Quantifying genetic load through joint modelling of inbreeding depression and inbreeding load for litter size in...

Genetic load, defined as the burden of deleterious variants carried by a population, has two components: a realized one that is expressed as reduced fitness, and a hidden one that is masked in heterozygotes. The hidden component, arising from recessive (or partially recessive) deleterious alleles and from overdominant loci, constitutes the inbreeding load (IL), which is unmasked under inbreeding and observed as inbreeding depression. Conventional analyses focus on average inbreeding depression and assume homogeneous effects across ancestors. In contrast, the IL framework allows heterogeneous ancestral contributions to be modelled through Mendelian decomposition. For composite reproductive traits, such as number born alive (NBA) in rabbits, inbreeding may act through distinct biological pathways associated with both the dam and the litter. We developed and validated an integrated model that jointly partitions maternal and litter IL underlying NBA in rabbits.

Data consisted of 33,521 kindling records from a Pannon White rabbit population and a pedigree of 43,858 individuals. Total inbreeding was decomposed into partial ancestral contributions using a tabular Mendelian decomposition, allowing IL effects to be modelled as additive genetic random effects. Bayesian linear mixed models varying in maternal and litter IL effects, inbreeding depression covariates, and genetic correlations genetic correlations between the additive effect and each of the two IL measures, as well as between the two IL measures, were compared by the Deviance Information Criterion; the model with both IL effects but no genetic correlations fitted best. Average inbreeding depression was consistently negative, with litter inbreeding showing a stronger and more precisely estimated effects on NBA than maternal inbreeding. Both maternal and litter IL variances were substantial, indicating marked heterogeneity among ancestors in their contributions to inbreeding depression. Analysis of genetic trends revealed sustained genetic progress for NBA and litter IL, accompanied by opposite temporal trends for maternal IL.

Joint modelling of maternal and litter IL provides a deeper and biologically coherent understanding of the genetic architecture of litter size in rabbits. This approach reveals hidden tensions between selection for production and biological fitness, highlighting the need for breeding strategies that balance additive genetic progress with the management of hidden genetic load.