Development of SNP genotyping arrays in two shellfish species

Type Article
Date 2014-07
Language English
Author(s) Lapegue Sylvie1, Harrang Estelle1, Heurtebise Serge1, Flahauw Emilie1, Donnadieu C.2, Gayral P.3, 4, Ballenghien M.3, Genestout L.5, Barbotte L.5, Mahla R.5, Haffray P.6, Klopp C.7
Affiliation(s) 1 : IFREMER, LGPMM, SG2M, Lab Genet & Pathol Mollusques Marins, La Tremblade, France.
2 : INRA, Lab Genet Cellulaire, Plateforme GeT PlaGe Genotoul, UMR444, F-31326 Castanet Tolosan, France.
3 : Univ Montpellier 2, Inst Sci Evolut Montpellier, CNRS, UMR 5554, Montpellier, France.
4 : Univ Tours, Fac Sci & Tech, Inst Rech Biol Insecte, CNRS,UMR 7261, Tours, France.
5 : LABOGENA, Domaine Vilvert, Jouy En Josas, France.
6 : INRA, SYSAAF, Stn LPGP, F-35042 Rennes, France.
7 : INRA, Sigenae, Biometrie & Intelligence Artificielle UR875, F-31326 Castanet Tolosan, France.
Source Molecular Ecology Resources (1755-098X) (Wiley-blackwell), 2014-07 , Vol. 14 , N. 4 , P. 820-830
DOI 10.1111/1755-0998.12230
WOS© Times Cited 23
Note Fig. S1 Percentage of SNPs for which the genotyping failed, or that were considered as polymorphic or monomorphic according to their in vitro or in silico origin and for each array. Fig. S2 Box plot representation of minor allele frequency (MAF) in a subset of four C. gigas populations (LAF = La Fumée, France; MAR = Marennes, France; ARE = Arcachon, France; DAN = Danemark) for a panel 203 SNPs that were polymorphic in this subset. Table S1 List and characteristics of the 384 SNPs of the Pacific oyster array. Table S2 List and characteristics of the 384 SNPs of the European flat oyster array.
Keyword(s) Crassostrea gigas, GoldenGate technology, Ostrea edulis, oysters, SNP genotyping
Abstract Use of SNPs has been favored due to their abundance in plant and animal genomes, accompanied by the falling cost and rising throughput capacity for detection and genotyping. Here, we present in vitro (obtained from targeted sequencing) and in silico discovery of SNPs, and the design of medium-throughput genotyping arrays for two oyster species, the Pacific oyster, Crassostrea gigas, and European flat oyster, Ostrea edulis. Two sets of 384 SNP markers were designed for two Illumina GoldenGate arrays and genotyped on more than 1000 samples for each species. In each case, oyster samples were obtained from wild and selected populations and from three-generation families segregating for traits of interest in aquaculture. The rate of successfully genotyped polymorphic SNPs was about 60% for each species. Effects of SNP origin and quality on genotyping success (Illumina functionality score) were analyzed and compared with other model and non-model species. Furthermore, a simulation was made based on a subset of the C. gigas SNP array with a minor allele frequency of 0.3 and typical crosses used in shellfish hatcheries. This simulation indicated that at least 150 markers were needed to perform an accurate parental assignment. Such panels might provide valuable tools to improve our understanding of the connectivity between wild (and selected) populations and could contribute to future selective breeding programs.
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Lapegue Sylvie, Harrang Estelle, Heurtebise Serge, Flahauw Emilie, Donnadieu C., Gayral P., Ballenghien M., Genestout L., Barbotte L., Mahla R., Haffray P., Klopp C. (2014). Development of SNP genotyping arrays in two shellfish species. Molecular Ecology Resources, 14(4), 820-830. Publisher's official version : , Open Access version :