Estimation of quantitative genetic parameters using marker-inferred relatedness in Japanese flounder: a case study of upward bias

Marker-based methods for estimating heritability have been proposed as an effective means to study quantitative traits in long-lived organisms and natural populations. However, practical examinations to evaluate the usefulness and robustness of a regression method are limited. Using several quantitative traits of Japanese flounder Paralichthys olivaceus, the present study examined the influence of relatedness estimator and population structure on the estimation of heritability and genetic correlation under a regression method with 7 microsatellite loci. Significant heritability and genetic correlation were detected for several quantitative traits in 2 laboratory populations but not in a natural population. In the laboratory populations, upward bias in heritability appeared depending on the relatedness estimators and the populations. Upward bias in heritability increased with decreasing the actual variance of relatedness, suggesting that the estimates of heritability under the regression method tend to be overestimated due to the underestimation of the actual variance of relatedness. Therefore, relationship structure and precise estimation of relatedness are critical for applying this method.