References of "Gengler, Nicolas"
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See detailGenetic variability of the Skyros pony breed and its relationship with other Greek and foreign horse breeds
Bömcke, Elisabeth ULg; Gengler, Nicolas ULg; Cothran, E. G.

in Book of Abstracts of the 59th Annual Meeeting of the European Association for Animal Production (EAAP) (2008, August)

On the basis of phenotypes and genotypes, seven native breeds were identified in Greece. The Skyros pony is the more distinctive of these breeds. Using blood group and microsatellite loci, the aim of this ... [more ▼]

On the basis of phenotypes and genotypes, seven native breeds were identified in Greece. The Skyros pony is the more distinctive of these breeds. Using blood group and microsatellite loci, the aim of this study was to assess the genetic diversity of Skyros breed, using also available genealogical information, and to investigate its relationships with the other Greek and foreign horse breeds. Results showed that the Skyros breed presented similar level of genetic diversity to other European breeds. Comparisons between DNA-based and pedigree-based results showed that the loss of genetic diversity has probably occurred before the beginning of breed registration. However, the relatively high levels of heterozygosity and Polymorphism Information Content values indicated still sufficient residual genetic variability that could be useful for planning future breeding strategies for the breed conservation. Relationship study showed no association between genetic variation of native Greek breed and population size or degree of geographic isolation. Compared to other domestic breeds, most of the Greek breed showed closest relationships with Middle Eastern breeds, while the Skyros breed clustered surprisingly with Lithuanian horses. [less ▲]

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See detailGenetic parameters of saturated and monounsaturated fatty acids estimated by test-day model in Walloon dairy cattle
Soyeurt, Hélène ULg; Bastin, Catherine ULg; Dardenne, Pierre et al

in Journal of Dairy Science (2008, July 07)

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See detailEffects of allele frequency estimation on genomic predictions and inbreeding coefficients.
VanRaden, P. M.; Tooker, M. E.; Gengler, Nicolas ULg

in Journal of Dairy Science (2008, July), 91

Genetic calculations often require estimating allele frequencies, which differ across time due to selection and drift. Data were 50,000 simulated markers and 39,985 actual markers for 2391 genotyped ... [more ▼]

Genetic calculations often require estimating allele frequencies, which differ across time due to selection and drift. Data were 50,000 simulated markers and 39,985 actual markers for 2391 genotyped Holstein bulls. Gene content of relatives and gene frequencies in the base (founder) population were estimated using pedigrees and a linear model. Ancestors born since 1950 were included, for a total of 22,088 animals. Because pedigrees were very complete, only one unknown-parent group was used. Convergence to 5 digits of accuracy required about 1000 iterations. Total time was 2 processor days and proportional to number of animals times markers, but actual clock time was reduced by processing loci on separate chromosomes in parallel. Simple allele frequencies were obtained from only the known genotypes. True base frequencies were correlated with estimated base frequencies by 0.98 versus 0.94 with simple frequencies. Genomic predictions and inbreeding coefficients were computed in four ways, using true or estimated base frequencies, simple frequencies, or an “estimate” of .5 for each marker. When allele frequencies estimates were used instead of 0.5 to assign mixed model coefficients, solutions converged more slowly but predictions were more accurate. From simulated data, realized reliabilities for young bulls were 62.8% using either true or estimated base frequencies, 62.6% using simple frequencies, and 62.0% using frequencies set to 0.5. Pedigree and genomic inbreeding coefficients were correlated by 0.73 using true base frequencies, 0.67 using estimated base frequencies, 0.12 using simple frequencies, and 0.72 when frequencies were set to 0.5. Genomic inbreeding coefficients were biased downward by 7% to 9% using either frequency estimate, upward by 31% using 0.5, but were reasonable when true frequencies were used. Frequency estimation had small effects on genomic predictions but large effects on genomic inbreeding coefficients in both simulated and real data. [less ▲]

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See detailStrategies to incorporate genomic prediction into population-wide genetic evaluations
Gengler, Nicolas ULg; VanRaden, P. M.

in Journal of Dairy Science (2008, July), 91

Most current research on genomic selection is focusing on the accurate prediction of genomic breeding values. However selection solely based on genomic breeding values, despite being theoretically ... [more ▼]

Most current research on genomic selection is focusing on the accurate prediction of genomic breeding values. However selection solely based on genomic breeding values, despite being theoretically promising, is in practice only suboptimal for several reasons. The two most important are that only few animals are genotyped therefore having genomic prediction directly available and that rankings will change. With genomic breeding values potentially available in the near future, strategies are required to avoid any confusion in the mind of users. The aim of this study is to present three different strategies that could be used to incorporate genomic prediction into population-wide genetic evaluation. The three strategies are: 1) using selection index theory to combine both sources of information into a single set of breeding values; 2) for ungenotyped animals, compute conditional expectation of gene contents for SNP given molecular and pedigree data and use these predicted gene contents; and 3) integrate genomic breeding values as external information into genetic evaluation using a Bayesian framework. If strategy 1) is straight forward, additional steps have to be done to adjust breeding values for changes in those of relatives. A practical implementation is to use reliabilities of the genomic prediction, the population-wide genetic evaluation PA, and PA from the genotyped subset to set up a 3 x 3 matrix for each animal, with off-diagonal elements being functions of the 3 reliabilities. The use of strategy 2) is computationally much more challenging but leads directly to the needed covariance structures combining genomic relationship if known with pedigree relationships. Strategy 3) is potentially a good compromise because the theory is well established and has already been used in beef cattle to incorporate external breeding values. Also current genetic evaluation software can be easily modified to incorporate genomic breeding values [less ▲]

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See detailGenetic parameters of stearoyl coenzyme-A desaturase 9 activity estimated by test-day model
Arnould, Valérie ULg; Gengler, Nicolas ULg; Soyeurt, Hélène ULg

Conference (2008, July)

Dairy and beef products account for a large part of fat intake in human nutrition and therefore can be linked to dietary diseases. The stearoyl Coenzyme-A desaturase 9 (delta-9) gene was identified as a ... [more ▼]

Dairy and beef products account for a large part of fat intake in human nutrition and therefore can be linked to dietary diseases. The stearoyl Coenzyme-A desaturase 9 (delta-9) gene was identified as a potential functional candidate gene affecting milk fat composition in dairy cattle. The objective of this research was to estimate the genetic parameters of delta-9 activity indicator traits and to study the relationship between delta-9 activity as described by these indicator traits and common milk production traits. A total of 126,331 test-day records were obtained from 14,259 Holstein (> 84% Holstein gene) heifers belonging to 105 herds. The studied traits were milk yield, percentages of fat and protein, content of monounsaturated fatty acids, and 3 ratios reflecting the delta-9 activity (C14:1/ C14:0; C16:1/C16:0 and C18:1/C18). The used model was a multiple-trait random regressions test-day model and included as fixed effects: herd x date of test, class of age, and month x year. Random effects were herd x year of calving, permanent environmental, additive genetic, and residual effects. The fatty acid contents were estimated by mid-infrared spectrometry. Delta-9 activity varied within year and lactation. The obtained heritability estimates of delta-9 as well as the genetic and phenotypic correlation varied also through lactation. This study suggests potential improvements of delta-9 activity and subsequently milk fat composition can be achieved by animal management but also by breeding and animal selection. [less ▲]

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See detailGenetic parameters of stearoyl coenzyme-A desaturase 9 activity estimated by test-day model
Arnould, Valérie ULg; Gengler, Nicolas ULg; Soyeurt, Hélène ULg

in Journal of Dairy Science (2008, July), 91(E-Suppl. 2), 542

Dairy and beef products account for a large part of fat intake in human nutrition and therefore can be linked to dietary diseases. The stearoyl Coenzyme-A desaturase 9 (delta-9) gene was identified as a ... [more ▼]

Dairy and beef products account for a large part of fat intake in human nutrition and therefore can be linked to dietary diseases. The stearoyl Coenzyme-A desaturase 9 (delta-9) gene was identified as a potential functional candidate gene affecting milk fat composition in dairy cattle. The objective of this research was to estimate the genetic parameters of delta-9 activity indicator traits and to study the relationship between delta-9 activity as described by these indicator traits and common milk production traits. A total of 126,331 test-day records were obtained from 14,259 Holstein (> 84% Holstein gene) heifers belonging to 105 herds. The studied traits were milk yield, percentages of fat and protein, content of monounsaturated fatty acids, and 3 ratios reflecting the delta-9 activity (C14:1/ C14:0; C16:1/C16:0 and C18:1/C18). The used model was a multiple-trait random regressions test-day model and included as fixed effects: herd x date of test, class of age, and month x year. Random effects were herd x year of calving, permanent environmental, additive genetic, and residual effects. The fatty acid contents were estimated by mid-infrared spectrometry. Delta-9 activity varied within year and lactation. The obtained heritability estimates of delta-9 as well as the genetic and phenotypic correlation varied also through lactation. This study suggests potential improvements of delta-9 activity and subsequently milk fat composition can be achieved by animal management but also by breeding and animal selection. [less ▲]

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See detailPotential Estimation of Minerals Content in Cow Milk Using Mid-Infrared Spectrometry
Soyeurt, Hélène ULg; Bruwier, Damien; Gengler, Nicolas ULg et al

in ICAR Proceedings of the Biennial Sessions (2008, June 16)

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See detailPredicting bovine milk urea concentration for future test-day records in a management perspective
Bastin, Catherine ULg; Laloux, Laurent; Bertozzi, Carlo et al

Conference (2008, April 02)

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See detailGenetic variability of fatty acids in bovine milk
Soyeurt, Hélène ULg; Gengler, Nicolas ULg

in Biotechnologie, Agronomie, Société et Environnement = Biotechnology, Agronomy, Society and Environment [=BASE] (2008), 12(2), 203-210

Fatty acids composition of bovine milk influences the technological properties of butterfat and also presents some potential benefits for human health. Impact of feeding on fat composition is well ... [more ▼]

Fatty acids composition of bovine milk influences the technological properties of butterfat and also presents some potential benefits for human health. Impact of feeding on fat composition is well described in the literature; less information is available about the impact of genetics. Based on few studies, essentially conducted to isolate some feeding effect, the breed seemed to influence the fatty acids composition. The variation in the activity of δ-9 desaturase, key enzyme in the production of monounsaturated fatty acids and conjugated linoleic acids in milk, could explain these differences. Very few studies have been focussing on the estimation of genetic parameters of fatty acids composition. However, the moderate heritability estimates observed by these studies for the major fatty acids could suggest a potential genetic effect. [less ▲]

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See detailDosage des sels minéraux du lait par la spectrométrie du moyen-infrarouge. Outil pratique à destination des chercheurs, éleveurs et industriels laitiers
Soyeurt, Hélène ULg; Bruwier, Damien; Dardenne, Pierre et al

in 13ième Carrefour des Productions animales: L'élevage des ruminants en question: vérités et contre-vérités (2008, January 23)

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See detailOptiVal: Vers de nouveaux outils de gestion pour les éleveurs laitiers wallons, Prédire la réussite à l’insémination
Laloux, Laurent; Bastin, Catherine ULg; Glorieux, Géry et al

Poster (2008, January 23)

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See detailGenotype x environment interaction for milk yield in Holsteins using Luxembourg and Tunisian populations.
Hammami, Hedi ULg; Rekik, Boulbaba; Soyeurt, Hélène ULg et al

in Journal of Dairy Science (2008), 91(9), 3661-71

Test-day (TD) milk yield records of first-lactation Holstein cows in Luxembourg and Tunisia were analyzed using within-and between-country random regression TD models. Edited data used for within-country ... [more ▼]

Test-day (TD) milk yield records of first-lactation Holstein cows in Luxembourg and Tunisia were analyzed using within-and between-country random regression TD models. Edited data used for within-country analysis included 661,453 and 281,913 TD records in Luxembourg and Tunisia, respectively. The joint data included 730,810 TD records of 87,734 cows and 231 common sires. Both data sets covered calving years 1995 to 2006. Fourth-order Legendre polynomials for random effects and a Gibbs sampling method were used to estimate variance components of lactation curve parameters in separate and joint analyses. Genetic variances of the first 3 coefficients from Luxembourg data were 46 to 69% larger than corresponding estimates from the Tunisian data. Inversely, the Tunisian permanent environment variances for the same coefficients were 52 to 65% larger than the Luxembourg ones. Posterior mean heritabilities of 305-d milk yield and persistency, defined as estimated breeding values (EBV) at 280 days in milk-EBV at 80 days in milk, from between-country analysis were 0.42 and 0.12 and 0.19 and 0.08 in Luxembourg and Tunisia, respectively. Heritability estimates for the same traits from within-country analyses, mainly from the Tunisian data, were lower than those from the joint analysis. Genetic correlations for 305-d milk yield and persistency between countries were 0.60 and 0.36. Product moment and rank correlations between EBV of common sires for 305-d milk yield and persistency from within-country analyses were 0.38 and 0.41 and 0.27 and 0.26, respectively. Differences between genetic variances found in both countries reflect different milk production levels. Moreover, low genetic and rank correlations suggest different ranking of sires in the 2 environments, which implies the existence of a genotype x environment interaction for milk yield in Holsteins. [less ▲]

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See detailGenetic parameters for Tunisian Holsteins using a test-day random regression model.
Hammami, Hedi ULg; Rekik, Boulbaba; Soyeurt, Hélène ULg et al

in Journal of Dairy Science (2008), 91(5), 2118-26

Genetic parameters of milk, fat, and protein yields were estimated in the first 3 lactations for registered Tunisian Holsteins. Data included 140,187; 97,404; and 62,221 test-day production records ... [more ▼]

Genetic parameters of milk, fat, and protein yields were estimated in the first 3 lactations for registered Tunisian Holsteins. Data included 140,187; 97,404; and 62,221 test-day production records collected on 22,538; 15,257; and 9,722 first-, second-, and third-parity cows, respectively. Records were of cows calving from 1992 to 2004 in 96 herds. (Co)variance components were estimated by Bayesian methods and a 3-trait-3-lactation random regression model. Gibbs sampling was used to obtain posterior distributions. The model included herd x test date, age x season of calving x stage of lactation [classes of 25 days in milk (DIM)], production sector x stage of lactation (classes of 5 DIM) as fixed effects, and random regression coefficients for additive genetic, permanent environmental, and herd-year of calving effects, which were defined as modified constant, linear, and quadratic Legendre coefficients. Heritability estimates for 305-d milk, fat and protein yields were moderate (0.12 to 0.18) and in the same range of parameters estimated in management systems with low to medium production levels. Heritabilities of test-day milk and protein yields for selected DIM were higher in the middle than at the beginning or the end of lactation. Inversely, heritabilities of fat yield were high at the peripheries of lactation. Genetic correlations among 305-d yield traits ranged from 0.50 to 0.86. The largest genetic correlation was observed between the first and second lactation, potentially due to the limited expression of genetic potential of superior cows in later lactations. Results suggested a lack of adaptation under the local management and climatic conditions. Results should be useful to implement a BLUP evaluation for the Tunisian cow population; however, results also indicated that further research focused on data quality might be needed. [less ▲]

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See detailAccuracy of prediction of gene content in large animal populations and its use for candidate gene detection and genetic evaluation
Gengler, Nicolas ULg; Abras, S.; Verkenne, C. et al

in Journal of Dairy Science (2008), 91(4), 1652-1659

To estimate and to use the effects of single genes on quantitative traits, genotypes need to be known. However, in large animal populations, the majority of animals are not genotyped. These missing ... [more ▼]

To estimate and to use the effects of single genes on quantitative traits, genotypes need to be known. However, in large animal populations, the majority of animals are not genotyped. These missing genotypes have to be estimated. However, currently used methods are impractical for large pedigrees. An alternative method to estimate missing gene content, defined as the number of copies of a particular allele, was recently developed. In this study, the proposed method was tested by assessing its accuracy in estimation and use of gene content in large animal populations. This was done for the bovine transmembrane growth hormone receptor and its effects on first-lactation milk, fat, and protein test-day yields and somatic cell score in Holstein cows. Estimated gene substitution effects of replacing a copy of the phenylalanine-coding allele with a copy of the tyrosine-coding allele were 295 g/d for milk, -8.14 g/d for fat, -1.83 g/d for protein, and -0.022/d for somatic cell score. However, only the gene substitution effect for milk was found to be significant. The accuracy of the estimated effects was evaluated by simulations and permutations. To validate the use of predicted gene content in a mixed inheritance model, a cross-validation study was done. The model with an additional regression of milk, fat, and protein yields and SCS on predicted gene content showed a better capacity to predict breeding values for milk, fat, and protein. Given these results, the estimation and use of allelic effects using this method proved functional and accurate. [less ▲]

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See detailSampling genotype configurations in a large complex pedigree
Szydlowski, M.; Gengler, Nicolas ULg

in Journal of Animal Breeding & Genetics (2008), 125(5), 330-338

Many genetic problems can be solved by Monte Carlo method. This often requires sampling genotype configurations over pedigree. Current available samplers are inefficient for large animal pedigrees. A new ... [more ▼]

Many genetic problems can be solved by Monte Carlo method. This often requires sampling genotype configurations over pedigree. Current available samplers are inefficient for large animal pedigrees. A new sampler suitable for large complex pedigrees has been developed and evaluated. The sampler uses simple and iterative peeling algorithms alternately. The sampler was compared to two other samplers on hypothetical pedigree of 79 individuals and recessive disease. The behaviour of the sampler was evaluated in four experimental designs on real bovine pedigree of 907 903 animals. The application of the sampler was also exemplified in identical by descent study. [less ▲]

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See detailVariabilité génétique des composés 'Santé' du lait prédits par la spectrométrie du moyen-infrarouge
Soyeurt, Hélène ULg; Dehareng, Frédéric; Dardenne, Pierre et al

in 13ième Carrefour des Productions Animales: L'Elevage des ruminants en question: vérités et contre-vérités (2008)

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