Differentiating diploid and triploid individuals using single nucleotide polymorphisms genotyped by amplicon sequencing

Delomas, Thomas A.

doi:10.1111/1755-0998.13073

Cited by 13 publications

(18 citation statements)

References 27 publications

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“…This would be especially beneficial if a study is performed on a batch of offspring in the industry itself, where the parental genotypes and family backgrounds of the offspring in the tanks or cages are not necessarily available as they were in the present study. Other approaches using amplicon sequencing can also be used to determine ploidy at the genomic level [49,50], and further developments there may well provide cost-effective approaches in the future.…”

Section: Limitations Of the Study And Future Improvements In Methodologymentioning

confidence: 99%

Chromosome aberrations in pressure-induced triploid Atlantic salmon

et al. 2020

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Background: Triploid organisms have three sets of chromosomes. In Atlantic salmon, hydrostatic pressure treatment of newly fertilized eggs has been extensively used to produce triploids which are functionally sterile due to their unpaired chromosomes. These fish often perform poorly on commercial farms, sometimes without explanation. Inheritance patterns in individuals subjected to pressure treatment have not been investigated in Atlantic salmon thus far. However, work on other species suggests that this treatment can result in aberrant inheritance. We therefore studied this in Atlantic salmon by genotyping 16 polymorphic microsatellites in eyed eggs and juveniles which had been subjected to pressure-induction of triploidy. Communally reared juveniles including fish subjected to pressure-induction of triploidy and their diploid siblings were included as a control. Results: No diploid offspring were detected in any of the eggs or juveniles which were subjected to hydrostatic pressure; therefore, the induction of triploidy was highly successful. Aberrant inheritance was nevertheless observed in 0.9% of the eggs and 0.9% of the juveniles that had been subjected to pressure treatment. In the communally reared fish, 0.3% of the fish subjected to pressure treatment displayed aberrant inheritance, while their diploid controls displayed 0% aberrant inheritance. Inheritance errors included two eyed eggs lacking maternal DNA across all microsatellites, and, examples in both eggs and juveniles of either the maternal or paternal allele lacking in one of the microsatellites. All individuals displaying chromosome aberrations were otherwise triploid. Conclusions: This is the first study to document aberrant inheritance in Atlantic salmon that have been subjected to pressure-induction of triploidy. Our experiments unequivocally demonstrate that even when induction of triploidy is highly successful, this treatment can cause chromosome aberrations in this species. Based upon our novel data, and earlier studies in other organisms, we hypothesize that in batches of Atlantic salmon where low to modest triploid induction rates have been reported, aberrant inheritance is likely to be higher than the rates observed here. Therefore, we tentatively suggest that this could contribute to the unexplained poor performance of triploid salmon that is occasionally reported in commercial aquaculture. These hypotheses require further investigation.

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Section: Limitations Of the Study And Future Improvements In Methodologymentioning

confidence: 99%

Chromosome aberrations in pressure-induced triploid Atlantic salmon

et al. 2020

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“…Moving forward, GT-seq and other targeted amplicon sequencing approaches hold great promise for informing conservation and management of biodiversity [66]. Originally demonstrated in steelhead trout [24], GT-seq has been subsequently applied to the study of other fish species, including redband trout [66], brook trout [67], Pacific lamprey [68], and walleye [69]. More recently, the efficacy of using GT-seq for genotyping minimally-invasive samples has been demonstrated [46], and successfully applied to further understanding of the molecular ecology and conservation status of the at-risk Western rattlesnake [70].…”

Section: Plos Onementioning

confidence: 99%

RapidRat: Development, validation and application of a genotyping-by-sequencing panel for rapid biosecurity and invasive species management

2020

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Invasive alien species (IAS) are among the main causes of global biodiversity loss. Invasive brown (Rattus norvegicus) and black (R. rattus) rats, in particular, are leading drivers of extinction on islands, especially in the case of seabirds where >50% of all extinctions have been attributed to rat predation. Eradication is the primary form of invasive rat management, yet this strategy has resulted in a~10-38% failure rate on islands globally. Genetic tools can help inform IAS management, but such applications to date have been largely reactive, time-consuming, and costly. Here, we developed a Genotyping-in-Thousands by sequencing (GT-seq) panel for rapid species identification and population assignment of invasive brown and black rats (RapidRat) in Haida Gwaii, an archipelago comprising~150 islands off the central coast of British Columbia, Canada. We constructed an optimized panel of 443 single nucleotide polymorphisms (SNPs) using previously generated double-digest restriction-site associated DNA (ddRAD) genotypic data (27,686 SNPs) from brown (n = 295) and black rats (n = 241) sampled throughout Haida Gwaii. The informativeness of this panel for identifying individuals to species and island of origin was validated relative to the ddRAD results; in all comparisons, admixture coefficients and population assignments estimated using RapidRat were consistent. To demonstrate application, 20 individuals from novel invasions of three islands (Agglomerate, Hotspring, Ramsay) were genotyped using RapidRat, all of which were confidently assigned (>98.5% probability) to Faraday and Murchison Islands as putative source populations. These results indicated that a previous eradication on Hotspring Island was conducted at an inappropriate geographic scale; future management should expand the eradication unit to include neighboring islands to prevent re-invasion. Overall, we demonstrated that RapidRat is an effective tool for managing invasive rat populations in Haida Gwaii and provided a clear framework for GT-seq panel development for informing biodiversity conservation in other systems.

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“…S2). Based on the distribution of the relative number of reference vs non-reference reads at each locus, the number of subgenome copies can be inferred (Delomas, 2019;Gompert & Mock, 2017). We chose the highest coverage individual from each of the three putative triploid genotypes and the diploid genotype with the greatest number of genotypicallyidentical accessions (to serve as a 1:1 control).…”

Section: Subgenome Comparisonsmentioning

confidence: 99%

Hybridization, polyploidy and clonality influence geographic patterns of diversity and salt tolerance in the model halophyte seashore paspalum (Paspalum vaginatum)

Goad

Baxter

Kellogg

et al. 2020

Preprint

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Seashore paspalum (Paspalum vaginatum Swartz) is a halophytic turfgrass and emerging genomic model system for the study of salt tolerance in cereals and other grasses. Despite recent interest and an increase in available tools, little is known about the diversity present in wild populations of P. vaginatum and its close relative P. distichum. Variation in ploidy, clonal propagation, hybridization, and subgenome composition appear to occur in the wild and may interact to influence geographic patterns of adaptation, particularly in response to environmental salinity levels. Using 218 accessions representing >170 wild collections from throughout the coastal southern United States plus existing USDA germplasm, we employed genotyping-by-sequencing, cpDNA sequencing and flow cytometry to identify genetic differentiation and ploidy variation. Within P. vaginatum, there are two morphologically distinct ecotypes: the fine-textured ecotype is diploid and appears to reproduce in the wild both sexually and by clonal propagation; in contrast, the coarse-textured ecotype consists largely of clonally-propagating triploid and diploid genotypes. The coarse-textured ecotype appears to be derived from hybridization between fine-textured P. vaginatum and an unidentified Paspalum species. These clonally propagating hybrid genotypes are more broadly distributed than clonal finetextured genotypes and may represent a transition to a more generalist adaptive strategy. The triploid genotypes vary in whether they carry one or two copies of the P. vaginatum subgenome, indicating multiple evolutionary origins. This variation in subgenome composition shows associations with local ocean salinity levels across the sampled populations and may play a role in local adaptation.

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Differentiating diploid and triploid individuals using single nucleotide polymorphisms genotyped by amplicon sequencing

Cited by 13 publications

References 27 publications

Chromosome aberrations in pressure-induced triploid Atlantic salmon

Chromosome aberrations in pressure-induced triploid Atlantic salmon

RapidRat: Development, validation and application of a genotyping-by-sequencing panel for rapid biosecurity and invasive species management

Hybridization, polyploidy and clonality influence geographic patterns of diversity and salt tolerance in the model halophyte seashore paspalum (Paspalum vaginatum)

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