Luis Varona | University of Zaragoza (original) (raw)

Papers by Luis Varona

The software program PQGen is presented as a complementary resource for an introductory course on... more The software program PQGen is presented as a complementary resource for an introductory course on Population and Quantitative Genetics, composed by 38 integrated modules, and specially oriented to animal breeding. Available modules for Population genetics covers the following topics: gene frequencies estimation, Hardy-Weinberg equilibrium, map distances and recombination coefficients, gametic frequencies estimation and evolution, linkage disequilibrium, predictive ability of a marker, assortative mating, migration, mutation, selection, hitchhiking effect, mutation-selection balance, selection for fitness defined by two loci, genetic drift, individual inbreeding, relationship matrices, founder effects and effective population size. Moreover, for Quantitative genetics, the software consist of the following modules: genetic structure of a quantitative trait, sampling of a quantitative trait, heritability estimation, effects of selection, inbreeding depression, heterosis, reciprocal recurrent selection, selection indexes and breeding values distribution, properties of the selection index, efficiency of selection indexes, Best Linear Unbiased Prediction, correlated response, threshold traits, comparison between criteria of selection and marker assisted selection. The program is shareware and it can be downloaded from the web. Suggestions that allow to improve this program will be appreciated by the authors.

Resumen Resulta complicado evaluar el ajuste de los modelos de riesgos proporcionales dado que lo... more Resumen Resulta complicado evaluar el ajuste de los modelos de riesgos proporcionales dado que los tests disponibles actualmente, en su mayoría gráficos, adolecen de un importante grado de subjetividad. En este sentido, hemos desarrollado un procedimiento de bootstrap paramétrico para testar el ajuste de los modelos de supervivencia.

Abstract The present study investigated differences in the allocation patterns of body stores in ... more Abstract The present study investigated differences in the allocation patterns of body stores in lactating female mice from a line selected for high litter size at birth (S-line, average litter size of 20) and dams from a nonselected control line (C-line, average litter size of 10). Body weight, litter size, litter weight, and absolute and relative lipid and protein mass were measured at peak lactation (2 wk in lactation) and at weaning (3 wk in lactation).

Abstract We identified 22 polymorphisms in the adipocyte fatty-acid binding protein (FABP4) gene,... more Abstract We identified 22 polymorphisms in the adipocyte fatty-acid binding protein (FABP4) gene, a strong positional candidate gene for the FAT1 locus in porcine chromosome 4. The most informative polymorphism, an insertion/deletion in intron 1, together with a single nucleotide polymorphism in intron 3, was genotyped in a cross between Iberian and Landrace pigs.

Abstract An analysis of litter size and average piglet weight at birth in Landrace and Yorkshire ... more Abstract An analysis of litter size and average piglet weight at birth in Landrace and Yorkshire using a standard two-trait mixed model (SMM) and a recursive mixed model (RMM) is presented. The RMM establishes a one-way link from litter size to average piglet weight. It is shown that there is a one-to-one correspondence between the parameters of SMM and RMM and that they generate equivalent likelihoods.

Abstract The objective of this work was to evaluate the Nelore beef cattle, growth curve paramete... more Abstract The objective of this work was to evaluate the Nelore beef cattle, growth curve parameters using the Von Bertalanffy function in a nested Bayesian procedure that allowed estimation of the joint posterior distribution of growth curve parameters, their (co) variance components, and the environmental and additive genetic components affecting them.

Gene expression data are influenced by multiple biological and technological factors leading to a... more Gene expression data are influenced by multiple biological and technological factors leading to a wide range of dispersion scenarios, although skewed patterns are not commonly addressed in microarray analyses. In this study, the distribution pattern of several human transcriptomes has been studied on free-access microarray gene expression data.

Abstract The Bayes factor (BF) procedure was applied to examine the additive genetic component of... more Abstract The Bayes factor (BF) procedure was applied to examine the additive genetic component of several physiological and vitality variables for newborn pigs. Nine variables were studied: heart rate, arterial oxygen saturation, rectal temperature (all at birth and 60 min later), birth weight, interval between birth and first teats contact, and interval between birth and first colostrum intake. The available numbers of data ranged from 288 (heart rate at 60 min) to 839 records (birth weight) from F 2 Iberian× Meishan newborn pigs.

Availability of dense marker maps of livestock species has opened new possibilities for genetic e... more Availability of dense marker maps of livestock species has opened new possibilities for genetic evaluation of individuals by whole genome association procedures (Meuwissen et al., 2001). However, an accurate prediction of breeding values ussually involves a huge genotyping effort that cannot be easily supported by populations with reduced population size.

Meat and carcass quality traits are becoming more important in beef cattle production (Eriksson e... more Meat and carcass quality traits are becoming more important in beef cattle production (Eriksson et al.(2003)). Some of them, such as conformation and fat cover scores, obtain their records from subjective grading that usually involve classification under a categorical and arbitrary predefined scale. Theoretically, the discrete nature of the performance should be taken into account for the genetic evaluation by using a threshold model (Gianola and Foulley (1983)).

Resumo: A seleção assistida por marcadores moleculares para características reprodutivas em progr... more Resumo: A seleção assistida por marcadores moleculares para características reprodutivas em programas de melhoramento de bovinos de corte foi até agora muito pouco explorada, essa situação pode mudar a partir da identificação de marcadores moleculares com efeitos sobre essas características. Esse estudo teve como objetivo comparar três modelos de análises de associação para a identificação de marcadores do tipo SNP associados ao perímetro escrotal.

Aproximadamente el 13% de los lechones nacidos vivos mueren antes del destete y cerca de la mitad... more Aproximadamente el 13% de los lechones nacidos vivos mueren antes del destete y cerca de la mitad de estas bajas se producen dentro de los primeros tres días de vida (Varley 1995). Obviamente, estas pérdidas son económicamente importantes y resulta por ello interesante identificar los factores que afectan la viabilidad de los lechones.

Abstract. Three models to analyze tenderness of two muscles with different fiber composition and ... more Abstract. Three models to analyze tenderness of two muscles with different fiber composition and functionality, M. Flexor digitorum and M. Psoas Major, were compared in terms of predictive ability: a linear animal mixed model with heterogeneous residual variance regarding muscle (M1), a model with heterogeneous thresholds regarding muscle (M2), and a model with heterogeneous thresholds for the combination of muscle and panelist (M3).

The advent of Genomic Selection (Meuwissen et al.(2001)) has promoted a renewal of the basic appr... more The advent of Genomic Selection (Meuwissen et al.(2001)) has promoted a renewal of the basic approach of Quantitative Genetics, giving actual value to the notion of gene effects which had remained an abstraction until large scale genotyping became available during the last five years. Developments remain however mainly restricted to an additive statistical framework, allowing improved estimates of genetic values to be obtained.

En los últimos años el tamaño de camada se ha convertido en uno de los objetivos principales en l... more En los últimos años el tamaño de camada se ha convertido en uno de los objetivos principales en los programas de selección de cerdos. Con el uso de líneas hiperprolíficas el número de tetinas que presenta una cerda puede condicionar el número de lechones destetados de la camada. En este escenario, la detección de QTL para el número de mamas puede ser de interés en futuros programas de mejora.

El peso al sacrificio es uno de los caracteres de interés en la producción de vacuno de carne (Go... more El peso al sacrificio es uno de los caracteres de interés en la producción de vacuno de carne (Golden. et al, 1998; MacNeil, 2003; Bouquet et al., 2010). En este carácter no se dispone de registros fenotípicos para los candidatos a la selección.

Resumen Los esquemas de selección en las especies ganaderas utilizan una amplia variedad de carac... more Resumen Los esquemas de selección en las especies ganaderas utilizan una amplia variedad de caracteres. En algunos casos, los registros fenotípicos se obtienen a partir de una valoración subjetiva por parte de evaluadores expertos. Esta valoración implica una clasificación en una escala arbitraria, y, por este motivo, puede diferir considerablemente de la distribución Normal. Por otra parte, cada evaluador puede utilizar criterios de clasificación específicos, y diferentes de los otros evaluadores.

El Caballo Trotador Español (CTE) es una raza equina criada específicamente para la disciplina qu... more El Caballo Trotador Español (CTE) es una raza equina criada específicamente para la disciplina que lleva su nombre. Su programa de mejora incluye como objetivo principal la consecución de un animal que destaque tanto en las competiciones nacionales como internacionales, con una conformación que favorezca su funcionalidad y un temperamento que le haga ansiar la victoria (http://www. mapa. es/ganaderia/pags/equino/seleccion/trotador. pdf).

Los modelos habituales de evaluación genética asumen que los caracteres expresados en machos y he... more Los modelos habituales de evaluación genética asumen que los caracteres expresados en machos y hembras están determinados por el mismo patrimonio genético. Pese a todo hay numerosas evidencias de heterogeneidad tanto en la media como en la varianza, que se han atribuido tanto a un efecto de escala, como al diferente grado de madurez alcanzado por cada sexo a una edad determinada.

Abstract A Bayesian procedure, which allows consideration of the individual variation in the feed... more Abstract A Bayesian procedure, which allows consideration of the individual variation in the feed resource allocation pattern, is described and implemented in 2 sire lines of rabbit (Caldes and R). The procedure is based on a hierarchical Bayesian scheme, where the first stage of the model consists of a multiple regression model of feed intake on metabolic BW and BW gain. In a second stage, an animal model was assumed including batch, parity order, litter size, and common environmental litter effects.

The software program PQGen is presented as a complementary resource for an introductory course on... more The software program PQGen is presented as a complementary resource for an introductory course on Population and Quantitative Genetics, composed by 38 integrated modules, and specially oriented to animal breeding. Available modules for Population genetics covers the following topics: gene frequencies estimation, Hardy-Weinberg equilibrium, map distances and recombination coefficients, gametic frequencies estimation and evolution, linkage disequilibrium, predictive ability of a marker, assortative mating, migration, mutation, selection, hitchhiking effect, mutation-selection balance, selection for fitness defined by two loci, genetic drift, individual inbreeding, relationship matrices, founder effects and effective population size. Moreover, for Quantitative genetics, the software consist of the following modules: genetic structure of a quantitative trait, sampling of a quantitative trait, heritability estimation, effects of selection, inbreeding depression, heterosis, reciprocal recurrent selection, selection indexes and breeding values distribution, properties of the selection index, efficiency of selection indexes, Best Linear Unbiased Prediction, correlated response, threshold traits, comparison between criteria of selection and marker assisted selection. The program is shareware and it can be downloaded from the web. Suggestions that allow to improve this program will be appreciated by the authors.

Resumen Resulta complicado evaluar el ajuste de los modelos de riesgos proporcionales dado que lo... more Resumen Resulta complicado evaluar el ajuste de los modelos de riesgos proporcionales dado que los tests disponibles actualmente, en su mayoría gráficos, adolecen de un importante grado de subjetividad. En este sentido, hemos desarrollado un procedimiento de bootstrap paramétrico para testar el ajuste de los modelos de supervivencia.

Abstract The present study investigated differences in the allocation patterns of body stores in ... more Abstract The present study investigated differences in the allocation patterns of body stores in lactating female mice from a line selected for high litter size at birth (S-line, average litter size of 20) and dams from a nonselected control line (C-line, average litter size of 10). Body weight, litter size, litter weight, and absolute and relative lipid and protein mass were measured at peak lactation (2 wk in lactation) and at weaning (3 wk in lactation).

Abstract We identified 22 polymorphisms in the adipocyte fatty-acid binding protein (FABP4) gene,... more Abstract We identified 22 polymorphisms in the adipocyte fatty-acid binding protein (FABP4) gene, a strong positional candidate gene for the FAT1 locus in porcine chromosome 4. The most informative polymorphism, an insertion/deletion in intron 1, together with a single nucleotide polymorphism in intron 3, was genotyped in a cross between Iberian and Landrace pigs.

Abstract An analysis of litter size and average piglet weight at birth in Landrace and Yorkshire ... more Abstract An analysis of litter size and average piglet weight at birth in Landrace and Yorkshire using a standard two-trait mixed model (SMM) and a recursive mixed model (RMM) is presented. The RMM establishes a one-way link from litter size to average piglet weight. It is shown that there is a one-to-one correspondence between the parameters of SMM and RMM and that they generate equivalent likelihoods.

Abstract The objective of this work was to evaluate the Nelore beef cattle, growth curve paramete... more Abstract The objective of this work was to evaluate the Nelore beef cattle, growth curve parameters using the Von Bertalanffy function in a nested Bayesian procedure that allowed estimation of the joint posterior distribution of growth curve parameters, their (co) variance components, and the environmental and additive genetic components affecting them.

Gene expression data are influenced by multiple biological and technological factors leading to a... more Gene expression data are influenced by multiple biological and technological factors leading to a wide range of dispersion scenarios, although skewed patterns are not commonly addressed in microarray analyses. In this study, the distribution pattern of several human transcriptomes has been studied on free-access microarray gene expression data.

Abstract The Bayes factor (BF) procedure was applied to examine the additive genetic component of... more Abstract The Bayes factor (BF) procedure was applied to examine the additive genetic component of several physiological and vitality variables for newborn pigs. Nine variables were studied: heart rate, arterial oxygen saturation, rectal temperature (all at birth and 60 min later), birth weight, interval between birth and first teats contact, and interval between birth and first colostrum intake. The available numbers of data ranged from 288 (heart rate at 60 min) to 839 records (birth weight) from F 2 Iberian× Meishan newborn pigs.

Availability of dense marker maps of livestock species has opened new possibilities for genetic e... more Availability of dense marker maps of livestock species has opened new possibilities for genetic evaluation of individuals by whole genome association procedures (Meuwissen et al., 2001). However, an accurate prediction of breeding values ussually involves a huge genotyping effort that cannot be easily supported by populations with reduced population size.

Meat and carcass quality traits are becoming more important in beef cattle production (Eriksson e... more Meat and carcass quality traits are becoming more important in beef cattle production (Eriksson et al.(2003)). Some of them, such as conformation and fat cover scores, obtain their records from subjective grading that usually involve classification under a categorical and arbitrary predefined scale. Theoretically, the discrete nature of the performance should be taken into account for the genetic evaluation by using a threshold model (Gianola and Foulley (1983)).

Resumo: A seleção assistida por marcadores moleculares para características reprodutivas em progr... more Resumo: A seleção assistida por marcadores moleculares para características reprodutivas em programas de melhoramento de bovinos de corte foi até agora muito pouco explorada, essa situação pode mudar a partir da identificação de marcadores moleculares com efeitos sobre essas características. Esse estudo teve como objetivo comparar três modelos de análises de associação para a identificação de marcadores do tipo SNP associados ao perímetro escrotal.

Aproximadamente el 13% de los lechones nacidos vivos mueren antes del destete y cerca de la mitad... more Aproximadamente el 13% de los lechones nacidos vivos mueren antes del destete y cerca de la mitad de estas bajas se producen dentro de los primeros tres días de vida (Varley 1995). Obviamente, estas pérdidas son económicamente importantes y resulta por ello interesante identificar los factores que afectan la viabilidad de los lechones.

Abstract. Three models to analyze tenderness of two muscles with different fiber composition and ... more Abstract. Three models to analyze tenderness of two muscles with different fiber composition and functionality, M. Flexor digitorum and M. Psoas Major, were compared in terms of predictive ability: a linear animal mixed model with heterogeneous residual variance regarding muscle (M1), a model with heterogeneous thresholds regarding muscle (M2), and a model with heterogeneous thresholds for the combination of muscle and panelist (M3).

The advent of Genomic Selection (Meuwissen et al.(2001)) has promoted a renewal of the basic appr... more The advent of Genomic Selection (Meuwissen et al.(2001)) has promoted a renewal of the basic approach of Quantitative Genetics, giving actual value to the notion of gene effects which had remained an abstraction until large scale genotyping became available during the last five years. Developments remain however mainly restricted to an additive statistical framework, allowing improved estimates of genetic values to be obtained.

En los últimos años el tamaño de camada se ha convertido en uno de los objetivos principales en l... more En los últimos años el tamaño de camada se ha convertido en uno de los objetivos principales en los programas de selección de cerdos. Con el uso de líneas hiperprolíficas el número de tetinas que presenta una cerda puede condicionar el número de lechones destetados de la camada. En este escenario, la detección de QTL para el número de mamas puede ser de interés en futuros programas de mejora.

El peso al sacrificio es uno de los caracteres de interés en la producción de vacuno de carne (Go... more El peso al sacrificio es uno de los caracteres de interés en la producción de vacuno de carne (Golden. et al, 1998; MacNeil, 2003; Bouquet et al., 2010). En este carácter no se dispone de registros fenotípicos para los candidatos a la selección.

Resumen Los esquemas de selección en las especies ganaderas utilizan una amplia variedad de carac... more Resumen Los esquemas de selección en las especies ganaderas utilizan una amplia variedad de caracteres. En algunos casos, los registros fenotípicos se obtienen a partir de una valoración subjetiva por parte de evaluadores expertos. Esta valoración implica una clasificación en una escala arbitraria, y, por este motivo, puede diferir considerablemente de la distribución Normal. Por otra parte, cada evaluador puede utilizar criterios de clasificación específicos, y diferentes de los otros evaluadores.

El Caballo Trotador Español (CTE) es una raza equina criada específicamente para la disciplina qu... more El Caballo Trotador Español (CTE) es una raza equina criada específicamente para la disciplina que lleva su nombre. Su programa de mejora incluye como objetivo principal la consecución de un animal que destaque tanto en las competiciones nacionales como internacionales, con una conformación que favorezca su funcionalidad y un temperamento que le haga ansiar la victoria (http://www. mapa. es/ganaderia/pags/equino/seleccion/trotador. pdf).

Los modelos habituales de evaluación genética asumen que los caracteres expresados en machos y he... more Los modelos habituales de evaluación genética asumen que los caracteres expresados en machos y hembras están determinados por el mismo patrimonio genético. Pese a todo hay numerosas evidencias de heterogeneidad tanto en la media como en la varianza, que se han atribuido tanto a un efecto de escala, como al diferente grado de madurez alcanzado por cada sexo a una edad determinada.

Abstract A Bayesian procedure, which allows consideration of the individual variation in the feed... more Abstract A Bayesian procedure, which allows consideration of the individual variation in the feed resource allocation pattern, is described and implemented in 2 sire lines of rabbit (Caldes and R). The procedure is based on a hierarchical Bayesian scheme, where the first stage of the model consists of a multiple regression model of feed intake on metabolic BW and BW gain. In a second stage, an animal model was assumed including batch, parity order, litter size, and common environmental litter effects.