Browsing by Author "Armentano, L. E."

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    Evaluation of the National Research Council (2001) dairy model and derivation of new prediction equations. 1. Digestibility of fiber, fat, protein, and nonfiber carbohydrate
    White, Robin R.; Roman-Garcia, Y.; Firkins, J. L.; VandeHaar, M. J.; Armentano, L. E.; Weiss, W. P.; McGill, Tyler R.; Garnett, R.; Hanigan, Mark D. (2017-05)
    Evaluation of ration balancing systems such as the National Research Council (NRC) Nutrient Requirements series is important for improving predictions of animal nutrient requirements and advancing feeding strategies. This work used a. literature data set (n = 550) to evaluate predictions of total-tract digested neutral detergent fiber (NDF), fatty acid (FA), crude protein (CP), and nonfiber carbohydrate (NFC) estimated by the NRC (2001) dairy model. Mean biases suggested that the NRC (2001) lactating cow model overestimated true FA and CP digestibility by 26 and 7%, respectively, and under-predicted NDF digestibility by 16%. All NR,C (2001) estimates had notable mean and slope biases and large root mean squared prediction error (RMSPE), and concordance (CCC) ranged from poor to good. Predicting NDF digestibility with independent equations for legumes, corn silage, other forages, and nonforage feeds improved CCC (0.85 vs. 0.76) compared with the re-derived NRC (2001) equation form (NRC equation with parameter estimates re-derived against this data set). Separate FA digestion coefficients were derived for different fat supplements (animal fats, oils. and other fat types) and for the basal diet. This equation returned improved (from 0.76 to 0.94) CCC compared with the re-derived NRC (2001) equation form. Unique CP digestibility equations were derived for forages, animal protein feeds, plant protein feeds, and other feeds, which improved CCC compared with the re-derived NRC (2001) equation form (0.74 to 0.85). New NFC digestibility coefficients were derived for grain-specific starch digestibilities, with residual organic matter assumed to be 98% digestible. A Monte Carlo cross-validation was performed to evaluate repeatability of model fit. In this procedure, data were randomly subsetted 500 tunes into derivation (60%) and evaluation (40%) data sets, and equations were derived using the derivation data and then evaluated against the independent evaluation data. Models derived with random study effects demonstrated poor repeatability of fit in independent evaluation. Similar equations derived without random study effects showed improved fit against independent data, and little evidence of biased parameter estimates associated with failure to include study effects. The equations derived in this analysis provide interesting insight, into how NDF, starch, FA, and CP digestibilities are affected by intake, feed type, and diet composition.
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    The genetic and biological basis of feed efficiency in mid-lactation Holstein dairy cows
    Hardie, L. C.; VandeHaar, M. J.; Tempelman, R. J.; Weigel, K. A.; Armentano, L. E.; Wiggans, G. R.; Veerkamp, R. F.; de Haas, Y.; Coffey, M. P.; Connor, E. E.; Hanigan, Mark D.; Staples, C. R.; Wang, Z.; Dekkers, J. C. M.; Spurlock, D. M. (2017-11)
    The objective of this study was to identify genomic regions and candidate genes associated with feed efficiency in lactating Holstein cows. In total, 4,916 cows with actual or imputed genotypes for 60,671 single nucleotide polymorphisms having individual feed intake, milk yield, milk composition, and body weight records were used in this study. Cows were from research herds located in the United States, Canada, the Netherlands, and the United Kingdom. Feed efficiency, defined as residual feed intake (RFI), was calculated within location as the residual of the regression of dry matter intake (DMI) on milk energy (MilkE), metabolic body weight (MBW), change in body weight, and systematic effects. For RFI, DMI, MilkE, and MBW, bivariate analyses were performed considering each trait as a separate trait within parity group to estimate variance components and genetic correlations between them. Animal relationships were established using a genomic relationship matrix. Genome-wide association studies were performed separately by parity group for RFI, DMI, MilkE, and MBW using the Bayes B method with a prior assumption that 1% of single nucleotide polymorphisms have a nonzero effect. One-megabase windows with greatest percentage of the total genetic variation explained by the markers (TGVM) were identified, and adjacent windows with large proportion of the TGVM were combined and reanalyzed. Heritability estimates for RFI were 0.14 (+/- 0.03; +/- SE) in primiparous cows and 0.13 (+/- 0.03) in multiparous cows. Genetic correlations between primiparous and multiparous cows were 0.76 for RFI, 0.78 for DMI, 0.92 for MBW, and 0.61 for MilkE. No single 1-Mb window explained a significant proportion of the TGVM for RFI; however, after combining windows, significance was met on Bos taurus autosome 27 in primiparous cows, and nearly reached on Bos taurus autosome 4 in multiparous cows. Among other genes, these regions contain 6-3 adrenergic receptor and the physiological candidate gene, leptin, respectively. Between the 2 parity groups, 3 of the 10 windows with the largest effects on DMI neighbored windows affecting RFI, but were not in the top 10 regions for MilkE or MBW. This result suggests a genetic basis for feed intake that is unrelated to energy consumption required for milk production or expected maintenance as determined by MBW. In conclusion, feed efficiency measured as RFI is a polygenic trait exhibiting a dynamic genetic basis and genetic variation distinct from that underlying expected maintenance requirements and milk energy output.
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    Modeling fatty acids for dairy cattle: Models to predict total fatty acid concentration and fatty acid digestion of feedstuffs
    Daley, Veridiana L.; Armentano, L. E.; Kononoff, P. J.; Hanigan, Mark D. (2020-08)
    Development of predictive models of fatty acid (FA) use by dairy cattle still faces challenges due to high variation in FA composition among feedstuffs and fat supplements. Two meta-analytical studies were carried out to develop empirical models for estimating (1) the total FA concentration of feedstuffs, and (2) the apparent total-tract digestibility of total FA (DCFA(TTa)) in dairy cows fed different fat types. In study 1, individual feedstuff data for total crude fat (EE) and FA were taken from commercial laboratories (total of 203 feeds, 1,170,937 samples analyzed for total FA, 1,510,750 samples analyzed for total EE), and data for FA composition were collected from the Cornell Net Carbohydrate and Protein System feed library. All feedstuffs were grouped into 7 classes based on their nutritional components. To predict total FA concentration (% of dry matter) for groups of feeds, the total EE (% of dry matter) was used as an independent variable in the model, and all models were linear. For forages, data were weighted using the inverse of the standard error (SE). Regression coefficients for predicting total FA from EE (% of dry matter) were 0.73 (SE, 0.04), 0.98 (0.02), 0.80 (0.02), 0.61 (0.04), 0.92 (0.03), and 0.93 (0.03), for animal protein, plant protein, energy sources, grain crop forage, by-product feeds, and oilseeds, respectively. The intercepts for plant protein and by-product groups were different from zero and included in the models. As expected, forages had the lowest total FA concentration (slope = 0.57, SE = 0.02). In study 2, data from 30 studies (130 treatment means) that reported DCFA(TTa) in dairy cows were used. Data for animal description, diet composition, intakes of total FA, and DCFA(TTa), were collected. Dietary sources of fat were grouped into 11 categories based on their fat characteristic and FA profile. A mixed model including the random effect of study was used to regress digested FA on FA intake with studies weighted according to the inverse of their variance (SE). Dietary intake of extensively saturated triglycerides resulted in markedly lower total FA digestion (DCFA(TTa) = 44%) compared with animals consuming unsaturated FA, such as Ca-salts of palm (DCFA(TTa) = 76%) and oilseeds (DCFA(TTa) = 73%). Cows fed saturated fats had lower total FA digestion among groups, but it was dependent on the FA profile of each fat source. The derived models provide additional insight into FA digestion in ruminants. Predictions of total FA supply and its digestion can be used to adjust fat supplementation programs for dairy cows.
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    Models to predict milk fat concentration and yield of lactating dairy cows: A meta-analysis
    Daley, Veridiana L.; Armentano, L. E.; Hanigan, Mark D. (Elsevier, 2022-10)
    Few models have attempted to predict total milk fat because of its high variation among and within herds. The objective of this meta-analysis was to develop models to predict milk fat concentration and yield of lactating dairy cows. Data from 158 studies consisting of 658 treatments from 2,843 animals were used. Data from several feed databases were used to calculate dietary nutrients when dietary nutrient composition was not reported. Digested intake (DI, g/d) of each fatty acid (FA; C12:0, C14:0, C16:0, C16:1, C18:0, C18:1 cis, C18:1 trans C18:2, C18:3) and absorbed amounts (g/d) of each AA (Arg, His, Ile, Leu, Lys, Met, Phe, Thr, Trp, Val) were calculated and used as candidate variables in the models. A multi-model inference method was used to fit a large set of mixed models with study as the random effect, and the best models were selected based on Akaike's information criterion corrected for sample size and evaluated further. Observed milk fat concentration (MFC) ranged from 2.26 to 4.78%, and milk fat yield (MFY) ranged from 0.488 to 1.787 kg/d among studies. Dietary levels of forage, starch, and total FA (dry matter basis) averaged 50.8 +/- 10.3% (mean +/- standard deviation), 27.5 +/- 7.0%, and 3.4 +/- 1.3%, respectively. The MFC was positively correlated with dietary forage (0.294) and negatively associated with dietary starch (-0.286). The DI of C18:2 (g/d) was more negatively correlated with MFC (-0.313) than that of the other FA. The best variables for predicting MFC were days in milk, FA-free dry matter intake, forage, starch, DI of C18:2, DI of C18:3, and absorbed Met, His, and Trp. The best predictor variables for MFY were FA-free dry matter intake, days in milk, absorbed Met and Ile, and intakes of digested C16:0 and C18:3. This model had a root mean square error of 14.1% and concordance correlation coefficient of 0.81. Surprisingly, DI of C18:3 was positively related to milk fat, and this relationship was consistently observed among models. The models developed can be used as a practical tool for predicting milk fat of dairy cows, while recognizing that additional factors are likely to also affect fat yield.
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    Use of genotype x environment interaction model to accommodate genetic heterogeneity for residual feed intake, dry matter intake, net energy in milk, and metabolic body weight in dairy cattle
    Yao, C.; de los Campos, G.; VandeHaar, M. J.; Spurlock, D. M.; Armentano, L. E.; Coffey, M.; de Haas, Y.; Veerkamp, R. F.; Staples, C. R.; Connor, E. E.; Wang, Z.; Hanigan, Mark D.; Tempelman, R. J.; Weigel, K. A. (2017-03)
    Feed efficiency in dairy cattle has gained much attention recently. Due to the cost-prohibitive measurement of individual feed intakes, combining data from multiple countries is often necessary to ensure an adequate reference population. It may then be essential to model genetic heterogeneity when making inferences about feed efficiency or selecting efficient cattle using genomic information. In this study, we constructed a marker x environment interaction model that decomposed marker effects into main effects and interaction components that were specific to each environment. We compared environment-specific variance component estimates and prediction accuracies from the interaction model analyses, an across-environment analyses ignoring population stratification, and a within-environment analyses using an international feed efficiency data set. Phenotypes included residual feed intake, dry matter intake, net energy in milk, and metabolic body weight from 3,656 cows measured in 3 broadly defined environments: North America (NAM), the Netherlands (NLD), and Scotland (SAC). Genotypic data included 57,574 single nucleotide polymorphisms per animal. The interaction model gave the highest prediction accuracy for metabolic body weight, which had the largest estimated heritabilities ranging from 0.37 to 0.55. The within environment model performed the best when predicting residual feed intake, which had the lowest estimated heritabilities ranging from 0.13 to 0.41. For traits (dry matter intake and net energy in milk) with intermediate estimated heritabilities (0.21 to 0.50 and 0.17 to 0.53, respectively), performance of the 3 models was comparable. Genomic correlations between environments also were computed using variance component estimates from the interaction model. Averaged across all traits, genomic correlations were highest between NAM and NLD, and lowest between NAM and SAC. In conclusion, the interaction model provided a novel way to evaluate traits measured in multiple environments in which genetic heterogeneity may exist. This model allowed estimation of environment-specific parameters and provided genomic predictions that approached or exceeded the accuracy of competing within- or across environment models.