Section: Mathematical & Computational Biology
Topic: Agricultural sciences, Computer sciences, Statistics
Conference: JOBIM

Simulating transgenerational hologenomes under selection with RITHMS

Pety, Solène1, 2 orcid ; David, Ingrid3 orcid; Rau, Andrea2 orcid; Mariadassou, Mahendra1 orcid
1Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
2Université Paris-Saclay, INRAE, GABI, 78350, Jouy-en-Josas, France
3Université de Toulouse, INRAE, ENVT, GenPhySE, 31326, Castanet-Tolosan, France

Corresponding author(s): Pety, Solène (solene.pety@inrae.fr)

10.24072/pcjournal.666 - Peer Community Journal, Volume 5 (2025), article no. e142

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A holobiont is made up of a host organism together with its microbiota. In the context of animal breeding, the holobiont can be viewed as the single unit upon which selection operates. Therefore, integrating microbiota data into genomic prediction models may be a promising approach to improve predictions of phenotypic and genetic values. Nevertheless, there is a paucity of hologenomic transgenerational data to address this hypothesis, and thus to fill this gap, we propose a new simulation framework. Our approach, an R Implementation of a Transgenerational Hologenomic Model-based Simulator (RITHMS) is an open-source package. It builds upon simulated transgenerational genotypes from the Modular Breeding Program Simulator (MoBPS) package and incorporates distinctive characteristics of the microbiota, notably vertical and horizontal transmission as well as modulation due to the environment and host genetics. In addition, RITHMS can account for a variety of selection strategies and is adaptable to different genetic architectures. We simulated transgenerational hologenomic data using RITHMS under a wide variety of scenarios, varying heritability, microbiability, and microbiota transmissibility. We found that simulated data accurately preserved key characteristics across generations, notably microbial diversity metrics, exhibited the expected behavior in terms of correlation between taxa and of modulation of vertical and horizontal transmission, response to environmental effects and the evolution of phenotypic values depending on selection strategy. Our results support the relevance of our simulation framework and illustrate its possible use for building a selection index balancing genetic gain and microbial diversity and for evaluating the impact of partially observed microbiota data. RITHMS is an advanced, flexible tool for generating transgenerational hologenomes under selection that incorporate the complex interplay between genetics, microbiota and environment.

Published online:
DOI: 10.24072/pcjournal.666
Type: Research article
Keywords: Methodology (stat.ME), FOS: Computer and information sciences, Holobiont, Genotypes, Microbiota data, Simulation framework, Selection

Pety, Solène  1 , 2 ; David, Ingrid  3 ; Rau, Andrea  2 ; Mariadassou, Mahendra  1

1 Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
2 Université Paris-Saclay, INRAE, GABI, 78350, Jouy-en-Josas, France
3 Université de Toulouse, INRAE, ENVT, GenPhySE, 31326, Castanet-Tolosan, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
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Pety, S.; David, I.; Rau, A.; Mariadassou, M. Simulating transgenerational hologenomes under selection with RITHMS. Peer Community Journal, Volume 5 (2025), article  no. e142. https://doi.org/10.24072/pcjournal.666

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.mcb.100417

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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