Inbreeding depression load for litter size in Entrepelado and Retinto Iberian pig varieties.

Individual-specific hidden inbreeding depression load (IDL) can be accounted for in livestock populations by appropriate best linear unbiased prediction approaches. This genetic effect has a recessive pattern and reveals when inherited in terms of identity-by-descent. Nevertheless, IDL inherits as a pure additive genetic background and can be selected using standard breeding values. The main target of this research was to evaluate IDL for litter size in 2 Iberian pig varieties (Entrepelado and Retinto) from a commercial breeding-stock. Analyses were performed on the total number of piglets born (both alive and dead) and used data from 3,200 (8.02 +/- 0.04 piglets/litter) Entrepelado and 4,744 Retinto litters (8.40 +/- 0.03 piglets/litter). Almost 50% of Entrepelado sows were inbred (1.7% to 25.0%), whereas this percentage reduced to 37.4% in the Retinto variety (0.2% to 25.0%). The analytical model was solved by Bayesian inference and accounted for 2 systematic effects (sow age and breed/variety of the artificial insemination boar), 2 permanent environmental effects (herd-year-season and sow), and 2 genetic effects (IDL and infinitesimal additive). In terms of posterior means (PM), additive genetic and IDL variances were similar in the Entrepelado variety (PM, 0.68 vs. 0.76 piglets(2), respectively) and their 95% credibility intervals (95CI) overlapped, although without including zero (0.38 to 0.94 vs. 0.15 to 1.31 piglets(2), respectively). The same pattern revealed in the Retinto variety, with IDL variance (PM, 0.41 piglets(2); 95CI, 0.07 to 0.88 piglets(2)) slightly larger than the additive genetic variance (PM, 0.37 piglets(2); 95CI, 0.16 to 0.59 piglets(2)). The relevance of IDL was also checked by a Bayes factor and the deviance information criterion, the model including this effect being clearly favored in both cases. Although the analysis assumed null genetic covariance between IDL and infinitesimal additive effects, a moderate negative correlation (-0.31) was suggested when plotting the PM of breeding values in the Entrepelado variety; a negative genetic trend for IDL was also revealed in this Iberian pig variety (-0.25 piglets for 100% inbred offspring of individuals born in 2014), whereas no trend was detected in Retinto breeding-stock. Those were the first estimates of IDL in a commercial livestock population, they giving evidence of a relevant genetic background with potential consequences on the reproductive performance of Iberian sows.