Theory and practice in the mapping of quantitative trait loci
Lead Research Organisation:
Roslin Institute
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
The basic tools to scan of livestock genomes to map quantitative trait loci (QTLs) are now in place and in use. Full exploitation of the tools in research and in commercial application requires developments in a number of areas. This project provides core support onto which will be built projects which will tackle three key areas: 1) Developing the analytical methods to allow high resolutions QTL mapping through exploitation of linkage disequilibrium in outbred populations. 2) Putting the developed methods into a user- friendly shell, allowing effective exploitation by both researchers and industry. 3) Applying the developed methodologies to both further our own experimental programme and to refine the approaches and demonstrate their efficiency in action. This work is essential underpinning for the research programmes of the Institute and the BBSRC.
Planned Impact
unavailable
People |
ORCID iD |
| Christopher Haley (Principal Investigator) |
Publications
Wei WH
(2011)
High throughput analyses of epistasis for swine body dimensions and organ weights.
in Animal genetics
Wei WH
(2011)
Mapping QTL in the porcine MHC region affecting fatness and growth traits in a Meishan/Large White composite population.
in Animal genetics
Hadjiconstantouras C
(2008)
Characterization of the porcine KIT ligand gene: expression analysis, genomic structure, polymorphism detection and association with coat colour traits.
in Animal genetics
Houston RD
(2008)
The cholecystokinin type A receptor g.179A>G polymorphism affects feeding rate.
in Animal genetics
Gutiérrez-Gil B
(2012)
Investigation of the genetic architecture of a bone carcass weight QTL on BTA6.
in Animal genetics
Huang Y
(2007)
Detection of quantitative trait loci for body weights and conformation traits in Beijing ducks.
in Animal genetics
Wei WH
(2007)
QTL modulating ear size and erectness in pigs.
in Animal genetics
Sauvage C
(2010)
QTL for resistance to summer mortality and OsHV-1 load in the Pacific oyster (Crassostrea gigas).
in Animal genetics
Tuiskula-Haavisto M
(2011)
Quantitative trait loci affecting eggshell traits in an F(2) population.
in Animal genetics
Wilkinson S
(2012)
Characterization of the genetic diversity, structure and admixture of British chicken breeds.
in Animal genetics
Powell JE
(2012)
Optimal use of regression models in genome-wide association studies.
in Animal genetics
Gheyas AA
(2010)
Segregation of infectious pancreatic necrosis resistance QTL in the early life cycle of Atlantic Salmon (Salmo salar).
in Animal genetics
Massault C
(2010)
QTL for body weight, morphometric traits and stress response in European sea bass Dicentrarchus labrax.
in Animal genetics
Gheyas AA
(2010)
Effect of a major QTL affecting IPN resistance on production traits in Atlantic salmon.
in Animal genetics
Cabrera CP
(2012)
Complex traits analysis of chicken growth using targeted genetical genomics.
in Animal genetics
Huang Y
(2007)
Genetic mapping of quantitative trait loci affecting carcass and meat quality traits in Beijing ducks (Anas platyrhynchos).
in Animal genetics
Gao Y
(2009)
Mapping quantitative trait loci regulating chicken body composition traits.
in Animal genetics
Houston RD
(2009)
Detection of QTL affecting harvest traits in a commercial Atlantic salmon population.
in Animal genetics
Guo YM
(2008)
Quantitative trait loci for production traits in pigs: a combined analysis of two Meishan x Large White populations.
in Animal genetics
Lallias D
(2007)
A first-generation genetic linkage map of the European flat oyster Ostrea edulis (L.) based on AFLP and microsatellite markers.
in Animal genetics
Massault C
(2011)
Quantitative trait loci for resistance to fish pasteurellosis in gilthead sea bream (Sparus aurata).
in Animal genetics
Chistiakov DA
(2008)
A combined AFLP and microsatellite linkage map and pilot comparative genomic analysis of European sea bass Dicentrarchus labrax L.
in Animal genetics
Alfonso L
(2010)
Power of different F 2 schemes for QTL detection in livestock
in Animal Science
Boulton K
(2011)
QTL affecting morphometric traits and stress response in the gilthead seabream (Sparus aurata)
in Aquaculture
Massault C
(2008)
QTL mapping designs for aquaculture
in Aquaculture
Houston R
(2007)
Mapping QTL affecting resistance to infectious pancreatic necrosis (IPN) in Atlantic salmon (Salmo salar)
in Aquaculture
Chatziplis D
(2007)
Mapping quantitative trait loci in European sea bass (Dicentrarchus labrax): The BASSMAP pilot study
in Aquaculture
Hernández-Sánchez J
(2009)
A web application to perform linkage disequilibrium and linkage analyses on a computational grid.
in Bioinformatics (Oxford, England)
Hemani G
(2011)
EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards.
in Bioinformatics (Oxford, England)
Ding N
(2009)
Genome-wide QTL mapping for three traits related to teat number in a White Duroc x Erhualian pig resource population.
in BMC genetics
Wilkinson S
(2012)
Development of a genetic tool for product regulation in the diverse British pig breed market.
in BMC genomics
Lam AC
(2009)
A combined strategy for quantitative trait loci detection by genome-wide association.
in BMC proceedings
Karacaören B
(2011)
Association analyses of the MAS-QTL data set using grammar, principal components and Bayesian network methodologies.
in BMC proceedings
Navarro P
(2006)
Genetic parameters for blood oxygen saturation, body weight and breast conformation in 4 meat-type chicken lines.
in British poultry science
Lam AC
(2008)
Optimal design of genetic studies of gene expression with two-color microarrays in outbred crosses.
in Genetics
Houston RD
(2008)
Major quantitative trait loci affect resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar).
in Genetics
Rowe SJ
(2008)
Detecting dominant QTL with variance component analysis in simulated pedigrees.
in Genetics research
Calus MP
(2010)
Including copy number variation in association studies to predict genotypic values.
in Genetics research
Rowe SJ
(2009)
Detecting parent of origin and dominant QTL in a two-generation commercial poultry pedigree using variance component methodology.
in Genetics, selection, evolution : GSE
Volckaert FA
(2012)
Heritability of cortisol response to confinement stress in European sea bass dicentrarchus labrax.
in Genetics, selection, evolution : GSE
Nagamine Y
(2009)
Detection of multiple quantitative trait loci and their pleiotropic effects in outbred pig populations.
in Genetics, selection, evolution : GSE
Wei WH
(2010)
Controlling false positives in the mapping of epistatic QTL.
in Heredity
Wilkinson S
(2011)
An empirical assessment of individual-based population genetic statistical techniques: application to British pig breeds.
in Heredity
Gutiérrez-Gil B
(2009)
Search for quantitative trait loci affecting growth and carcass traits in a cross population of beef and dairy cattle.
in Journal of animal science
Brockmann GA
(2007)
Genetic control of lipids in the mouse cross DU6i x DBA/2.
in Mammalian genome : official journal of the International Mammalian Genome Society
Murphy AM
(2007)
Linkage mapping of the locus for inherited ovine arthrogryposis (IOA) to sheep chromosome 5.
in Mammalian genome : official journal of the International Mammalian Genome Society
Haley C
(2011)
A cornucopia of maize genes.
in Nature genetics
| Description | We identified genes involved in terrestrial and aquatic livestock performance that contribute to improved sustainability of production in these sectors. |
| Exploitation Route | Improved sustainability of livestock production and impact to improve animal welfare. |
| Sectors | Agriculture Food and Drink |
| Description | Tools and Resources Development Fund |
| Amount | £107,308 (GBP) |
| Funding ID | BB/H024484/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2010 |
| End | 05/2012 |
| Description | Agricygen |
| Organisation | Agricultural Research Institute |
| Country | Cyprus |
| Sector | Public |
| PI Contribution | Use of genomics to optimise sheep and cattle breeding in order to maximise milk production for halloumi cheese |
| Collaborator Contribution | Local livestock expertise and husbandry and nutrition expertise for the optimisation of milk production in Cyprus |
| Impact | Project is in its early stages. No outputs as yet. |
| Start Year | 2017 |
| Description | LNS - IPN |
| Organisation | Landcatch Natural Selection Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Design if studies, joint grant application, advice on data analysis |
| Collaborator Contribution | Joint publication |
| Impact | Publications listed separately |
| Start Year | 2006 |
| Description | WAU - CNV |
| Organisation | Wageningen University & Research |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | Input to design of study and analysis of results |
| Collaborator Contribution | Joint publication |
| Impact | Joint publication listed separately |
| Start Year | 2007 |
| Description | Edinburgh Alliance for Complex Trait Genetics |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Co-organise a twice-yearly meeting to coordinate complex trait genetic research focussed on Edinburgh but with national participation. |
| Year(s) Of Engagement Activity | 2011,2012,2013,2014,2015,2016,2017,2018,2019,2020 |
| URL | https://www.wiki.ed.ac.uk/display/eactg/Edinburgh+Alliance+for+Complex+Trait+Genetics |