Le Touquet – Paris-Plage, France
Le Touquet – Paris-Plage, France
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Fritz S.,UNCEIA | Fritz S.,French National Institute for Agricultural Research | Capitan A.,UNCEIA | Capitan A.,French National Institute for Agricultural Research | And 12 more authors.
PLoS ONE | Year: 2013

The regular decrease of female fertility over time is a major concern in modern dairy cattle industry. Only half of this decrease is explained by indirect response to selection on milk production, suggesting the existence of other factors such as embryonic lethal genetic defects. Genomic regions harboring recessive deleterious mutations were detected in three dairy cattle breeds by identifying frequent haplotypes (>1%) showing a deficit in homozygotes among Illumina Bovine 50k Beadchip haplotyping data from the French genomic selection database (47,878 Holstein, 16,833 Montbéliarde, and 11,466 Normande animals). Thirty-four candidate haplotypes (p<10-4) including previously reported regions associated with Brachyspina, CVM, HH1, and HH3 in Holstein breed were identified. Haplotype length varied from 1 to 4.8 Mb and frequencies from 1.7 up to 9%. A significant negative effect on calving rate, consistent in heifers and in lactating cows, was observed for 9 of these haplotypes in matings between carrier bulls and daughters of carrier sires, confirming their association with embryonic lethal mutations. Eight regions were further investigated using whole genome sequencing data from heterozygous bull carriers and control animals (45 animals in total). Six strong candidate causative mutations including polymorphisms previously reported in FANCI (Brachyspina), SLC35A3 (CVM), APAF1 (HH1) and three novel mutations with very damaging effect on the protein structure, according to SIFT and Polyphen-2, were detected in GART, SHBG and SLC37A2 genes. In conclusion, this study reveals a yet hidden consequence of the important inbreeding rate observed in intensively selected and specialized cattle breeds. Counter-selection of these mutations and management of matings will have positive consequences on female fertility in dairy cattle. © 2013 Fritz et al.

Lund M.S.,University of Aarhus | De Roos A.P.,Crv Inc. | De Vries A.G.,Crv Inc. | Druet T.,University of Liège | And 10 more authors.
Genetics Selection Evolution | Year: 2011

Background: Size of the reference population and reliability of phenotypes are crucial factors influencing the reliability of genomic predictions. It is therefore useful to combine closely related populations. Increased accuracies of genomic predictions depend on the number of individuals added to the reference population, the reliability of their phenotypes, and the relatedness of the populations that are combined. Methods. This paper assesses the increase in reliability achieved when combining four Holstein reference populations of 4000 bulls each, from European breeding organizations, i.e. UNCEIA (France), VikingGenetics (Denmark, Sweden, Finland), DHV-VIT (Germany) and CRV (The Netherlands, Flanders). Each partner validated its own bulls using their national reference data and the combined data, respectively. Results: Combining the data significantly increased the reliability of genomic predictions for bulls in all four populations. Reliabilities increased by 10%, compared to reliabilities obtained with national reference populations alone, when they were averaged over countries and the traits evaluated. For different traits and countries, the increase in reliability ranged from 2% to 19%. Conclusions: Genomic selection programs benefit greatly from combining data from several closely related populations into a single large reference population. © 2011 Lund et al; licensee BioMed Central Ltd.

Dassonneville R.,French National Institute for Agricultural Research | Dassonneville R.,Institute Of Lelevage | Fritz S.,UNCEIA | Ducrocq V.,French National Institute for Agricultural Research | Boichard D.,French National Institute for Agricultural Research
Journal of Dairy Science | Year: 2012

Low-density chips are appealing alternative tools contributing to the reduction of genotyping costs. Imputation enables researchers to predict missing genotypes to recreate the denser coverage of the standard 50K (∼50,000) genotype. Two alternative in silico chips were defined in this study that included markers selected to optimize minor allele frequency and spacing. The objective of this study was to compare the imputation accuracy of these custom low-density chips with a commercially available 3K chip. Data consisted of genotypes of 4,037 Holstein bulls, 1,219 Montbéliarde bulls, and 991 Blonde d'Aquitaine bulls. Criteria to select markers to include in low-density marker panels are described. To mimic a low-density genotype, all markers except the markers present on the low-density panel were masked in the validation population. Imputation was performed using the Beagle software. Combining the directed acyclic graph obtained with Beagle with the PHASEBOOK algorithm provides fast and accurate imputation that is suitable for routine genomic evaluations based on imputed genotypes. Overall, 95 to 99% of alleles were correctly imputed depending on the breed and the low-density chip used. The alternative low-density chips gave better results than the commercially available 3K chip. A low-density chip with 6,000 markers is a valuable genotyping tool suitable for both dairy and beef breeds. Such a tool could be used for preselection of young animals or large-scale screening of the female population. © 2012 American Dairy Science Association.

Nuttinck F.,ENVA | Gall L.,French National Institute for Agricultural Research | Ruffini S.,French National Institute for Agricultural Research | Laffont L.,French National Institute for Agricultural Research | And 6 more authors.
Biology of Reproduction | Year: 2011

During the periovulatory period, the induction of prostaglandin G/H synthase-2 (PTGS2) expression in cumulus cells and associated prostaglandin E2 (PGE2) production are implicated in the terminal differentiation of the cumulus-oocyte complex. During the present study, the effects of the PTGS2/PGE2 pathway on the developmental competence of bovine oocytes were investigated using an in vitro model of maturation, fertilization, and early embryonic development. The specific inhibition of PTGS2 activity with NS-398 during in vitro maturation (IVM) significantly restricted mitogen-activated protein kinase (MAPK) activation in oocytes at the germinal vesicle breakdown stage and reduced both cumulus expansion and the maturation rate after 22 h of culture. In addition, significantly higher rates of abnormal meiotic spindle organization were observed after 26 h of culture. Periconceptional PTGS2 inhibition did not affect fertilization but significantly reduced the speed of embryo development. Embryo output rates were significantly decreased on Day 6 postfertilization but not on Day 7. However, total blastomere number was significantly lower in embryos obtained after PTGS2 inhibition. The addition of PGE2 to IVM and in vitro fertilization cultures containing NS-398 overrode oocyte maturation and early embryonic developmental defects. Protein and mRNA expression for the prostaglandin E receptor PTGER2 were found in oocytes, whereas the PTGER2, PTGER3, and PTGER4 subtypes were expressed in cumulus cells. This study is the first to report the involvement of PGE2 in oocyte MAPK activation during the maturation process. Taken together, these results indicate that PGE2-mediated interactions between somatic and germ cells during the periconceptional period promote both in vitro oocyte maturation and preimplantation embryonic development in cattle. © 2011 by the Society for the Study of Reproduction, Inc.

Van Den Berg I.,French National Institute for Agricultural Research | Van Den Berg I.,Agro ParisTech | Van Den Berg I.,University of Aarhus | Fritz S.,UNCEIA | And 2 more authors.
Genetics Selection Evolution | Year: 2013

Background: Accurate QTL mapping is a prerequisite in the search for causative mutations. Bayesian genomic selection models that analyse many markers simultaneously should provide more accurate QTL detection results than single-marker models. Our objectives were to (a) evaluate by simulation the influence of heritability, number of QTL and number of records on the accuracy of QTL mapping with Bayes Cπ and Bayes C; (b) estimate the QTL status (homozygous vs. heterozygous) of the individuals analysed. This study focussed on the ten largest detected QTL, assuming they are candidates for further characterization. Methods. Our simulations were based on a true dairy cattle population genotyped for 38 277 phased markers. Some of these markers were considered biallelic QTL and used to generate corresponding phenotypes. Different numbers of records (4387 and 1500), heritability values (0.1, 0.4 and 0.7) and numbers of QTL (10, 100 and 1000) were studied. QTL detection was based on the posterior inclusion probability for individual markers, or on the sum of the posterior inclusion probabilities for consecutive markers, estimated using Bayes C or Bayes Cπ. The QTL status of the individuals was derived from the contrast between the sums of the SNP allelic effects of their chromosomal segments. Results: The proportion of markers with null effect (π) frequently did not reach convergence, leading to poor results for Bayes Cπ in QTL detection. Fixing π led to better results. Detection of the largest QTL was most accurate for medium to high heritability, for low to moderate numbers of QTL, and with a large number of records. The QTL status was accurately inferred when the distribution of the contrast between chromosomal segment effects was bimodal. Conclusions: QTL detection is feasible with Bayes C. For QTL detection, it is recommended to use a large dataset and to focus on highly heritable traits and on the largest QTL. QTL statuses were inferred based on the distribution of the contrast between chromosomal segment effects. © 2013 van den Berg et al.; licensee BioMed Central Ltd.

Dassonneville R.,French National Institute for Agricultural Research | Dassonneville R.,Institute Of Lelevage | Baur A.,UNCEIA | Fritz S.,UNCEIA | And 2 more authors.
Genetics Selection Evolution | Year: 2012

Background: Today, genomic evaluations are an essential feature of dairy cattle breeding. Initially, genomic evaluation targeted young bulls but recently, a rapidly increasing number of females (both heifers and cows) are being genotyped. A rising issue is whether and how own performance of genotyped cows should be included in genomic evaluations. The purpose of this study was to assess the impact of including yield deviations, i.e. own performance of cows, in genomic evaluations. Methods. Two different genomic evaluations were performed: one including only reliable daughter yield deviations of proven bulls based on their non-genotyped daughters, and one including both daughter yield deviations for males and own yield deviations for genotyped females. Milk yield, the trait most prone to preferential treatment, and somatic cell count, for which such a bias is very unlikely, were studied. Data consisted of two groups of animals from the three main dairy breeds in France: 11 884 elite females genotyped by breeding companies and 7032 cows genotyped for a research project (and considered as randomly selected from the commercial population). Results: For several measures that could be related to preferential treatment bias, the elite group presented a different pattern of estimated breeding values for milk yield compared to the other combinations of trait and group: for instance, for milk yield, the average difference between estimated breeding values with or without own yield deviations was significantly different from 0 for this group. Correlations between estimated breeding values with or without yield deviations were lower for elite females than for randomly selected cows for milk yield but were very similar for somatic cell count. Conclusions: This study demonstrated that including own milk performance of elite females leads to biased (over-estimated) genomic evaluations. Thus, milk production records of elite cows require specific treatment in genomic evaluation. © 2012 Dassonneville et al.; licensee BioMed Central Ltd.

Colombani C.,French National Institute for Agricultural Research | Croiseau P.,French National Institute for Agricultural Research | Fritz S.,UNCEIA | Guillaume F.,Institute Of Lelevage | And 3 more authors.
Journal of Dairy Science | Year: 2012

Genomic selection involves computing a prediction equation from the estimated effects of a large number of DNA markers based on a limited number of genotyped animals with phenotypes. The number of observations is much smaller than the number of independent variables, and the challenge is to find methods that perform well in this context. Partial least squares regression (PLS) and sparse PLS were used with a reference population of 3,940 genotyped and phenotyped French Holstein bulls and 39,738 polymorphic single nucleotide polymorphism markers. Partial least squares regression reduces the number of variables by projecting independent variables onto latent structures. Sparse PLS combines variable selection and modeling in a one-step procedure. Correlations between observed phenotypes and phenotypes predicted by PLS and sparse PLS were similar, but sparse PLS highlighted some genome regions more clearly. Both PLS and sparse PLS were more accurate than pedigree-based BLUP and generally provided lower correlations between observed and predicted phenotypes than did genomic BLUP. Furthermore, PLS and sparse PLS required similar computing time to genomic BLUP for the study of 6 traits. © 2012 American Dairy Science Association.

Touzard E.,French National Institute for Agricultural Research | Reinaud P.,French National Institute for Agricultural Research | Dubois O.,French National Institute for Agricultural Research | Guyader-Joly C.,UNCEIA | And 3 more authors.
Reproduction | Year: 2013

Pregnancy-associated glycoproteins (PAGs) constitute a multigenic family of aspartic proteinases expressed in the trophoblast of the ruminant placenta. In Bos taurus, this family comprises 21 members segregated into ancient and modern phylogenetic groups. Ancient PAGs have been reported to be synthesized throughout the trophoblastic cell layer whereas modern PAGs are produced by binucleate cells of cotyledons. The aim of this study was to investigate modern and ancient PAGs during gestation in cotyledonary and intercotyledonary tissues. To obtain convincing and innovative results despite the high sequence identity shared between PAGs, we designed specific tools such as amplification primers and antibodies. Using real-time RT-PCR, we described the transcript expression of 16 bovine PAGs. Overall, PAGs are characterized by an increase in their expression during gestation. However, we demonstrated a segregation of modern PAGs in cotyledons and of ancient PAGs in the intercotyledonary chorion, except for the ancient PAG2 expressed in cotyledons. By raising specific antibodies against the modern PAG1 and ancient PAG11 and PAG2, we established the expression kinetics of the proteins using western blotting. Immunohistochemistry showed that PAGs were produced by specific cellular populations: PAG1 by binucleate cells in the whole trophoblastic layer, PAG11 was localized in binucleate cells of the intercotyledonary trophoblast and the chorionic plate of the cotyledon, while PAG2 was produced in mononucleate cells of the internal villi of the cotyledon. These results revealed a highly specific regulation of PAG expression and cell localization as a function of their phylogenetic status, suggesting distinct biological functions within placental tissues. © 2013 Society for Reproduction and Fertility.

Bruyere P.,VetAgro Sup | Baudot A.,University of Paris Descartes | Guyader-Joly C.,UNCEIA | Guerin P.,VetAgro Sup | And 2 more authors.
Theriogenology | Year: 2012

This study evaluates a new synthetic substitute (CRYO3, Ref. 5617, Stem Alpha, France) for animal-based products in bovine embryo cryopreservation solutions. During the experiment, fetal calf serum (FCS) and bovine serum albumin (BSA) were used as references. A combination of a thermodynamic approach using differential scanning calorimetry and a biological approach using in vitro-produced bovine embryo slow-freezing was used to characterize cryopreservation solutions containing CRYO3, FCS and BSA. The CRYO3 and fetal calf serum (FCS) slow-freezing solutions were made from Dulbecco's phosphate-buffered saline containing 1.5 m ethylene glycol, 0.1 m sucrose and 20% (v.v-1) of CRYO3 or FCS. The bovine serum albumin (BSA) solution was made by adding 0.1 m sucrose to a commercial solution containing 1.5 m ethylene glycol and 4 g L-1 BSA. These solutions were evaluated using three characteristics: the end of melting temperature, the enthalpy of crystallization (thermodynamic approach) and the embryo survival and hatching rates after in vitro culture (biological approach). The CRYO3 and FCS solutions had similar thermodynamic properties. In contrast, the thermodynamic characteristics of the BSA solution were different from those of the FCS and CRYO3 solutions. Nevertheless, the embryo survival and hatching rates obtained with the BSA and FCS solutions were not different. Similar biological properties can thus be obtained with slow freezing solutions that have different physical properties within a defined range. The embryo survival rate after 48 h of in vitro culture obtained with the CRYO3 solution (81.5%) was higher than that obtained with the BSA (42.2%, P = 0.000 12) and FCS solutions (58%, P = 0.016). Similarly, the embryo hatching rate after 72 h of in vitro culture was higher with the CRYO3 solution (61.1%) than with the BSA (31.1%, P = 0.0055) and FCS solutions (36%, P = 0.018). We conclude that CRYO3 can be used as a chemically defined substitute for animal-based products in in vitro-produced bovine embryo cryopreservation solutions. © 2012 Elsevier Inc..

Rico C.,CNRS Physiology of Reproduction and Behaviors | Drouilhet L.,CNRS Physiology of Reproduction and Behaviors | Salvetti P.,UNCEIA | Dalbis-Tran R.,CNRS Physiology of Reproduction and Behaviors | And 6 more authors.
Reproduction, Fertility and Development | Year: 2012

High between-animal variability in the number of embryos produced by multiple ovulation and embryo transfer (MOET) and ovum pick-up and in vitro production (OPUIVP) methods remains a major limit to the development of embryo biotechnologies in cattle. The measurement of anti-Mllerian hormone (AMH) endocrine concentrations in cows can help to predict their follicular and ovulatory responses to gonadotrophin treatment. The present study aimed to provide practical information for a simple prognostic method based on AMH measurement in Holstein cows. Accurate AMH concentrations could be measured with ELISA in blood or plasma. In cows undergoing repeated OPU protocols over 1 year, the AMH concentrations measured in plasma samples collected before each gonadotrophin treatment were found to be highly repeatable and were tightly correlated with follicular responses. From data obtained at both an experimental station and farm settings, it was possible to propose AMH cut-off values to identify low-responding cows. Gonadotrophin-stimulated cows producing fewer than 15 large follicles at oestrus and fewer than 10 embryos in MOET protocols could be discarded efficiently with plasma AMH concentrations below 87 and 74pgmL-1, respectively. In conclusion, we propose a prognostic method based on a single AMH measurement to improve the results of embryo biotechnologies. © CSIRO 2012.

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