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Functional prediction of genetic variation within and between two chicken lines selected for body-weight

with bioinformatic methods

Li, Xidan (2014). Functional prediction of genetic variation within and between two chicken lines selected for body-weight. Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2014:24
ISBN 978-91-576-7996-3
eISBN 978-91-576-7997-0
[Doctoral thesis]

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Abstract

Identifying genetic variation influencing complex traits is often a big challenge. Paul Siegel at the Virginia Polytechnic Institute and State University (USA) initiated a breeding experiment in the 1950s, where White Plymouth Rock (WPR) chicken lines were bi-directionally selected for body-weight at 56 days of age. After more than 50 generations of selection, the High Weight Selected (HWS) line is more than 10-fold bigger than the Low Weight Selected (LWS) line. These HWS and LWS lines have become a good model to investigate the genetic mechanisms underlying the body weight changes under long-term selection. Moreover, as a result of the recently rapid development of next generation sequencing technologies, with high throughput, a large number of genetics polymorphisms have been identified and can be used to explore the genetic factors underlying complex traits. In this thesis, we used NGS resequencing data and several leading databases to search for genes and mutations within previously mapped epistasic QTL regions, which could explain the differences in growth-related traits between the HWS and LWS lines. In consequence, a number of genetic factors have been detected and provide a good basis for further experimental investigation in relation to the observed effects on growth and other metabolic traits. Additionally, we also developed three softwares, which can be useful in the process of identifying genes and variations with phenotypic effects. One of these softwares were also applied within genetic studies in this thesis. Our softwares could be widely applied in many species and are likely to benefit many other research projects.

Authors/Creators:Li, Xidan
Title:Functional prediction of genetic variation within and between two chicken lines selected for body-weight
Subtitle:with bioinformatic methods
Series/Journal:Acta Universitatis agriculturae Sueciae (1652-6880)
Year of publishing :5 March 2014
Volume:2014:24
Number of Pages:57
Papers/manuscripts:
NumberReferences
I.Xidan Li, Muhammad Ahsan, Andreas E Lundberg, Marcin Kierczak, Paul B Siegel, Örjan Carlborg, Stefan Marklund. Identification of candidate genes and SNPs within epistatic chicken growth QTL regions. (Manuscript)
II.Muhammad Ahsan, Xidan Li, Andreas E Lundberg, Marcin Kierczak, Paul B Siegel, Örjan Carlborg, Stefan Marklund. (2013) Identification of candidate genes and mutations in QTL regions for chicken growth using bioinformatic analysis of NGS and SNP-­‐chip data. Frontiers in Genetics, doi: 10.3389/fgene.2013.00226
III.Xidan Li§, Marcin Kierczak§, Xia Shen, Muhammad Ahsan, Örjan Carlborg, Stefan Marklund. (2013) PASE: a novel method for functional prediction of amino acid substitutions based on physicochemical properties. Frontiers in Genetics, doi: 10.3389/fgene.2013.00021
IV.Xidan Li, Zheya Sheng and Stefan Marklund. Profat: A novel method for prediction of novel protein function using the motif profile classification prior to sequence alignments. (Manuscript)
V.Xidan Li, Martin Norling and Ronald Nelson. DIPT: Software for detecting interactions and pathways between expression phenotypes and associated QTL/GWAS defined region. (Manuscript)
UNSPECIFIED§ Authors contributed equally
Place of Publication:Uppsala
Publisher:Dept. of Clinical Sciences, Swedish University of Agricultural Sciences
ISBN for printed version:978-91-576-7996-3
ISBN for electronic version:978-91-576-7997-0
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) > Bioinformatics and Systems Biology (methods development to be 10203)
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 403 Veterinary Science > Clinical Science
Agrovoc terms:chickens, body weight, quantitative trait loci, quantitative genetics, genetic polymorphism, growth, gene interaction, phenotypes, computer software, bioinformatics, methods
Keywords:NGS, SNP, amino acid substitution, chicken, body weight, protein motif, expression phenotype
URN:NBN:urn:nbn:se:slu:epsilon-e-1804
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-1804
ID Code:11054
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Clinical Sciences
Deposited By: Xidan Li
Deposited On:11 Mar 2014 12:05
Metadata Last Modified:02 Dec 2014 11:05

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