A genetic method to infer ploidy and aberrant inheritance in triploid organisms

Polyploidy occurs naturally across eukaryotic lineages and has been harnessed in the domestication of many crops and vertebrates. In aquaculture, triploidy can be induced as a biocontainment strategy, as it creates a reproductive barrier preventing farm-to-wild introgression, which is currently a major conservation issue for the industry. However, recent work suggests that triploidization protocols may, on occasion, produce ‘failed triploids’ displaying diploidy, aneuploidy, and aberrant inheritance. The potentially negative consequences for conservation and animal welfare motivate the need for methods to evaluate the success of ploidy-manipulation protocols early in the production process. We developed a semi-automated version of the MAC-PR (microsatellite DNA allele counting – peak ratios) method to resolve the allelic configuration of large numbers of individuals across a panel of microsatellite markers, that can be used to infer ploidy, pedigree, and inheritance aberrations. We demo..., , , ### Title: A genetic method to infer ploidy and aberrant inheritance in triploid organisms

### Authors: Aurélien Delaval, Kevin A. Glover, Monica F. Solberg, John B. Taggart, François Besnier, Anne Grete Eide Sørvik, Johanne Øyro, Sofie Nordaune Garnes-Gutvik, Per Gunnar Fjelldal, Tom Hansen, Alison Harvey

### Upload date: 8 July 2024

1\. MAC-PR folder:

* MAC-PR_analysis.R: Main script used to perform MAC-PR and estimate ploidy.
* Scripts folder: Contains an additional script sourced by the main script.
* Genotypes folder: Contains raw data for MAC-PR, and curated data for ploidy assessment.
* Reference_dips_trips.csv: A curated GeneMapper dataset containing reference diploids and triploids.
* egg_genotypes_raw.csv: Raw GeneMapper data of salmon eggs, as an example of raw genotyping data to run MAC-PR analysis.
* eggs_MAC-PR_genotypes.csv: Resolved egg genotypes after MAC-PR, in full allele format for downstream pedigree and inheritance analysis.
* eggs_MAC-PR_genotype_categories.cs...