Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array

Gidskehaug, Lars, Kent, Matthew, Hayes, Ben J. and Lien, Sigbjorn (2011) Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array. Bioinformatics, 27 3: 303-310. doi:10.1093/bioinformatics/btq673


Author Gidskehaug, Lars
Kent, Matthew
Hayes, Ben J.
Lien, Sigbjorn
Title Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array
Journal name Bioinformatics   Check publisher's open access policy
ISSN 1367-4803
1460-2059
Publication date 2011-02-01
Sub-type Article (original research)
DOI 10.1093/bioinformatics/btq673
Open Access Status Not yet assessed
Volume 27
Issue 3
Start page 303
End page 310
Total pages 8
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
Formatted 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 MSVmarkers. 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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
 
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