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TriPoly: a haplotype estimation approach for polyploids using sequencing data of related individuals

View ORCID ProfileEhsan Motazedi, View ORCID ProfileDick de Ridder, View ORCID ProfileRichard Finkers, Chris Maliepaard
doi: https://doi.org/10.1101/163162
Ehsan Motazedi
1Bioinformatics Group, Wageningen University and Research, The Netherlands
2Wageningen UR Plant Breeding, Postbus 386, 6700AJ, Wageningen, The Netherlands
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  • ORCID record for Ehsan Motazedi
Dick de Ridder
1Bioinformatics Group, Wageningen University and Research, The Netherlands
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Richard Finkers
2Wageningen UR Plant Breeding, Postbus 386, 6700AJ, Wageningen, The Netherlands
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Chris Maliepaard
2Wageningen UR Plant Breeding, Postbus 386, 6700AJ, Wageningen, The Netherlands
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  • For correspondence: chris.maliepaard@wur.nl
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Abstract

Knowledge of “haplotypes”, i.e. phased and ordered marker alleles on a chromosome, is essential to answer many questions in genetics and genomics. By generating short pieces of DNA sequence, high-throughput modern sequencing technologies make estimation of haplotypes possible for single individuals. In polyploids, however, haplotype estimation methods usually require deep coverage to achieve sufficient accuracy. This often renders sequencing-based approaches too costly to be applied to large populations needed in studies of Quantitative Trait Loci (QTL).

We propose a novel haplotype estimation method for polyploids, TriPoly, that combines sequencing data with Mendelian inheritance rules to infer haplotypes in parent-offspring trios. Using realistic simulations of short- read sequencing data for potato (Solanum tuberosum) and banana (Musa acuminata) trios, we show that TriPoly yields more accurate progeny haplotypes at low coverages compared to the existing methods that work on single individuals.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 13, 2017.
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TriPoly: a haplotype estimation approach for polyploids using sequencing data of related individuals
Ehsan Motazedi, Dick de Ridder, Richard Finkers, Chris Maliepaard
bioRxiv 163162; doi: https://doi.org/10.1101/163162
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TriPoly: a haplotype estimation approach for polyploids using sequencing data of related individuals
Ehsan Motazedi, Dick de Ridder, Richard Finkers, Chris Maliepaard
bioRxiv 163162; doi: https://doi.org/10.1101/163162

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