On Thursday 15th December, around 300 people from academia and industry gathered in Orion for the 1st WURomics Symposium “Technology-driven innovation for plant breeding”, bringing up to date with the latest scientific developments and the opportunities to stimulate innovation in both fundamental and applied science and in industry. The Symposium was organized by Wageningen UR (Bioscience) and generously sponsored by Shared Research Facilities (CAT-AgroFood), EPS Theme 4 and the main sequencing providers (Bionano Genomics, Illumina, PacBio and 10x Genomics).
The Symposium started with a presentation by Jaroslav Dolezel, director of the Center of Plant Structural and Functional Genomics at the Institute of Experimental Botany in Olomouc (Czech Republic). His lab is a worldwide reference to study structure, evolution and function of complex plant genomes with long tradition on innovating protocols for flow cytometry and recently optical mapping. He provided an excellent overview on the progress to characterize plant genomes using complexity reduction approaches (e.g. chromosome sorting), instead of whole genome sequencing. Also, Jaroslav showed the promising results on improving genome assemblies using Bionano Genomics.
The next presentation was by Giovanni Giuliano, professor at ENEA, Rome (Italy) that presented the latest sequenced genome from the Solanaceae family: eggplant. Using a combination of Illumina and Bionano Genomics, an international consortium has unraveled key evolutionary events and new insights in economically important traits (e.g. fruit ripening) in the genome of this appreciated vegetable when it was compared to the other sequenced members within this important family (potato, tomato and pepper).
Next speaker was professor Paul Schulze-Lefer, head of Department of Plant Microbe Interactions at MPI for Plant Breeding, Cologne (Germany). His pioneering work on plant metagenomics is bringing light at the complex interactions that microbes establish with plants both at the rhizosphere as at the phyllosphere. During his inspiring presentation, he showed some of the mechanisms in which plants establish intimate associations with microbial communities and how the plants are able to discriminate between beneficial and pathogenic microbes. Interestingly, Paul is using the analogy between human gut and plant root as specialized organs for nutrient mobilization and how similarly in both systems microbes interact with the host.
Professor Toni Granell from the Plant Genomics and Biotechnology lab at IBMCP in Valencia (Spain) gave an overview on fruit quality using tomato as model system. Toni works in establishing links between what makes different each type of tomato from each other and the underlying genomic diversity, using a combination of different omics technologies (mainly metabolomics and transcriptomics). He also showed the first steps in the Traditom project, to assess genetic diversity in traditional tomato varieties with the goal to improve them so they remain attractive to farmers and consumers.
The next speaker, Korbinian Schneeberger, Group leader at Department of Plant Developmental Biology in MPI for Plant Breeding Research, Cologne (Germany) broadened this idea to associate phenotypic diversity with differences at the genome level, using an evolutionary comparative genomics approach. Korbinian advocated to intensify efforts in order to obtain full-length reference genomes to facilitate downstream bioinformatics comparisons, by taking advantage of the recent technological breakthroughs on sequencing technology (PacBio, Illumina and Bionano Genomics).
In the last session, professor Klaas Vandepoele from the Department of Plant Biotechnology and Bioinformatics at Ghent University (Belgium) explained the advantages of integrating large-scale omics datasets for comparative sequence and expression analyses to understand the mechanisms controlling developmental switches. Klaas showed some examples of integration of transcription factors and cis-regulatory elements into gene regulatory networks and predict new genes involved in relevant processes.
The Symposium concluded with professor Barbara Gravendeel, who has a joint Biodiversity Chair at the University of Applied Sciences Leiden and Naturalis Biodiversity Center in Leiden. She gave a fascinating lecture, opening the door to musea and the valuable specimens there waiting to tell an amazing story and maybe helping to answer some of the current world problems. Barbara showed the possibilities and challenges of the Ancient DNA lab she supervises, an ultra-clean facility for DNA extractions on very old specimens (e.g. mammoths, tomatos, tulips) and how using sequencing information we are able now to understand the impact of human on the evolution of domesticated species.