Chris Gaynor is a creator of the AlphaSimR software package for stochastic simulations of breeding programs. He trained breeders and quantitative geneticists in the use of the breeding scheme optimisation method based on project management (continuous improvement) and simulation-based tools (AlphaSimR) at the Breeding Scheme Optimisation Training in Netherlands organised by Excellence in Breeding Platform and CGIAR.

Christian Werner, helped with tutorials at the Training.

Training Background

Breeders and Quantitative Geneticists play an important role in the seed sector as pipeline engineers (not products), but for a long time breeders have been commissioned with the responsibility of executing many other aspects. As plant breeding programs are starting to grow and become a team of specialists, the role of the breeders and quantitative geneticists as pipeline designers becomes clearer. In any process, the design of manufacturing pipelines is a complicated task that requires knowledge of the materials used (germplasm), process optimization (simulation and other mathematical approaches) and project management tools. This training aims to provide knowledge on what are these tools and how to use them in the context of plant breeding to enable continuous improvement/optimisation of the breeding schemes.

Training Objectives

Excellence in Breeding is committed with bringing all CGIAR breeding programs as close as possible to state of the art programs for them to be competitive, increase impact and fulfil the mission of the CGIAR. This training has as main objective to train breeders and quantitative geneticists in the use of the breeding scheme optimisation method based on project management (continuous improvement) and simulation – based tools (AlphaSimR).

Royal Dick Christmas Bag Appeal

The Royal Dick Christmas Bag Appeal is a yearly donation scheme to aid the homeless of Edinburgh. Staff, students and friends of the Dick Vet and the Roslin Institute provide bags of essential items to be distributed, with the help of local homeless charities and soup kitchens, throughout the streets of Edinburgh close to Christmas.

AlphaGenes is proud to contribute to the Royal Dick Christmas Bag Appeal this year, and hope to bring some Christmas spirit to ones in need.

Pruthviraj is a graduate of veterinary science with a research interest in animal genetics & breeding. During his masters, he worked on expression profiling & genetic polymorphism of porcine beta defensin-1 gene in which they could identify a novel SNP. In his PhD research, he is working on the phenotypic data of Vrindavani cattle to obtain genetic parameters, breeding value and genetic trend for various performance traits. At Alphagenes group, Pruthviraj is interested to learn methods to incorporate genomic information in the estimation of breeding value either with the help of some real data set or through simulation studies.


Peter Bradbury is a USDA-ARS computational biologist working in the lab of Edward Buckler in Ithaca, NY and affiliated with Cornell University. He is one of the developers of the TASSEL software package and the PHG (Practical Haplotype Graph). His current research projects involve genotype imputation and phasing using DNA sequence data. One of the primary objectives of that research is the development of a low cost genotyping platform that can be used by plant breeders and that will be implemented by the PHG software. Peter is visiting the AlphaGenes lab to learn about the methods we have developed to help improve and extend the methods used by the PHG software and to explore the potential for future collaboration in other areas.