Investigating gene function in cereals

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Overview
Welcome to the Functional Genomics group at the University of Bristol In addition to traditional micro-array based studies of cereal genomics were are currently developing new tools to further our understanding of the importance of sequence variation (including variation between homeologous genes in polyploids) in crops.

Functional SNPs
For wheat, barley and maize we have a large number of SNPs available which have been mined from public EST databases using our autoSNP software. In addition to DNA sequence alignment and haplotype views, an amino acid sequence alignment view of the effect of SNPs is avialable, overlayed with reading frame and PROSITE domain data. Go to SNP page.

244K wheat Array
Based on the SNPs generated in wheat we have recently developed a 244K feature Agilent array. This array has a series of 25-mer oligonucleotide probes designed to discriminate the expression values of closely related haplotypes including allelic variants, gene family memebers and homeologs. This is currently being evaluated in house but will be avialable to order from Agilent later in 2007.

Molecular inversion probes
We are currently optimising Molecular Inversion Probe (MIPs) technology in wheat. MIPs facilitates high throughput array based detection of sequence polymorhpisms.

Other resources
We have 26K quality and vector trimmed EST's from 35 cDNA libraries relating to different stages of grain development and various stress treatments. These sequences have be used to produce a ~10K feature unigene set, which has been arrayed on to glass slides. These arrays are currently being used for high-throughput gene expression studies. The Unigene set is avialable on request.

Selected publications:

• Alteration of the embryo transcriptome of hexaploid winter wheat (Triticum aestivum cv. Mercia) during maturation and germination
  Ian D. Wilson, Gary L. A. Barker, Chungui Lu, Jane A. Coghill, Richard W. Beswick, John R. Lenton and Keith J. Edwards. 2005. Functional integrative genomics
• A transcriptomics resource for wheat functional genomics. Wilson, I.D., Barker, G.L.A., Beswick, R.W., Shepherd, S.K., Lu, C., Coghill, J.A., Edwards, D., Owen, P., Lyons, R., Parker, J.S., Lenton, J.R., Holdsworth, M.J., Shewry, P.R. & Edwards, K.J. 2004. Plant Biotechnology 2 (6): 495-506.

Maintained by Gary Barker Last updated Jan 2007
 
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