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| 15. |  | LEGARRA, A.; AGUILAR, I.; MISZTAL, I. Single step methods with a view towards poultry breeding. Volume Species Breeding: Poultry, 324. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.324. Acknowledgements: This work has been financed by X-Gen and GenSSeq actions from SelGen metaprogram (INRA).| Biblioteca(s): INIA Las Brujas. |
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| 17. | | MASUDA, Y.; AGUILAR, I.; TSURUTA, S.; MISZTAL, I. Acceleration of computations in AI REML for single-step GBLUP models. Volume Methods and Tools: Statistical methods - linear and nonlinear models (Posters), 703. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.703.| Biblioteca(s): INIA Las Brujas. |
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| 20. | | AGUILAR, I.; MISZTAL, I.; LEGARRA, A.; TSURUTA, S. Efficient computations of genomic relationship matrix and other matrices used in the single-step evaluation. Volume Methods and tools: Software and bioinformatics - Lecture Sessions, 0768. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 9., Leipzig, Germany, August 1-6, 2010. p. 0768. Acknowledgments: This study was partially funded by the Holstein Association USA Inc. and by AFRI grants 2009-65205-05665 and 2010-65205-20366 from the USDA NIFA Animal Genome Program. The authors thank P.M. VanRaden from Animal...| Biblioteca(s): INIA Las Brujas. |
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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha actual : |
13/11/2015 |
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Actualizado : |
08/02/2023 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Circulación / Nivel : |
Internacional - -- |
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Autor : |
LEGARRA, A.; CHRISTENSEN, O.F.; VITEZICA, Z.G.; AGUILAR, I.; MISZTAL, I. |
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Afiliación : |
IGNACIO AGUILAR GARCIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. |
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Título : |
Ancestral relationships using metafounders: Finite ancestral populations and across population relationships. |
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Fecha de publicación : |
2015 |
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Fuente / Imprenta : |
Genetics, 2015, v.200, no.2, p. 455-468. OPEN ACCESS. doi: https://doi.org/10.1534/genetics.115.177014 |
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ISSN : |
0016-6731 |
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DOI : |
10.1534/genetics.115.177014 |
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Idioma : |
Inglés |
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Notas : |
Article history: Received 12 February 2015; Accepted 03 April 2015; Published 14 April 2015. -- |
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Contenido : |
ABSTRACT.
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. MenosABSTRACT.
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... Presentar Todo |
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Palabras claves : |
Base populations; Genetic drift; GenPred; Marker genotypes; Pedigree; Relationships; Shared data resource. |
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Thesagro : |
GENOMICA; GENOTIPOS; MARCADORES MOLECULARES. |
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Asunto categoría : |
L10 Genética y mejoramiento animal |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/5186/1/Aguilar-I.-2015.-Genetics.pdf
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Marc : |
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022 $a0016-6731
024 7 $a10.1534/genetics.115.177014$2DOI
100 1 $aLEGARRA, A.
245 $aAncestral relationships using metafounders$bFinite ancestral populations and across population relationships.$h[electronic resource]
260 $c2015
500 $aArticle history: Received 12 February 2015; Accepted 03 April 2015; Published 14 April 2015. --
520 $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.
650 $aGENOMICA
650 $aGENOTIPOS
650 $aMARCADORES MOLECULARES
653 $aBase populations
653 $aGenetic drift
653 $aGenPred
653 $aMarker genotypes
653 $aPedigree
653 $aRelationships
653 $aShared data resource
700 1 $aCHRISTENSEN, O.F.
700 1 $aVITEZICA, Z.G.
700 1 $aAGUILAR, I.
700 1 $aMISZTAL, I.
773 $tGenetics, 2015$gv.200, no.2, p. 455-468. OPEN ACCESS. doi: https://doi.org/10.1534/genetics.115.177014
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