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Monnaie, France
Monnaie, France
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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.


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.


Kadri N.K.,University of Liège | Harland C.,University of Liège | Harland C.,Livestock Improvement Corporation | Faux P.,University of Liège | And 12 more authors.
Genome Research | Year: 2016

We herein study genetic recombination in three cattle populations from France, New Zealand, and the Netherlands. We identify 2, 395, 177 crossover (CO) events in 94, 516 male gametes, and 579, 996 CO events in 25, 332 female gametes. The average number of COs was found to be larger in males (23.3) than in females (21.4). The heritability of global recombination rate (GRR) was estimated at 0.13 in males and 0.08 in females, with a genetic correlation of 0.66 indicating that shared variants are influencing GRR in both sexes. A genome-wide association study identified seven quantitative trait loci (QTL) for GRR. Fine-mapping following sequence-based imputation in 14, 401 animals pinpointed likely causative coding (5) and noncoding (1) variants in genes known to be involved in meiotic recombination (HFM1, MSH4, RNF212, MLH3, MSH5) for 5/7 QTL, and noncoding variants (3) in RNF212B for 1/7 QTL. This suggests that this RNF212 paralog might also be involved in recombination. Most of the identified mutations had significant effects in both sexes, with three of them each accounting for ∼10% of the genetic variance in males. © 2016 Aldrup-MacDonald et al.


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.


PubMed | ALLICE and French National Institute for Agricultural Research
Type: Journal Article | Journal: Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie | Year: 2016

An important prerequisite for high prediction accuracy in genomic prediction is the availability of a large training population, which allows accurate marker effect estimation. This requirement is not fulfilled in case of regional breeds with a limited number of breeding animals. We assessed the efficiency of the current French routine genomic evaluation procedure in four regional breeds (Abondance, Tarentaise, French Simmental and Vosgienne) as well as the potential benefits when the training populations consisting of males and females of these breeds are merged to form a multibreed training population. Genomic evaluation was 5-11% more accurate than a pedigree-based BLUP in three of the four breeds, while the numerically smallest breed showed a<1% increase in accuracy. Multibreed genomic evaluation was beneficial for two breeds (Abondance and French Simmental) with maximum gains of 5 and 8% in correlation coefficients between yield deviations and genomic estimated breeding values, when compared to the single-breed genomic evaluation results. Inflation of genomic evaluation of young candidates was also reduced. Our results indicate that genomic selection can be effective in regional breeds as well. Here, we provide empirical evidence proving that genetic distance between breeds is only one of the factors affecting the efficiency of multibreed genomic evaluation.


PubMed | ALLICE and French National Institute for Agricultural Research
Type: | Journal: Genetics, selection, evolution : GSE | Year: 2016

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 dAquitaine beef cattle breeds.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.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.


PubMed | Allice and French National Institute for Agricultural Research
Type: Journal Article | Journal: 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 genotypeenvironment interactions.


Sellem E.,ALLICE | Broekhuijse M.L.W.J.,CRV B.V. | 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.


PubMed | CRV B.V., IMV Technologies and ALLICE
Type: Journal Article | Journal: Theriogenology | Year: 2015

Predicting invivo fertility of bull ejaculates using invitro-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 4hours at 37C. 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 [m/s], r(2)=-0.12; polarized mitochondria sperm (%), r(2)=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 r(2) 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.


Duittoz A.H.,University of Tours | Tillet Y.,University of Tours | Le Bourhis D.,Allice | Schibler L.,Allice
Animal Reproduction | Year: 2016

This review aims at giving an overview on the physiological events leading to puberty onset in mammals and more specifically in cattle. Puberty is an important developmental milestone in mammals involving numerous changes in various physiological regulations and behaviors. It is a physiological unique event integrating several important central regulations at the crossroad of adaptation to environment: reproductive axis, feeding behavior and nutritional controls, growth, seasonal rhythm and stress. Puberty onset is also an important economic parameter in replacement heifer program and in genomic selection (genomic bulls). The quest for advanced puberty onset should be carefully balanced by its impact on physiological parameters of the animal and its offspring. Thus one has to carefully consider each step leading to puberty onset and set up a strategy that will lead to early puberty without being detrimental in the long term. In this review, major contributions in the understanding of puberty process obtained in rodents, primates and farm animals such as sheep and cattle are discussed. In the first part we will detail the endocrine events leading to puberty onset with a special focus on the regulation of GnRH secretion. In the second part we will describe the neural mechanisms involved in silencing and reactivating the GnRH neuronal network. These central mechanisms are at the crossroad of the integration of environmental factors such as the nutritional status, the stress and the photoperiod that will be discussed in the third part. In the fourth part, we will discuss the genetic determinants of puberty onset and more particularly in humans, where several pathologies are associated with puberty delay or advance and in cattle where several groups have now identified genomic regions or gene networks associated with puberty traits. Last but not least, in the last part we will focus on the embryologist point of view, how to get good oocytes for in vitro fertilization and embryo development from younger animals.

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