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Application 2.2.6 Tool 8.2 Molecular Breeding Design Tool

The Molecular Breeding Design Tool (Functionality and linkages within the Integrated Breeding Workbench)

Figure 1: Workflow for the Molecular Breeding Design Tool and its linkages to other Modules of the IB WorkBench

Functionality of the Molecular Breeding Design Tool:

Read input files consisting of genotype data, map data, results of QTL mapping – This functionality currently works on reading in flat files, but eventually will be integrated to read from the database(s) underlying the IBWB. The files read in currently are the linkage map and the genotyping data file (these two are mandatory). The other two files, the QTL data and the phenotyping data file are optional. A validation step will take place to determine the marker system in use as well as other checks such as missing data, duplication of markers or genotypes, consistency of the linkage map etc.

Display linkage and QTL maps as well as graphical genotypes – The QTL and linkage map information will be displayed in the graphical view as coaligned bars. The genotyping information is then displayed in the form of heat maps.

Selecting parental germplasm – The donor and recurrent parents may be selected based on (a) presence or absence of traits in potential parents (b) level of polymorphism among the selected lines or (c) analysis of background similarity via similarity matrix

Track information throughout the backcrossing process – This functionality will allow one to manage and visualize data collected over several segregating populations. It will also use the information from previous generations of the MAB program.

Create lists/input files for Laboratory Information Management System (LIMS) – This will allow researchers to identify the unscreened markers in a region of interest and provide the input to the LIMS system for screening of markers on selected lines / accessions.

Design target genotype by dragging and dropping alleles from donor to target genotype – The creation of the ideal genotype by dragging and dropping alleles therefore allowing one to select foreground/background markers (possible regions for introgression from donor to recipient). This may also be done by selection of flanking markers for multiple QTLs.

Decision support tools for Backcrossing projects – Third part tools such as Popmin that would aid in calculating the population size and the number of backcross generations. It would also calculate percentage recovery of the recurrent genome.

Figure 2: Annotated screenshot of the available prototype

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