MoBPSweb: A web-based framework to simulate and compare breeding programs.

In this study, we introduce a new web-based simulation framework ("MoBPSweb") that combines a unified language to describe breeding programs with the simulation software MoBPS, standing for "Modular Breeding Program Simulator." Thereby, MoBPSweb provides a flexible environment to log, simulate, evaluate, and compare breeding programs. Inputs can be provided via modules ranging from a Vis.js-based environment for "drawing" the breeding program to a variety of modules to provide phenotype information, economic parameters, and other relevant information. Similarly, results of the simulation study can be extracted and compared to other scenarios via output modules (e.g., observed phenotypes, the accuracy of breeding value estimation, inbreeding rates), while all simulations and downstream analysis are executed in the highly efficient R-package MoBPS.

A unifying concept of animal breeding programmes.

Modern animal breeding programmes are constantly evolving with advances in breeding theory, biotechnology and genetics. Surprisingly, there seems to be no generally accepted succinct definition of what exactly a breeding programme is, neither is there a unified language to describe breeding programmes in a comprehensive, unambiguous and reproducible way. In this work, we try to fill this gap by suggesting a general definition of breeding programmes that also pertains to cases where genetic progress is not achieved through selection, but, for example, through transgenic technologies, or the aim is not to generate genetic progress, but, for example, to maintain genetic diversity. The key idea of the underlying concept is to represent a breeding programme in modular form as a directed graph that is composed of nodes and edges, where nodes represent cohorts of breeding units, usually individuals, and edges represent breeding activities, like "selection" or "reproduction." We claim, that by defining a comprehensive set of nodes and edges, it is possible to represent any breeding programme of arbitrary complexity by such a graph, which thus comprises a full description of the breeding programme. This concept is implemented in a web-based tool (MoBPSweb, available at www.mobps.de) and has a link to the R-package MoBPS (Modular Breeding Program Simulator) to simulate the described breeding programmes. The approach is illustrated by showcasing three different breeding programmes of increasing complexity. The concept allows a formal description of breeding programmes, which is requested, for example, in legal regulations of the European Union, but so far cannot be provided in a standardized format. In the discussion, we point out potential limitations of the concept and argue that the general approach can be easily extended to account for novel breeding technologies, to breeding of crops or experimental species, but also to modelling diversity dynamics in natural populations.

Simulation Study on the Integration of Health Traits in Horse Breeding Programs.

Osteochondrosis dissecans (OCD) is a degenerative disease of the cartilage leading to osseous fragments in the joints. It is important in horse breeding both from an animal welfare and an economic perspective. To study adequate breeding strategies to reduce OCD prevalence, a lifelike simulation of the breeding program of German Warmblood horses was performed with the R package MoBPS. We simulated complex breeding schemes of riding horses with different selection steps and realistic age structure, mimicking the German situation. As an example, osseous fragments in fetlock and hock joints were considered. Different scenarios, either using threshold selection, index selection or genomic index selection, respectively, were compared regarding their impact on health and performance traits. A rigorous threshold selection as well as the integration of OCD in a selection index at the stage of stallion licensing and chosen frequency of use in breeding cases on a selection index that includes breeding values for OCD traits performed best on a comparable level. Simply integrating OCD in this breeding value was less effective in terms of OCD reduction. Scenarios with a higher reduction of OCD also showed a slightly reduced improvement in the riding horse performance traits.