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]
![]() |
PDF
12MB |
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 Name/Journal: | Acta Universitatis Agriculturae Sueciae | ||||||||||||||
Year of publishing : | 5 March 2014 | ||||||||||||||
Number: | 2014:24 | ||||||||||||||
Number of Pages: | 57 | ||||||||||||||
Papers/manuscripts: |
| ||||||||||||||
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 |
Repository Staff Only: item control page