University of Oulu

Mathew, B., Léon, J., Sannemann, W., Sillanpää, M. (2017) Detection of Epistasis for Flowering Time Using Bayesian Multilocus Estimation in a Barley MAGIC Population. GENETICS, 208 (2), 525-536. doi:10.1534/genetics.117.300546

Detection of epistasis for flowering time using Bayesian multilocus estimation in a barley MAGIC population

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Author: Mathew, Boby1; Léon, Jens1; Sannemann, Wiebke2;
Organizations: 1Institute of Crop Science and Resource Conservation, University of Bonn, 53115, Germany
2Plant Breeding, Martin Luther University of Halle-Wittenberg, 06120, Germany
3Department of Mathematical Sciences, University of Oulu, FIN-90014, Finland
4Biocenter Oulu, University of Oulu, FIN-90014, Finland
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 1.5 MB)
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Language: English
Published: Genetics Society of America, 2018
Publish Date: 2019-07-09


Gene-by-gene interactions, also known as epistasis, regulate many complex traits in different species. With the availability of low-cost genotyping it is now possible to study epistasis on a genome-wide scale. However, identifying genome-wide epistasis is a high-dimensional multiple regression problem and needs the application of dimensionality reduction techniques. Flowering Time (FT) in crops is a complex trait that is known to be influenced by many interacting genes and pathways in various crops. In this study, we successfully apply Sure Independence Screening (SIS) for dimensionality reduction to identify two-way and three-way epistasis for the FT trait in a Multiparent Advanced Generation Inter-Cross (MAGIC) barley population using the Bayesian multilocus model. The MAGIC barley population was generated from intercrossing among eight parental lines and thus, offered greater genetic diversity to detect higher-order epistatic interactions. Our results suggest that SIS is an efficient dimensionality reduction approach to detect high-order interactions in a Bayesian multilocus model. We also observe that many of our findings (genomic regions with main or higher-order epistatic effects) overlap with known candidate genes that have been already reported in barley and closely related species for the FT trait.

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Series: Genetics
ISSN: 0016-6731
ISSN-E: 1943-2631
ISSN-L: 0016-6731
Volume: 208
Issue: 2
Pages: 525 - 536
DOI: 10.1534/genetics.117.300546
Type of Publication: A1 Journal article – refereed
Field of Science: 111 Mathematics
1181 Ecology, evolutionary biology
Funding: The phenotyping work was supported by the German Federal Ministry of Education and Research and was conducted in the network (Förder-Nr. 0315529). The genotyping work was funded by Europäische Fonds für Regionale Entwicklung (Förderkennzeichen: z1011bc001).
Copyright information: © 2018 by the Genetics Society of America Available freely online through the author-supported open access option. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.