References of "Colinet, Frédéric"
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See detailBayesian single-step genomic evaluations combining local and foreign information in Walloon Holsteins
Colinet, Frédéric ULiege; Vandenplas, J.; Vanderick, Sylvie ULiege et al

in Animal (2017)

Most dairy cattle populations found in different countries around the world are small to medium sized and use many artificial insemination bulls imported from different foreign countries. The Walloon ... [more ▼]

Most dairy cattle populations found in different countries around the world are small to medium sized and use many artificial insemination bulls imported from different foreign countries. The Walloon population in the southern part of Belgium is a good example for such a small-scale population. Wallonia has also a very active community of Holstein breeders requesting high level genetic evaluation services. Single-step Genomic BLUP (ssGBLUP) methods allow the simultaneous use of genomic, pedigree and phenotypic information and could reduce potential biases in the estimation of genomically enhanced breeding values (GEBV). Therefore, in the context of implementing a Walloon genomic evaluation system for Holsteins, it was considered as the best option. However, in contrast to multi-step genomic predictions, natively ssGBLUP will only use local phenotypic information and is unable to use directly important other sources of information coming from abroad, for example Multiple Across Country Evaluation (MACE) results as provided by the Interbull Center (Uppsala, Sweden). Therefore, we developed and implemented single-step Genomic Bayesian Prediction (ssGBayes), as an alternative method for the Walloon genomic evaluations. The ssGBayes method approximated the correct system of equations directly using estimated breeding values (EBV) and associated reliabilities (REL) without any explicit deregression step. In the Walloon genomic evaluation, local information refers to Walloon EBV and REL and foreign information refers to MACE EBV and associated REL. Combining simultaneously all available genotypes, pedigree, local and foreign information in an evaluation can be achieved but adding contributions to left-hand and right-hand sides subtracting double-counted contributions. Correct propagation of external information avoiding double counting of contributions due to relationships and due to records can be achieved. This ssGBayes method computed more accurate predictions for all types of animals. For example, for genotyped animals with low Walloon REL (<0.25) without MACE results but sired by genotyped bulls with MACE results, the average increase of REL for the studied traits was 0.38 points of which 0.08 points could be traced to the inclusion of MACE information. For other categories of genotyped animals, the contribution by MACE information was also high. The Walloon genomic evaluation system passed for the first time the Interbull GEBV tests for several traits in July 2013. Recent experiences reported here refer to its use in April 2016 for the routine genomic evaluations of milk production, udder health and type traits. Results showed that the proposed methodology should also be of interest for other, similar, populations. [less ▲]

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See detailGenetic evaluation for birth and conformation traits in dual-purpose Belgian Blue cattle using a mixed inheritance model
REIS MOTA, Rodrigo ULiege; Mayeres, P.; Bastin, Catherine et al

in Journal of Animal Science (2017)

The segregation of the causal mutation (mh) in the muscular hypertrophy gene in dual-purpose Belgian Blue (dpBB) cattle is considered to result in greater calving difficulty (dystocia). Establishing ... [more ▼]

The segregation of the causal mutation (mh) in the muscular hypertrophy gene in dual-purpose Belgian Blue (dpBB) cattle is considered to result in greater calving difficulty (dystocia). Establishing adapted genetic evaluations might overcome this situation through efficient selection. However, the heterogeneity of dpBB populations at the mh locus implies separating the major gene and other polygenic effects in complex modeling. The use of mixed inheritance models may be an interesting option because they simultaneously assume both influences. A genetic evaluation in dpBB based on a mixed inheritance model was developed for birth and conformation traits: gestation length (GL), calving difficulty (CD), birth weight (BiW), and body conformation score (BC). A total of 27,362 animals having records were used for analyses. The total number of animals in the pedigree used to build the numerator relationship matrix was 62,617. Genotypes at the mh locus were available for 2,671 animals. Missing records at this locus were replaced with genotype probabilities. A total of 13,221 (48.3%) were registered as dpBB, 1,287 (4.7%) as beef Belgian Blue, and 12,854 (47.0%) were unknown. From those 13,221dpBB animals, 650, 849, and 534 had double or single copies or no copy, respectively, of the causal mutation (mh) in the muscular hypertrophy gene, whereas 11,188 had missing genotypes. This heterogeneity at the mh locus may be the reason for high variability in the studied traits, that is, high heritability estimates of 0.33, 0.30, 0.38, and 0.43 for GL, CD, BiW, and BC, respectively. In general, additive (P < 0.05) and dominance (P < 0.001) allele substitution for calves and dams had significant impact for all traits. The moderate coefficient of genetic variation (27.80%) and high direct heritability (0.28) for CD suggested genetic variability in dpBB and possible genetic improvement through selection. This variability has allowed dpBB breeders to successfully apply mass selection in the past. Genetic trend means from 1988 to 2016 showed that sire selection for CD within genotype was progressively applied by breeders. The selection intensity was more important for CD in double-muscled lines than in segregated lines. Our study illustrated the possible confusion caused by the use of major genes in selection and the importance of fitting appropriate models such as mixed inheritance models that combine polygenic and gene content information. [less ▲]

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See detailCow milk coagulation: process description, variation factors and evaluation methodologies. A review.
Troch, Thibault; Lefebure, Emilie ULiege; Baeten, Vincent et al

in Biotechnologie, Agronomie, Société et Environnement = Biotechnology, Agronomy, Society and Environment (2017), 21

Introduction. For dairy producers who want to transform their milk, the ability of milk to coagulate is an important parameter. It makes it possible to transform milk into cheese. Therefore, it is ... [more ▼]

Introduction. For dairy producers who want to transform their milk, the ability of milk to coagulate is an important parameter. It makes it possible to transform milk into cheese. Therefore, it is necessary to understand the coagulation process and the techniques to measure it in order to achieve the best transformation performance. The objective of this review is to describe the milk coagulation process, the factors influencing it and the methods for measuring the coagulation of milk at lab level. Literature. The processing of milk into cheese involves three steps: coagulation, dewatering and refining. Coagulation is a key step which involves the use of rennet and depends on several parameters (pH, calcium content, temperature, etc.). Some milks never coagulate. To measure the coagulation ability of milk and identify different parameters in milk coagulation properties, the Formagraph, the computerized renneting meter and the Optigraph have been developed (reference methods). Equations have been developed using infrared spectrometry to predict the parameters obtained by the reference methods. Conclusions. The milk coagulation mechanism is known. However, the issue of non-coagulating milk persists and represents a real challenge in terms of yield. The use of infrared is a faster alternative to reference methods that measure the coagulation properties of milk, but still requires an improvement in prediction equations. [less ▲]

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See detailGenomics of a revived breed: Case study of the Belgian campine cattle.
Francois, Liesbeth; Wijnrocx, Katrien; Colinet, Frédéric ULiege et al

in PLoS ONE (2017), 12(4), 0175916

Through centuries of both natural and artificial selection, a variety of local cattle populations arose with highly specific phenotypes. However, the intensification and expansion of scale in animal ... [more ▼]

Through centuries of both natural and artificial selection, a variety of local cattle populations arose with highly specific phenotypes. However, the intensification and expansion of scale in animal production systems led to the predominance of a few highly productive cattle breeds. The loss of local populations is often considered irreversible and with them specific qualities and rare variants could be lost as well. Over these last years, the interest in these local breeds has increased again leading to increasing efforts to conserve these breeds or even revive lost populations, e.g. through the use of crosses with similar breeds. However, the remaining populations are expected to contain crossbred individuals resulting from introgressions. They are likely to carry exogenous genes that affect the breed's authenticity on a genomic level. Using the revived Campine breed as a case study, 289 individuals registered as purebreds were genotyped on the Illumina BovineSNP50. In addition, genomic information on the Illumina BovineHD and Illumina BovineSNP50 of ten breeds was available to assess the current population structure, genetic diversity, and introgression with phenotypically similar and/or historically related breeds. Introgression with Holstein and beef cattle genotypes was limited to only a few farms. While the current population shows a substantial amount of within-breed variation, the majority of genotypes can be separated from other breeds in the study, supporting the re-establishment of the Campine breed. The majority of the population is genetically close to the Deep Red (NL), Improved Red (NL) and Eastern Belgium Red and White (BE) cattle, breeds known for their historical ties to the Campine breed. This would support an open herdbook policy, thereby increasing the population size and consequently providing a more secure future for the breed. [less ▲]

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See detailAssessing the effect of pregnancy stage on milk composition of dairy cows using mid-infrared spectra
Laine, Aurélie ULiege; Bastin, C.; Grelet, C. et al

in Journal of Dairy Science (2017), 100(4), 2863-2876

ABSTRACT Changes in milk production traits (i.e., milk yield, fat, and protein contents) with the pregnancy stage are well documented. To our knowledge, the effect of pregnancy on the detailed milk ... [more ▼]

ABSTRACT Changes in milk production traits (i.e., milk yield, fat, and protein contents) with the pregnancy stage are well documented. To our knowledge, the effect of pregnancy on the detailed milk composition has not been studied so far. The mid-infrared (MIR) spectrum reflects the detailed composition of a milk sample and is obtained by a nonexhaustive and widely used method for milk analysis. Therefore, this study aimed to investigate the effect of pregnancy on milk MIR spectrum in addition to milk production traits (milk yield, fat, and protein contents). A model including regression on the number of days pregnant was applied on milk production traits (milk yield, fat, and protein contents) and on 212 spectral points from the MIR spectra of 9,757 primiparous Holstein cows from Walloon herds. Effects of pregnancy stage were expressed on a relative scale (effect divided by the squared root of the phenotypic variance); this allowed comparisons between effects on milk traits and on 212 spectral points. Effect of pregnancy stage on production traits were in line with previous studies indicating that the model accounted well for the pregnancy effect. Trends of the relative effect of the pregnancy stage on the 212 spectral points were consistent with known and observed effect on milk traits. The highest effect of the pregnancy was observed in the MIR spectral region from 968 to 1,577 cm−1. For some specific wavenumbers, the effect was higher than for fat and protein contents in the beginning of the pregnancy (from 30 to 90 or 120 d pregnant). In conclusion, the effect of early pregnancy can be observed in the detailed milk composition through the analysis of the MIR spectrum of bovine milk. Further analyses are warranted to explore deeply the use of MIR spectra of bovine milk for breeding and management of dairy cow pregnancy. [less ▲]

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See detailStandardization of milk mid-infrared spectrometers for the transfer and use of multiple models
Grelet, C.; Pierna, J. A. Fernández; Dardenne, P. et al

in Journal of Dairy Science (2017), 100(10), 7910-7921

An increasing number of models are being developed to provide information from milk Fourier transform mid-infrared (FT-MIR) spectra on fine milk composition, technological properties of milk, or even cows ... [more ▼]

An increasing number of models are being developed to provide information from milk Fourier transform mid-infrared (FT-MIR) spectra on fine milk composition, technological properties of milk, or even cows' physiological status. In this context, and to take advantage of these existing models, the purpose of this work was to evaluate whether a spectral standardization method can enable the use of multiple equations within a network of different FT-MIR spectrometers. The piecewise direct standardization method was used, matching “slave” instruments to a common reference, the “master.” The effect of standardization on network reproducibility was assessed on 66 instruments from 3 different brands by comparing the spectral variability of the slaves and the master with and without standardization. With standardization, the global Mahalanobis distance from the slave spectra to the master spectra was reduced on average from 2,655.9 to 14.3, representing a significant reduction of noninformative spectral variability. The transfer of models from instrument to instrument was tested using 3 FT-MIR models predicting (1) the quantity of daily methane emitted by dairy cows, (2) the concentration of polyunsaturated fatty acids in milk, and (3) the fresh cheese yield. The differences, in terms of root mean squared error, between master predictions and slave predictions were reduced after standardization on average from 103 to 17 g/d, from 0.0315 to 0.0045 g/100 mL of milk, and from 2.55 to 0.49 g of curd/100 g of milk, respectively. For all the models, standard deviations of predictions among all the instruments were also reduced by 5.11 times for methane, 5.01 times for polyunsaturated fatty acids, and 7.05 times for fresh cheese yield, showing an improvement of prediction reproducibility within the network. Regarding the results obtained, spectral standardization allows the transfer and use of multiple models on all instruments as well as the improvement of spectral and prediction reproducibility within the network. The method makes the models universal, thereby offering opportunities for data exchange and the creation and use of common robust models at an international level to provide more information to the dairy sector from direct analysis of milk. [less ▲]

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See detailThe Impact of Diseases Transmission in Pollinators Decline
Noël, Grégoire ULiege; Bebermans, Julien ULiege; Colinet, Frédéric ULiege et al

Scientific conference (2016, December 02)

Ongoing global biodiversity loss is a growing concern for our society. This involves also the pollinators community which ensures insect-pollinated plant reproduction in our natural environment and ... [more ▼]

Ongoing global biodiversity loss is a growing concern for our society. This involves also the pollinators community which ensures insect-pollinated plant reproduction in our natural environment and provides a great ecosystem service to mankind, particularly for food safety and human welfare. The aim of this study is two-fold: i) to produce a comprehensive update of the decline of pollinators at global scale and ii) to focus especially on the issue of pollinators disease transmission. In this research we argue that the cause of insect-pollinator decline is multi-factorial, including anthropogenic pressures such as land-use change (habitats loss, agricultural intensification…), climate change, pesticides and the spread of alien species and diseases. It also appears that the high prevalence of a broad range of insects and commercial use of pollinators are key drivers of pathogens transmission (virus, parasites …). However, the dynamics of pathogens transmission is still poorly known and, in turn, more scientific research must be performed to have a better insight of this issue. Finally, pollinators decline results from synergetic actions among these stress generators at different spatio-temporal levels emphasized by the globalization of commercial exchanges. [less ▲]

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See detailNovel innovative possibilities for the dairy industry opened by common format of FT-MIR instruments
Grelet, Clément ULiege; Fernandez Pierna, Juan Antonio; Dardenne, Pierre et al

Poster (2016, October)

FT-MIR technology is worldwide used for fast and cost effective determination of major milk components. However, due to the different individual response of each instrument the potential of this ... [more ▼]

FT-MIR technology is worldwide used for fast and cost effective determination of major milk components. However, due to the different individual response of each instrument the potential of this technology is currently underexploited as new tools cannot be easily ported to other instruments. Recently a standardization method was developed in order to harmonize the spectral response format between instruments of different brands and models but also across time for each spectrometer. The method matches monthly the infrared response of all spectrometers on the response of a reference instrument, making all machines talking a common language. The objective is to allow the creation and the use of common, new and innovative concepts by pooling resources and sharing data. Using this method, new tools for analysis of milk quality and milk technological properties have been created and shared within the network, as fatty acids and minerals predictions or milk coagulation properties. New concepts requiring a common spectral format have been developed like the untargeted detection of milk contaminant and abnormal milk or the determination of milk geographic origin. Models in relation with the status of the dairy cow were also created and shared as to predict ketosis, negative energy balance or methane emissions. Therefore models can be developed at one place and deployed within the entire network, in which 90 instruments are currently monthly standardized. [less ▲]

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See detailUtiliser les résultats du contrôle laitier pour améliorer son rendement fromager
Colinet, Frédéric ULiege; Troch, Thibault ULiege

Conference given outside the academic context (2016)

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See detailImprovement of robustness of forward selection of variables using split datasets: Mid-infrared methane equation
Soyeurt, Hélène ULiege; Vanlierde, Amélie; Grelet, Clément ULiege et al

Conference (2016, January)

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See detailCapitalizing on fine milk composition for breeding and management of dairy cows
Gengler, Nicolas ULiege; Soyeurt, Hélène ULiege; Dehareng, Fréderic et al

in Journal of Dairy Science (2016), 99

The challenge of managing and breeding dairy cows is permanently adapting to changing production circumstances under socio-economic constraints. If managing and breeding address different timeframes of ... [more ▼]

The challenge of managing and breeding dairy cows is permanently adapting to changing production circumstances under socio-economic constraints. If managing and breeding address different timeframes of action, both need relevant phenotypes that allow for precise monitoring of the status of the cows, and their health, behavior, and well-being as well as their environmental impact and the quality of their products (i.e., milk and subsequently dairy products). Milk composition has been identified as an important source of information because it could reflect, at least partially, all these elements. Major conventional milk components such as fat, protein, urea, and lactose contents are routinely predicted by mid-infrared (MIR) spectrometry and have been widely used for these purposes. But, milk composition is much more complex and other nonconventional milk components, potentially predicted by MIR, might be informative. Such new milk-based phenotypes should be considered given that they are cheap, rapidly obtained, usable on a large scale, robust, and reliable. In a first approach, new phenotypes can be predicted from MIR spectra using techniques based on classical prediction equations. This method was used successfully for many novel traits (e.g., fatty acids, lactoferrin, minerals, milk technological properties, citrate) that can be then useful for management and breeding purposes. An innovation was to consider the longitudinal nature of the relationship between the trait of interest and the MIR spectra (e.g., to predict methane from MIR). By avoiding intermediate steps, prediction errors can be minimized when traits of interest (e.g., methane, energy balance, ketosis) are predicted directly from MIR spectra. In a second approach, research is ongoing to detect and exploit patterns in an innovative manner, by comparing observed with expected MIR spectra directly (e.g., pregnancy). All of these traits can then be used to define best practices, adjust feeding and health management, improve animal welfare, improve milk quality, and mitigate environmental impact. Under the condition that MIR data are available on a large scale, phenotypes for these traits will allow genetic and genomic evaluations. Introduction of novel traits into the breeding objectives will need additional research to clarify socio-economic weights and genetic correlations with other traits of interest. [less ▲]

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See detailUn noyau génétique confirmé par la génomique
Colinet, Frédéric ULiege

Article for general public (2016)

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See detailGenetic variability of MIR predicted milk technological properties in Walloon dairy cattle
Colinet, Frédéric ULiege; Troch, Thibault ULiege; Baeten, Vincent et al

in Book of Abstracts of the 66th Annual Meeting of the European Federation of Animal Science (2015, August)

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See detailPotential of visible-near infrared spectroscopy for the characterization of butter properties
Troch, Thibault ULiege; Baeten, Vincent; Dehareng, Frédéric et al

in Book of Abstracts of the 66th Annual Meeting of the European Federation of Animal Science (2015, August)

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See detailOn the use of novel milk phenotypes as predictors of difficult-to-record traits in breeding programs
Bastin, Catherine ULiege; Colinet, Frédéric ULiege; Dehareng, Frédéric et al

in Book of Abstracts of the 66th Annual Meeting of the European Federation of Animal Science (2015, August)

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See detailGenetic heritage of the Eastern Belgium Red and White breed, an endangered local breed
Colinet, Frédéric ULiege; Bouffioux, Aude; Mayeres, Patrick et al

Poster (2015, August)

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See detailOverview of possibilities and challenges of the use of infrared spectrometry in cattle breeding
Gengler, Nicolas ULiege; Soyeurt, Hélène ULiege; Dehareng, Frédéric et al

in Book of Abstracts of the 66th Annual Meeting of the European Federation of Animal Science (2015, August)

Detailed reference viewed: 48 (11 ULiège)