{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T23:27:56Z","timestamp":1778974076421,"version":"3.51.4"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability and implementation: R-package beadarrayMSV freely available on the web at http:\/\/cran.r-project.org\/<\/jats:p>\n               <jats:p>Contact: \u00a0lg@camo.no<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq673","type":"journal-article","created":{"date-parts":[[2010,12,14]],"date-time":"2010-12-14T04:21:31Z","timestamp":1292300491000},"page":"303-310","source":"Crossref","is-referenced-by-count":61,"title":["Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array"],"prefix":"10.1093","volume":"27","author":[{"given":"Lars","family":"Gidskehaug","sequence":"first","affiliation":[{"name":"1 CIGENE\/Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, N-1432 Aas, Norway and 2Biosciences Research Division, Department of Primary Industries, Victoria, Melbourne 3083, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew","family":"Kent","sequence":"additional","affiliation":[{"name":"1 CIGENE\/Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, N-1432 Aas, Norway and 2Biosciences Research Division, Department of Primary Industries, Victoria, Melbourne 3083, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ben J.","family":"Hayes","sequence":"additional","affiliation":[{"name":"1 CIGENE\/Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, N-1432 Aas, Norway and 2Biosciences Research Division, Department of Primary Industries, Victoria, Melbourne 3083, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sigbj\u00f8rn","family":"Lien","sequence":"additional","affiliation":[{"name":"1 CIGENE\/Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, N-1432 Aas, Norway and 2Biosciences Research Division, Department of Primary Industries, Victoria, Melbourne 3083, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,12,12]]},"reference":[{"key":"2023012511550347300_B1","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1139\/g05-067","article-title":"A comparative analysis of the rainbow trout genome with 2 other species of fish (Arctic charr and Atlantic salmon) within the tetraploid derivative Salmonidae family (subfamily: Salmoninae)","volume":"48","author":"Danzmann","year":"2005","journal-title":"Genome"},{"key":"2023012511550347300_B2","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1186\/1471-2164-9-557","article-title":"Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon)","volume":"9","author":"Danzmann","year":"2008","journal-title":"BMC Genomics"},{"key":"2023012511550347300_B3","doi-asserted-by":"crossref","first-page":"2183","DOI":"10.1093\/bioinformatics\/btm311","article-title":"beadarray: R classes and methods for Illumina bead-based data","volume":"23","author":"Dunning","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012511550347300_B4","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1038\/ng1401","article-title":"Complex SNP-related sequence variation in segmental genome duplications","volume":"36","author":"Fredman","year":"2004","journal-title":"Nat. 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