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See detailGenomic screening in family-based association testing and the multiple testing problem
Van Steen, Kristel ULg; McQueen, M. B.; Herbert, A. et al

in Genetic Epidemiology. Supplement (2005), 28

The Human Genome Project and its spin- offs are making it increasingly feasible to determine the genetic basis of complex traits using genome- wide association studies. The statistical challenge of ... [more ▼]

The Human Genome Project and its spin- offs are making it increasingly feasible to determine the genetic basis of complex traits using genome- wide association studies. The statistical challenge of analyzing such studies stems from the severe multiple-comparison problem resulting from the analysis of thousands of SNPs. Our methodology for genome- wide family- based association studies, using single SNPs or haplotypes, can identify associations that achieve genome- wide significance. In relation to developing guidelines for our screening tools, we determined lower bounds for the estimated power to detect the gene underlying the disease- susceptibility locus, which hold regardless of the linkage disequilibrium structure present in the data. We also assessed the power of our approach in the presence of multiple disease- susceptibility loci. Our screening tools accommodate genomic control and use the concept of haplotype- tagging SNPs. Our methods use the entire sample and do not require separate screening and validation samples to establish genome- wide significance, as population- based designs do. [less ▲]

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See detailGenomic selection and scan for major genes for a new lamb survival trait for the New Zealand sheep industry
Auvray, Benoit; Vanderick, Sylvie ULg; Newman, Sheryl-Anne et al

Poster (2012, July)

Lambing percentage is one of the most significant factors affecting profitability on New Zealand sheep farms. Since the early 1990s, lambing percentage has increased at about 1% per year from a relatively ... [more ▼]

Lambing percentage is one of the most significant factors affecting profitability on New Zealand sheep farms. Since the early 1990s, lambing percentage has increased at about 1% per year from a relatively stable level of approximately 100%, and top performing sheep farms are now consistently achieving 150% or more. As lambing percentage increases, the proportion of ewes bearing twins and triplets increases accordingly. Lamb mortality rate in these multiples is higher than in singles, with triplets being particularly susceptible. Consequently, lamb survival has become increasingly important to the New Zealand sheep industry. Sheep Improvement Ltd. (SIL, New Zealand’s national sheep genetic evaluation system owned by Beef + Lamb NZ) records lamb survival to weaning but genetic improvement has been limited due to the low heritability of the trait and the current method of recording. To address those issues, we have developed an improved survival to weaning trait for industry implementation, which is more accurate and more heritable than the current SIL trait. This poster will present results of applying genome-enabled prediction procedures to the new trait to obtain molecular breeding values. It will also describe results from a genome wide association study using the new trait. [less ▲]

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See detailGenomic selection in French dairy cattle
Boichard, D; Guillaume, François ULg; Baur, A et al

in Animal Production Science (2012), 52(12), 115-120

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See detailGENOMIC SELECTION IN FRENCH DAIRY CATTLE
Boichard, D.; Guillaume, F.; Baur, A. et al

in Proceedings of the 9th World Congress on Genetics Applied to Livestock Production (2010)

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See detailGenomic structure and chromosomal mapping of the mouse transcription factor TEF-5 (Tead3) gene
Jacquemin, Patrick; Chen, Zhi; Martial, Joseph ULg et al

in Mammalian Genome : Official Journal of the International Mammalian Genome Society (1999), 10(6), 632-4

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See detailGenomic structure of new Peach Mosaic viroid variants in Tunisia
Fekih Hassen, I.; Massart, Sébastien ULg; Kummert, J. et al

Poster (2006)

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See detailGenomic structure of new tunisian peach latent mosaic viroid variants
Fekih Hassen, I.; Massart, Sébastien ULg; Roussel, S. et al

Poster (2006)

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See detailGenomic structure of new Tunisian peach latent mosaic viroid variants.
Hassen, I Fekih; Massart, Sébastien ULg; Roussel, S. et al

in Communications in agricultural and applied biological sciences (2006), 71(3 Pt B), 1257-1265

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See detailGenomic structure, organisation, and promoter analysis of the bovine (Bos taurus) Mx1 gene
Gérardin; Baise, Etienne ULg; Pire, Grégory et al

in Gene (2004), 326

Some MX proteins are known to confer a specific resistance against a panel of single-stranded RNA viruses. Many diseases due to such viruses are known to affect cattle worldwide, raising the possibility ... [more ▼]

Some MX proteins are known to confer a specific resistance against a panel of single-stranded RNA viruses. Many diseases due to such viruses are known to affect cattle worldwide, raising the possibility that the identification of an antiviral isoform of a bovine MX protein would allow the implementation of genetic selection programs aimed at improving innate resistance of cattle. With this potential application in mind, the present study was designed to isolate the bovine Mx1 gene including its promoter region and to investigate its genomic organisation and promoter reactivity. The bovine Mx1 gene is made up of 15 exons. All exon-intron boundaries conformed to the consensus sequences. A PCR product that contained a approximately 1-kb, 5'-flanking region upstream from the putative transcription start site was sequenced. Unexpectedly, this DNA region did not contain TATA or CCAAT motifs. A computer scan of the region disclosed a series of putative binding sites for known cytokines and transcription factors. There was a GAAAN(1-2)GAAA(C/G) motif, typical of an interferon-sensitive responsive element, between -118 and -107 from the putative transcription start site. There were also a NF-kappaB, two interleukin-6 binding sites, two Sp1 sites and five GC-rich boxes. The region also contained 12 stretches of the GAAA type, as described in all IFN-inducible genes. Bovine Mx1 expression was assessed by Northern blotting and immunofluorescence in the Madin Darby bovine kidney cells (MDBK) cell line treated with several stimuli. In conclusion, the bovine Mx1 gene and promoter region share the major structural and functional characteristics displayed by their homologs described in the rainbow trout, chicken, mouse and man. [less ▲]

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See detailGenomic structure, promoter analysis and expression of the porcine (Sus scrofa) TLR4 gene.
Thomas, Anne; Broers, Aurore ULg; Vandegaart, Hélène ULg et al

in Molecular Immunology (2006), 43(6), 653-659

Toll-like receptor 4 (TLR4) is essential for initiating the innate response to lipopolysaccharide (LPS) from Gram-negative bacteria by acting as a signal-transducing receptor. As the pig industry faces a ... [more ▼]

Toll-like receptor 4 (TLR4) is essential for initiating the innate response to lipopolysaccharide (LPS) from Gram-negative bacteria by acting as a signal-transducing receptor. As the pig industry faces a unique array of related pathogens, it is anticipated that the genotype of swine TLR4 could be of crucial importance in future strategies aimed at improving genetic resistance to infectious diseases. In order to help in investigating TLR4 as a candidate disease-resistance gene in pigs, we established its genomic structure and produced sufficient flanking intronic sequences to enable simple PCR amplification of the coding portions of the gene. Expression in different porcine tissues was studied and showed splicing variations in mRNA sequences. The cDNA sequence for poTLR4 contains an open reading frame of 2526bp that codes for 841 aa, 98 and 568bp in the 5'- and 3'-UTRs, respectively. Overall, the general organization of porcine, human, murine, and avian TLR4 genes is quite similar: three exons with the third one very long. A high level of conservation of the size and the sequence, especially for the two last exons and particularly in the sequence corresponding to the LRRs and TIR domain, is observed between species. The important antimicrobial properties of these proteins may account for a conservative selection pressure on these TLR4 coding sequences. Several putative binding sites described in the human and murine promoter of TLR4 genes have been identified in the 5'-flanking region of poTLR4. Conversely, this region lacks a TATA box, consensus initiator sequences, or GC-rich regions. The basic sequence data gathered will allow the establishment of an inventory of naturally occurring variation in porcine TLR4, so that alleles can be tested for disease association studies. [less ▲]

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See detailGenomic structure, promoter analysis, and expression of the porcine (Sus scrofa) Mx1 gene
Thomas, Anne; Palm, Mélanie; Broers, Aurore ULg et al

in Immunogenetics (2006), 58

Allelic polymorphisms at the mouse Mx1 locus affect the probability of survival after experimental influenzal disease, raising the possibility that marker-assisted selection using the homologous locus ... [more ▼]

Allelic polymorphisms at the mouse Mx1 locus affect the probability of survival after experimental influenzal disease, raising the possibility that marker-assisted selection using the homologous locus could improve the innate resistance of pigs to natural influenza infections. Several issues need to be resolved before efficient large scale screening of the allelic polymorphism at the porcine (Sus scrofa) Mx1 locus can be implemented. First, the Mx1 genomic structure has to be established and sufficient flanking intronic sequences have to be gathered to enable simple PCR amplification of the coding portions of the gene. Then, a basic knowledge of the promoter region needs to be obtained as an allelic variation there can significantly alter absolute levels and/or tissue-specificity of MX protein expression. The results gathered here show that the porcine Mx1 gene and promoter share the major structural and functional characteristics displayed by their homologs described in cattle, mouse, chicken, and man. The crucial function of the proximal interferon-sensitive response elements motif for gene expression is also demonstrated. The sequence data compiled here will allow an extensive analysis of the polymorphisms present among the widest spectrum possible of porcine breeds with the aim to identify an Mx1 allele providing antiviral resistance. [less ▲]

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See detailGénomique des maladies inflammatoires intestinales
Louis, Edouard ULg; Libioulle, Cécile ULg; Reenaers, Catherine ULg et al

in Revue Médicale de Liège (2009), 64

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See detailGenomische Selektion: ein Meilenstein auch in der Schweinezucht?
Buske, Bernd ULg; Gengler, Nicolas ULg

Article for general public (2009)

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See detailGenophotodermatoses.
Arrese Estrada, Jorge ULg; Henry, Frédérique ULg; Pierard, Gérald ULg

in Revue Médicale de Liège (2005), 60 Suppl 1

Genophotodermatoses can result from a defect in melanin synthesis, a defect in DNA repair or a congenital photosensibility.

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See detailGenotoxic potential of aqueous extracts of Artemisia verlotorum on the cell cycle of Allium cepa
Souza, LFB; Laughinghouse IV, Haywood ULg; Pastori, T et al

in International Journal of Environmental Studies (2010), 67(6), 871-877

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See detailGénotrichoses alopéciantes de l'enfance.
Franchimont, Claudine ULg; Pierard, Gérald ULg

in Dermatologie Actualité (2007), 104

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See detailLe genotypage RHD foetal sur sang maternel dans le suivi prenatal des patientes Rh D negatif
Dricot, J. F.; Minon, J. M.; Schaaps, Jean-Pierre ULg et al

in Revue Médicale de Liège (2006), 61(12), 820-6

Since the beginning of RHD genotyping in maternal plasma, no Rh D positive baby was diagnosed RHD negative in our institution. Genotyping from circulating DNA in maternal plasma is as efficient as ... [more ▼]

Since the beginning of RHD genotyping in maternal plasma, no Rh D positive baby was diagnosed RHD negative in our institution. Genotyping from circulating DNA in maternal plasma is as efficient as genotyping on amniocyts but without the associated risks. We propose a prophylactic injection based on fetal genotyping RHD in maternal blood with 300 microg anti-D immunoglobulin at 28 weeks of amenhorrea in all of Rh D negative pregnant women whitch fetuses positive RHD. [less ▲]

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See detailGenotype by Environment Interaction for Production Traits of Holsteins Using Two Countries as Model: Luxembourg and Tunisia
Hammami, Hedi ULg

Doctoral thesis (2009)

Under globalization, breeding organizations are selecting animals and exchanging germplasm across various environments. Ignoring genotype by environment interaction (G x E) may affect the efficiency of ... [more ▼]

Under globalization, breeding organizations are selecting animals and exchanging germplasm across various environments. Ignoring genotype by environment interaction (G x E) may affect the efficiency of breeding strategies and limit outcomes from cooperation between breeding programs. Quantifying the effectiveness of indirect selection and effects of G x E for different breeds is therefore necessary. The objective of this thesis was to evaluate the magnitude of G x E for milk yield using Luxembourg and Tunisian Holstein populations. In fact, these two countries rely considerably on importation of superior genes from diverse origins for their breeding programs. This study needed records on both the genotype and the environment. In the first part of this thesis, genetic ties between the two populations were studied. Additive relationships and genetic similarity were important and genetic links have been strengthened with time which allowed the analysis of the phenotypic expression of daughters of common sires under each of these tow production environments. In the second part, genetic parameters for production traits of Tunisian Holsteins were estimated by a test-day random regression model (RRTD). Heritability estimates for 305-d milk, fat and protein yields were low to moderate (0.12 to 0.18) suspecting difficulties of high-producing cows to express their potential under limiting production conditions. In the third part, G x E for milk yield and persistency were investigated using character state models, where milk yield in each country was considered as a separate trait, and where the country border delimitation was designed as an environmental character state. A RRTD sire model was applied and was extended to a RRTD animal model. Significant G x E was detected for milk yield and persistency by both models. Large differences in genetic and permanent environmental variances between the two countries were observed. Genetic correlations for 305-d milk yield and persistency between Luxembourg and Tunisian Holsteins were 0.50 and 0.43 (sire model) and 0.60 and 0.36 (animal model). Moreover, low rank correlations obtained between estimated breeding values of common sires translate a significant re-ranking between the two environments. At the end of this thesis, a herd management (HM) parameter reflecting feeding and management intensity was defined. Three HM levels were identified in each country and G x E was investigated within- and across-environments. Significant G x E was detected between the Tunisian HM levels, whereas, only heterogeneous genetic variance for milk yield with limited re-ranking of sires across the three Luxembourg environments was observed. Overall, this thesis shows that under constraining environmental effects, selection for adaptive traits among economically valuable traits under their specific conditions is needed for low-input systems. When satisfactory feeding resources, management and husbandry practices are available, high degree environmental sensitivity is desired and the use of a high yielding breed may be encouraged. [less ▲]

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See detailGenotype by environment interaction in dairy cattle
Hammami, Hedi ULg; Rekik, Boulbaba; Gengler, Nicolas ULg

in Biotechnologie, Agronomie, Société et Environnement = Biotechnology, Agronomy, Society and Environment [=BASE] (2009), 13(1), 155-164

The aim of this literature review was to identify the existence and scope of genotype by environment interaction (G x E) from reports on dairy cattle populations in different management systems, Methods ... [more ▼]

The aim of this literature review was to identify the existence and scope of genotype by environment interaction (G x E) from reports on dairy cattle populations in different management systems, Methods applied to deal with G x E (controlled experiments and large data modeling) were discussed. A G x E was confirmed essentially when high differences between production environments and/or genotypes (genetically distant genotypes) were observed. Environmental effects were aggregated in most studies and identification of the components of the environment was largely unresolved, with only a few studies based on more definite-descriptors of environment. The implications of G x E on breeding decisions are discussed. Breeders should select genotypes on production traits within environmental conditions comparable to where candidate animals are intended to perform. [less ▲]

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See detailGenotype x Climate interactions for protein yield using four European Holstein Populations
Hammami, Hedi ULg; Carabaño, Maria-Jesus; Logar, Betka et al

Conference (2014)

Detailed reference viewed: 10 (1 ULg)