Estimation of coancestry in Iberian pigs using molecular markers

Genetic markers provide a useful tool to estimate pairwise coancestry between individuals in the absence of a known pedigree. In the present work 62 pigs from two related strains of Iberian breed, Guadyerbas and Torbiscal, belonging to a conservation programme with completely known pedigrees since 1945, have been genotyped for 49 microsatellites. Four coefficients that summarise molecular resemblance between individuals together with eight estimators of coancestry have been calculated from this information. Their values were compared with the genealogical coancestry, calculated from the complete or partial pedigree. The eight estimations obtained using molecular information substantially underestimate the coancestry calculated using the genealogical analysis. The correlation between the estimates and the genealogical values was also calculated. This correlation was high, between 0.78 and 0.93 for different estimators, when all pairwise comparisons among the 62 animals were considered. However, the correlation decreases remarkably to 0.49-0.69 and 0.37-0.47 for the Guadyerbas and Torbiscal populations respectively, when they were analysed separately. All the correlations were similar to those obtained when using simple coefficients of molecular resemblance such as molecular coancestry or similarity indexes. Finally, simulations were carried out to further explore the results obtained. It is concluded that lack of information on the allele frequencies in the base population may explain the bias of these estimators in populations with complex pedigrees.