title: Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana.
abstract: 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 http://signal.salk.edu/cgi-bin/AtSFP.
authors.affiliation: Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA. borevitz@uchicago.edu
authors.forename: Justin O
authors.initials: JO
authors.lastname: Borevitz
authors.forename: Samuel P
authors.initials: SP
authors.lastname: Hazen
authors.forename: Todd P
authors.initials: TP
authors.lastname: Michael
authors.forename: Geoffrey P
authors.initials: GP
authors.lastname: Morris
authors.forename: Ivan R
authors.initials: IR
authors.lastname: Baxter
authors.forename: Tina T
authors.initials: TT
authors.lastname: Hu
authors.forename: Huaming
authors.initials: H
authors.lastname: Chen
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Werner
authors.forename: Magnus
authors.initials: M
authors.lastname: Nordborg
authors.forename: David E
authors.initials: DE
authors.lastname: Salt
authors.forename: Steve A
authors.initials: SA
authors.lastname: Kay
authors.forename: Joanne
authors.initials: J
authors.lastname: Chory
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
authors.forename: Jonathan D G
authors.initials: JD
authors.lastname: Jones
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Ecker
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D032461:Chromosomes, Plant / Q000235:genetics; D017343:Genes, Plant; D018745:Genome, Plant / Q000235:genetics*; D006239:Haplotypes; D011110:Polymorphism, Genetic; D012641:Selection, Genetic