The imprinting patterns were determined using the mixed model approach and are given by the relationship between the additive (a), dominance (d) and parent-of-origin genotype value (i) [ 36].
The exact origin of the P. tremuloides parent of these genotypes was often less precisely known but represented various states and regions along the border of the USA with Canada.
Whether the genome-wide preferential expression as effected by water-limiting conditions is maternal parent-of-origin or genotype-dependent is yet to be concluded.
A popular design for the investigation of such effects, including effects of parent-of-origin (imprinting), maternal genotype, and maternal-fetal genotype interactions, is to collect DNA from affected offspring and their mothers (case/mother duos) and to compare with an appropriate control sample.
The 'conditioning on exchangeable parental genotypes' (CEPG) method [ Cordell et al., 2004] is an extension of the CPG approach to detecting parent-of-origin or maternal genotype effects by assuming exchangeability of parental genotypes.
In sum, we here observed that if a genotype network is connected at size n, the genotype network formed by the parents of its genotypes is also connected.
Likewise, the application of three levels of reduced density SNP panels (approximately one marker every 5, 0.7 and 0.35 cM) in pigs showed that imputation accuracy would be higher than 0.9 provided that both parents of individuals genotyped at low density are genotyped at high density.
We compared this approach to a prospective aproach, the QTDTM and also extended the QTDTM to allow analysis of multiple linked loci (including multi-locus haplotypes), parent-of-origin or maternal genotype effects.
Like Cordell et al. [2004], we introduce an additional conditioning event χ corresponding to the event that parent-of-origin and maternal genotype can be deduced in the trio.
The method allows genotype and haplotype analysis at an arbitrary number of linked and unlinked multiallelic loci, as well as modelling of more complex effects such as epistasis, parent-of-origin effects, maternal genotype and mother-child interaction effects, and gene-environment interactions.
