Briefly, we first determined the most likely marker linkage phase for all genotyped animals (i.e. sires and daughters) using purpose-built software (Farnir, unpublished).
More recently, Lin et al 15 have proposed a likelihood model for estimating QTL locations and QTL effects in an outcrossed family by jointly considering possible QTL-marker linkage phases.
For the sex-specific markers, the linkage phases were inferred automatically, while for the markers with 1 : 2 : 1 segregation type (AB × AB), the linkage phase was deduced based on the genotypes of grandparents to assist the map construction.
Presently, MAS could be done on the bulk of the population using linkage information, since QTL genotypes and marker-QTL linkage phases were established for 72% of the parents of the current generation (a number that can be increased by adding genotypes).
The overall genotyping error rate was estimated within the 0.0005-0.05 range, the "checkalleles" function was used to detect markers with erroneous linkage phases and the "droponemarker" function to spot suspicious markers.
Validation failure may be due to a lack of true associations between the trait and marker but could also be caused by differences in SNP frequencies, different marker-causative mutation linkage phases, genotype-by-environment interactions or epistasis as well as sample size effects and the way the trait is measured.
The use of a subset of markers (i.e. eight initial markers or five ripple markers) that is made up of BI markers of both maternal linkage phases and less than two anchoring markers, results in an unreliable suggested marker order.
When the marker is present in both grandparents, the linkage phase is determined by the software based on co-segregation in the F2 with markers for which linkage phases are known.
For example, even if the same quantitative trait loci is segregating in both populations, different allele frequencies of either the marker or causative mutation, or different linkage phases between marker and quantitative trait loci, can lead to different results.
Because of differences in LD and linkage phases, marker effects estimated in one breeding population cannot easily be transferred to another, and this at least partly explains the low accuracies observed within breeding populations using marker effects estimated in the other breeding populations (V4 and V5).
