however, we envisage that such lines could be a valuable source of novel alleles for any number of interesting genes.
View complete publications list in the University of Bristol publications system
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