Genesys rolls out the Subsetting Tool

8 May 2023

You can now create your own subsets of accessions by using the climate and soil variables of your choice.

The Subsetting Tool, developed by the Alliance of Bioversity International & CIAT and the International Center for Agricultural Research in the Dry Areas (ICARDA), allows Genesys users to use combinations of abiotic factors to create subsets of accessions that can grow under specific environmental conditions. Think of it as the Do-It-Yourself method for subsets with particular adaptations.

The tool considers only accessions that, for starters, are (obviously) published in Genesys, and that include the coordinates of their collecting site in the passport data. You can then use 20 agroclimatic indicators related to the site of collecting to do the subsetting, grouped into six categories: drought, flooding, heat, photoperiod, soil and (if you’re lucky) additional crop-specific indicators.

We will use as an example a breeder who wants to find 10 to 15 accessions of beans that are tolerant to high rainfall and low temperatures to include in their breeding program. Searching Genesys for the genus Phaseolus yields about 160,000 accessions conserved at over 97 genebanks. Where does our breeder go from there?

Well she can further narrow the search down to lima beans (Phaseolus lunatus). That doesn’t help too much because now she’s at about 8,200 accessions in 37 different genebanks. This is precisely where the Subsetting Tool comes in: when the search is narrowed down, but not quite enough to make a decision on what to select. 

Out of those 8,200 lima bean accessions, around 4,200 have the geographical coordinates of their collecting sites included in their passport data. Luckily, each location in the world has a set of climatic and soil data associated with it, thanks to CLIMAP.

This ecographical dataset provides data on consecutive dry days, total precipitation, average minimum temperature, and so on for all the locations in the world (Figure 1).

image.pngFigure 1

Every accession with coordinate data in Genesys is then associated with the particular climatic and soil parameters at that location.

The tool then groups the accessions according to their similar climate and soil conditions. The breeder gets to specify which of the variables to consider in order to create a subset relevant to her needs, and also how many subsets the tool should create.

What the breeder cannot control however, is the number of accessions that this tool yields. The set highlighted in yellow (Figure 2) is the one she is interested in: accessions collected from areas with high average temperatures and extremely low average precipitation. This set, however, still contains a lot of accessions: 1,200 of them.

image.pngFigure 2

But don’t worry. The tool also provides different ways to get to a more manageable number, and also the means to directly request the accessions from the genebanks through Genesys (Figure 3).

image.pngFigure 3

Interested? If you are curious to test the tool out for yourself and see how it works, here’s how you can access it:

Tip: It is important to use passport data filters to reduce the analysis from over 4 million accessions published in Genesys to a few thousand before running the tool, in order not to fry your computer.

  1. Navigate to Passport data in Genesys.

  2. Specify the filters.

  3. Apply the selected filters.


When you’re satisfied with the constraints on the accession passport data, then you:

4. Open the Subsetting tool tab.

5. Expand the categories with the indicators of interest.

6. Select the indicators.


7. Select how many subsets you want to generate.

8. Examine the results in a table.

9. Examine the results through charts.

10. Select the subset that fits your criteria. For example, set 1 below has the highest total precipitation, and the lowest number of consecutive dry days.


11. Select a more manageable number of accessions using one of the three options.

12. In the case of a Random Selection or Core Collection, select the total number of accessions to generate.

13. From the generated accessions, select the ones you want to add to My List to request from the genebank(s).


The tool provides descriptive statistics and charts for each subset to help make a more informed decision. 

The tool is accessible only to registered Genesys users, so make sure to create your Genesys account if you haven’t done so, and be logged in while applying the steps of our detailed user guide. The tool offers two modes for selecting indicators: basic and advanced. Our detailed guide is where you can get more information on the advanced mode.

We thank the development team at Alliance of Bioversity International & CIAT and the International Center for Agricultural Research in the Dry Areas (ICARDA) for their dedication and hard work over many months that resulted in making this tool a reality.

This work would not have been possible without the support of the CGIAR Genebank Platform, all contributors to the CGIAR Trust Fund, and all the donors of the Crop Trust Endowment Fund.

You may also be interested in