Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel

Matthew W. Horton, Angela M. Hancock, Yu S. Huang, Christopher Toomajian, Susanna Atwell, Adam Auton, N. Wayan Muliyati, Alexander Platt, F. Gianluca Sperone, Bjarni J. Vilhjálmsson, Magnus Nordborg, Justin O. Borevitz, Joy Bergelson

Research output: Contribution to journalArticle

253 Citations (Scopus)

Abstract

Arabidopsis thaliana is native to Eurasia and is naturalized across the world. Its ability to be easily propagated and its high phenotypic variability make it an ideal model system for functional, ecological and evolutionary genetics. To date, analyses of the natural genetic variation of A. thaliana have involved small numbers of individual plants or genetic markers. Here we genotype 1,307 worldwide accessions, including several regional samples, using a 250K SNP chip. This allowed us to produce a high-resolution description of the global pattern of genetic variation. We applied three complementary selection tests and identified new targets of selection. Further, we characterized the pattern of historical recombination in A. thaliana and observed an enrichment of hotspots in its intergenic regions and repetitive DNA, which is consistent with the pattern that is observed for humans but which is strikingly different from that observed in other plant species. We have made the seeds we used to produce this Regional Mapping (RegMap) panel publicly available. This panel comprises one of the largest genomic mapping resources currently available for global natural isolates of a non-human species.

Original languageEnglish (US)
Pages (from-to)212-216
Number of pages5
JournalNature Genetics
Volume44
Issue number2
DOIs
StatePublished - Feb 2012
Externally publishedYes

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Arabidopsis
Genome
Intergenic DNA
Genetic Markers
Genetic Recombination
Single Nucleotide Polymorphism
Ecosystem
Seeds
Genotype
DNA

ASJC Scopus subject areas

  • Genetics

Cite this

Horton, M. W., Hancock, A. M., Huang, Y. S., Toomajian, C., Atwell, S., Auton, A., ... Bergelson, J. (2012). Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nature Genetics, 44(2), 212-216. https://doi.org/10.1038/ng.1042

Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. / Horton, Matthew W.; Hancock, Angela M.; Huang, Yu S.; Toomajian, Christopher; Atwell, Susanna; Auton, Adam; Muliyati, N. Wayan; Platt, Alexander; Sperone, F. Gianluca; Vilhjálmsson, Bjarni J.; Nordborg, Magnus; Borevitz, Justin O.; Bergelson, Joy.

In: Nature Genetics, Vol. 44, No. 2, 02.2012, p. 212-216.

Research output: Contribution to journalArticle

Horton, MW, Hancock, AM, Huang, YS, Toomajian, C, Atwell, S, Auton, A, Muliyati, NW, Platt, A, Sperone, FG, Vilhjálmsson, BJ, Nordborg, M, Borevitz, JO & Bergelson, J 2012, 'Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel', Nature Genetics, vol. 44, no. 2, pp. 212-216. https://doi.org/10.1038/ng.1042
Horton, Matthew W. ; Hancock, Angela M. ; Huang, Yu S. ; Toomajian, Christopher ; Atwell, Susanna ; Auton, Adam ; Muliyati, N. Wayan ; Platt, Alexander ; Sperone, F. Gianluca ; Vilhjálmsson, Bjarni J. ; Nordborg, Magnus ; Borevitz, Justin O. ; Bergelson, Joy. / Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. In: Nature Genetics. 2012 ; Vol. 44, No. 2. pp. 212-216.
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