Association between days open and milk spectral data in dairy cows.

Data on 19,489 Brown Swiss cows reared in northeastern Italy were used to associate absorbances of individual wavenumbers within the mid-infrared range with days open (DO). Different postcalving days in milk (DIM) intervals were studied to determine the most informative milk sampling periods for predicting DO. Milk samples were analyzed using a MilkoScan (Foss Electric, Hillerød, Denmark) Fourier-transform infrared (FTIR) spectrometer for 1,060 wavenumbers (wn) ranging from 5,011 to 925 cm-1. To determine DO, we considered an insemination to lead to conception when there was no return of heat (i.e., no successive insemination) and the cow had a subsequent calving date whereby gestation length was required to be within ±30 d of 290 d. Only milk records within the first 90 DIM were considered. Associations were inferred by (1) fitting linear regression models between the DO and each individual wavenumber or milk component, and (2) fitting a Bayesian regression model that included the complete FTIR spectral data. The effects of including systematic effects (parity number, year-season, herd) in the model on these associations were also studied. These analyses were performed for the complete data (5-90 DIM) and for data stratified by DIM period (5 to 30, 31 to 60, and 61 to 90 DIM). Overall, regions of wavenumbers of the milk FTIR spectra that were associated with DO included wn 2,973 to 2,830 cm-1 [related to fat-B (C-H stretch)], wn 2,217 to 1,769 cm-1 [related to fat-A (C = O stretch)], wn 1,546 cm-1 (related to protein), wn 1,465 cm-1 (related to urea and fat), wn 1,399 to 1,245 cm-1 (related to acetone), and wn 1,110 cm-1 (related to lactose). Estimated effects depended on the DIM period, with milk samples drawn during DIM intervals 31 to 60 d and 61 to 90 d being most strongly associated with DO. These DIM intervals are also typically most associated with negative energy balance and peak lactation.

Effect of claw disorders on milk production, fertility, and longevity, and their economic impact in Spanish Holstein cows.

The aims of this study were (1) to estimate the phenotypic association between different degrees of severity of claw disorders and production, fertility performance, and longevity in Spanish dairy cattle, and (2) to quantify its economic impact at the animal and herd level. In this study, claw data comprised 108,468 trimmings collected between 2012 and 2014 by 25 trimmers from 804 Holstein dairy herds. The claw disorders considered were the 3 most frequent disorders in Spanish dairy herds: dermatitis (DE), sole ulcer (SU), and white line disease (WL). The presence of SU or WL was associated with a significant decrease in milk production and was more important in cows in second or later lactations. A severe lesion of SU or WL lead to twice the milk losses associated with a mild lesion, ranging from 1.47 to 2.66kg/d of energy-corrected milk. The presence of SU or WL during the early lactation period was associated with more days open, fewer inseminations to get pregnant, and longer calving to first service interval (4.83 and 8.0 d longer due to mild and severe lesions of SU, respectively, and 4.94 and 17.43 d longer due to mild and severe lesions of WL, respectively). The occurrence of a case of SU or WL in first lactation had a significant effect on longevity, with severe lesions reducing up to 71 d of productive life. The cost of a mild lesion ranged from $53 to $232 per affected cow and year, whereas the cost of a severe lesion ranged from $402 to $622 per affected cow and year. The annual costs per cow for DE, SU, and WL were $10.80, $50.9, and $43.2, respectively. An average herd with 64 cows had an extra expenditure of $691/yr due to DE, $3,256/yr due to SU, and $2,765/year due to WL. Milk losses, longer calving intervals, and premature culling contributed to more than half of the costs. Therefore, providing this information to farmers could help decide on strategies to reduce the incidence of claw disorders on the farm.

Short communication: Association of foot and leg conformation and body weight with claw disorders in Spanish Holstein cows.

Data of first-lactation Holstein cows including claw disorders, foot and leg type traits, and structure and capacity type traits were used to study the phenotypic association of conformation and body weight with claw health status. The claw disorders studied were digital and interdigital dermatitis, sole ulcer, white line disease, and an overall claw disorder trait, indicating the presence of any of the 6 claw disorders recorded by the Spanish I-SAP program. Body weight was estimated indirectly with the Von Bertalanffy equation using live weight, which was also estimated from body depth, stature, and chest width. Cows with poor scores for foot and leg traits were more likely to have a claw disorder, with the exception of rear leg rear view and foot and leg composite that did not show any association with the studied disorders. The heavier the cow was, the higher was the probability of having sole ulcer, white line disease, or overall claw disorder trait, but digital and interdigital dermatitis, as an infectious disorder, did not show any association with body weight. Therefore, it is recommended that the preventive trimming routine be improved, which means checking each cow at least once per lactation and trimming if necessary, to achieve balanced weight-bearing for heavier cows and cows with poor feet and leg classification.

Models for genetic evaluations of claw health traits in Spanish dairy cattle.

Genetic parameters of 7 claw health traits from Spanish dairy cattle were estimated and the predictive ability of linear and ordinal threshold models were compared and assessed. This study included data on interdigital and digital dermatitis (DE), sole ulcer (SU), white line disease (WL), interdigital hyperplasia (IH), interdigital phlegmon (IP), and chronic laminitis (CL) collected between July 2012 and June 2013 from 834 dairy herds visited by 21 trained trimmers. An overall claw disorder (OCD) was also considered an indicator the absence or the presence of at least 1 of the 6 disorders. Claw health traits were scored as categorical traits with 3 degrees of severity (nonaffected, mild, and severe disorder). Genetic parameters were estimated by fitting both a standard linear model and an ordinal threshold animal model. Around 21% of cows had at least 1 claw disorder, and the most frequent disorders were SU, DE, WL, and CL. Heritabilities of claw disorders estimated with a linear model ranged from 0.01 (IP) to 0.05 (OCD), whereas estimates from the ordinal threshold models ranged from 0.06 to 0.39 (for IP and IH, respectively). Repeatabilities of claw health estimated with the linear model varied from 0.03 to 0.18 and estimates with the ordinal threshold model ranged from 0.33 to 0.69. The global trait OCD was correlated with all disorders, except for IH and IP when the linear model was fitted. Two different genetic backgrounds of claw disorders were found. Digital dermatitis showed positive correlations with IH and IP, whereas SU was positively correlated with WL and CL. The predictive ability of the models was assessed using mean squared error and Pearson correlation between the real observation and the corresponding prediction using cross-validation. Regardless of the claw health status, the linear model led to smaller mean squared error. However, differences in predictive ability were found when predicting nonaffected and affected animals. For most traits, healthy cows were better predicted using the threshold model, whereas the linear model fitted affected cows better. Correlations between the observed data and corresponding predictions support those results ranging from 0.01 to 0.34. Claw health traits showed enough genetic variance to be included in the selection goal for Spanish Holsteins to select animals with less susceptibility to claw health problems, and we suggest the linear model for implementing genetic evaluations of claw heath traits.

Weighting fibre and morphological traits in a genetic index for an alpaca breeding programme.

Nowadays, the fibre diameter (FD) is considered the main selection objective in alpaca populations all over the world. International Committee for Animal Recording recommendations define the FD and its CV as the first two traits to be considered in breeding programmes for this specie. In addition to these main criteria, other selection criteria of economic value used are comfort factor (CF) or standard deviation (s.d.); also other less important traits being used as selection objectives are these morphological traits: density (DE), crimp (CR) or lock structure (LS) for, respectively, Huacaya (HU) and Suri (SU) ecotypes, head (HE), coverage (CO) and balance (BA). The goal of this study was to establish how to implement a combined selection index starting from genetic parameters and to study the expected correlation between genetic trends by considering different alternative procedures of weighting all the involved traits, and the consequences of a wrongly proceeding way. Heritabilities and genetic and phenotypic correlations were estimated from the data set belonging to the PACOMARCA experimental farm for SU and HU. Two approaches were used to check the consequences of a set of subjective weights essayed. The coefficients of selection indexes were obtained for two sets of reference weights. In addition, equivalent weights were drawn if applied those reference values as coefficients of hypothetical selection indexes directly on phenotypes; relative expected genetic responses were computed in different cases. Results showed that almost in all cases for both ecotypes, the weight applied to CF should be surprisingly negative. Concerning genetic responses, only CO was compromised in some cases for the HU ecotype. The essayed methodology allowed explaining the differences between ecotypes in the genetic trends. The proposed methodology was shown to be effective to study the relative importance of the traits granted by the manager of a breeding scheme.

Genetic parameters for birthweight environmental variability in mice.

Data from a divergent experiment for birthweight (BrW) environmental variability were used to estimate genetic parameters for BrW trait and its environmental variability by fitting both homoscedastic (HO) and heteroscedastic (HE) models. A total of 5 475 records of BrW from animals born from inbred dams, and 7 140 pedigree records were used. The heritability of BrW using the model HO was 0.27, with the litter effect much more important, 0.43. The model HE provided a genetic correlation between the trait and its environmental variability that was very high and negative, -0.97, and a high value for the additive genetic variance for environmental variability, suggesting an artefact in the model. The residual skewness was found to be essentially null. A model considering the genetic correlation null was also fitted, and used to obtain the breeding values for the selection process. Moreover, the trait was considered as maternal resulting in similar estimates under the model HO, but more reasonable for the genetic correlation between the trait and its environmental variability of 0.48 with a value of 0.25 for the additive genetic variance regarding environmental variability under the model HE. This led to the conclusion that environmental variability of BrW in mice must be selected via dams. Estimated parameters in a reduced dataset without inbred animals did not substantially change this conclusion.

Predictive ability of alternative models for genetic analysis of clinical mastitis.

Mastitis in cows can be defined as a binary trait, reflecting presence or absence of clinical mastitis (CM), or as a count variable, number of mastitis cases (NCM), within a defined time interval. Many different models have been proposed for genetic analyses of mastitis, and the objective of this study was to evaluate the predictive ability and sire predictions of a set of models for genetic evaluation of CM or NCM. Linear- and threshold liability models for CM, and linear, censored ordinal threshold, and zero-inflated Poisson (ZIP) models for NCM were compared in a cross-validation study. To assess the ability of these models to predict future data, records from 620492 first-lactation Norwegian Red cows, which were daughters of 3064 sires, were evaluated in a fourfold cross-validation scheme. The mean squared error of prediction was used for model comparison. All models but ordinal threshold model equally performed when comparing the overall predictive ability. This result was on average, across sick and healthy cows; however, the models behaved differently for each category of animals. For example, healthy cows were predicted better by the threshold and linear models for binary data and ZIP model, whereas for mastitic cows, the ordinal threshold model was by far the best model. Predicted sire effects and rankings of sires were highly correlated across all models. For practical purposes, the linear models are very competitive with the nonlinear models.

Genetic parameters for growth of fiber diameter in alpacas.

The alpaca is the most important fiber producer of the South American camelid species, and is an important source of income for the Andean communities. Nowadays, fiber diameter is considered the main selection objective in alpaca populations throughout the world. However, fiber diameter increases with the age of the animals, and it would be preferable to select those animals that maintain a thin fiber throughout their life span. The goal of this study was to describe the genetic relationship between fiber diameter at weaning age (6 mo) and the evolution of fiber diameter along the life span. The analysis of the evolution of fiber diameter was studied as a useful model for canalization and as a longitudinal trait by hierarchical Bayesian analysis. The results suggested that substantial genetic variation exists for fiber diameter and also for the variability and linear growth of the fiber diameter. Thus, a genetic selection program is plausible to modify the evolution of fiber diameter with time, together with a favorable correlated decrease in fiber diameter.

Analysis of the existence of major genes affecting alpaca fiber traits.

The aim of this study was to determine the presence of major genes for fiber diameter (FD), SD of FD (SDFD), CV of FD, and comfort factor (CF) in Huacaya (HU) and Suri (SU) Peruvian alpaca breeds. Bayesian segregation analyses with relaxed transmission probabilities were performed using 1,906 and 6,592 available records for SU and HU breeds. Evidence for the presence of major genes was statistically supported when the 95% posterior density did not include zero. Significant major genes were found associated with decreased FD, SDFD, CV values, and increased CF values. Additive effects of the major genes were 4.18 and 4.23 µm for FD, 1.67 and 1.61 µm for SDFD, 3.32 and 3.76% for CV, and 15.03 and 14.90% for CF in HU and SU breeds, respectively. Dominance effects were -1.98 and -2.03 µm for FD, -0.88 and -1.11 µm for SDFD, -1.37 and -2.17% for CV, and 13.0 and 11.8% for CF in HU and SU breeds, respectively. Major gene variance was larger than the polygenic variance for all traits. Major gene allelic frequencies for FD, SDFD, and CV ranged from 0.81 to 0.86 for HU breed and from 0.70 to 0.77 for the SU breed and were 0.24 and 0.36, respectively, for CF. It can be concluded that a major gene affecting these traits could be segregating. Then, molecular identification and monitoring of animals carrying favorable genes throughout the worldwide alpaca population would allow for a quick genetic improvement.

Poisson versus threshold models for genetic analysis of clinical mastitis in US Holsteins.

Typically, clinical mastitis is coded as the presence or absence of disease in a given lactation, and records are analyzed with either linear models or binary threshold models. Because the presence of mastitis may include cows with multiple episodes, there is a loss of information when counts are treated as binary responses. Poisson models are appropriated for random variables measured as the number of events, and although these models are used extensively in studying the epidemiology of mastitis, they have rarely been used for studying the genetic aspects of mastitis. Ordinal threshold models are pertinent for ordered categorical responses; although one can hypothesize that the number of clinical mastitis episodes per animal reflects a continuous underlying increase in mastitis susceptibility, these models have rarely been used in genetic analysis of mastitis. The objective of this study was to compare probit, Poisson, and ordinal threshold models for the genetic evaluation of US Holstein sires for clinical mastitis. Mastitis was measured as a binary trait or as the number of mastitis cases. Data from 44,908 first-parity cows recorded in on-farm herd management software were gathered, edited, and processed for the present study. The cows were daughters of 1,861 sires, distributed over 94 herds. Predictive ability was assessed via a 5-fold cross-validation using 2 loss functions: mean squared error of prediction (MSEP) as the end point and a cost difference function. The heritability estimates were 0.061 for mastitis measured as a binary trait in the probit model and 0.085 and 0.132 for the number of mastitis cases in the ordinal threshold and Poisson models, respectively; because of scale differences, only the probit and ordinal threshold models are directly comparable. Among healthy animals, MSEP was smallest for the probit model, and the cost function was smallest for the ordinal threshold model. Among diseased animals, MSEP and the cost function were smallest for the Poisson model, followed by the ordinal threshold model. In general, the models for count variables more accurately identified diseased animals and more accurately predicted mastitis costs. Healthy animals were more accurately identified by the probit model.

Genetic evaluation of susceptibility to clinical mastitis in Spanish Holstein cows.

This study had 3 objectives: to estimate genetic parameters and predict sires' transmitting abilities for clinical mastitis in a Spanish Holstein population, to propose a methodology for comparing models with different response variables by using a cost-based loss function, and to evaluate alternative genetic evaluation models by using this methodology. On-farm records for clinical mastitis from herds in 3 Spanish regions were analyzed as a binary trait (CM) and as number of episodes (NCM) per lactation. Linear and probit models were fitted for CM, whereas linear and Poisson models were used for NCM. Predictive ability of the models was evaluated by using the average predicted residual sum of squares from cross-validation and an alternative cost-based loss function. The loss function for model comparison was calculated by using average mastitis costs depending on the NCM and average cost per infected lactation. The average cost per infected lactation was $345.58, whereas the cost per lactation ranged from $204.86 to $985.44 for lactations with 1 to 5 cases, respectively. Management and hygiene practices on individual farms had a large impact on clinical mastitis because the herd-year variance was larger than that of other random effects considered. The sire variance was significantly different from zero, confirming that genetic variation exists for clinical mastitis. Estimates of heritability for CM using the linear and probit models were 0.07 and 0.10 on the underlying scale, respectively. For NCM, the estimate of heritability for the linear model was 0.10 and estimates for the Poisson model evaluated at the mean and the median of lambda on the underlying scale were 0.09 and 0.07, respectively. Regarding ranking of sires, the definition of response variable (CM or NCM) was of greater importance than the choice of statistical model. Cross-validation results indicated that models with the best fit for CM and NCM were the probit model and the linear model, respectively. However, a comparison across all models using the alternative cost-based loss function showed that using NCM as a response variable with a Poisson model provided the most accurate predictions of future costs associated with clinical mastitis.

Genetic and phenotypic relationships among locomotion type traits, profit, production, longevity, and fertility in Spanish dairy cows.

The phenotypic and genetic relationships of 3 locomotion traits with profit, production, longevity, and fertility traits were studied to determine the importance of locomotion traits for dairy producers. Two data sets including official milk records and type classification scores of 62,293 cows, and reproductive records of 24,561 cows from the Basque and Navarra Autonomous Regions were analyzed. Higher scores for feet and legs (FL), foot angle (FA), and rear legs set (RLS) were positively related to production and functional traits, whereas fertility was not significantly affected. The cows that scored the highest for FL were $213/yr more profitable, produced 575 kg more milk per year, and remained in the herd for 307 more functional days than the cows scoring the lowest. Feet and legs was the trait most genetically correlated to profit, although a low value (0.10) was obtained, whereas RLS was the trait most correlated to milk production (0.12). Genetic correlations among FL, FA, RLS, and longevity traits (from -0.10 to 0.05) were low. Quadratic curves were the best fit for both profit and functional herd life for EBV of each of the 3 locomotion traits. Further studies dealing with profitability and lameness, instead of using conformation traits, could be performed directly if a larger data pool of lameness was routinely recorded.

Economic value of female fertility and its relationship with profit in Spanish dairy cattle.

A data file of 225,085 inseminations and 120,713 lactations from 63,160 Holstein cows was analyzed to obtain female fertility economic value according to number of inseminations per service period (INS). Fertility cost (FCOST) was included in a bioeconomic model, taking into account number of doses of semen, hormonal treatments, fertility culling cost, and delayed milk and calf sales. A profit equation was elaborated to estimate fertility cost and profit according to INS. Fertility in Spanish dairy cattle has worsened >10% over the last 14 yr. Days open have increased by about 15 d, and INS has increased from 1.7 to 2.0. A quadratic relationship was found between FCOST and INS. Similar profitability was estimated for cows who needed one or 2 INS, but when >3 INS were needed, profit decreased by >205 (US dollars)/yr per cow. Cows that needed more INS had higher milk yield per lactation, but also had a higher culling risk and lower productive life and lifetime production, therefore, lower profit. Calving interval (CI) and INS economic values were, respectively, -4.90 and -67.32 (US dollars)/yr per cow and per one unit of change. The economic values of productive traits were 4.04, 1.02, and 1.19 (US dollars)/yr per cow and per one unit of change for kg protein, kg fat, and days in milk, respectively. A mature body weight economic value of -0.67 (US dollars)/yr per cow and per kg was estimated. The relative importance of fertility traits with respect to protein was 64% for CI and 24% for INS, although the CI economic value is highly influenced by phenotypic standard deviation considered.

Lifetime profit as an individual trait and prediction of its breeding values in Spanish Holstein cows.

Genetic parameters for lifetime profit and some productive traits were estimated from records of 42,401 Holstein cows with first calving before May 1996 from Navarra and Basque Autonomous Regions of Spain. Profit from the first, first two, and first three lactations were tested as early measures of profitability. Profit prediction was tested for another population of 2127 cows using selection indexes (Type-Production and economic indexes) and multitrait analysis for directly predicting profit from first-lactation records. High genetic correlations of actual profit with estimated profit from the first two or first three lactation records, (0.97 and 0.99, respectively) suggest that lifetime profit can be accurately estimated from data in second lactation. Profit was positively correlated to production traits (0.79 to 0.83), functional herd life (0.38), mature body weight (0.25), and days in milk (0.35), but genetic correlation was found to be close to zero with calving interval. Complicated relationships among profit and economic traits (i.e., calving interval, days in milk, and functional herd life) were found. Although the correlation between calving interval and profit was near zero, calving interval was the most important trait after production in prediction of sire profit by a stepwise regression analysis. Profit breeding values from multitrait analysis obtained higher correlation (0.48) with actual profit than Spanish official Type-Production index ICO (0.44) and economic index MEG (0.46). A correlation of 0.49 between profit breeding values and the economic index MEG2002, where stature and calving interval were included as new traits, was obtained.

Genetic relationships between lifetime profit and type traits in Spanish Holstein cows.

Genetic parameters and relationships were estimated for profit and type traits for Spanish Holstein cows. In this study, 46,316 cows with official production and type data from Navarra and Basque autonomous regions of Spain were used to calculate profit per cow and year of productive life. Data from 239 Basque Autonomous Region herds in year 1995 were considered to obtain average prices system for yield, meat, feeding, and housing costs. An average cow had a net profit of 78.56 euros per year of productive life, with 7334 kg of milk, 3.85 lactations and 28.0 mo of age at first calving. Heritability of profit was 0.25. Genetic correlations between profit and almost all conformation traits were low to moderate, from 0.12 for leg side view to 0.37 for suspensory ligament while stature, body depth, and udder depth had close to zero correlations with profit. Significant quadratic relationships were found between breeding values for profit and feet and legs, foot angle, fore-udder attachment, rear-udder height and udder depth. The most influential type trait on profit adjusted for production was feet and legs. Animals with negative breeding values for legs were not less profitable than another with zero value, but positive values increased profit per cow and year with a quadratic and positive relationship. Other traits affecting profit out of production and longevity, such as fertility and mastitis, should be considered in future studies.