Genotyping SNPs and inferring ploidy by amplicon sequencing for polyploid, ploidy-variable organisms

Whole genome duplication is hypothesized to have played a critical role in the evolution of several major organism groups, 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 provide a strategy for developing an amplicon sequencing panel of single nucleotide polymorphisms for high-throughput genotyping of polyploid organisms. We then developed 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...学界假说，全基因组复制（Whole genome duplication）在包括脊椎动物在内的多个主要生物类群的演化过程中发挥了关键作用；尽管多数演化支已完成二倍体化，但仍有部分类群保留多倍体基因组。此外，倍性变异可自然发生，亦可在特定动植物物种中通过人工手段诱导产生。现代遗传学技术尚未广泛应用于多倍体或倍性可变物种，部分原因在于难以从多倍体生物中获取基因型数据。本研究提出了一种开发单核苷酸多态性（Single Nucleotide Polymorphism, SNP）扩增子测序组合（amplicon sequencing panel）的策略，用于多倍体生物的高通量基因分型。随后我们开发了一种从扩增子测序数据中推断个体倍性的方法，该方法可推广至任意倍性水平，且无需预先识别杂合基因型。将这两种技术相结合，将使研究人员能够同时完成个体倍性推断并生成兼顾倍性信息的基因型数据……