CIGENE/Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, N-1432 Aas, Norway.
Bioinformatics. 2011 Feb 1;27(3):303-10. doi: 10.1093/bioinformatics/btq673. Epub 2010 Dec 12.
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.
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.
R-package beadarrayMSV freely available on the web at http://cran.r-project.org/.
由于鲑鱼科鱼类在近代发生了一次基因组加倍事件，现代大西洋鲑（Salmo salar）拥有镶嵌式基因组，大约三分之一为四倍体。这给基因分型和遗传作图带来了复杂因素，因为重复区域内的多态性（多座位变异体；MSVs）难以被检出和被分配到正确的同源基因上。Illumina 提供的标准基因分型软件并未被编写用于解释 MSVs，因此要么无法检出这些多态性，要么会错误检出。对于非二倍体物种的作图、连锁或关联研究，迫切需要一种软件，除了常规的单核苷酸多态性（SNP）标记外，还能分析 MSVs。
我们提出了一个用于分析使用 Illumina Infinium BeadArray（Illumina Inc.）部分四倍体基因组的软件包，该软件包包括预处理、聚类、绘图和验证例程。在挪威一个水产养殖品系的 266 个全同胞家系中，分布着 3000 多条鲑鱼，这些鲑鱼在包含 SNP 和 MSV 标记的 15K BeadArray 上进行了基因分型。总共鉴定出 4268 个 SNP 和 1471 个 MSV，平均检出率分别为 0.97 和 0.86。对 150 个在两个同源基因上均表现为多态性的 MSV 进行了剖析和作图，揭示了鲑鱼基因组返祖为二倍体的情况，并提高了标记基因组的覆盖度。发现并报告了几个保留的同源性。
beadarrayMSV R 包可在网上免费获取，网址为 http://cran.r-project.org/。
