Framework for dissection of complex cytonuclear epistasis by a two-dimensional genome scan

Epistasis between cytoplasmic and nuclear genes is the primary genetic component of complex quantitative traits. Genetic dissection of cytonuclear epistasis is fundamentally important to understand the genetic architecture of complex traits. In this study, a two-dimensional genome scan strategy was employed to evaluate the contribution of cytoplasm, quantitative trait loci (QTL), QTL×QTL interactions and QTL×QTL×cytoplasm interactions to the phenotypic variation. The p-value and parameter value for each genetic effect were calculated by multiple regression analysis. A stepwise approach was suggested to build confidence in candidate QTL on the basis of q-value estimation, false discovery rate calculation and Bonferroni adjustment. A fine-scale grid scan strategy was proposed for further analysis of peaks of interest. Plant height in maize was used as an example to illustrate the efficiency of the two-dimensional genome scan strategy.