Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

    We have a manual that explains all the features 

Record number 551904
Title Family-based haplotype estimation and allele dosage correction for polyploids using short sequence reads
Author(s) Motazedi, Ehsan; Maliepaard, Chris; Finkers, Richard; Visser, Richard; Ridder, Dick De
Source Frontiers in Genetics Livestock Genomics 10 (2019)MAR. - ISSN 1664-8021
DOI https://doi.org/10.3389/fgene.2019.00335
Department(s) Bioinformatics
Plant Breeding
EPS
PE&RC
Plant Breeding
PBR Quantitative aspects of Plant Breeding
Publication type Refereed Article in a scientific journal
Publication year 2019
Keyword(s) Estimation - Family - Haplotype - Polyploid - Sequence data
Abstract

DNA sequence reads contain information about the genomic variants located on a single chromosome. By extracting and extending this information using the overlaps between the reads, the haplotypes of an individual can be obtained. Using parent-offspring relationships in a population can considerably improve the quality of the haplotypes obtained from short reads, as pedigree information can be used to correct for spurious overlaps (due to sequencing errors) and insufficient overlaps (due to short read lengths, low genomic variation and shallow coverage). We developed a novel method, PopPoly, to estimate polyploid haplotypes in an F1-population from short sequence data by taking into consideration the transmission of the haplotypes from the parents to the offspring. In addition, this information is employed to improve genotype dosage estimation and to call missing genotypes in the population. Through simulations, we compare PopPoly to other haplotyping methods and show its better performance. We evaluate PopPoly by applying it to a tetraploid potato cross at nine genomic regions involved in tuber formation.

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