References of "Charlier, Carole"
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See detailHigher male than female recombination rate in cattle is controlled by genetic variants effective in both sexes
Kadri, Naveen Kumar ULg; Harland, Chad ULg; Coppieters, Wouter ULg et al

Poster (2015, May 05)

We herein study genetic recombination in three dairy cattle populations from France, New-Zealand and the Netherlands. We apply a new phasing algorithm extracting familial information suited for large half ... [more ▼]

We herein study genetic recombination in three dairy cattle populations from France, New-Zealand and the Netherlands. We apply a new phasing algorithm extracting familial information suited for large half-sib families to reconstruct haplotypes and detect cross-overs (CO). The software is robust to genotyping and map errors. We identify more than 2,000,000 CO events in sperm cells transmitted by 3008 sires to 94,603 offspring, and more than 500,000 CO events in oocytes transmitted by 11,497 cows to 25,390 offspring. When measured in identical family structures, the average number of CO in males (24.0) was found to be larger than in females (21.8). In males, recombination rates were higher closer to telomeres whereas in females, recombination rates dropped at both centromeres and telomeres (probably as a result of lower informativity). The heritability of the global recombination rate (GRR) was close to 0.20 in males and to 0.08 in females. Genetic correlation ranged from 0.38 to 0.69 depending on the population, indicating that shared variants are influencing GRR in both genders. Haplotype-based genome-wide association studies revealed four genome-wide significant QTL, including two previously identified ones (involving REC8 and RNF212). For all QTLs, there was a positive correlation between haplotype effects across sexes, ranging from 0.35 to 0.68. We selected two reference panels of respectively 122 and 215 bulls sequenced at cover > 15x to impute variants in the New-Zealand and French populations. All variants identified by next-generating sequencing in 5 Mb windows encompassing the QTL peaks were imputed with Beagle in order to perform a sequence-based association study. For three QTLs, we identified missense mutations in genes known to be involved in meiosis among the most significantly associated variants. These variants were perfectly associated with the haplotypes underlying the QTL effects. The variant identified in RNF212 had already been reported, whereas missense mutations in MLH3 (N408S) and HFM1 (S1189L) are new findings. Surprisingly, variants previously identified in REC8 did not capture the QTL effect whereas variants in RNF212B, PPP1R3E, BCL2L2, HOMEZ and PABPN1 had much stronger association with the phenotype. The three missense mutations were significant in both genders with two of them accounting for approximately 10% of the genetic variance in males (the allelic substitution effect being approximately equal to one additional CO per genome). Our results are very different from reports of recombination in other species. For instance, in human, recombination rate is higher in females, distinct variants affect recombination rate in males and females and the genetic correlation is close to 0 whereas in cattle, we observed a higher recombination rate in males controlled by shared variants effective in both sexes. [less ▲]

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See detailScanning the genome for QTL affecting the recombination process in the male and female cattle germline
Kadri, Naveen Kumar ULg; Harland, Chad ULg; Coppieters, Wouter ULg et al

Poster (2015, February)

We herein study genetic recombination in three dairy cattle population from France, New-Zealand and The Netherlands. We apply a new phasing algorithm extracting familial information suited for large half ... [more ▼]

We herein study genetic recombination in three dairy cattle population from France, New-Zealand and The Netherlands. We apply a new phasing algorithm extracting familial information suited for large half-sib families to reconstruct haplotypes and detect cross-overs. The software is robust to genotyping errors and map errors (genome builts still contain errors for non-model organisms). We identify more than 2,000,000 cross-over events in sperm cells transmitted by 2942 sires to 94,049 offspring, and more than 500,000 cross-over events in oocytes transmitted by 10,943 cows to 23,850 offspring. The estimated number of cross-overs per gamete and its accuracy were influenced by the family structure (number of offsprings, parents and grand-parents genotyped). The average number of cross-overs in males (24.0) was larger than in females (21.8), even after correction for family structure. In males, recombination rates were higher closer to telomeres whereas in females, recombination rates dropped at both centromeres and telomeres (probably as a result of lower informativity). The heritability of the global recombination rate was close to 0.20 in males and to 0.10 in females and the genetic correlation was ~0.70, indicating that common genes are influencing both traits. Genome-wide association studies clearly confirmed QTL located close to REC8 and RNF212 in males. The QTL associated to REC8 was also detected in females and there was a positive correlation between QTL effects in males and females. The QTL associated to REC8 accounted for ~10% of the genetic variance in both males and females. [less ▲]

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See detailSelection in action: dissecting the molecular underpinnings of the increasing muscle mass of Belgian Blue Cattle
Druet, Tom ULg; Ahariz, Naïma ULg; Cambisano, Nadine ULg et al

Conference (2014, October 17)

Belgian Blue cattle are famous for their exceptional muscular development or “double-muscling”. This defining feature emerged following the fixation of a loss-of-function variant in the myostatin gene in ... [more ▼]

Belgian Blue cattle are famous for their exceptional muscular development or “double-muscling”. This defining feature emerged following the fixation of a loss-of-function variant in the myostatin gene in the eighties. Since then, sustained selection has further increased muscle mass of Belgian Blue animals to a comparable extent. In the present paper, we study the genetic determinants of this second wave of muscle growth. A scan for selective sweeps did not reveal the recent fixation of another allele with major effect on muscularity. However, a genome-wide association study identified two genome-wide significant and three suggestive QTLs affecting specific muscle groups and jointly explaining 8-21% of the heritability. The top two QTL are caused by presumably recent mutations on unique haplotypes that have rapidly risen in frequency in the population. While one appears on its way to fixation, the ascent of the other is compromised as the underlying MRC2 mutation causes crooked tail syndrome in homozygotes. Genomic prediction models indicate that the residual additive variance is largely polygenic. Contrary to complex traits in humans which have a near-exclusively polygenic architecture, muscle mass in beef cattle (as other production traits under directional selection), appears to be controlled by (i) a handful of recent mutations with large effect that rapidly sweep through the population, and (ii) a large number of presumably older variants with very small effects that rise slowly in the population (polygenic adaptation). [less ▲]

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See detailA 660-Kb Deletion with Antagonistic Effects on Fertility and Milk Production Segregates at High Frequency in Nordic Red Cattle: Additional Evidence for the Common Occurrence of Balancing Selection in Livestock
Kumar Kadri, Naveen; Sahana, Goutam; Charlier, Carole ULg et al

in PLoS Genetics (2014), 10(1), 1004049

In dairy cattle, the widespread use of artificial insemination has resulted in increased selection intensity, which has led to spectacular increase in productivity. However, cow fertility has ... [more ▼]

In dairy cattle, the widespread use of artificial insemination has resulted in increased selection intensity, which has led to spectacular increase in productivity. However, cow fertility has concomitantly severely declined. It is generally assumed that this reduction is primarily due to the negative energy balance of high-producing cows at the peak of lactation. We herein describe the fine-mapping of a major fertility QTL in Nordic Red cattle, and identify a 660-kb deletion encompassing four genes as the causative variant. We show that the deletion is a recessive embryonically lethal mutation. This probably results from the loss of RNASEH2B, which is known to cause embryonic death in mice. Despite its dramatic effect on fertility, 13%, 23% and 32% of the animals carry the deletion in Danish, Swedish and Finnish Red Cattle, respectively. To explain this, we searched for favorable effects on other traits and found that the deletion has strong positive effects on milk yield. This study demonstrates that embryonic lethal mutations account for a non-negligible fraction of the decline in fertility of domestic cattle, and that associated positive effects on milk yield may account for part of the negative genetic correlation. Our study adds to the evidence that structural variants contribute to animal phenotypic variation, and that balancing selection might be more common in livestock species than previously appreciated. [less ▲]

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See detailA missense mutation accelerating the gating of the lysosomal Cl-/H+-exchanger ClC-7/Ostm1 causes osteopetrosis with gingival hamartomas in cattle.
Sartelet, Arnaud ULg; Stauber, Tobias; Coppieters, Wouter ULg et al

in Disease Models & Mechanisms (2014), 7

Chloride/proton exchange by the lysosomal anion transporter ClC-7/Ostm1 is of pivotal importance for the physiology of lysosomes and bone resorption. Mice lacking either ClC-7 or Ostm1 develop a lysosomal ... [more ▼]

Chloride/proton exchange by the lysosomal anion transporter ClC-7/Ostm1 is of pivotal importance for the physiology of lysosomes and bone resorption. Mice lacking either ClC-7 or Ostm1 develop a lysosomal storage disease and mutations in either protein have been found to underlie osteopetrosis in mice and humans. Some human disease-causing CLCN7 mutations accelerate the usually slow voltage-dependent gating of ClC-7/Ostm1. However, it has remained unclear whether the fastened kinetics is indeed causative for the disease. Here we identified and characterized a new deleterious ClC-7 mutation in Belgian Blue Cattle with a severe symptomatology including peri-natal lethality and in most cases gingival hamartomas. By autozygosity mapping and genome-wide sequencing we found a handful of candidate variants, including a cluster of three private SNPs causing the substitution of a conserved tyrosine in the CBS2 domain of ClC-7 by glutamine. The case for ClC-7 was strengthened by subsequent examination of affected calves that revealed severe osteopetrosis. The Y750Q mutation largely preserved the lysosomal localization and assembly of ClC-7/Ostm1, but drastically accelerated its activation by membrane depolarization. These data provide first evidence that accelerated ClC-7/Ostm1 gating per se is deleterious, highlighting a physiological importance of the slow voltage-activation of ClC-7/Ostm1 in lysosomal function and bone resorption. [less ▲]

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See detailSelection in action: dissecting the molecular underpinnings of the increasing muscle mass of Belgian Blue Cattle.
Druet, Tom ULg; Ahariz, Naima; Cambisano, Nadine et al

in BMC genomics (2014), 15(1), 796

BACKGROUND: Belgian Blue cattle are famous for their exceptional muscular development or "double-muscling". This defining feature emerged following the fixation of a loss-of-function variant in the ... [more ▼]

BACKGROUND: Belgian Blue cattle are famous for their exceptional muscular development or "double-muscling". This defining feature emerged following the fixation of a loss-of-function variant in the myostatin gene in the eighties. Since then, sustained selection has further increased muscle mass of Belgian Blue animals to a comparable extent. In the present paper, we study the genetic determinants of this second wave of muscle growth. RESULTS: A scan for selective sweeps did not reveal the recent fixation of another allele with major effect on muscularity. However, a genome-wide association study identified two genome-wide significant and three suggestive quantitative trait loci (QTL) affecting specific muscle groups and jointly explaining 8-21% of the heritability. The top two QTL are caused by presumably recent mutations on unique haplotypes that have rapidly risen in frequency in the population. While one appears on its way to fixation, the ascent of the other is compromised as the likely underlying MRC2 mutation causes crooked tail syndrome in homozygotes. Genomic prediction models indicate that the residual additive variance is largely polygenic. CONCLUSIONS: Contrary to complex traits in humans which have a near-exclusive polygenic architecture, muscle mass in beef cattle (as other production traits under directional selection), appears to be controlled by (i) a handful of recent mutations with large effect that rapidly sweep through the population, and (ii) a large number of presumably older variants with very small effects that rise slowly in the population (polygenic adaptation). [less ▲]

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See detailA splice-acceptor site variant in the bovine PIGH gene causes glycosylphosphatidyl inositol deficiency and lethal arthrogryposis syndrome.
Sartelet, Arnaud ULg; Li, Wanbo; Pailhoux Eric et al

in Bayrou, Calixte; Cabaraux, Jean-François; Delguste, Catherine (Eds.) et al Proccedings of the 3rd Scientific Meetingof the Faculty of Veterinary Medecine (2013, October 11)

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See detailRilouke, une cellule de surveillance des défauts génétiques dans la race blanc bleu belge
Sartelet, Arnaud ULg; Tamma, Nico ULg; Chapon, Samuel et al

in Point Vétérinaire (2013), 339

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See detailScan for selective sweeps associated with muscular devolpment in Belgian Blue beef cattle
Druet, Tom ULg; Ahariz, Naïma ULg; Cambisano, Nadine ULg et al

Poster (2013, February)

The Belgian Blue beef cattle is well known for its double muscling phenotype resulting from fixation of a deletion in the myostatin gene. Since this fixation, further intensive selection for muscular ... [more ▼]

The Belgian Blue beef cattle is well known for its double muscling phenotype resulting from fixation of a deletion in the myostatin gene. Since this fixation, further intensive selection for muscular development has been particularly succesful. This response to selection might be due to fixation of more genetic variants increasing muscular development. In the present study, we search for selective sweeps in the Belgian Blue genome which might result from the fixation of such variants. To that end we used data from 593 sires genotyped with the BovineHD SNP array. In addition, we used the Belgian Blue dual purpose and the Holstein breeds as controls. We first performed scans for regions of complete homozygosity resulting from fixation. Large fixed regions were found around major genes known to be fixed in the Belgian Blue cattle breed (MSTN, PLAG1 and MC1R) but no other regions of the same magnitude was found. Among the smaller identified regions, only few of them were unique to the Belgian Blue breed. Statistical tests based on long range haplotype information were also implemented, revealing large regions in the genome of reduced haplotype homozygosity specific to the Belgian Blue breed. Some of these regions corresponded to known major genes (MSTN, roan locus, PLAG1 or MC1R) while other regions were new. To determine whether these regions might be the result of selection for muscular development, we performed association studies for muscular development. None of the identified QTL matched with the regions of reduced haplotype homozygosity and the largest QTLs did not presented evidence of strong selective sweeps. These results suggest that the response to selection for muscular development in Belgian Blue beef cattle is probably the result of polygenic selection. [less ▲]

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See detailSevrage rapide aux opiaces sous anesthesie (RODA).
DUBOIS, Nathalie ULg; Hallet, C.; Luppens, D. et al

in Revue medicale de Liege (2013), 68(5-6), 298-302

Rapid Opiate Detoxification under Anesthesia (RODA) involves the use of opiate antagonists combined with anesthesia and pharmacotherapy to reduce withdrawal symptoms. The aim of our study was to measure ... [more ▼]

Rapid Opiate Detoxification under Anesthesia (RODA) involves the use of opiate antagonists combined with anesthesia and pharmacotherapy to reduce withdrawal symptoms. The aim of our study was to measure the plasma concentrations of heroin metabolites and methadone during anesthesia and patient stay at the hospital in order to assess the amount of active substances at each protocol step. Plasma concentrations of antagonists were also quantified and compared to the recommended target values. Blood samples were drawn in 10 patients undergoing RODA at different times of the procedure (during anesthesia, in post-anesthesia care unit and in psychiatry unit). The plasma concentrations of heroin metabolites, methadone and antagonists were measured using a previously described method. Heroin active metabolites were no longer detected in the patient blood when helshe left the hospital; by contrast, methadone was still present at significant concentrations 3 days after the beginning of the detoxification procedure. Naltrexone analysis allowed us to adjust doses to insure opiate receptor blockade during acute withdrawal, which is a critical period. [less ▲]

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See detailIdentification of large selective sweeps associated with major genes in cattle.
Druet, Tom ULg; Perez-Pardal, L.; Charlier, Carole ULg et al

in Animal Genetics (2013), 44(6), 758-62

Selection for new favorable variants can lead to selective sweeps. However, such sweeps might be rare in the evolution of different species for which polygenic adaptation or selection on standing ... [more ▼]

Selection for new favorable variants can lead to selective sweeps. However, such sweeps might be rare in the evolution of different species for which polygenic adaptation or selection on standing variation might be more common. Still, strong selective sweeps have been described in domestic species such as chicken lines or dog breeds. The goal of our study was to use a panel of individuals from 12 different cattle breeds genotyped at high density (800K SNPs) to perform a whole-genome scan for selective sweeps defined as unexpectedly long stretches of reduced heterozygosity. To that end, we developed a hidden Markov model in which one of the hidden states corresponds to regions of reduced heterozygosity. Some unexpectedly long regions were identified. Among those, six contained genes known to affect traits with simple genetic architecture such as coat color or horn development. However, there was little evidence for sweeps associated with genes underlying production traits. [less ▲]

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See detailDetection of copy number variants in the horse genome and examination of their association with recurrent laryngeal neuropathy
Dupuis, Marie-Capucine; Zhang, Zhiyan ULg; Durkin, Keith ULg et al

in Animal Genetics (2013)

We used the data from a recently performed genome-wide association study using the Illumina Equine SNP50 beadchip for the detection of copy number variants (CNVs) and examined their association with ... [more ▼]

We used the data from a recently performed genome-wide association study using the Illumina Equine SNP50 beadchip for the detection of copy number variants (CNVs) and examined their association with recurrent laryngeal neuropathy (RLN), an important equine upper airway disease compromising performance. A total of 2797 CNVs were detected for 477 horses, covering 229 kb and seven SNPs on average. Overlapping CNVs were merged to define 478 CNV regions (CNVRs). CNVRs, particularly deletions, were shown to be significantly depleted in genes. Fifty-two of the 67 common CNVRs (frequency ! 1%) were validated by association mapping, Mendelian inheritance, and/or Mendelian inconsistencies. None of the 67 common CNVRs were significantly associated with RLN when accounting for multiple testing. However, a duplication on chromosome 10 was detected in 10 cases (representing three breeds) and two unphenotyped parents but in none of the controls. The duplication was embedded in an 8-Mb haplotype shared across breeds. [less ▲]

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See detailA missense mutation in the ClC-7 chloride channel causes hamartomas with osteopetrosis in cattle.
Sartelet, Arnaud ULg; Stauber, Tobias; Coppieters, Wouter ULg et al

Conference (2012, October 19)

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See detailAllelic heterogeneity of Crooked Tail Syndrome: result of balancing selection?
Sartelet, Arnaud ULg; Klingbeil, Pamela; Franklin, Chris et al

in Animal Genetics (2012), 43(5), 604-607

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See detailAncestral haplotype-based association mapping with generalized linear mixed models accounting for stratification
Zhang, Zhiyan; Guillaume, François; Sartelet, Arnaud ULg et al

in Bioinformatics (2012), 28(19), 2467-2473

Detailed reference viewed: 29 (12 ULg)