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doi:10.1534/genetics.105.051110
A more recent version of this article appeared on May 1, 2006.
REGULAR RESEARCH PAPERS |
Patterns of nucleotide diversity in wild and cultivated sunflower
Aizhong Liu 1 and John M Burke 1*
1 Vanderbilt University
* To whom correspondence should be addressed. E-mail: john.m.burke{at}vanderbilt.edu.
Submitted on September 13, 2005
Revised on November 10, 2005
Accepted on 16 November 2005
Interest in the level and organization of nucleotide diversity in domesticated plant lineages has recently been motivated by the potential for using association-based mapping techniques as a means for identifying the genes underlying complex traits. To date, however, such data have only been available for a relatively small number of well-characterized plant taxa. Here we provide the first detailed description of patterns of nucleotide polymorphism in wild and cultivated sunflower (Helianthus annuus) using sequence data from nine nuclear genes. The results of this study indicate that wild sunflower harbors at least as much nucleotide diversity as has been reported in other wild plant taxa, with randomly selected sequence pairs being expected to differ at one out of every 70 base pairs. In contrast, cultivated sunflower has retained only 40-50% of the diversity present in the wild. Consistent with this dramatic reduction in polymorphism, a phylogenetic analysis of our data revealed that the cultivars form a monophyletic clade, adding to the growing body of evidence that sunflower is the product of a single domestication. Eight of the nine loci surveyed appeared to be evolving primarily under purifying selection, while the remaining locus may have been the subject of positive selection. Linkage disequilibrium (LD) decayed very rapidly in the self-incompatible wild sunflower, with the expected LD falling to negligible levels within 200 bp. The cultivars, on the other hand, exhibited somewhat higher levels of LD, with nonrandom associations persisting up to ~1100 bp. Taken together, these results suggest that association-based approaches will provide a high degree of resolution for the mapping of functional variation in sunflower.
Key Words: Helianthus annuus, domestication, linkage disequilibrium, nucleotide variation, sunflower
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