FN Archimer Export Format
PT J
TI Transcriptome based SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata
BT 
AF HARNEY, Ewan
   LACHAMBRE, Sebastien
   ROUSSEL, Sabine
   HUCHETTE, Sylvain
   ENEZ, Florian
   MORVEZEN, Romain
   HAFFRAY, Pierrick
   BOUDRY, Pierre
AS 1:1,2;2:1,3;3:1;4:3;5:4;6:4;7:4;8:2;
FF 1:PDG-RBE-PFOM-PI;2:;3:;4:;5:;6:;7:;8:PDG-RBE-PFOM;
C1 Univ Brest UBO, Lab Sci Environm Marin LEMAR, Inst Univ Europeen Mer, UMR 6539,CNRS,IRD,Ifremer,UBO, Technopole Brest Iroise, F-29280 Plouzane, France.
   UBO, Ctr Bretagne, IFREMER, UMR LEMAR 6539,CNRS,IRD, F-29280 Plouzane, France.
   France Haliotis, F-29880 Plouguerneau, France.
   Syndicat Selectionneurs Avicoles & Aquacoles Fran, F-35000 Rennes, France.
C2 UBO, FRANCE
   IFREMER, FRANCE
   FRANCE HALIOTIS, FRANCE
   SYSAAF, FRANCE
SI BREST
SE PDG-RBE-PFOM-PI
   PDG-RBE-PFOM
UM LEMAR
IN WOS Ifremer jusqu'en 2018
   copubli-france
   copubli-univ-france
IF 3.022
TC 13
UR https://archimer.ifremer.fr/doc/00429/54061/55396.pdf
LA English
DT Article
DE ;Abalone;Parentage assignment;Pedigree;Selective breeding;Transcriptome;SNP
AB 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 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. 
PY 2018
PD APR
SO Aquaculture
SN 0044-8486
PU Elsevier Science Bv
VL 491
UT 000431009400014
BP 105
EP 113
DI 10.1016/j.aquaculture.2018.03.006
ID 54061
ER

EF