Genetic polyploid phasing from low-depth progeny samples

Sven Schrinner*, Rebecca Serra Mari, Richard Finkers, Paul Arens, Björn Usadel, Tobias Marschall, Gunnar W. Klau

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)

Abstract

An important challenge in genome assembly is haplotype phasing, that is, to reconstruct the different haplotype sequences of an individual genome. Phasing becomes considerably more difficult with increasing ploidy, which makes polyploid phasing a notoriously hard computational problem. We present a novel genetic phasing method for plant breeding with the aim to phase two deep-sequenced parental samples with the help of a large number of progeny samples sequenced at low depth. The key ideas underlying our approach are to (i) integrate the individually weak Mendelian progeny signals with a Bayesian log-likelihood model, (ii) cluster alleles according to their likelihood of co-occurrence, and (iii) assign them to haplotypes via an interval scheduling approach. We show on two deep-sequenced parental and 193 low-depth progeny potato samples that our approach computes high-quality sparse phasings and that it scales to whole genomes.

Original languageEnglish
Article number104461
JournaliScience
Volume25
Issue number6
DOIs
Publication statusPublished - 17 Jun 2022

Keywords

  • Bioinformatics
  • Genomics
  • Sequence analysis

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