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Originally published as Genetics Published Articles Ahead of Print on May 23, 2005.
Genetics, Vol. 170, 1897-1911, August 2005, Copyright © 2005
doi:10.1534/genetics.104.036152
High-Diversity Genes in the Arabidopsis Genome
Jennifer M. Cork and Michael D. Purugganan1
Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695
1 Corresponding author: Department of Genetics, Box 7614, 3513 Gardner Hall, North Carolina State University, Raleigh, NC 27695.
E-mail: michael_purugganan{at}ncsu.edu
High-diversity genes represent an important class of loci in organismal genomes. Since elevated levels of nucleotide variation are a key component of the molecular signature for balancing selection or local adaptation, high-diversity genes may represent loci whose alleles are selectively maintained as balanced polymorphisms. Comparison of 4300 random shotgun sequence fragments of the Arabidopsis thaliana Ler ecotype genome with the whole genomic sequence of the Col-0 ecotype identified 60 genes with putatively high levels of intraspecific variability. Eleven of these genes were sequenced in multiple A. thaliana accessions, 3 of which were found to display elevated levels of nucleotide polymorphism. These genes encode the myb-like transcription factor MYB103, a putative soluble starch synthase I, and a homeodomain-leucine zipper transcription factor. Analysis of these genes and 4–7 flanking genes in 14–20 A. thaliana ecotypes revealed that two of these loci show other characteristics of balanced polymorphisms, including broad peaks of nucleotide diversity spanning multiple linked genes and an excess of intermediate-frequency polymorphisms. Scanning genomes for high-diversity genomic regions may be useful in approaches to adaptive trait locus mapping for uncovering candidate balanced polymorphisms.
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