DOI: 10.5061/dryad.931zcrjv1
title: A genetic method to infer ploidy and aberrant inheritance in triploid organisms

description: 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 demonstrate an application of the approach using material from a series
 of Atlantic salmon (Salmo salar) breeding experiments where ploidy was
 manipulated using a hydrostatic pressure treatment. We validated the
 approach to infer ploidy against blood smears, finding a &gt;99%
 agreement between these methods, and demonstrate its potential utility to
 infer ploidy as early as the embryonic stage. Furthermore, we present
 tools to assign diploid and triploid progeny to families and to detect
 aberrant inheritance, which may be useful for breeding programmes that
 utilize ploidy manipulation techniques. The approach adds to the ploidy
 verification toolbox. The increased precision in detecting ploidy and
 inheritance aberrations will facilitate the ability of triploidization
 programmes to prevent farm-to-wild introgression.
description: ### 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.csv: Resolved egg genotypes after MAC-PR,
 in a genotypic category format for downstream ploidy analysis. *
 parr_MAC-PR_genotypes.csv: Resolved parr genotypes after MAC-PR, in full
 allele format for downstream pedigree and inheritance analysis. *
 parr_MAC-PR_genotype_categories.csv: Resolved parr genotypes after MAC-PR,
 in a genotypic category format for downstream ploidy analysis. *
 parr_bloodsmears.csv: raw parr bloodsmear data used to validate the MAC-PR
 ploidy assessment. 2\. tripFAP folder: * tripFAP v1.92.xlsm: Family
 Analysis Program, with information on how to run the program, tabulated
 with Atlantic salmon parr genotypes. 3\. Mismatch script folder: *
 script_check.R: Main script used to identify types of inheritance
 aberrations (i.e. mismatches between parent and offspring genotypes) *
 Scripts folder: Contains additional scripts sourced by the main script. *
 offspring_genotypes.csv: genotypes of offspring determined by MAC-PR, with
 family assignment information (determined by tripFAP) *
 parents_genotypes.csv: genotypes of the parents. Three dams (M1-M3) and
 one sire (M13). * genotypes_comments_baseshift.csv: Output file generated
 by script_check.R Note: R scripts were written in version 4.2.2 (R Core
 Team (2022). R: A language and environment for statistical computing. R
 Foundation for Statistical Computing, Vienna, Austria. URL
 [https://www.R-project.org/](https://www.R-project.org/).)