Multiple alleles at a single locus control seed dormancy in Swedish Arabidopsis

Envel Kerdaffrec; Danièle L. Filiault; Arthur Korte; Eriko Sasaki; Viktoria Nizhynska; Ümit Seren; Magnus Nordborg

doi:10.7554/eLife.22502

Multiple alleles at a single locus control seed dormancy in Swedish Arabidopsis

Envel Kerdaffrec, Danièle L. Filiault, Arthur Korte, Eriko Sasaki, Viktoria Nizhynska, Ümit Seren, Magnus Nordborg

Research output: Contribution to journal › Article › peer-review

40 Citations (Scopus)

Abstract

Seed dormancy is a complex life history trait that determines the timing of germination and is crucial for local adaptation. Genetic studies of dormancy are challenging, because the trait is highly plastic and strongly influenced by the maternal environment. Using a combination of statistical and experimental approaches, we show that multiple alleles at the previously identified dormancy locus DELAY OF GERMINATION1 jointly explain as much as 57% of the variation observed in Swedish Arabidopsis thaliana, but give rise to spurious associations that seriously mislead genome-wide association studies unless modeled correctly. Field experiments confirm that the major alleles affect germination as well as survival under natural conditions, and demonstrate that locally adaptive traits can sometimes be dissected genetically.

Original language	English
Article number	e22502
Journal	eLife
Volume	5
Issue number	DECEMBER2016
DOIs	https://doi.org/10.7554/eLife.22502
Publication status	Published - Dec 14 2016
Externally published	Yes

All Science Journal Classification (ASJC) codes

Neuroscience(all)
Immunology and Microbiology(all)
Biochemistry, Genetics and Molecular Biology(all)

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10.7554/eLife.22502

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abstract = "Seed dormancy is a complex life history trait that determines the timing of germination and is crucial for local adaptation. Genetic studies of dormancy are challenging, because the trait is highly plastic and strongly influenced by the maternal environment. Using a combination of statistical and experimental approaches, we show that multiple alleles at the previously identified dormancy locus DELAY OF GERMINATION1 jointly explain as much as 57% of the variation observed in Swedish Arabidopsis thaliana, but give rise to spurious associations that seriously mislead genome-wide association studies unless modeled correctly. Field experiments confirm that the major alleles affect germination as well as survival under natural conditions, and demonstrate that locally adaptive traits can sometimes be dissected genetically.",

author = "Envel Kerdaffrec and Filiault, {Dani{\`e}le L.} and Arthur Korte and Eriko Sasaki and Viktoria Nizhynska and {\"U}mit Seren and Magnus Nordborg",

note = "Funding Information: This work was supported by European Research Council grant 268962 (MAXMAP) to MN. We thank members of the Nordborg lab for illuminating discussions, Caroline Broyart, Malte J{\"o}nsson, Nils J{\"o}nsson, Svante Holm, Torbj{\"o}rn S{\"a}ll and Ann Espelund for help with the field experiments, Wim Soppe and Santosh Satbhai for providing us with biological material, Bjarni J Vilhj{\'a} lmsson for making the {\textquoteleft}mixmogam{\textquoteright} package available, the VBCF NGS Unit (www.vbcf.ac.at) for performing Illumina sequencing, Harald Scheuch for running the 384-SNP Illumina GoldenGate genotyping assays, and Joy Bergelson and Caroline Dean for comments on the manuscript. Publisher Copyright: {\textcopyright} Kerdaffrec et al.",

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AU - Filiault, Danièle L.

AU - Korte, Arthur

AU - Sasaki, Eriko

AU - Nizhynska, Viktoria

AU - Seren, Ümit

AU - Nordborg, Magnus

N1 - Funding Information: This work was supported by European Research Council grant 268962 (MAXMAP) to MN. We thank members of the Nordborg lab for illuminating discussions, Caroline Broyart, Malte Jönsson, Nils Jönsson, Svante Holm, Torbjörn Säll and Ann Espelund for help with the field experiments, Wim Soppe and Santosh Satbhai for providing us with biological material, Bjarni J Vilhjá lmsson for making the ‘mixmogam’ package available, the VBCF NGS Unit (www.vbcf.ac.at) for performing Illumina sequencing, Harald Scheuch for running the 384-SNP Illumina GoldenGate genotyping assays, and Joy Bergelson and Caroline Dean for comments on the manuscript. Publisher Copyright: © Kerdaffrec et al.

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Multiple alleles at a single locus control seed dormancy in Swedish Arabidopsis

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