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]
![]() |
PDF
1MB |
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 | ||||||||||||
Number: | 2014:92 | ||||||||||||
Number of Pages: | 56 | ||||||||||||
Papers/manuscripts: |
| ||||||||||||
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 |
Repository Staff Only: item control page