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Genome-wide association mapping reveals epistasis and genetic interaction networks in sugar beet

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Abstract

Epistasis is defined as interactions between alleles of two or more genetic loci. Detection of epistatic interactions is the key to understand the genetic architecture and gene networks underlying complex traits. Here, we examined the extent of epistasis for seven quantitative traits with an association mapping approach in a large population of elite sugar beet lines. We found that correction for population stratification is required and that in terms of reducing the false-positive rate the mixed model approach including the kinship matrix performed best. In genome-wide scans, we detected both main effects and epistatic QTL. For physiological traits, the detected digenic and higher-order epistasis explained a considerable proportion of the genotypic variance. We illustrate that the identified epistatic interactions define comprehensive genetic networks, which may serve as starting points towards a systems-oriented approach to understand the regulation of complex traits.

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Acknowledgments

This research was conducted within the Biometric and Bioinformatic Tools for Genomics based Plant Breeding project supported by the German Federal Ministry of Education and Research (BMBF) within the framework of GABI-FUTURE initiative.

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Authors and Affiliations

  1. State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany

    Tobias Würschum, Hans Peter Maurer & Jochen Christoph Reif

  2. Bioinformatics Unit, Institute for Crop Production and Grassland Research, University of Hohenheim, 70593, Stuttgart, Germany

    Jens Möhring

  3. KWS SAAT AG, 37574, Einbeck, Germany

    Britta Schulz

Authors
  1. Tobias Würschum
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  2. Hans Peter Maurer
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  3. Britta Schulz
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  4. Jens Möhring
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  5. Jochen Christoph Reif
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Corresponding author

Correspondence to Tobias Würschum.

Additional information

Communicated by F. van Eeuwijk.

Electronic supplementary material

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122_2011_1570_MOESM1_ESM.eps

Supplementary Figure S1 The 22 parents (1-22) with their male and female grandparents (23-40) are shown and the number of genotypes in the data set to which these parents contributed either as male or as female parent (progeny) (EPS 674 kb)

122_2011_1570_MOESM2_ESM.eps

Supplementary Figure S2 Plot of observed vs. expected P values for the epistasis scan with the model including the kinship matrix (K). (WSY, white sugar yield, SY, sugar yield, SC, sugar content, BY, beet yield, K, potassium, Na, sodium, N, α-amino nitrogen) (EPS 3480 kb)

122_2011_1570_MOESM3_ESM.eps

Supplementary Figure S3 (A) 2-way epistatic QTL and (B) 3-way epistatic QTL. The chromosomes are depicted as black lines. Interacting loci are connected by lines where the line strength indicates the size of the QTL effects for white sugar yield (WSY), sugar yield (SY), sugar content (SC), beet yield (BY), potassium (K), sodium (Na), and α-amino nitrogen (N). (EPS 1257 kb)

Supplementary Table S1 (DOCX 14 kb)

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Würschum, T., Maurer, H.P., Schulz, B. et al. Genome-wide association mapping reveals epistasis and genetic interaction networks in sugar beet. Theor Appl Genet 123, 109–118 (2011). https://doi.org/10.1007/s00122-011-1570-3

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  • DOI: https://doi.org/10.1007/s00122-011-1570-3

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