Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array
Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array
复制标题
DOI：
10.1093/bioinformatics/btq673
复制
发表时间：
2011-02-01
期刊：
影响因子：
5.8
通讯作者：
Lien, Sigbjorn
中科院分区：
文献类型：
--
作者：
Gidskehaug, Lars;Kent, Matthew;Lien, Sigbjorn
动机：由于鲑科鱼类近代史上的一次基因组复制事件，现代大西洋鲑鱼(Salmo Salar)的基因组是马赛克的，大约三分之一是四倍体。这在基因分型和遗传作图中是一个复杂的因素，因为重复区域(多点变种；MSVS)中的多态很难调用和分配到正确的并列。Illumina提供的标准基因分型软件还没有被编写来解释MSVS，并且将失败或错误地调用这些多态。为了在非二倍体物种中进行作图、连锁或关联研究，除了常规的单核苷酸多态(SNP)标记外，迫切需要包括MSVS分析的软件。结果：开发了一个用于利用Illumina Infinium BeadArray(Illumina Inc.)这包括预处理、聚类、绘图和验证例程。来自挪威水产养殖品系的3000多条鲑鱼分布在266个全同胞家庭中，在包括SNP和MSV标记的15K珠状阵列上进行了基因分型。共识别了4268个SNP和1471个MSV，平均呼叫准确率分别为0.97和0.86。在这两种近亲海豚中，共有150个MSVS被解剖并定位到它们各自的染色体上，从而获得了关于鲑鱼基因组恢复到二倍体的见解，并提高了标记基因组的覆盖率。发现并报道了几个保留的同源序列。
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.