Wageningen University and Research - Plant Breeding, Wageningen, The Netherlands.
BMC Bioinformatics. 2022 Oct 23;23(1):442. doi: 10.1186/s12859-022-04989-0.
For genetic analyses, multi-allelic markers have an advantage over bi-allelic markers like SNPs (single nucleotide polymorphisms) in that they carry more information about the genetic constitution of individuals. This is especially the case in polyploids, where individuals carry more than two alleles at each locus. Haploblocks are multi-allelic markers that can be derived by phasing sets of closely-linked SNP markers. Phased haploblocks, similarly to other multi-allelic markers, will therefore be advantageous in genetic tasks like linkage mapping, QTL mapping and genome-wide association studies.
We present a new method to reconstruct haplotypes from SNP dosages derived from genotyping arrays, which is applicable to polyploids. This method is implemented in the software package PolyHaplotyper. In contrast to existing packages for polyploids it makes use of full-sib families among the samples to guide the haplotyping process. We show that in this situation it is much more accurate than other available software, using experimental hexaploid data and simulated tetraploid data.
Our method and the software package PolyHaplotyper in which it is implemented extend the available tools for haplotyping in polyploids. They perform especially well in situations where one or more full-sib families are present.
对于遗传分析，多等位基因标记比单核苷酸多态性 (SNP) 等双等位基因标记具有优势，因为它们携带更多关于个体遗传构成的信息。在多倍体中尤其如此，个体在每个基因座携带两个以上的等位基因。单倍型块是多等位基因标记，可以通过相位紧密连锁的 SNP 标记集来衍生。与其他多等位基因标记类似，相位单倍型块在连锁作图、QTL 作图和全基因组关联研究等遗传任务中具有优势。
我们提出了一种从基因分型阵列中得出的 SNP 剂量重建单倍型的新方法，该方法适用于多倍体。该方法在软件包 PolyHaplotyper 中实现。与现有的多倍体软件包不同，它利用样本中的全同胞家系来指导单倍型分析过程。我们表明，在这种情况下，它比其他可用的软件更准确，使用实验性六倍体数据和模拟四倍体数据。
我们的方法和其中实现的软件包 PolyHaplotyper 扩展了多倍体中单倍型分析的可用工具。它们在存在一个或多个全同胞家系的情况下表现尤其出色。
