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Inbreeding load is the fraction of the mutation load that is due to hidden recessive alleles in heterozygous state. This load, when exposed by inbreeding, is responsible for inbreeding depression, the decrease in performance and fitness in inbred individuals [1].
Inbreeding depression is thought to be due to the presence of recessive alleles in populations or from the reduction of heterozygous loci under overdominance. Usually, inbreeding depression is expected to be larger for fitness traits (e.g. fertility) than in traits less related to fitness (e.g. milk yield). However, there is evidence that inbreeding depression can occur in any trait [2]. For fitness traits, inbreeding depression is mainly endorsed to recessive deleterious mutations. However, for traits under directional selection such as milk yield (selection to increase the mean), dominance deviation effects are on average favourable; and inbreeding depression is due to the reduced expression of dominance effects by an increase in homozygosity [2].
In livestock, inbreeding load can vary among founders, particularly if the founder families were exposed to different selection pressures on deleterious alleles [3]. Inbreeding load of individuals can be predicted in the same manner that we do for additive genetic values based on linear models [4, 5]. However, previous authors [4, 5–6] have never expressed inbreeding load in terms of simple locus effects, e.g. as a substitution effect. In fact, the inbreeding load of individuals is a heritable additive trait, proportional to the gene count of recessive alleles (as it will be shown below), and this trait is only expressed when inbreeding occurs in the descendants [5]. Further, inbreeding load can have a favorable or unfavorable effect on the studied trait (e.g. milk yield) [6]. For instance, one could in principle find out if different individuals carry different inbreeding loads by producing e.g. equally inbred descendance (say mating sires to their daughters) and comparing descendants across sires. In complex pedigrees this becomes more complicated because each individual possesses parts of inbreeding coming potentially from different ancestors. The inbreeding partitioning in fractions attributed to each ancestor can be computed using pedigree, using the Mendelian decomposition of inbreeding, which traces back the specific ancestral paths through which the identical by descent (IBD) alleles are inherited. Using these fractions, a linear model can predict the...