A Statistical Variance Components Framework for Mapping Imprinted Quantitative Trait Locus in Experimental Crosses

Current methods for mapping imprinted quantitative trait locus (iQTL) with inbred line crosses assume fixed QTL effects. When an iQTL segregates in experimental line crosses, combining different line crosses with similar genetic background can improve the accuracy of iQTLs inference. In this article, we develop a general interval-based statistical variance components framework to map iQTLs underlying complex traits by combining different backcross line crosses. We propose a new iQTL variance partition method based on the nature of marker alleles shared identical-by-decent (IBD) in inbred lines. Maternal effect is adjusted when testing imprinting. Efficient estimation methods with the maximum likelihood and the restricted maximum likelihood are derived and compared. Statistical properties of the proposed mapping strategy are evaluated through extensive simulations under different sampling designs. An extension to multiple QTL analysis is given. The proposed method will greatly facilitate genetic dissection of imprinted complex traits in inbred line crosses.

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