Mixed linear model approaches in mapping QTLs with epistatic effects by a simulation study

Abstract

Epistasis refers to the phenotypic effects of interactions between alleles of different loci. Statistical detection of such interactions remains to be the subject of presented studies. A method based on mixed linear model was developed for mapping QTLs with digenic epistasis. Reliable estimates of QTL additive and epistasis effects can be obtained by the maximum-likelihood estimate methods. Likelihood ratio and t statistics were combined for testing hypotheses about QTL effects (additive and epistasis effects). Monte Carlo simulations were conducted for evaluating the unbiasedness, accuracy and power for parameter estimation in QTL mapping. The results indicated that the mixed-model approaches could provide unbiased estimates for effects of QTLs. Additionally, the mixed-model approaches also showed high accuracy in mapping QTLs with epistasis effects. The information obtained in this study will be useful for manipulating the QTLs for plant breeding by marker assisted selection.

<b>Identification of QTL underlying agronomic, morphological and physiological traits in barley under rainfed conditions using SNP markers

“…This method requires the identification of groups of extreme lines, i.e., lines with the minimal and maximal expression levels of the trait under consideration. The group of minimal lines consists of the lines that contain, theoretically, only alleles reducing the value of the trait, and the group of maximal lines contains the lines that only have alleles increasing the trait value (Bocianowski & Nowosad, 2015). These groups were determined using the quantile method described by Bocianowski Krajewski and Kaczmarek, (1999 …”

Estimation of heterosis for yield-related traits for single cross and three-way cross hybrids of oilseed rape (Brassica napus L.)

“…This is one of the mechanisms that maintains polymorphism in the population. Epistasis (Goodnight 1999;Bocianowski 2012;Bocianowski and Nowosad 2015) is the interaction of non-allelic genes. One gene masks the expression of another, and several pairs of alleles determine a single feature in hybrids.…”

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).…”