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

Date 2018
Author(s) Harney EwanORCID1, 2, Lachambre Sebastien1, 3, Roussel Sabine1, Huchette Sylvain3, Enez Florian4, Morvezen RomainORCID4, Haffray Pierrick4, Boudry PierreORCID2
Affiliation(s) 1 : Univ Brest, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des Sciences de l'Environnement Marin, 29280 Plouzané, France
2 : Ifremer, UMR 6539 UBO/CNRS/IRD/Ifremer, Laboratoire des Sciences de l'Environnement Marin, Centre Bretagne, 29280 Plouzané, France
3 : France Haliotis, 29880 Plouguerneau, France
4 : Syndicat des Sélectionneurs Avicoles et Aquacoles Français, 35000 Rennes, France
DOI 10.17882/51704
Publisher SEANOE
Keyword(s) abalone, parentage assignment, pedigree, selective breeding, transcriptome, SNP
Abstract

Selective 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.

Licence CC-BY
Data
File Size Format Processing Access
Data file 1: Information about the 500 SNPs that were genotyped 372 KB CSV Processed data Open access
Data file 2: Genotypes of 1065 individual abalone for 298 SNPs 1 MB CSV Processed data Open access
Data description 1 KB TEXTE Open access
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How 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's official version : https://doi.org/10.1016/j.aquaculture.2018.03.006 , Open Access version : https://archimer.ifremer.fr/doc/00429/54061/