Building a bioinformatics pipeline to predict the genomic shift of cultivated and wild fruit trees in response to climate change

PhD Thesis Co-supervised by CNRS, Université Grenoble Alpes, IRD.

  • Title : "Construction of a Bioinformatics Pipeline to Predict the Genomic Shift of Cultivated and Wild Fruit Trees in Response to Climate Change," CNRS & Université Grenoble Alpes & IRD;
    • PhD Student: Maxime Criado;
    • Affiliated Unit: INRAE, GQE (Génétique Quantitative et evolution);
    • Co-supervision:
      • Olivier François, Université Grenoble Alpes, TIMC (Recherche Translationnelle et Innovation en Médecine et Complexité);
      • Yann Bourgeois, IRD, Diade (Diversité, Adaptation et DEveloppement des plantes);
    • Doctoral School: SEVE, Université Paris-Saclay


To mitigate the impact of climate change on food production, it is essential to tap into the diversity of cultivated crops and their wild relatives. This is especially true for fruit trees planted in orchards years ago under different climatic conditions. The doctoral candidate will combine available genomic, climatic, and phenotypic data with population genomics, statistics, and modeling to provide an overview of the genomic compensation of fruit tree crops and their wild counterparts in response to climate change. They will construct a reproducible analysis pipeline using apple as a training model and then optimize it using other fruit trees studied in the context of a project by the BNP Foundation (FRUITRESCUE), including apricots, peaches, grapes, and olives. The project will provide (i) a list of varieties already available in orchards that can be used for future breeding programs to meet the food production requirements in the context of climate change, (ii) a bioinformatics pipeline for genomic compensation analyses that will be made accessible to the public. The project involves an interdisciplinary consortium of experts interacting with project partners from AgroDiv, who are exploring related issues in livestock. The project will promote the creation of scientific networks to discuss tools and concepts for evaluating genomic shifts in crops and livestock, with their commonalities and specificities.

See also

Modification date : 10 April 2024 | Publication date : 28 July 2023 | Redactor : AgroEcoNum