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Can metafounders improve inbreeding estimation?

Z. G. Vitezica



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Can metafounders improve inbreeding estimation?
Z. G. Vitezica*1,2, I. Aguilar3, J. M. Astruc4, A. Legarra1. 1INRAE Toulouse, France, 2INPT Toulouse, France, 3INIA Montevideo, Uruguay, 4IDELE Toulouse, France.

In sheep, there are considerable difficulties to control pedigrees because of the use of natural mating. This incomplete pedigree information is typically 20% of unknown sire or dam, and inbreeding tends to be underestimated. The concept of metafounder deals with important issues in animal genetic evaluation. Metafounders allow to accommodate and conciliate pedigree and genomic relationships. Inclusion of metafounder relationships also compensates for missing pedigrees, resulting in inbred animals born from unknown parents. Thus, if all animals have estimates of inbreeding, regardless of pedigree completion, more accurate estimates of inbreeding depression could be obtained. The goal of this study is to test the usefulness of metafounder relationships in the estimation of inbreeding depression. Inbreeding coefficients were computed with pedigree and/or markers by considering or not metafounders in Basco-B�arnaise rams. Data comprised 16,196 phenotypic records (semen traits) for 620 rams, 533 of them genotyped with 36,464 SNPs (Illumina OvineSNP50 BeadChip). There were 8,266 animals in the pedigree including these rams and 5 generations of ancestors. Inbreeding coefficients were estimated using 4 methods. The first method used the traditional pedigree-based inbreeding. The second used pedigree-based inbreeding but accounting for nonzero relationships for unknown parents. The third method used the metafounder relationships in pedigree-based inbreeding. The fourth method calculates inbreeding from a combined relationship matrix using pedigree and genotypes with metafounder relationships. Inbreeding depression was estimated as regression on inbreeding coefficient in an animal model including environmental effects, permanent environment and breeding values. These were modeled with pedigree in models 1 and 2, pedigree + metafounders in model 3 and Single-Step with metafounders in model 4. Models 3 and 4 (with metafounders) show that motility was unfavorably impacted (significant estimate of inbreeding depression) by inbreeding in Basco-B�arnaise rams. Metafounders allows more accurate inbreeding depression estimations in motility. Thus, this approach compensates missing pedigree information.

Keywords: inbreeding, genomic, depression.