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

Abstract In this work, 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.

Download Full-text

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

10.1101/2020.07.08.193227 ◽

2020 ◽

Cited By ~ 1

Author(s):

T. Pook ◽

L. Büttgen ◽

A. Ganesan ◽

N.T. Ha ◽

H. Simianer

Keyword(s):

Selection Index ◽

Relevant Information ◽

Simulation Software ◽

Breeding Program ◽

Breeding Value ◽

Long Term Effects ◽

General Applicability ◽

Breeding Programs ◽

Web Based ◽

Value Estimation

ABSTRACTSelective breeding is a continued element of both crop and livestock breeding since early prehistory. In this work, we are proposing a new web-based simulation framework (“MoBPSweb”) that is combining a unified language to describe breeding programs with the simulation software MoBPS, standing for ‘Modular Breeding Program Simulator’. Thereby, MoBPSweb is providing a flexible environment to enter, simulate, evaluate and compare breeding programs. Inputs can be provided via modules ranging from a Vis.js-based flash 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, accuracy of breeding value estimation, inbreeding rates). Usability of the framework is showcased along a toy example of a dairy cattle breeding program on farm level, with comparing scenarios differing in implemented breeding value estimation, selection index and selection intensity being considered. Comparisons are made considering both short and long-term effects of the different scenarios in terms of genomic gains, rates of inbreeding and the accuracy of the breeding value estimation. Lastly, general applicability of the MoBPSweb framework and the general potential for simulation studies for genetics and in particular in breeding are discussed.

Download Full-text

AlphaSimR: an R package for breeding program simulations

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkaa017 ◽

2020 ◽

Vol 11 (2) ◽

Author(s):

R Chris Gaynor ◽

Gregor Gorjanc ◽

John M Hickey

Keyword(s):

Software Package ◽

R Package ◽

Animal Breeding ◽

Breeding Program ◽

Stochastic Simulations ◽

Breeding Programs ◽

Detailed Design ◽

Building Simulations ◽

Wide Range ◽

Commercial Breeding

Abstract This paper introduces AlphaSimR, an R package for stochastic simulations of plant and animal breeding programs. AlphaSimR is a highly flexible software package able to simulate a wide range of plant and animal breeding programs for diploid and autopolyploid species. AlphaSimR is ideal for testing the overall strategy and detailed design of breeding programs. AlphaSimR utilizes a scripting approach to building simulations that is particularly well suited for modeling highly complex breeding programs, such as commercial breeding programs. The primary benefit of this scripting approach is that it frees users from preset breeding program designs and allows them to model nearly any breeding program design. This paper lists the main features of AlphaSimR and provides a brief example simulation to show how to use the software.

Download Full-text

A unifying concept of animal breeding programs

10.1101/2020.07.08.193201 ◽

2020 ◽

Author(s):

H. Simianer ◽

A. Ganesan ◽

L. Buettgen ◽

N.T. Ha ◽

T. Pook

Keyword(s):

R Package ◽

Companion Paper ◽

Animal Breeding ◽

Breeding Program ◽

General Definition ◽

Full Description ◽

Genetic Progress ◽

Breeding Programs ◽

Definition Of ◽

Transgenic Technologies

ABSTRACTModern 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.

Download Full-text

Estimation of realized rates of genetic gain and indicators for breeding program assessment

10.1101/409342 ◽

2018 ◽

Cited By ~ 2

Author(s):

J.E. Rutkoski

Keyword(s):

Oryza Sativa ◽

Genetic Gain ◽

Program Assessment ◽

Careful Consideration ◽

Breeding Program ◽

Stochastic Simulations ◽

Breeding Value ◽

Estimation Methods ◽

Breeding Programs ◽

The Past

AbstractRoutine estimation of the rate of genetic gain (ΔGt) realized by a breeding program has been proposed as a means to monitor its effectiveness. Several methods of realized ΔGt estimation have been utilized in other studies, but none have been objectively evaluated in a plant breeding context. Stochastic simulations of 80 rice (Oryza sativa) breeding programs over 28 years were done to generate data used to evaluate five methods of realized ΔGt estimation in terms of error, precision, efficiency and correlation between true and predicted annual mean breeding values. Two indicators of ΔGt, the expected ΔGt and the average number of equivalent complete generations (EqCg), were described and evaluated. At best, estimates of realized ΔGt were over or underestimated by 15% and 27% when considering all 28 years and the past 15 years of breeding respectively. The best methods were the control population, estimated breeding value, and ERA trial methods. Among these, correlations between true and estimated ΔGt were at best 0.59, indicating that these methods cannot very accurately rank breeding programs in terms of realized ΔGt. The expected ΔGt and the average EqCg were shown to be useful indicators for determining if a non-zero genetic gain is expected. Determining which of the three best realized ΔGt estimation methods evaluated, if any, would be appropriate for any given breeding program should be done with careful consideration of the objectives, resources, seed stocks, and structure of the data available.

Download Full-text

Breeding Value of Cocoa (Theobroma cacao L.) for Pod and Bean Traits: A Consequential Advance in Nigerian Cocoa Breeding Program

Notulae Scientia Biologicae ◽

10.15835/nsb629291 ◽

2014 ◽

Vol 6 (2) ◽

pp. 214-219

Author(s):

Daniel Babasola ADEWALE ◽

Oluwatosin O. ADEIGBE ◽

Olalekan I. SOBOWALE ◽

Oluwaseun S. DADA

Keyword(s):

Block Design ◽

Breeding Program ◽

Breeding Value ◽

Hybrid Breeding ◽

Cross Combination ◽

Breeding Programs ◽

Six Traits ◽

Sources Of Variation ◽

Additive Gene ◽

Pod Length

The understanding of the generated hybrids’ breeding value gives a measure of probable advances in a breeding program. Four cocoa genotypes (testers) were crossed with two distinct lines (T65/7 and T86/2). The parents and the hybrids were separately established in randomized complete block design with six replications. The fourteen genotypes were evaluated for pod length (PL), weight (PW), beans/pod (NoB), bean length (BL), width (Bwi) and thickness (BT). The treatment, parent, crosses and Line x Tester sources of variation were significant (P ≤ 0.05). Hybrids from the same maternal parent differed significantly (P < 0.05) for the six traits. Contribution to the total variance of PL, PW and Bwi were in the following order: Tester > Line x Tester > Lines. The highest general combining ability (0.42) occurred in T65/7 for PW; the least (-0.081) occurred in T86/2 for PL. Cross combination T65/7xT57/22 produced the highest specific ability of combination (4.33) for NoB. Variance of GCA and SCA were significant (P < 0.05) for the six traits. The GCA/SCA ratios revealed the inheritance of PL, PW, Bwi and BT to be additive. Non-additive gene effect controlled NoB and BL. Heterosis for the six traits ranged between -17.82% for BT (T65/7xT57/22) to 52.40% for PW (T65/7xT53/8). Increased productivity in cocoa is possible through hybrid breeding programs.

Download Full-text

QTL mapping and breeding value estimation through pedigree-based analysis of fruit size and weight in four diverse peach breeding programs

Tree Genetics & Genomes ◽

10.1007/s11295-016-0985-z ◽

2016 ◽

Vol 12 (2) ◽

Cited By ~ 28

Author(s):

Jonathan Fresnedo-Ramírez ◽

Terrence J. Frett ◽

Paul J. Sandefur ◽

Alejandra Salgado-Rojas ◽

John R. Clark ◽

...

Keyword(s):

Qtl Mapping ◽

Fruit Size ◽

Breeding Value ◽

Breeding Programs ◽

Value Estimation ◽

Peach Breeding

Download Full-text

AlphaSimR: An R-package for Breeding Program Simulations

10.1101/2020.08.10.245167 ◽

2020 ◽

Cited By ~ 6

Author(s):

R. Chris Gaynor ◽

Gregor Gorjanc ◽

John M. Hickey

Keyword(s):

Software Package ◽

R Package ◽

Animal Breeding ◽

Breeding Program ◽

Stochastic Simulations ◽

Breeding Programs ◽

Detailed Design ◽

Building Simulations ◽

Wide Range ◽

Commercial Breeding

AbstractThis paper introduces AlphaSimR, an R package for stochastic simulations of plant and animal breeding programs. AlphaSimR is a highly flexible software package able to simulate a wide range of plant and animal breeding programs for diploid and autopolyploid species. AlphaSimR is ideal for testing the overall strategy and detailed design of breeding programs. AlphaSimR utilizes a scripting approach to building simulations that is particularly well suited for modeling highly complex breeding programs, such as commercial breeding programs. The primary benefit of this scripting approach is that it frees users from preset breeding program designs and allows them to model nearly any breeding program design. This paper lists the main features of AlphaSimR and provides a brief example simulation to show how to use the software.

Download Full-text

Matoa (Pometia Pinata Foster): Local Fruit Papua and Strategy Development

Beccariana Botanical Research Bulletin ◽

10.30862/bbrp.v7i1.276 ◽

2010 ◽

Vol 7 (1) ◽

Author(s):

Julius D. Nugroho

Keyword(s):

Genetic Resources ◽

Fruit Tree ◽

Breeding Program ◽

Strategy Development ◽

Local Market ◽

Font Size ◽

Breeding Programs ◽

Irian Jaya ◽

Forest Exploitation ◽

Program Strategy

Matoa (Pometia pinnata) is a local fruit of  Papua (formerly called Irian Jaya) which has high potensial to develop as comercial fruit. Highly significant genetic resources of matoa potentially for breeding program in Papua are being threatened as a result of cutting down trees for fruit harvesting and of forest exploitation for timber. Besides the loss of genetic resources facing now, other major problems should be consider for conservation and domestication of this fruit tree species i.e. lack of silviculture and agronomy knowledge for further breeding programs; matoa production only for local market; and inadequate government policy for matoa breeding program. Strategy developed for matoa conservation and domestication should also concern about time limited due to the fast loss of genetic poll. This paper provides a general overview of strategy for conservation and domestication of Pometia pinnata with special reference to Papua.

Download Full-text

A voyage to Ancient Greek Harbours on board Limenoscope

Water Science & Technology Water Supply ◽

10.2166/ws.2007.029 ◽

2007 ◽

Vol 7 (1) ◽

pp. 253-260 ◽

Cited By ~ 1

Author(s):

T. Theodoulou ◽

C. Memos

Keyword(s):

Black Sea ◽

General Public ◽

Aegean Sea ◽

Relevant Information ◽

The Black Sea ◽

Ancient Greek ◽

Web Based ◽

Database Structure ◽

Historical Role ◽

Concise Information

Limenoscope is a web based database aiming at promoting the cultural heritage regarding ancient Greek harbours and disseminate the relevant information equally to the general public and to researchers with an interest in that particular cognitive field. The scope of the project is the realization of a database, where one can search for concise information relevant to the historical role, the topography, the morphology, as well as the technical works and installations of ancient harbours in the Mediterranean and the Black Sea. The Database started off with the registration of harbours located in the Aegean Sea and Cyprus, dating from Archaic to Byzantine times. Special emphasis is laid on the bibliographical update of the data forms of the harbour sites, as well as on the related references in ancient literature. The database enables the locating of these sites on a general map, where photographs, plans etc. are also archived. The principles of the database structure are briefly presented along with an example, that of the harbour of Phalasarna, among the harbours registered therein.

Download Full-text

NoRCE: non-coding RNA sets cis enrichment tool

BMC Bioinformatics ◽

10.1186/s12859-021-04112-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Gulden Olgun ◽

Afshan Nabi ◽

Oznur Tastan

Keyword(s):

Expression Patterns ◽

Target Prediction ◽

Enrichment Analysis ◽

Fruit Fly ◽

Relevant Information ◽

R Package ◽

Data Repository ◽

Biologically Relevant ◽

Gene Sets ◽

Data Files

Abstract Background While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint at a functional association. Results We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast. Conclusions NoRCE is a platform-independent, user-friendly, comprehensive R package that can be used to gain insight into the functional importance of a list of ncRNAs of any type. The tool offers flexibility to conduct the users’ preferred set of analyses by designing their own pipeline of analysis. NoRCE is available in Bioconductor and https://github.com/guldenolgun/NoRCE.

Download Full-text