Multivariate survival mixed models for genetic analysis of longevity traits

Maia, Rafael Costa Lima; Madsen, Per; Labouriau, Rodrigo

doi:10.1080/02664763.2013.868416

Cited by 17 publications

(10 citation statements)

References 29 publications

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“…The possibilities to analyse multivariate mixed survival models for continuous and discrete time in a context of quantitative genetic applications were discussed by Maia et al . (). They found that the likelihood function of a continuous time model is typically much flatter than the likelihood function of a corresponding discrete time model.…”

Section: Resultsmentioning

confidence: 97%

Phenotypic and genetic variation in longevity of Polish Landrace sows

Sobczyńska

Blicharski

2015

J Animal Breeding Genetics

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The influence of some production traits on the longevity of Polish Landrace sows was evaluated using survival analysis. Estimates of genetic parameters were obtained from the sire and animal components in linear and survival methodologies. Comparison between survival and linear models was based on heritabilities and ranking of estimated breeding values of sires. The same data set, 13,031 sows, was used for both methodologies, even in the presence of censored observations. The effects of herd*year and year*season of the first farrowing had the largest influence on the risk of culling of sows. Sows born in spring season (March-May) had a 24% (p < 0.001) lower hazard for removal than those born in winter (December-February). The age at first farrowing had a small but significant effect on culling: the hazard regression coefficient for this trait was 0.002 per day. Sows that had more piglets born alive and fewer stillborn in the first litter had a decreased risk of being culled. Within a contemporary group, slower growing gilts had decreased removal risk. The relative risk ratios show a marginal decreased rate of culling for sows with backfat thickness between 9.5 and 11 mm compared to the leaner sows. Loin depth had no effect on sow longevity. Heritability estimates ranged from 0.09 to 0.38 depending on the model and type of analysis. In survival analysis, all heritabilities for longevity were higher when analysed with sire models (0.21 and 0.38) compared to animal models (0.09 and 0.16). The use of animal or sire models in the linear analysis gave similar heritability estimates (0.12 and 0.10). Correlations between breeding values for sires were moderate and high, with absolute values from 0.51 to 0.99, depending on the model fitted and methodology. A stronger correlations within methodologies (0.83-0.99) than within models with different methodologies (0.51-0.63) were obtained.

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Section: Resultsmentioning

confidence: 97%

Phenotypic and genetic variation in longevity of Polish Landrace sows

Sobczyńska

Blicharski

2015

J Animal Breeding Genetics

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“…The deaths of hens that occurred in the time period from 30 weeks to 37 weeks of age (both extremes included) were studied using a discrete time proportional hazards model (DTPHM, see Kalbfleisch and Prentice 2002, Maia and others 2014a, b for technical details). This is a discrete-time version of the classic Cox proportional hazards model.…”

Section: Methodsmentioning

confidence: 99%

“…The inference was performed defining a suitable generalised linear mixed model as specified in Maia and others (2014a, b). Hypotheses tests on fixed effects were performed by applying parametrical bootstrap tests on the likelihood ratio statistics (100,000 bootstrap samples).…”

Section: Methodsmentioning

confidence: 99%

Helminth infection is associated with hen mortality in Danish organic egg production

et al. 2016

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The aim of this study was to investigate whether two highly prevalent helminth infections (Ascaridia galli and Heterakis species) are associated with an increased mortality rate for hens at the peak of lay. An observational event study with 11 farms was conducted between 2012 and 2013, with weekly mortality recordings and grouping of the farms into low-infected with A galli and Heterakis species (0-200 epg of faeces) or high-infected (over 200 epg of faeces). Survival analysis was performed using a discrete time proportional hazards model. The difference between the hazard functions for low-infected farms and high-infected farms in either summer (August to September) or winter (January to March) were analysed. No statistically significant associations were found between the mortality rate in winter and summer in low-infected farms. However, the mortality rate was doubled for hens from high-infected farms observed in the summer season compared with hens from low-infected farms (winter and summer), whereas high-infected farms observed in the winter did not have a significant association between mortality rate and season compared with low-infected farms (summer and winter). The results suggest that the mortality in organic egg production may be reduced by measures to control A galli and Heterakis species infections.

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“…Therefore, this part of the variability should be represented in the residual variance; but this is not possible to occur if the residual variance is set to be constant (Breslow & Clayton ; Maia et al . ). Hence, the probit model was performed with the free dispersion parameter.…”

Section: Methodsmentioning

confidence: 99%

Genetic evaluation of calf and heifer survival in Iranian Holstein cattle using linear and threshold models

Forutan

Mahyari

Sargolzaei

2014

J Animal Breeding Genetics

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Calf and heifer survival are important traits in dairy cattle affecting profitability. This study was carried out to estimate genetic parameters of survival traits in female calves at different age periods, until nearly the first calving. Records of 49,583 female calves born during 1998 and 2009 were considered in five age periods as days 1-30, 31-180, 181-365, 366-760 and full period (day 1-760). Genetic components were estimated based on linear and threshold sire models and linear animal models. The models included both fixed effects (month of birth, dam's parity number, calving ease and twin/single) and random effects (herd-year, genetic effect of sire or animal and residual). Rates of death were 2.21, 3.37, 1.97, 4.14 and 12.4% for the above periods, respectively. Heritability estimates were very low ranging from 0.48 to 3.04, 0.62 to 3.51 and 0.50 to 4.24% for linear sire model, animal model and threshold sire model, respectively. Rank correlations between random effects of sires obtained with linear and threshold sire models and with linear animal and sire models were 0.82-0.95 and 0.61-0.83, respectively. The estimated genetic correlations between the five different periods were moderate and only significant for 31-180 and 181-365 (r(g) = 0.59), 31-180 and 366-760 (r(g) = 0.52), and 181-365 and 366-760 (r(g) = 0.42). The low genetic correlations in current study would suggest that survival at different periods may be affected by the same genes with different expression or by different genes. Even though the additive genetic variations of survival traits were small, it might be possible to improve these traits by traditional or genomic selection.

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Multivariate survival mixed models for genetic analysis of longevity traits

Cited by 17 publications

References 29 publications

Phenotypic and genetic variation in longevity of Polish Landrace sows

Phenotypic and genetic variation in longevity of Polish Landrace sows

Helminth infection is associated with hen mortality in Danish organic egg production

Genetic evaluation of calf and heifer survival in Iranian Holstein cattle using linear and threshold models

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