Genetic polyploid phasing from low-depth progeny samples - Kölner UniversitätsPublikationsServer

Schrinner, Sven ORCID: 0000-0002-6712-2198, Mari, Rebecca Serra, Finkers, Richard ORCID: 0000-0002-4368-8058, Arens, Paul, Usadel, Bjoern, Marschall, Tobias and Klau, Gunnar W. (2022). Genetic polyploid phasing from low-depth progeny samples. iScience, 25 (6). CAMBRIDGE: CELL PRESS. ISSN 2589-0042

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DOI:10.1016/j.isci.2022.104461

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.

Item Type:

Journal Article

Creators:

Creators	Email	ORCID	ORCID Put Code
Schrinner, Sven	UNSPECIFIED	orcid.org/0000-0002-6712-2198	UNSPECIFIED
Mari, Rebecca Serra	UNSPECIFIED	UNSPECIFIED	UNSPECIFIED
Finkers, Richard	UNSPECIFIED	orcid.org/0000-0002-4368-8058	UNSPECIFIED
Arens, Paul	UNSPECIFIED	UNSPECIFIED	UNSPECIFIED
Usadel, Bjoern	UNSPECIFIED	UNSPECIFIED	UNSPECIFIED
Marschall, Tobias	UNSPECIFIED	UNSPECIFIED	UNSPECIFIED
Klau, Gunnar W.	UNSPECIFIED	UNSPECIFIED	UNSPECIFIED