FN Archimer Export Format
PT J
TI Potential of genomic selection for growth, meat content and colour traits in mixed-family breeding designs for the Pacific oyster Crassostrea gigas
BT 
AF Jourdan, Antoine
   Morvezen, Romain
   Enez, Florian
   Haffray, Pierrick
   Lange, Adeline
   Vétois, Emilie
   Allal, Francois
   Phocas, Florence
   Bugeon, Jérôme
   Dégremont, Lionel
   Boudry, Pierre
AS 1:1,2;2:1;3:1;4:1;5:3;6:4;7:5;8:6;9:7;10:2;11:8;
FF 1:;2:;3:;4:;5:;6:;7:PDG-RBE-MARBEC-LAAAS;8:;9:;10:PDG-RBE-ASIM;11:PDG-RBE;
C1 SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, Rennes 35042, France
   Ifremer, RBE, ASIM, Avenue lede Mus de Loup – Ronce-les-Bains, La Tremblade 17390, France
   France Naissain, Bouin 85230, France
   SATMAR, Gatteville 50760, France
   MARBEC, Université Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
   Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas 78350, France
   INRAE, LPGP, Rennes 35000, France
   Ifremer, Département Ressources Biologiques et Environnement, Plouzané 29280, France
C2 SYSAAF, FRANCE
   IFREMER, FRANCE
   FRANCE NAISSAIN, FRANCE
   SATMAR, FRANCE
   IFREMER, FRANCE
   UNIV PARIS-SACLAY, FRANCE
   INRAE, FRANCE
   IFREMER, FRANCE
SI LA TREMBLADE
   PALAVAS
   BREST
SE PDG-RBE-ASIM
   PDG-RBE-MARBEC-LAAAS
   PDG-RBE
UM MARBEC
IN WOS Ifremer UPR
   WOS Ifremer UMR
   copubli-france
   copubli-p187
   copubli-univ-france
IF 4.5
TC 4
UR https://archimer.ifremer.fr/doc/00846/95839/106236.pdf
LA English
DT Article
DE ;Mollusc;Aquaculture;Genomic selection;Prediction accuracy;Breeding program;Linkage disequilibrium
AB 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. 
PY 2023
PD NOV
SO Aquaculture
SN 0044-8486
PU Elsevier BV
VL 576
UT 001043810200001
DI 10.1016/j.aquaculture.2023.739878
ID 95839
ER

EF