Bayesian linear-threshold censored models for genetic evaluation of age at first calving and stayability in Nellore cattle

Costa, Edson Vinícius; Ventura, Henrique Torres; Veroneze, Renata; Silva, Fabyano F.; Pereira, Mariana; Lopes, Paulo Sávio

doi:10.1016/j.livsci.2019.103833

Cited by 14 publications

(8 citation statements)

References 18 publications

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“…According to López-Paredes et al (2018), there was a 0.27 genetic correlation between the AFC and the calving difficulty at first calving in Blonde d'Aquitaine herds. In the Nellore herd Costa et al (2019) found negative (-0.23 and -0.52) correlation between AFC and longevity. According to the results of Lesmeister et al (1973), the average annual calf rearing capacity of early mated heifers was higher than that of those calved later.…”

Section: Introduction and Literature Reviewmentioning

confidence: 81%

Environmental effects, population genetic parameters, breeding value, phenotypic and genetic trend for age at first calving of Limousin cows

Bene¹,

Polgár²,

Szűcs³

et al. 2021

JCEA

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Some environmental effects, population genetic parameters, breeding value of Limousin breeding bulls, also phenotypic and genetic trends in the age at first calving (AFC) of cows between 1992 and 2013 were estimated. Data were served by the Limousin and Blonde d'Aquitaine Breeders Association, in Hungary. The study was extended to three herds and 1157 cows. GLM method was used for the study of different effects, the BLUP animal model for estimation of population genetic parameters and breeding values (BV), and one-way linear regression analysis for trend calculations.The overall mean value of the AFC was estimated to be 34.7±0.4 months. The contribution of the evaluated factors to the phenotype was as follows: herd 73.51%, birth year of cow 13.02%, sire 6.74%, birth season of cow 1.62%. The heritability of AFC proved to be low (h 2 = 0.08±0.07 and h 2 = 0.01±0.04). There were relatively small differences in the estimated BV of the studied sires for the AFC. Based on the phenotypic trend calculation, the AFC of cows decreased by an average of 0.33 months per year, however no significant change was found in the genetic trend during the study period.

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Section: Introduction and Literature Reviewmentioning

confidence: 81%

Environmental effects, population genetic parameters, breeding value, phenotypic and genetic trend for age at first calving of Limousin cows

Bene¹,

Polgár²,

Szűcs³

et al. 2021

JCEA

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“…Despite the fact that the statistical models and the longevity definitions used in their study are not conceptually the same as in our study, the authors reported heritability estimates close to the ones found in our study when considering the group combining all culling reasons under the FLa definition (heritabilities ranging from 0.09 to 0.13). Similar heritabilities (ranging from 0.09 to 0.16) were also estimated for stayability (defined as probability that a cow had calved at least three times before 6.3 years) in Brazilian Nellore cattle [ 57 ]. On the other hand, higher heritability estimates (ranging from 0.18 to 0.25) were found for stayability (defined as stayability to calving, from 2 to 6 years) in Hereford cattle, using a traditional linear model [ 14 ].…”

Section: Discussionmentioning

confidence: 99%

“…Stronger genetic correlations were found by Martínez-Velázquez et al [ 72 ] for scrotal circumference and stayability (0.76 ± 0.04) and between heifer fertility and stayability (0.57 ± 0.07) in a population composed by Charolais, Charbray, and Charolais–Zebu crosses. Costa et al [ 57 ] reported genetic correlations between age at first calving and stayability ranging from −0.23 to −0.51, depending on the statistical model used for the analysis (linear-threshold, penalty-threshold, modified penalty-threshold, and linear-threshold-threshold model) in Nellore cattle.…”

Section: Discussionmentioning

confidence: 99%

Using Random Regression Models to Genetically Evaluate Functional Longevity Traits in North American Angus Cattle

Oliveira

Brito

Miller³

et al. 2020

Animals

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This study aimed to propose novel longevity indicators by comparing genetic parameters for traditional (TL; i.e., the cow’s lifespan after the first calving) and functional (FL; i.e., how long the cow stayed in the herd while also calving; assuming no missing (FLa) or missing (FLb) records for unknown calving) longevity, considering different culling reasons (natural death, structural problems, disease, fertility, performance, and miscellaneous). Longevity definitions were evaluated from 2 to 15 years of age, using single- and multiple-trait Bayesian random regression models (RRM). The RRM fitting heterogenous residual variance and fourth order Legendre polynomials were considered as the optimal models for the majority of longevity indicators. The average heritability estimates over ages for FLb (from 0.08 to 0.25) were always higher than those for FLa (from 0.07 to 0.19), and higher or equal to the ones estimated for TL (from 0.07 to 0.23), considering the different culling reasons. The average genetic correlations estimated between ages were low to moderate (~0.40), for all longevity definitions and culling reasons. However, removing the extreme ages (i.e., 2 and >12 years) increased the average correlation between ages (from ~0.40 to >0.70). The genetic correlations estimated between culling reasons were low (0.12 and 0.20 on average, considering all ages and ages between 3 and 12 years old, respectively), indicating that longevity based on different culling reasons should be considered as different traits in the genetic evaluations. Higher average genetic correlations (estimated from 3 to 12 years old) were observed between TL and FLb (0.73) in comparison to TL and FLa (0.64), or FLa and FLb (0.65). Consequently, a higher average proportion of commonly-selected sires, for the top 1% sires, was also observed between TL and FLb (91.74%), compared to TL and FLa (59.68%), or FLa and FLb (61.01%). Higher prediction accuracies for the expected daughter performances (calculated based on the pedigree information) were obtained for FLb in comparison to TL and FLa. Our findings indicate that FLb is preferred for the genetic evaluation of longevity. In addition, it is recommended including multiple longevity traits based on different groups of culling reasons in a selection sub-index, as they are genetically-different traits. Genetic selection based on breeding values at the age of four years is expected to result in greater selection responses for increased longevity in North American Angus cattle.

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“…However, the authors pointed out that similar EBV correlations were observed using either uncensored or penalized data, which suggests that there was not relevant re-ranking of animals when censored records were used [ 11 ]. Similarly, Costa et al [ 40 ] also found that the linear-threshold model without censored data showed the best predictive ability (computed based on the EBV correlation estimated between the complete and reduced datasets) for the genetic evaluation of both age at first calving and stayability in Nellore cattle. On the other hand, Veerkamp et al [ 41 ] showed that RRM were relatively robust to censoring in genetic evaluations of survival in dairy cattle, as similar EBV predictions were made based on uncensored and censored data.…”

Section: Discussionmentioning

confidence: 96%

Impact of Censored or Penalized Data in the Genetic Evaluation of Two Longevity Indicator Traits Using Random Regression Models in North American Angus Cattle

Oliveira

Miller²,

Brito

et al. 2021

Animals

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This study aimed to evaluate the impact of different proportions (i.e., 20%, 40%, 60% and 80%) of censored (CEN) or penalized (PEN) data in the prediction of breeding values (EBVs), genetic parameters, and computational efficiency for two longevity indicators (i.e., traditional and functional longevity; TL and FL, respectively). In addition, three different criteria were proposed for PEN: (1) assuming that all cows with censored records were culled one year after their last reported calving; (2) assuming that cows with censored records older than nine years were culled one year after their last reported calving, while censored (missing) records were kept for cows younger than nine years; and (3) assuming that cows with censored records older than nine years were culled one year after their last reported calving, while cows younger than nine years were culled two years after their last reported calving. All analyses were performed using random regression models based on fourth order Legendre orthogonal polynomials. The proportion of commonly selected animals and EBV correlations were calculated between the complete dataset (i.e., without censored or penalized data; COM) and all simulated proportions of CEN or PEN. The computational efficiency was evaluated based on the total computing time taken by each scenario to complete 150,000 Bayesian iterations. In summary, increasing the CEN proportion significantly (p-value <0.05 by paired t-tests) decreased the heritability estimates for both TL and FL. When compared to CEN, PEN tended to yield heritabilities closer to COM, especially for FL. Moreover, similar heritability patterns were observed for all three penalization criteria. High proportions of commonly selected animals and EBV correlations were found between COM and CEN with 20% censored data (for both TL and FL), and COM and all levels of PEN (for FL). The proportions of commonly selected animals and EBV correlations were lower for PEN than CEN for TL, which suggests that the criteria used for PEN are not adequate for TL. Analyses using COM and CEN took longer to finish than PEN analyses. In addition, increasing the amount of censored records also tended to increase the computational time. A high proportion (>20%) of censored data has a negative impact in the genetic evaluation of longevity. The penalization criteria proposed in this study are useful for genetic evaluations of FL, but they are not recommended when analyzing TL.

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Bayesian linear-threshold censored models for genetic evaluation of age at first calving and stayability in Nellore cattle

Cited by 14 publications

References 18 publications

Environmental effects, population genetic parameters, breeding value, phenotypic and genetic trend for age at first calving of Limousin cows

Environmental effects, population genetic parameters, breeding value, phenotypic and genetic trend for age at first calving of Limousin cows

Using Random Regression Models to Genetically Evaluate Functional Longevity Traits in North American Angus Cattle

Impact of Censored or Penalized Data in the Genetic Evaluation of Two Longevity Indicator Traits Using Random Regression Models in North American Angus Cattle

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