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Mapping and functional characterization of candidate genes and mutations for chicken growth

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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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
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
Volume:2014:49
Number of Pages:58
Papers/manuscripts:
NumberReferences
I.Xidan Li, Marcin Kierczak, Xia Shen, Muhammad Ahsan, Örjan Carlborg and Stefan Marklund. PASE: a novel method for functional prediction of amino acid substitutions based on physicochemical properties. Frontiers in Genetics, 2013, doi: 10.3389/fgene.2013.00021
II.Muhammad Ahsan, Paul B. Siegel and Örjan Carlborg. Evaluation of an imputation-based fine-mapping strategy in an outbred chicken Advanced Intercross Line (AIL). (manuscript)
III.Muhammad Ahsan, Xidan Li, Andreas E Lundberg, Marcin Kierczak, Paul B Siegel, Örjan Carlborg and Stefan Marklund. Identification of candidate genes and mutations in QTL regions for chicken growth using bioinformatic analysis of NGS and SNP-chip data. Frontiers in Genetics, 2013. doi: 10.3389/fgene.2013.00226.
IV.Xidan Li, Muhammad Ahsan, Andreas E Lundberg, Marcin Kierczak, Paul B Siegel, Örjan Carlborg and Stefan Marklund. Revealing candidate biological interactions underlying epistatic QTLs for chicken growth. (manuscript)
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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