Maintenance of genetic diversity in subdivided populations using genomic coancestry matrices

Maintenance of genetic diversity in subdivided populations using genomic coancestry matrices

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Main Authors: Morales-González, Elisabeth, Villanueva, Beatriz, Toro, Miguel Ángel, Fernández, Jesús
Other Authors: Agencia Estatal de Investigación (España)
Format: artículo biblioteca
Language:English
Published: John Wiley & Sons 2023-03-12
Subjects:Allele frequency changes, Allelic diversity, Expected heterozygosity, Genomic coancestry, Optimal contributions, Subdivided populations,
Online Access:http://hdl.handle.net/10261/330020
http://dx.doi.org/10.13039/501100004837
http://dx.doi.org/10.13039/501100011033
https://api.elsevier.com/content/abstract/scopus_id/85150885754
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spelling dig-inia-es-10261-3300202024-11-04T21:39:42Z Maintenance of genetic diversity in subdivided populations using genomic coancestry matrices Morales-González, Elisabeth Villanueva, Beatriz Toro, Miguel Ángel Fernández, Jesús Agencia Estatal de Investigación (España) Ministerio de Ciencia e Innovación (España) Morales-González, Elisabeth [0000-0002-5614-5044] Villanueva, Beatriz [0000-0003-4645-8853] Toro, M. A. [0000-0001-7460-2483] Fernández, Jesús [0000-0001-8269-1893] Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72] Allele frequency changes Allelic diversity Expected heterozygosity Genomic coancestry Optimal contributions Subdivided populations 15 Pág. For both undivided and subdivided populations, the consensus method to maintain genetic diversity is the Optimal Contribution (OC) method. For subdivided populations, this method determines the optimal contribution of each candidate to each subpopulation to maximize global genetic diversity (which implicitly optimizes migration between subpopulations) while balancing the relative levels of coancestry between and within subpopulations. Inbreeding can be controlled by increasing the weight given to within-subpopulation coancestry (λ). Here we extend the original OC method for subdivided populations that used pedigree-based coancestry matrices, to the use of more accurate genomic matrices. Global levels of genetic diversity, measured as expected heterozygosity and allelic diversity, their distributions within and between subpopulations, and the migration pattern between subpopulations, were evaluated via stochastic simulations. The temporal trajectory of allele frequencies was also investigated. The genomic matrices investigated were (i) the matrix based on deviations of the observed number of alleles shared by two individuals from the expected number under Hardy-Weinberg equilibrium; and (ii) a matrix based on a genomic relationship matrix. The matrix based on deviations led to higher global and within-subpopulation expected heterozygosities, lower inbreeding and similar allelic diversity than the second genomic and pedigree-based matrices when a relatively high weight was given to the within-subpopulation coancestries (λ ≥ 5). Under this scenario, allele frequencies moved only slightly away from the initial frequencies. Therefore, the recommended strategy is to use the former matrix in the OC methodology giving a high weight to the within-subpopulation coancestry. This research was funded by MCIN/AEI/10.13039/501100011033 (Project PID2020-114426GB-C22). Peer reviewed 2023-06-29T11:34:09Z 2023-06-29T11:34:09Z 2023-03-12 artículo http://purl.org/coar/resource_type/c_6501 Publisher's version Molecular Ecology Resources 00 :1-15 (2023) 1755-098X http://hdl.handle.net/10261/330020 10.1111/1755-0998.13781 1755-0998 http://dx.doi.org/10.13039/501100004837 http://dx.doi.org/10.13039/501100011033 36906916 2-s2.0-85150885754 https://api.elsevier.com/content/abstract/scopus_id/85150885754 en #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-114426GB-C22/ES/ESTIMACION DEL CENSO EFECTIVO Y LA DEPRESION CONSANGUINEA UTILIZANDO DATOS GENOMICOS: APLICACIONES EN MEJORA GENETICA ANIMAL/ Departamento de ​Mejora Genética Animal https://doi.org/10.1111/1755-0998.13781 Sí open application/pdf John Wiley & Sons
institution INIA ES
collection DSpace
country España
countrycode ES
component Bibliográfico
access En linea
databasecode dig-inia-es
tag biblioteca
region Europa del Sur
libraryname Biblioteca del INIA España
language English
topic Allele frequency changes
Allelic diversity
Expected heterozygosity
Genomic coancestry
Optimal contributions
Subdivided populations
Allele frequency changes
Allelic diversity
Expected heterozygosity
Genomic coancestry
Optimal contributions
Subdivided populations
spellingShingle Allele frequency changes
Allelic diversity
Expected heterozygosity
Genomic coancestry
Optimal contributions
Subdivided populations
Allele frequency changes
Allelic diversity
Expected heterozygosity
Genomic coancestry
Optimal contributions
Subdivided populations
Morales-González, Elisabeth
Villanueva, Beatriz
Toro, Miguel Ángel
Fernández, Jesús
Maintenance of genetic diversity in subdivided populations using genomic coancestry matrices
description 15 Pág.
author2 Agencia Estatal de Investigación (España)
author_facet Agencia Estatal de Investigación (España)
Morales-González, Elisabeth
Villanueva, Beatriz
Toro, Miguel Ángel
Fernández, Jesús
format artículo
topic_facet Allele frequency changes
Allelic diversity
Expected heterozygosity
Genomic coancestry
Optimal contributions
Subdivided populations
author Morales-González, Elisabeth
Villanueva, Beatriz
Toro, Miguel Ángel
Fernández, Jesús
author_sort Morales-González, Elisabeth
title Maintenance of genetic diversity in subdivided populations using genomic coancestry matrices
title_short Maintenance of genetic diversity in subdivided populations using genomic coancestry matrices
title_full Maintenance of genetic diversity in subdivided populations using genomic coancestry matrices
title_fullStr Maintenance of genetic diversity in subdivided populations using genomic coancestry matrices
title_full_unstemmed Maintenance of genetic diversity in subdivided populations using genomic coancestry matrices
title_sort maintenance of genetic diversity in subdivided populations using genomic coancestry matrices
publisher John Wiley & Sons
publishDate 2023-03-12
url http://hdl.handle.net/10261/330020
http://dx.doi.org/10.13039/501100004837
http://dx.doi.org/10.13039/501100011033
https://api.elsevier.com/content/abstract/scopus_id/85150885754
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AT toromiguelangel maintenanceofgeneticdiversityinsubdividedpopulationsusinggenomiccoancestrymatrices
AT fernandezjesus maintenanceofgeneticdiversityinsubdividedpopulationsusinggenomiccoancestrymatrices
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