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The principles of animal and plant breeding are increasingly coalescing due to advances in technology and increasing demands and opportunities for agriculture. This two-week graduate level course of integrated lectures and practicals is designed to equip students, academics and practitioners with theoretical and applied knowledge, skills and tools to design, optimise and deploy Data Driven Animal and Plant Breeding and Genetics techniques. The course will take place in Edinburgh from April 27th to May 8th. It will be jointly delivered by scientists and teachers from the University of Edinburgh, Scotland’s Rural College and the CGIAR’s Excellence in Breeding Platform, with guest lectures from industry collaborators.
Lecturers
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| John Hickey, University of Edinburgh Chair of Animal Breeding and leading a research programme that develops tools and strategies to empower local and global animal and plant breeding programmes. | Gregor Gorjanc, University of Edinburgh Chancellor's Fellow in Data Driven Innovation for AgriTech using data science, genetics and breeding to manage and improve populations used for production of food, feed and fibre. |
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| Ian Mackay, Scotland’s Rural College Professor of Plant Breeding, SRUC. Application of quantitative methods in plant breeding, teaching, Founder/director of Implant Consultancy Ltd. | Chris Gaynor, University of Edinburgh Research fellow at the Roslin Institute, improvement and optimization of plant and animal breeding programmes. |
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| Eduardo Covarrubias, CGIAR Excellence in Breeding Breeding scheme optimization lead at Excellence in Breeding using quantitative genetics theory, project management and mathematical optimization tools to modernize CGIAR and NARs breeding programmes. | |
Guest lecturers
Geoff Simm, UoE, Director of the Global Academy of Agriculture and Food Security, and Chair of Global Agriculture and Food Security www.ed.ac.uk/profile/geoff-simm
Ross Houston, UoE, Personal Chair of Aquaculture Genetics www.ed.ac.uk/profile/ross-houston
Andrea Wilson, UoE, Personal Chair in Infectious Disease Genetics and Modelling www.ed.ac.uk/profile/andrea-wilson
Andreas Kranis, UoE & Aviagen, Senior Research Fellow and Group Leader www.ed.ac.uk/profile/andreas-kranis
Wayne Powell, SRUC, The Principal and Chief Executive, FLSW, FRSE at SRUC, member of the Science Advisory Council of DEFRA, The Scottish Science Advisory Council and Convenor of the Research and Knowledge Exchange Committee of Universities Scotland www.sruc.ac.uk/wpowell
Mike Coffey, SRUC, Professor of Livestock Informatics / Team Leader – Animal Breeding & Genomics and EGENES www.sruc.ac.uk/mcoffey
Scott Denholm, SRUC, Postdoctoral researcher www.sruc.ac.uk/sdenholm
Tim Byrne, AbacusBio, Managing Director AbacusBio International abacusbio.com/people/tim-byrne
Brian Gardunia, Bayer CropSciences, Discovery Breeding Methodology Lead www.linkedin.com/in/brian-gardunia-3694397/
Demonstrators
Andrew Whalen, UoE, Research Fellow in Quantitative Genetics alphagenes.roslin.ed.ac.uk/wp/andrew-whalen
Christian Werner, UoE, Research Fellow in Computational Genetics and Genomics alphagenes.roslin.ed.ac.uk/wp/christian-werner
Martin Johnsson, UoE & The Swedish University of Agricultural Sciences, Research Fellow alphagenes.roslin.ed.ac.uk/wp/martin-johnsson
Steve Thorne, UoE, Research Fellow in Quantitative Genetics alphagenes.roslin.ed.ac.uk/wp/steve-thorn-2
Ivan Pocrnic, UoE, Research Fellow in Quantitative Genetics www.ed.ac.uk/profile/ivan-pocrnic
Lorena Batista, UoE, Research Fellow in Quantitative Genetics alphagenes.roslin.ed.ac.uk/wp/lorena-batista-2
Leticia Lara, UoE, Research Fellow in Quantitative Genetics and Insect Breeding www.ed.ac.uk/profile/leticia-de-castro-lara
Stephanie Smith, UoE, Teaching Fellow at The Global Academy for Agriculture and Food Security www.ed.ac.uk/profile/steph-smith
Daniel Tolhurst, UoE, PhD student in in Quantitative Genetics alphagenes.roslin.ed.ac.uk/wp/daniel-tolhurst
CJ Yang, SRUC, Postdoctoral Researcher in Quantitative Genetics pure.sruc.ac.uk/en/persons/cj-yang
Rajiv Sharma, SRUC, Postdoctoral Researcher in Quantitative Genetics and Plant Breeding pure.sruc.ac.uk/en/persons/rajiv-sharma
Prerequisites
Participants are expected to have some prior exposure to breeding, genetics or data science. As a preparation for the course we suggest a refresh of basic genetic and statistics principles as well as R (www.r-project.org). Participants should bring their own laptop with an installation of the most recent R version and RStudio and the AlphaSimR (alphagenes.roslin.ed.ac.uk/wp/software-2/alphasimr) and AlphaLearn (alphagenes.roslin.ed.ac.uk/wp/software-2/alphalearn) R packages.
Programme
Day 1 (April 27th) Introduction to breeding
- Introductions and grouping of participants for group work
- Why do we do selective breeding?
- Compare and contrast breeding programmes in different species
- R crash course, including the tidyverse and ggplot
- Genomes, inheritance and phenotypes
- Guest lecture (Wayne Powell: Global agriculture to secure societies future)*
- Welcome dinner
Day 2 (April 28th) Breeding programme design
- Breeder’s equation.
- Manipulating parameters of the breeder’s equation deterministically
- Introduction to AlphaSimR & simulating genomes, inheritance and phenotypes
- Designing basic breeding programmes
- Evaluating alternative breeding scenarios via simulation
- Guest lecture (Ross Houston: Breeding in aquaculture)*
Day 3 (April 29th) Genomic data in breeding
- Genomic data: SNP array genotyping and sequencing
- Phasing genomic data with heuristic and probabilistic methods
- Imputation of genomic data
- Strategies to generate genomic data in breeding programmes
- Guest lecture (Andreas Kranis: How does a major multinational animal breeding programme operate in the 21stcentury)*
Day 4 (April 30th) Modelling phenotype data to estimate environmental effects
- Group allocation
- Introduction to linear mixed models for breeders
- General principles of experimental design (the 3 Rs)
- Design and analysis of experimental data (field trials), including spatial
- Design and analysis of series of trials, including handling of GxE
- Analysingobservational data
- Guest lecture (Eduardo Covarrubias: Genetic evaluations in multinational plant breeding programmes)*
Day 5 (May 1st ) Population and Quantitative genetics for breeding
- Group presentations
- Change of allele, genotype and haplotype frequencies due to admixture, drift and selection, including linkage disequilibrium and founder effects
- Additive effects
- Non-additive effects: dominance and epistasis
- Heterosis and inbreeding depression
- Guest lecture (Scott Denholm: Artificial intelligence to model and generate phenotypes)*
Weekend break (2nd & 3rdMay)
Day 6 (May 4th) Quantitative genetics for breeding II
- Variances, covariances and correlations
- Heritability and reliability
- Correlated response to selection
- Recurrent selection – half sib, full, sib, S1, clonal etc.
- Guest lecture (Brian Gardunia: How does a major multinational plant breeding programme operate in the 21stcentury)*
Day 7 (May 5th) Modelling phenotype data to estimate genetic effects
- Pedigree BLUP
- Linkage analysis
- Genome-wide association studies
- Genomic BLUP and the Bayesian Alphabet
- Guest lecture (Mike Coffey: National genetic evaluations in livestock – what, why, how)*
Day 8 (May 6th) Sustainable breeding
- Management of selection and diversity with optimal contributions and mate/cross allocation
- Detection and management of deleterious variation in breeding
- Breeding goals
- Multi-trait genetic evaluation
- Desired gains, selection index and economic weights
- Guest lecture (Tim Byrne: Economic objectives in animal and plant breeding)*
Day 9 (May 7th) Exploiting technologies in breeding
- Reproductive technologies in animals and plants
- Use of genome editing and gene drives in breeding programmes
- Tool and strategies to exploit high-throughput phenotyping, sensors and “Omics”
- Guest lecture (Andrea Wilson: Breeding for disease resistance in animals)*
- Group work on breeding programmes for specific species
(design and deploy resources for alternative breeding programmes and compare them over a short- and long-term period using the course tool and techniques) - Farewell dinner
Day 10 (May 8th) Exploiting modern technologies in breeding programmes
- Group work on breeding programmes for specific species
(design and deploy resources for alternative breeding programmes and compare them over a short- and long-term period using the course tool and techniques) - Group presentations
- Guest lecture (Geoff Simm: The role of livestock in global food security)*
- Wrap-up
*The order and title of guest lectures is subject to change.
Organizational information
Dates: April 27th - May 8th 2020
Venue: South Hall, 18 Holyrood Park Rd, Edinburgh EH16 5AY
Maximum participants: 65
Registration is closed
Travel and accommodation
Participants have to arrange and cover their travel and accommodation. There are multiple accommodation options in Edinburgh, for example Travelodge (www.travelodge.co.uk), University of Edinburgh (Salisbury Green Hotel, KM Central Hotel or Richmond Place Apartments via www.book.accom.ed.ac.uk– use promotion code EVENT for a 15 % discount; payment at the time of booking) and others.
Contact
Romana Gorjanc romana.gorjanc@ed.ac.uk
