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

Fransz, P., Linc, G., Lee, C. R., Aflitos, S. A., Lasky, J. R., Toomajian, C., Ali, H., Peters, J., van Dam, P., Ji, X., Kuzak, M., Gerats, T., Schubert, I., Schneeberger, K., Colot, V., Martienssen, R., Koornneef, M., Nordborg, M., Juenger, T. E., de Jong, H., Schranz, M. E. (October 2016) Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana. Plant J, 88 (2). pp. 159-178. ISSN 1365-313X (Electronic)0960-7412 (Linking)

URL: https://www.ncbi.nlm.nih.gov/pubmed/27436134
DOI: 10.1111/tpj.13262

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.

Item Type: Paper
Uncontrolled Keywords: Arabidopsis thaliana chromosome rearrangement haplotype pattern introgression phylogenetic relationship transposon
Subjects: organism description > plant > Arabidopsis
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosome
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosomes, structure and function > chromosome

bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transposons
CSHL Authors:
Communities: CSHL labs > Martienssen lab
Depositing User: Matt Covey
Date: October 2016
Date Deposited: 15 Dec 2016 20:35
Last Modified: 15 Dec 2016 20:35
PMCID: PMC5113708
Related URLs:
URI: http://repository.cshl.edu/id/eprint/33939

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