Whole genome duplication is hypothesized to have played a critical role in the evolution of several major taxa, including vertebrates, and while many lineages have rediploidized, some retain polyploid genomes. Additionally, variation in ploidy can occur naturally or be artificially induced within select plant and animal species. Modern genetic techniques have not been widely applied to polyploid or ploidy-variable species, in part due to the difficulty of obtaining genotype data from polyploids. In this study, we demonstrate a strategy for developing an amplicon sequencing panel of single nucleotide polymorphisms for high-throughput genotyping of polyploid organisms. We then develop a method to infer ploidy of individuals from amplicon sequencing data that is generalized to apply to any ploidy and does not require prior identification of heterozygous genotypes. Combining these two techniques will allow researchers to both infer ploidy and generate ploidy-aware genotypes with the same amplicon sequencing panel. We demonstrate this approach with white sturgeon Acipenser transmontanus, a ploidy-variable (octoploid, decaploid and dodecaploid) imperiled species under conservation management in the Pacific Northwest and obtained a panel of 325 loci. These loci were validated by examining inheritance in known-cross families, and the ploidy inference method was validated with known ploidy samples. We provide scripts that adapt existing pipelines to genotype polyploids and an R package for application of the ploidy inference method. We expect that these techniques will empower studies of genetic variation and inheritance in polyploid organisms that vary in ploidy level, either naturally or as a result of artificial propagation practices.

中文翻译：

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基因分型单核苷酸多态性并通过扩增子测序推断多倍体、倍性可变生物体的倍性

全基因组复制被假设在包括脊椎动物在内的几个主要分类群的进化中发挥了关键作用，虽然许多谱系已经重新二倍体化，但有些仍保留了多倍体基因组。此外，倍性的变异可以自然发生，也可以在选定的植物和动物物种中人工诱导。现代遗传技术尚未广泛应用于多倍体或倍性可变物种，部分原因是难以从多倍体中获得基因型数据。在这项研究中，我们展示了一种开发单核苷酸多态性扩增子测序面板的策略，用于多倍体生物的高通量基因分型。然后，我们开发了一种从扩增子测序数据推断个体倍性的方法，该方法适用于任何倍性，并且不需要事先鉴定杂合基因型。结合这两种技术将使研究人员能够使用相同的扩增子测序面板推断倍性并生成具有倍性意识的基因型。我们用白鲟证明了这种方法Acipenser transmontanus，一种倍性变异（八倍体、十倍体和十二倍体）在太平洋西北部受到保护管理的濒危物种，并获得了 325 个基因座的面板。通过检查已知交叉家族中的遗传来验证这些基因座，并使用已知倍性样本验证倍性推断方法。我们提供了使现有管道适应基因型多倍体的脚本和用于应用倍性推理方法的 R 包。我们预计这些技术将有助于研究倍性水平不同的多倍体生物的遗传变异和遗传，无论是自然的还是人工繁殖实践的结果。