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

Quan Long, Fernando A. Rabanal, Dazhe Meng, Christian D. Huber, Ashley Farlow, Alexander Platzer, Qingrun Zhang, Bjarni J. Vilhjálmsson, Arthur Korte, Viktoria Nizhynska, Viktor Voronin, Pamela Korte, Laura Sedman, Terezie Mandáková, Martin A. Lysak, Ümit Seren, Ines Hellmann, Magnus Nordborg

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Abstract

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.

Original languageEnglish (US)
Pages (from-to)884-890
Number of pages7
JournalNature Genetics
Volume45
Issue number8
DOIs
StatePublished - Aug 2013

All Science Journal Classification (ASJC) codes

  • Genetics

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