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Full-factorial breeding experiment with lake char (Lake Geneva, winter 2017/2018)

Citation

Garaud, Laura et al. (2022), Full-factorial breeding experiment with lake char (Lake Geneva, winter 2017/2018), Dryad, Dataset, https://doi.org/10.5061/dryad.0p2ngf23r

Abstract

We sampled 16 wild lake char (Salvelinus umbla) and used their gametes to investigate the genetic consequences of different mating scenarios. A full-factorial breeding was used to separate additive genetic from maternal environmental effects, and embryos were raised singly after sublethal exposures to a pathogen, a common pollutant, or water only. In all treatment groups, embryo development was strongly reduced with increased genetic relatedness between the parents. Contrary to predictions of ‘good genes’ sexual selection, pathogen tolerance of offspring declined with increasing coloration of their fathers.

Determination of inbreeding and kinship coefficients: All 10 males and 4 of the 6 females were used in a parallel study that included sperm competition experiments (Nusbaumer et a. 2021). These 14 parents had been prepared in one library for ddRAD sequencing on 2 lanes on an Illumina HIseq 2500 (see de Guttry et al. 2022 for the corresponding 14 gzipped .fastq of these individuals). The remaining 2 females were later genotyped in a different library but again on an Illumina HIseq 2500. After demultiplexing, the 16 individuals were processed together using stacks 2.53, and with the resulting filtered VCF file estimations of kinship and inbreeding have been done. For each individual, the fastq files of the 2 sequencings lanes (2018/2019), or of the replicates within the same library (2021), were merged after demultiplexing using process_radtags (Stacks 2.53). The bash and R scripts are provided. There are no legal or ethical considerations regarding the above-mentioned data.

Methods

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Garaud L., Nusbaumer D., de Guttry C., Ançay L., Jacquet S., Lasne E., Wedekind C. 2022 Genomic compatibility excels possible good genes effects of sexual selection in lake char. bioRxiv. (doi:https://doi.org/10.1101/2022.03.03.482834).

Usage Notes

Nusbaumer D., Garaud L., de Guttry C., Ançay L., Wedekind C. 2021 Sperm of more colorful males are better adapted to ovarian fluids in lake char (Salmonidae). bioRxiv. (doi: https://doi.org/10.1101/2021.10.02.462848).

de Guttry C., Nusbaumer D., Garaud L., Ançay L., Wedekind C. 2022 Inbreeding and kinship coefficients of parents of sperm competition experiment with lake char (Lake Geneva 2017/18). Dryad Digital Repository. (doi:10.5061/dryad.rn8pk0pct).

Funding

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Award: 31003A_182265