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Le Touquet – Paris-Plage, France

Boichard D.,French National Institute for Agricultural Research | Ducrocq V.,French National Institute for Agricultural Research | Croiseau P.,French National Institute for Agricultural Research | Fritz S.,ALLICE
Comptes Rendus - Biologies | Year: 2016

The principles of genomic selection are described, with the main factors affecting its efficiency and the assumptions underlying the different models proposed. The reasons of its fast adoption in dairy cattle are explained and the conditions of its application to other species are discussed. Perspectives of development include: selection for new traits and new breeding objectives; adoption of more robust approaches based on information on causal variants; predictions of genotype. ×. environment interactions. © 2016 Académie des sciences.

Montazer-Torbati F.,French National Institute for Agricultural Research | Boutinaud M.,French National Institute for Agricultural Research | Boutinaud M.,Agrocampus Ouest | Brun N.,French National Institute for Agricultural Research | And 12 more authors.
Journal of Dairy Science | Year: 2016

Lactation performance is dependent on both the genetic characteristics and the environmental conditions surrounding lactating cows. However, individual variations can still be observed within a given breed under similar environmental conditions. The role of the environment between birth and lactation could be better appreciated in cloned cows, which are presumed to be genetically identical, but differences in lactation performance between cloned and noncloned cows first need to be clearly evaluated. Conflicting results have been described in the literature, so our aim was to clarify this situation. Nine cloned Prim' Holstein cows were produced by the transfer of nuclei from a single fibroblast cell line after cell fusion with enucleated oocytes. The cloned cows and 9 noncloned counterparts were raised under similar conditions. Milk production and composition were recorded monthly from calving until 200 d in milk. At 67 d in milk, biopsies were sampled from the rear quarter of the udder, their mammary epithelial cell content was evaluated, and mammary cell renewal, RNA, and DNA were then analyzed in relevant samples. The results showed that milk production did not differ significantly between cloned and noncloned cows, but milk protein and fat contents were less variable in cloned cows. Furthermore, milk fat yield and contents were lower in cloned cows during early lactation. At around 67 DIM, milk fat and protein yields, as well as milk fat, protein, and lactose contents, were also lower in cloned cows. These lower yields could be linked to the higher apoptotic rate observed in cloned cows. Apoptosis is triggered by insulin-like factor growth binding protein 5 (IGFBP5) and plasminogen activator inhibitor (PAI), which both interact with CSN1S2. During our experiments, CSN1S2 transcript levels were lower in the mammary gland of cloned cows. The mammary cell apoptotic rate observed in cloned cows may have been related to the higher levels of DNA (cytosine-5-)-methyltransferase 1 (DNMT1) transcripts, coding for products that maintain the epigenetic status of cells. We conclude, therefore, that milk production in cloned cows differs slightly from that of noncloned cows. These differences may be due, in part, to a higher incidence of subclinical mastitis. They were associated with differences in cell apoptosis and linked to variations in DNMT1 mRNA. However, milk protein and fat contents were more similar among cloned cows than among noncloned cows. © 2016 American Dairy Science Association.

Ramayo-Caldas Y.,French National Institute for Agricultural Research | Renand G.,French National Institute for Agricultural Research | Ballester M.,French National Institute for Agricultural Research | Ballester M.,IRTA - Institute of Agricultural-Alimentary Research and Technology | And 2 more authors.
Genetics Selection Evolution | Year: 2016

Background: Studies to identify markers associated with beef tenderness have focused on Warner-Bratzler shear force (WBSF) but the interplay between the genes associated with WBSF has not been explored. We used the association weight matrix (AWM), a systems biology approach, to identify a set of interacting genes that are co-associated with tenderness and other meat quality traits, and shared across the Charolaise, Limousine and Blonde d'Aquitaine beef cattle breeds. Results: Genome-wide association studies were performed using ~500K single nucleotide polymorphisms (SNPs) and 17 phenotypes measured on more than 1000 animals for each breed. First, this multi-trait approach was applied separately for each breed across 17 phenotypes and second, between- and across-breed comparisons at the AWM and functional levels were performed. Genetic heterogeneity was observed, and most of the variants that were associated with WBSF segregated within rather than across breeds. We identified 206 common candidate genes associated with WBSF across the three breeds. SNPs in these common genes explained between 28 and 30 % of the phenotypic variance for WBSF. A reduced number of common SNPs mapping to the 206 common genes were identified, suggesting that different mutations may target the same genes in a breed-specific manner. Therefore, it is likely that, depending on allele frequencies and linkage disequilibrium patterns, a SNP that is identified for one breed may not be informative for another unrelated breed. Well-known candidate genes affecting beef tenderness were identified. In addition, some of the 206 common genes are located within previously reported quantitative trait loci for WBSF in several cattle breeds. Moreover, the multi-breed co-association analysis detected new candidate genes, regulators and metabolic pathways that are likely involved in the determination of meat tenderness and other meat quality traits in beef cattle. Conclusions: Our results suggest that systems biology approaches that explore associations of correlated traits increase statistical power to identify candidate genes beyond the one-dimensional approach. Further studies on the 206 common genes, their pathways, regulators and interactions will expand our knowledge on the molecular basis of meat tenderness and could lead to the discovery of functional mutations useful for genomic selection in a multi-breed beef cattle context. © 2016 Ramayo-Caldas et al.

Michot P.,French National Institute for Agricultural Research | Fantini O.,VetAgro Sup | Braque R.,Cabinet des Vignes de la Fontaine | Allais-Bonnet A.,ALLICE | And 10 more authors.
Genetics Selection Evolution | Year: 2015

Background: Since 2010, four Charolais calves with a congenital mechanobullous skin disorder that were born in the same herd from consanguineous matings were reported to us. Clinical and histopathological examination revealed lesions that are compatible with junctional epidermolysis bullosa (JEB). Results: Fifty-four extended regions of homozygosity (>1 Mb) were identified after analysing the whole-genome sequencing (WGS) data from the only case available for DNA sampling at the beginning of the study. Filtering of variants located in these regions for (i) homozygous polymorphisms observed in the WGS data from eight healthy Charolais animals and (ii) homozygous or heterozygous polymorphisms found in the genomes of 234 animals from different breeds did not reveal any deleterious candidate SNPs (single nucleotide polymorphisms) or small indels. Subsequent screening for structural variants in candidate genes located in the same regions identified a homozygous deletion that includes exons 17 to 23 of the integrin beta 4 (ITGB4), a gene that was previously associated with the same defect in humans. Genotyping of a second case and of six parents of affected calves (two sires and four dams) revealed a perfect association between this mutation and the assumed genotypes of the individuals. Mining of Illumina BovineSNP50 Beadchip genotyping data from 6870 Charolais cattle detected only 44 heterozygous animals for a 5.6-Mb haplotype around ITGB4 that was shared with the carriers of the mutation. Interestingly, none of the 16 animals genotyped for the deletion carried the mutation, which suggests a rather recent origin for the mutation. Conclusions: In conclusion, we successfully identified the causative mutation for a very rare autosomal recessive mutation with only one case by exploiting the most recent DNA sequencing technologies. © 2015 Michot et al.; licensee BioMed Central.

Sellem E.,ALLICE | Broekhuijse M.L.W.J.,CRV BV | Chevrier L.,IMV Technologies | Camugli S.,IMV Technologies | And 3 more authors.
Theriogenology | Year: 2015

Predicting in vivo fertility of bull ejaculates using in vitro-assessed semen quality criteria remains challenging for the breeding industry. New technologies such as computer-assisted semen analysis (CASA) and flow cytometry may provide accurate and objective methods to improve semen quality control. The aim of this study was to evaluate the relationship between semen quality parameters and field fertility of bull ejaculates. A total of 153 ejaculates from 19 Holstein bulls have been analyzed using CASA (postthawing semen motility and morphology) and several flow cytometric tests, including sperm DNA integrity, viability (estimated by membrane integrity), acrosomal integrity, mitochondria aerobic functionality and oxidation. Samples were analyzed both immediately after thawing and after 4 hours at 37 °C. A fertility value (FV), based on nonreturn rate at 56 days after insemination and adjusted for environment factors, was calculated for each ejaculate. Simple and multiple regressions have been used to correlate FV with CASA and flow cytometric parameters. Significant simple correlations have been observed between some parameters and FV (e.g., straight line velocity [μm/s], r2 = -0.12; polarized mitochondria sperm (%), r2 = 0.07), but the relation between simple parameter and FV was too week to predict the fertility. Partial least square procedure identified several mathematical models combining flow cytometer and CASA variables and had better correlations with FV (adjusted r2 ranging between 0.24 and 0.40 [P < 0.0001], depending on the number of included variables). In conclusion, this study suggests that quality assessment of thawed bull sperm using CASA and flow cytometry may provide a reasonable prediction of bovine semen fertility. Additional work will be required to increase the prediction reliability and promote this technology in routine artificial insemination laboratory practice. © 2015 Elsevier Inc.

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