Assessment of Poisson, Probit and linear models for genetic analysis of presence and number of black spots in Corriedale sheep

Peñagaricano, Francisco; Urioste, J. I.; Naya, Hugo; Campos, Gustavo de los; Gianola, Daniel

doi:10.1111/j.1439-0388.2010.00893.x

Cited by 17 publications

(11 citation statements)

References 26 publications

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“…Alternatively, number of mastitis cases can be analysed with linear models, ordinal threshold models , Poisson models (Pé rez-Cabal et al 2009;Vazquez et al 2009a,b) or with zero-inflated Poisson (ZIP) models (Rodrigues-Motta et al 2007; the latter has been used successfully in animal breeding studies in other species (e.g. Naya et al 2008;Penagaricano et al 2011).…”

Section: Discussionmentioning

confidence: 99%

Predictive ability of alternative models for genetic analysis of clinical mastitis

Vázquez

Pérez-Cabal

Heringstad

et al. 2011

J Animal Breeding Genetics

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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.

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Section: Discussionmentioning

confidence: 99%

Predictive ability of alternative models for genetic analysis of clinical mastitis

Vázquez

Pérez-Cabal

Heringstad

et al. 2011

J Animal Breeding Genetics

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“…It is well known that the age of the animals affects spot presence (Naya et al 2008;Peñagaricano et al 2011). Nevertheless, and given the paucity of results in this area, we decided, as a first approximation, to sample across ages to concentrate on identifying those candidate genes that are responsible for the development of black spots under white coats independent of the age of the animal.…”

Section: Microarray Analysismentioning

confidence: 99%

Gene expression analysis identifies new candidate genes associated with the development of black skin spots in Corriedale sheep

et al. 2011

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The white coat colour of sheep is an important economic trait. For unknown reasons, some animals are born with, and others develop with time, black skin spots that can also produce pigmented fibres. The presence of pigmented fibres in the white wool significantly decreases the fibre quality. The aim of this work was to study gene expression in black spots (with and without pigmented fibres) and white skin by microarray techniques, in order to identify the possible genes involved in the development of this trait. Five unrelated Corriedale sheep were used and, for each animal, the three possible comparisons (three different hybridisations) between the three samples of interest were performed. Differential gene expression patterns were analysed using different t-test approaches. Most of the major genes with well-known roles in skin pigmentation, e.g. ASIP, MC1R and C-KIT, showed no significant difference in the gene expression between white skin and black spots. On the other hand, many of the differentially expressed genes (raw P-value < 0.005) detected in this study, e.g. C-FOS, KLF4 and UFC1, fulfil biological functions that are plausible to be involved in the formation of black spots. The gene expression of C-FOS and KLF4, transcription factors involved in the cellular response to external factors such as ultraviolet light, was validated by quantitative polymerase chain reaction (PCR). This exploratory study provides a list of candidate genes that could be associated with the development of black skin spots that should be studied in more detail. Characterisation of these genes will enable us to discern the molecular mechanisms involved in the development of this feature and, hence, increase our understanding of melanocyte biology and skin pigmentation. In sheep, understanding this phenomenon is a first step towards developing molecular tools to assist in the selection against the presence of pigmented fibres in white wool.

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“…For this purpose, the use of appropriated statistic methodologies are needed. Methods often used to evaluate tick count data are linear models using data log transformation (WHARTON et al, 1970;SEIFERT, 1971;MARUFU et al, 2011;IBELLI et al, 2012;BIEGELMEYER et al, 2015;MAPHOLI et al, 2016) or Poisson models (VAZQUEZ et al 2009;PEÑAGARICANO et al 2010;AYRES et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Comparative Study of Cattle Tick Resistance Using Generalized Linear Mixed Models

et al. 2019

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Comparison of tick resistance in Bos taurus indicus (Nelore) and Bos taurus taurus (Simmental and Caracu) subspecies was investigated utilizing generalized linear mixed models (GLMMs) with Poisson and Negative binomial distributions. Nelore animals (NE) are known to present greater resistance than t. taurus. Difference between tick resistance in Simmental (SI) and Caracu (CA) breeds has never been reported previously. Three artificial tick infestations were conducted to evaluate tick resistance in these breeds. The statistic point of the present study was to show alternative models for the evaluation of tick count data, the GLMMs. Analysis for tick resistance by GLMM with Negative binomial distribution has never been assessed previously. The analyses were performed by the use of the PROC GLIMMIX procedure of the SAS program. The results showed that GLMM with Negative binomial distribution is appropriated to evaluate tick count data with excess of zero observations avoiding overdispersion problems. Finally, considering multiple comparisons with the Bonferroni test, different pattern of tick infestation was observed for the studied breeds, suggesting that NE is the most resistant breed followed by CA.

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Assessment of Poisson, Probit and linear models for genetic analysis of presence and number of black spots in Corriedale sheep

Cited by 17 publications

References 26 publications

Predictive ability of alternative models for genetic analysis of clinical mastitis

Predictive ability of alternative models for genetic analysis of clinical mastitis

Gene expression analysis identifies new candidate genes associated with the development of black skin spots in Corriedale sheep

Comparative Study of Cattle Tick Resistance Using Generalized Linear Mixed Models

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