Gene-based sequence diversity analysis of field pea (Pisum)

Runchun Jing, Richard Johnson, Andrea Seres, G. Kiss, Mike J. Ambrose, Maggie R. Knox, T. H Noel Ellis, Andrew J. Flavell

Research output: Contribution to journalArticle

53 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)2263-2275
Number of pages13
JournalGenetics
Volume177
Issue number4
DOIs
Publication statusPublished - Dec 2007

Fingerprint

Peas
Sequence Analysis
Intergenic DNA
Genes
Haplotypes
Genetic Recombination
Retroelements
Inbreeding
Genetic Structures
Linkage Disequilibrium
DNA

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Jing, R., Johnson, R., Seres, A., Kiss, G., Ambrose, M. J., Knox, M. R., ... Flavell, A. J. (2007). Gene-based sequence diversity analysis of field pea (Pisum). Genetics, 177(4), 2263-2275. https://doi.org/10.1534/genetics.107.081323

Gene-based sequence diversity analysis of field pea (Pisum). / Jing, Runchun; Johnson, Richard; Seres, Andrea; Kiss, G.; Ambrose, Mike J.; Knox, Maggie R.; Ellis, T. H Noel; Flavell, Andrew J.

In: Genetics, Vol. 177, No. 4, 12.2007, p. 2263-2275.

Research output: Contribution to journalArticle

Jing, R, Johnson, R, Seres, A, Kiss, G, Ambrose, MJ, Knox, MR, Ellis, THN & Flavell, AJ 2007, 'Gene-based sequence diversity analysis of field pea (Pisum)', Genetics, vol. 177, no. 4, pp. 2263-2275. https://doi.org/10.1534/genetics.107.081323
Jing R, Johnson R, Seres A, Kiss G, Ambrose MJ, Knox MR et al. Gene-based sequence diversity analysis of field pea (Pisum). Genetics. 2007 Dec;177(4):2263-2275. https://doi.org/10.1534/genetics.107.081323
Jing, Runchun ; Johnson, Richard ; Seres, Andrea ; Kiss, G. ; Ambrose, Mike J. ; Knox, Maggie R. ; Ellis, T. H Noel ; Flavell, Andrew J. / Gene-based sequence diversity analysis of field pea (Pisum). In: Genetics. 2007 ; Vol. 177, No. 4. pp. 2263-2275.
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