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Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array.
Lars Gidskehaug1, Matthew Kent, Ben J Hayes
1CIGENE/Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, N-1432 Aas, Norway. lg@camo.no
Bioinformatics (Oxford, England)
|December 15, 2010
Summary
A new R-package, beadarrayMSV, analyzes Atlantic salmon genomes, accurately identifying single nucleotide polymorphisms (SNPs) and multisite variants (MSVs) in their complex tetraploid regions for improved genetic mapping.
Area of Science:
- Genomics
- Bioinformatics
- Aquaculture Genetics
Background:
- Atlantic salmon (Salmo salar) possess a mosaic genome due to a recent genome duplication, with approximately one-third being tetraploid.
- This tetraploidy complicates genotyping and genetic mapping, as multisite variants (MSVs) are difficult to accurately call and assign to paralogous regions.
- Existing genotyping software, such as Illumina's, is not designed to interpret MSVs, leading to errors in data analysis.
Purpose of the Study:
- To develop and present a novel software package for the comprehensive analysis of partially tetraploid salmonid genomes.
- To enable accurate genotyping and genetic mapping in Atlantic salmon by incorporating analysis of both single nucleotide polymorphisms (SNPs) and multisite variants (MSVs).
- To improve marker genome coverage and gain insights into genome reversion to diploidy in salmonids.
Main Methods:
- Development of an R-package named beadarrayMSV, incorporating pre-processing, clustering, plotting, and validation routines.
- Genotyping of over 3000 Atlantic salmon from an aquacultural strain using an Illumina 15K BeadArray, including both SNP and MSV markers.
- Analysis of multisite variants (MSVs) within duplicated genomic regions, alongside standard single nucleotide polymorphism (SNP) analysis.
Main Results:
- The study identified a total of 4268 SNPs and 1471 MSVs with high average call accuracies (0.97 for SNPs, 0.86 for MSVs).
- A total of 150 MSVs that were polymorphic in both paralogs were successfully dissected and mapped to their respective chromosomes.
- The mapping of MSVs provided insights into the reversion of the salmon genome to diploidy and enhanced overall marker genome coverage.
Conclusions:
- The beadarrayMSV R-package provides a robust solution for analyzing complex tetraploid genomes in salmonids.
- Accurate identification and mapping of MSVs significantly improve genetic mapping resolution and genomic insights in Atlantic salmon.
- This software facilitates advanced genetic studies, including linkage and association analyses, in non-diploid species.
