Software synergies: reimagining the future of crop breeding

May 3, 2023

 

Across almost all industry and research domains, it is becoming increasingly evident that the faster we can share data, the faster we can collaboratively invent new solutions and products. Of course, this is also true for the research and development of future-proof crop varieties.

This is why the people behind Genesys and Germinate have formed an alliance, and are working together to create greater synergy between their software, both of which have earned their place as essential tools in the crop science community.

Genesys is an online data portal for agricultural genebank accessions. Developed by the Crop Trust, the website stores passport and basic characterization data for more than 4 million genebank accessions – around half the estimated total number worldwide.

It’s become an indispensable tool for breeders and researchers alike. An eggplant breeder hoping to create more high-yielding, drought-tolerant strains, may begin her search for seed on Genesys. There, she can use search filters to look for accessions of a particular variety, provenance, or biological status (e.g. crop wild relatives or landraces). What’s more, once she’s identified the germplasm she is interested in, she can query its availability and even request it directly from the genebank.

But how does she know which seeds to request? While Genesys stores important passport data on all accessions, this information. For that, she is going to need experimental data.

That’s where Germinate comes in. This software helps crop breeders to analyze, visualize, and share experimental data from their pre-breeding trials. Germinate offers the possibility for breeders around the world to share data with one another, so that previously isolated efforts to produce better cultivars can turn into a collective global effort.

Or at least, in theory. “Germinate provides researchers and breeders with a convenient way to visualize and share large volumes of experimental data,” explains project lead Paul Shaw, from the James Hutton Institute (JHI) in Scotland. “But the ultimate goal is to point people in the direction of actually getting hold of the underlying germplasm which exhibits characteristics of interest.”

This brings us back to Genesys. “The breadth and depth of data that Germinate provides complements the characterization data already held in Genesys, making a synergistic pairing,“ says Shaw. “Researchers can go straight to Genesys to find germplasm based on passport or characterization data, and they can then explore the larger volumes or trials data stored in Germinate databases as the means to identify interesting germplasm.”

As luck would have it, the teams behind Genesys and Germinate are old bedfellows. Matija Obreza, head of Genebank Information Systems at the Crop Trust, explains: “The Crop Trust has encouraged and supported the use of Germinate for publishing the results of pre-breeding activities of its past projects, which has resulted in several new databases, from chickpea to barley. This collaboration with JHI continues in the current BOLD project.”

Obreza and Shaw envisage a future where crop breeders can move seamlessly between Genesys and Germinate. “At the moment, Germinate stores simple web links to Genesys for plant lines, so a user can jump between systems,“ explains Shaw. “But what we would really like to see is for Germinate users to be able to add germplasm they have found to a shopping cart within Germinate.”

“This shopping cart could then tell you if stocks are available through Germinate interacting with Genesys behind the scenes,” he says. “Ideally, users could then post requests for germplasm directly to genebanks for consideration and fulfilment, without ever having to switch between platforms.”

There’s scope for synergies on the Genesys side of things too, according to Obreza. Future versions of Genesys may be able to query Germinate on whether it contains any additional information on specific lines, which it could then point its users to.

“We have already started discussing how we can improve the links between our tools, which really would give any users of germplasm a great way to explore data and find exactly what they are looking for,” he says.

“The challenge for Genesys would be to link to the many different breeding information systems in use today,” says Obreza, “but luckily there is the Breeding API (BrAPI) standard, which most of them, including Germinate, implement.”

 

Written by: Kiri Marker

Back