Genotype calling of triploid offspring from diploid parents
International audience AbstractBackgroundPolyploidy is widespread in animals and especially in plants. Different kinds of ploidies exist, for example, hexaploidy in wheat, octaploidy in strawberries, and diploidy, triploidy, tetraploidy, and pseudo-tetraploidy (partly tetraploid) in fish. Triploid o...
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ftccsdartic:oai:HAL:hal-02514815v1 2023-05-15T15:31:07+02:00 Genotype calling of triploid offspring from diploid parents Grashei, Kim Erik Ødegård, Jørgen Meuwissen, Theo H. E. 2020-12 https://hal.archives-ouvertes.fr/hal-02514815 https://hal.archives-ouvertes.fr/hal-02514815/document https://hal.archives-ouvertes.fr/hal-02514815/file/12711_2020_Article_534.pdf https://doi.org/10.1186/s12711-020-00534-w en eng HAL CCSD BioMed Central info:eu-repo/semantics/altIdentifier/doi/10.1186/s12711-020-00534-w hal-02514815 https://hal.archives-ouvertes.fr/hal-02514815 https://hal.archives-ouvertes.fr/hal-02514815/document https://hal.archives-ouvertes.fr/hal-02514815/file/12711_2020_Article_534.pdf doi:10.1186/s12711-020-00534-w info:eu-repo/semantics/OpenAccess ISSN: 0999-193X EISSN: 1297-9686 Genetics Selection Evolution https://hal.archives-ouvertes.fr/hal-02514815 Genetics Selection Evolution, BioMed Central, 2020, 52 (1), pp.15. ⟨10.1186/s12711-020-00534-w⟩ [SDV]Life Sciences [q-bio] info:eu-repo/semantics/article Journal articles 2020 ftccsdartic https://doi.org/10.1186/s12711-020-00534-w 2021-02-20T23:44:48Z International audience AbstractBackgroundPolyploidy is widespread in animals and especially in plants. Different kinds of ploidies exist, for example, hexaploidy in wheat, octaploidy in strawberries, and diploidy, triploidy, tetraploidy, and pseudo-tetraploidy (partly tetraploid) in fish. Triploid offspring from diploid parents occur frequently in the wild in Atlantic salmon (Salmo salar) and, as with triploidy in general, the triploid individuals are sterile. Induced triploidy in Atlantic salmon is common practice to produce sterile fish. In Norwegian aquaculture, production of sterile triploid fish is an attempt by government and industry to limit genetic introgression between wild and farmed fish. However, triploid fish may have traits and properties that differ from those of diploids. Investigating the genetics behind traits in triploids has proved challenging because genotype calling of genetic markers in triploids is not supported by standard software. Our aim was to develop a method that can be used for genotype calling of genetic markers in triploid individuals.ResultsAllele signals were produced for 381 triploid Atlantic salmon offspring using a 56 K Thermo Fisher GeneTitan genotyping platform. Genotypes were successfully called by applying finite normal mixture models to the (transformed) allele signals. Subsets of markers were filtered by quality control statistics for use with downstream analyses. The quality of the called genotypes was sufficient to allow for assignment of diploid parents to the triploid offspring and to discriminate between maternal and paternal parents from autosomal inheritance patterns. In addition, as the maternal inheritance in triploid offspring is identical to gynogenetic inheritance, the maternal recombination pattern for each chromosome could be mapped by using a similar approach as that used in gene-centromere mapping.ConclusionsWe show that calling of dense marker genotypes for triploid individuals is feasible. The resulting genotypes can be used in parentage ... Article in Journal/Newspaper Atlantic salmon Salmo salar Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) Genetics Selection Evolution 52 1 |
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Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) |
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ftccsdartic |
language |
English |
topic |
[SDV]Life Sciences [q-bio] |
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[SDV]Life Sciences [q-bio] Grashei, Kim Erik Ødegård, Jørgen Meuwissen, Theo H. E. Genotype calling of triploid offspring from diploid parents |
topic_facet |
[SDV]Life Sciences [q-bio] |
description |
International audience AbstractBackgroundPolyploidy is widespread in animals and especially in plants. Different kinds of ploidies exist, for example, hexaploidy in wheat, octaploidy in strawberries, and diploidy, triploidy, tetraploidy, and pseudo-tetraploidy (partly tetraploid) in fish. Triploid offspring from diploid parents occur frequently in the wild in Atlantic salmon (Salmo salar) and, as with triploidy in general, the triploid individuals are sterile. Induced triploidy in Atlantic salmon is common practice to produce sterile fish. In Norwegian aquaculture, production of sterile triploid fish is an attempt by government and industry to limit genetic introgression between wild and farmed fish. However, triploid fish may have traits and properties that differ from those of diploids. Investigating the genetics behind traits in triploids has proved challenging because genotype calling of genetic markers in triploids is not supported by standard software. Our aim was to develop a method that can be used for genotype calling of genetic markers in triploid individuals.ResultsAllele signals were produced for 381 triploid Atlantic salmon offspring using a 56 K Thermo Fisher GeneTitan genotyping platform. Genotypes were successfully called by applying finite normal mixture models to the (transformed) allele signals. Subsets of markers were filtered by quality control statistics for use with downstream analyses. The quality of the called genotypes was sufficient to allow for assignment of diploid parents to the triploid offspring and to discriminate between maternal and paternal parents from autosomal inheritance patterns. In addition, as the maternal inheritance in triploid offspring is identical to gynogenetic inheritance, the maternal recombination pattern for each chromosome could be mapped by using a similar approach as that used in gene-centromere mapping.ConclusionsWe show that calling of dense marker genotypes for triploid individuals is feasible. The resulting genotypes can be used in parentage ... |
format |
Article in Journal/Newspaper |
author |
Grashei, Kim Erik Ødegård, Jørgen Meuwissen, Theo H. E. |
author_facet |
Grashei, Kim Erik Ødegård, Jørgen Meuwissen, Theo H. E. |
author_sort |
Grashei, Kim Erik |
title |
Genotype calling of triploid offspring from diploid parents |
title_short |
Genotype calling of triploid offspring from diploid parents |
title_full |
Genotype calling of triploid offspring from diploid parents |
title_fullStr |
Genotype calling of triploid offspring from diploid parents |
title_full_unstemmed |
Genotype calling of triploid offspring from diploid parents |
title_sort |
genotype calling of triploid offspring from diploid parents |
publisher |
HAL CCSD |
publishDate |
2020 |
url |
https://hal.archives-ouvertes.fr/hal-02514815 https://hal.archives-ouvertes.fr/hal-02514815/document https://hal.archives-ouvertes.fr/hal-02514815/file/12711_2020_Article_534.pdf https://doi.org/10.1186/s12711-020-00534-w |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
ISSN: 0999-193X EISSN: 1297-9686 Genetics Selection Evolution https://hal.archives-ouvertes.fr/hal-02514815 Genetics Selection Evolution, BioMed Central, 2020, 52 (1), pp.15. ⟨10.1186/s12711-020-00534-w⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1186/s12711-020-00534-w hal-02514815 https://hal.archives-ouvertes.fr/hal-02514815 https://hal.archives-ouvertes.fr/hal-02514815/document https://hal.archives-ouvertes.fr/hal-02514815/file/12711_2020_Article_534.pdf doi:10.1186/s12711-020-00534-w |
op_rights |
info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1186/s12711-020-00534-w |
container_title |
Genetics Selection Evolution |
container_volume |
52 |
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1 |
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1766361603330015232 |