Haplotype estimation in polyploids using DNA sequence data

Ehsan Motazedi

Research output: Thesisinternal PhD, WU

Abstract

Polyploid organisms possess more than two copies of their core genome and therefore contain k>2 haplotypes for each set of ordered genomic variants. Polyploidy occurs often within the plant kingdom, among others in important corps such as potato (k=4) and wheat (k=6). Current sequencing technologies enable us to read the DNA and detect genomic variants, but cannot distinguish between the copies of the genome, each inherited from one of the parents. To detect inheritance patterns in populations, it is necessary to know the haplotypes, as alleles that are in linkage over the same chromosome tend to be inherited together. In this work, we develop mathematical optimisation algorithms to indirectly estimate haplotypes by looking into overlaps between the sequence reads of an individual, as well as into the expected inheritance of the alleles in a population. These algorithm deal with sequencing errors and random variations in the counts of reads observed from each haplotype. These methods are therefore of high importance for studying the genetics of polyploid crops. 

Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
Supervisors/Advisors
  • de Ridder, Dick, Promotor
  • Maliepaard, Chris, Co-promotor
  • Finkers, Richard, Co-promotor
Award date7 Nov 2019
Place of PublicationWageningen
Publisher
Print ISBNs9789463951210
DOIs
Publication statusPublished - 2019

Fingerprint

polyploidy
haplotypes
nucleotide sequences
inheritance (genetics)
alleles
genomics
genome
linkage (genetics)
potatoes
chromosomes
wheat
organisms
DNA
crops
methodology

Cite this

Motazedi, Ehsan. / Haplotype estimation in polyploids using DNA sequence data. Wageningen : Wageningen University, 2019. 153 p.
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Motazedi, E 2019, 'Haplotype estimation in polyploids using DNA sequence data', Doctor of Philosophy, Wageningen University, Wageningen. https://doi.org/10.18174/500092

Haplotype estimation in polyploids using DNA sequence data. / Motazedi, Ehsan.

Wageningen : Wageningen University, 2019. 153 p.

Research output: Thesisinternal PhD, WU

TY - THES

T1 - Haplotype estimation in polyploids using DNA sequence data

AU - Motazedi, Ehsan

N1 - WU thesis 7364 Includes bibliographical references. - With summaries in English and Dutch

PY - 2019

Y1 - 2019

N2 - Polyploid organisms possess more than two copies of their core genome and therefore contain k>2 haplotypes for each set of ordered genomic variants. Polyploidy occurs often within the plant kingdom, among others in important corps such as potato (k=4) and wheat (k=6). Current sequencing technologies enable us to read the DNA and detect genomic variants, but cannot distinguish between the copies of the genome, each inherited from one of the parents. To detect inheritance patterns in populations, it is necessary to know the haplotypes, as alleles that are in linkage over the same chromosome tend to be inherited together. In this work, we develop mathematical optimisation algorithms to indirectly estimate haplotypes by looking into overlaps between the sequence reads of an individual, as well as into the expected inheritance of the alleles in a population. These algorithm deal with sequencing errors and random variations in the counts of reads observed from each haplotype. These methods are therefore of high importance for studying the genetics of polyploid crops. 

AB - Polyploid organisms possess more than two copies of their core genome and therefore contain k>2 haplotypes for each set of ordered genomic variants. Polyploidy occurs often within the plant kingdom, among others in important corps such as potato (k=4) and wheat (k=6). Current sequencing technologies enable us to read the DNA and detect genomic variants, but cannot distinguish between the copies of the genome, each inherited from one of the parents. To detect inheritance patterns in populations, it is necessary to know the haplotypes, as alleles that are in linkage over the same chromosome tend to be inherited together. In this work, we develop mathematical optimisation algorithms to indirectly estimate haplotypes by looking into overlaps between the sequence reads of an individual, as well as into the expected inheritance of the alleles in a population. These algorithm deal with sequencing errors and random variations in the counts of reads observed from each haplotype. These methods are therefore of high importance for studying the genetics of polyploid crops. 

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SN - 9789463951210

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CY - Wageningen

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Motazedi E. Haplotype estimation in polyploids using DNA sequence data. Wageningen: Wageningen University, 2019. 153 p. https://doi.org/10.18174/500092