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 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 >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.