| 1. |
- Rönnegård, Lars, et al.
(författare)
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Genetic heterogeneity of residual variance - estimation of variance components using double hierarchical generalized linear models
- 2010
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Ingår i: Genetics Selection Evolution. - : Springer Science and Business Media LLC. - 0999-193X .- 1297-9686. ; 42
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Tidskriftsartikel (refereegranskat)abstract
- Background: The sensitivity to microenvironmental changes varies among animals and may be under genetic control. It is essential to take this element into account when aiming at breeding robust farm animals. Here, linear mixed models with genetic effects in the residual variance part of the model can be used. Such models have previously been fitted using EM and MCMC algorithms.Results: We propose the use of double hierarchical generalized linear models (DHGLM), where the squared residuals are assumed to be gamma distributed and the residual variance is fitted using a generalized linear model. The algorithm iterates between two sets of mixed model equations, one on the level of observations and one on the level of variances. The method was validated using simulations and also by re-analyzing a data set on pig litter size that was previously analyzed using a Bayesian approach. The pig litter size data contained 10,060 records from 4,149 sows. The DHGLM was implemented using the ASReml software and the algorithm converged within three minutes on a Linux server. The estimates were similar to those previously obtained using Bayesian methodology, especially the variance components in the residual variance part of the model.Conclusions: We have shown that variance components in the residual variance part of a linear mixed model can be estimated using a DHGLM approach. The method enables analyses of animal models with large numbers of observations. An important future development of the DHGLM methodology is to include the genetic correlation between the random effects in the mean and residual variance parts of the model as a parameter of the DHGLM.
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| 2. |
- Ahlman, Therese, et al.
(författare)
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Culling reasons in organic and conventional dairy herds and genotype by environment interaction for longevity
- 2011
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Ingår i: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 94, s. 1568-1575
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Tidskriftsartikel (refereegranskat)abstract
- Dairy cow longevity combines all functional traits and is thought to be especially important in organic production, which is an established, increasing part of Swedish dairy production, representing approximately 6% of the market. The aim of this study was to compare dynamics in culling reasons between organic and conventional production and to analyze genotype by environment interactions for longevity. The data contained information from all organic herds with information available from official recording (n = 402) and from approximately half of the conventional herds (n = 5,335). Records from Swedish Holsteins (n = 155,379) and Swedish Red cows (n = 160,794) that had their first calf between January 1998 and September 2003 were included. The opportunity period for longevity was at least 6 yr. Six longevity traits were defined: length of productive life; survival through first, second, and third lactations; fertility-determined survival; and udder health-determined survival. Twenty codes were used to describe the cause of culling, and these were divided into 8 groups: udder health, low fertility, low production, leg problems, metabolic diseases, other diseases, other specified causes, and unspecified cause. The main reason for culling cows in organic herds was poor udder health, whereas for cows in conventional herds it was low fertility. Furthermore, the shift in main culling reason from fertility, which was most common in first lactation regardless of production system, to udder health occurred at a lower age in organic production. Heritabilities and genetic correlations for the longevity traits expressed in organic and conventional herds were estimated from a bivariate animal model. The genetic correlations were close to unity (>0.88), except for fertility-determined survival in the Swedish Red breed (0.80). Heritabilities were low to moderate, and no clear pattern was identified for production system or breed. In general, the results indicate that farmers' culling criteria differ between organic and conventional production. Different preferences may influence the need for alternative selection indexes for organic production, with different weightings of traits, or a separate breeding program. However, no genotype by environment interaction of importance was found between the production systems.
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| 3. |
- Ahlman, Therese, et al.
(författare)
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Fertility, somatic cell count and milk production in Swedish organic and conventional dairy herds
- 2009
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Ingår i: Livestock Science. - : Elsevier BV. - 1871-1413 .- 1878-0490. ; 126, s. 176-182
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Tidskriftsartikel (refereegranskat)abstract
- The share of organic dairy production in EU is increasing and this study describes the herd structure and cow performance in organic and conventional dairy production systems in Sweden. The data included records from 2902718 lactations, collected in organic (n=471) and conventional (n = 13976) herds between 1998 and 2005. Compared with conventional herds, the organic herds were larger and increased more rapidly in size. The replacement rate was slightly lower in organic herds and fewer Swedish Holsteins were used. The statistical analysis of cow performance in the first three lactations showed lower milk, fat and protein production in organic herds, but the increase in production from first to second lactation was larger when expressed in kg milk. Fertility was better for organically managed cows compared to conventionally managed cows, but the somatic cell count (SCC) was higher. However. at a given production level the fertility was slightly worse in organic herds while there was no difference in SCC. No interactions of importance were found between production system and breed for any trait.The results showed that organic and conventional dairy production differed regarding herd structure and cow performance. However, the differences in fertility and SCC found were to a high extent explained by the lower milk yield in organic production and no breed was found to perform better in either system. (C) 2009 Elsevier B.V. All rights reserved.
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| 6. |
- Carlén, Emma, et al.
(författare)
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Random regression models for genetic evaluation of clinical mastitis in dairy cattle
- 2009
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Ingår i: Animal. - 1751-7311 .- 1751-732X. ; 3, s. 1100-1108
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Tidskriftsartikel (refereegranskat)abstract
- A genetic analysis of longitudinal binary clinical mastitis (CM) data recorded on about 90000 first-lactation Swedish Holstein cows was carried out using linear random regression models (RRM). This method for genetic evaluation of CM has theoretical advantages compared to the method of linear cross-sectional models (CSM), which is currently being used The aim of this study was to investigate the feasibility and suitability of estimating genetic parameters and predicting breeding values for CM with a linear sire RRM. For validation purposes, the estimates and predictions from the RRM were compared to those from linear sire longitudinal multivariate models (LMVM) and CSM. For each cow, the period from 10 days before to 241 days after calving was divided into four 1-week intervals followed by eight 4-week intervals. Within each interval, presence or absence of CM was scored as '1' or '0' The linear RRM used to explain the trajectory of CM over time included a set of explanatory variables plus a third-order Legendre polynomial function of time for the sire effect The time-dependent heritabilities and genetic correlations from the chosen RRM corresponded fairly well with estimates obtained from the linear LMVM for the separate intervals. Some discrepancy between the two methods was observed, with the more unstable results being obtained from the linear LMVM. Both methods indicated clearly that CM was not genetically the same trait throughout lactation. The correlations between predicted sire breeding values from the RRM, summarized over different time periods, and from linear CSM were rather high. They were, however, less than unity (0.74 to 0.96), which indicated some re-ranking of sires. Sire curves based on the time-specific breeding values from the RRM illustrated differences in intercept and slope among the best and the worst sires. To conclude, a linear sire RRM seemed to work well for genetic evaluation purposes, but was sensitive for estimation of genetic parameters.
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| 7. |
- Emanuelson, Ulf, et al.
(författare)
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Relationship between somatic cell count and milk yield in different stages of lactation
- 2009
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Ingår i: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 92, s. 3124-3133
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Tidskriftsartikel (refereegranskat)abstract
- The association between somatic cell count (SCC) and daily milk yield in different stages of lactation was investigated in cows free of clinical mastitis (CM). Data were recorded between 1989 and 2004 in a research herd, and consisted of weekly test-day (TD) records from 1,155 lactations of Swedish Holstein and Swedish Red cows. The main data set (data set A) containing 36,117 records excluded TD affected by CM. In this data set, the geometric mean SCC was 55,000 and 95,000 cells/mL in primiparous and multiparous cows, respectively. A subset of data set A (data set B), containing 27,753 records excluding all TD sampled in lactations affected by CM, was created to investigate the effect of subclinical mastitis (SCM) in lactations free of CM. Daily milk yields were analyzed using a mixed linear model with lactation stage; linear, quadratic and cubic regressions of log(2)-transformed and centered SCC nested within lactation stage; weeks in lactation; TD season; parity; breed; pregnancy status; year-season of calving; calving, reproductive, metabolic and claw disorders; and housing system as fixed effects. A random regression was included to further improve the modeling of the lactation curve. Primiparous and multiparous cows were analyzed separately. The magnitude of daily milk loss associated with increased SCC depended on stage of lactation and parity, and was most extensive in late lactation irrespective of parity. In data set A, daily milk loss at an SCC of 500,000 cells/mL ranged from 0.7 to 2.0 kg (3 to 9%) in primiparous cows, depending on stage of lactation. In multiparous cows, corresponding loss was 1.1 to 3.7 kg (4 to 18%). Regression coefficients of primiparous cows estimated from data set B were consistent with those obtained from data set A, whereas data set B generated more negative regression coefficients of multiparous cows suggesting a higher milk loss associated with increased SCC in lactations in which the cow did not develop CM. The 305-d milk loss in the average lactation affected with SCM was 155 kg of milk (2%) in primiparous cows and 445 kg of milk (5%) in multiparous cows. It was concluded that multiparous cows in late lactation can be expected to be responsible for the majority of the herd-level production loss caused by SCM, and that preventive measures need to focus on reducing the incidence of SCM in such cows.
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| 10. |
- Malm, Sofia, et al.
(författare)
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Association between radiographic assessment of hip status and subsequent incidence of veterinary care and mortality related to hip dysplasia in insured Swedish dogs
- 2010
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Ingår i: Preventive Veterinary Medicine. - : Elsevier BV. - 0167-5877 .- 1873-1716. ; 93, s. 222-232
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Tidskriftsartikel (refereegranskat)abstract
- Our objective was to evaluate the association between grading of hip status as assessed by radiographic examination (hip screening) and subsequent incidence of veterinary care and mortality related to hip dysplasia (HD) in five breeds of insured dogs in Sweden. Screening results for hip status from the Swedish Kennel Club and data on veterinary care and mortality from the insurance company Agria were merged based on the registration number of the dog. Dogs of five breeds (Bernese Mountain Dogs, German Shepherds, Golden Retrievers, Labrador Retrievers, and Rottweilers) screened during 1995-2004 and covered by an insurance plan for veterinary care or life at the time of screening were included. The study populations included between 1667 and 10,663 dogs per breed. Breed-specific multivariable Cox proportional-hazards analyses were performed to evaluate the impact of radiographic hip status on time from hip screening to first HD-related veterinary and life claim, respectively. The effects of gender, birth season, and a time-varying covariate of year were also studied. Additional analyses, on the five breeds combined, were performed to investigate the effects of hip status, breed, and the interaction between hip status and breed. The effect of hip status was highly significant (P < 0.001) for both life and veterinary claims related to HD in all five breeds with increased hazard ratio (HR) for deteriorating hip status. Dogs with moderate or severe hip status at screening had a markedly increased hazard of HD-related veterinary care and mortality compared with dogs assessed as free or mild. The time-varying covariate of year showed a significantly higher HR in the last time period for German Shepherds and Labrador Retrievers in the analyses of veterinary claims. In the analyses on all five breeds, German Shepherds had the highest HR for both veterinary care and mortality related to HD, followed by Bernese Mountain Dogs. Golden and Labrador Retrievers had the lowest HR. The effect of hip status on the hazard was the same irrespective of breed. However, as a consequence of differences between breeds in overall risk, the predictive ability of screening results for subsequent incidence of HD-related problems for individual dogs was breed-dependent. Based on the strong association between radiographic hip status and incidence of HD-related veterinary care and mortality, and the previously reported moderate heritability of hip status, we conclude that selection based on screening results for hip status can be expected to reduce the risk of HD-related clinical problems. (C) 2009 Elsevier B.V. All rights reserved.
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