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See detailMilk mid-infrared spectra based biomarkers contributing to genetic improvement for udder health, fertility and longevity
Gengler, Nicolas ULiege; Mineur, Axelle ULiege; Vanderick, Sylvie ULiege et al

in Proceedings ICAR 2018 (2018)

Recent research showed the usefulness of using estimated breeding values (EBV) for midinfrared (MIR) based biomarkers in genetic improvement. Similarly, research has also shown that genetic variation is ... [more ▼]

Recent research showed the usefulness of using estimated breeding values (EBV) for midinfrared (MIR) based biomarkers in genetic improvement. Similarly, research has also shown that genetic variation is contained in the absorbance traits along the MIR band of wavelengths. Targeted extraction of the useful genetic variance can be achieved by the combination of EBV. Direct estimation of EBV for absorbance traits was demonstrated. Our first objective was to show that the reduction of the rank of the (co)variance structure among spectral traits is possible by imposing linear functions, even if these functions represent lower accuracy MIR biomarkers. MIR based biomarkers traits were derived from ongoing research in the FP7 GplusE project. In this study, the pathway from MIR spectra to the use in genetic improvement will be described. First, blood reference phenotypic data was collected on Holstein cows, at early lactation for IGF-1, glucose, urea, cholesterol, fructosamine, β- hydroxybutyric (BHB) acid and non-esterified fatty acids (NEFA). These traits were calibrated against corresponding MIR spectral data. Calibration 2 cv R ranged from 0.21 to 0.51, very low from a chemometrical point of view, but potentially sufficient to extract useful spectral variation. This was validated, using EBV that were based on these MIR predictions for 144,623 records (closest to days in milk 25), from 73,378 cows, in the Walloon region of Belgium. Single-trait, but multi-lactation (1, 2, 3+) models yielded h2 estimates ranging from 0.07 to 0.27. At least 20 daughters with novel traits and official EBV for udder health, fertility and longevity with minimum reliabilities of 70% were required; a total of 124 bulls met this criteria. Standard selection index theory would usually rely on prediction error variance minimisation and estimated population (co)variances. Alternatively in this study, Partial Least Squares were applied to EBV for the milk MIR based biomarkers to develop novel genetic predictors, for udder health, fertility and longevity, by extracting genetic variation along the wave band after rank reduction. Using all bulls, correlations between best predictors and EBV for udder health, fertility and longevity were at least 0.63, 0.67 and 0.62. Using selection index theory and based on significant increases of prediction abilities of longevity (0.76 compared to 0.68 from udder health or fertility alone) using also milk MIR based blood biomarkers, their potential contribution to genetic improvement of udder health, fertility and longevity will be demonstrated. [less ▲]

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See detailDefining and using novel milk composition based heat stress resilience traits in the context of genomic selection for more robust dairy cows in Wallonia
Mineur, Axelle ULiege; REIS MOTA, Rodrigo ULiege; Gengler, Nicolas ULiege et al

in Proceedings ICAR 2018 (2018)

Recent research showed the usefulness of using estimated breeding values (EBV) for mid-infrared (MIR) based biomarkers in genetic improvement. A novel class of biomarkers was defined based on modelling ... [more ▼]

Recent research showed the usefulness of using estimated breeding values (EBV) for mid-infrared (MIR) based biomarkers in genetic improvement. A novel class of biomarkers was defined based on modelling responses of milk composition (e.g., mid-infrared (MIR) based) to stress expressed on continuous scales using reaction norm models. Heat stress is an important aspect of dairy production even in temperate climates as shown in recent studies. Implementation of genomic selection for tolerance to heat stress is therefore not only an issue for Australian dairy cattle, a country that introduced recently such an evaluation. The question remains open if using milk composition based heat stress resilience genomically enhanced EBV (GEBV) is not a viable option. Genetic parameters were estimated for production and milk composition traits. Data included 155,977 test-day records for milk, fat, and protein yields, fat and protein percentages, 9 individual milk fatty acids (FA), 7 FA groups, 5 minerals, and 3 ketone bodies) predicted by mid-infrared spectrometry., and 7 FA groups. Data were from 21,375 first-lactation Holstein cows in 473 herds in the Walloon region of Belgium and were collected between 2008 and 2014. Test-day records were merged with daily temperature-humidity index (THI) values based on meteorological records from public weather stations. The maximum distance between each farm and its corresponding weather station was 13 km. Linear reaction norm models were used to estimate the intercept and slope responses of 23 traits to increasing THI values. Most yield and FA traits had phenotypic and genetic declines as THI increased, whereas C18:0, C18:1 cis-9, and 4 FA groups (unsaturated FA, monounsaturated FA, polyunsaturated FA, and long-chain FA) increased with THI. Moreover, the latter traits had the largest slope-to-intercept genetic variance ratios, which indicate that they are more affected by heat stress at high THI levels and therefore good candidate traits. Among all traits, C18:1 cis-9 was the most sensitive to heat stress. As this trait is known to reflect body reserve mobilization, using its response to THI could be a very affordable milk biomarker of heat stress for dairy cattle expressing the equilibrium between intake and mobilization, and therefore adaptation, under warm conditions. By including novel milk based composition traits to traditional production traits, correlations between EBVs and also GEBVs of those milk based traits and udder health, fertility and longevity increased considerably. This study demonstrated that milk composition resilience heat stress traits could be used as early indicators of robustness traits. Our results also suggest that marker information tend to lead to higher accuracies of prediction. Therefore, new options to improve robustness through genomic selection in Walloon Holsteins are now presented. [less ▲]

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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 detailGrowth and carcass performances of guinea fowls reared under intensive system in Benin
Houndonougbo, Pascal ULiege; REIS MOTA, Rodrigo ULiege; Chrysostome, A.A.M. Christophe et al

in Livestock of Research for Rural Development (LRRD) (2017), 29(10),

Several local guinea fowl varieties continued to be reared in extensive systems in Benin, even though productivity remains low. Improving rearing conditions through feeding and housing may enhance local ... [more ▼]

Several local guinea fowl varieties continued to be reared in extensive systems in Benin, even though productivity remains low. Improving rearing conditions through feeding and housing may enhance local guinea fowls productivity in Benin. Therefore, the objective of this study was to verify growth and carcass performances of five (Common, Bonaparte, Grey, White and Black) local guinea fowl varieties under intensive management conditions. At birth, 36 keets (young guinea fowls) of each identified variety were randomly divided into six batches and reared up to 16 weeks old under the same feeding and housing conditions. Body weights were recorded up to week 15. At week 16, carcass measurements were also taken. Growth performances and carcass measurements (morphological and visceral) differed among guinea fowl varieties. The heaviest body weight was observed in Common (832±24g) and the lowest in Black variety (698±39g). Highest carcass yield was observed in Grey variety. Liver weight, intestine length and caecum length were highest in Bonaparte variety. Gizzard weight and thigh proportion were highest in Common variety. Breast weight and breast proportion were highest in Grey guinea fowls. Body weight was moderately correlated with drumstick length, body length, wing size, tarsus diameter, thigh length and thorax circumference (range r = 0.34-0.60). The phenotypic variability and its impact on the characterization of these varieties implies that they are genetically different strains, supporting the hypothesis that the guinea fowl population in Benin presents opportunities for genetic improvement. [less ▲]

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See detailCharacteristic of Guinea Fowl breeding in West Africa: Review
Houndonougbo, Pascal ULiege; Bindelle, Jérôme ULiege; Chrysostome, A.A.M. Christophe et al

in Tropicultura (2017), 35(3), 222-230

Guinea fowl production in sub-Saharan Africa (SSA) is generally practiced under family and traditional rearing systems mainly for consumption and income generation, but this species plays also a major ... [more ▼]

Guinea fowl production in sub-Saharan Africa (SSA) is generally practiced under family and traditional rearing systems mainly for consumption and income generation, but this species plays also a major socio-cultural role in specific ceremonies. Birds are kept in free range or in confinement with outdoor access and fed on grain cereals, vegetables, edible termites and kitchen residues found in nature or occasionally supplied by the farmers. Several Guinea fowl varieties are observed and all are characterized by slow growth, high mortality of young and a relatively wild instinct. Although this avian species is less sensitive to some poultry diseases (Newcastle disease, Marek disease, Gumboro disease, etc), local guinea fowl are very sensitive to other poorly controlled diseases that require further study. These varieties differ greatly by their feather color, their morphological characteristics and growth performance, but further thorough and sustained research is needed to quantify these differences. Several researches established the nutritional requirements of local Guinea fowl but in terms of breeding, little works were done compared to chicken. Some recessive and dominant genes as well as genotypic differences were highlighted between varieties. [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 detailRelationships between methane emissions and technico-economic data from commercial dairy herds
Delhez, Pauline ULiege; Wyzen, Benoit; Dalcq, Anne-Catherine ULiege et al

Conference (2017, September 01)

Considering economic and environmental issues is important for the sustainability of dairy farms. Regarding environment, direct methane (CH4) emissions from cows are of increasing concern. Many studies ... [more ▼]

Considering economic and environmental issues is important for the sustainability of dairy farms. Regarding environment, direct methane (CH4) emissions from cows are of increasing concern. Many studies examined CH4 variation factors but often on a low number of experimental cows. Also, few studies linked CH4 to economic aspects of dairy farms. The innovative aim of this study was to highlight technical factors associated with dairy cow CH4 emissions and gain insight into the relationships between CH4 and herd economic results by the use of large scale and on-farm data. A total of 525,697 individual CH4 predictions from milk mid-infrared (MIR) spectra [MIR-CH4 (g/day)] of milk samples collected on 206 farms during the Walloon milk recording were used to create a CH4 proxy at the herd by year (herd*year) level. This proxy was merged with accounting data. This allowed a simultaneous study of CH4 emissions and 56 technico-economic variables for 1,024 herd*year records from 2007 to 2014. Significant effects were detected from ANOVA analyses and correlations (r). MIR-CH4 was weakly linked to technical variables considered individually (r < 0.38), suggesting complex associations between variables. Lower MIR-CH4 was associated with lower fat and protein corrected milk (FPCM) yield (r=0.18), lower milk fat and protein content (r=0.38 and 0.33, respectively), lower quantity of milk produced from forages (r=0.12) and suboptimal reproduction and health performances (e.g. higher calving interval (r=-0.21), higher culling rate (r=-0.15)). On an economic point of view, lower MIR-CH4 was associated with lower gross margin per cow (r=0.19) and per litre FPCM (r=0.09). To conclude, this study suggested that low dairy cow CH4 emissions tended to be associated with suboptimal and also less profitable herd management practices. Further research is needed to confirm and expand on these results. [less ▲]

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See detailPhenotypic, socio-economic and growth features of Guinea fowls raised under different village systems in West Africa
Houndonougbo, Pascal ULiege; Chrysostome, A. A. M. Christophe; REIS MOTA, Rodrigo ULiege et al

in African Journal of Agricultural Research (AJAR) (2017), 12(26), 2232-2241

In Benin, family poultry farming has become an important activity in economic and social aspects that contribute to food security, poverty reduction and well-being. However, current information about ... [more ▼]

In Benin, family poultry farming has become an important activity in economic and social aspects that contribute to food security, poverty reduction and well-being. However, current information about poultry production and consumption is still limited. This information would be useful to improve the sustainable exploitation of agricultural and commercial genetic resources. We aimed to identify and assess the socio-economic and phenotypic features as well as to investigate phenotypic variability and growth performance of guinea fowls raised under different environments. Growth performance and survival rates of local guinea fowl varieties were recorded in three zones of Benin: Collines, Atacora and Borgou. Seven varieties, Gray, Common, Bonaparte, White, Black, Isabelle and Multicolored, were identified in Benin. The farmers choose a variety to be raised based on breeding system, agro-ecological zone, disease resistance, market price and production purpose. Bonaparte, Common and Gray varieties emerged as the most resistant whereas White, Black and Gray outperformed in growth and may be used for breeding purposes. The semi-confinement system could be recommended for startup as a temporary solution to improve production of local guinea fowls in Benin. The existence of several varieties on farms does not encourage genetic conservation and improvement of these resources. Establishing selection or crossbreeding programs in controlled environments would be more appropriate for guinea fowls raised in Benin. [less ▲]

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See detailConsequences of genetic selection for environmental impact traits on economically important traits in dairy cows
Kandel, Purna ULiege; Vanderick, Sylvie ULiege; Vanrobays, Marie-Laure ULiege et al

in Animal Production Science (2017)

Methane (CH4) emission is an important environmental trait in dairy cows. Breeding aiming to mitigate CH4 emissions require the estimation of genetic correlations with other economically important traits ... [more ▼]

Methane (CH4) emission is an important environmental trait in dairy cows. Breeding aiming to mitigate CH4 emissions require the estimation of genetic correlations with other economically important traits and the prediction of their selection response. In this study, test-day CH4 emissions were predicted from milk mid-infrared spectra of Holstein cows. Predicted CH4 emissions (PME) and log-transformed CH4 intensity (LMI) computed as the natural logarithm of PME divided by milk yield (MY). Genetic correlations of PME and LMI with traits used currently were approximated from correlations between estimated breeding values of sires. Values were for PME with MY 0.06, fat yield (FY) 0.09, protein yield (PY) 0.13, fertility 0.17; body condition score (BCS) –0.02; udder health (UDH) 0.22; and longevity 0.22. As expected by its definition, values were negative for LMI with production traits (MY –0.61; FY –0.15 and PY –0.40) and positive with fertility (0.36); BCS (0.20); UDH (0.08) and longevity (0.06). The genetic correlations of 33 type traits with PME ranged from –0.12 to 0.25 and for LMI ranged from –0.22 to 0.18. Without selecting PME and LMI (status quo) the relative genetic change through correlated responses of other traits were in PME by 2% and in LMI by –15%, but only due to the correlated response to MY. Results showed for PME that direct selection of this environmental trait would reduce milk carbon foot print but would also affect negatively fertility. Therefore, more profound changes in current indexes will be required than simply adding environmental traits as these traits also affect the expected progress of other traits. [less ▲]

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See detailGenetic parameters of mid-infrared methane predictions and their relationships with milk production traits in Holstein cattle
Kandel, Purna ULiege; Vanrobays, Marie-Laure ULiege; Vanlierde, Amélie ULiege et al

in Journal of Dairy Science (2017), 100(7), 5578-5591

Many countries have pledged to reduce greenhouse gases. In this context, the dairy sector is one of the identified sectors to adapt production circumstances to address socio-environmental constraints due ... [more ▼]

Many countries have pledged to reduce greenhouse gases. In this context, the dairy sector is one of the identified sectors to adapt production circumstances to address socio-environmental constraints due to its large carbon footprint related to CH4 emission. This study aimed mainly to estimate (1) the genetic parameters of 2 milk mid-infrared-based CH4 proxies [predicted daily CH4 emission (PME, g/d), and log-transformed predicted CH4 intensity (LMI)] and (2) their genetic correlations with milk production traits [milk (MY), fat (FY), and protein (PY) yields] from first- and second-parity Holstein cows. A total of 336,126 and 231,400 mid-infrared CH4 phenotypes were collected from 56,957 and 34,992 first- and second-parity cows, respectively. The PME increased from the first to the second lactation (433 vs. 453 g/d) and the LMI decreased (2.93 vs. 2.86). We used 20 bivariate random regression test-day models to estimate the variance components. Moderate heritability values were observed for both CH4 traits, and those values decreased slightly from the first to the second lactation (0.25 ± 0.01 and 0.22 ± 0.01 for PME; 0.18 ± 0.01 and 0.17 ± 0.02 for LMI). Lactation phenotypic and genetic correlations were negative between PME and MY in both first and second lactations (−0.07 vs. −0.07 and −0.19 vs. −0.24, respectively). More close scrutiny revealed that relative increase of PME was lower with high MY levels even reverting to decrease, and therefore explaining the negative correlations, indicating that higher producing cows could be a mitigation option for CH4 emission. The PME phenotypic correlations were almost equal to 0 with FY and PY for both lactations. However, the genetic correlations between PME and FY were slightly positive (0.11 and 0.12), whereas with PY the correlations were slightly negative (−0.05 and −0.04). Both phenotypic and genetic correlations between LMI and MY or PY or FY were always relatively highly negative (from −0.21 to −0.88). As the genetic correlations between PME and LMI were strong (0.71 and 0.72 in first and second lactation), the selection of one trait would also strongly influence the other trait. However, in animal breeding context, PME, as a direct quantity CH4 proxy, would be preferred to LMI, which is a ratio trait of PME with a trait already in the index. The range of PME sire estimated breeding values were 22.1 and 29.41 kg per lactation in first and second parity, respectively. Further studies must be conducted to evaluate the effect of the introduction of PME in a selection index on the other traits already included in this index, such as, for instance, fertility or longevity. [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 detailAssessing the effect of pregnancy stage on milk composition of dairy cows using mid-infrared spectra
Laine, Aurélie ULiege; Bastin, Catherine; Grelet, Clément ULiege et al

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

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 ... [more ▼]

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 detailUsefulness of multi-breed models in genetic evaluation of direct and maternal calving ease in Holstein and Belgian Blue Walloon purebreds and crossbreds
Vanderick, Sylvie ULiege; Gillon, Alain; Glorieux, Géry et al

in Livestock Science (2017), 198

The objective of this study was to verify the feasibility of a joint genetic evaluation system for calving ease trait of Belgian Blue (BBB) and Holstein (HOL) Walloon cattle based on data of purebred and ... [more ▼]

The objective of this study was to verify the feasibility of a joint genetic evaluation system for calving ease trait of Belgian Blue (BBB) and Holstein (HOL) Walloon cattle based on data of purebred and crossbred animals. Variance components and derived genetic parameters for purebred BBB and HOL animals were estimated by using single-breed linear animal models. This analysis showed clear genetic differences between breeds. Estimates of direct and maternal heritabilities (± standard error) were 0.34 (±0.02) and 0.09 (±0.01) for BBB, respectively, but only 0.09 (±0.01) and 0.04 (±0.01) for HOL, respectively. Moreover, a significant negative genetic correlation between direct and maternal effects was obtained in both breeds: −0.46 (±0.04) for BBB and −0.29 (±0.11) for HOL. Variance components and derived genetic parameters for purebred BBB and HOL and crossbred BBB ×× HOL cattle were then estimated by using two multi-breed linear animal models: a multi-breed model based on a random regression test-day model (Model MBV), and a multi-breed model based on the random regression multi-breed model (Model MBSM). Both multi-breed models use different functions of breed proportions as random regressions, thereby enabling modelling different additive effects according to animal's breed composition. The main difference between these models is the way in which relationships between breeds are accounted for in the genetic (co)variance structure. Genetic parameters differed between single-breed and multi-breed analysis, but are similar to the literature. For BBB, estimates of direct and maternal heritabilities (±SE) were 0.45 (±0.07) and 0.08 (±0.01) by using Model MBV, and 0.45 (±0.08) and 0.09 (±0.02) for Model MBSM, respectively. For HOL, these estimates were 0.18 (±0.04) and 0.05 (±0.01) using Model MBV, and 0.16 (±0.04) and 0.05 (±0.01) for Model MBSM, respectively. Reliability gains (up to 25%) indicated that the use of crossbred data in the multi-breed models had a positive influence on the estimation of genetic merit of purebred animals. A slight re-ranking of purebred sires and maternal grandsires was observed between single-breed and multi-breed models. Moreover, both multi-breed models can be considered as quasi-equivalent models because they performed almost equally well with respect to MSE and correlations, for purebred and crossbred animals. [less ▲]

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See detailRelationships between methane emissions from dairy cows and farm technico-economic results
Delhez, Pauline ULiege; Wyzen, Benoit; Dalcq, Anne-Catherine ULiege et al

Poster (2017, February 07)

Considering economic and environmental issues is important for the sustainability of dairy farms. Regarding environment, direct methane (CH4) emissions from cows are of increasing concern. Many studies ... [more ▼]

Considering economic and environmental issues is important for the sustainability of dairy farms. Regarding environment, direct methane (CH4) emissions from cows are of increasing concern. Many studies examined CH4 variation factors but often on a low number of experimental cows. Also, few studies linked CH4 to economic aspects of dairy farms. The innovative aim of this study was to highlight technical factors associated with dairy cow CH4 emissions and gain insight into the relationships between CH4 and herd economic results by the use of large scale and on-farm data. A total of 525,697 individual CH4 predictions from milk mid-infrared (MIR) spectra [MIR-CH4 (g/day)] of milk samples collected on 206 farms during the Walloon milk recording were used to create a CH4 proxy at the herd by year (herd*year) level. This proxy was merged with accounting data. This allowed a simultaneous study of CH4 emissions and 56 technico-economic variables for 1,024 herd*year records from 2007 to 2014. Significant effects were detected from ANOVA analyses and correlations (r). MIR-CH4 was weakly linked to technical variables considered individually (r < 0.38), suggesting complex associations between variables. Lower MIR-CH4 was associated with lower fat and protein corrected milk (FPCM) yield (r=0.18), lower milk fat and protein content (r=0.38 and 0.33, respectively), lower quantity of milk produced from forages (r=0.12) and suboptimal reproduction and health performances (e.g. higher calving interval (r=-0.21), higher culling rate (r=-0.15)). On an economic point of view, lower MIR-CH4 was associated with lower gross margin per cow (r=0.19) and per litre FPCM (r=0.09). To conclude, this study suggested that low dairy cow CH4 emissions tended to be associated with suboptimal and also less profitable herd management practices. Further research is needed to confirm and expand on these results. [less ▲]

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See detailRelationships between milk mid-infrared predicted gastro-enteric methane production and the technical and financial performance of commercial dairy herds
Delhez, Pauline ULiege; Wyzen, Benoit; Dalcq, Anne-Catherine ULiege et al

in Animal (2017)

Considering economic and environmental issues is important in ensuring the sustainability of dairy farms. The objective of this study was to investigate univariate relationships between lactating dairy ... [more ▼]

Considering economic and environmental issues is important in ensuring the sustainability of dairy farms. The objective of this study was to investigate univariate relationships between lactating dairy cow gastro-enteric methane (CH4) production predicted from milk mid-infrared spectra and technico-economic variables by the use of large scale and on-farm data. A total of 525 697 individual CH4 predictions from milk mid-infrared spectra [MIR-CH4 (g/day)] of milk samples collected on 206 farms during the Walloon milk recording scheme were used to create a MIR-CH4 prediction for each herd and year (HYMIR-CH4). These predictions were merged with dairy herd accounting data. This allowed a simultaneous study of HYMIR-CH4 and 42 technical and economic variables for 1 024 herd and year records from 2007 to 2014. Pearson correlation coefficients (r) were used to assess significant relationships (P < 0.05). Low HYMIR-CH4 was significantly associated with, amongst others, lower fat and protein corrected milk (FPCM) yield (r = 0.18), lower milk fat and protein content (r = 0.38 and 0.33, respectively), lower quantity of milk produced from forages (r = 0.12) and suboptimal reproduction and health performance (e.g. longer calving interval (r = -0.21) and higher culling rate (r = -0.15)). Concerning economic results, low HYMIR-CH4 was significantly associated with lower gross margin per cow (r = 0.19) and per litre FPCM (r = 0.09). To conclude, this study suggested that low lactating dairy cow gastro-enteric CH4 production tended to be associated with more extensive or suboptimal management practices, which could lead to lower profitability. The observed low correlations suggest complex interactions between variables due to the use of on-farm data with large variability in technical and management practices. [less ▲]

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See detailFirst results in the use of milk mid-infrared spectra in the detection of lameness in Austrian dairy cows
Mineur, Axelle ULiege; Köck, Astrid; Grelet, Clément ULiege et al

in Agriculturae Conspectus Scientificus (2017)

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See detailStandardization of milk mid-infrared spectrometers for the transfer and use of multiple models
Grelet, Clément ULiege; 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 detailInvited review: Large-scale indirect measurements for enteric methane emissions in dairy cattle: A review of proxies and their potential for use in management and breeding decisions
Negussie, E.; Haas, Y. De; Dehareng, F. et al

in Journal of Dairy Science (2017), 100(4), 2433-2453

Efforts to reduce the carbon footprint of milk production through selection and management of low-emitting cows require accurate and large-scale measurements of methane (CH4) emissions from individual ... [more ▼]

Efforts to reduce the carbon footprint of milk production through selection and management of low-emitting cows require accurate and large-scale measurements of methane (CH4) emissions from individual cows. Several techniques have been developed to measure CH4 in a research setting but most are not suitable for large-scale recording on farm. Several groups have explored proxies (i.e., indicators or indirect traits) for CH4; ideally these should be accurate, inexpensive, and amenable to being recorded individually on a large scale. This review (1) systematically describes the biological basis of current potential CH4 proxies for dairy cattle; (2) assesses the accuracy and predictive power of single proxies and determines the added value of combining proxies; (3) provides a critical evaluation of the relative merit of the main proxies in terms of their simplicity, cost, accuracy, invasiveness, and throughput; and (4) discusses their suitability as selection traits. The proxies range from simple and low-cost measurements such as body weight and high-throughput milk mid-infrared spectroscopy (MIR) to more challenging measures such as rumen morphology, rumen metabolites, or microbiome profiling. Proxies based on rumen samples are generally poor to moderately accurate predictors of CH4, and are costly and difficult to measure routinely on-farm. Proxies related to body weight or milk yield and composition, on the other hand, are relatively simple, inexpensive, and high throughput, and are easier to implement in practice. In particular, milk MIR, along with covariates such as lactation stage, are a promising option for prediction of CH4 emission in dairy cows. No single proxy was found to accurately predict CH4, and combinations of 2 or more proxies are likely to be a better solution. Combining proxies can increase the accuracy of predictions by 15 to 35%, mainly because different proxies describe independent sources of variation in CH4 and one proxy can correct for shortcomings in the other(s). The most important applications of CH4 proxies are in dairy cattle management and breeding for lower environmental impact. When breeding for traits of lower environmental impact, single or multiple proxies can be used as indirect criteria for the breeding objective, but care should be taken to avoid unfavorable correlated responses. Finally, although combinations of proxies appear to provide the most accurate estimates of CH4, the greatest limitation today is the lack of robustness in their general applicability. Future efforts should therefore be directed toward developing combinations of proxies that are robust and applicable across diverse production systems and environments. [less ▲]

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See detailNational single-step genomic method that integrates multi-national genomic information
Vandenplas, J.; Spehar, M.; Potocnik, K. et al

in Journal of Dairy Science (2017), 100(1), 465-478

The aim of this paper was to develop a national single-step genomic BLUP that integrates multi-national genomic estimated breeding values (EBV) and associated reliabilities without double counting ... [more ▼]

The aim of this paper was to develop a national single-step genomic BLUP that integrates multi-national genomic estimated breeding values (EBV) and associated reliabilities without double counting dependent data contributions from the different evaluations. Simultaneous use of all data, including phenotypes, pedigree, and genotypes, is a condition to obtain unbiased EBV. However, this condition is not always fully met, mainly due to unavailability of foreign raw data for imported animals. In dairy cattle genetic evaluations, this issue is traditionally tackled through the multiple across-country evaluation (MACE) of sires, performed by Interbull Centre (Uppsala, Sweden). Multiple across-country evaluation regresses all the available national information onto a joint pedigree to obtain country-specific rankings of all sires without sharing the raw data. In the context of genomic selection, the issue is handled by exchanging sire genotypes and by using MACE information (i.e., MACE EBV and reliabilities), as a valuable source of “phenotypic” data. Although all the available data are considered, these “multi-national” genomic evaluations use multi-step methods assuming independence of various sources of information, which is not met in all situations. We developed a method that handles this by single-step genomic evaluation that jointly (1) uses national phenotypic, genomic, and pedigree data; (2) uses multi-national genomic information; and (3) avoids double counting dependent data contributions from an animal’s own records and relatives’ records. The method was demonstrated by integrating multi-national genomic EBV and reliabilities of Brown Swiss sires, included in the InterGenomics consortium at Interbull Centre, into the national evaluation in Slovenia. The results showed that the method could (1) increase reliability of a national (genomic) evaluation; (2) provide consistent ranking of all animals: bulls, cows, and young animals; and (3) increase the size of a genomic training population. These features provide more efficient and transparent selection throughout a breeding program. [less ▲]

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