An evaluation of inbreeding measures using a whole-genome sequenced cattle pedigree

The estimation of the inbreeding coefficient (F) is essential for the study of inbreeding depression (ID) or for the management of populations under conservation. Several methods have been proposed to estimate the realized F using genetic markers, but it remains unclear which one should be used. Here we used whole-genome sequence data for 245 individuals from a Holstein cattle pedigree to empirically evaluate which estimators best capture homozygosity at variants causing ID, such as rare deleterious alleles or loci presenting heterozygote advantage and segregating at intermediate frequency. Estimators relying on the correlation between uniting gametes (FUNI) or on the genomic relationships (FGRM) presented the highest correlations with these variants. However, homozygosity at rare alleles remained poorly captured. A second group of estimators relying on excess homozygosity (FHOM), homozygous-by-descent segments (FHBD), runs-of-homozygosity (FROH) or on the known genealogy (FPED) was better at capturing whole-genome homozygosity, reflecting the consequences of inbreeding on all variants, and for young alleles with low to moderate frequencies (0.10 < . < 0.25). The results indicate that FUNI and FGRM might present a stronger association with ID. However, the situation might be different when recessive deleterious alleles reach higher frequencies, such as in populations with a small effective population size. For locus-specific inbreeding measures or at low marker density, the ranking of the methods can also change as FHBD makes better use of the information from neighboring markers. Finally, we confirmed that genomic measures are in general superior to pedigree-based estimates. In particular, FPED was uncorrelated with locus-specific homozygosity.

Effects of inbreeding on four families of Peppin Merinos. IV. The expression of heterosis

Whereas Inbreeding in Merino sheep seems to have an adverse effect on many fitness characters, it does not appear to limit the potential maternal ability of the ewes in respect to the rearing of a single lamb. There is, however, a complex effect on fertility such that inbred ewes appear to be more variable in their response to environmental fluctuations in terms of successful pregnancies. The variance of body weight is significantly increased by inbreeding, as would be expected following a disturbance of the "developmental homeostasis". However, the variance of fleece weight, which is a character strongly depressed by inbreeding, does not appear to be affected. It is suggested that the 'inbreeding syndrome' is related to excess homozygosity but that the variance changes in the depressed characters result from the consequent disturbance of physiological mechanisms. Outcrossing, both between two Inbred lines from the same strain and between inbred lines and unrelated sheep of the same strain, produces the same results, namely, a reversion of the progeny to the normal characteristics of the original random-bred populations.