Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana

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 JongEric Schranz

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

61 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)159-178
JournalThe Plant Journal
Issue number2
Publication statusPublished - 2016


  • Arabidopsis thaliana
  • Chromosome rearrangement
  • Haplotype pattern
  • Introgression
  • Phylogenetic relationship
  • Transposon


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