Complex Genetic Determinism of Male-Fertility Restoration in the Gynodioecious Snail Physa acuta

Overview

This repository contains data and code related to the study:
“Complex genetic determinism of male-fertility restoration in the gynodioecious snail Physa acuta”
(Preprint available here)

Male fertility in plants is often controlled by the interaction between mitochondrial and nuclear genes. Some mitotypes confer cytoplasmic male sterility (CMS), making the individual male-sterile, unless the nuclear background contains alleles called restorers, that suppress the effects of CMS and restore the hermaphroditic phenotype. Restorers in cultivated crops are often alleles with strong and dominant effect, but in wild plants, data often suggest more complex systems. Here, we characterized the inheritance and specificity of restoration in a new CMS model, the freshwater snail Physa acuta. We explored two different populations (i) a naive population i.e., without contact with CMS in the past 80 generations, (ii) a non-naive population, where CMS is present and largely restored. Although we found male fertility of individuals with CMS mitogenomes to be heritable in both contexts, this heritability was of a different nature depending on population history. In naïve populations not coevolved with CMS the background variation may include alleles that happen to act as weak quantitative modifiers of the penetrance of CMS, while in populations coevolved with CMS, selection may have favored, when such variants were available, the emergence of strong alleles with a dominant effect.

How to Use

Clone or download this repository to access the data and analysis files. To reproduce the results, open and execute the .Rmd file in a suitable R environment. See below for repository structure and details.

Layout

The repository is organized into the following files:

data/

Raw data collected during the experiments.

  • inbredlines.csv: Dataset from inbred lines experiments.
  • inbredlines_mothers.csv: Dataset on the maternal lineages used in the inbred lines.
  • G0.csv: Data on offspring from “G0” mothers, part of the HFR/LFR selection experiment.
  • G1.csv: Corresponding “G1” experimental individuals, part of the HFR/LFR selection experiment..

analysis/

  • analysis_inbredlines&HFRLFR.Rmd: Main analysis file. Contains all statistical procedures, data wrangling, figures, and interpretation for both the inbred lines and HFR/LFR experiments.

Figures:

Figures generated by the analysis are saved during RMarkdown execution and illustrate the patterns of fertility restoration across lines and populations.

miscellaneous/

protocols/

  • Our objective was to characterize, within both the naive and the non-naive backgrounds, genetic variation for the potential to restore male fertility in CMS mitotypes. We did this in two ways (i) first, we tested whether we could select for high versus low restoration potential within the naive population (hereafter, “selected lines” dataset) (ii) second, we produced inbred lines from both populations and characterized genetic variance in restoration potential among lines, specially aiming to identify lines fixed for either restorer or maintainer (i.e., non-restorer) alleles (hereafter, “inbred lines” dataset). In both cases, lines were of the N mitotype, and their restoration potential was evaluated by crossing them with either a K or a D snail and then evaluating the male fertility of the offspring.

study system/

  • Freshwater snails (Physa acuta), handling conditions: 25°C, 12/12 photoperiod using ground water changed at least once a week, and grinded boiled lettuce ad libitum as food.

software details/

  • R version and key packages: tidyverse, lme4, ggplot2, etc. See the .Rmd file for full session info.

Project Description

Authors:
Elpida Skarlou*, Fanny Laugier*, Kévin Béthune, Timothée Chenin, Jean-Marc Donnay, Céline Froissard, Patrice David
(*co-first authors)
Affiliation: CEFE, CNRS, Univ Montpellier, EPHE, IRD, France