Breeding Management Systems

Integrated Breeding Platform

The Breeding Management System (BMS) is a suite of interconnected software specifically designed to help breeders manage their day-to-day activities through all phases of their breeding programmes. From straightforward phenotyping to complex genotyping, it provides all the tools you need to conduct modern breeding in one comprehensive package.

The VSNi Group is a lead commercial and development partner of the Integrated Breeding Platform (IBP) providing statistical analytics, such as Breeding View, along with commercial and licensing resources.

 

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Setting the standard for statistical analysis in plant breeding

 

In modern plant breeding today, breeders have an increasing amount of data to analyse and need to make rapid decisions.

Breeding View (BV) links an easy user interface to a statistical analysis package allowing rapid phenotypic and genotypic analyses of field trial observations. Results include:

  • summary statistics
  • adjusted means of all traits
  • mixed model comparisons of genotypes and locations

all through a set of simple, visual and easy-to-use analytical pipelines and quality insurance measures.

“Breeding View enables easy and comprehensive data analysis and presentation of data very soon after completion of the study.  It facilitates the work of breeders who will focus on plant selection rather than data management and analysis of technical aspects.”  

— Dr Ibnou Dieng, Head of the Data Integration and Biometrics Unit,
Africa Rice Center


 

Analytical pipelines

These pipelines are presented as graphical workflows where you can choose to run the complete pipeline at once, or to run each separate element of the pipeline. Each element of each pipeline has a set of default statistical parameters which can be modified by the user before an analysis.

Single-site analysis – phenotypic analysis

 

Multi-site (genotype by environment) analysis – phenotypic analysis

 

Single trait (single environment) QTL analysis using external sources of data.

 

Results of each analysis are saved in a time stamped folder in your personal workspace or, for the phenotypic analysis, can be saved to the BMS database for later review or further analysis. The phenotypic analyses are fully integrated into the BMS so that data can be selected in the BMS and sent to Breeding View for analysis, and resulting means and summary statistics saved back to the BMS database, allowing database searches based on germplasm performance within and between locations.

QTL analysis with Breeding View

The BMS comes with a standalone QTL analysis package as part of the Breeding View statistical tool. Combine phenotypic, genotypic and linkage map information to identify potential quantitative trait loci (QTL) through simple and composite interval mapping. The QTL package creates a report with easy-to-interpret publication-ready graphics.

Quality assurance

A quality assurance step in the single-site analysis displays a list of potential outliers for each trait by environment combination and allows the user to re-run the analysis with specified outliers treated as missing values to verify the effect of these aberrant values on the conclusions of the study.