WIAS Course: Simulation of breeding programs with the Modular Breeding Program Simulator (MoBPS) (0.6 ECTS)

Course description

Background: Breeding programs aim at improving the genetic characteristics of livestock and plant populations. As breeding is affected by a variety of interdependent factors, the analysis of the effect of certain breeding actions and the optimization of a breeding program are highly complex tasks. Although quantitative genetic theory can give approximations for simple breeding schemes, this typically is not sufficient for todays’ complex breeding programs and thus requires stochastic simulations with software like MoBPS for extended analysis.

Course topics: The course will include a general introduction to the MoBPS framework and breeding programs, as well as a series of exercises on how to use MoBPSweb (www.mobps.de) and the MoBPS R-package. In addition, there will be room for open discussion and specific questions regarding own breeding programs. After completion of the course, participants should be able to simulate common breeding programs in both plant and animal breeding including features such as:

• Use of real genotype and phenotype data as input
• Generation of traits
• Simulation of multiple breeding cycles
• Selection, phenotyping, breeding value estimation
• Comparison of scenarios of a breeding scheme
• MoBPS analysis functions
• Linking MoBPS to other software (MiXBLUP / blupf90 etc.)

Assumed background knowledge: Basic understanding of genomic prediction and breeding programs. Basic programming knowledge in R is encouraged, but not mandatory. Participants are expected to have access to a running version of R (version 3.4+) and a web-browser.

Background reading material:

https://doi.org/10.1534/g3.120.401193

https://doi.org/10.1093/g3journal/jkab023

https://github.com/tpook92/MoBPS/blob/master/Guidelines%20to%20MoBPS.pdf