an approach combining computational genetics and bioinformatics
Ahsan, Muhammad
(2014).
Mapping and functional characterization of candidate genes and mutations for chicken growth.
Diss. (sammanfattning/summary)
Uppsala :
Sveriges lantbruksuniv.,
Acta Universitatis Agriculturae Sueciae, 1652-6880
; 2014:49
ISBN 978-91-576-8046-4
eISBN 978-91-576-8047-1
[Doctoral thesis]
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PDF
9MB |
Abstract
Knowledge of the genetics related to growth is important for breeding chickens with the desired traits of rapid and efficient growth. A long-term selection experiment in the domestic chicken (Gallus gallus) has resulted in two highly divergent lines selected for juvenile body weight. These lines are a great genetic resource to identify the genetic basis of phenotypic variation mainly for growth traits.
The aim of this thesis was to map the relationship between the genotype and phenotype and thereby reveal the genetic architecture of growth in the chicken. To this end, high-density genotyping and whole-genome resequencing of the lines were used to explore the genetics of the body weight difference between these lines. We further fine- mapped previously identified Quantitative Trait Loci (QTLs) for body weight and used bioinformatics approaches to identify the most promising candidate genes, mutations and biological pathways for growth for further functional evaluations. We also studied a previously mapped radial network of interacting QTLs to reveal potential biological interactions by analyzing biological pathways. In addition, we developed new computational genetic method and tools and used them to functionally explore specific genetic variants in selected regions in the genome. To functionally evaluate the effect of identified amino acid substitutions (AAS), we developed and implemented a bioinformatics method in a tool called PASE.
The predictions of PASE, using physicochemical properties of amino acids, were consistent with other widely available homology-based tools. Our mapping strategy successfully fine-mapped the QTLs, and our bioinformatic strategies were efficient in identifying the candidate mutations and biological pathways for growth. The methods we developed could be applied to the genetic dissection of other complex traits.
Authors/Creators: | Ahsan, Muhammad | ||||||||||
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Title: | Mapping and functional characterization of candidate genes and mutations for chicken growth | ||||||||||
Subtitle: | an approach combining computational genetics and bioinformatics | ||||||||||
Series/Journal: | Acta Universitatis Agriculturae Sueciae (1652-6880) | ||||||||||
Year of publishing : | May 2014 | ||||||||||
Number: | 2014:49 | ||||||||||
Number of Pages: | 58 | ||||||||||
Papers/manuscripts: |
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Place of Publication: | Uppsala | ||||||||||
Publisher: | Dept. of Clinical Sciences, Swedish University of Agricultural Sciences | ||||||||||
ISBN for printed version: | 978-91-576-8046-4 | ||||||||||
ISBN for electronic version: | 978-91-576-8047-1 | ||||||||||
ISSN: | 1652-6880 | ||||||||||
Language: | English | ||||||||||
Additional Information: | The Higher Education Commission of Pakistan (HEC) provided the scholarship for the PhD education of the author. | ||||||||||
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 > 102 Computer and Information Science > 10203 Bioinformatics (Computational Biology) (applications to be 10610) (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) | ||||||||||
Agrovoc terms: | chickens, body weight, growth, genes, mutation, quantitative trait loci, chromosome mapping, computer software, bioinformatics | ||||||||||
Keywords: | SNP, QTL, NGS, Candidate mutations, Association mapping, Imputation, Virginia chicken lines, Divergent selection, Functional characterization | ||||||||||
URN:NBN: | urn:nbn:se:slu:epsilon-e-1928 | ||||||||||
Permanent URL: | http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-1928 | ||||||||||
ID Code: | 11216 | ||||||||||
Faculty: | VH - Faculty of Veterinary Medicine and Animal Science | ||||||||||
Department: | (VH) > Dept. of Clinical Sciences | ||||||||||
Deposited By: | Muhammad Ahsan | ||||||||||
Deposited On: | 23 May 2014 12:02 | ||||||||||
Metadata Last Modified: | 02 Dec 2014 11:06 |
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