Molecular Breeding Design Tool (MBDT)
The design tool has the following functions:
- Assist breeders in selecting parental germplasm based on phenotypic data, known adaptation, economic importance.
- What traits are present and which are absent in potential recipients?
- Find and display known genes and QTL available for supplying the missing traits.
- List potential donors for missing traits.
- Develop and display trait maps
This function relies heavily on integration and assimilation of external knowledge and information. Initially the application interface should facilitate appropriate queries, but even then most results are likely to come from external analysis and the interface should enable capture of the information from that external analysis.
- Verify and display genotypic and trait association data
- Check availability of genotyping data for potential recipients and donors.
- If not available, formulate lists of germplasm and required marker analysis and pass the information to the Molecular LIMS for field and lab requests.
- Display graphical genotypes and known trait associations for potential recipients.
- Display genotype and trait association information on potential donors.
- Analyse compatibility between donors and recipients
- how donor and recipient regions
- Choose markers (exact or flanking) for important regions. These must be polymorphic between donors and recipients, as close as possible to genes of interest, and should mark regions for introgression from donors or specific regions for retention of genotype in recipient germplasm.
- Identify potential linkage drag
- Analyse background similarity via genetic distances of coefficients of parentage.
- Select background markers, polymorphic between recipients and donors and suitably spaced over the genome.
- Select recipient and donor germplasm, design crosses and pass crossing lists to the Molecular LIMS for making crosses.
This function will benefit substantially from integration of simulation tools like QULine to pick crossing strategies, population sizes and most compatible parents. However this will not be attempted in year 1 of the use case development.
The MBDT has two main display formats, one for trait maps and one for displaying genotyping and trait association data for specific recipients and donors. The first has a mapping flavor and technology could draw heavily on the CMTV, while the second is a graphical genotyping tool which also lies at the heart of the third component - MOSEL.