The difference between the variance explained by genome-wide significant (GWS) SNPs (hGWS2) and heritability estimate from family studies (h2) has been called the “missing heritability” and the difference between hGWS2 and hM2 the “hidden” heritability, so that the difference between hM2 is the “still missing heritability”, i.e., hGWS2 < hM2 < h2. The still missing heritability may simply reflect genomic variants not well tagged by SNPs. In livestock populations, when missing heritability is defined in this way, little is missing with up to 97% of the heritability captured by common SNPs31, 32, probably because the smaller effective population size leads to long range LD and hence even rare alleles can be predicted by a linear combination of SNPs in LD with the causal variant. Even in dairy cattle however, traits that could reasonably be assumed to be under strong natural selection, such as fertility, have greater missing heritability31. Moreover, when the SNPs are fitted together with a pedigree as much as half of the genetic variance is explained by the pedigree and not the SNPs33. The simplest explanation is that in livestock as in humans some causal variants are rare and in poor LD with the SNPs.
