Academic journal article Genetics

Nucleotide Polymorphism and Linkage Disequilibrium within and among Natural Populations of European Aspen (Populus Tremula L., Salicaceae)

Academic journal article Genetics

Nucleotide Polymorphism and Linkage Disequilibrium within and among Natural Populations of European Aspen (Populus Tremula L., Salicaceae)

Article excerpt

ABSTRACT

Populus is an important model organism in forest biology, but levels of 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 of genetic variation. Levels of silent site polymorphisms, π^sub S^, averaged 0.016 across the five genes. Linkage disequilibrium was generally low, extending only a few hundred base pairs, 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 F^sub ST^ = 0.116. Levels of polymorphism in P. tremula are 2- to 10-fold higher than those in 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.

QFL mapping is currently the key tool for identifying the genetic basis of quantitative traits. However, an approach that has gained in popularity recently is the use of natural populations to map traits by means of association analysis. Association analysis, or linkage disequilibrium (LD) mapping, has been used extensively to dissect traits in species where traditional QTL-mapping approaches are not feasible, such as in humans (RAFALSKI and MORGANTE 2004). Association methods have also been extended to plants and have helped increase the resolution considerably compared to standard mapping populations (FLINT-GARCIA et al. 2003). In principle, association studies can identify variation down to the single-nucleotide substitutions that are responsible for variation in phenotypes (quantitative trait nucleotides, QTNs). However, a move from a traditional QTLmapping approach to association-based population surveys requires detailed knowledge about basic population genetic parameters, such as levels of genetic variation and the extent of linkage disequilibrium and population structure, and also how these parameters vary across the genome of the species in question.

The long generation times of most forest trees have led to slow progress in elucidating the genetic architecture of complex traits through traditional QTL-mapping approaches, and suggestions have been made that linkage-disequilibrium mapping approaches might be more fruitful (BRUNNER el al. 2004; NEALE and SAVOLAINEN 2004). However, in plants, the majority of polymorphism data at the nucleotide level come from a few, well-studied model species such as Arabidopsis, maize, rice, and barley and from only a few studies that have estimated levels of nucleotide polymorphism and linkage disequilibrium in long-lived outcrossing plants, such as woody perennials (DvORNYK et al 2002; GARCIA-&L et al 2003; KADO et al 2003; SEMERIKOV and LASCOUX 2003).

It is hard to know to what extent results from shortlived, selfing, or domesticated species generalize to plants with different life histories, mating systems, and/or domestication histories. For instance, even though levels of nucleotide polymorphism at the alcohol dehydrogenase (AdK) locus were comparable in selfing Arabidopsis thaliana and outcrossing A. lyrata, the distribution of segregating sites across the gene was very different in the two species (SAVOLAINEN et al. 2000). Furthermore, in predominantly selfing species like selfing A. thaliana and rice (Oryza sativa) linkage disequilibrium extends over large physical distances [>150 kb in Arabidopsis (NORDBORG et al. 2000) and ^1OO kb in rice (GARRIS et al. 2003)] whereas in outcrossing maize, linkage disequilibrium declines to negligible levels in < 1 kb (REMINGTON et al 2001).

The genus Populus has a long tradition as a model system for tree physiology and Populus has recently also been established as the de facto model species for tree genomics (WULLSCHLEGER et al. …

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