Molecular,genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana |
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| Authors: | Paul Fransz Gabriella Linc Cheng‐Ruei Lee Saulo Alves Aflitos Jesse R. Lasky Christopher Toomajian Hoda Ali Janny Peters Peter van Dam Xianwen Ji Mateusz Kuzak Tom Gerats Ingo Schubert Korbinian Schneeberger Vincent Colot Rob Martienssen Maarten Koornneef Magnus Nordborg Thomas E. Juenger Hans de Jong Michael E. Schranz |
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| Affiliation: | 1. Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands;2. Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria;3. Biosystematics Group, Wageningen University, Wageningen, the Netherlands;4. Department of Biology, Pennsylvania State University, University Park, PA, USA;5. Department of Plant Pathology, Kansas State University, Manhattan, KS, USA;6. Department of Cytogenetics and Genome Analysis, The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany;7. Section 8. Plant Genetics, Institute for Wetland and Water Research Faculty of Science, Radboud University, Nijmegen, the Netherlands;9. Laboratory of Genetics, Wageningen University, Wageningen, the Netherlands;10. MAD, Dutch Genomics Service & Support Provider, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands;11. Max Planck Institute for Plant Breeding Research, K?ln, Germany;12. Unité de Recherche en Génomique Végétale (URGV), INRA/CNRS/UEVE 2 Rue Gaston Crémieux, Evry Cedex, France;13. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA;14. Department of Integrative Biology, University of Texas, Austin, TX, USA |
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| 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. |
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| Keywords: | chromosome rearrangement
Arabidopsis thaliana
transposon phylogenetic relationship introgression haplotype pattern |
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