A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication
Diploidization, which follows whole genome duplication events, does not occur evenly across the genome. In salmonid fishes, certain pairs of homeologous chromosomes preserve tetraploid loci in higher frequencies toward the telomeres due to residual tetrasomic inheritance. Research suggests this occu...
Published in: | G3 Genes|Genomes|Genetics |
---|---|
Main Authors: | , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Oxford University Press
2017
|
Subjects: | |
Online Access: | https://doi.org/10.1534/g3.116.038026 https://doaj.org/article/300331bc46204920a6020b2e0b6a26b4 |
id |
ftdoajarticles:oai:doaj.org/article:300331bc46204920a6020b2e0b6a26b4 |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:300331bc46204920a6020b2e0b6a26b4 2023-05-15T14:30:03+02:00 A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication Cameron M. Nugent Anne A. Easton Joseph D. Norman Moira M. Ferguson Roy G. Danzmann 2017-02-01T00:00:00Z https://doi.org/10.1534/g3.116.038026 https://doaj.org/article/300331bc46204920a6020b2e0b6a26b4 EN eng Oxford University Press http://g3journal.org/lookup/doi/10.1534/g3.116.038026 https://doaj.org/toc/2160-1836 2160-1836 doi:10.1534/g3.116.038026 https://doaj.org/article/300331bc46204920a6020b2e0b6a26b4 G3: Genes, Genomes, Genetics, Vol 7, Iss 2, Pp 543-556 (2017) diploidization duplicated genes epigenetic modification linkage map salmonid fishes transmission genetics transposition Genetics QH426-470 article 2017 ftdoajarticles https://doi.org/10.1534/g3.116.038026 2022-12-31T09:59:33Z Diploidization, which follows whole genome duplication events, does not occur evenly across the genome. In salmonid fishes, certain pairs of homeologous chromosomes preserve tetraploid loci in higher frequencies toward the telomeres due to residual tetrasomic inheritance. Research suggests this occurs only in homeologous pairs where one chromosome arm has undergone a fusion event. We present a linkage map for Arctic charr (Salvelinus alpinus), a salmonid species with relatively fewer chromosome fusions. Genotype by sequencing identified 19,418 SNPs, and a linkage map consisting of 4508 markers was constructed from a subset of high quality SNPs and microsatellite markers that were used to anchor the new map to previous versions. Both male- and female-specific linkage maps contained the expected number of 39 linkage groups. The chromosome type associated with each linkage group was determined, and 10 stable metacentric chromosomes were identified, along with a chromosome polymorphism involving the sex chromosome AC04. Two instances of a weak form of pseudolinkage were detected in the telomeric regions of homeologous chromosome arms in both female and male linkage maps. Chromosome arm homologies within the Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) genomes were determined. Paralogous sequence variants (PSVs) were identified, and their comparative BLASTn hit locations showed that duplicate markers exist in higher numbers on seven pairs of homeologous arms, previously identified as preserving tetrasomy in salmonid species. Homeologous arm pairs where neither arm has been part of a fusion event in Arctic charr had fewer PSVs, suggesting faster diploidization rates in these regions. Article in Journal/Newspaper Arctic charr Arctic Atlantic salmon Salmo salar Salvelinus alpinus Directory of Open Access Journals: DOAJ Articles Arctic G3 Genes|Genomes|Genetics 7 2 543 556 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
diploidization duplicated genes epigenetic modification linkage map salmonid fishes transmission genetics transposition Genetics QH426-470 |
spellingShingle |
diploidization duplicated genes epigenetic modification linkage map salmonid fishes transmission genetics transposition Genetics QH426-470 Cameron M. Nugent Anne A. Easton Joseph D. Norman Moira M. Ferguson Roy G. Danzmann A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication |
topic_facet |
diploidization duplicated genes epigenetic modification linkage map salmonid fishes transmission genetics transposition Genetics QH426-470 |
description |
Diploidization, which follows whole genome duplication events, does not occur evenly across the genome. In salmonid fishes, certain pairs of homeologous chromosomes preserve tetraploid loci in higher frequencies toward the telomeres due to residual tetrasomic inheritance. Research suggests this occurs only in homeologous pairs where one chromosome arm has undergone a fusion event. We present a linkage map for Arctic charr (Salvelinus alpinus), a salmonid species with relatively fewer chromosome fusions. Genotype by sequencing identified 19,418 SNPs, and a linkage map consisting of 4508 markers was constructed from a subset of high quality SNPs and microsatellite markers that were used to anchor the new map to previous versions. Both male- and female-specific linkage maps contained the expected number of 39 linkage groups. The chromosome type associated with each linkage group was determined, and 10 stable metacentric chromosomes were identified, along with a chromosome polymorphism involving the sex chromosome AC04. Two instances of a weak form of pseudolinkage were detected in the telomeric regions of homeologous chromosome arms in both female and male linkage maps. Chromosome arm homologies within the Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) genomes were determined. Paralogous sequence variants (PSVs) were identified, and their comparative BLASTn hit locations showed that duplicate markers exist in higher numbers on seven pairs of homeologous arms, previously identified as preserving tetrasomy in salmonid species. Homeologous arm pairs where neither arm has been part of a fusion event in Arctic charr had fewer PSVs, suggesting faster diploidization rates in these regions. |
format |
Article in Journal/Newspaper |
author |
Cameron M. Nugent Anne A. Easton Joseph D. Norman Moira M. Ferguson Roy G. Danzmann |
author_facet |
Cameron M. Nugent Anne A. Easton Joseph D. Norman Moira M. Ferguson Roy G. Danzmann |
author_sort |
Cameron M. Nugent |
title |
A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication |
title_short |
A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication |
title_full |
A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication |
title_fullStr |
A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication |
title_full_unstemmed |
A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication |
title_sort |
snp based linkage map of the arctic charr (salvelinus alpinus) genome provides insights into the diploidization process after whole genome duplication |
publisher |
Oxford University Press |
publishDate |
2017 |
url |
https://doi.org/10.1534/g3.116.038026 https://doaj.org/article/300331bc46204920a6020b2e0b6a26b4 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic charr Arctic Atlantic salmon Salmo salar Salvelinus alpinus |
genre_facet |
Arctic charr Arctic Atlantic salmon Salmo salar Salvelinus alpinus |
op_source |
G3: Genes, Genomes, Genetics, Vol 7, Iss 2, Pp 543-556 (2017) |
op_relation |
http://g3journal.org/lookup/doi/10.1534/g3.116.038026 https://doaj.org/toc/2160-1836 2160-1836 doi:10.1534/g3.116.038026 https://doaj.org/article/300331bc46204920a6020b2e0b6a26b4 |
op_doi |
https://doi.org/10.1534/g3.116.038026 |
container_title |
G3 Genes|Genomes|Genetics |
container_volume |
7 |
container_issue |
2 |
container_start_page |
543 |
op_container_end_page |
556 |
_version_ |
1766303970153725952 |