- THIS ARTICLE
- Full Text
- Full Text (PDF)
- Data Supplement
- Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
- Reprints & Permissions
- CITING ARTICLES
- Citing Articles via Google Scholar
- GOOGLE SCHOLAR
- Articles by Jing, R.
- Articles by Flavell, A. J.
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Jing, R.
- Articles by Flavell, A. J.
Genetics, Vol. 177, 2263-2275, December 2007, Copyright © 2007
doi:10.1534/genetics.107.081323
Gene-Based Sequence Diversity Analysis of Field Pea (Pisum)
Runchun Jing*,1,
Richard Johnson*,
Andrea Seres
,
Gyorgy Kiss,
Mike J. Ambrose
,
Maggie R. Knox,
T. H. Noel Ellis and
Andrew J. Flavell*,2
* Plant Research Unit, University of Dundee at Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Institute of Genetics–Agricultural Biotechnology Center, Szent-Györgyi u. 4, 2100 Gödöll
, Hungary and John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom
2 Corresponding author: Division of Plant Sciences, University of Dundee at SCRI, Invergowrie, Dundee DD2 5DA, United Kingdom.
E-mail: a.j.flavell{at}dundee.ac.uk
Sequence diversity of 39 dispersed gene loci was analyzed in 48 diverse individuals representative of the genus Pisum. The different genes show large variation in diversity parameters, suggesting widely differing levels of selection and a high overall diversity level for the species. The data set yields a genetic diversity tree whose deep branches, involving wild samples, are preserved in a tree derived from a polymorphic retrotransposon insertions in an identical sample set. Thus, gene regions and intergenic "junk DNA" share a consistent picture for the genomic diversity of Pisum, despite low linkage disequilibrium in wild and landrace germplasm, which might be expected to allow independent evolution of these very different DNA classes. Additional lines of evidence indicate that recombination has shuffled gene haplotypes efficiently within Pisum, despite its high level of inbreeding and widespread geographic distribution. Trees derived from individual gene loci show marked differences from each other, and genetic distance values between sample pairs show high standard deviations. Sequence mosaic analysis of aligned sequences identifies nine loci showing evidence for intragenic recombination. Lastly, phylogenetic network analysis confirms the non-treelike structure of Pisum diversity and indicates the major germplasm classes involved. Overall, these data emphasize the artificiality of simple tree structures for representing genomic sequence variation within Pisum and emphasize the need for fine structure haplotype analysis to accurately define the genetic structure of the species.