Polyploidy is widespread in animals and especially in plants. Different kinds of ploidies exist, for example, hexaploidy in wheat, octaploidy in strawberries, and diploidy, triploidy, tetraploidy, and pseudo-tetraploidy (partly tetraploid) in fish. Triploid offspring from diploid parents occur frequently in the wild in Atlantic salmon (Salmo salar) and, as with triploidy in general, the triploid individuals are sterile. Induced triploidy in Atlantic salmon is common practice to produce sterile fish. In Norwegian aquaculture, production of sterile triploid fish is an attempt by government and industry to limit genetic introgression between wild and farmed fish. However, triploid fish may have traits and properties that differ from those of diploids. Investigating the genetics behind traits in triploids has proved challenging because genotype calling of genetic markers in triploids is not supported by standard software. Our aim was to develop a method that can be used for genotype calling of genetic markers in triploid individuals. Allele signals were produced for 381 triploid Atlantic salmon offspring using a 56 K Thermo Fisher GeneTitan genotyping platform. Genotypes were successfully called by applying finite normal mixture models to the (transformed) allele signals. Subsets of markers were filtered by quality control statistics for use with downstream analyses. The quality of the called genotypes was sufficient to allow for assignment of diploid parents to the triploid offspring and to discriminate between maternal and paternal parents from autosomal inheritance patterns. In addition, as the maternal inheritance in triploid offspring is identical to gynogenetic inheritance, the maternal recombination pattern for each chromosome could be mapped by using a similar approach as that used in gene-centromere mapping. We show that calling of dense marker genotypes for triploid individuals is feasible. The resulting genotypes can be used in parentage assignment of triploid offspring to diploid parents, to discriminate between maternal and paternal parents using autosomal inheritance patterns, and to map the maternal recombination pattern using an approach similar to gene-centromere mapping. Genotyping of triploid individuals is important both for selective breeding programs and unravelling the underlying genetics of phenotypes recorded in triploids. In principle, the developed method can be used for genotype calling of other polyploid organisms.

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来自二倍体父母的三倍体后代的基因型鉴定

多倍体在动物尤其是植物中广泛存在。存在不同种类的倍性，例如小麦中的六倍体，草莓中的八倍体以及鱼中的二倍体，三倍体，四倍体和伪四倍体（部分为四倍体）。来自二倍体父母的三倍体后代在大西洋鲑（Salmo salar）的野外经常发生，并且与三倍体一样，三倍体个体是不育的。在大西洋鲑中诱导三倍体是生产不育鱼的普遍做法。在挪威的水产养殖中，政府和工业界试图生产无菌三倍体鱼类，以限制野生和养殖鱼类之间的基因渗入。但是，三倍体鱼类的性状和特性可能与二倍体不同。研究三倍体性状背后的遗传学已证明具有挑战性，因为标准软件不支持三倍体中遗传标记的基因型调用。我们的目标是开发一种可用于三倍体个体中遗传标记基因型调用的方法。使用56 K Thermo Fisher GeneTitan基因分型平台，为381个三倍体大西洋鲑鱼后代产生了等位基因信号。通过将有限的正常混合模型应用于（转化的）等位基因信号，成功地确定了基因型。标记的子集通过质量控制统计数据进行过滤，以用于下游分析。所谓基因型的质量足以允许将二倍体亲本分配给三倍体后代，并从常染色体遗传模式中区分母本和父本。此外，由于三倍体后代的母体遗传与妇科遗传学相同，因此可以使用与基因着丝粒作图相似的方法对每个染色体的母体重组模式进行作图。我们表明三倍体个体的密集标记基因型的调用是可行的。产生的基因型可用于将三倍体后代与二倍体亲本的亲本分配中，使用常染色体遗传模式来区分母本和父本亲本，并使用类似于基因着丝粒作图的方法来绘制母体重组模式。三倍体个体的基因分型对于选择育种计划和揭示三倍体中记录的表型的潜在遗传学都非常重要。原则上，