Evaluating different genomic coancestry matrices for managing genetic variability in turbot
8 Pág. In population management, the most efficient method to control the increase of inbreeding and the associated loss of genetic variability is the Optimal Contributions method. This method optimizes the contributions of breeding candidates by minimizing the weighted global coancestry. Traditiona...
Published in: | Aquaculture |
---|---|
Main Authors: | , , , , , , , , |
Other Authors: | , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Elsevier BV
2020
|
Subjects: | |
Online Access: | http://hdl.handle.net/10261/341800 https://doi.org/10.1016/j.aquaculture.2020.734985 https://doi.org/10.13039/501100000780 https://doi.org/10.13039/501100000268 https://api.elsevier.com/content/abstract/scopus_id/85078095468 |
id |
ftcsic:oai:digital.csic.es:10261/341800 |
---|---|
record_format |
openpolar |
spelling |
ftcsic:oai:digital.csic.es:10261/341800 2024-06-23T07:56:37+00:00 Evaluating different genomic coancestry matrices for managing genetic variability in turbot Morales-González, Elisabeth Saura, María Fernández, Almudena Fernández, Jesús Pong-Wong, Ricardo Cabaleiro, Santiago Martínez, Paulino Martín-García, Anaís Villanueva, Beatriz European Commission Ministerio de Ciencia, Innovación y Universidades (España) Biotechnology and Biological Sciences Research Council (UK) Morales-González, Elisabeth Saura, María Fernández, Almudena Fernández, Jesús Pong-Wong, Ricardo Cabaleiro, Santiago Martínez, Paulino Villanueva, Beatriz 2020-04-15 http://hdl.handle.net/10261/341800 https://doi.org/10.1016/j.aquaculture.2020.734985 https://doi.org/10.13039/501100000780 https://doi.org/10.13039/501100000268 https://api.elsevier.com/content/abstract/scopus_id/85078095468 en eng Elsevier BV #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/EC/FP7/613611 info:eu-repo/grantAgreement/MICIU//CGL2016-75904-C2-2-P Departamento de Mejora Genética Animal Publisher's version https://doi.org/10.1016/j.aquaculture.2020.734985 Sí Aquaculture 520: e734985 (2020) 0044-8486 http://hdl.handle.net/10261/341800 doi:10.1016/j.aquaculture.2020.734985 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100000268 2-s2.0-85078095468 https://api.elsevier.com/content/abstract/scopus_id/85078095468 open Coancestry Expected heterozygosity Loss of variability Optimal contributions RAD-Seq Scophthalmus maximus artículo http://purl.org/coar/resource_type/c_6501 2020 ftcsic https://doi.org/10.1016/j.aquaculture.2020.73498510.13039/50110000078010.13039/501100000268 2024-05-29T00:05:22Z 8 Pág. In population management, the most efficient method to control the increase of inbreeding and the associated loss of genetic variability is the Optimal Contributions method. This method optimizes the contributions of breeding candidates by minimizing the weighted global coancestry. Traditionally, coancestry coefficients have been estimated from pedigree data but the current availability of genome-wide information allows us to estimate them with higher precision. In recent years, developments of genomic tools in aquaculture species have been very significant. For turbot, a species with an increasing aquaculture value, the whole genome has been recently assembled and genetic and physical maps have been refined. Although several measures of genomic coancestry have been proposed, their relative efficiency for maintaining genetic variability is unknown. The objectives of this study were to compare different measures of genomic coancestry for turbot, and to evaluate their efficiency for retaining genetic variability when using the Optimal Contributions method. We used genomic data obtained through 2b-RAD technology for a domesticated population to achieve the objectives. The different genome-wide coancestry matrices compared were based on: i) the proportion of shared alleles; ii) deviations of the observed number of alleles shared by two individuals from the expected number; iii) the realized relationship matrix obtained by VanRaden's method 1; iv) the realized relationship matrix obtained by VanRaden's method 2; v) the realized relationship matrix obtained by Yang's method; and vi) identical by descent segments. The amount of genetic variability retained when using each coancestry matrix was measured as the expected heterozygosity in the next generation. Results revealed that coancestry coefficients showing high correlations between them gave similar results from the optimization. The genetic variability retained was about 5% higher when using the matrices based on the proportion of shared alleles, ... Article in Journal/Newspaper Scophthalmus maximus Turbot Digital.CSIC (Spanish National Research Council) Aquaculture 520 734985 |
institution |
Open Polar |
collection |
Digital.CSIC (Spanish National Research Council) |
op_collection_id |
ftcsic |
language |
English |
topic |
Coancestry Expected heterozygosity Loss of variability Optimal contributions RAD-Seq Scophthalmus maximus |
spellingShingle |
Coancestry Expected heterozygosity Loss of variability Optimal contributions RAD-Seq Scophthalmus maximus Morales-González, Elisabeth Saura, María Fernández, Almudena Fernández, Jesús Pong-Wong, Ricardo Cabaleiro, Santiago Martínez, Paulino Martín-García, Anaís Villanueva, Beatriz Evaluating different genomic coancestry matrices for managing genetic variability in turbot |
topic_facet |
Coancestry Expected heterozygosity Loss of variability Optimal contributions RAD-Seq Scophthalmus maximus |
description |
8 Pág. In population management, the most efficient method to control the increase of inbreeding and the associated loss of genetic variability is the Optimal Contributions method. This method optimizes the contributions of breeding candidates by minimizing the weighted global coancestry. Traditionally, coancestry coefficients have been estimated from pedigree data but the current availability of genome-wide information allows us to estimate them with higher precision. In recent years, developments of genomic tools in aquaculture species have been very significant. For turbot, a species with an increasing aquaculture value, the whole genome has been recently assembled and genetic and physical maps have been refined. Although several measures of genomic coancestry have been proposed, their relative efficiency for maintaining genetic variability is unknown. The objectives of this study were to compare different measures of genomic coancestry for turbot, and to evaluate their efficiency for retaining genetic variability when using the Optimal Contributions method. We used genomic data obtained through 2b-RAD technology for a domesticated population to achieve the objectives. The different genome-wide coancestry matrices compared were based on: i) the proportion of shared alleles; ii) deviations of the observed number of alleles shared by two individuals from the expected number; iii) the realized relationship matrix obtained by VanRaden's method 1; iv) the realized relationship matrix obtained by VanRaden's method 2; v) the realized relationship matrix obtained by Yang's method; and vi) identical by descent segments. The amount of genetic variability retained when using each coancestry matrix was measured as the expected heterozygosity in the next generation. Results revealed that coancestry coefficients showing high correlations between them gave similar results from the optimization. The genetic variability retained was about 5% higher when using the matrices based on the proportion of shared alleles, ... |
author2 |
European Commission Ministerio de Ciencia, Innovación y Universidades (España) Biotechnology and Biological Sciences Research Council (UK) Morales-González, Elisabeth Saura, María Fernández, Almudena Fernández, Jesús Pong-Wong, Ricardo Cabaleiro, Santiago Martínez, Paulino Villanueva, Beatriz |
format |
Article in Journal/Newspaper |
author |
Morales-González, Elisabeth Saura, María Fernández, Almudena Fernández, Jesús Pong-Wong, Ricardo Cabaleiro, Santiago Martínez, Paulino Martín-García, Anaís Villanueva, Beatriz |
author_facet |
Morales-González, Elisabeth Saura, María Fernández, Almudena Fernández, Jesús Pong-Wong, Ricardo Cabaleiro, Santiago Martínez, Paulino Martín-García, Anaís Villanueva, Beatriz |
author_sort |
Morales-González, Elisabeth |
title |
Evaluating different genomic coancestry matrices for managing genetic variability in turbot |
title_short |
Evaluating different genomic coancestry matrices for managing genetic variability in turbot |
title_full |
Evaluating different genomic coancestry matrices for managing genetic variability in turbot |
title_fullStr |
Evaluating different genomic coancestry matrices for managing genetic variability in turbot |
title_full_unstemmed |
Evaluating different genomic coancestry matrices for managing genetic variability in turbot |
title_sort |
evaluating different genomic coancestry matrices for managing genetic variability in turbot |
publisher |
Elsevier BV |
publishDate |
2020 |
url |
http://hdl.handle.net/10261/341800 https://doi.org/10.1016/j.aquaculture.2020.734985 https://doi.org/10.13039/501100000780 https://doi.org/10.13039/501100000268 https://api.elsevier.com/content/abstract/scopus_id/85078095468 |
genre |
Scophthalmus maximus Turbot |
genre_facet |
Scophthalmus maximus Turbot |
op_relation |
#PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/EC/FP7/613611 info:eu-repo/grantAgreement/MICIU//CGL2016-75904-C2-2-P Departamento de Mejora Genética Animal Publisher's version https://doi.org/10.1016/j.aquaculture.2020.734985 Sí Aquaculture 520: e734985 (2020) 0044-8486 http://hdl.handle.net/10261/341800 doi:10.1016/j.aquaculture.2020.734985 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100000268 2-s2.0-85078095468 https://api.elsevier.com/content/abstract/scopus_id/85078095468 |
op_rights |
open |
op_doi |
https://doi.org/10.1016/j.aquaculture.2020.73498510.13039/50110000078010.13039/501100000268 |
container_title |
Aquaculture |
container_volume |
520 |
container_start_page |
734985 |
_version_ |
1802649879043899392 |