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

Abstract
Data availability
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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.

Data availability

The following data sets were generated

1. Kerdaffrec E
2. Filiault DL
3. Korte A
4. Sasaki E
5. Nizhynska V
6. Seren U
7. Nordborg M
(2016) Low coverage sequencing of three A. thaliana F2 populations for QTL mapping
Publicly available at the NCBI BioProject (accession no: PRJNA343766).

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA343766
1. Kerdaffrec E
2. Filiault DL
3. Korte A
4. Sasaki E
5. Nizhynska V
6. Seren U
7. Nordborg M
(2016) Low coverage sequencing of A. thaliana samples from Swedish field experiments
Publicly available at the NCBI BioProject (accession no: PRJNA343768).

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA343768

The following previously published data sets were used

1. Long Q
2. Rabanal FA
3. Meng D
4. Huber CD
5. Farlow A
6. Platzer A
7. Zhang Q
8. Vilhjálmsson BJ
9. Korte A
10. Nizhynska V
11. Voronin V
12. Korte P
13. Sedman L
14. Mandáková T
15. Lysak MA
16. Seren Ü
17. Hellmann I
18. Nordborg M
(2013) Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden
Publicly available at Github (https://github.com).

https://github.com/Gregor-Mendel-Institute/swedish-genomes

Article and author information

Author details

Envel Kerdaffrec

Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0001-8667-6850
Danièle L Filiault

Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria

Competing interests
No competing interests declared.
Arthur Korte

Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0003-0831-1463
Eriko Sasaki

Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria

Competing interests
No competing interests declared.
Viktoria Nizhynska

Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria

Competing interests
No competing interests declared.
Ümit Seren

Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria

Competing interests
No competing interests declared.
Magnus Nordborg

Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria

For correspondence
magnus.nordborg@gmi.oeaw.ac.at

Competing interests
Magnus Nordborg, Reviewing editor, eLife.

"This ORCID iD identifies the author of this article:" 0000-0001-7178-9748

Funding

European Research Council (268962 (MAXMAP))

Magnus Nordborg

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.