Mapping Quantitative Trait Loci Interactions From the Maternal and Offspring Genomes

Abstract

The expression of most developmental or behavioral traits involves complex interactions between quantitative trait loci (QTL) from the maternal and offspring genomes. The maternal-offspring interactions play a pivotal role in shaping the direction and rate of evolution in terms of their substantial contribution to quantitative genetic (co)variation. To study the genetics and evolution of maternal-offspring interactions, a unifying statistical framework that embraces both the direct and indirect genetic effects of maternal and offspring QTL on any complex trait is developed. This model is derived for a simple backcross design within the maximum-likelihood context, implemented with the EM algorithm. Results from extensive simulations suggest that this model can provide reasonable estimation of additive and dominant effects of the QTL at different generations and their interaction effects derived from the maternal and offspring genomes. Although our model is framed to characterize the actions and interactions of maternal and offspring QTL affecting offspring traits, the idea can be readily extended to decipher the genetic machinery of maternal traits, such as maternal care. Our model provides a powerful means for studying the evolutionary significance of indirect genetic effects in any sexually reproductive organisms.

Mixed linear model approach for mapping quantitative trait loci underlying crop seed traits

“…False positive QTL(s) could be eliminated by model selection, while higher power and more accurate estimation of QTL effects could be achieved, benefiting from smaller and more accurate estimation of the residual effects because of background control. It should be noted that we have integrated the maternal genome into the model in addition to the offspring genome (Foolad and Jones, 1992;Cui et al, 2004;Hu and Xu, 2005;Wen and Wu, 2007), based on the view that development of embryo/endosperm traits partially depends on its own maternal plant.…”

“…It is well evidenced that additive and/or epistatic maternal effects, embryo effects, endosperm effects and gene-environment interaction effects are involved in the genetic development and evolution of crop seed (Zhang et al, 1999;Shi et al, 2000;Cui et al, 2004;Cui and Wu, 2005a,b;Cui et al, 2006). A considerable body of genetic models and statistical methods have been developed and applied to the analysis of real data.…”

Dissecting Genetic Architecture Underlying Seed Traits in Multiple Environments

“…With increasing recognition of the importance of epistasis in complex traits, it is appealing to develop a statistical model that integrates maternal and offspring genome into one mapping framework for dissecting the genetic networks of seed traits. General epistasis is defined as the interaction of two genes at different loci of the same genome; however, some studies have indicated that two epistatic genes can reside in different genomes (Cui et al 2004;Cui and Wu 2005a, b). Zhang et al (2004) proposed a statistical model for testing and estimating the effects of maternal-offspring genome interactions on embryo and endosperm traits during seed development in autogamous plants.…”

“…This approach can detect epistasis from different genomes, but at the price of ignoring maternal effects of a single QTL. Cui et al (2004;Cui and Wu 2005a,b) proposed a statistical method to detect the genetic mechanism of maternal-offspring genome interactions. Under the assumption that genetic expression of endosperm traits is controlled by both the maternal and the offspring genomes, the method can estimate the direct (offspring) effect, the indirect (maternal) effect, and the effects of maternal-offspring genome interaction simultaneously.…”

“…But this method is based on the arguable assumption that the two interacting QTL cannot have maternal and offspring effects simultaneously. In other words, the methods proposed by Cui et al (2004;Cui and Wu 2005a,b) can handle only an interaction of paired QTL in which one QTL has only a maternal effect while the other has only an endosperm effect. As the endosperm develops from the maternal plant, it is natural to consider that both maternal and offspring QTL can have phenotypic manifestations.…”