Heritability Estimates Using 60K Porcine SNPs Indicate No ‘missing heritability problem’ in Domesticated Animals

The concern of missing heritability problem in complex traits has stimulated debate on a wide array of explanations and possible solutions to this dark matter of the genome. Missing heritability has been reported on human, leaving further investigation on animals. We estimated the variances explained by autosomal SNPs on meat quality traits and found no evidence of missing heritability when compared with pedigree based heritability. We observed a large difference on the extent of LD between human and pig. The long extent of LD cause common variants to capture neighboring genetic variants that were not detected by commercial SNP chip. We believe that no missing heritability for domesticated animals on complex traits, especially meat-quality of pig, can be attributed to the common variants representing the whole genetic variation due to the strong LD. Therefore we can infer that heritability of complex phenotypes for domesticated animals can be thoroughly estimated by current SNP commercial chips.