The accuracy of a heritability estimator using molecular information

Abstract

The heritability of a quantitative trait is a key parameter to quantify the genetic variation present in a population. Although estimates of heritability require accurate information on the genetic relationship among individuals, pedigree data is generally lacking in natural populations. Nowadays, the increasing availability of DNA markers is making possible the estimation of coancestries from neutral molecular information. In 1996, K. Ritland developed an approach to estimate heritability from the regression of the phenotypic similarity on the marker-based coancestry. We carried out simulations to analyze the accuracy of the estimates of heritability obtained by this method using information from a variable number of neutral codominant markers. Because the main application of the estimator is on populations with no family structure, such as natural populations, its accuracy was tested under this scenario. However, the method was also investigated under other scenarios, in order to test the influence of different factors (family structure, assortative mating and phenotypic selection) on the precision. Our results suggest that the main factor causing a directional bias in the estimated heritability is the presence of phenotypic selection, and that very noisy estimates are obtained in the absence of a familiar structure and for small population sizes. The estimated heritabilities from marker-based coancestries showed lower accuracy than the estimated heritabilities from genealogical coancestries. However, a large amount of bias occurred even in the most favourable situation where genealogical coancestries are known. The results also indicate that the molecular markers are more suitable to infer coancestry than inbreeding.

Wild pedigrees: the way forward

“…The observed correlation between pedigree inbreeding coefficients and marker-based estimates of inbreeding is often low despite good data (Markert et al 2004;Slate et al 2004;Overall et al 2005;Rodriguez-Ramilo et al 2007) and this is largely because the mean and variance of inbreeding coefficients are both low in those natural populations so far studied (Slate et al 2004). Similar conclusions were reached by a simulation study (Balloux et al 2004).…”

Comparison of marker- and pedigree-based methods for estimating heritability in an agroforestry population of Vitellaria paradoxa C.F. Gaertn. (shea tree)

“…In a recent paper, Rodrıguez-Ramilo et al (2007) analysed scenarios including different numbers of molecular markers, different population structures and different management population regimes (presence or absence of selection). Their simulations indicate that Ritland's regression method gives unreliable heritability estimates in most scenarios, especially in unstructured populations (like our example of a shea tree population).…”

“…The most serious point lies in the poor performance of the regression approach itself. Rodrıguez-Ramilo et al (2007) have implemented the method with the known coancestries calculated from the pedigree, which would imply the most favourable situation for the estimation method. However, biased estimates were found even when using these genealogical coancestries.…”

Estimating heritability of disease resistance and factors that contribute to long-term survival in butternut (Juglans cinerea L.)

“…Wild populations of trees are a difficult case for this method (Klaper et al 2001) because they typically contain mostly unrelated trees and low V r . When adequate variance is present, estimates of heritability can be made (Andrew et al 2005), and although their accuracy is low when compared with h 2 estimates derived from known pedigrees (Rodriguez-Ramilo et al 2007;Bessega et al 2008), marker-derived estimates can generally discriminate between heritable and non-heritable traits (Coltman 2005).…”