Estimating Breeding Values With Molecular Relatedness and Reconstructed Pedigrees in Natural Mating Populations of Common Sole, Solea Solea
Captive populations where natural mating in groups is used to obtain offspring typically yield unbalanced population structures with highly skewed parental contributions and unknown pedigrees. Consequently, for genetic parameter estimation, relationships need to be reconstructed or estimated using D...
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ftunivwagenin:oai:library.wur.nl:wurpubs/387220 2024-02-04T10:00:30+01:00 Estimating Breeding Values With Molecular Relatedness and Reconstructed Pedigrees in Natural Mating Populations of Common Sole, Solea Solea Blonk, R.J.W. Komen, J. Kamstra, A. van Arendonk, J.A.M. 2010 application/pdf https://research.wur.nl/en/publications/estimating-breeding-values-with-molecular-relatedness-and-reconst https://doi.org/10.1534/genetics.109.110536 en eng https://edepot.wur.nl/108137 https://research.wur.nl/en/publications/estimating-breeding-values-with-molecular-relatedness-and-reconst doi:10.1534/genetics.109.110536 info:eu-repo/semantics/restrictedAccess Wageningen University & Research Genetics 184 (2010) ISSN: 0016-6731 body-weight cod gadus-morhua computer-program heritability marker-inferred relatedness oncorhynchus-mykiss pairwise relatedness quantitative genetic-parameters rainbow-trout turbot scophthalmus-maximus info:eu-repo/semantics/article Article/Letter to editor info:eu-repo/semantics/publishedVersion 2010 ftunivwagenin https://doi.org/10.1534/genetics.109.110536 2024-01-10T23:22:52Z Captive populations where natural mating in groups is used to obtain offspring typically yield unbalanced population structures with highly skewed parental contributions and unknown pedigrees. Consequently, for genetic parameter estimation, relationships need to be reconstructed or estimated using DNA marker data. With missing parents and natural mating groups, commonly used pedigree reconstruction methods are not accurate and lead to loss of data. Relatedness estimators, however, infer relationships between all animals sampled. In this study, we compared a pedigree relatedness method and a relatedness estimator ("molecular relatedness") method using accuracy of estimated breeding values. A commercial data set of common sole, Solea solea, with 51 parents and 1953 offspring ("full data set") was used. Due to missing parents, for 1338 offspring, a pedigree could be reconstructed with 10 microsatellite markers ("reduced data set"). Cross-validation of both methods using the reduced data set showed an accuracy of estimated breeding values of 0.54 with pedigree reconstruction and 0.55 with molecular relatedness. Accuracy of estimated breeding values increased to 0.60 when applying molecular relatedness to the full data set. Our results indicate that pedigree reconstruction and molecular relatedness predict breeding values equally well in a population with skewed contributions to families. This is probably due to the presence of few large full-sib families. However, unlike methods with pedigree reconstruction, molecular relatedness methods ensure availability of all genotyped selection candidates, which results in higher accuracy of breeding value estimation Article in Journal/Newspaper Gadus morhua Scophthalmus maximus Turbot Wageningen UR (University & Research Centre): Digital Library Genetics 184 1 213 219 |
institution |
Open Polar |
collection |
Wageningen UR (University & Research Centre): Digital Library |
op_collection_id |
ftunivwagenin |
language |
English |
topic |
body-weight cod gadus-morhua computer-program heritability marker-inferred relatedness oncorhynchus-mykiss pairwise relatedness quantitative genetic-parameters rainbow-trout turbot scophthalmus-maximus |
spellingShingle |
body-weight cod gadus-morhua computer-program heritability marker-inferred relatedness oncorhynchus-mykiss pairwise relatedness quantitative genetic-parameters rainbow-trout turbot scophthalmus-maximus Blonk, R.J.W. Komen, J. Kamstra, A. van Arendonk, J.A.M. Estimating Breeding Values With Molecular Relatedness and Reconstructed Pedigrees in Natural Mating Populations of Common Sole, Solea Solea |
topic_facet |
body-weight cod gadus-morhua computer-program heritability marker-inferred relatedness oncorhynchus-mykiss pairwise relatedness quantitative genetic-parameters rainbow-trout turbot scophthalmus-maximus |
description |
Captive populations where natural mating in groups is used to obtain offspring typically yield unbalanced population structures with highly skewed parental contributions and unknown pedigrees. Consequently, for genetic parameter estimation, relationships need to be reconstructed or estimated using DNA marker data. With missing parents and natural mating groups, commonly used pedigree reconstruction methods are not accurate and lead to loss of data. Relatedness estimators, however, infer relationships between all animals sampled. In this study, we compared a pedigree relatedness method and a relatedness estimator ("molecular relatedness") method using accuracy of estimated breeding values. A commercial data set of common sole, Solea solea, with 51 parents and 1953 offspring ("full data set") was used. Due to missing parents, for 1338 offspring, a pedigree could be reconstructed with 10 microsatellite markers ("reduced data set"). Cross-validation of both methods using the reduced data set showed an accuracy of estimated breeding values of 0.54 with pedigree reconstruction and 0.55 with molecular relatedness. Accuracy of estimated breeding values increased to 0.60 when applying molecular relatedness to the full data set. Our results indicate that pedigree reconstruction and molecular relatedness predict breeding values equally well in a population with skewed contributions to families. This is probably due to the presence of few large full-sib families. However, unlike methods with pedigree reconstruction, molecular relatedness methods ensure availability of all genotyped selection candidates, which results in higher accuracy of breeding value estimation |
format |
Article in Journal/Newspaper |
author |
Blonk, R.J.W. Komen, J. Kamstra, A. van Arendonk, J.A.M. |
author_facet |
Blonk, R.J.W. Komen, J. Kamstra, A. van Arendonk, J.A.M. |
author_sort |
Blonk, R.J.W. |
title |
Estimating Breeding Values With Molecular Relatedness and Reconstructed Pedigrees in Natural Mating Populations of Common Sole, Solea Solea |
title_short |
Estimating Breeding Values With Molecular Relatedness and Reconstructed Pedigrees in Natural Mating Populations of Common Sole, Solea Solea |
title_full |
Estimating Breeding Values With Molecular Relatedness and Reconstructed Pedigrees in Natural Mating Populations of Common Sole, Solea Solea |
title_fullStr |
Estimating Breeding Values With Molecular Relatedness and Reconstructed Pedigrees in Natural Mating Populations of Common Sole, Solea Solea |
title_full_unstemmed |
Estimating Breeding Values With Molecular Relatedness and Reconstructed Pedigrees in Natural Mating Populations of Common Sole, Solea Solea |
title_sort |
estimating breeding values with molecular relatedness and reconstructed pedigrees in natural mating populations of common sole, solea solea |
publishDate |
2010 |
url |
https://research.wur.nl/en/publications/estimating-breeding-values-with-molecular-relatedness-and-reconst https://doi.org/10.1534/genetics.109.110536 |
genre |
Gadus morhua Scophthalmus maximus Turbot |
genre_facet |
Gadus morhua Scophthalmus maximus Turbot |
op_source |
Genetics 184 (2010) ISSN: 0016-6731 |
op_relation |
https://edepot.wur.nl/108137 https://research.wur.nl/en/publications/estimating-breeding-values-with-molecular-relatedness-and-reconst doi:10.1534/genetics.109.110536 |
op_rights |
info:eu-repo/semantics/restrictedAccess Wageningen University & Research |
op_doi |
https://doi.org/10.1534/genetics.109.110536 |
container_title |
Genetics |
container_volume |
184 |
container_issue |
1 |
container_start_page |
213 |
op_container_end_page |
219 |
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1789965837656915968 |