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

Abstract

Epistasis, 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 9 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 9 Sahara 3771 cross, 145 doubled haploid lines from the Harrington 9 TR306 cross and 150 doubled haploid lines from the Steptoe 9 Morex cross. In total, 157 sets of observations were analyzed and altogether 728 pairs of loci were observed for the three datasets.

Genome wide genetic dissection of wheat quality and yield related traits and their relationship with grain shape and size traits in an elite × non-adapted bread wheat cross

“…The role of epistasis in the genetic control of quantitative traits has been documented in many crops [92], including wheat [1, 70, 71], barley [93], maize [94], and rice [95, 96]. For grain protein content in two RIL populations, Kulwal et al [1] reported that epistatic interactions contributed a significantly higher portion of phenotypic variation than main effect QTL.…”

Genotype by environment interaction using AMMI model and estimation of additive and epistasis gene effects for 1000-kernel weight in spring barley (Hordeum vulgare L.)

“…Assessment of genetic parameters has a considerable role in spring barley breeding (Pal et al 2010 ; Bocianowski 2008 , 2014 ; Bocianowski et al 2016 ). The result reveals the significance of additive as well as epistasis gene effects of 1000-kernel weight in 2 years (2011 and 2013) of the research.…”

Estimation of additive and epistatic gene effects of doubled haploid lines of winter oilseed rape (Brassica napus L.)

“…parental, F 1 , F 2 , BC 1 . However, more effective estimation of additive and epistasis effects is on the basis of homozygous lines (Bocianowski 2012a(Bocianowski , 2013(Bocianowski , 2014Bocianowski and Nowosad 2015;Kim et al 2015;Monnahan and Kelly 2015;Ober et al 2015).…”