MoBPS - Modular Breeding Program Simulator

Abstract

The R-package MoBPS provides a computationally efficient and flexible framework to simulate complex breeding programs and compare their economic and genetic impact. Simulations are performed on the base of individuals and haplotypes are calculated on-the-fly by only saving founder haplotypes, points of recombination and mutations. MoBPS utilizes a highly efficient implementation with bit-wise storage of data and matrix multiplications from the associated R-package miraculix allowing to handle large scale populations. The modular structure of MoBPS allows to combine rather coarse simulations, as needed to generate founder populations, with a very detailed modeling of todays complex breeding programs, making use of all available biotechnologies. MoBPS provides pre-implemented functions for common breeding practices such as optimum genetic contributions and single-step GBLUP but also allows the user to replace certain steps with personalized and/or self-written solutions.