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

doi:10.1038/ng.2678

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

Biology

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286 Scopus citations

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 language	English (US)
Pages (from-to)	884-890
Number of pages	7
Journal	Nature Genetics
Volume	45
Issue number	8
DOIs	https://doi.org/10.1038/ng.2678
State	Published - Aug 2013

All Science Journal Classification (ASJC) codes

Genetics

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10.1038/ng.2678

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Long, Q., Rabanal, F. A., Meng, D., Huber, C. D., Farlow, A., Platzer, A., Zhang, Q., Vilhjálmsson, B. J., Korte, A., Nizhynska, V., Voronin, V., Korte, P., Sedman, L., Mandáková, T., Lysak, M. A., Seren, Ü., Hellmann, I., & Nordborg, M. (2013). Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nature Genetics, 45(8), 884-890. https://doi.org/10.1038/ng.2678

@article{b3345709cdb1487fa6d09fb0671aef9c,

title = "Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden",

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.",

author = "Quan Long and Rabanal, {Fernando A.} and Dazhe Meng and Huber, {Christian D.} and Ashley Farlow and Alexander Platzer and Qingrun Zhang and Vilhj{\'a}lmsson, {Bjarni J.} and Arthur Korte and Viktoria Nizhynska and Viktor Voronin and Pamela Korte and Laura Sedman and Terezie Mand{\'a}kov{\'a} and Lysak, {Martin A.} and {\"U}mit Seren and Ines Hellmann and Magnus Nordborg",

note = "Funding Information: Programme 7 grant 283496 transPLANT to M.N., by the Austrian Science Fund (Vienna Graduate School of Population Genetics, FWF W1225) to I.H. and by Czech Science Foundation grants P501/12/G090 and P506/12/0668 to M.A.L. Funding Information: We thank O. Mittelsten Scheid for comments on the manuscript, J. Dolezel for providing a size standard for flow cytometry, G. Schmauss for technical assistance with flow cytometry, N. Lettner for help with sample preparation, A. Sommer for help with sequencing and the Gregor Mendel Institute IT team (in particular, P. Forai) for excellent cluster support. This work was supported by European Research Council grant 268962 MAXMAP and European Community Framework",

year = "2013",

month = aug,

doi = "10.1038/ng.2678",

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Long, Q, Rabanal, FA, Meng, D, Huber, CD, Farlow, A, Platzer, A, Zhang, Q, Vilhjálmsson, BJ, Korte, A, Nizhynska, V, Voronin, V, Korte, P, Sedman, L, Mandáková, T, Lysak, MA, Seren, Ü, Hellmann, I & Nordborg, M 2013, 'Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden', Nature Genetics, vol. 45, no. 8, pp. 884-890. https://doi.org/10.1038/ng.2678

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T1 - Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

AU - Long, Quan

AU - Rabanal, Fernando A.

AU - Meng, Dazhe

AU - Huber, Christian D.

AU - Farlow, Ashley

AU - Platzer, Alexander

AU - Zhang, Qingrun

AU - Vilhjálmsson, Bjarni J.

AU - Korte, Arthur

AU - Nizhynska, Viktoria

AU - Voronin, Viktor

AU - Korte, Pamela

AU - Sedman, Laura

AU - Mandáková, Terezie

AU - Lysak, Martin A.

AU - Seren, Ümit

AU - Hellmann, Ines

AU - Nordborg, Magnus

N1 - Funding Information: Programme 7 grant 283496 transPLANT to M.N., by the Austrian Science Fund (Vienna Graduate School of Population Genetics, FWF W1225) to I.H. and by Czech Science Foundation grants P501/12/G090 and P506/12/0668 to M.A.L. Funding Information: We thank O. Mittelsten Scheid for comments on the manuscript, J. Dolezel for providing a size standard for flow cytometry, G. Schmauss for technical assistance with flow cytometry, N. Lettner for help with sample preparation, A. Sommer for help with sequencing and the Gregor Mendel Institute IT team (in particular, P. Forai) for excellent cluster support. This work was supported by European Research Council grant 268962 MAXMAP and European Community Framework

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N2 - 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.

AB - 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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JO - Nature Genetics

JF - Nature Genetics

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

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