title: Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana.
abstract: Chromosomal inversions can provide windows onto the cytogenetic, molecular, evolutionary and demographic histories of a species. Here we investigate a paracentric 1.17-Mb inversion on chromosome 4 of Arabidopsis thaliana with nucleotide precision of its borders. The inversion is created by Vandal transposon activity, splitting an F-box and relocating a pericentric heterochromatin segment in juxtaposition with euchromatin without affecting the epigenetic landscape. Examination of the RegMap panel and the 1001 Arabidopsis genomes revealed more than 170 inversion accessions in Europe and North America. The SNP patterns revealed historical recombinations from which we infer diverse haplotype patterns, ancient introgression events and phylogenetic relationships. We find a robust association between the inversion and fecundity under drought. We also find linkage disequilibrium between the inverted region and the early flowering Col-FRIGIDA allele. Finally, SNP analysis elucidates the origin of the inversion to South-Eastern Europe approximately 5000 years ago and the FRI-Col allele to North-West Europe, and reveals the spreading of a single haplotype to North America during the 17th to 19th century. The 'American haplotype' was identified from several European localities, potentially due to return migration.
authors.affiliation: Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Paul
authors.initials: P
authors.lastname: Fransz
authors.affiliation: Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Gabriella
authors.initials: G
authors.lastname: Linc
authors.affiliation: Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, Vienna, 1030, Austria.
authors.forename: Cheng-Ruei
authors.initials: CR
authors.lastname: Lee
authors.affiliation: Biosystematics Group, Wageningen University, Wageningen, the Netherlands.
authors.forename: Saulo Alves
authors.initials: SA
authors.lastname: Aflitos
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, PA, USA.
authors.forename: Jesse R
authors.initials: JR
authors.lastname: Lasky
authors.affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Toomajian
authors.affiliation: Department of Cytogenetics and Genome Analysis, The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
authors.forename: Hoda
authors.initials: H
authors.lastname: Ali
authors.affiliation: Section Plant Genetics, Institute for Wetland and Water Research Faculty of Science, Radboud University, Nijmegen, the Netherlands.
authors.forename: Janny
authors.initials: J
authors.lastname: Peters
authors.affiliation: Section Plant Genetics, Institute for Wetland and Water Research Faculty of Science, Radboud University, Nijmegen, the Netherlands.
authors.forename: Peter
authors.initials: P
authors.lastname: van Dam
authors.affiliation: Laboratory of Genetics, Wageningen University, Wageningen, the Netherlands.
authors.forename: Xianwen
authors.initials: X
authors.lastname: Ji
authors.affiliation: MAD, Dutch Genomics Service & Support Provider, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Mateusz
authors.initials: M
authors.lastname: Kuzak
authors.affiliation: Section Plant Genetics, Institute for Wetland and Water Research Faculty of Science, Radboud University, Nijmegen, the Netherlands.
authors.forename: Tom
authors.initials: T
authors.lastname: Gerats
authors.affiliation: Department of Cytogenetics and Genome Analysis, The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
authors.forename: Ingo
authors.initials: I
authors.lastname: Schubert
authors.affiliation: Max Planck Institute for Plant Breeding Research, Köln, 50829, Germany.
authors.forename: Korbinian
authors.initials: K
authors.lastname: Schneeberger
authors.affiliation: Unité de Recherche en Génomique Végétale (URGV), INRA/CNRS/UEVE 2 Rue Gaston Crémieux, Evry Cedex, 91057, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Colot
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA.
authors.forename: Rob
authors.initials: R
authors.lastname: Martienssen
authors.affiliation: Laboratory of Genetics, Wageningen University, Wageningen, the Netherlands.|Max Planck Institute for Plant Breeding Research, Köln, 50829, Germany.
authors.forename: Maarten
authors.initials: M
authors.lastname: Koornneef
authors.affiliation: Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, Vienna, 1030, Austria.
authors.forename: Magnus
authors.initials: M
authors.lastname: Nordborg
authors.affiliation: Department of Integrative Biology, University of Texas, Austin, TX, USA.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Juenger
authors.affiliation: Laboratory of Genetics, Wageningen University, Wageningen, the Netherlands.
authors.forename: Hans
authors.initials: H
authors.lastname: de Jong
authors.affiliation: Biosystematics Group, Wageningen University, Wageningen, the Netherlands.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Schranz
mesh_terms: D017360:Arabidopsis / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D032461:Chromosomes, Plant / Q000235:genetics; D019143:Evolution, Molecular; D006239:Haplotypes / Q000235:genetics; D015810:Linkage Disequilibrium / Q000235:genetics; D010802:Phylogeny
chemical_list: D029681:Arabidopsis Proteins
keywords: 
  Arabidopsis thaliana
  ; chromosome rearrangement; haplotype pattern; introgression; phylogenetic relationship; transposon