Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana

Justin O. Borevitz, Samuel P. Hazen, Todd P. Michael, Geoffrey P. Morris, Ivan R. Baxter, Tina T. Hu, Huaming Chen, Jonathan D. Werner, Magnus Nordborg, David E. Salt, Steve A. Kay, Joanne Chory, Detlef Weigel, Jonathan D.G. Jones, Joseph R. Ecker

Research output: Contribution to journalArticlepeer-review

143 Scopus citations


We used hybridization to the ATH1 gene expression array to interrogate genomic DNA diversity in 23 wild strains (accessions) of Arabidopsis thaliana (arabidopsis), in comparison with the reference strain Columbia (Col). At <1% false discovery rate, we detected 77,420 single-feature polymorphisms (SFPs) with distinct patterns of variation across the genome. Total and pair-wise diversity was higher near the centromeres and the heterochromatic knob region, but overall diversity was positively correlated with recombination rate (R 2 = 3.1%). The difference between total and pair-wise SFP diversity is a relative measure contrasting diversifying or frequency-dependent selection, similar to Tajima's D, and can be calibrated by the empirical genome-wide distribution. Each unique locus, centered on a gene, has a diversity and selection score that suggest a relative role in past evolutionary processes. Homologs of disease resistance (R) genes include members with especially high levels of diversity often showing frequency-dependent selection and occasionally evidence of a past selective sweep. Receptor-like and S-locus proteins also contained members with elevated levels of diversity and signatures of selection, whereas other gene families, bHLH, F-box, and RING finger proteins, showed more typical levels of diversity. SFPs identified with the gene expression array also provide an empirical hybridization polymorphism background for studies of gene expression polymorphism and are available through the genome browser

Original languageEnglish
Pages (from-to)12057-12062
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number29
StatePublished - Jul 17 2007


  • Evolutionary genomics
  • Gene array
  • Nucleotide diversity


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