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Desbiez-Piat A, Ressayre A, Marchadier E, Noly A, Remoué C, Vitte C, Belcram H, Bourgais A, Galic N, Le Guilloux M, Tenaillon MI, Dillmann C. Pervasive G × E interactions shape adaptive trajectories and the exploration of the phenotypic space in artificial selection experiments. Genetics 2023; 225:iyad186. [PMID: 37824828 DOI: 10.1093/genetics/iyad186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 07/27/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023] Open
Abstract
Quantitative genetics models have shown that long-term selection responses depend on initial variance and mutational influx. Understanding limits of selection requires quantifying the role of mutational variance. However, correlative responses to selection on nonfocal traits can perturb the selection response on the focal trait; and generations are often confounded with selection environments so that genotype by environment (G×E) interactions are ignored. The Saclay divergent selection experiments (DSEs) on maize flowering time were used to track the fate of individual mutations combining genotyping data and phenotyping data from yearly measurements (DSEYM) and common garden experiments (DSECG) with four objectives: (1) to quantify the relative contribution of standing and mutational variance to the selection response, (2) to estimate genotypic mutation effects, (3) to study the impact of G×E interactions in the selection response, and (4) to analyze how trait correlations modulate the exploration of the phenotypic space. We validated experimentally the expected enrichment of fixed beneficial mutations with an average effect of +0.278 and +0.299 days to flowering, depending on the genetic background. Fixation of unfavorable mutations reached up to 25% of incoming mutations, a genetic load possibly due to antagonistic pleiotropy, whereby mutations fixed in the selection environment (DSEYM) turned to be unfavorable in the evaluation environment (DSECG). Global patterns of trait correlations were conserved across genetic backgrounds but exhibited temporal patterns. Traits weakly or uncorrelated with flowering time triggered stochastic exploration of the phenotypic space, owing to microenvironment-specific fixation of standing variants and pleiotropic mutational input.
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Affiliation(s)
- Arnaud Desbiez-Piat
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
- Université Montpellier, INRAE, Institut Agro Montpellier, LEPSE, Montpellier 34000, France
| | - Adrienne Ressayre
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Elodie Marchadier
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Alicia Noly
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institut of Plants Sciences Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Carine Remoué
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Clémentine Vitte
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Harry Belcram
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Aurélie Bourgais
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Nathalie Galic
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Martine Le Guilloux
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Maud I Tenaillon
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Christine Dillmann
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
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