Dundee University at SCRI,Plant Research Group,Invergowrie,DD2 5DA Dundee,UKMini-biographyThe main interest of my lab is the structure and genetic diversity of plant genomes. This has grown from my studies on the transposons, which are a major factor in shaping the genomes of plants. I have been interested in exploiting transposons as molecular markers for genetic and genomic studies. This has led us into new fields, namely i) developing new high-throughput molecular marker technologies based on transposon insertions or single nucleotide polymorphisms. These markers are being used both for biodiversity assessment of gene banks and as linkage markers for marker-assisted breeding. ii) developing a database (
GERMINATE) for storing plant biodiversity data. I became involved in GL-TTP through my commitment to the "Grain Legumes" Integrated Project (
GLIP) and the desire to make the results of the project available for exploitation by the broad user community. As member of GL-TTP council, I am part of the decision-making process that decides upon the directions taken by GL-TTP.
High-throughput molecular marker analysis of Pisum sativum germplasmAndrew J. Flavell
1, Runchun Jing
1, Viacheslav N. Bolshakov
3, Maggie R. Knox
2, Jennifer M. Lee
4 Jo Dicks
2, Robert Davey
2, Michael Ambrose
2 and T.H. Noel Ellis
21Plant Research Unit, University of Dundee at SCRI, Invergowrie, Dundee DD2 5DA, UK.
2John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK.
3 Post-Genomics and Molecular Interactions Centre, University of Dundee at SCRI, Invergowrie, Dundee DD2 5DA, UK.
4Current address, Evolution and Ecology, Storer Hall, University of California at Davis, One Shields Ave, Davis, CA 95616.
a.j.flavell@dundee.ac.ukWe have combined three different genotyping approaches, namely the retrotransposon-based SSAP (1-2) and RBIP (3-5) methods, together with partial gene intron sequencing, to study the diversity of wild and cultivated Pisum. The intron sequence data set yield a phylogenetic tree that closely resembles an SSAP-based tree (2), suggesting that both methods are giving a true picture of the diversity in this species. Despite this, the intron tree is unstable with respect to data removal, because the individual gene trees show large deviations from the overall tree. This suggests that diverse, ancient gene haplotypes inherited from the wild progenitors
P. elatius and
P. fulvum are segregating in cultivated
P. sativum and recombination has scrambled these distributions in an unpredictable way. If this is true, then large numbers of markers will be needed for preliminary genome-wide scans before choosing samples for marker-assisted breeding in Pisum.
We also will present the latest information on the genetic diversity of the entire John Innes Pisum collection (~ 3000 accessions), using high throughput Tagged Microarray Marker (TAM) scoring of RBIP markers (3-5). These data are accessible via the web from the GERMINATE database (7).
1. Ellis et al (1998) Mol. Gen. Genet. 260: 9-19
2. Vershinin et al. (2003) Mol. Biol. Evol. 20: 2067-2075
3. Flavell et al. (1998) Plant J 16: 643-650
4. Flavell et al. (2003) Nucleic Acids Res. 31: e115.
5. http://www.dundee.ac.uk/biocentre/SLSBDIV7ajf.htm
6. http://cbr.jic.ac.uk/dicks/software/index.html
7. Lee et al. (2005) Plant Physiol. 139: 619-631
