Koning, D.J. de

Haley, Chris

Law, Andy

Cabrera Cárdenas, Claudia Paola

Dorothy Hodgkin Postgraduate Award (DHPA)

CONACYT

2010-10-06T10:18:17Z

2010-10-06T10:18:17Z

2009

This thesis explores the genetic characterization of the mechanisms underlying complex traits in chicken through the use and development of bioinformatics tools. The characterization of quantitative trait loci controlling complex traits has proven to be very challenging. This thesis comprises the study of experimental designs, annotation procedures and functional analyses. These represent some of the main ‘bottlenecks’ involved in the integration of QTLs with the biological interpretation of high-throughput technologies. The thesis begins with an investigation of the bioinformatics tools and procedures available for genome research, briefly reviewing microarray technology and commonly applied experimental designs. A targeted experimental design based on the concept of genetical genomics is then presented and applied in order to study a known functional QTL responsible for chicken body weight. This approach contrasts the gene expression levels of two alternative QTL genotypes, hence narrowing the QTL-phenotype gap, and, giving a direct quantification of the link between the genotypes and the genetic responses. Potential candidate genes responsible for the chicken body weight QTL are identified by using the location of the genes, their expression and biological significance. In order to deal with the multiple sources of information and exploit the data effectively, a systematic approach and a relational database were developed to improve the annotation of the probes of the ARK-Genomics G. gallus 13K v4.0 cDNA array utilized on the experiment. To follow up the investigation of the targeted genetical genomics study, a detailed functional analysis is performed on the dataset. The aim is to identify the downstream effects through the identification of functional variation found in pathways, and secondly to achieve a further characterization of potential candidate genes by using comparative genomics and sequence analyses. Finally the investigation of the body weight QTL syntenic regions and their reported QTLs are presented.

http://hdl.handle.net/1842/3864

en

The University of Edinburgh

de Koning, D. J., C. P. Cabrera, and C. S. Haley, 2007 Genetical Genomics: Combining Gene Expression with Marker Genotypes in Poultry. Poultry Science 86: 1501-1509

CP Cabrera, CS Haley and DJ de Koning 2007 Integrating technologies for the Analysis of Complex Traits. Otto Warburg - International Summer School and Workshop 2007 on Computational Systems Biology.

CP Cabrera, CS Haley and DJ de Koning 2007 Integrative and comparative genomics to target potential pathways for a functional body weight QTL in poultry. Pathways, Networks, and Systems, International Conference.

CP Cabrera, I Dunn, M Fell, P Wilson, DW Burt, D Waddington, R Talbot, PM Hocking, A Lam, A Law, CS Haley, S Knott & DJ de Koning 2007 Genetical Genomics for a marked QTL. International Chick Meeting 2007

CP Cabrera, I Dunn, M Fell, P Wilson, DW Burt, D Waddington, R Talbot, PM Hocking, A Law, CS Haley, S Knott & DJ de Koning 2006 Application of genetical genomics to a marked QTL in poultry. 8th World Congress on Genetics Applied to Livestock Production.

quantitative trait loci

chickens

chicken body weight

genetical genomics

Bioinformatics tools for the genetic dissection of complex traits in chickens

Thesis or Dissertation

Doctoral

PhD Doctor of Philosophy