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/.
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/.
Authors: David B Jones; Dean R Jerry; Sylvain Forêt; Dmitry A Konovalov; Kyall R Zenger Journal: Mar Biotechnol (NY) Date: 2013-05-30 Impact factor: 3.619
Authors: Sigbjørn Lien; Lars Gidskehaug; Thomas Moen; Ben J Hayes; Paul R Berg; William S Davidson; Stig W Omholt; Matthew P Kent Journal: BMC Genomics Date: 2011-12-19 Impact factor: 3.969
Authors: Michael J Gilchrist; Daniel Sobral; Pierre Khoueiry; Fabrice Daian; Batiste Laporte; Ilya Patrushev; Jun Matsumoto; Ken Dewar; Kenneth E M Hastings; Yutaka Satou; Patrick Lemaire; Ute Rothbächer Journal: Dev Biol Date: 2015-05-27 Impact factor: 3.582
Authors: Susan E Johnston; Meri Lindqvist; Eero Niemelä; Panu Orell; Jaakko Erkinaro; Matthew P Kent; Sigbjørn Lien; Juha-Pekka Vähä; Anti Vasemägi; Craig R Primmer Journal: BMC Genomics Date: 2013-07-03 Impact factor: 3.969