Inferring relatedness and heritability using molecular markers in radiata pine

A set of eight unlinked microsatellite markers was used to estimate relatedness among 355 individuals of a Pinus radiata breeding population. The average performance of open-pollinated progeny of each individual, for wood density, was considered to represent the phenotype of all 355 individuals. Marker-based estimates of relationship were compared with the pedigree-based coefficients of relationships. The phenotypic similarity among all pairs of individuals was regressed on marker-estimated relatedness to estimate the inheritance of wood density. The marker-based estimate of heritability was compared with that obtained using classical quantitative genetic methods. Overall, a low correlation (0.13) was observed between marker-based and pedigree-based estimates of relatedness. After discarding negative estimates of relatedness, the average coefficient of relationship among ‘known’ groups of maternal half-sibs, full-sibs and unrelated individuals, increased from 0.24 to 0.29 (0.25 expected), from 0.43 to 0.48 (0.50 expected) and from −0.04 to 0.15 (0 expected), respectively. Marker-based and conventional estimates of heritability of wood density were 0.79 and 0.38, respectively. However, by using only marker loci with expected Hardy–Weinberg frequencies, marker-based estimate of heritability was 0.33, which is very similar to that obtained from conventional approaches. The use of molecular markers to understand quantitative genetic variation is discussed.