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Details of SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata

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Dataset identification

Title of datasetSNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata
Narrative summary of datasetSelective breeding strategies require pedigree information over generations, but many species produced in aquaculture are too small to be physically tagged at early stages. Consequently, maintaining a sufficient number of separate families is often needed but costly and logistically difficult. Alternatively, parentage assignment can be obtained using DNA markers. We developed a panel of single nucleotide polymorphism (SNP) markers for the European abalone Haliotis tuberculata using an existing transcriptomic resource. An initial set of 2,176,887 SNPs was filtered to select 500 for high throughput genotyping. Of these, 298 SNPs were amplified in at least 90% of our H. tuberculata samples, consisting of a mixed family cohort (945 offspring) generated by crossing 40 abalones, and 5 full-sib training families. Based on amplification success among parents, minimum allele frequency and checks carried out against the training families, a subset of 123 markers was used to carry out parentage assignment in our mixed family cohorts. Maximum likelihood and exclusion-based methods of parentage assignment yielded consistent results, allowing parentage to be assigned in 98.9% of the studied progeny. Optimization of markers suggests that the 60 most informative SNPs may be sufficient for 95% assignment success in these progeny. The panel was also used to estimate effective population size, and revealed a low Ne due to high variance of reproductive success between parents. Our panel could be used to estimate genetic parameters of traits in mixed family cohorts, an essential stage to initiate selective breeding in H. tuberculata. It could also be useful tool in the context of monitoring stock enhancement and population genetics studies.
Supporting documentationHow to cite: Harney Ewan, Lachambre Sebastien, Roussel Sabine, Huchette Sylvain, Enez Florian, Morvezen Romain, Haffray Pierrick, Boudry Pierre (2018). SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata. SEANOE. https://doi.org/10.17882/51704 In addition to properly cite this dataset, it would be appreciated that the following work(s) be cited too, when using this dataset in a publication : Harney Ewan, Lachambre Sebastien, Roussel Sabine, Huchette Sylvain, Enez Florian, Morvezen Romain, Haffray Pierrick, Boudry Pierre (2018). Transcriptome based SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata. Aquaculture, 491, 105-113. Publisher
Start date1900-01-01
End date2018-01-01

Responsible organisations

CountryFrance
Organisation nameIFREMER
Role of organisationDataset Holding Organisation

Dataset availability

Original dataset download linkhttps://cloud.emodnet-ingestion.eu/index.php/s/pQsN4EygT7ifiFR
Dataset formatDelimited
Text or Plaintext
Public accessNo limitations
License for useCC-BY 4.0
TypeDataset
DOIhttps://doi.org/10.17882/51704

Locations

Map
Latitude north boundary48.913738
Longitude east boundary-3.282045
Latitude south boundary48.449509
Longitude west boundary-4.85309
Coordinate reference systemWorld Geodetic System 84
Sea areaNorth Atlantic Ocean
Celtic Sea
English Channel
Atlantic Ocean
European mainland
Northeast Atlantic Ocean (40W)

Data types, collection and processing

Observation typeFisheries
Aquaculture
ParameterConcentration of phycotoxins in biota

Process information

Submitting organisationLABORATORY OF SCIENCES OF MARINE ENVIRONMENT (LEMAR)
Submission identifier (UUID)300f4abc-6143-45be-8fd7-40b51ecfbcb1
Date of dataset creation2018-01-01
Date of metadata creation2019-05-16
Date of metadata latest revision2019-07-19
Date of publishing2019-08-06
Processing data centreIFREMER / IDM / SISMER - Scientific Information Systems for the SEA
Summary record-ID545