Hologenomic methods to include host microbiota in genetic evaluations

• Title: "Hologenomic methods to include host microbiota in genetic evaluations", INRAE.
  • Doctoral student: Solène Pety
  • Affiliated unit: INRAE, UMR 1313 - GABI – GiBBs.
  • Supervision:
    • Andrea Rau (INRAE).
  • Doctoral school: École doctorale Agriculture, Alimentation, Biologie, Environnement, Santé.
  • Project duration: 2023–2026.

Project summary:

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. The host's genes and the environment influence the colonization, development, and functioning of various microbiomes, which in turn help shape the host's phenotypes. Additionally, the microbiome is also transmitted from mother to offspring, thus contributing to the non-genetic transmission of phenotypes. A major challenge for animal breeding is the development of integrative hologenomic approaches capable of jointly analyzing genomic data sets of the host and its microbiome, as well as the phenotypes and environmental parameters in which the holobionts evolve. Such methods are promising for improving the precision of prediction and understanding of traits involved in the adaptation of animals to agroecological production systems across different species of agronomic interest. This thesis project focuses on the development, optimization, and evaluation of integrative methods that allow the simultaneous consideration of genomic variability and metagenomic indicators of the host, as well as their interaction. This project will contribute to establishing clear guidelines for simulating realistic hologenomic data, constructing similarity matrices based on microbiota, and optimally combining genomic, microbiota, and multi-omics data in a wide variety of scenarios.