Next Generation Plant and Animal Breeding Programs

21st to 25th March 2016

Animal Science Department

University of Nebraska – Lincoln

Animal Science Complex
Lectures: room A132
Workshops: rooms A222/A223

The lectures are open to the public while the workshops will be capped to 30 participants – priority will be given to graduate and undergraduate students. In order to provide access to those that really want to participate please register only if you really plan to attend.

Register here

Prof. John Hickey (The Roslin Institute, UK)
Dr. Gregor Gorjanc (The Roslin Institute, UK)
Dr. Chris Gaynor (The Roslin Institute, UK)

Dr. John Hickey is a Professor and Chair of Animal Breeding at The University of Edinburgh and the Roslin Institute, one of a leading agriculture institutions in the world. His work contributed (i) to the theoretical understanding of genomic selection; (ii) haplotyping and imputation methods; (iii) genotyping and sequencing strategies to underpin imputation in animals and plants; (iv) statistical methods for estimating marker effects and predicting breeding values in plants and animals with applications in humans; (v) data analysis in a range of animal and crop species; (vi) methods for simulation of breeding programs in plants and animals; and (vii) novel breeding program designs including the development of a novel way for using genome editing to improve quantitative traits and a novel strategy for incorporating genomic selection in plant breeding programs. His software applications, algorithms, and strategies underpin 3 of the 7 largest animal breeding programs globally and are widely used by researchers.

Dr. Gregor Gorjanc is a Research Fellow in Computational Genetics and Genomics at The University of Edinburgh and the Roslin Institute. His work spans animal and plant breeding. He contributed to a broad range of topics including (i) quantitative genetic modelling, (ii) design of breeding programs, (iii) use of high-throughput genotyping technologies (SNP arrays, Genotyping-By-Sequencing, and imputation), and (iv) phenotyping and genotyping strategies.

Dr. Chris Gaynor is a Research Fellow in Computational Genetics and Genomics at The University of Edinburgh and the Roslin Institute. He is a former assistant wheat breeder and has worked on a range of research projects in wheat breeding including: (i) QTL mapping of agronomic traits, (ii) applying genomic selection in an active breeding program, and (iii) simulating breeding strategies for incorporating genomic selection in plant breeding programs.


The lectures/workshops will start each day at 8:30 am with a break from 12 pm to 1:30 pm.
For those attending the workshop you need to setup an HCC (Holland Computer Center Account) account and able to log in using your own laptop. A link with information on signing up and quick start guides: A member of the HCC team will be in attendance to provide technical support.
Monday: Introduction to Genomics in Breeding

  • General overview (Hickey)
  • Practical factors effecting animal breeding programs (Hickey)
  • Practical factors effecting plant breeding programs (Gorjanc)
  • Practical: Introduction to Linux scripting (Gorjanc)
  • Practical: Introduction to AlphaSim (Gaynor)

Tuesday: BLUP

  • GBLUP (Hickey)
  • Practical: BLUP using Excel (Gorjanc)
  • Gauss-Seidel method (Hickey)
  • Practical: Gauss-Seidel using R (Gorjanc)
  • Practical: Making predictions using AlphaSim (Gaynor)

Wednesday: Imputation

  • Mechanics of imputation (Hickey)
  • Economics of genotyping (Gorjanc)
  • Practical: Imputation in plants and animals (Gaynor)

Thursday: Practical Implementation of genomic selection

  • Maintaining genetic diversity (Hickey)
  • Introducing genetic diversity (Gorjanc)
  • Practical: Designing a breeding program - AlphaSim (Gaynor)
  • Current progress in plants (Hickey)
  • Current progress in animals (Gorjanc)

Friday: Future

  • Genomic Selection 2.0 (Hickey)
  • Practical: Simulating Genome Editing using AlphaSim (Gaynor)

Please fill out the registration below