References of "Gengler, Nicolas"
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See detailExpressing female fertility in the Walloon region of Belgium: how to do?
Vanderick, Sylvie ULiege; Bastin, Catherine ULiege; Gengler, Nicolas ULiege

Conference (2009, August)

Since September 2007, the Walloon Region of Belgium has used a genetic evaluation system for pregnancy rate in Holsteins and has participated in 3 of the 5 MACE trait INTERBULL runs for female fertility ... [more ▼]

Since September 2007, the Walloon Region of Belgium has used a genetic evaluation system for pregnancy rate in Holsteins and has participated in 3 of the 5 MACE trait INTERBULL runs for female fertility. In order to define general way of female fertility expression, a principal component analysis was carried out on six published foreign female fertility indexes. Results of were used to compute a direct female fertility index with the INTERBULL international female fertility proofs available on the Walloon scale. An indirect female fertility index was also developed in order to increase reliability of young bulls. Approximate procedure based on selection index was used to combine both indexes in an overall index called combined female fertility index. This index was highly correlated with the direct female fertility index (.96) and the first principal component (.85), therefore it was considered as good expression of female fertility. Moreover, this allowed recovering 4,019 INTERBULL bulls with a publishable female fertility index. [less ▲]

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See detailEvaluations génétiques des verrats Piétrain en Wallonie
Dufrasne, Marie ULiege; Gengler, Nicolas ULiege

Diverse speeche and writing (2009)

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See detailGenetic variability of test-day stearoyl coenzyme-A desaturase 9 activity
Arnould, Valérie ULiege; Gengler, Nicolas ULiege; Soyeurt, Hélène ULiege

Conference (2009, July)

Milk fatty acid (FA) profile is far from the optimal fat composition in regards to human health. Different natural sources of variation such as feeding or genetics could be used to modify the contents of ... [more ▼]

Milk fatty acid (FA) profile is far from the optimal fat composition in regards to human health. Different natural sources of variation such as feeding or genetics could be used to modify the contents of unsaturated fatty acids. The impact of feeding is well described; however, genetics effects on the milk FA composition are not well studied. Increasing the unsaturated fatty acids contents of bovine milk could have the potential to raise the nutritive and therapeutic values of dairy products. 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 study the genetic variability on this enzyme activity across lactations. A total of 199,977 test-day records were obtained from 29,603 Holstein cows in first lactation, 154,267 records from 23,453 Holstein cows in second lactation, and 173,244 records from 75,887 Holstein cows in third and later lactations. The used model was a multiple-trait random regressions test-day model. Fixed effects were: herd × date of test, and class of age. Random effects were: herd × year of calving, permanent environmental, additive genetic, and residual effects. The studied traits were milk yield, protein content, percentage of fat, monounsaturated fatty acids estimated by mid-infrared spectrometry, and the ratios reflecting the delta-9 activity. Obtained heritability estimates of delta-9 as well as the genetic and phenotypic correlations varied across lactations. These results suggest potential improvements of milk fat composition based on delta-9 activity using animal selection and appropriate management practices. [less ▲]

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See detailEquivalent mixed model for joint genetic evaluation considering molecular and phenotypic information
Gengler, Nicolas ULiege; Colinet, Frédéric ULiege

Conference (2009, July)

Currently efforts are underway to introduce molecular information into genetic evaluation systems. A particular situation is genomic selection however simpler cases exists where major genes are known and ... [more ▼]

Currently efforts are underway to introduce molecular information into genetic evaluation systems. A particular situation is genomic selection however simpler cases exists where major genes are known and used by breeders. A new alternative strategy for the prediction of gene effects and especially their smooth integration into genetic evaluations based on an equivalent method was developed from existing theory. Underlying hypothesis were based on the idea that knowledge of genotypes will not affect overall additive genetic variance but only change expected values of genetic effects for animals with known genotypes. The developed equations were modified to allow that not all animals were genotyped. As the underlying mixed model is open a very large range of models can be used in situations including random regression models, multipletrait, maternal effects and multiple-across-country-evaluation models. Computations involved successive solving of two mixed models, with the use of an linear extrapolation to speed up convergence of gene effects. The method was tested for several known major genes and QTL, e.g. for the mh gene in the dual-purpose Belgian Blue population in Belgium. Modifications of the method could also be developed to be useful in the context of genomic selection. [less ▲]

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See detailPotential estimation of major mineral contents in cow milk using mid-infrared spectrometry.
Soyeurt, Hélène ULiege; Bruwier, Damien; Romnee, Jean-Michel et al

in Journal of Dairy Science (2009), 92(6), 2444-2454

Milk and dairy products are a major source of minerals, particularly calcium, involved in several metabolic functions in humans. Currently, several dairy products are enriched with calcium to prevent ... [more ▼]

Milk and dairy products are a major source of minerals, particularly calcium, involved in several metabolic functions in humans. Currently, several dairy products are enriched with calcium to prevent osteoporosis. The development of an inexpensive and fast quantitative analysis for minerals is required to offer dairy farmers an opportunity to improve the added value of the produced milk. The aim of this study was to develop 5 equations to measure Ca, K, Mg, Na, and P contents directly in bovine milk using mid-infrared (MIR) spectrometry. A total of 1,543 milk samples were collected between March 2005 and May 2006 from 478 cows during the Walloon milk recording and analyzed by MIR spectrometry. Using a principal component approach, 62 milk samples were selected by their spectral variability and separated in 2 calibration sets. Five outliers were detected and deleted. The mineral contents of the selected samples were measured by inductively coupled plasma atomic emission spectrometry. Using partial least squares combined with a repeatability file, 5 calibration equations were built to estimate the contents of Ca, K, Mg, Na, and P in milk. To assess the accuracy of the developed equations, a full cross-validation and an external validation were performed. The cross-validation coefficients of determination (R(2)cv) were 0.80, 0.70, and 0.79 for Ca, Na, and P, respectively (n = 57), and 0.23 and 0.50 for K and Mg, respectively (n = 31). Only Ca, Na, and P equations showed sufficient R(2)cv for a potential application. These equations were validated using 30 new milk samples. The validation coefficients of determination were 0.97, 0.14, and 0.88 for Ca, Na, and P, respectively, suggesting the potential to use the Ca and P calibration equations. The last 30 samples were added to the initial milk samples and the calibration equations were rebuilt. The R(2)cv for Ca, K, Mg, Na, and P were 0.87, 0.36, 0.65, 0.65, and 0.85, respectively, confirming the potential utilization of the Ca and P equations. Even if new samples should be added in the calibration set, the first results of this study showed the feasibility to quantify the calcium and phosphorus directly in bovine milk using MIR spectrometry. [less ▲]

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See detailEvaluation génétique du porcs en Wallonie
Dufrasne, Marie ULiege; Hammami, Hedi ULiege; Gengler, Nicolas ULiege

Diverse speeche and writing (2009)

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See detailCombine pedigree and marker information into a single estimator for the calculation of relationships
Bömcke, Elisabeth ULiege; Gengler, Nicolas ULiege

Poster (2009, May)

Relationship coefficients are particularly useful to improve genetic management of endangered populations. Estimation of relationships was traditionally based on pedigree data but, today, numerous methods ... [more ▼]

Relationship coefficients are particularly useful to improve genetic management of endangered populations. Estimation of relationships was traditionally based on pedigree data but, today, numerous methods already exist to replace pedigrees by molecular data. However, genotyping a complete population for a sufficient number of markers can be impossible, e.g., in case of local and/or rare breeds. The idea was therefore to develop a new method to estimate relationship by combining molecular with pedigree data into a single estimator. Originally developed for the management of an endangered horse population, it will be useful for specific situations, where neither pedigree nor molecular data are complete. Two questions appeared: What and how to combine? Following the principle that things have to be similar to be combined, we compared two coefficients that have the advantage to be similarly defined: the additive relationship coefficient (axy) calculated from pedigrees and the total allelic relationship (taxy) obtained from markers. Wright relationship coefficient (rped,xy) were also compared to taxy, transformed into rmol,xy, to highlight the influence of inbreeding. The results showed the influence of inbreeding, of marker quality and the tendency of molecular coefficients to overestimate the relationship among individuals. The method to combine the selected coefficients was also determined. Various parameters were taken into account in the model: number of markers and quality (e.g. marker informativeness), mutation rate, pedigree quality (e.g. generation-equivalents), … The combined estimator has several advantages. Especially, negative relationship values obtained in literature with molecular-based estimators in case of small inbred populations can be avoided. [less ▲]

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See detailEstimation of test-day model (co)variance components across breeds using New Zealand dairy cattle data
Vanderick, Sylvie ULiege; Harris, Bevin; Pryce, Jenny et al

in Journal of Dairy Science (2009), 92(3), 1240-1252

In New Zealand, a large proportion of cows are currently crossbreds, mostly Holstein-Friesians (HF) x Jersey (JE). The genetic evaluation system for milk yields is considering the same additive genetic ... [more ▼]

In New Zealand, a large proportion of cows are currently crossbreds, mostly Holstein-Friesians (HF) x Jersey (JE). The genetic evaluation system for milk yields is considering the same additive genetic effects for all breeds. The objective was to model different additive effects according to parental breeds to obtain first estimates of correlations among breed-specific effects and to study the usefulness of this type of random regression test-day model. Estimates of (co) variance components for purebred HF and JE cattle in purebred herds were computed by using a single-breed model. This analysis showed differences between the 2 breeds, with a greater variability in the HF breed. (Co) variance components for purebred HF and JE and crossbred HF x JE cattle were then estimated by using a complete multibreed model in which computations of complete across-breed (co)variances were simplified by correlating only eigenvectors for HF and JE random regressions of the same order as obtained from the single-breed analysis. Parameter estimates differed more strongly than expected between the single-breed and multibreed analyses, especially for JE. This could be due to differences between animals and management in purebred and nonpurebred herds. In addition, the model used only partially accounted for heterosis. The multibreed analysis showed additive genetic differences between the HF and JE breeds, expressed as genetic correlations of additive effects in both breeds, especially in linear and quadratic Legendre polynomials (respectively, 0.807 and 0.604). The differences were small for overall milk production (0.926). Results showed that permanent environmental lactation curves were highly correlated across breeds; however, intraherd lactation curves were also affected by the breed-environment interaction. This result may indicate the existence of breed-specific competition effects that vary through the different lactation stages. In conclusion, a multibreed model similar to the one presented could optimally use the environmental and genetic parameters and provide breed-dependent additive breeding values. This model could also be a useful tool to evaluate crossbred dairy cattle populations like those in New Zealand. However, a routine evaluation would still require the development of an improved methodology. It would also be computationally very challenging because of the simultaneous presence of a large number of breeds. [less ▲]

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See detailLe BCS, une méthode simple à la source de conseils variés : ration, repro et santé
Laloux, Laurent; Bastin, Catherine ULiege; Gillon, Alain ULiege et al

Poster (2009, February 11)

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See detailEvaluation génétique du porc en Wallonie
Dufrasne, Marie ULiege; Hammami, Hedi ULiege; Gengler, Nicolas ULiege

Diverse speeche and writing (2009)

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See detailEnvironmental sensitivity for milk yield in Luxembourg and Tunisian Holsteins by herd management level.
Hammami, Hedi ULiege; Rekik, Boulbaba; Bastin, Catherine ULiege et al

in Journal of Dairy Science (2009), 92(9), 4604-12

Milk production data of Luxembourg and Tunisian Holstein cows were analyzed using herd management (HM) level. Herds in each country were clustered into high, medium, and low HM levels based on solutions ... [more ▼]

Milk production data of Luxembourg and Tunisian Holstein cows were analyzed using herd management (HM) level. Herds in each country were clustered into high, medium, and low HM levels based on solutions of herd-test-date and herd-year of calving effects from national evaluations. Data from both populations included 730,810 test-day (TD) milk yield records from 87,734 first-lactation cows. A multi-trait, random regression TD model was used to estimate (co)variance components for milk yield within and across country HM levels. Additive genetic and permanent environmental variances of TD milk yields varied with management level in Tunisia and Luxembourg. Additive variances were smaller across HM levels in Tunisia than in Luxembourg, whereas permanent environmental variances were larger in Tunisian HM levels. Highest heritability estimates of 305-d milk yield (0.41 and 0.21) were found in high HM levels, whereas lowest estimates (0.31 and 0.12, respectively) were associated with low HM levels in both countries. Genetic correlations among Luxembourg HM levels were >0.96, whereas those among Tunisian HM levels were below 0.80. Respective rank orders of sires ranged from 0.73 to 0.83 across Luxembourg environments and from 0.33 to 0.42 across Tunisian HM levels indicating high re-ranking of sires in Tunisia and only a scaling effect in Luxembourg. Across-country environment analysis showed that estimates of genetic variance in the high, medium, and low classes of Tunisian environments were 45, 69, and 81% lower, respectively, than the estimate found in the high Luxembourg HM level. Genetic correlations among 305-d milk yields in Tunisian and Luxembourg HM environments ranged from 0.39 to 0.79. The largest estimated genetic correlation was found between the medium Luxembourg and high Tunisian HM levels. Rank correlations for common sires' estimated breeding values among HM environments were low and ranged from 0.19 to 0.39, implying the existence of genotype by environment interaction. These results indicate that daughters of superior sires in Luxembourg have their genetic expression for milk production limited under Tunisian environments. Milk production of cows in the medium and low Luxembourg environments were good predictors of that of their paternal half-sisters in the high Tunisian HM level. Breeding decisions in low-input Tunisian environment should utilize semen from sires with daughters in similar production environments rather than semen of bulls proven in higher management levels. [less ▲]

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See detailAccessing genotype by environment interaction using within- and across-country test-day random regression sire models
Hammami, Hedi ULiege; Rekik, Boulbaba; Soyeurt, Hélène ULiege et al

in Journal of Animal Breeding & Genetics (2009), 126(5), 366-377

First-lactation test-day (TD) milk records of Luxembourg and Tunisian Holsteins were analysed for evidence of genotype by environment interaction (G · E). The joint data included 730 810 TD records of 87 ... [more ▼]

First-lactation test-day (TD) milk records of Luxembourg and Tunisian Holsteins were analysed for evidence of genotype by environment interaction (G · E). The joint data included 730 810 TD records of 87 734 cows and 231 common sires. Random regression TD sire models with fourth-order Legendre polynomials were used to estimate genetic parameters via within- and across-country analyses. Daily heritability estimates of milk yield from within-country analysis were between 0.11 and 0.32, and 0.03 and 0.13 in Luxembourg and Tunisia, respectively. Heritability estimates for 305-day milk yield and persistency (defined as the breeding value for milk yield on DIM 280 minus the breeding value on DIM 80) were lower for Tunisian Holsteins compared with the Luxembourg population. Specifically, heritability for 305-day milk yield was 0.16 for within- and 0.11 for across-country analyses for Tunisian Holsteins and 0.38 for within- and 0.40 for across-country analyses for Luxembourg Holsteins. Heritability for apparent persistency was 0.02 for both within and across-country analyses for Tunisian Holsteins and 0.08 for within and 0.09 for across-country analyses for Luxembourg Holsteins. Genetic correlations between the two countries were 0.50 for 305-day milk yield and 0.43 for apparent persistency. Moreover, rank correlations between the estimated breeding values of common sires for 305-day milk yield and persistency, estimated separately in each country, were low. Low genetic correlations are evidence for G · E for milk yield production while low rank correlations suggest different rankings of sires in both environments. Results from this study indicate that milk production of daughters of the same sires depends greatly on the production environment and that importing high merit semen for limited input systems might not be an effective strategy to improve milk production. [less ▲]

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See detailModeling milk urea of Walloon dairy cows in management perspectives.
Bastin, Catherine ULiege; Laloux, Laurent; Gillon, Alain ULiege et al

in Journal of Dairy Science (2009), 92(7), 3529-40

The aim of this study was to develop an adapted random regression test-day model for milk urea (MU) and to study the possibility of using predictions and solutions given by the model for management ... [more ▼]

The aim of this study was to develop an adapted random regression test-day model for milk urea (MU) and to study the possibility of using predictions and solutions given by the model for management purposes. Data included 607,416 MU test-day records of first-lactation cows from 632 dairy herds in the Walloon Region of Belgium. Several advanced features were used. First, to detect the herd influence, the classical herd x test-day effect was split into 3 new effects: a fixed herd x year effect, a fixed herd x month-period effect, and a random herd test-day effect. A fixed time period regression was added in the model to take into account the yearly oscillations of MU on a population scale. Moreover, first autoregressive processes were introduced and allowed us to consider the link between successive test-day records. The variance component estimation indicated that large variance was associated with the random herd x test-day effect (48% of the total variance), suggesting the strong influence of herd management on the MU level. The heritability estimate was 0.13. By comparing observed and predicted MU levels at both the individual and herd levels, target ranges for MU concentrations were defined to take into account features of each cow and each herd. At the cow level, an MU record was considered as deviant if it was <200 or >400 mg/L (target range used in the field) and if the prediction error was >50 mg/L (indicating a significant deviation from the expected level). Approximately 7.5% of the MU records collected between June 2007 and May 2008 were beyond these thresholds. This combination allowed for the detection of potentially suspicious cows. At the herd level, the expected MU level was considered as the sum of the solutions for specific herd effects. A herd was considered as deviant from its target range when the prediction error was greater than the standard deviation of MU averaged by herd test day. Results showed that 6.7% of the herd test-day MU levels between June 2007 and May 2008 were considered deviant. These deviations seemed to occur more often during the grazing period. Although theoretical considerations developed in this study should be validated in the field, this research showed the potential use of a test-day model for analyzing functional traits to advise dairy farmers. [less ▲]

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See detailEquivalent mixed model for joint genetic evaluation considering molecular and phenotypic information
Gengler, Nicolas ULiege; Colinet, Frédéric ULiege

in Journal of Dairy Science (2009), 92(E-suppl.1), 315

Currently efforts are underway to introduce molecular information into genetic evaluation systems. A particular situation is genomic selection however simpler cases exists where major genes are known and ... [more ▼]

Currently efforts are underway to introduce molecular information into genetic evaluation systems. A particular situation is genomic selection however simpler cases exists where major genes are known and used by breeders. A new alternative strategy for the prediction of gene effects and especially their smooth integration into genetic evaluations based on an equivalent method was developed from existing theory. Underlying hypothesis were based on the idea that knowledge of genotypes will not affect overall additive genetic variance but only change expected values of genetic effects for animals with known genotypes. The developed equations were modified to allow that not all animals were genotyped. As the underlying mixed model is open a very large range of models can be used in situations including random regression models, multipletrait, maternal effects and multiple-across-country-evaluation models. Computations involved successive solving of two mixed models, with the use of an linear extrapolation to speed up convergence of gene effects. The method was tested for several known major genes and QTL, e.g. for the mh gene in the dual-purpose Belgian Blue population in Belgium. Modifications of the method could also be developed to be useful in the context of genomic selection. [less ▲]

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See detailMulti-trait animal model estimation of genetic parameters for linear type and gait traits in the Belgian warmblood horse
Rustin, M.; Janssens, S.; Buys, N. et al

in Journal of Animal Breeding & Genetics (2009), 126(5), 378--386

Summary Genetic parameters for the height at withers, 27 linear type and six linear gait traits were estimated for the Belgian warmblood horse. Observations on 987 mares, mostly 3 years old, were analysed ... [more ▼]

Summary Genetic parameters for the height at withers, 27 linear type and six linear gait traits were estimated for the Belgian warmblood horse. Observations on 987 mares, mostly 3 years old, were analysed using a multi-trait animal model. The statistical model included appraiser, age and location (date × place of appraisal) as fixed effects. Genetic parameters were estimated using a canonical transformation and an expectation-maximization restricted maximum likelihood algorithm with an additional deceleration step. Estimates of heritability for the 33 linear traits were between 0.15 and 0.55. Heritability of the height at withers was 0.34 ± 0.06. Estimated genetic correlations ranged from −0.60 to 0.98 with an average SE of 0.10. The highest positive correlations were found among traits of walk and among traits of trot. Volume and the quality of legs were the most negatively correlated. Estimated genetic parameters indicated that the linear scoring system is a valuable tool to assess conformation. The full (co)variance matrix is now available for breeding value estimation to support selection for conformation and gaits. [less ▲]

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See detailSystéme d'évaluation génétique pour les verrats Piétrain en croisement en Wallonie
Dufrasne, Marie ULiege; Rustin, Maïté; Hammami, Hedi ULiege et al

Computer development (2009)

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See detailDetection and Correction of Outliers for Fatty Acids Contents Measured by Mid-Infrared Spectrometry Using Random Regression Test-Day Models
Soyeurt, Hélène ULiege; Dardenne, Pierre; Gengler, Nicolas ULiege

in Book of Abstracts of the 60th Annual Meeting of the European Association for Animal Production (2009)

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See detailCombining microsatellite and pedigree data to estimate relationships among Skyros ponies.
Bömcke, Elisabeth ULiege; Gengler, Nicolas ULiege

in Journal of Applied Genetics (2009), 50(2), 133-43

Relationship coefficients are particularly useful to improve genetic management of endangered populations. These coefficients are traditionally based on pedigree data, but in case of incomplete or ... [more ▼]

Relationship coefficients are particularly useful to improve genetic management of endangered populations. These coefficients are traditionally based on pedigree data, but in case of incomplete or inexistent pedigrees they are replaced by coefficients calculated from molecular data. The main objective of this study was to develop a new method to estimate relationship coefficients by combining molecular with pedigree data, which is useful for specific situations where neither pedigree nor molecular data are complete. The developed method was applied to contribute to the conservation of the Skyros pony breed, which consists of less than 200 individuals, divided into 3 main herds or subpopulations. In this study, relationships between individuals were estimated using traditional estimators as well as the newly developed method. For this purpose, 99 Skyros ponies were genotyped at 16 microsatellite loci. It appeared that the limitation of the most common molecular-based estimators is the use of weights that assume relationships equal to 0. The results showed that, as a consequence of this limitation, negative relationship values can be obtained in small inbred populations, for example. By contrast, the combined estimator gave no negative values. Using principal component analysis, the combined estimator also enabled a better graphic differentiation between the 3 subpopulations defined previously. In conclusion, this new estimator can be a promising alternative to traditionally used estimators, especially in inbred populations, with both incomplete pedigree and molecular information. [less ▲]

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