Genetics of Complex Traits

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute

Abstract

The aim of this theme is to exploit advances in genomics and numerical genetics to test and develop more precise models of the genetic control of complex traits, primarily in farmed animal species but also in companion animals. The objectives of this theme are: To develop advanced analytical, mathematical and modelling approaches for complex trait dissection. To dissect the genetic control of specific complex traits, including: Production efficiency in the context of not only economics but also environmental impact. Reproductive fitness. Pain and stress. To identify key nodes of regulatory pathways and their relationship to phenotypic variation. To evaluate the role of epigenetics, epistasis and other interactions in the genetic control of complex traits.

Publications

10 25 50
 
Description Using our targeted genetical genomics approach, we identified a putative mutation in the AADAT gene as the prime candidate underlying a functional QTL on chicken chromosome 4, which shows differential alternative splicing at the mRNA level.

Identification of the Thoka locus affecting litter size in sheep.

An important epistatic gene interaction for QTL on chromosomes 4 and 13 was identified for the number of yellow ovarian follicles, a proxy for the daily ovulation rate in broilers, using newly developed software tools. This interaction may prove central to the development of strategies to address this important welfare problem.

The first fine mapped QTL affecting boar taint was localized to SNPs in the CYP2E region, explaining up to 6% of phenotypic variation (in humans GWAS often explain <1%).

In chicken eggshells, cuticle coverage is correlated with bacterial penetration and novel measurement techniques have uncovered useful genetic variation in both cuticle coverage and CaCO3 crystal size. Measurement is being further refined for potential use. Crystal size's effect on material properties was the opposite of that expected from man-made materials and changes our understanding of how shell strength is determined.

Genetic markers for eggshell matrix genes and genes involved in oviduct function have been identified that can repeatably predict egg shell quality, important to food safety and supply. QTL regions for egg shell quality are now being fine mapped and tested in pedigree populations.

Quantification of genetic control of beef quality and carcass traits on implementation pathway for Marker-Assisted-Selection.

Tools for complex traits dissection have continued to be developed.
Exploitation Route The discoveries made and the tools developed within this programme have underpinned further advances in selective animal breeding.
Sectors Agriculture, Food and Drink

 
Description Contributed to the Society of Biology submission to the Smith Commission
Geographic Reach National 
Policy Influence Type Participation in a national consultation
 
Description A global shared data biological sample resource to support productivity improvement for tropical livestock
Amount £5,000,000 (GBP)
Organisation Bill and Melinda Gates Foundation 
Sector Charity/Non Profit
Country United States
Start 10/2015 
End 09/2020
 
Description ANIHWA call 2: Better bone quality in laying hens
Amount £836,262 (GBP)
Funding ID BB/M028291/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2015 
End 10/2018
 
Description GCRF Data and Resources round 1
Amount £946,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2016 
End 07/2017
 
Title Better bones 
Description Phenotyped laying hen population with/without DNA for bone quality 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Collaboration with colleagues in Germany, Sweden and Spain has resulted in GWAS and other publications 
 
Title PRJEB10338 
Description This collection of data represents whole metagenome sequence data for 8 cattle chosen for low and high methane emissions after matching for breed and diet 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact This is a critically important dataset for linking genotype to phenotype (methane) in the cattle rumen microbiome. Since its release, the papers based on these data have been cited over 100 times 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB10338
 
Description Centre for Tropical Livestock Genetics and Health 
Organisation International Livestock Research Institute (ILRI)
Country Kenya 
Sector Charity/Non Profit 
PI Contribution This project formed part of the establishment of a joint centre with ILRI to develop new approaches to improving the productivity of African Livestock
Collaborator Contribution There is a formal joint venture
Impact The Centre attracted funding from the Bill and Melinda Gates Foundation. It is too early to identify outcomes, but the centre is fully functional and pursuing multiple collaborative projects
Start Year 2015
 
Description Centre for tropical livestock genetics and health (CTLGH) 
Organisation International Livestock Research Institute (ILRI)
Country Kenya 
Sector Charity/Non Profit 
PI Contribution Mick Watson is co-leading programme 5 (informatics and bioresources) programme of CTLGH which aims to collect data on genotype and phenotype into a central database which can subsequently be mined for useful associations. So far we have ensured that scientists have access to the latest high performance computing environment for research, we have analysed and continue to analyse hundreds of farm animal genomes from LMIC countries, and we have built the data portal (http://data.ctlgh.org)
Collaborator Contribution The partners are involved in all programmes, which include:Program 1: Harnessing genetic variability among indigenous and exotic breeds of cattle (as well as their crosses) to develop genetic and genomic tools that will be used to improve productivity under harsh tropical conditions and to mitigate the impact of cattle on climate change. Program 2: Harnessing genetic variability in tropical productivity and adaptation among various breeds of Chickens. Program 3: Development and application of precision breeding (through novel reproductive and germplasm technologies) to achieve step changes in livestock genetic improvement. Program 4: Understanding the genetic and molecular mechanisms underlying the tolerance of certain cattle and poultry breeds to tropical diseases and pests. Program 5: A shared global data and biological sample resource to support continued research and development on tropical livestock genetics and health.
Impact The data portal so far: http://data.ctlgh.org The collaboration is multi-disciplinary, bringing together geneticists, parasitologists, virologists, epidemiologists and data scientists together.
Start Year 2016
 
Description Centre for tropical livestock genetics and health (CTLGH) 
Organisation Scotland's Rural College
Country United Kingdom 
Sector Academic/University 
PI Contribution Mick Watson is co-leading programme 5 (informatics and bioresources) programme of CTLGH which aims to collect data on genotype and phenotype into a central database which can subsequently be mined for useful associations. So far we have ensured that scientists have access to the latest high performance computing environment for research, we have analysed and continue to analyse hundreds of farm animal genomes from LMIC countries, and we have built the data portal (http://data.ctlgh.org)
Collaborator Contribution The partners are involved in all programmes, which include:Program 1: Harnessing genetic variability among indigenous and exotic breeds of cattle (as well as their crosses) to develop genetic and genomic tools that will be used to improve productivity under harsh tropical conditions and to mitigate the impact of cattle on climate change. Program 2: Harnessing genetic variability in tropical productivity and adaptation among various breeds of Chickens. Program 3: Development and application of precision breeding (through novel reproductive and germplasm technologies) to achieve step changes in livestock genetic improvement. Program 4: Understanding the genetic and molecular mechanisms underlying the tolerance of certain cattle and poultry breeds to tropical diseases and pests. Program 5: A shared global data and biological sample resource to support continued research and development on tropical livestock genetics and health.
Impact The data portal so far: http://data.ctlgh.org The collaboration is multi-disciplinary, bringing together geneticists, parasitologists, virologists, epidemiologists and data scientists together.
Start Year 2016
 
Description Genetics of laying hen welfare traits 
Organisation Lohmann Tierzucht GmbH
Country Germany 
Sector Private 
PI Contribution Measuring new phenotypes related to bone quality and egg quality related to preventing pathogen transfer, developing new methods of preventing injurious feather pecking. Calculating genetic parameters and establishing genetic loci underlying the trait.
Collaborator Contribution Access to large populations, logistic help, pedigree information. Collaborative discussion. Making measurements, financial support.
Impact New phenotypes, support from BBSRC flexible talent mobility award, New grants from the Foundation for Food and Agricultural Research on bone phenotyping and a PhD student on beak morphology.
 
Description Genetics of one-carbon metabolism 
Organisation University of Nottingham
Country United Kingdom 
Sector Academic/University 
PI Contribution The Roslin Institute partners in this collaboration provide expertise in genome analysis in farmed animal species and expertise in molecular, quantitative and population genetic analyses.
Collaborator Contribution The University of Nottingham group bring expertise in reproductive biology, physiology, epigenetics and bioinformatics as well as the biological questions which the "Genetics of one-carbon metabolism in sheep in relation to productivity, fertility and health" project has been designed to address.
Impact This BBSRC-funded research project (2013-17) supported by grants to University of Nottingham (BB/K017810/1) and The Roslin Institute, University of Edinburgh (BB/K017993/1) is an outcome from this collaborative link that started three years earlier. Whilst this collaboration is multi-disciplinary, the disciplines involved are specialisms within biology: reproductive biology; physiology; genetics; genomics; bioinformatics.
Start Year 2010
 
Description ILRI 
Organisation International Livestock Research Institute (ILRI)
Country Kenya 
Sector Charity/Non Profit 
PI Contribution We work with ILRI on all aspects of genomics and data science, including whole genome sequencing of multiple African animals, data recording and database design, web and web content development, and bioinformatics training.
Collaborator Contribution We work with ILRI on all aspects of genomics and data science, including whole genome sequencing of multiple African animals, data recording and database design, web and web content development, and bioinformatics training.
Impact So far we have sequenced the genomes of approx 800 African farm animals from diverse breeds and ecotypes
Start Year 2016
 
Description SRUC: genetic and environmental dissection of behavioural traits 
Organisation Scotland's Rural College
Country United Kingdom 
Sector Academic/University 
PI Contribution We are managing a study of genetic and non-genetic factors associated with behaviour in dogs, incorporating data collection, analysis and interpretation. Funded by the Dogs Trust, we are employing a postdoctoral researcher to carry out the research.
Collaborator Contribution They provide expertise in animal behaviour and are collaborating on data collection, analysis and interpretation.
Impact Several publications have resulted from this collaboration and further funding has been secured. This multi-disciplinary collaboration involves genetics and animal behaviour.
Start Year 2012
 
Description Universidad de León: signatures of selection in sheep 
Organisation University of Leon
Country Spain 
Sector Academic/University 
PI Contribution We have contributed to the identification of selected regions in domestic sheep from genomic data.
Collaborator Contribution They are carrying out large-scale studies of domestication and selection in domestic sheep.
Impact Two papers have been published on the identification of signatures of selection in domestic sheep. The results of these analyses suggest convergent selection for dairy traits in cattle and sheep and also confirm strong signatures of selection on several genes associated with carcass composition and growth.
Start Year 2012
 
Title resSpecies 
Description Database and associated web interface to handle pedigree populations, genotypes and phenotypes for genetic linkage mapping and quantitative trait linkage mapping studies. System checks inheritance of markers and formats/reformats data in readiness for import into common analysis programs. 
Type Of Technology Webtool/Application 
Year Produced 2008 
Impact Non computer-literate scientists can manipulate data - error free - within minutes rather than days 
URL http://www.resspecies.org/
 
Description Improving egg quality; win - win traits 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Presentation to breeders and geneticists from main breeding companies . X European Symposium on Poultry Genetics
Year(s) Of Engagement Activity 2017
URL http://www.wpsa.com/index.php/publications/wpsa-proceedings/2017/x-european-symposium-on-poultry-gen...
 
Description Animal and Plant Health in the UK 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact working group at Animal and Plant Health in the UK (2014): an assessment of future national capability, emerging technologies, 14 Feb 2014, BIS Conference Centre, London, UK
Year(s) Of Engagement Activity 2014
 
Description Avian genome evolution and the origins of species diversity. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited lecture: Avian genome evolution and the origins of species diversity. In "Molecular evolution of avian species", SMBE2016, Queensland's Gold Coast, Australia, 3-7 July, 2016.
Year(s) Of Engagement Activity 2016
 
Description BUAS Schools Countryside Day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Primary 5 children and teachers from the entire Scottish Borders region. Ran activities around the cuticle and its importance.
Year(s) Of Engagement Activity 2017
URL http://www.buas.org/calendar/buas_schools_countryside_day_23_may_17.html
 
Description CUTE EGG: PROVIDING A SAFE SUPPLY OF EGGS TO HATCH THE NEXT GENERATION OF CHICKENS 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Article on Cute egg featured in LOHMANN TIERZUCHT "Poultry News". Reaches huge number of farmers across the world
Year(s) Of Engagement Activity 2017
URL http://www.ltz.de/de-wAssets/docs/poultry-news/2017/Poultry-News-02-2017.pdf
 
Description CUTICLE DEPOSITION DOES NOT AFFECT WATER VAPOUR CONDUCTANCE AND CAN BE MEASURED IN HATCHING EGGS WITHOUT COMPROMISING EMBRYO DEVELOPMENT 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Presentation to specialists in egg science, breeders and state veterinarians, an industry Science meeting. XVIIth European Symposium on the Quality of Eggs and Egg Products, XXIIIth European Symposium on the Quality of Poultry Meat. Increases awareness across Europe of applications in poultry science.
Year(s) Of Engagement Activity 2017
URL http://www.wpsa.com/index.php/publications/wpsa-proceedings/2017/xxiii-european-symposium-on-the-qua...
 
Description CUTICLE DEPOSITION ENHANCES THE EGGS NATURAL DEFENCE AND IS A TRAIT WHICH DOES NOT TEND TO DECREASE WITH BIRD AGE 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Presentation to specialists in egg science, breeders and state veterinarians, an industry Science meeting. XVIIth European Symposium on the Quality of Eggs and Egg Products, XXIIIth European Symposium on the Quality of Poultry Meat. Increases awareness across Europe of applications in poultry science.
Year(s) Of Engagement Activity 2017
URL http://www.wpsa.com/index.php/publications/wpsa-proceedings/2017/xxiii-european-symposium-on-the-qua...
 
Description CUTICLE QUALITY GENETICS IN LAYERS AND BROILERS 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Presentation to specialists in egg science, breeders and state veterinarians, an industry Science meeting. XVIIth European Symposium on the Quality of Eggs and Egg Products, XXIIIth European Symposium on the Quality of Poultry Meat. Increases awareness across Europe of applications in poultry science.
Year(s) Of Engagement Activity 2017
URL http://www.wpsa.com/index.php/publications/wpsa-proceedings/2017/xxiii-european-symposium-on-the-qua...
 
Description Chicken Genome: Current Status and Future Trends from Next Generation Sequencing 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a talk at the 3rd Annual NGS Asia Congress. Talk: Chicken Genome: Current Status and Future Trends from Next Generation Sequencing. 8 - 9 Oct 2013, Singapore.
Year(s) Of Engagement Activity 2013
 
Description Contributed to the Society of Biology submission to the Smith Commission 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Contributed to the Society of Biology submission to the Smith Commission: "Research and the further devolution of powers to the Scottish government" (2014).
Year(s) Of Engagement Activity 2014
 
Description Development of New Tools for Genetic Selection for a Sustainable Poultry Industry 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a talk: Development of New Tools for Genetic Selection for a Sustainable Poultry Industry (2014), Veterinary Advances in Animal Health and Welfare Research - Impact and Opportunities, Feb 20-24, 2014, NIANP Auditorium, Adugodi, Bangalore, India
Year(s) Of Engagement Activity 2014
 
Description Edinburgh scientists working to create safer eggs 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact News coverage of egg cuticle story. 'Cute egg'
Year(s) Of Engagement Activity 2018
URL https://www.bbc.co.uk/news/uk-scotland-edinburgh-east-fife-43605254
 
Description From Sequences to Consequences 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact talk and meet industry at "21st Century Genomics for Animal Breeding and Animal Health. In "From Sequences to Consequences: What The Roslin Institute can do for you in the livestock sector", Industry Day. The Roslin Institute Building, Edinburgh, 18th March 2016."
Year(s) Of Engagement Activity 2016
 
Description ISAG Conference 2012. Talk: NGS of multiple chicken lines and development of a high-density 600K SNP genotyping array, 16-20 July, Cairns, Australia 2012. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a talk at ISAG Conference 2012. Talk: NGS of multiple chicken lines and development of a high-density 600K SNP genotyping array, 16-20 July, Cairns, Australia 2012.
Year(s) Of Engagement Activity 2012
 
Description Invited talk University of Guelph, The 'Who ate all the pies gene', University of Guelph, 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited talk at the Animal Science department of the University of Guelph
Year(s) Of Engagement Activity 2018
URL http://animalbiosciences.uoguelph.ca/events/2018/07/who-ate-all-pies-gene-and-its-implications
 
Description New tools and prospects for chicken genomics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk at Genetics Society of Australia (GSA), July 2015, University of Adelaide, Australia
Year(s) Of Engagement Activity 2015
 
Description Next Generation Sequencing of multiple chicken lines reveals a rich source of Single nucleotide polymorphisms for high resolution genetic studies 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk at The 1st International Conference on Genomics in the Americas. Talk: Next Generation Sequencing of multiple chicken lines reveals a rich source of Single nucleotide polymorphisms for high resolution genetic studies, 27-28 Sept, Philadelphia, USA.
Year(s) Of Engagement Activity 2012
 
Description Opportunities and applications of in poultry genomics 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Presentation to Agri-Tech Catalyst Funding Consortia Building Workshop - Edinburgh, 27 Jan 2014
Year(s) Of Engagement Activity 2014
 
Description Past, Present and Future of Genomics in Poultry Breeding. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk: Past, Present and Future of Genomics in Poultry Breeding. 25th World's Poultry Congress, Beijing, 5-9 September, 2016.
Year(s) Of Engagement Activity 2016
 
Description Poultry Genome: Implications for Immunity, Poultry Productivity and Health, Poultry beyond 2020 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact talk and roundtable discussion to "Poultry Genome: Implications for Immunity, Poultry Productivity and Health, Poultry beyond 2020, 13-17th April, Queenstown, New Zealand."
Year(s) Of Engagement Activity 2014
 
Description Poultry Genomics: Current Status and Future Trends from Next Generation Sequencing 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a talk at the 8th International Conference on Genomics (ICG-8). Talk: Poultry Genomics: Current Status and Future Trends from Next Generation Sequencing. 29 Oct - 1 Nov 2013, Shenzhen, China.
Year(s) Of Engagement Activity 2013
 
Description Poultry Genomics: Current Status and Future Trends from Next Generation Sequencing 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Talk at Animal Genomics Research Group "The global genomic approaches to climate change impact on livestock production". Talk: Poultry Genomics: Current Status and Future Trends from Next Generation Sequencing. 10-15 July, Seoul, Korea, 2013.
Year(s) Of Engagement Activity 2013
 
Description Production Animal Health and Welfare Research: Impacts and Opportunities. 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk at Production Animal Health and Welfare Research: Impacts and Opportunities. 19-20 Feb, 2015, Indian Council for Agricultural Research (ICAR), New Delhi, India
Year(s) Of Engagement Activity 2015
 
Description Science festivals 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact As a result of a Beltane grant and workshop an activity was built up to engage the public including children in the research. Specifically to understand the role of the cuticle in keeping bacteria out of the egg (in a fun way!).
This was used at a number of different science festival events running through to this year and has included the highland show.

Developed an interactive tool to explain the research aim which can be used in the future.
Year(s) Of Engagement Activity 2014,2017,2018,2019
URL http://scoffingscottishscience.com/about/
 
Description Structural aspects of genomes across species 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a talk at The 8th European Poultry Genetics Symposium. Talk: Structural aspects of genomes across species. 25-27 Sept, Venice Italy, 2013.
Year(s) Of Engagement Activity 2013
 
Description The chicken genome 10 years on. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Keynote lecture: chicken genome - 10 years on. Avian Model Systems - the 8th International Meeting, Cold Spring Harbour, USA, 4-8th March, 2014.

CSHL Leading Strand - Keynote Lecture Series (http://theleadingstrand.cshl.edu/Course/Keynote/2014/AVIAN/150

The chicken genome 10 years on - BBSRC (http://www.bbsrc.ac.uk/news/events/1403-chicken-genome.aspx)
Year(s) Of Engagement Activity 2014
 
Description UK-Brazil Animal Health Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact talk and round table discussion with UK-Brazil Animal Health Workshop, Edinburgh University UK, 3-5 Dec, 2014
Year(s) Of Engagement Activity 2014