Genotype calling of triploid offspring from diploid parents
BACKGROUND: Polyploidy 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...
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ftpubmed:oai:pubmedcentral.nih.gov:7081531 2023-05-15T15:31:05+02:00 Genotype calling of triploid offspring from diploid parents Grashei, Kim Erik Ødegård, Jørgen Meuwissen, Theo H. E. 2020-03-18 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7081531/ http://www.ncbi.nlm.nih.gov/pubmed/32188420 https://doi.org/10.1186/s12711-020-00534-w en eng BioMed Central http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7081531/ http://www.ncbi.nlm.nih.gov/pubmed/32188420 http://dx.doi.org/10.1186/s12711-020-00534-w © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. CC0 PDM CC-BY Research Article Text 2020 ftpubmed https://doi.org/10.1186/s12711-020-00534-w 2020-03-29T01:32:49Z BACKGROUND: Polyploidy 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. RESULTS: Allele 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. CONCLUSIONS: We show that calling of dense marker genotypes for triploid individuals is feasible. The resulting genotypes can be used in parentage assignment of triploid offspring ... Text Atlantic salmon Salmo salar PubMed Central (PMC) Genetics Selection Evolution 52 1 |
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Research Article Grashei, Kim Erik Ødegård, Jørgen Meuwissen, Theo H. E. Genotype calling of triploid offspring from diploid parents |
topic_facet |
Research Article |
description |
BACKGROUND: Polyploidy 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. RESULTS: Allele 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. CONCLUSIONS: We show that calling of dense marker genotypes for triploid individuals is feasible. The resulting genotypes can be used in parentage assignment of triploid offspring ... |
format |
Text |
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 |
BioMed Central |
publishDate |
2020 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7081531/ http://www.ncbi.nlm.nih.gov/pubmed/32188420 https://doi.org/10.1186/s12711-020-00534-w |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7081531/ http://www.ncbi.nlm.nih.gov/pubmed/32188420 http://dx.doi.org/10.1186/s12711-020-00534-w |
op_rights |
© The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
op_rightsnorm |
CC0 PDM CC-BY |
op_doi |
https://doi.org/10.1186/s12711-020-00534-w |
container_title |
Genetics Selection Evolution |
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52 |
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1 |
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1766361571306504192 |