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Forsberg, Simon K. G.ORCID iD iconorcid.org/0000-0002-7451-9222
Publications (3 of 3) Show all publications
Zan, Y., Forsberg, S. K. G. & Carlborg, Ö. (2018). On the Relationship Between High-Order Linkage Disequilibrium and Epistasis. G3: Genes, Genomes, Genetics, 8(8), 2817-2824
Open this publication in new window or tab >>On the Relationship Between High-Order Linkage Disequilibrium and Epistasis
2018 (English)In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 8, no 8, p. 2817-2824Article in journal (Refereed) Published
Abstract [en]

A plausible explanation for statistical epistasis revealed in genome wide association analyses is the presence of high order linkage disequilibrium (LD) between the genotyped markers tested for interactions and unobserved functional polymorphisms. Based on findings in experimental data, it has been suggested that high order LD might be a common explanation for statistical epistasis inferred between local polymorphisms in the same genomic region. Here, we empirically evaluate how prevalent high order LD is between local, as well as distal, polymorphisms in the genome. This could provide insights into whether we should account for this when interpreting results from genome wide scans for statistical epistasis. An extensive and strong genome wide high order LD was revealed between pairs of markers on the high density 250k SNP-chip and individual markers revealed by whole genome sequencing in the Arabidopsis thaliana 1001-genomes collection. The high order LD was found to be more prevalent in smaller populations, but present also in samples including several hundred individuals. An empirical example illustrates that high order LD might be an even greater challenge in cases when the genetic architecture is more complex than the common assumption of bi-allelic loci. The example shows how significant statistical epistasis is detected for a pair of markers in high order LD with a complex multi allelic locus. Overall, our study illustrates the importance of considering also other explanations than functional genetic interactions when genome wide statistical epistasis is detected, in particular when the results are obtained in small populations of inbred individuals.

Place, publisher, year, edition, pages
GENETICS SOCIETY AMERICA, 2018
Keywords
Arabidopsis thaliana, epistasis, high order linkage disequilibrium, leaf, molybdenum
National Category
Genetics
Research subject
Biology
Identifiers
urn:nbn:se:uu:diva-356530 (URN)10.1534/g3.118.200513 (DOI)000440327400025 ()29945968 (PubMedID)
Funder
Swedish Research Council Formas, 2013-450Swedish Research Council, 2012-4634
Available from: 2018-07-31 Created: 2018-07-31 Last updated: 2018-11-12Bibliographically approved
Forsberg, S. K. G., Bloom, J. S., Sadhu, M. J., Kruglyak, L. & Carlborg, Ö. (2017). Accounting for genetic interactions improves modeling of individual quantitative trait phenotypes in yeast. Nature Genetics, 49(4), 497-503
Open this publication in new window or tab >>Accounting for genetic interactions improves modeling of individual quantitative trait phenotypes in yeast
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2017 (English)In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 49, no 4, p. 497-503Article in journal (Refereed) Published
Abstract [en]

Experiments in model organisms report abundant genetic interactions underlying biologically important traits, whereas quantitative genetics theory predicts, and data support, the notion that most genetic variance in populations is additive. Here we describe networks of capacitating genetic interactions that contribute to quantitative trait variation in a large yeast intercross population. The additive variance explained by individual loci in a network is highly dependent on the allele frequencies of the interacting loci. Modeling of phenotypes for multilocus genotype classes in the epistatic networks is often improved by accounting for the interactions. We discuss the implications of these results for attempts to dissect genetic architectures and to predict individual phenotypes and long-term responses to selection.

National Category
Medical Genetics
Identifiers
urn:nbn:se:uu:diva-316620 (URN)10.1038/ng.3800 (DOI)000397603700012 ()28250458 (PubMedID)
Funder
NIH (National Institute of Health), R01 GM102308 F32 GM116318Swedish Research Council, 621-2012-4632
Available from: 2017-03-06 Created: 2017-03-06 Last updated: 2018-01-18
Forsberg, S. K. G. & Carlborg, Ö. (2017). On the relationship between epistasis and genetic variance heterogeneity.. Journal of Experimental Botany, 68(20), 5431-5438
Open this publication in new window or tab >>On the relationship between epistasis and genetic variance heterogeneity.
2017 (English)In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, no 20, p. 5431-5438Article in journal (Refereed) Published
Abstract [en]

Epistasis and genetic variance heterogeneity are two non-additive genetic inheritance patterns that are often, but not always, related. Here we use theoretical examples and empirical results from earlier analyses of experimental data to illustrate the connection between the two. This includes an introduction to the relationship between epistatic gene action, statistical epistasis, and genetic variance heterogeneity, and a brief discussion about how genetic processes other than epistasis can also give rise to genetic variance heterogeneity.

Keywords
Epistasis, gene action, genetic variance heterogeneity, genotype–phenotype maps, non-additive, quantitative genetics
National Category
Genetics Medical Genetics
Identifiers
urn:nbn:se:uu:diva-332732 (URN)10.1093/jxb/erx283 (DOI)000417159100004 ()28992256 (PubMedID)
Funder
Swedish Research Council Formas, 2013-450
Available from: 2017-11-01 Created: 2017-11-01 Last updated: 2018-04-06Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-7451-9222

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