Edeline Gagnon

Project title: A museomics approach  to study the diversity and loss of disease resistance genes in a crop wild relative of tomato (Solanum chilense L.)

Host Institution: Technical University of Munich (TUM)

Host Supervisor: Dr Remco Stam

Co-host Institution: Technical University of Denmark (DTU)

Co-host Supervisor: Dr Gabriel Renaud

Summary project: Unlocking the genetic diversity of Crop Wild Relatives (CWRs) is crucial to improve crop resistance to abiotic and biotic stress, but CWRs are at the risk of losing genetic diversity due to anthropogenic pressures and climate change. Recent advances in high throughput sequencing now facilitates sequencing of CWR herbarium collections, which are more widely distributed than germplasm collections and contain historical specimens from extinct populations. Through target enrichment capture, they represent a quick way to screen species and populations for large numbers of loci, such as polygenic disease resistance genes. Sequencing historical herbarium and germplasm collections of CWRs can be used to develop time-series analyses, to gain a more direct and realistic understanding of how these genes evolve in the face of habitat loss. Using Solanum chilense, a well-studied CWR of tomato in germplasm collections, I am using a bait set designed for population genomics and the study of disease resistance genes to answer the following questions: (1) Are germplasm collections representative of the genomic diversity present in the entire population of S. chilense? (2) Are there signs of loss of genetic diversity in populations of S. chilense in the past 70 years due to habitat loss? This will be achieved by studying contemporary field-collected samples alongside historical collections from both herbarium and germplasm collections.