Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

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Authors

LONG Quan RABANAL Fernando A. MENG Dazhe HUBER Christian D. FARLOW Ashley PLATZER Alexander ZHANG Qingrun VILHJÁLMSSON Bjarni J. KORTE Arthur NIZHYNSKA Viktoria VORONIN Viktor KORTE Pamela SEDMAN Laura MANDÁKOVÁ Terezie LYSÁK Martin SEREN Uemit HELLMANN Ines NORDBORG Magnus

Year of publication 2013
Type Article in Periodical
Magazine / Source Nature Genetics
MU Faculty or unit

Central European Institute of Technology

Citation
Web http://www.nature.com/ng/journal/v45/n8/full/ng.2678.html
Doi http://dx.doi.org/10.1038/ng.2678
Field Genetics and molecular biology
Keywords RIBOSOMAL-RNA GENES; LINKAGE DISEQUILIBRIUM; WIDE ASSOCIATION; NATURAL VARIATION; DNA; POPULATIONS; SEQUENCE; POLYMORPHISM; METHYLATION; ACCESSIONS
Description Despite advances in sequencing, the goal of obtaining a comprehensive view of genetic variation in populations is still far from reached. We sequenced 180 lines of A. thaliana from Sweden to obtain as complete a picture as possible of variation in a single region. Whereas simple polymorphisms in the unique portion of the genome are readily identified, other polymorphisms are not. The massive variation in genome size identified by flow cytometry seems largely to be due to 45S rDNA copy number variation, with lines from northern Sweden having particularly large numbers of copies. Strong selection is evident in the form of long-range linkage disequilibrium (LD), as well as in LD between nearby compensatory mutations. Many footprints of selective sweeps were found in lines from northern Sweden, and a massive global sweep was shown to have involved a 700-kb transposition.
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