The genetics of flowering: a new database
2/2/16

The database developed by the Laboratory of Plant Physiology at the University of Liège is not only an educational tool, but also a valuable resource for researchers, in a field where knowledge is growing exponentially. It is comprised of fully ‘clickable’ snapshots allowing users to access the underlying information. On the website, they can also find all the references of the scientific articles (currently 1646!) that have contributed to this data, with direct links to the publications.

The Laboratory of Plant Physiology at ULg has been specialising in the study of flowering for several decades. “Our diet is mostly based on the availability of fruits. For instance, flour, which is obtained from wheat grain. The grain of wheat is a fruit. So if plants don’t flower, there’s no fruit”, Professor Claire Périlleux, director of the laboratory, reminds us. While flowering is essential to the human diet, controlling this process is just as important. “If a lettuce flowers, it can’t be sold anymore”, explains the researcher. Owing to its central role in the preservation and evolution of plant species, flowering, which lies at the basis of reproduction, is also key to the stakes of biodiversity.

“Flowering began to be investigated from a genetic point of view in the 1990s, based on the Arabidopsis thaliana model”, continues Professor Claire Périlleux. Nicknamed the ‘white mouse of plant biology’, this plant had its genome entirely sequenced in 2000. From this moment on, it served as a gateway for many genetic research in flowering. “A fundamental discovery concerning this species often opens the door to equally fundamental discoveries in other species. For instance, many Asian teams are working on rice. And up until now, the majority of data concerning Arabidopsis thaliana has improved knowledge about the flowering of rice. But this is also true for tomato, potato, etc.”

Arabidopsis thaliana

1646 articles in just a few clicks

Over the years, knowledge in the genetics of flowering has grown exponentially thanks to this key model. “For people who are starting out in this field, the subject has become very difficult to deal with. Researchers write reviews several times a year. We also use an increasing number of schemes – known as snapshots – to better visualise this mass of data and keep an overview”, explains Professor Claire Périlleux. Confronted with this information management problem while doing his PhD at the Laboratory of Plant Physiology, Frédéric Bouché, who is also passionate about IT and graphics, set up his own database. “We realised that what he was doing could be very useful, not only for the researchers of the laboratory who didn’t necessarily find it easy to manage and represent the literature, but also for the rest of the scientific community”, continues Claire Périlleux. Frédéric Bouché then met Guillaume Lobet, an FNRS postdoctoral researcher, who was also passionate about new technologies. Together they decided to transform this database into a website called the ‘Flowering Interactive Database’ [FLOR-ID]. “This database contains approximately 1646 scientific articles. The interactive format allows the information to be easily accessed.”

The snapshots are entirely ‘clickable’ both as regards the listed genes and the lines that show the interactions between these genes. The website also provides all the references of the scientific articles that contribute to this data, with direct links to the publications. “We make sure that the information is easy to extract, so that researchers can re-use it in their own analyses and presentations. This is a real time-saver”, Guillaume Lobet points out. “It’s also possible to query the database regarding a specific gene”, Claire Périlleux adds. These different entries and levels of complexity allow students and senior researchers alike to tailor its use to their needs. “We offer pre-digested information but this does not mean the reader doesn't need to think”, Professor Périlleux underlines. In fact, these shortcuts to knowledge leave more time and availability for the most inventive part of research.

(1) FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana, in Nucleic Acids Research.    

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