Recombinant Inbred Line (RIL) Summary

Provides functionality for summarizing Recombinant Inbred Lines (RILs) including the following:

  1. Tabular matrix which summarizes how many RILs are available for each species combination. This is particularly helpful if you have a cultivated and associated wild species for a single genus.
  2. Listing of all RILs for a specific species combination including information about the number of F2 families for each F-generation.
  3. ChadoField for RIL pages which summarizes information about the number of F2 families for each F-generation.

Functionality

The RIL summary matrix can be found at [mytripalsite.com]/germplasm/summary/[genus]. This is what it looks like for a fake Tripalus example.

../_images/rilsummary.png

When you click on any of the cells in the RIL summary matrix you are taken to the following listing:

../_images/rillist.png

The details for a given RIL can be summarized on the RIL Tripal Content Page using the field provided by this module.

../_images/rilfield.png

Adding RILs to the summary

  1. Create a Recombinant Inbred Line with the name of your RIL population (e.g. TR-01).
  2. Create a germplasm line (type doesn’t matter; suggested Generated Germplasm (Breeding Line)) with the name of the original cross giving rise to the RIL population (e.g. 1234S) and add a relationship: TR-01 is_selection_of 1234S.
  3. Create parents for the Breeding cross (type does not matter) and related them using the is_maternal_parent and is_paternal_parent relationship types (e.g. CDC FRED is_maternal_parent_of 1234S and AABC is_paternal_parent_of 1234S).
  4. Each subline for a RIL (i.e. TR-01-123) should be of type stock_type:F2.

Adding the summary to RIL pages.

  1. Go to Admin > Structure > Tripal Content Types > Recombinant Inbred Lines > Manage Fields.
  2. Add a new field where the type is Germplasm RIL Summary.
  3. Make sure it is not disabled on the Manage Display tab.