GeneSys: a gateway into the world’s gene banksMarch 19, 2023
“Databases, databases, and more databases.”
These are the words Matija Obreza uses to describe the digital landscape that crop scientists enter when faced with the challenge of locating data and germplasm for their next project.
Obreza is head of genebank information systems at the Crop Trust, the only organization whose sole mission it is to ensure humanity conserves crop genetic diversity in genebanks, and to make it more accessible. Among other things, the Crop Trust works closely with the International Treaty on Plant Genetic Resources for Food and Agriculture to create a global information system for crop diversity.
Crop genetic diversity is currently housed in many different forms. Amidst the vast pipeline of global agribusiness, genetic diversity is stored across farms, fields and pastures (in-situ) . But it is also stored ex-situ: in genebanks, laboratories, glasshouses, museums and herbaria worldwide.
This long-term ex-situ form of diversity conservation is the focus of the Crop Trust, where Obreza leads the ongoing development of Genesys. This online portal enables genebanks to share information about their crop diversity with users around the world.
It also allows scientists and breeders to quickly search for germplasm, to query its availability, and even to initiate requests for material. Genesys now contains more than 4 million genebank accessions, around half of the estimated total number in the world. But for the Genesys team, this is only the beginning.
“Many genebanks already participate in Genesys, but that’s not enough,” says Obreza. “We would like all genebanks to become part of Genesys, and so ensure that users have access to the most comprehensive and up-to-date information, which eventually translates into the development of new crop varieties that are better suited to the changing needs of agriculture.”
Since Genesys aggregates data from multiple sources in its central database, the various approaches to data management followed by different genebanks pose a challenge, and every partnership demands a different solution, he explains. “We invest a lot in improving information systems at genebanks, so that they are comfortable sharing their data with the outside world.”
Shout out to the genebanks!
The strategy stresses the importance of meeting the needs of existing partner genebanks, saying that they deserve priority attention. “It is crucial that we address the needs of our partners,” says Obreza, “as they are in the best position to recommend Genesys to other genebanks. They wouldn’t do that if Genesys doesn’t work for them first.”
Genesys is a powerful tool for genebanks to share their data without losing ownership or autonomy. Many Genesys features are specifically designed to help genebanks in their work, such as tools for data cleaning and validation, or for embedding their Genesys database directly into their own websites, saving them time and money.
“Over the years we’ve developed many advanced tools that are not yet fully utilized by genebanks. We aim to change that with additional documentation and tutorials.”
Users of crop data, rejoice!
Genesys considers itself an interface between providers (genebanks, genebank curators, data managers) and users (breeders, scientists, etc.) – of both germplasm and data. As such, their strategy also focuses on strengthening ties with the plant breeder community in order to better understand their needs.
Earlier this year, Obreza gave a presentation about Genesys to a room full of genomic scientists at DivSeek International Network’s PAG30 workshop. Training and networking events like this help to raise awareness of Genesys within the plant genetic resources (PGR) community and promote its use.
They also provide a platform for community discussion between users of plant genetic data (like breeders and scientists) and those at the forefront of developing information systems for those data.
Ultimately, the more breeders use Genesys to access data and germplasm, the better our global scientific community will become at developing future-proof crop varieties. To this effect, Genesys also places emphasis on developing features that meet the demands of their community of data users. While of course never forgetting that genebanks need to be happy first of all.
Written by: Kiri Marker
Corresponding authors: Matija Obreza, Luigi Guarino