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Bioinformatic analysis of whole genome sequencing data

detection of selective sweeps and structural changes

Maqbool, Khurram (2014). Bioinformatic analysis of whole genome sequencing data. Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2014:58
ISBN 978-91-576-8064-8
eISBN 978-91-576-8065-5
[Doctoral thesis]

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Abstract

Evolution has shaped the life forms for billion of years. Domestication is an accelerated process that can be used as a model for evolutionary changes. The aim of this thesis project has been to carry out extensive bioinformatic analyses of whole genome sequencing data to reveal SNPs, InDels and selective sweeps in the chicken, pig and dog genome.

Pig genome sequencing revealed loci under selection for elongation of back and increased number of vertebrae, associated with the NR6A1, PLAG1, and LCORL genes. The scan for copy number variations (CNVs) revealed four duplications at the KIT locus associated with dominant white and belt colour phenotypes. Selective sweeps in the dog genome included genes involved in adaptation to a starch rich diet, fat metabolism and behavior. Identification of a selective sweep and a CNV in the AMY2B gene, which correlates with variation in α-amylase expression, along with selective sweeps in MGAM and SGLT1, in dogs revealed adaptation to a starch-rich diet after domestication. Analysis of chicken genome resequencing data identified hundreds of regions under selection shared among all domestic chicken and others that were
specific for layers or broiler chickens and 68 fixed large deletions and 70 small InDels in domestic chicken populations.

Structural variations are changes in the genome that may affect the copy number of genes, their regulation or their coding sequence. Current methods utilize sequence information from either single sample or pair of samples to scan for CNVs across the genome. We developed a fast algorithm and a tool, MultiSV, to identify structural variations using short reads from massively parallel sequencing of multiple populations.

This thesis demonstrates the importance of structural variations as a factor contributing to phenotypic diversity in domestic animals and has revealed regions under strong selection during animal domestication and breeding. It also presents a new method for the identification of structural variations in populations using short reads from NextGen sequencers.

Authors/Creators:Maqbool, Khurram
Title:Bioinformatic analysis of whole genome sequencing data
Subtitle:detection of selective sweeps and structural changes
Series/Journal:Acta Universitatis agriculturae Sueciae (1652-6880)
Year of publishing :2014
Volume:2014:58
Number of Pages:55
Papers/manuscripts:
NumberReferences
I.Carl-Johan Rubin, Hendrik-Jan Megens, Alvaro Martinez Barrio, Khurram Maqbool, Shumaila Sayyab, Doreen Schwochow, Chao Wang, Örjan Carlborg, Patric Jern, Claus B. Jørgensen, Alan L. Archibald, Merete Fredholm, Martien A. M. Groenen, and Leif Andersson (2012). Strong signatures of selection in the domestic pig genome. Proc Natl Acad Sci USA. 109, 19529–19536.
II.Erik Axelsson, Abhirami Ratnakumar, Maja-Louise Arendt, Khurram Maqbool, Matthew Webster, Olof Liberg, Jon M. Arnemo, Åke Hedhammar and Kerstin Lindblad-Toh (2013). Whole genome resequencing reveals dog domestication genes and pathways including adaptation to a starch-rich diet. Nature 495, 360-364.
III.Khurram Maqbool, Shumaila Sayyab, Alvaro Martinez Barrio, Bertrand Bed'hom, Michele Tixier-Boichard, Paul Siegel, Carl-Johan Rubin and Leif Andersson. Detecting signatures of selection in broiler and layer chickens using whole genome resequencing of pooled samples. (manuscript)
IV.Khurram Maqbool, Lars Rönnegård and Leif Andersson. MultiSV: an R package for identification of structural variations in multiple populations based on whole genome resequencing. (manuscript)
Place of Publication:Uppsala
Publisher:Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences
ISBN for printed version:978-91-576-8064-8
ISBN for electronic version:978-91-576-8065-5
ISSN:1652-6880
Language:English
Publication Type:Doctoral thesis
Full Text Status:Public
Agris subject categories.:L Animal production > L10 Animal genetics and breeding
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Bioinformatics and Systems Biology (methods development to be 10203)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Evolutionary Biology
Agrovoc terms:molecular genetics, dogs, chickens, swine, genomes, evolution, genetic inheritance, selection, domestication, nucleotides, polymorphism, bioinformatics
Keywords:Molecular Evolution, domestication, chicken, pig, dog, next-generation sequencing, selective sweep, structural variation, copy number variation, duplication, deletion, genome, SNP
URN:NBN:urn:nbn:se:slu:epsilon-e-2120
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-2120
ID Code:11506
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
External funders:FORMAS and Higher Education Commission, Pakistan
Deposited By: Khurram Maqbool
Deposited On:12 Sep 2014 12:45
Metadata Last Modified:02 Dec 2014 11:08

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