Heritability estimates and predictive ability for pig meat quality traits using identity-by-state and identity-by-descent relationships in an F₂ population

Genomic relationships can be computed with dense genome-wide genotypes through different methods, either based on identity-by-state (IBS) or identity-by-descent (IBD). The latter has been shown to increase the accuracy of both estimated relationships and predicted breeding values. However, it is not clear whether an IBD approach would achieve greater heritability ((Formula presented.)) and predictive ability ((Formula presented.)) than its IBS counterpart for data with low-depth pedigrees. Here, we compare both approaches in terms of the estimated of (Formula presented.) and (Formula presented.), using data on meat quality and carcass traits recorded in experimental crossbred pigs, with a pedigree constrained to only three generations. Three animal models were fitted which differed on the relationship matrix: an IBS model ((Formula presented.)), an IBD (defined within the known pedigree) model ((Formula presented.)), and a pedigree model ((Formula presented.)). In 9 of 20 traits, the range of increase for the estimates of (Formula presented.) and (Formula presented.) was 1.2–2.9 times greater with (Formula presented.) and (Formula presented.) models than with (Formula presented.). Whereas for all traits, both parameters were similar between genomic models. The (Formula presented.) of the genomic models was higher compared to (Formula presented.). A scarce increment in (Formula presented.) was found with (Formula presented.) when compared to (Formula presented.), most likely due to the former recovering sizeable relationships among founder F₀ animals.