Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array
Abstract Motivation: Due to a genome duplication event in the recent history of salmonids, modern Atlantic salmon (Salmo salar) have a mosaic genome with roughly one-third being tetraploid. This is a complicating factor in genotyping and genetic mapping since polymorphisms within duplicated regions...
Published in: | Bioinformatics |
---|---|
Main Authors: | , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Oxford University Press (OUP)
2010
|
Subjects: | |
Online Access: | http://dx.doi.org/10.1093/bioinformatics/btq673 https://academic.oup.com/bioinformatics/article-pdf/27/3/303/48865750/bioinformatics_27_3_303.pdf |
id |
croxfordunivpr:10.1093/bioinformatics/btq673 |
---|---|
record_format |
openpolar |
spelling |
croxfordunivpr:10.1093/bioinformatics/btq673 2024-09-09T19:30:34+00:00 Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array Gidskehaug, Lars Kent, Matthew Hayes, Ben J. Lien, Sigbjørn 2010 http://dx.doi.org/10.1093/bioinformatics/btq673 https://academic.oup.com/bioinformatics/article-pdf/27/3/303/48865750/bioinformatics_27_3_303.pdf en eng Oxford University Press (OUP) Bioinformatics volume 27, issue 3, page 303-310 ISSN 1367-4811 1367-4803 journal-article 2010 croxfordunivpr https://doi.org/10.1093/bioinformatics/btq673 2024-08-19T04:22:47Z Abstract Motivation: Due to a genome duplication event in the recent history of salmonids, modern Atlantic salmon (Salmo salar) have a mosaic genome with roughly one-third being tetraploid. This is a complicating factor in genotyping and genetic mapping since polymorphisms within duplicated regions (multisite variants; MSVs) are challenging to call and to assign to the correct paralogue. Standard genotyping software offered by Illumina has not been written to interpret MSVs and will either fail or miscall these polymorphisms. For the purpose of mapping, linkage or association studies in non-diploid species, there is a pressing need for software that includes analysis of MSVs in addition to regular single nucleotide polymorphism (SNP) markers. Results: A software package is presented for the analysis of partially tetraploid genomes genotyped using Illumina Infinium BeadArrays (Illumina Inc.) that includes pre-processing, clustering, plotting and validation routines. More than 3000 salmon from an aquacultural strain in Norway, distributed among 266 full-sib families, were genotyped on a 15K BeadArray including both SNP- and MSV-markers. A total of 4268 SNPs and 1471 MSVs were identified, with average call accuracies of 0.97 and 0.86, respectively. A total of 150 MSVs polymorphic in both paralogs were dissected and mapped to their respective chromosomes, yielding insights about the salmon genome reversion to diploidy and improving marker genome coverage. Several retained homologies were found and are reported. Availability and implementation: R-package beadarrayMSV freely available on the web at http://cran.r-project.org/ Contact: lg@camo.no Supplementary information: Supplementary data are available at Bioinformatics online. Article in Journal/Newspaper Atlantic salmon Salmo salar Oxford University Press Norway Bioinformatics 27 3 303 310 |
institution |
Open Polar |
collection |
Oxford University Press |
op_collection_id |
croxfordunivpr |
language |
English |
description |
Abstract Motivation: Due to a genome duplication event in the recent history of salmonids, modern Atlantic salmon (Salmo salar) have a mosaic genome with roughly one-third being tetraploid. This is a complicating factor in genotyping and genetic mapping since polymorphisms within duplicated regions (multisite variants; MSVs) are challenging to call and to assign to the correct paralogue. Standard genotyping software offered by Illumina has not been written to interpret MSVs and will either fail or miscall these polymorphisms. For the purpose of mapping, linkage or association studies in non-diploid species, there is a pressing need for software that includes analysis of MSVs in addition to regular single nucleotide polymorphism (SNP) markers. Results: A software package is presented for the analysis of partially tetraploid genomes genotyped using Illumina Infinium BeadArrays (Illumina Inc.) that includes pre-processing, clustering, plotting and validation routines. More than 3000 salmon from an aquacultural strain in Norway, distributed among 266 full-sib families, were genotyped on a 15K BeadArray including both SNP- and MSV-markers. A total of 4268 SNPs and 1471 MSVs were identified, with average call accuracies of 0.97 and 0.86, respectively. A total of 150 MSVs polymorphic in both paralogs were dissected and mapped to their respective chromosomes, yielding insights about the salmon genome reversion to diploidy and improving marker genome coverage. Several retained homologies were found and are reported. Availability and implementation: R-package beadarrayMSV freely available on the web at http://cran.r-project.org/ Contact: lg@camo.no Supplementary information: Supplementary data are available at Bioinformatics online. |
format |
Article in Journal/Newspaper |
author |
Gidskehaug, Lars Kent, Matthew Hayes, Ben J. Lien, Sigbjørn |
spellingShingle |
Gidskehaug, Lars Kent, Matthew Hayes, Ben J. Lien, Sigbjørn Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array |
author_facet |
Gidskehaug, Lars Kent, Matthew Hayes, Ben J. Lien, Sigbjørn |
author_sort |
Gidskehaug, Lars |
title |
Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array |
title_short |
Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array |
title_full |
Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array |
title_fullStr |
Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array |
title_full_unstemmed |
Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array |
title_sort |
genotype calling and mapping of multisite variants using an atlantic salmon iselect snp array |
publisher |
Oxford University Press (OUP) |
publishDate |
2010 |
url |
http://dx.doi.org/10.1093/bioinformatics/btq673 https://academic.oup.com/bioinformatics/article-pdf/27/3/303/48865750/bioinformatics_27_3_303.pdf |
geographic |
Norway |
geographic_facet |
Norway |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Bioinformatics volume 27, issue 3, page 303-310 ISSN 1367-4811 1367-4803 |
op_doi |
https://doi.org/10.1093/bioinformatics/btq673 |
container_title |
Bioinformatics |
container_volume |
27 |
container_issue |
3 |
container_start_page |
303 |
op_container_end_page |
310 |
_version_ |
1809899559175847936 |