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

Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Research Abstract Details 

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Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Abstract Text:

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,

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.

Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Publishing Authors By Initials

JO Borevitz,SP Hazen,TP Michael,GP Morris,IR Baxter,TT Hu,H Chen,JD Werner,M Nordborg,DE Salt,SA Kay,J Chory,D Weigel,JD Jones,JR Ecker,

For similar genetic processes: selection (genetics) research abstracts see: genetic processes: selection (genetics) research

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Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Proceedings of the National Academy of Sciences of

VOLUME: 104

Page Numbers: 12057-62

Journal Abbreviation: Proc. Natl. Acad. Sci. U.S.A.

ISSN: 0027-8424

DAY: 12

MONTH: 07

YEAR: 2007

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

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LANGUAGE: eng

NlmUniqueID: 7505876

Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Keywords Mesh Terms:

KEYWORDS: Selection (Genetics)

MESH TERMS: genetics

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Grant and Affiliation Information for Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana.

AFFILIATION: Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA. borevitz@uchicago.edu

Country: United States

AGENCY: United States NIGMS

GRANT: R01GM073822

ACRONYM: GM

MEDLINETA: Proc Natl Acad Sci U S A

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