Required marker properties for unbiased estimates of the genetic correlation between populations
Populations generally differ in environmental and genetic factors, which can create differences in allele substitution effects between populations. Therefore, a single genotype may have different additive genetic values in different populations. The correlation between the two additive genetic values of a single genotype in both populations is known as the additive genetic correlation between populations and can differ from one. Our objective was to investigate whether differences in linkage disequilibrium (LD) and allele frequencies of markers and causal loci between populations affect bias of the estimated genetic correlation. We simulated two populations that were separated for 50 generations. Markers and causal loci were selected to either have similar or different allele frequencies in the two populations. Differences in consistency of LD between populations were obtained by using different marker density panels. Results showed that when the difference in allele frequencies of causal loci between populations was reflected by the markers, genetic correlations were only slightly underestimated using markers. This was even the case when LD patterns, measured by LD statistic r, were different between populations. When the difference in allele frequencies of causal loci between populations was not reflected by the markers, genetic correlations were severely underestimated. We conclude that for an unbiased estimate of the genetic correlation between populations, marker allele frequencies should reflect allele frequencies of causal loci so that marker-based relationships can accurately predict the relationships at causal loci, i.e. E(Gcausal loci|Gmarkers) = Gmarkers. Differences in LD between populations have little effect on the estimated genetic correlation.