A unifying concept of animal breeding programs

Abstract

<jats:p>Modern animal breeding programs 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 program is, neither is there a unified language to describe breeding programs in a comprehensive, unambiguous and reproducible way. In this work, we try to fill this gap by suggesting a general definition of breeding programs that also pertains to cases where genetic progress is not achieved through selection, but e.g. through transgenic technologies, or the aim is not to generate genetic progress, but e.g. to maintain genetic diversity. The key idea of the underlying concept is to represent a breeding program 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 program of arbitrary complexity by such a graph, which thus comprises a full description of the breeding program. This concept is implemented in a web-based tool (MoBPSweb, available at www.mobps.de) which is described in a companion paper, and has a link to the R-package MoBPS (Modular Breeding Program Simulator) to simulate the described breeding programs. The approach is illustrated by showcasing three different breeding programs of increasing complexity. Finally, potential limitations of the concept are indicated and extensions to other fields, like plant breeding, are discussed.</jats:p>

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

“…As described in Simianer et al (2020) a breeding scheme can be represented by a set of cohorts (nodes) and breeding actions (edges). This is implemented in an interactive environment based on the dynamic and browser-based visualization library Vis.js.…”

“…In a companion paper, Simianer et al (2020) proposed a unifying concept to describe breeding programs. Even though the focus in that work was mostly on animal breeding, concepts can readily be extended to plant breeding.…”

“…Even though the focus in that work was mostly on animal breeding, concepts can readily be extended to plant breeding. The key idea of the concept introduced by Simianer et al (2020) is to describe each breeding program via a set of nodes and edges, with nodes representing cohorts of individuals and edges representing a set of potential breeding actions ( e.g. , generation of offspring, performing phenotyping or selection of individuals).…”

“…, generation of offspring, performing phenotyping or selection of individuals). By this, Simianer et al (2020) are providing a comprehensive, unambiguous, and reproducible way to describe a breeding program.…”

“…In this study, we combine the ideas of Simianer et al (2020) with the highly efficient breeding program simulator MoBPS ( Pook et al 2020 ) to provide a web-based application (“MoBPSweb”) to log, simulate, evaluate, and compare breeding programs in an user-friendly and intuitive web-based environment.…”