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Doctoral thesis, 2014

Bioinformatic screening for candidate mutations underlying phenotypic traits in domestic animals

Sayyab, Shumaila


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.


Bioinformatics; Next generation sequencing; Genome-wide association; SNP; Structural Variations; Rabbits; Dogs; Pigs; Domestication

Published in

Acta Universitatis Agriculturae Sueciae
2014, number: 2014:92
ISBN: 978-91-576-8132-4, eISBN: 978-91-576-8133-1
Publisher: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences

Authors' information

Sayyab, Shumaila
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics

UKÄ Subject classification

Genetics and Breeding
Bioinformatics and Systems Biology
Clinical Science

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