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Bioinformatic screening for candidate mutations underlying phenotypic traits in domestic animals

Sayyab, Shumaila (2014). Bioinformatic screening for candidate mutations underlying phenotypic traits in domestic animals. Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2014:92
ISBN 978-91-576-8132-4
eISBN 978-91-576-8133-1
[Doctoral thesis]

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Abstract

Domestic animals represent excellent model organisms for gene mapping and identification of mutations underlying phenotypic traits. Humans have selected spontaneous mutations in farm and companion animals since they were domesticated and this has resulted in large phenotypic variation among different breeds. In this thesis, we evaluate the candidate mutations in domesticated animals from NGS and SNP genotype data using bioinformatic analysis. Functional significance of coding sequence polymorphisms was assessed using both available bioinformatics resources and in-house pipelines. In consequence, pig and rabbit sequencing revealed major sweeps for genes (NR6A1, LCORL and PLAG1) for body length and increased number of vertebrae in domestic pigs and genes (GRIK2 and SOX2) affecting brain and neuronal development in rabbit domestication. Genome-wide association mapping for demodicosis disease in Staffordshire Bull Terrier dog show several preliminary candidate risk loci (CFA17, 18, 28 and 29) containing interesting candidate genes providing a good basis for further evaluation. Additionally, we also highlight some opportunities and pitfalls of whole genome resequencing using the Ion Proton platform and developed a tool DevRO (using deviant read paired orientation) for detection of large structural variants for NGS data from paired-end sequencing or mate pair. This method will be useful when large numbers of populations are resequenced as compared to traditional methods that can detect the structural variants in a pair wise manner.

Authors/Creators:Sayyab, Shumaila
Title:Bioinformatic screening for candidate mutations underlying phenotypic traits in domestic animals
Series/Journal:Acta Universitatis agriculturae Sueciae (1652-6880)
Year of publishing :31 October 2014
Depositing date:31 October 2014
Volume:2014:92
Number of Pages:56
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 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(48), 19529-36
II.Miguel Carneiro*, Carl-Johan Rubin*, Federica Di Palma*, Frank W. Albert, Jessica Alföldi, Alvaro Martinez Barrio, Gerli Pielberg, Nima Rafati, Shumaila Sayyab, Jason Turner-Maier, Shady Younis, Sandra Afonso, Bronwen Aken, Joel M. Alves, Daniel Barrell, Gerard Bolet, Samuel Boucher, Hernán A. Burbano, Rita Campos, Jean L. Chang, Veronique Duranthon, Luca Fontanesi, Hervé Garreau, David Heiman, Jeremy Johnson, Rose G. Mage, Ze Peng, Guillaume Queney, Claire Rogel- Gaillard, Magali Ruffier, Steve Searle, Rafael Villafuerte, Anqi Xiong, Sarah Young, Karin Forsberg-Nilsson, Jeffrey M. Good, Eric S. Lander, Nuno Ferrand*, Kerstin Lindblad-Toh*, Leif Andersson* (2014). Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science 345, 1074-1079
III.Shumaila Sayyab, Susanne Åhman, Katarina Varjonen, Tomas Bergström, Kerstin Bergvall, Frode Lingaas, Göran Andersson (2014). Genome-wide association mapping identifies candidate risk loci for a canine juvenileonset demodicosis disease in Staffordshire Bull Terriers. (Manuscript)
IV.Agnese Viluma*, Shumaila Sayyab*, Sofia Mikko, Göran Andersson, Tomas Bergström (2014). Whole genome sequencing for variant detection of four chinese crested dogs. (Submitted)
V.Shumaila Sayyab, Nima Rafati, Miguel Carneiro, Göran Andersson, Leif Andersson, Carl Johan Rubin. Computational method for detection of structural variants using Deviant Reads and read pair Orientation: DevRO. (Manuscript)
Place of Publication:Uppsala
Publisher:Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences
ISBN for printed version:978-91-576-8132-4
ISBN for electronic version:978-91-576-8133-1
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 > 4 Agricultural Sciences > 402 Animal and Dairy Science > Animal and Dairy Science.
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 403 Veterinary Science > Clinical Science
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
Agrovoc terms:bioinformatics, rabbits, dogs, swine, domestication, genes, mutation, genetic variation, genetic inheritance, loci
Keywords:Bioinformatics, Next generation sequencing, Genome-wide association, SNP, Structural Variations, Rabbits, Dogs, Pigs, Domestication
URN:NBN:urn:nbn:se:slu:epsilon-e-2198
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-2198
ID Code:11623
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
Deposited By: Shumaila Sayyab
Deposited On:03 Nov 2014 13:26
Metadata Last Modified:02 Dec 2014 11:09

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