Visualising QTLs

In this Use Case, we will visualise wheat QTLs from Cheng et al. 2024 (https://doi.org/10.1038/s41586-024-07682-9).

Step 1: Locating the QTL dataset

The dataset containing the QTLs is called Triticum aestivum - IWGSC_RefSeq_v1.0 - QTL - Watkins natural population GWAS - Cheng 2024.

Use the Search Bar in the Explorer tab to find the dataset more easily.

Step 2: Loading the QTL dataset

Click the black plus icon to the left of the dataset name to show the available chromosomes within the dataset.

Click the green plus button to the left of the chromosome of interest. Once the chromosome is loaded, the plus button will change to a minus button which can be used to remove the dataset from the view.

The QTLs should now be displayed on the right hand side of the chromosome axis. By default the QTLs within the dataset are the same colour.

QTLs defined by a single position are shown as a diamond while QTLs defined as an interval are displayed as a rectangle spanning the interval.

Step 3 (Optional): Selecting traits of interest and colour coding by trait

Click on the View tab in the left panel and click the Trait sub-tab. By default, all traits become deselected.

Select traits of interest by checking the box to the right of each trait. Alternatively, check the Show / Hide QTLs of all Traits box to view all traits.

Each trait is shown in a different colour.

Step 4 (Optional): Label the QTL

Click on the QTL (shown as a diamond or rectangle to the right of the axis) to add an arrow to the left of the axis.

Click on the arrow to add the label corresponding to the QTL name.