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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
Fecha : |
13/11/2015 |
Actualizado : |
08/02/2023 |
Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
Autor : |
LEGARRA, A.; CHRISTENSEN, O.F.; VITEZICA, Z.G.; AGUILAR, I.; MISZTAL, I. |
Afiliación : |
IGNACIO AGUILAR GARCIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. |
Título : |
Ancestral relationships using metafounders: Finite ancestral populations and across population relationships. |
Fecha de publicación : |
2015 |
Fuente / Imprenta : |
Genetics, 2015, v.200, no.2, p. 455-468. OPEN ACCESS. doi: https://doi.org/10.1534/genetics.115.177014 |
ISSN : |
0016-6731 |
DOI : |
10.1534/genetics.115.177014 |
Idioma : |
Inglés |
Notas : |
Article history: Received 12 February 2015; Accepted 03 April 2015; Published 14 April 2015. -- |
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 |
Palabras claves : |
Base populations; Genetic drift; GenPred; Marker genotypes; Pedigree; Relationships; Shared data resource. |
Thesagro : |
GENOMICA; GENOTIPOS; MARCADORES MOLECULARES. |
Asunto categoría : |
L10 Genética y mejoramiento animal |
URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/5186/1/Aguilar-I.-2015.-Genetics.pdf
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Marc : |
LEADER 03053naa a2200325 a 4500 001 1053877 005 2023-02-08 008 2015 bl uuuu u00u1 u #d 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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INIA Las Brujas (LB) |
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Registros recuperados : 218 | |
81. | | MASUDA, Y.; AGUILAR, I.; TSURUTA, S.; MISZTAL, I. Technical note: Acceleration of sparse operations for average-information REML analyses with supernodal methods and sparse-storage refinements. Journal of Animal Science, 2015, v. 93, p. 4670 - 4674. Published October 9, 2015 Article history: Received June 8, 2015.; Accepted August 7, 2015.
1. We acknowledge the work by François Guillaume in programming a hash function. We greatly appreciate the work of the two anonymous reviewers.
2. The AIREMLF90 program...Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Las Brujas. |
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84. | | ZHANG, X.; LOURENCO, D.; MISZTAL, I.; AGUILAR, I.; LEGARRA, A. Weighted single-step genomic BLUP: an iterative approach for accurate calculation of GEBV and GWAS. Volume Methods and Tools: Statistical and genomic tools for mapping QTL and genes (Posters), 681. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.681.Tipo: Trabajos en Congresos/Conferencias |
Biblioteca(s): INIA Las Brujas. |
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85. | | ZHANG, X.; LOURENCO, D.; AGUILAR, I.; LEGARRA, A.; MISZTAL, I. Weighting strategies for single-step genomic BLUP: An iterative approach for accurate calculation of GEBV and GWAS. Frontiers in Genetics, 19 August 2016, Volume 7, Issue AUG, Article number 151. OPEN ACCESS Article history: Received 15 May 2016 // Accepted 04 August 2016 // Published 19 August 2016.
Specialty section:
This article was submitted to Statistical Genetics and Methodology, a section of the journal Frontiers in Genetics.Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : A - 2 |
Biblioteca(s): INIA Las Brujas. |
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90. | | LEMA, O.M.; BRITO, G.; CLARIGET, J.; PEREZ, E.; RAVAGNOLO, O.; AGUILAR, I.; MONTOSSI, F. Dos años de evaluación de ganancia diaria invernal de terneros con paternidad conocida y su efecto sobre la recría
y terminación. In: CONGRESO ARGENTINO DE PRODUCCIÓN ANIMAL, 38., 2015. Resúmenes. Santa Rosa, La Pampa, AR: ASAS/AAPA, 2015 Revista Argentina de Producción Animal, 2015, v.35, Supl.1, p.62Tipo: Abstracts/Resúmenes |
Biblioteca(s): INIA La Estanzuela; INIA Treinta y Tres. |
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92. | | LOURENÇO, D. A. L.; MISZTAL, I.; TSURUTA, S.; FRAGOMENI, B.; AGUILAR, I.; MASUDA, Y.; MOSER, D. Direct and indirect genomic evaluations in beef cattle. Interbull Bulletin, 2015, v. 49, p.80 - 84.Tipo: Artículos Indexados |
Biblioteca(s): INIA Las Brujas. |
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94. | | LOURENCO, D; MISZTAL, I.; TSURUTA, S.; AGUILAR, I.; LAWLOR, T. J.; WELLER, J. I. Are evaluations on young genotyped dairy bulls benefiting from the past generations? [conference paper]. Volume Species Breeding: Dairy cattle, 297. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.297.Tipo: Trabajos en Congresos/Conferencias |
Biblioteca(s): INIA Las Brujas. |
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97. | | NAVAJAS, E.; MACEDO, F.; LEMA, O.M.; LUZARDO, S.; AGUILAR, I. Accuracy of genomic predictions for carcass and meat quality traits in the Uruguayan Hereford breed. Volume Species - Bovine (beef) 1, p. 636. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 11., Aotea Centre Auckland, New Zealand: WCGALP, ICAR, 11-16 feb 2018. 6 p. Acknowledgements: This work was supported by the Agencia Nacional de Investigación e Innovación (ANII) (grants RTS_1_2012_1_3489 and FMV_1_2011_1_6671), Instituto Nacional de Investigación Agropecuaria (INIA), Sociedad de Criadores de...Tipo: Trabajos en Congresos/Conferencias |
Biblioteca(s): INIA Las Brujas. |
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98. | | GARCÍA, A.; AGUILAR, I.; LEGARRA, A.; MILLER, S.; TSURUTA, S.; MISZTAL, I.; LOURENCO, D. Accuracy of indirect predictions for large datasets based on prediction error covariance of SNP effects from single-step GBLUP. [abstract 22]. Issue Section: Animal Breeding and Genetics. Journal of Animal Science, 2020, Volume 98, Issue Supplement 4, Pages 6-7. doi: https://doi.org/10.1093/jas/skaa278.012 Article history: 30 November 2020.
ASAS Annual 2020 Meeting Abstracts.Tipo: Abstracts/Resúmenes |
Biblioteca(s): INIA Las Brujas. |
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99. | | LEGARRA, A.; CHRISTENSEN, O. F.; VITEZICA, Z. G.; AGUILAR, I.; MISZTAL, I. Across-breeds ancestral relationships and metafounders for genomic evaluation. Volume Genetic Improvement Programs: Selection using molecular information, 075. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.075. Acknowledgements: This project has been financed by X-Gen and GenSSeq actions from SelGen metaprogram (INRA). We are grateful to the genotoul bioinformatics platform Toulouse Midi-Pyrenees for providing computing resources.Tipo: Trabajos en Congresos/Conferencias |
Biblioteca(s): INIA Las Brujas. |
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100. | | LEMA, O.M.; AGUILAR, I.; DIONELLO, N.J.L.; CARDOSO, F.F.; RAVAGNOLO, O.; GIMENO, D. Additive, heterotic and recombination losses for direct and maternal effects in growth for British, Continental and Zebu crosses. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 11., Aotea Centre Auckland, New Zealand: WCGALP, ICAR, 11-16 feb 2018.Tipo: Trabajos en Congresos/Conferencias |
Biblioteca(s): INIA La Estanzuela. |
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Registros recuperados : 218 | |
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