Of the set of expressed probes (15,966), 10,580 (66%) had an estimated narrow-sense heritability (h2) greater than zero with a mean (median) value of 0.192 0.1422).
We then estimated narrow-sense heritabilities (h) using a mixed model including an overall mean, a fixed parity effect, an individual animal effect, a random herd effect and a random error (e.g. [ 41]).
The estimated narrow-sense heritability equals the slope of the regression line at the average relatedness value multiplied by 1− the average kinship value, where the average kinship value is half the average relatedness value.
We used the same methods as reported in Åkesson et al. [20] to estimate (narrow sense) heritabilities and additive variances.
For example, parents and offspring only share additive genetic effects so that estimates of heritability based on parent offspring designs estimate narrow heritability.
For estimating narrow sense heritability, the additive kinship matrix described in the rrBLUP package was used as the relationship matrix, and, for estimating broad sense heritability, the non-additive Gaussian kernel was used.
The PED model is the classical polygenic model, using family structure to estimate narrow sense heritability, which yielded estimates of 42%, 53%, and 58% for BW, FI, and FE, respectively.
Our focus in this study is on estimating narrow-sense heritability.
In principle, estimating narrow-sense heritability for a binomially distributed trait, such as coral settlement, is straightforward, see Gilmour et al. (1985); Foulley et al. (1987); Vazquez et al. (2009); Biscarini et al. (2014, 2015).
