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Ancestral Relationships Using Metafounders: Finite Ancestral Populations and Across Population Relationships

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  • Andres Legarra, INRA, France
  • Ole Fredslund Christensen
  • Zulma G Vitezica, Université de Toulouse, INP, ENSAT, GenPhySE (Génétique, Physiologie et Systèmes 9 d’Elevage), France
  • Ignacio Aguilar, Instituto Nacional de Investigación Agropecuaria, Las Brujas, Canelones, Uruguay, Uruguay
  • Ignacy Misztal, University og Georgia, United States
Recent use of genomic (marker-based) relationships shows that relationships exist within and across base population (breeds or lines). However, current treatment of pedigree relationships is unable to consider relationships within or across base populations, although such relationships must exist due to finite size of the ancestral population and connections between populations. This complicates the conciliation of both approaches and, in particular, combining pedigree with genomic relationships. We present a coherent theoretical framework to consider base population in pedigree relationships. We suggest a conceptual framework that considers each ancestral population as a finite-sized pool of gametes. This generates across-individual relationships and contrasts with the classical view where each population is considered as an infinite, unrelated pool. Several ancestral populations may be connected and therefore related. Each ancestral population can be represented as a "metafounder", a pseudo-individual included as founder of the pedigree and similar to an "unknown parent group". Metafounders have self- and across- relationships according to a set of parameters, which measure ancestral relationships, i.e. homozygozities within populations and relationships across populations. These parameters can be estimated from existing pedigree and marker genotypes using maximum likelihood or a method based on summary statistics, for arbitrarily complex pedigrees. Equivalences of genetic variance and variance components between the classical and this new parameterization are shown. Segregation variance on crosses of populations is modeled. Efficient algorithms for computation of relationship matrices, their inverses, and inbreeding coefficients are presented. Use of metafounders leads to compatibility of genomic and pedigree relationship matrices, and to simple computing algorithms. Examples and code are given.
Original languageEnglish
JournalGenetics (Print)
Pages (from-to)455-468
Number of pages14
Publication statusPublished - 1 Jun 2015

    Research areas

  • base populations, genetic drift, Marker genotypes, pedigree, Relationships

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