03053naa a2200325 a 450000100080000000500110000800800410001902200140006002400370007410000160011124501370012726000090026450001000027352019920037365000130236565000140237865000270239265300210241965300180244065300120245865300210247065300130249165300180250465300250252270000220254770000190256970000160258870000160260477301070262010538772023-02-08       2015    bl uuuu     u00u1 u    #d  a0016-67317 a10.1534/genetics.115.1770142DOI1 aLEGARRA, A.  aAncestral relationships using metafoundersbFinite ancestral populations and across population relationships.h[electronic resource]  c2015  aArticle history: Received 12 February 2015; Accepted 03 April 2015; Published 14 April 2015. --  aABSTRACT.  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 which 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.   © 2015 by the Genetics Society of America.  aGENOMICA  aGENOTIPOS  aMARCADORES MOLECULARES  aBase populations  aGenetic drift  aGenPred  aMarker genotypes  aPedigree  aRelationships  aShared data resource1 aCHRISTENSEN, O.F.1 aVITEZICA, Z.G.1 aAGUILAR, I.1 aMISZTAL, I.  tGenetics, 2015gv.200, no.2, p. 455-468. OPEN ACCESS. doi: https://doi.org/10.1534/genetics.115.177014