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

Pook, Torsten; Büttgen, Lisa; Ganesan, Amudha; Ha, Ngoc-Thuy; Simianer, Henner

doi:10.1101/2020.07.08.193227

Cited by 2 publications

(9 citation statements)

References 24 publications

(8 reference statements)

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“…This general concept was implemented in a web‐based graphical user interface MoBPSweb (Pook, Büttgen, et al, 2020) which is accessible under http://www.mobps.de. This interface offers a wide range of options to define breeding programmes along the concept outlined above and subsequently simulate the breeding programme with the MoBPS R‐package (Pook, Schlather, et al, 2020) as the backend simulator.…”

Section: Methodsmentioning

confidence: 99%

“…Later we provide a formal framework to describe a breeding programme in a modular way and discuss a possible set of modules of a breeding programme without claiming this set to be comprehensive. This modular concept was implemented in an interactive software tool, the graphical user interface of the Modular Breeding Program Simulator as described in a companion paper (Pook et al, 2020) which will be introduced and illustrated with a few examples of increasing complexity. Finally, the usefulness of the concept and potential extensions to other fields of application will be discussed.…”

Section: Introductionmentioning

confidence: 99%

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A unifying concept of animal breeding programmes

Simianer

Büttgen

Ganesan

et al. 2021

J Animal Breeding Genetics

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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 http://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.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A unifying concept of animal breeding programmes

Simianer

Büttgen

Ganesan

et al. 2021

J Animal Breeding Genetics

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show abstract

“…Finally, a formal breeding program description can be used as input for a software to simulate breeding programs. In fact, the JSON file to be exported from MoBPSweb (Pook et al 2020a) can be used as an input parameter file in the R-package MoBPS Breeding scheme for line A of a four-line cross in a commercial layer breeding program as described in Sitzenstock et al (2013). Details on the attributes of all nodes and edges can be found in Supplementary File S3.…”

Section: Commercial Layer Breeding Programmentioning

confidence: 99%

“…This general concept was implemented in a web-based graphical user interface MoBPSweb (Pook et al 2020a) which is accessible under www.mobps.de. This interface offers a wide range of options to define breeding programs along the concept outlined above and subsequently simulate the breeding program with the MoBPS R-package (Pook et al 2020b) as the backend simulator.…”

mentioning

confidence: 99%

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A unifying concept of animal breeding programs

Simianer¹,

Ganesan²,

Buettgen³

et al. 2020

Preprint

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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.

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

Cited by 2 publications

References 24 publications

A unifying concept of animal breeding programmes

A unifying concept of animal breeding programmes

A unifying concept of animal breeding programs

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