Skew distribution of founder-specific inbreeding depression effects on the longevity of Landrace sows

Abstract

Inbreeding is a biological phenomenon of special relevance in domestic species in which its influence has been typically associated with reductions in animal fitness. Nevertheless, recent research suggests substantial founder-specific variability in terms of inbreeding depression on some productive traits, although this centred on a very reduced number of founders. This research focuses on the modelling of founder-specific inbreeding depression (FSID) effects from a more general point of view, characterizing the expected distribution of FSID effects on sow longevity. Under a change-point Weibull proportional hazards model solved through Bayesian inference, a skew-normal a priori distribution for the FSID effects of 19 founders was assumed. In terms of the deviance information criterion, this model was clearly preferred to other prior distributions for FSID effects as well as to a standard analysis of the overall inbreeding depression effect, although all models were consistent with an overall negative genetic effect of inbreeding on sow longevity. The joint posterior distribution of FSID effects showed a skewed pattern with substantial right-tail overexpression, in which the mean (0.036), mode (0.034), S.D. (0.032) and asymmetry parameter (0.045) reported a higher incidence of positive estimates (85.2%) with an unfavourable effect on sow longevity. The founder with the worst inbreeding depression effect reduced sow longevity by 32 days for 1% or 167 days for 10% partial inbreeding. As a whole, our analyses highlighted substantial variability in FSID effects, with unfavourable, neutral and even favourable influences on sow longevity. This heterogeneity could be related to an uneven distribution of the recessive deleterious genetic load among founder genomes, and also with the different selection pressures applied to each founder line. The implementation of skew-normal priors also proved an appealing way to bypass the strict scenario imposed by the standard symmetric-Gaussian distribution, allowing right- and left-tail overexpression as well as non-zero modal estimates.