4.6 Article

PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data

Journal

BMC BIOINFORMATICS
Volume 23, Issue 1, Pages -

Publisher

BMC
DOI: 10.1186/s12859-022-04989-0

Keywords

Haplotype; SNP array; Multi-allelic marker; Polyploid

Funding

  1. Ministry of Agriculture, Nature and Food Quality of the Netherlands, through TKI projects `Novel genetic and genomic tools for polyploid [BO-50-002-022]
  2. `Application of sequence-based multi-allelic markers in genetics and breeding of polyploids' [LWV20.112]

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This study presents a new method to reconstruct haplotypes from SNP dosages derived from genotyping arrays in polyploids. The method shows higher accuracy compared to existing software, especially in the presence of full-sib families. The results demonstrate the usefulness of this method in polyploid genetic analysis.
Background 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. Results 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. Conclusions 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.

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