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See detailFeasibility of a genetic evaluation for milk fatty acids in dairy cattle
Soyeurt, Hélène ULg; Arnould, Valérie ULg; Vanderick, Sylvie ULg et al

in Journal of Dairy Science (2010), 93(E-Suppl 1), 744

Recent development of equations based on mid-infrared (MIR) spectrometry for the prediction of milk fatty acid (FA) contents allows their measurement on a large scale during performance recording. The ... [more ▼]

Recent development of equations based on mid-infrared (MIR) spectrometry for the prediction of milk fatty acid (FA) contents allows their measurement on a large scale during performance recording. The objective was to show that a genetic evaluation for milk FA in dairy cattle is feasible in the Walloon region of Belgium and to report first results. Estimated breeding values (EBV) and associated reliabilities (REL) were computed using a multi-trait test-day animal model similar to the one used for the routine genetic evaluation for yield traits. Studied traits were first lactation test-day milk, fat and protein yields, fat (FAT) and protein contents, and content of saturated fatty acids in milk (g/100g of milk, SAT). More than 6,700,000 records were available for common production and content traits and 194,000 records were used for SAT. Used variance components were estimated using REML. The average SAT content was 2.79% with a standard deviation (SD) of 0.50%. A total of 1,707 Holstein bulls used in Walloon Region had REL superior to 0.49 for all studied traits. REL for SAT ranged from 0.53 to 0.99. A total of 1,217 bulls had REL superior to 0.74. SD of EBV for SAT was 0.20%. The maximum and minimum SAT EBV values were 0.89% and -0.69%, respectively. In order to have a direct measure of the part of FAT that is not due to SAT, a new trait (dSAT) was post-evaluated and defined as difference between expected SAT EBV for a given FAT EBV and the estimated EBV for SAT. This new trait can be assumed to be a direct predictor of the content of unsaturated fatty acids in fat. The interest is that this trait cannot be accurately predicted directly by MIR. The maximum and minimum EBV for dSAT for the 1,707 bulls were -0.28% and 0.24%, respectively. Based on these results, a genetic evaluation for milk fatty acids is feasible. In the bull population used recently, a genetic variability for dSAT exists and could be used to improve the milk fat composition. [less ▲]

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See detailGenetic relationships between body condition score and reproduction traits in Canadian Holstein and Ayrshire first-parity cows.
Bastin, Catherine ULg; Loker, Sarah; Gengler, Nicolas ULg et al

in Journal of Dairy Science (2010), 93(5), 2215-28

The objective of this study was to investigate the genetic relationship between body condition score (BCS) and reproduction traits for first-parity Canadian Ayrshire and Holstein cows. Body condition ... [more ▼]

The objective of this study was to investigate the genetic relationship between body condition score (BCS) and reproduction traits for first-parity Canadian Ayrshire and Holstein cows. Body condition scores were collected by field staff several times over the lactation in herds from Quebec, and reproduction records (including both fertility and calving traits) were extracted from the official database used for the Canadian genetic evaluation of those herds. For each breed, six 2-trait animal models were run; they included random regressions that allowed the estimation of genetic correlations between BCS over the lactation and reproduction traits that are measured as a single lactation record. Analyses were undertaken on data from 108 Ayrshire herds and 342 Holstein herds. Average daily heritabilities of BCS were close to 0.13 for both breeds; these relatively low estimates might be explained by the high variability among herds and BCS evaluators. Genetic correlations between BCS and interval fertility traits (days from calving to first service, days from first service to conception, and days open) were negative and ranged between -0.77 and -0.58 for Ayrshire and between -0.31 and -0.03 for Holstein. Genetic correlations between BCS and 56-d nonreturn rate at first insemination were positive and moderate. The trends of these genetic correlations over the lactation suggest that a genetically low BCS in early lactation would increase the number of days that the primiparous cow was not pregnant and would decrease the chances of the primiparous cow to conceive at first service. Genetic correlations between BCS and calving traits were generally the strongest at calving and decreased with increasing days in milk. The correlation between BCS at calving and maternal calving ease was 0.21 for Holstein and 0.31 for Ayrshire and emphasized the relationship between fat cows around calving and dystocia. Genetic correlations between calving traits and BCS during the subsequent lactation were moderate and favorable, indicating that primiparous cows with a genetically high BCS over the lactation would have a greater chance of producing a calf that survived (maternal calf survival) and would transmit the genes that allowed the calf to be born more easily (maternal calving ease) and to survive (direct calving ease). [less ▲]

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

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

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

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

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

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

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

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

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See detailEstimates of genetic parameters among body condition score and fertility traits in first-parity Canadian cows
Bastin, Catherine ULg; Loker, Sarah; Gengler, Nicolas ULg et al

in Journal of Dairy Science (2009), 92 - E-Suppl 1

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

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

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

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

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See detailGenetic analysis of lactoferrin content in bovine milk
Arnould, Valérie ULg; Soyeurt, Hélène ULg; Gengler, Nicolas ULg et al

in Journal of Dairy Science (2009), 92(5), 2151-2158

Bovine lactoferrin (LF) is mainly present in milk and shows important physiological and biological functions. The aim of this study was to estimate the heritability and correlation values of LF content in ... [more ▼]

Bovine lactoferrin (LF) is mainly present in milk and shows important physiological and biological functions. The aim of this study was to estimate the heritability and correlation values of LF content in bovine milk with different economic traits as milk yield (MY), fat and protein percentages, and somatic cell score (SCS). Variance components of the studied traits were estimated by REML using a multiple-trait mixed model. The obtained heritability (0.22) for LF content predicted using mid-infrared spectrometry (pLF) suggested the possibility of animal selection based on the increase of LF content in milk. The phenotypic and genetic correlation values calculated between pLF and SCS were moderate (0.31 and 0.24, respectively). Furthermore, a preliminary study of bovine LF gene polymorphism effects was performed on the same production traits. By PCR, all exons of the LF gene were amplified and then sequenced. Three new polymorphisms were detected in exon 2, exon 11, and intron 8. We examined the effects of LF gene polymorphisms of exons 2, 4, 9, 11, and 15, and intron 8 on pLF, MY, fat and protein percentages, and SCS. The different observed effects did not reach a significant level probably because of the characteristics of the studied population. However, the results were promising, and LF may be a potential indicator of mastitis. Further studies are necessary to evaluate the effect of genetic selection based on LF content on the improvement of mastitis resistance. [less ▲]

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

in Journal of Dairy Science (2009), 92(E-suppl.1), 353-354

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

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

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

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

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

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

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

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

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

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

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See detailGenetic parameters of saturated and monounsaturated fatty acid content and the ratio of saturated to unsaturated fatty acids in bovine milk.
Soyeurt, Hélène ULg; Dardenne, Pierre; Dehareng, Frédéric et al

in Journal of Dairy Science (2008), 91(9), 3611-26

Fatty acid composition influences the nutritional quality of milk and the technological properties of butter. Using a prediction of fatty acid (FA) contents by mid-infrared (MIR) spectrometry, a large ... [more ▼]

Fatty acid composition influences the nutritional quality of milk and the technological properties of butter. Using a prediction of fatty acid (FA) contents by mid-infrared (MIR) spectrometry, a large amount of data concerning the FA profile in bovine milk was collected. The large number of records permitted consideration of more complex models than those used in previous studies. The aim of the current study was to estimate the effects of season and stage of lactation as well as genetic parameters of saturated (SAT) and monounsaturated (MONO) fatty acid contents in bovine milk and milk fat, and the ratio of SAT to unsaturated fatty acids (UNSAT) that reflect the hardness of butter (SAT:UNSAT), using 7 multiple-trait, random-regression test-day models. The relationship between these FA traits with common production traits was also studied. The data set contained 100,841 test-day records of 11,626 Holstein primiparous cows. The seasonal effect was studied based on unadjusted means. These results confirmed that milk fat produced during spring and summer had greater UNSAT content compared with winter (63.13 vs. 68.94% of SAT in fat, on average). The effect of stage of lactation on FA profile was studied using the same methodology. Holstein cows in early first lactation produced a lower content of SAT in their milk fat. Variance components were estimated using a Bayesian method via Gibbs sampling. Heritability of SAT in milk (0.42) was greater than heritability of SAT in milk fat (0.24). Estimates of heritability for MONO were also different in milk and fat (0.14 vs. 0.27). Heritability of SAT:UNSAT was moderate (0.27). For all of these traits, the heritability estimates and the genetic and phenotypic correlations varied through the lactation. [less ▲]

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See detailVariation of delta(9)-desaturase activity in dairy cattle
Soyeurt, Hélène ULg; Dehareng, Frédéric; Mayeres, Patrick et al

in Journal of Dairy Science (2008), 91(8), 3211-3224

The endogenous production of unsaturated fatty acids (FA), particularly some monounsaturated FA (%MONO) and nearly all conjugated linoleic acids, is regulated by the 9-desaturase activity. The aims of ... [more ▼]

The endogenous production of unsaturated fatty acids (FA), particularly some monounsaturated FA (%MONO) and nearly all conjugated linoleic acids, is regulated by the 9-desaturase activity. The aims of this study were to assess the variation of this enzymatic activity within lactation, across dairy breeds, and to estimate its genetic parameters. The ratios of C14:1 cis-9 to C14:0, C16:1 cis-9 to C16:0, and C18:1 cis to C18:0 were calculated from FA contents predicted by mid-infrared spectrometry. Variance components and standard errors were estimated using average information REML. The multitrait mixed model included as fixed effects herd × test date × class of lactation number, class of days in milk × class of lactation number, class of age × class of lactation number, and regressions on breed composition. Four random effects were also included: animal genetic effect, 2 permanent environments (within and across lactations), and residual effect. Under the assumption that the calculated ratios are an approximate measurement of 9-desaturase activity, this study showed different sources of variation for this enzymatic activity. A slight difference was observed within lactation. The ratios of C14:1 cis-9 to C14:0 and C16:1 cis-9 to C16:0 increased as a function of days in milk. Differences across 7 dairy breeds were observed. The values of 9-desaturase indices observed for Jersey and Brown-Swiss cows were lower compared with Holstein. The opposite was observed for dual-purpose Belgian Blue cows. Values of heritability for the ratios of C14:1 cis-9 to C14:0, C16:1 cis-9 to C16:0, and C18:1 cis to C18:0 were 20, 20, and 3%, respectively. Negative genetic correlations observed between fat or protein contents and the 3 indices suggested that an increased activity of 9-desaturase could inhibit the synthesis of fat and protein in bovine milk. Negative correlations were also observed between fat or protein contents and the contents of 3 studied unsaturated FA in milk fat (C14:1 cis-9, C16:1 cis-9, and C18:1 cis). The positive genetic correlations observed between %MONO and the ratios of C14:1 cis-9 to C14:0 (0.72), C16:1 cis-9 to C16:0 (0.62), and C18:1 cis to C18:0 (0.97) showed that %MONO is linked to the 9-desaturase activity. [less ▲]

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See detailGenetic parameters of saturated and monounsaturated fatty acids estimated by test-day model in Walloon dairy cattle
Soyeurt, Hélène ULg; Bastin, Catherine ULg; Dardenne, Pierre et al

in Journal of Dairy Science (2008, July 07)

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See detailGenetic parameters of stearoyl coenzyme-A desaturase 9 activity estimated by test-day model
Arnould, Valérie ULg; Gengler, Nicolas ULg; Soyeurt, Hélène ULg

in Journal of Dairy Science (2008, July), 91(E-Suppl. 2), 542

Dairy and beef products account for a large part of fat intake in human nutrition and therefore can be linked to dietary diseases. The stearoyl Coenzyme-A desaturase 9 (delta-9) gene was identified as a ... [more ▼]

Dairy and beef products account for a large part of fat intake in human nutrition and therefore can be linked to dietary diseases. The stearoyl Coenzyme-A desaturase 9 (delta-9) gene was identified as a potential functional candidate gene affecting milk fat composition in dairy cattle. The objective of this research was to estimate the genetic parameters of delta-9 activity indicator traits and to study the relationship between delta-9 activity as described by these indicator traits and common milk production traits. A total of 126,331 test-day records were obtained from 14,259 Holstein (> 84% Holstein gene) heifers belonging to 105 herds. The studied traits were milk yield, percentages of fat and protein, content of monounsaturated fatty acids, and 3 ratios reflecting the delta-9 activity (C14:1/ C14:0; C16:1/C16:0 and C18:1/C18). The used model was a multiple-trait random regressions test-day model and included as fixed effects: herd x date of test, class of age, and month x year. Random effects were herd x year of calving, permanent environmental, additive genetic, and residual effects. The fatty acid contents were estimated by mid-infrared spectrometry. Delta-9 activity varied within year and lactation. The obtained heritability estimates of delta-9 as well as the genetic and phenotypic correlation varied also through lactation. This study suggests potential improvements of delta-9 activity and subsequently milk fat composition can be achieved by animal management but also by breeding and animal selection. [less ▲]

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See detailEffects of allele frequency estimation on genomic predictions and inbreeding coefficients.
VanRaden, P. M.; Tooker, M. E.; Gengler, Nicolas ULg

in Journal of Dairy Science (2008, July), 91

Genetic calculations often require estimating allele frequencies, which differ across time due to selection and drift. Data were 50,000 simulated markers and 39,985 actual markers for 2391 genotyped ... [more ▼]

Genetic calculations often require estimating allele frequencies, which differ across time due to selection and drift. Data were 50,000 simulated markers and 39,985 actual markers for 2391 genotyped Holstein bulls. Gene content of relatives and gene frequencies in the base (founder) population were estimated using pedigrees and a linear model. Ancestors born since 1950 were included, for a total of 22,088 animals. Because pedigrees were very complete, only one unknown-parent group was used. Convergence to 5 digits of accuracy required about 1000 iterations. Total time was 2 processor days and proportional to number of animals times markers, but actual clock time was reduced by processing loci on separate chromosomes in parallel. Simple allele frequencies were obtained from only the known genotypes. True base frequencies were correlated with estimated base frequencies by 0.98 versus 0.94 with simple frequencies. Genomic predictions and inbreeding coefficients were computed in four ways, using true or estimated base frequencies, simple frequencies, or an “estimate” of .5 for each marker. When allele frequencies estimates were used instead of 0.5 to assign mixed model coefficients, solutions converged more slowly but predictions were more accurate. From simulated data, realized reliabilities for young bulls were 62.8% using either true or estimated base frequencies, 62.6% using simple frequencies, and 62.0% using frequencies set to 0.5. Pedigree and genomic inbreeding coefficients were correlated by 0.73 using true base frequencies, 0.67 using estimated base frequencies, 0.12 using simple frequencies, and 0.72 when frequencies were set to 0.5. Genomic inbreeding coefficients were biased downward by 7% to 9% using either frequency estimate, upward by 31% using 0.5, but were reasonable when true frequencies were used. Frequency estimation had small effects on genomic predictions but large effects on genomic inbreeding coefficients in both simulated and real data. [less ▲]

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See detailStrategies to incorporate genomic prediction into population-wide genetic evaluations
Gengler, Nicolas ULg; VanRaden, P. M.

in Journal of Dairy Science (2008, July), 91

Most current research on genomic selection is focusing on the accurate prediction of genomic breeding values. However selection solely based on genomic breeding values, despite being theoretically ... [more ▼]

Most current research on genomic selection is focusing on the accurate prediction of genomic breeding values. However selection solely based on genomic breeding values, despite being theoretically promising, is in practice only suboptimal for several reasons. The two most important are that only few animals are genotyped therefore having genomic prediction directly available and that rankings will change. With genomic breeding values potentially available in the near future, strategies are required to avoid any confusion in the mind of users. The aim of this study is to present three different strategies that could be used to incorporate genomic prediction into population-wide genetic evaluation. The three strategies are: 1) using selection index theory to combine both sources of information into a single set of breeding values; 2) for ungenotyped animals, compute conditional expectation of gene contents for SNP given molecular and pedigree data and use these predicted gene contents; and 3) integrate genomic breeding values as external information into genetic evaluation using a Bayesian framework. If strategy 1) is straight forward, additional steps have to be done to adjust breeding values for changes in those of relatives. A practical implementation is to use reliabilities of the genomic prediction, the population-wide genetic evaluation PA, and PA from the genotyped subset to set up a 3 x 3 matrix for each animal, with off-diagonal elements being functions of the 3 reliabilities. The use of strategy 2) is computationally much more challenging but leads directly to the needed covariance structures combining genomic relationship if known with pedigree relationships. Strategy 3) is potentially a good compromise because the theory is well established and has already been used in beef cattle to incorporate external breeding values. Also current genetic evaluation software can be easily modified to incorporate genomic breeding values [less ▲]

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See detailRelationship between lactoferrin, minerals, and somatic cells in bovine milk
Soyeurt, Hélène ULg; Arnould, Valérie ULg; Bruwier, Damien et al

in Journal of Dairy Science (2008), 91(E-Suppl. 1), 542

Selection for increased mastitis resistance is hampered by lack of available data. Currently, somatic cell count or score are proven indicators. However, it should be a priority to increase the number of ... [more ▼]

Selection for increased mastitis resistance is hampered by lack of available data. Currently, somatic cell count or score are proven indicators. However, it should be a priority to increase the number of available indicator traits for mastitis resistance. The aim of this research was to study the relationships among potential indicator traits as lactoferrin content, concentrations of major minerals in milk (calcium, Ca; sodium, Na; phosphore, P), and somatic cell count. First, 3 calibration equations Breeding and Genetics: Breeding for Milk Quality and Test-Day Model Applications J. Anim. Sci. Vol. 86, E-Suppl. 2/J. Dairy Sci. Vol. 91, E-Suppl. 1 543 were developed using partial least squares regressions to predict the contents of Ca, Na, and P in milk by mid-infrared spectrometry. A total of 1,609 milk samples were collected between March 2005 and May 2006 for 475 cows from 6 dairy breeds. Based on their spectral variability, 100 samples were selected using a principal components approach. The contents of these minerals were estimated by emission spectrometry (ICP-AES). The ratio of standard deviation to standard error of cross validation obtained for the equations predicted the contents of Ca, Na, and P were superior to 2 suggesting the use of these equations in this research. Second, the relationship between lactoferrin, minerals and somatic cells was studied using a random regressions multi-trait animal test-day model. A total of 57,973 milk samples were collected from 94 herds between April 2005 and January 2008 during milk recording in the Walloon part of Belgium. [less ▲]

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See detailGenotype x environment interaction for milk yield in Holsteins using Luxembourg and Tunisian populations.
Hammami, Hedi ULg; Rekik, Boulbaba; Soyeurt, Hélène ULg et al

in Journal of Dairy Science (2008), 91(9), 3661-71

Test-day (TD) milk yield records of first-lactation Holstein cows in Luxembourg and Tunisia were analyzed using within-and between-country random regression TD models. Edited data used for within-country ... [more ▼]

Test-day (TD) milk yield records of first-lactation Holstein cows in Luxembourg and Tunisia were analyzed using within-and between-country random regression TD models. Edited data used for within-country analysis included 661,453 and 281,913 TD records in Luxembourg and Tunisia, respectively. The joint data included 730,810 TD records of 87,734 cows and 231 common sires. Both data sets covered calving years 1995 to 2006. Fourth-order Legendre polynomials for random effects and a Gibbs sampling method were used to estimate variance components of lactation curve parameters in separate and joint analyses. Genetic variances of the first 3 coefficients from Luxembourg data were 46 to 69% larger than corresponding estimates from the Tunisian data. Inversely, the Tunisian permanent environment variances for the same coefficients were 52 to 65% larger than the Luxembourg ones. Posterior mean heritabilities of 305-d milk yield and persistency, defined as estimated breeding values (EBV) at 280 days in milk-EBV at 80 days in milk, from between-country analysis were 0.42 and 0.12 and 0.19 and 0.08 in Luxembourg and Tunisia, respectively. Heritability estimates for the same traits from within-country analyses, mainly from the Tunisian data, were lower than those from the joint analysis. Genetic correlations for 305-d milk yield and persistency between countries were 0.60 and 0.36. Product moment and rank correlations between EBV of common sires for 305-d milk yield and persistency from within-country analyses were 0.38 and 0.41 and 0.27 and 0.26, respectively. Differences between genetic variances found in both countries reflect different milk production levels. Moreover, low genetic and rank correlations suggest different ranking of sires in the 2 environments, which implies the existence of a genotype x environment interaction for milk yield in Holsteins. [less ▲]

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See detailPregnancy incidence in Norwegian red cows using nonreturn to estrus, rectal palpation, pregnancy-associated glycoproteins, and progesterone.
Garmo, R. T.; Refsdal, A. O.; Karlberg, K. et al

in Journal of Dairy Science (2008), 91(8), 3025-3033

The objectives of the study were to estimate pregnancy incidence and calving rate after first artificial insemination (AI) in Norwegian Red cows undergoing spontaneous estrus, to assess the relationship ... [more ▼]

The objectives of the study were to estimate pregnancy incidence and calving rate after first artificial insemination (AI) in Norwegian Red cows undergoing spontaneous estrus, to assess the relationship between pregnancy and management factors at herd or cow level, to evaluate differences between 60-d nonreturn rate (NRR60d) and pregnancy incidence, and to compare the accuracy of pregnancy diagnosis by rectal palpation and plasma pregnancy-associated glycoproteins (PAG) analysis supported by progesterone measurements. In total, 829 animals (n = 229 heifers, 234 first-lactation, 173 second-lactation, and 193 >second-lactation cows) were included. Milk samples for progesterone analysis were collected both at AI and 3 wk later. Cows with progesterone concentrations <3 ng/mL at AI were considered in estrus or having nonactive ovaries, whereas cows with progesterone concentrations >7 ng/ mL 3 wk later were considered pregnant. Blood sampling for PAG analysis and pregnancy diagnosis by rectal palpation were conducted 57.6 +/- 0.92 d after AI. Pregnancy-associated glycoprotein concentrations equal to 2.5 ng/mL gave the greatest sensitivity (94.3%) and specificity (94.6%) in the assessment of pregnancy. The number of days from calving to first AI was 85.3 +/- 1.71. Overall NRR60d after first AI was 72.5%. The corresponding values for heifers, first-lactation, second-lactation, and >second-lactation cows were 76.9, 67.1, 69.9, and 76.2%. Overall pregnancy incidence after first AI was 63.7%. The corresponding values for heifers, first-lactation, second-lactation, and >second-lactation cows were 70.0, 58.2, 61.6, and 64.9%. Overall calving rate to first AI was 57.2%. The corresponding values for heifers, first-lactation, second-lactation, and >second-lactation cows were 64.9, 54.3, 54.7, and 53.9%. The overall difference between NRR60d and pregnancy incidence was 8.8%, whereas the parity-specific differences were 6.9, 8.9, 8.3, and 11.3% for heifers, first-lactation, second-lactation, and >second-lactation cows, respectively. Eight animals with PAG <2.5 ng/mL and classified as pregnant by rectal palpation calved, whereas 5 animals with PAG >or=2.5 ng/mL and classified as non-pregnant by rectal palpation also calved. The study showed that Norwegian Red cows have relatively high reproductive performance. Breeding for fertility traits over 35 yr is probably an important reason for such high fertility. [less ▲]

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See detailAccuracy of prediction of gene content in large animal populations and its use for candidate gene detection and genetic evaluation
Gengler, Nicolas ULg; Abras, S.; Verkenne, C. et al

in Journal of Dairy Science (2008), 91(4), 1652-1659

To estimate and to use the effects of single genes on quantitative traits, genotypes need to be known. However, in large animal populations, the majority of animals are not genotyped. These missing ... [more ▼]

To estimate and to use the effects of single genes on quantitative traits, genotypes need to be known. However, in large animal populations, the majority of animals are not genotyped. These missing genotypes have to be estimated. However, currently used methods are impractical for large pedigrees. An alternative method to estimate missing gene content, defined as the number of copies of a particular allele, was recently developed. In this study, the proposed method was tested by assessing its accuracy in estimation and use of gene content in large animal populations. This was done for the bovine transmembrane growth hormone receptor and its effects on first-lactation milk, fat, and protein test-day yields and somatic cell score in Holstein cows. Estimated gene substitution effects of replacing a copy of the phenylalanine-coding allele with a copy of the tyrosine-coding allele were 295 g/d for milk, -8.14 g/d for fat, -1.83 g/d for protein, and -0.022/d for somatic cell score. However, only the gene substitution effect for milk was found to be significant. The accuracy of the estimated effects was evaluated by simulations and permutations. To validate the use of predicted gene content in a mixed inheritance model, a cross-validation study was done. The model with an additional regression of milk, fat, and protein yields and SCS on predicted gene content showed a better capacity to predict breeding values for milk, fat, and protein. Given these results, the estimation and use of allelic effects using this method proved functional and accurate. [less ▲]

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