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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.


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.


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.,French National Institute for Agricultural Research | Bugeon J.,French National Institute for Agricultural Research | Rivard Q.,French National Institute for Agricultural Research | Quittet B.,French National Institute for Agricultural Research | And 5 more authors.
Aquaculture | Year: 2013

Selection to improve processing yields relies on sib selection, in which live candidates are ranked according to their family breeding value. This approach limits genetic progress, as it only exploits genetic variability between families and not within them. Indirect criteria measured on live candidates could overcome this limitation. The present study (1) proposes a procedure to identify indirect criteria to predict processing yields in rainbow trout (head, carcass and fillet yields), (2) estimates genetic parameters of these indirect criteria, and (3) predicts relative genetic gains in processing yields using full-sib selection or indirect individual selection on those indirect criteria.DNA-pedigreed all-female rainbow trout Oncorhynchus mykiss (. n=. 2029, 1631.0. ±. 355.6. g) from 600 families produced from 100 sires and 60 dams were characterized by external and internal non-lethal morphological measures using digital pictures and real time ultrasound tomography. Nineteen landmarks were recorded on the digital pictures to define the outline of the body, head and lateral line. Their coordinates were used to calculate different lengths, heights and areas. Five different internal thicknesses were measured by ultrasound tomography.In the first phase of this study, processing yields were predicted using multiple linear regressions including both external and internal morphometric variables. In a second phase, the heritability of the predicted values and their genetic correlations with real processing yields were estimated using animal models. Predicted yields exhibited intermediate heritabilities (0.25-0.28) that were half the value of heritabilities for real processing yields (0.47-0.55), but had high genetic correlations with these real yields (0.87-0.90). The relative efficiency of indirect selection (IS) on these indirect criteria was compared to theoretical mass selection (MS) or sib selection (FS) with different family sizes (10 or 100) and two different selection pressures (10% or 40%). At the same selection pressure (10%, with 100 sibs per family %), full-sib selection created genetic progress 49.6% to 60.5% higher than indirect selection according to the processing yield targeted. However, when sib-selection pressure was limited to a more realistic between family selection pressure (40% and 10 sibs per family), indirect selection with 10% selection pressure was 21.9% to 32.7% more efficient than sib selection. © 2013 Elsevier B.V.


Boitard S.,French National Institute for Agricultural Research | Chevalet C.,French National Institute for Agricultural Research | Mercat M.-J.,Institute du Porc | Meriaux J.C.,LABOGENA | And 3 more authors.
Animal Genetics | Year: 2010

The Spanish and French pig populations share the common practice of quasi systematic paternity control of pure breed and composite line males. Ten microsatellite markers are in common between Spain and France controls, among the 17 markers used in France and the 13 used in Spain. After the adjustment of allele sizes, it is possible to merge the two datasets and to obtain a set of 5791 animals, including the vast majority of the males in the Duroc, Landrace, Large White and Piétrain French and Spanish breeds. Twelve French composite lines are also available. The genetic diversity analysis of these pig populations is presented, as well as the assignment of an individual to its breed. The effects of heterogeneous sampling across time and of relatedness among animals are also assessed. Consistent with the results of the previous studies, we found that different populations from the same breed clearly clustered together. In addition, all populations of this study, whether purebred or composite, are quite well differentiated from the other ones. As a result, we note that the 10 microsatellites commonly used for paternity control ensure a powerful detection of the breed of origin, with the power of detection being 95-99%. The detection of the exact population within breed is more difficult, but the power exceeds 70% for most of the populations. Practical implications include, for instance, the detection of outlier animals, crosses and admixture events. © 2010 Stichting International Foundation for Animal Genetics.


Lapegue S.,French Research Institute for Exploitation of the Sea | Harrang E.,French Research Institute for Exploitation of the Sea | Heurtebise S.,French Research Institute for Exploitation of the Sea | Flahauw E.,French Research Institute for Exploitation of the Sea | And 9 more authors.
Molecular Ecology Resources | Year: 2014

Use of SNPs has been favoured 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 analysed and compared with other model and nonmodel 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 programmes. © 2014 John Wiley & Sons Ltd.


PubMed | French National Institute for Agricultural Research
Type: Journal Article | Journal: Plant physiology | Year: 2016

Plant mutants for genes encoding subunits of mitochondrial complex I (CI; NADH:ubiquinone oxidoreductase), the first enzyme of the respiratory chain, display various phenotypes depending on growth conditions. Here, we examined the impact of photoperiod, a major environmental factor controlling plant development, on two Arabidopsis (Arabidopsis thaliana) CI mutants: a new insertion mutant interrupted in both ndufs8.1 and ndufs8.2 genes encoding the NDUFS8 subunit and the previously characterized ndufs4 CI mutant. In the long day (LD) condition, both ndufs8.1 and ndufs8.2 single mutants were indistinguishable from Columbia-0 at phenotypic and biochemical levels, whereas the ndufs8.1 ndufs8.2 double mutant was devoid of detectable holo-CI assembly/activity, showed higher alternative oxidase content/activity, and displayed a growth retardation phenotype similar to that of the ndufs4 mutant. Although growth was more affected in ndufs4 than in ndufs8.1 ndufs8.2 under the short day (SD) condition, both mutants displayed a similar impairment of growth acceleration after transfer to LD compared with the wild type. Untargeted and targeted metabolomics showed that overall metabolism was less responsive to the SD-to-LD transition in mutants than in the wild type. The typical LD acclimation of carbon and nitrogen assimilation as well as redox-related parameters was not observed in ndufs8.1 ndufs8 Similarly, NAD(H) content, which was higher in the SD condition in both mutants than in Columbia-0, did not adjust under LD We propose that altered redox homeostasis and NAD(H) content/redox state control the phenotype of CI mutants and photoperiod acclimation in Arabidopsis.


PubMed | University of Aarhus, Union Nationale des Cooperatives dElevage et dInsemination Animale, La Trobe University, Australian Department of Primary Industries and Fisheries and 7 more.
Type: Journal Article | Journal: 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.


PubMed | Labogena, Paris-Sorbonne University, CNRS Developmental Biology Laboratory, University of Basel and 3 more.
Type: | Journal: Nature communications | Year: 2015

Caprine-like Generalized Hypoplasia Syndrome (SHGC) is an autosomal-recessive disorder in Montbliarde cattle. Affected animals present a wide range of clinical features that include the following: delayed development with low birth weight, hind limb muscular hypoplasia, caprine-like thin head and partial coat depigmentation. Here we show that SHGC is caused by a truncating mutation in the CEP250 gene that encodes the centrosomal protein C-Nap1. This mutation results in centrosome splitting, which neither affects centriole ultrastructure and duplication in dividing cells nor centriole function in cilium assembly and mitotic spindle organization. Loss of C-Nap1-mediated centriole cohesion leads to an altered cell migration phenotype. This discovery extends the range of loci that constitute the spectrum of autosomal primary recessive microcephaly (MCPH) and Seckel-like syndromes.

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