Structural variations in pig genomes

Y. Paudel

Research output: Thesisinternal PhD, WUAcademic

Abstract

Abstract

Paudel, Y. (2015). Structural variations in pig genomes. PhD thesis, Wageningen University, the Netherlands

Structural variations are chromosomal rearrangements such as insertions-deletions (INDELs), duplications, inversions, translocations, and copy number variations (CNVs). It has been shown that structural variations are as important as single nucleotide polymorphisms (SNPs) in regards to phenotypic variations. The general aim of this thesis was to use next generation sequencing data to improve our understanding of the evolution of structural variations such as CNVs, and INDELs in pigs. We found that: 1) the frequency of copy number variable regions did not change during pig domestications but rather reflected the demographic history of pigs. 2) CNV of olfactory receptor genes seems to play a role in the on-going speciation of the genus Sus. 3) Variation in copy number of olfactory receptor genes in pigs (Sus scrofa) seems to be shaped by a combination of selection and genetic drift, where the clustering of ORs in the genome is the major source of variation in copy number. 4) Analysis on short INDELs in the pig genome shows that the level of purifying selection of INDELs positively correlates with the functional importance of a genomic region, i.e. strongest purifying selection was observed in gene coding regions. This thesis provides a highly valuable resource for copy number variable regions, INDELs, and SNPs, for future pig genetics and breeding research. Furthermore, this thesis discusses the limitations and improvements of the available tools to conduct structural variation analysis and insights into the future trends in the detection of structural variations.

 

LanguageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
Supervisors/Advisors
  • Groenen, Martien, Promotor
  • Madsen, Ole, Co-promotor
  • Megens, Hendrik-Jan, Co-promotor
Award date20 Jan 2015
Place of PublicationWageningen
Publisher
Print ISBNs9789462572171
Publication statusPublished - 2015

Fingerprint

swine
genome
olfactory receptors
single nucleotide polymorphism
genes
Sus scrofa
genetic drift
domestication
phenotypic variation
Netherlands
demographic statistics
genomics
history
breeding

Keywords

  • pigs
  • animal breeding
  • genomes
  • genomics
  • single nucleotide polymorphism
  • dna sequencing
  • phenotypic variation
  • chromosome aberrations
  • evolution
  • speciation

Cite this

Paudel, Y. (2015). Structural variations in pig genomes. Wageningen: Wageningen University.
Paudel, Y.. / Structural variations in pig genomes. Wageningen : Wageningen University, 2015. 204 p.
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}

Paudel, Y 2015, 'Structural variations in pig genomes', Doctor of Philosophy, Wageningen University, Wageningen.

Structural variations in pig genomes. / Paudel, Y.

Wageningen : Wageningen University, 2015. 204 p.

Research output: Thesisinternal PhD, WUAcademic

TY - THES

T1 - Structural variations in pig genomes

AU - Paudel, Y.

N1 - WU thesis 5963

PY - 2015

Y1 - 2015

N2 - Abstract Paudel, Y. (2015). Structural variations in pig genomes. PhD thesis, Wageningen University, the Netherlands Structural variations are chromosomal rearrangements such as insertions-deletions (INDELs), duplications, inversions, translocations, and copy number variations (CNVs). It has been shown that structural variations are as important as single nucleotide polymorphisms (SNPs) in regards to phenotypic variations. The general aim of this thesis was to use next generation sequencing data to improve our understanding of the evolution of structural variations such as CNVs, and INDELs in pigs. We found that: 1) the frequency of copy number variable regions did not change during pig domestications but rather reflected the demographic history of pigs. 2) CNV of olfactory receptor genes seems to play a role in the on-going speciation of the genus Sus. 3) Variation in copy number of olfactory receptor genes in pigs (Sus scrofa) seems to be shaped by a combination of selection and genetic drift, where the clustering of ORs in the genome is the major source of variation in copy number. 4) Analysis on short INDELs in the pig genome shows that the level of purifying selection of INDELs positively correlates with the functional importance of a genomic region, i.e. strongest purifying selection was observed in gene coding regions. This thesis provides a highly valuable resource for copy number variable regions, INDELs, and SNPs, for future pig genetics and breeding research. Furthermore, this thesis discusses the limitations and improvements of the available tools to conduct structural variation analysis and insights into the future trends in the detection of structural variations.  

AB - Abstract Paudel, Y. (2015). Structural variations in pig genomes. PhD thesis, Wageningen University, the Netherlands Structural variations are chromosomal rearrangements such as insertions-deletions (INDELs), duplications, inversions, translocations, and copy number variations (CNVs). It has been shown that structural variations are as important as single nucleotide polymorphisms (SNPs) in regards to phenotypic variations. The general aim of this thesis was to use next generation sequencing data to improve our understanding of the evolution of structural variations such as CNVs, and INDELs in pigs. We found that: 1) the frequency of copy number variable regions did not change during pig domestications but rather reflected the demographic history of pigs. 2) CNV of olfactory receptor genes seems to play a role in the on-going speciation of the genus Sus. 3) Variation in copy number of olfactory receptor genes in pigs (Sus scrofa) seems to be shaped by a combination of selection and genetic drift, where the clustering of ORs in the genome is the major source of variation in copy number. 4) Analysis on short INDELs in the pig genome shows that the level of purifying selection of INDELs positively correlates with the functional importance of a genomic region, i.e. strongest purifying selection was observed in gene coding regions. This thesis provides a highly valuable resource for copy number variable regions, INDELs, and SNPs, for future pig genetics and breeding research. Furthermore, this thesis discusses the limitations and improvements of the available tools to conduct structural variation analysis and insights into the future trends in the detection of structural variations.  

KW - varkens

KW - dierveredeling

KW - genomen

KW - genomica

KW - single nucleotide polymorphism

KW - dna-sequencing

KW - fenotypische variatie

KW - chromosoomafwijkingen

KW - evolutie

KW - soortvorming

KW - pigs

KW - animal breeding

KW - genomes

KW - genomics

KW - single nucleotide polymorphism

KW - dna sequencing

KW - phenotypic variation

KW - chromosome aberrations

KW - evolution

KW - speciation

M3 - internal PhD, WU

SN - 9789462572171

PB - Wageningen University

CY - Wageningen

ER -

Paudel Y. Structural variations in pig genomes. Wageningen: Wageningen University, 2015. 204 p.