References of "Gengler, Nicolas"
     in
Bookmark and Share    
Full Text
Peer Reviewed
See detailA review of inversion techniques related to the use of relationship matrices in animal breeding
Faux, Pierre ULg; Gengler, Nicolas ULg

in Biotechnologie, Agronomie, Société et Environnement = Biotechnology, Agronomy, Society and Environment [=BASE] (in press)

In animal breeding, prediction of genetic effects is usually obtained through the use of mixed models. For any of these genetic effects, mixed models require the inversion of the covariance matrix ... [more ▼]

In animal breeding, prediction of genetic effects is usually obtained through the use of mixed models. For any of these genetic effects, mixed models require the inversion of the covariance matrix associated to that effect, which is equal to the associated relationship matrix times the associated component of the genetic variance. Given the size of many genetic evaluation systems, computing the inverses of these relationship matrices is not trivial. In this review, we aim to cover computational techniques that ease inversion of relationship matrices used in animal breeding for prediction of the following different types of genetic effects: additive effect, gametic effect, effect due to presence of marked quantitative trait loci, dominance effect and different epistasis effects. Construction rules and inversion algorithms are detailed for each relationship matrix. In the final discussion, we draw up a common theoretical frame to most of the reviewed techniques. Two computational constraints come out of this theoretical frame: setting up the matrix of dependencies between levels of the effect and setting up some parts (diagonal or block-diagonal elements) of the relationship matrix to be inverted. [less ▲]

Detailed reference viewed: 21 (6 ULg)
Full Text
Peer Reviewed
See detailGenetic parameters for mid-infrared methane indicators based on milk fatty acids in dairy cows
Kandel, Purna Bhadra ULg; Gengler, Nicolas ULg; Soyeurt, Hélène ULg

in Journal of Applied Animal Research (in press)

Dairy production is identified as a major source of methane (CH4) emissions. Selective breeding canbe one method used to mitigate CH4 emissions but practical and cheap measurement of this trait is not ... [more ▼]

Dairy production is identified as a major source of methane (CH4) emissions. Selective breeding canbe one method used to mitigate CH4 emissions but practical and cheap measurement of this trait is not currently available. The mid-infrared (MIR) prediction of milk fatty acids is relevant in this context. Five MIR methane indicators were derived from the literature and were calibrated from 600 samples analyzed by gas chromatography. Genetic parameters for these traits were estimated using single trait random regression test-day models from 619,265 records collected from 2007 to 2011 on 71,188 Holstein cows in their first three lactations. For the published indicator showing the highest relationship with the methane data (R2 = 0.88), the average daily heritability was 0.34±0.01, 0.37±0.01 and 0.34±0.01 for the first three lactations, respectively. The methane emission (g/day) was increased from beginning of lactation, reached at the highest in peak of lactation and decreased towards end of lactation. The largest differences between estimated breeding values (EBV) of sires having daughters in production eructing the highest and the lowest methane content was 21.80, 22.75 and 24.89 kg per lactation for the first three parities. Positive genetic correlations were estimated between indicator traits and milk fat and protein content. Low negative correlation was observed with milk yield. In conclusion, this study shows the feasibility to predict methane indicator traits by MIR. Moreover, the estimated genetic parameters suggest also a potential genetic variability of the quantity of methane eructed by dairy cows. [less ▲]

Detailed reference viewed: 88 (41 ULg)
Full Text
See detailInnovative lactation stage specific prediction of CH4 from milk MIR spectra
Vanlierde, Amélie; Vanrobays, Marie-Laure ULg; Dehareng, Frédéric et al

Conference (2014, August 28)

Detailed reference viewed: 11 (2 ULg)
Full Text
See detailUse of high performance computing in animal breeding
Vandenplas, Jérémie ULg; Gengler, Nicolas ULg

Poster (2014, August 28)

High-perfomance computing facilities proposing shared-memory and distributed-memory multiprocessors are becoming available. With those clusters, parallel computing could lead to increased performances and ... [more ▼]

High-perfomance computing facilities proposing shared-memory and distributed-memory multiprocessors are becoming available. With those clusters, parallel computing could lead to increased performances and problem sizes. However, to our knowledge and especially for variance components estimations, most software available in animal breeding, based on sparse matrices computations, do not allow parallel computing and are limited by memory accessible by the central processing unit, or allow parallel computing only for options with dense matrices computations, which limits anyway problem sizes due to storage of dense matrices. The aim was to propose simple and effective modifications for the BLUPF90 family of programs to reduce computing time with consideration of required memory. Modifications were based on academic free packages proposing solver and sparse inversion for sparse symmetric indefinite linear systems. First, modifications concerned the sparse inversion subroutine implemented in the package FSPAK. Rearrangements of 'do' loops to allow optimizations of computer operations by some compilers and addition of OpenMP directives were performed. The ordering operation was modified to more easily compare a multiple minimum degree algorithm (MMD; implemented in FSPAK) and a multilevel nested dissection algorithm (implemented in METIS 4.0.3). Second, the package PARDISO Version 5.0.0 was used instead of FSPAK. This package proposes in particular a parallel solver and sparse inversion on shared-memory multiprocessors. Modified FSPAK and PARDISO were compared to original FSPAK using MMD through REMLF90. Different models, such as univariate or bivariate (random regressions) test-day animal and single-step genomic models, were tested. All jobs were run 5 times. With an appropriate ordering algorithm, speedup for each REMLF90 iteration were up to 7.5 for modified FSPAK and up to 22.8 for PARDISO with 2 threads. With 4 threads, speedup increased to 8.3 and 32.5, respectively. [less ▲]

Detailed reference viewed: 5 (0 ULg)
See detailBayesian approach integrating correlated foreign information into a multivariate genetic evaluation
Vandenplas, Jérémie ULg; Gengler, Nicolas ULg

in Book of Abstracts of the 65th Annual Meeting of the European Federation of Animal Science (2014, August 28)

High-perfomance computing facilities proposing shared-memory and distributed-memory multiprocessors are becoming available. With those clusters, parallel computing could lead to increased performances and ... [more ▼]

High-perfomance computing facilities proposing shared-memory and distributed-memory multiprocessors are becoming available. With those clusters, parallel computing could lead to increased performances and problem sizes. However, to our knowledge and especially for variance components estimations, most software available in animal breeding, based on sparse matrices computations, do not allow parallel computing and are limited by memory accessible by the central processing unit, or allow parallel computing only for options with dense matrices computations, which limits anyway problem sizes due to storage of dense matrices. The aim was to propose simple and effective modifications for the BLUPF90 family of programs to reduce computing time with consideration of required memory. Modifications were based on academic free packages proposing solver and sparse inversion for sparse symmetric indefinite linear systems. First, modifications concerned the sparse inversion subroutine implemented in the package FSPAK. Rearrangements of 'do' loops to allow optimizations of computer operations by some compilers and addition of OpenMP directives were performed. The ordering operation was modified to more easily compare a multiple minimum degree algorithm (MMD; implemented in FSPAK) and a multilevel nested dissection algorithm (implemented in METIS 4.0.3). Second, the package PARDISO Version 5.0.0 was used instead of FSPAK. This package proposes in particular a parallel solver and sparse inversion on shared-memory multiprocessors. Modified FSPAK and PARDISO were compared to original FSPAK using MMD through REMLF90. Different models, such as univariate or bivariate (random regressions) test-day animal and single-step genomic models, were tested. All jobs were run 5 times. With an appropriate ordering algorithm, speedup for each REMLF90 iteration were up to 7.5 for modified FSPAK and up to 22.8 for PARDISO with 2 threads. With 4 threads, speedup increased to 8.3 and 32.5, respectively. [less ▲]

Detailed reference viewed: 5 (2 ULg)
Full Text
See detailUsing milk spectral data for large-scale phenotypes linked to mitigation and efficiency
Soyeurt, Hélène ULg; Vanlierde, Amélie; Vanrobays, Marie-Laure ULg et al

Conference (2014, August 26)

Even if producing milk efficiently has always been a major concern for producers, the direct environmental impact of their cows is becoming a novel one. Traits linked to this issue were identified as ... [more ▼]

Even if producing milk efficiently has always been a major concern for producers, the direct environmental impact of their cows is becoming a novel one. Traits linked to this issue were identified as methane emission (CH4), dry matter intake (DMI) and feed efficiency (FE); however they are available on a small scale. Researches showed that CH4 could be predicted from milk mid-infrared (MIR) spectra, allowing large-scale recording at low cost. The main objective of this study was to show, using a modelling approach, that DMI and FE could be derived from milk MIR spectra. For that, knowledge of body weight (BW) is required; however it was unknown in this study. Derived procedure was based on milk yield and composition, MIR CH4, and modelled standard animal requirements, allowing the prediction of expected BW. An external validation was conducted based on 91 actual records. 95% confidence limit for the difference ranged between -0.66 and 18.84 kg for BW, from -0.02 to 0.26 kg/day for DMI, and from -0.02 to 0.002 kg of fat corrected milk/kg DM for FE. Root mean square errors were 39.66 kg, 0.56 kg/d, and 0.03 kg/DM for the 3 studied traits. P-value for the t-test was not significant for BW and DMI. This suggests the possibility to obtain expected BW and therefore DMI from MIR spectra. Single trait animal test-day models used 1,291,850 records to assess the variability of studied traits. Significant variations were observed for the lactation stage, parity, genetics, and age. These findings were in agreement with the literature except for early lactation. This suggests in conclusion that the MIR information gave similar results for DMI and CH4 for the major part of lactation. The use of this novel method to predict expected BW offers new possibilities interesting for the development of genomic and genetic tools. [less ▲]

Detailed reference viewed: 5 (0 ULg)
Full Text
See detailCreation of universal MIR calibration by standardization of milk spectra: example of fatty acids
Grelet, Clément; Fernandez Pierna, Juan; Soyeurt, Hélène ULg et al

Poster (2014, August 25)

Detailed reference viewed: 7 (0 ULg)
Full Text
See detailMitigation strategies versus Adaptation strategies
Gengler, Nicolas ULg

Conference (2014, August 17)

Detailed reference viewed: 10 (3 ULg)
Full Text
See detailUsing milk spectral data for large-scale phenotypes linked to mitigation and efficiency
Soyeurt, Hélène ULg; Vanlierde, Amélie; Vanrobays, Marie-Laure ULg et al

in Book of abstracts of the 65th annual meeting of the European Federation of Animal Science (2014, August)

Even if producing milk efficiently has always been a major concern for producers, the direct environmental impact of their cows is becoming a novel one. Traits linked to this issue were identified as ... [more ▼]

Even if producing milk efficiently has always been a major concern for producers, the direct environmental impact of their cows is becoming a novel one. Traits linked to this issue were identified as methane emission (CH4), dry matter intake (DMI) and feed efficiency (FE); however they are available on a small scale. Researches showed that CH4 could be predicted from milk mid-infrared (MIR) spectra, allowing large-scale recording at low cost. The main objective of this study was to show, using a modelling approach, that DMI and FE could be derived from milk MIR spectra. For that, knowledge of body weight (BW) is required; however it was unknown in this study. Derived procedure was based on milk yield and composition, MIR CH4, and modelled standard animal requirements, allowing the prediction of expected BW. An external validation was conducted based on 91 actual records. 95% confidence limit for the difference ranged between -0.66 and 18.84 kg for BW, from -0.02 to 0.26 kg/day for DMI, and from -0.02 to 0.002 kg of fat corrected milk/kg DM for FE. Root mean square errors were 39.66 kg, 0.56 kg/d, and 0.03 kg/DM for the 3 studied traits. P-value for the t-test was not significant for BW and DMI. This suggests the possibility to obtain expected BW and therefore DMI from MIR spectra. Single trait animal test-day models used 1,291,850 records to assess the variability of studied traits. Significant variations were observed for the lactation stage, parity, genetics, and age. These findings were in agreement with the literature except for early lactation. This suggests in conclusion that the MIR information gave similar results for DMI and CH4 for the major part of lactation. The use of this novel method to predict expected BW offers new possibilities interesting for the development of genomic and genetic tools. [less ▲]

Detailed reference viewed: 7 (0 ULg)
Full Text
See detailInnovative lactation stage specific prediction of CH4 from milk MIR spectra
Vanlierde, Amélie; Vanrobays, Marie-Laure ULg; Dehareng, Frédéric et al

in Book of abstracts of the 65th annual meeting of the European Federation of Animal Science (2014, August)

Detailed reference viewed: 12 (2 ULg)
Full Text
Peer Reviewed
See detailConsequences of Selection for Environmental Impact Traits in Dairy Cows
Kandel, Purna Bhadra ULg; Vanderick, Sylvie ULg; Vanrobays, Marie-Laure ULg et al

in Proceedings, 10th World Congress of Genetics Applied to Livestock Production (2014, August)

Genetic selection programs aiming to mitigate methane (CH4) emissions require the estimation of genetic correlations with other production and economical traits and predicted selection response. CH4 ... [more ▼]

Genetic selection programs aiming to mitigate methane (CH4) emissions require the estimation of genetic correlations with other production and economical traits and predicted selection response. CH4 intensity was predicted from Mid-infrared spectra of milk samples from Holstein cows. Genetic correlations between CH4 intensity and milk yield (MY) was -0.68, fat yield (FY) -0.13, protein yield (PY) -0.47, somatic cell score (SCS) 0.07, longevity 0.05, fertility 0.31, body condition score (BCS) 0.17. Adding 25% relative weight on CH4 intensity to the current Walloon selection index, the response to selection would reduce CH4 intensity by 24%, increase MY by 30%, FY by 17%, PY by 29%, SCS by -14%, longevity by 24% but also reduce fertility by 11% and BCS by 13%. In conclusion, environmental traits can be added without jeopardizing production traits, but energy balance related traits have to be protected. [less ▲]

Detailed reference viewed: 8 (0 ULg)
Full Text
See detailCreation of universal MIR calibration by standardization of milk spectra: example of fatty acids
Grelet, Clément; Fernandez Pierna, Juan; Soyeurt, Hélène ULg et al

in Book of abstracts of the 65th annual meeting of the European Federation of Animal Science (2014, August)

Detailed reference viewed: 11 (3 ULg)
Full Text
See detailGenetic parameters for individual birth weight, weaning weight and final weight of crossbred pigs from Piétrain boars
Dufrasne, Marie ULg; Wavreille, José; Piedboeuf, Maureen et al

Poster (2014, August)

Genetic parameters for birth weight (BWT), weaning weight (WWT), and final weight (BW) were estimated for crossbred pigs from Piétrain boars raised in test station. Estimates of direct heritability were ... [more ▼]

Genetic parameters for birth weight (BWT), weaning weight (WWT), and final weight (BW) were estimated for crossbred pigs from Piétrain boars raised in test station. Estimates of direct heritability were moderate (0.25 to 0.42), suggesting that genetic improvement of growth would be possible. Estimates of maternal heritability were 0.24 for BWT and WWT, and 0.05 for BW, indicating that the genetic influence of the dam on growth was not negligible until weaning. Genetic correlations between direct and maternal effects for BWT and WWT were moderate and unfavorable (-0.52 and -0.57 respectively). Direct genetic correlations were high and favorable between traits (0.40 to 0.75), suggesting that a high BWT is a good predictor to produce pigs with high final weight. Maternal genetic correlations between traits were low (0.01 to 0.03). Selection for higher BWT would increase final market weight but should be balanced with survival traits. [less ▲]

Detailed reference viewed: 6 (0 ULg)
Peer Reviewed
See detailPrediction of Body Weight of Primiparous Dairy Cows Throughout Lactation
Vanrobays, Marie-Laure ULg; Vandenplas, Jérémie ULg; Hammami, Hedi ULg et al

in Proceedings of the 10th World Congress on Genetics Applied to Livestock Production (2014, August)

Body weight (BW) can be computed using linear conformation traits (CBW). However, these traits are recorded mostly once during a lactation. Therefore, predicted BW (PBW) is needed throughout the lactation ... [more ▼]

Body weight (BW) can be computed using linear conformation traits (CBW). However, these traits are recorded mostly once during a lactation. Therefore, predicted BW (PBW) is needed throughout the lactation (e.g., allowing feed intake prediction in milk recording systems). A two-step procedure was developed to obtain PBW using a random regression test-day model using CBW as observations. Added second step consisted in changing prior distribution for additive genetic random effects using results from first step to predict again PBW. This method was applied on 24,919 primiparous Holstein cows having 25,061 CBW to obtain PBW for 232,436 test-days. Results showed that applying both steps provided more accurate estimates than using only the first step. Furthermore, this procedure predicting PBW throughout lactation is also extremely flexible because actual BW can also be used together with CBW, the prediction model being able to accommodate different levels of accuracies. [less ▲]

Detailed reference viewed: 21 (9 ULg)
Full Text
See detailQuel système d'évaluations génétiques pour les verrats Piétrain en Wallonie
Dufrasne, Marie ULg; Piedboeuf, Maureen; Wavreille, José et al

Article for general public (2014)

Detailed reference viewed: 10 (2 ULg)
Full Text
See detailStrategies to combine novel traits across countries: example of heat stress
Hammami, Hedi ULg; Vandenplas, Jérémie ULg; Carabaño, Maria Jesus et al

Conference (2014, May 21)

Nowadays, novel traits are of great interest. However, phenotypes are siloed and mainly not shared. Heat stress is becoming problematic affecting animals’ performances and their well-being. Heat stress ... [more ▼]

Nowadays, novel traits are of great interest. However, phenotypes are siloed and mainly not shared. Heat stress is becoming problematic affecting animals’ performances and their well-being. Heat stress tolerance as a novel trait is only addressed by isolated within-country research studies. Integration and combination of local and foreign information sources is needed for better accuracy genetic evaluations. Therefore, this study was aimed to test the potential combination of sources of external information towards the evaluation of heat stress tolerance of dairy cattle. Long-term cow performances linked to environmental descriptors (weather parameters as proxy to climate change) collected over 10 years under the temperate conditions of the Walloon Region of Belgium and the hotter and warm Mediterranean conditions of Andalusia and Castile-La-Mancha Spanish regions were available. A total of 1,604,775 milk, fat, and protein test-day (TD) records linked to average daily temperature humidity (THI) values for 3-day lag before each TD were considered. Under a first strategy considering free-access to raw-data (phenotype and pedigree), a joint evaluation was firstly run using reaction norm models where production traits were considered as function of THI. A Belgian and a Spanish evaluation were also run using the same model. An alternative strategy considering only access to external information (i.e. regression coefficients for additive genetic effects (â and their associated REL)) was tested. In this case, foreign â and their REL resulting from the Spanish evaluation were first converted to the Belgian trait and thereafter integrated in the Belgian evaluation using a Bayesian approach. Rank correlations between regression coefficients, â (of the 1,104 bulls having daughters only in Spain) estimated by Belgian evaluation and â estimated by the joint evaluation were moderate (<=0.70). Corresponding rank correlations between â estimated by joint and Bayesian evaluations were significantly higher (ranging from 0.967 to 0.998), indicating that the Bayesian evaluation integrating external information was in good concordance with the joint evaluation. Results from this study indicated that the integration of external information via the Bayesian approach has a good potential to improve the genetic evaluation of sparse and siloed novel traits. [less ▲]

Detailed reference viewed: 19 (4 ULg)
Full Text
See detailContributions à l’amélioration des systèmes d’évaluations génétiques
Vanderick, Sylvie ULg; Gengler, Nicolas ULg

Conference given outside the academic context (2014)

Detailed reference viewed: 13 (6 ULg)
Full Text
See detailConsequences of Selection for Environmental Impact Trait in Dairy Cows
Kandel, Purna Bhadra ULg; Vanderick, Sylvie ULg; Vanrobays, Marie-Laure ULg et al

Scientific conference (2014, February 07)

Environmental sustainability is gaining importance in dairy industry due to enteric methane (CH4) emission from dairy cows. We predicted CH4 indicator trait (CH4 intensity: CH4 g/kg of milk) from Mid ... [more ▼]

Environmental sustainability is gaining importance in dairy industry due to enteric methane (CH4) emission from dairy cows. We predicted CH4 indicator trait (CH4 intensity: CH4 g/kg of milk) from Mid-infrared spectra of milk samples and recorded milk yield. Genetic correlations between CH4 intensity and milk production traits were estimated on Holstein cows from correlations of estimated breeding values. Genetic correlations between CH4 intensity and milk yield (MY) was -0.67, fat yield (FY) -0.13, protein yield (PY) -0.46, somatic cell score (SCS) 0.02, longevity -0.07, fertility 0.31, body condition score (BCS) 0.27 and average of confirmation traits -0.23. Currently, there is no CH4 emission trait in genetic evaluation selection index. Putting an hypothetical 25% weight on CH4 intensity on current Walloon genetic evaluation selection index and proportional reduction on other selection traits, the response to selection will be reduction of CH4 emission intensity by 24%, increase in MY by 30%, FY by 17%, PY by 29%, SCS by -15%, longevity by 24%, fertility by -11%, BCS by -13% and conformation traits by 24%. In conclusion, introduction of environmental traits in current selection index will affect selection responses. As there is no economic value of these traits presently alternative methods like putting correlated traits with clear economic value (e.g. feed efficiency) in the selection objective could generate appropriate index weights. [less ▲]

Detailed reference viewed: 46 (17 ULg)
Full Text
See detailEfficient computation of genomically-enhanced inbreeding coefficients
Faux, Pierre ULg; Gengler, Nicolas ULg

Poster (2014, February 07)

Detailed reference viewed: 19 (6 ULg)