References of "Gengler, Nicolas"
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See detailUnified method to integrate and blend several, potentially related, sources of information for genetic evaluation
Vandenplas, Jérémie ULg; Colinet, Frédéric ULg; Gengler, Nicolas ULg

in Genetics, Selection, Evolution (in press)

Background A condition to predict unbiased estimated breeding values by best linear unbiased prediction is to use simultaneously all available data. However, this condition is not often fully met. For ... [more ▼]

Background A condition to predict unbiased estimated breeding values by best linear unbiased prediction is to use simultaneously all available data. However, this condition is not often fully met. For example, in dairy cattle, internal (i.e. local) populations lead to evaluations based only on internal records while widely used foreign sires have been selected using internally unavailable external records. In such cases, internal genetic evaluations may be less accurate and biased. Because external records are unavailable, methods were developed to combine external information that summarizes these records, i.e. external estimated breeding values and associated reliabilities, with internal records to improve accuracy of internal genetic evaluations. Two issues of these methods concern double-counting of contributions due to relationships and due to records. These issues could be worse if external information came from several evaluations, at least partially based on the same records, and combined into a single internal evaluation. Based on a Bayesian approach, the aim of this research was to develop a unified method to integrate and blend simultaneously several sources of information into an internal genetic evaluation by avoiding double-counting of contributions due to relationships and due to records. Results This research resulted in equations that integrate and blend simultaneously several sources of information and avoid double-counting of contributions due to relationships and due to records. The performance of the developed equations was evaluated using simulated and real datasets. The results showed that the developed equations integrated and blended several sources of information well into a genetic evaluation. The developed equations also avoided double-counting of contributions due to relationships and due to records. Furthermore, because all available external sources of information were correctly propagated, relatives of external animals benefited from the integrated information and, therefore, more reliable estimated breeding values were obtained. Conclusions The proposed unified method integrated and blended several sources of information well into a genetic evaluation by avoiding double-counting of contributions due to relationships and due to records. The unified method can also be extended to other types of situations such as single-step genomic or multi-trait evaluations, combining information across different traits. [less ▲]

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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 ▲]

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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 ▲]

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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 ▲]

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See detailMitigation strategies versus Adaptation strategies
Gengler, Nicolas ULg

Conference (2014, August 17)

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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)

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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 ▲]

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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 ▲]

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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)

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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 ▲]

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See detailContributions à l’amélioration des systèmes d’évaluations génétiques
Vanderick, Sylvie ULg; Gengler, Nicolas ULg

Conference given outside the academic context (2014)

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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 ▲]

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See detailEfficient computation of genomically-enhanced inbreeding coefficients
Faux, Pierre ULg; Gengler, Nicolas ULg

Poster (2014, February 07)

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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)

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 ▲]

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See detailEstimation of dominance variance for live body weight in a crossbred population of pigs
Dufrasne, Marie ULg; Faux, Pierre ULg; Piedboeuf, Maureen et al

in Journal of Animal Science (2014), 92

The objective of this study was to estimate the dominance variance for repeated live BW records in a crossbred population of pigs. Data were provided by the Walloon Pig Breeding Association and included ... [more ▼]

The objective of this study was to estimate the dominance variance for repeated live BW records in a crossbred population of pigs. Data were provided by the Walloon Pig Breeding Association and included 22,197 BW records of 2,999 crossbred Piétrain × Landrace K+ pigs from 50 to 210 d of age. The BW records were standardized and adjusted to 210 d of age for analysis. Three single-trait random regression animal models were used: Model 1 without parental subclass effect, Model 2 with parental subclasses considered unrelated, and Model 3 with the complete parental dominance relationship matrix. Each model included sex, contemporary group, and heterosis as fixed effects as well as additive genetic, permanent environment, and residual as random effects. Variance components and their SE were estimated using a Gibbs sampling algorithm. Heritability tended to increase with age: from 0.50 to 0.64 for Model 1, from 0.19 to 0.42 for Model 2, and from 0.31 to 0.53 for Model 3. Permanent environmental variance tended to decrease with age and accounted for 29 to 44% of total variance with Model 1, 29 to 37% of total variance with Model 2, and 34 to 51% of total variance with Model 3. Residual variance explained <10% of total variance for the 3 models. Dominance variance was computed as 4 times the estimated parental subclass variance. Dominance variance accounted for 22 to 40% of total variance for Model 2 and 5 to 11% of total variance for Model 3, with a decrease with age for both models. Results showed that dominance effects exist for growth traits in pigs and may be reasonably large. The use of the complete dominance relationship matrix may improve the estimation of additive genetic variances and breeding values. Moreover, a dominance effect could be especially useful in selection programs for individual matings through the use of specific combining ability to maximize growth potential of crossbred progeny. [less ▲]

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See detailGenetic analysis of pig survival up to commercial weight in a crossbred population
Dufrasne, Marie ULg; Misztal, Ignacy; Tsuruta, Shogo et al

in Livestock Science (2014), 167

Records from 99,384 crossbred pigs from Duroc sires and Large White x Landrace dams were used to estimate genetic parameters for survival traits at different stages of the fattening period, and their ... [more ▼]

Records from 99,384 crossbred pigs from Duroc sires and Large White x Landrace dams were used to estimate genetic parameters for survival traits at different stages of the fattening period, and their relations with final weight. Traits analyzed were preweaning mortality (PWM), culling between weaning and harvesting (Call), culling during the farrowing period (Cfar), in the nursery site (Cnur), during the finishing phase (Cfin), and hot carcass weight (HCW). Because of the binary nature of PWM and culling traits, threshold-linear models were used: Model 1, including PWM, Call, and HCW; Model 2, including PWM, Cfar, Cnur, Cfin, and HCW. Both models included sex and parity number as fixed effects for all traits. Contemporary groups were considered as fixed effect for HCW and as random effects for the binary traits. Random effects were sire additive genetic, common litter, and residual effects for all traits and models. Heritability estimates were 0.03 for PWM, and 0.15 for HCW with both models, 0.06 for Call with Model 1, and 0.06 for Cfar, 0.14 for Cnur, and 0.10 for Cfin with Model 2. Litter variance explained a large part of the total variance and its influence declined slightly with age. For Model 1, genetic correlations were -0.36 between PWM and Call, -0.02 between PWM and HCW, and -0.25 between Call and HCW; correlations for litter effect were -0.15 between PWM and Call, -0.19 between PWM and HCW, and -0.21 between Call and HCW. For Model 2, genetic correlations were all positive between PWM and culling traits, except between PWM and Cnur (-0.61). Genetic correlations between HCW and the other traits were moderate and negative to null. Correlations for common litter effect were all negative between traits, except between Cfar and Cfin, and between Cnur and Cfin. Heritability of PWM and culling traits increased with age period. Therefore, selection for survival after weaning may be more efficient. The low genetic correlations between PWM and culling traits suggest that different genes influence pre- and postweaning mortality. The HCW was not correlated with the other traits. However, relationships are not strongly unfavorable, therefore selection for survival and high final weight is possible. [less ▲]

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See detailUse of high performance computing in animal breeding
Vandenplas, Jérémie ULg; Gengler, Nicolas ULg

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

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 ▲]

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See detailUse of high performance computing in animal breeding
Vandenplas, Jérémie ULg; Gengler, Nicolas ULg

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

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 ▲]

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