Adaptability, Origin and Genome Evolution of an emerging plant-devastating nematode

• Applicant: Dr. Sebastian Kiewnick
• Subject Area: Plant Breeding and Plant Pathology
• Term: from 2019 to 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 431627824

Feeding more than 9 billion people by 2050 while limiting the impact of agriculture on the planet will be one of the major challenges the humanity will have to face. Plant-parasitic nematodes are responsible for agricultural losses estimated at >100 billion € every year. The most damaging species are the root-knot nematodes (or Meloidogyne). These obligatory root parasites have a worldwide distribution with a wide host range. For control, mostly cultivars bearing nematode resistance genes are used. However, for Meloidogyne enterolobii an emerging species, no resistance is available. Described for the first time in Europe in 2008 (in Switzerland) and has been detected in France and in Portugal. As no resistance is available in the main crops in Europe, the only solutions following infestation by M. enterolobii are either to deploy non-host plants or use black fallow. The origin of M. enterolobii, its invasion routes to Europe, its potential to adapt to new plants and environments and to spread are still unknown. Thus, it is important to gain more insights on these aspects to guide future policies and control methods. We will use comparative analyzes at the whole genome level and adaptation experiments to tackle these different points. The two partners of the project (INRA, France and JKI, Germany) have recently sequenced and assembled the genome of the M. enterolobii strain that was identified in Switzerland in 2008. As a preliminary step in this project, we want to improve the quality and completeness of the genome assembly to produce the best possible reference genome for further comparative analysis. We will then use 2nd and 3rd generation sequencing to decode the genomes of a diversity of M. enterolobii isolates from different crop plants around the world and compare them to the reference Swiss strain of M. enterolobii. We will identify both short-scale (SNPs) and longer scale (inversions, translocations, movements of mobile elements) variations at the whole genome level between the different collected isolates and the reference genomes. Based on the identified variations we will use both phylogenomics and population genomics to classify the isolates and determine phylo-geographic relationships between the isolates. In parallel, we will assess several biological traits such as the range of compatible plants and the ability to adapt to poor or non-host plants. Because the only acceptable option to control M. enterolobii is to deploy non-host plants, it is necessary to assess the ability of the different strains to adapt to bad host or new hosts. By conducting association studies between genomic variations and biological traits we aim at identifying genome regions and markers of isolates associated to these traits. The data and information generated in the framework of this project will be of high value in support of risk assessment and to drive future policies aiming at preventing the spread of this emerging plant pest in Europe.

• DFG Programme: Research Grants
• International Connection: France
• Cooperation Partner: Dr. Etienne Danchin