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Vandeputte M.,French National Institute for Agricultural Research | Vandeputte M.,French Research Institute for Exploitation of the Sea | Rossignol M.-N.,LABOGENA | Pincent C.,SYSAAF Section Aquacole
Aquaculture | Year: 2011

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 parent-set specific simulations to observed values in offspring with valid genotypes at all loci (- 0.5% on average) and 4) from observed values in offspring with valid genotypes at all loci to observed values in all offspring sampled (- 2.4% on average). For all steps, we provide a regression equation which models the loss of assignment power, or at least a maximal practical value for the loss of assignment power. Finally, equations are provided to model the expected true assignment rate from the theoretical assignment power or from the combined exclusion probability of the loci used. They show that the expected true assignment rates are considerably lower than the theoretical ones, for example achieving 99% true assignment requires a theoretical assignment power of 99.999996%, while 95% already requires 99.9989% theoretical assignment rate. © 2011 Elsevier B.V.

Amigues Y.,LABOGENA | Boitard S.,French National Institute for Agricultural Research | Bertrand C.,French National Institute for Agricultural Research | Sancristobal M.,French National Institute for Agricultural Research | Rocha D.,CNRS Animal Molecular Genetics Unit
Journal of Animal Breeding and Genetics | Year: 2011

This study was conducted to evaluate the genetic diversity of Blonde d'Aquitaine, a well-muscled native French beef breed, and to understand the relationships between Blonde d'Aquitaine, Limousin and Salers. We also compared these three beef breeds to the Holstein dairy breed. For this purpose, a set of 16 microsatellite markers were investigated. The obtained results show that Blonde d'Aquitaine has a high level of genetic diversity. Our study shows also that the French beef breeds have genetic differentiation among them, with approximately 9% of the total variation owing to breed differences. Our results show also that Blonde d'Aquitaine and Salers populations are genetically more similar to each other than to the Limousin. © 2011 Blackwell Verlag GmbH.

Daetwyler H.D.,Australian Department of Primary Industries and Fisheries | Daetwyler H.D.,La Trobe University | Daetwyler H.D.,Dairy Futures Cooperative Research Center | Capitan A.,French National Institute for Agricultural Research | And 35 more authors.
Nature Genetics | Year: 2014

The 1000 bull genomes project supports the goal of accelerating the rates of genetic gain in domestic cattle while at the same time considering animal health and welfare by providing the annotated sequence variants and genotypes of key ancestor bulls. In the first phase of the 1000 bull genomes project, we sequenced the whole genomes of 234 cattle to an average of 8.3-fold coverage. This sequencing includes data for 129 individuals from the global Holstein-Friesian population, 43 individuals from the Fleckvieh breed and 15 individuals from the Jersey breed. We identified a total of 28.3 million variants, with an average of 1.44 heterozygous sites per kilobase for each individual. We demonstrate the use of this database in identifying a recessive mutation underlying embryonic death and a dominant mutation underlying lethal chrondrodysplasia. We also performed genome-wide association studies for milk production and curly coat, using imputed sequence variants, and identified variants associated with these traits in cattle. © 2014 Nature America, Inc.

Marty A.,Genopole | Amigues Y.,LABOGENA | Servin B.,French National Institute for Agricultural Research | Renand G.,French National Institute for Agricultural Research | And 2 more authors.
Molecular Biotechnology | Year: 2010

Correlation between expression level of the bovine DNAJA1 gene and meat tenderness was recently found in Charolais longissimus thoracis muscle samples, suggesting that this gene could play an important role in meat tenderness. Here, we report the validation of polymorphisms within the bovine DNAJA1 gene, and the haplotype variability and extent of linkage disequilibrium in the three main French beef breeds (Blonde d'Aquitaine, Charolais, Limousin). Genotyping 18 putative SNPs revealed that 16 SNPs were polymorphic within the breeds tested. Two SNPs were removed from further analyses as one SNP had a low genotyping call rate, while the other SNP was not in Hardy-Weinberg equilibrium. The degree of heterozygosity observed for the remaining 14 SNPs varied between breeds, with Charolais being the breed with the highest genetic variation and Blonde d'Aquitaine the lowest. Linkage disequilibrium and haplotype structure of DNAJA1 were different between breeds. Eighteen different haplotypes, including three shared by all breeds, were discovered, and two to three tag SNPs (depending on the breed) are sufficient to capture all the genetic variability seen in these haplotypes. The results of this study will facilitate the design of optimal future association studies evaluating the role of the DNAJA1 gene in meat tenderness. © 2009 Springer Science+Business Media, LLC.

Haffray P.,SYSAAF | Vandeputte M.,French National Institute for Agricultural Research | Vandeputte M.,French Research Institute for Exploitation of the Sea | Petit V.,Aqualande | And 7 more authors.
Livestock Science | Year: 2012

Application of DNA parentage assignment for commercial selection in aquaculture is still rare. An experiment was performed to quantify and to minimize maternal effects on growth in rainbow trout. Six hundred families were reared until 198 day post fertilization (dpf) according to two different procedures. In the first procedure (NORM), all families were pooled at eyed stage. In the second procedure (MIN), where maternal effects due to differences in egg size were expected to be minimal, the spawns were divided into sub-groups with similar mean egg weight at eyed stage. These sub-groups were then pooled when they achieved the same mean body length (147. dpf). Genetic parameters were estimated for body weight, body length and condition factor at 198. dpf, with 2964 fish assigned to their parents using microsatellites. Significant maternal effects were observed in the NORM group for body weight and body length (m2=0.08±0.03). The heritability of body weight was 0.16±0.07 in the NORM group and 0.36±0.06 in the MIN group, in which maternal effects were not significant. It is concluded that, when eggs of different females are mixed at eyed stage, maternal effects persist at least until 198. dpf. The proposed procedure efficiently limits maternal effects, substantially increasing the heritability for growth, and therefore the expected selection response. © 2012 Elsevier B.V.

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