We used the linear mixed model (LMM)-based approach to estimate the variance components. We note two key assumptions under this modeling framework when we interpret the results. First, the model assumes additive genetic effects. As a result, the estimated variance should be less than the total variance that can be explained by all genetic factors, e.g., dominance effects and epistasis are excluded. Second, the estimation is based on the genotyped markers. However, information from non-genotyped markers may be partially captured in this estimation due to linkage disequilibrium. For convenience, the estimated variance is referred to as “chip heritability” (see ref. [26] for a more detailed discussion of heritability estimation).
