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Hologenomic methods to account for host microbiota in genetic evaluations

• Dr. Andrea Rau (andrea.rau@inrae.fr; INRAE GABI, Jouy-en-Josas)
• Dr. Mahendra Mariadassou (mahendra.mariadassou@inrae.fr; INRAE MaIAGE, Jouy-en-Josas)
• Dr. Ingrid David (ingrid.david@inrae.fr; INRAE GenPhySE, Toulouse)

Keywords: holobiont, hologenomics, genomic prediction, transmissibility, simulation, biostatistics

Animals and their microbiota form a composite organism, called the holobiont, which can be considered as the ultimate unit on which evolution and selection act. Host genes and the environment influence the colonization, development and functioning of various microbiota, which in turn help shape host phenotypes. In addition, the microbiota is also transmitted from mother to offspring (for example, during birth, breastfeeding and maternal care in mammals), thus participating in the non-genetic transmission of phenotypes. A major challenge for animal breeding is therefore the development of integrative hologenomic approaches capable of jointly analyzing host and microbiota genomic data, as well as the phenotypes and environmental parameters in which holobionts evolve. Such methods are promising for improving prediction accuracy and our understanding of traits involved in animal adaptation to agroecological production systems in various species of agronomic interest. In this context, this thesis project focuses on the development, optimization, and evaluation of integrative methods to simultaneously take into account host genomic variability and metagenomic indicators, as well as their interaction. This project will contribute to establishing clear guidelines for the simulation of realistic hologenomic data, the construction of microbiota-based similarity matrices, and the optimal combination of genomic, microbiota, and multi-omics data in a wide variety of scenarios.