Estimation of epistasis in doubled haploid barley populations considering interactions between all possible marker pairs

Jan Bocianowski

doi:10.1007/s10681-013-1018-8

Abstract

AbstractEpistasis, is the interaction between alleles from two or more loci determining complex traits, and thus plays an important role in the development of quantitative traits of crops. In mapping studies of inbreeding species epistasis is usually defined as the interactions between quantitative trait loci with significant additive gene effects. Indeed, in many studies, genes with small effects do not come into the final model and thus the total epistasis interaction effect is biased. Many loci may not have a significant direct effect on the trait under consideration, but they may still affect trait expression by interacting with other loci. In this paper the benefits of using all loci, not only the loci with significant main effects, for estimation of the epistatic effects are presented. The particular examples are with doubled haploids lines and so are restricted to homozygotes and thus additive genetic effects and additive × additive interactions. Numerical analyses were carried out on three populations of doubled haploid lines of barley (Hordeum vulgare L.): 120 doubled haploid lines from the Clipper × Sahara 3771 cross, 145 doubled haploid lines from the Harrington × TR306 cross and 150 doubled haploid lines from the Steptoe × Morex cross. In total, 157 sets of observations were analyzed and altogether 728 pairs of loci were observed for the three datasets.

Highlights

In homozygotes, additive-by-additive interactions (QTL-by-quantitative trait locus (QTL) interaction, gene–gene interaction or epistasis) can play a very important role in controlling the expression of quantitative traits and are typically defined as statistical deviation from the additive genetic effects
The genetic variation in continuous traits is usually governed by a polygenic network system, composed of many genes with small effect, and sometimes including one or a few genes with large effect
The statistical power to detect pairwise epistatic interactions is lower than for the main QTL because the tests of significance must be conducted for two intervals rather than just one, and a higher critical threshold per test must be applied to overcome the problem of multiple tests (Melchinger et al 2007)

Summary

Introduction

Additive-by-additive interactions (QTL-by-QTL interaction, gene–gene interaction or epistasis) can play a very important role in controlling the expression of quantitative traits and are typically defined as statistical deviation from the additive genetic effects. MAS schemes should be designed to exploit it. In the presence of epistasis, MAS generally yields more persistent responses than that based exclusively on additive or additive—dominance model. Neglecting epistasis could result in considerable loss in response, that will become more pronounced in later generations. Tests of epistasis are a powerful tool that developmental biologists use to determine the order of developmental triggers in gene regulation pathways, but such tests are most effective when alleles conferring complete loss-of-function of the genes under study are used

Objectives

Methods

Results

Conclusion