Potential of genomic selection for growth, meat content and colour traits in mixed-family breeding designs for the Pacific oyster Crassostrea gigas

• Published in: Aquaculture
• Main Authors: Jourdan, Antoine, Morvezen, Romain, Enez, Florian, Haffray, Pierrick, Lange, Adeline, Vétois, Emilie, Allal, François, Phocas, Florence, Bugeon, Jérôme, Degremont, Lionel, Boudry, Pierre
• Other Authors: Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), France Naissain, SATMAR, MARine Biodiversity Exploitation and Conservation Sète (UMR MARBEC SETE), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Physiologie et Génomique des Poissons = Fish Physiology and Genomics Institute (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), This work was supported by the European Maritime and Fisheries Fund (EMFF) and FranceAgriMer as part of ‘Quality Huitre’ under grant number PFEA470018FA1000011.
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2023
• Subjects: Mollusc; Aquaculture; Genomic selection; Prediction accuracy; Breeding program; Linkage disequilibrium; [SDE.BE]Environmental Sciences/Biodiversity and Ecology; [SDE.MCG]Environmental Sciences/Global Changes; Crassostrea gigas; Pacific oyster
• Online Access: https://hal.science/hal-04158060; https://doi.org/10.1016/j.aquaculture.2023.739878

International audience Selective breeding programs have been initiated worldwide for the Pacific oyster Crassostrea gigas to improve economically important traits such as growth and disease resistance. The emergence of genomic tools has allowed novel perspectives for using genomic selection (GS) in mixed-family breeding designs, which are cheaper and easier to develop than classical breeding schemes. In this study, we evaluated the potential of GS for different growth-related and shell colour traits in two independent commercially selected populations (P1 and P2), based on mixed-family designs. From ≈14.5K informative SNPs genotyped with the bi-species Axiom Affymetrix 57K oyster array, ≈12.5K were mapped on the reference genome. A strong heterogeneity of marker density between and within chromosomes was reported, with a low linkage disequilibrium (below 0.1 at 0.1 Mb) between pairs of SNPs. The within-population structure was homogenous for each population, with effective sizes of 107 for P1 and 76 for P2. Heritability was estimated for each trait and population and ranged from 0.08 ± 0.04 (for mean darkness intensity in P1) to 0.56 ± 0.08 (for the mean upper valve b* value in P2) for a pedigree-based model and from 0.04 ± 0.02 (for mean darkness intensity in P1) to 0.69 ± 0.04 (for the mean darkness intensity in P2) for a genomic-based model. Growth-related traits were generally highly genetically and positively correlated with each other, but weakly correlated with colour traits. Accuracy of prediction was generally higher with the genomic model (GBLUP) than with the classical BLUP model, with a maximum gain of accuracy (from 0.38 to 0.66) for flesh weight adjusted by total weight in P2. Accuracy of breeding values was slightly higher for colour traits for P2, with higher heritability estimates. Overall, our results indicate that GS has a good potential to be implemented in mixed-family breeding programs in a shellfish such as C. gigas.