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Genetics. Published Articles Ahead of Print: October 16, 2004, Copyright © 2004
doi:10.1534/genetics.104.034959

A more recent version of this article appeared on February 1, 2005.
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REGULAR RESEARCH PAPERS

Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae)

Pär K Ingvarsson 1*

1 University of Umeå

* To whom correspondence should be addressed. E-mail: pelle{at}eg.umu.se.

Submitted on August 12, 2004
Revised on September 27, 2004
Accepted on 11 October 2004


  Abstract
Populus is an important model organism in forest biology, but levels on nucleotide polymorphisms and linkage disequilibrium have never been investigated in natural populations. Here I present a study on levels of nucleotide polymorphism, haplotype structure and population subdivision in five nuclear genes in the European aspen Populus tremula. Results show substantial levels genetic variation. Levels of silent site polymorphisms, ps, averaged 0.016 across the five genes. Linkage disequilibrium was generally low, extending only a few hundred bp, suggesting that rates of recombination are high in this obligate outcrossing species. Significant genetic differentiation was found at all five genes, with an average estimate of FST =0.116. Levels of polymorphism in P. tremula are two to ten-fold higher that other woody, long-lived perennial plants, such as Pinus and Cryptomeria. The high levels of nucleotide polymorphism and low linkage disequilibrium suggest that it may be possible to map functional variation to very fine scales in P. tremula using association mapping approaches.

Key Words: <I>Populus tremula </I>, linkage disequilibrium, nucleotide polymorphism, population structure




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