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Development of four EST-SSR multiplex PCRs in the Pacific oyster (Crassostrea gigas) and their validation in parentage assignment ArchiMer
Li, Ronghua; Li, Qi; Cornette, Florence; Degremont, Lionel; Lapegue, Sylvie.
We report four highly informative multiplex PCRs developed from twelve previously described ESTSSRs in Crassostrea gigas. We evaluated and validated these multiplex PCRs in twelve full-sib families. The average allelic richness and the polymorphism information content (PIC) were 11.1 and 0.811 respectively. The combined power of exclusion was greater than 99.99% using all four multiplex assays. A hundred and forty three tests of segregation ratios revealed 11 significant departures from expected Mendelian ratios. The frequency of null alleles was estimated as 4.9% of all the alleles segregating based on a within-family analysis of Mendelian segregation patterns. Parentage analysis of real offspring demonstrated that 97% of all offspring were unambiguously...
Tipo: Text Palavras-chave: Pacific oyster; Crassostrea gigas; Microsatellite; EST; Multiplex PCR; Parentage assignment.
Ano: 2010 URL: http://archimer.ifremer.fr/doc/00013/12419/9999.pdf
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From theory to practice: Empirical evaluation of the assignment power of marker sets for pedigree analysis in fish breeding ArchiMer
Vandeputte, Marc; Rossignol, Marie-noelle; Pincent, Cedric.
The use of marker-based pedigrees is increasing in aquaculture breeding, and obtaining high assignment rates is necessary for practical use of this methodology. In this paper, we used 12 real parentage assignment datasets from three species (European sea bass Dicentrarchus labrax, common carp Cyprinus carpio and rainbow trout Oncorhynchus mykiss) to investigate the relationships between theoretical, simulated and real assignment power. We found out that there was a large decrease between the theoretical and the observed values, which we modeled in four independent steps: 1) from theoretical values to population-wise simulations (-2.8% on average), 2) from population-wise simulations to true parent set specific simulations (-2.6% on average), 3) from true...
Tipo: Text Palavras-chave: Aquaculture; Parentage assignment; Exclusion probability; Microsatellites.
Ano: 2011 URL: http://archimer.ifremer.fr/doc/00035/14586/11964.pdf
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From theory to practice: Empirical evaluation of the assignment power of marker sets for pedigree analysis in fish breeding Inra
Vandeputte, M.; Rossignol; Pincent.
The use of marker-based pedigrees is increasing in aquaculture breeding, and obtaining high assignment ratesis necessary for practical use of this methodology. In this paper, we used 12 real parentage assignmentdatasets from three species (European sea bass Dicentrarchus labrax, common carp Cyprinus carpio andrainbow trout Oncorhynchus mykiss) to investigate the relationships between theoretical, simulated and realassignment power. We found out that there was a large decrease between the theoretical and the observedvalues, which we modeled in four independent steps: 1) from theoretical values to population-wisesimulations (−2.8% on average), 2) from population-wise simulations to true parent set specific simulations(−2.6% on average), 3) from true...
Tipo: Journal Article Palavras-chave:  Aquaculture; Parentage assignment; Exclusion probability; Microsatellites.
Ano: 2011 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2011e9b164a5&uri=/notices/prodinra1/2011/03/
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Genetic variation for growth at one and two summers of age in the common carp (Cyprinus carpio L.): Heritability estimates and response to selection ArchiMer
Vandeputte, Marc; Kocour, M; Mauger, S; Rodina, M; Launay, A; Gela, D; Dupont Nivet, M; Hulak, M; Linhart, O.
We estimated the heritability of growth-related traits (weight and length at ages one summer, first spring and two summers) in a synthetic mirror carp strain (HSM) in the Czech Republic. The four generation pedigree was obtained from parentage assignment of three factorial mating designs with microsatellite markers, and included 195 fish without phenotypes (48 G0, 147 G1) and 1321 fish with phenotypes (674 G2, 647 G3). Animal model heritability estimates over generations were in the range 0.21-0.33 for length and in the range 0.31-0.44 for weight. The genetic correlation between length and weight was high (0.97). The correlations between growth measurements in the first and in the second summer of age were moderate to low (0.34-0.67). Divergent selection...
Tipo: Text Palavras-chave: Quantitative genetics; Performance; Microsatellites; Parentage assignment; Realized heritability; Selection response; Selection; Growth; Heritability; Cyprinus carpio; Common carp.
Ano: 2008 URL: http://archimer.ifremer.fr/doc/2008/publication-4076.pdf
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Response to domestication and selection for growth in the European sea bass (Dicentrarchus labrax) in separate and mixed tanks ArchiMer
Vandeputte, Marc; Dupont Nivet, M; Haffray, P; Chavanne, H; Cenadelli, S; Parati, K; Vidal, Marie-odile; Vergnet, Alain; Chatain, Beatrice.
Selective breeding of European sea bass (Dicentrarchus labrax) receives a growing interest, as the estimated heritability of growth is medium to high. In this study, we compared the offspring of four groups of sea bass sires, mated with the same wild dams: wild (W), first generation of domestication (D), first generation of mass selection for length (M), first generation of PROSPER-like selection for length (P). The comparison was done both in replicated tanks (separate rearing) and in mixed tanks (mixed rearing) where sire origins were recovered by genotyping of eight microsatellite markers. Weight, length and growth rate were measured from day 238 post-fertilization (69 g mean weight) to day 611 post-fertilization (390 g mean weight). Both in mixed and...
Tipo: Text Palavras-chave: Nephrocalcinosis; Competition; Microsatellites; Parentage assignment; Realized heritability; Selection response; Growth; Selective breeding; Dicentrarchus labrax; European sea bass.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/2009/publication-5303.pdf
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Transcriptome based SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata ArchiMer
Harney, Ewan; Lachambre, Sebastien; Roussel, Sabine; Huchette, Sylvain; Enez, Florian; Morvezen, Romain; Haffray, Pierrick; Boudry, Pierre.
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...
Tipo: Text Palavras-chave: Abalone; Parentage assignment; Pedigree; Selective breeding; Transcriptome; SNP.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00429/54061/55396.pdf
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