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

• Published in: Aquaculture
• Main Authors: Harney, Ewan, Lachambre, Sebastien, Roussel, Sabine, Huchette, Sylvain, Enez, Florian, Morvezen, Romain, Haffray, Pierrick, Boudry, Pierre
• Other Authors: Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Scea France Haliotis, ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2018
• Subjects: effective population-size; genetic diversity; linkage disequilibrium; ACL; Transcriptome; pacific oyster; Abalone; atlantic salmon; Selective breeding; oyster crassostrea-gigas; pecten-maximus; reproductive success; microsatellite markers; Parentage assignment; Pedigree; single-nucleotide polymorphisms; snp; [SDE.BE]Environmental Sciences/Biodiversity and Ecology; Pacific; Atlantic salmon; Crassostrea gigas; Pacific oyster
• Online Access: https://hal.archives-ouvertes.fr/hal-02626095; https://hal.archives-ouvertes.fr/hal-02626095/document; https://hal.archives-ouvertes.fr/hal-02626095/file/Harney_etal_Aquaculture_2018.pdf; https://doi.org/10.1016/j.aquaculture.2018.03.006

WOS:000431009400014 International audience 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 (70 offspring). 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 N-e 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.