Maintenance of genetic diversity in subdivided populations using genomic coancestry matrices

Morales-González, Elisabeth; Villanueva, Beatriz; Toro, M. A.; Fernández, Jesús; Agencia Estatal de Investigación (España)

Maintenance of genetic diversity in subdivided populations using genomic coancestry matrices

15 Pág.

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Bibliographic Details
Main Authors:	Morales-González, Elisabeth, Villanueva, Beatriz, Toro, M. A., 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 https://api.elsevier.com/content/abstract/scopus_id/85150885754
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id	dig-inia-es-10261-330020
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spelling	dig-inia-es-10261-3300202023-06-29T20:37:54Z Maintenance of genetic diversity in subdivided populations using genomic coancestry matrices Morales-González, Elisabeth Villanueva, Beatriz Toro, M. A. 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] 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 Molecular Ecology Resources 00 :1-15 (2023) 1755-098X http://hdl.handle.net/10261/330020 10.1111/1755-0998.13781 1755-0998 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 Publisher's version 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, M. A. 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, M. A. 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, M. A. 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 https://api.elsevier.com/content/abstract/scopus_id/85150885754
work_keys_str_mv	AT moralesgonzalezelisabeth maintenanceofgeneticdiversityinsubdividedpopulationsusinggenomiccoancestrymatrices AT villanuevabeatriz maintenanceofgeneticdiversityinsubdividedpopulationsusinggenomiccoancestrymatrices AT toroma maintenanceofgeneticdiversityinsubdividedpopulationsusinggenomiccoancestrymatrices AT fernandezjesus maintenanceofgeneticdiversityinsubdividedpopulationsusinggenomiccoancestrymatrices
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Maintenance of genetic diversity in subdivided populations using genomic coancestry matrices

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