Romdhane Rekaya - Academia.edu (original) (raw)

Papers by Romdhane Rekaya

Research paper thumbnail of Use of phenotypic and molecular information to ascertain paternity

Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Minas Gerais, Brazil, 13-18 August, 2006., 2006

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Research paper thumbnail of 330 Multivariate genome wide association for continuous and discrete responses using multivariate Bernoulli prior

Journal of Animal Science, Dec 1, 2018

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Research paper thumbnail of Genetic evaluation in the presence of uncertain additive relationships. I. Use of phenotypic information to ascertain paternity

Journal of Animal Science, Oct 1, 2007

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Research paper thumbnail of High density marker panels, SNPs prioritizing and accuracy of genomic selection

BMC Genetics, Jan 5, 2018

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Research paper thumbnail of National evaluation for calving ease, gestation length and birth weight by linear and threshold model methodologies

PubMed, 2002

Data included 393,097 calving ease, 129,520 gestation length, and 412,484 birth weight records on... more Data included 393,097 calving ease, 129,520 gestation length, and 412,484 birth weight records on 412,484 Gelbvieh cattle. Additionally, pedigrees were available on 72,123 animals. Included in the models were effects of sex and age of dam, treated as fixed, as well as direct, maternal genetic and permanent environmental effects and effects of contemporary group (herd-year-season), treated as random. In all analyses, birth weight and gestation length were treated as continuous traits. Calving ease (CE) was treated either as a continuous trait in a mixed linear model (LM), or as a categorical trait in linear-threshold models (LTM). Solutions in TM obtained by empirical Bayes (TMEB) and Monte Carlo (TMMC) methodologies were compared with those by LM. Due to the computational cost, only 10,000 samples were obtained for TMMC. For calving ease, correlations between LM and TMEB were 0.86 and 0.78 for direct and maternal genetic effects, respectively. The same correlations but between TMEB and TMMC were 1.00 and 0.98, respectively. The correlations between LM and TMMC were 0.85 and 0.75, respectively. The correlations for the linear traits were above.97 between LM and TMEB but as low as 0.91 between LM and TMMC, suggesting insufficient convergence of TMMC. Computing time required was about 2 hrs, 5 hrs, and 6 days for LM, TMEB and TMMC, respectively, and memory requirements were 169, 171, and 445 megabytes, respectively. Bayesian implementation of threshold model is simple, can be extended to multiple categorical traits, and allows easy calculation of accuracies; however, computing time is prohibitively long for large models.

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Research paper thumbnail of Longitudinal multiple-trait versus cumulative single-trait analysis of male and female fertility and hatchability in chickens

Poultry Science, Jul 1, 2005

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Research paper thumbnail of Disease class prediction using gene expression data: dealing with potential misdiagnosis

Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Minas Gerais, Brazil, 13-18 August, 2006, 2006

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Research paper thumbnail of Genetic evaluation of calving to first insemination using natural and artificial insemination mating data1

Journal of Animal Science, Feb 1, 2004

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Research paper thumbnail of SNPxGE2: a database for human SNP-coexpression associations

Bioinformatics, Nov 30, 2011

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Research paper thumbnail of Longitudinal random effects models for genetic analysis of binary data with application to mastitis in dairy cattle

Genetics Selection Evolution, Sep 15, 2003

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Research paper thumbnail of Male and female fertility and hatchability in chickens: a longitudinal mixed model approach

Poultry Science, Aug 1, 2004

The objective of the current study was to investigate different approaches for handling missing r... more The objective of the current study was to investigate different approaches for handling missing records and to develop and implement a multivariate longitudinal mixed model for the genetic evaluation of male and female fertility and hatchability in chickens. The traits recorded on a weekly basis were eggs set (E), percentage fertility (F), and percentage hatch of fertile eggs (H). Three approaches for handling missing records were investigated: 1) all records with zero weekly laid eggs were removed and remaining records with missing F and H were predicted (M1); 2) missing records, including zero weekly laid eggs, were assumed known and equal to zero (M2); and 3) zero weekly laid eggs were assumed as a valid record and missing F and H were predicted (M3). A longitudinal mixed model was used for the multiple trait analysis of E, F, and H. Fixed effects included week-flock, age of service sire (rooster in the pen at data collection), and age of hen. Unrelated service sire, additive hen, permanent environmental, and the residual term were included as random effects. Heritability estimates ranged from 0.06 to 0.13 for E, F, and H. Heritability estimates of F and H were overestimated using M2. Correlations among the 3 traits were highest using M2 and lowest using M1. Pearson correlations indicated that reranking of birds and service sires could occur when using M1. Therefore, M1 should not be used for the analysis of longitudinal data of fertility and hatchability in chickens. Furthermore, M3 seems to be the most ideal method for handling missing records.

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Research paper thumbnail of Growth Rate Distribution and Potential Non-Linear Relationship between Body Weight and Walking Ability in Turkeys

Animals

The aim of this study was to investigate the potential non-linear relationship between growth and... more The aim of this study was to investigate the potential non-linear relationship between growth and walking ability (WA). The phenotypic data included body weights at 12 and 20 weeks and WA at 20 weeks of age measured on 276,059 male turkeys. The growth rate at three age periods (0 to 12, 12 to 20 and 0 to 20 weeks) was calculated. Each bird was assigned to one of the quartiles of the growth rate distribution for each age period. Between the first and fourth quartiles, the incidence of score 1 (bad WA) increased by 31, 18, and 33% for the first, second, and third age periods, respectively. For good WA (scores 4, 5, and 6), the incidence decreased by 55, 66, and 72% between the first and fourth quartiles for the first, second, and third age periods, respectively. Estimates of heritability of WA ranged between 0.18 and 0.26. The genetic correlations between adjacent growth rate quartiles were high and decayed as the interval between quartiles increased. The magnitude of the variation in...

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Research paper thumbnail of 54 Image Based Sampling to Assess Horn Fly Abundance on Cattle

Journal of Animal Science

Horn flies are a major irritant to livestock. In cattle, horn flies can cause increased heart and... more Horn flies are a major irritant to livestock. In cattle, horn flies can cause increased heart and respiratory rates, decreased feed efficiency, decreased weaning weights, and reduced milk production, resulting in substantial economic loss. Fly abundance varies within and across breeds, and genetic analyses have shown sufficient variation to permit selection of hosts for resistance to horn flies. A major limitation for selecting against horn fly abundance is the difficulty associated with measuring on-animal fly counts under pasture conditions. Traditionally, trained evaluators examine cattle in the pasture and estimate fly numbers. Fly movement and animal movements, as well as evaluator expertise are major sources of variation. Image analysis has also been proposed as a means to evaluate horn fly abundance. However, several issues related to image acquisition and processing need to be resolved before reliable estimates can be obtained. Cows (n = 752) and heifers (n = 129) were asses...

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Research paper thumbnail of Poultry Breeding

Springer eBooks, Nov 2, 2022

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Research paper thumbnail of Genomic selection using Bayesian methods

Advances in poultry genetics and genomics, 2020

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Research paper thumbnail of Estimation of parameters of structural model for genetic covariances in international genetic evaluations

Interbull Bulletin, 1999

In international genetic evaluations, genetic correlations between countries are computed using d... more In international genetic evaluations, genetic correlations between countries are computed using deregressed proofs as dependent variables (Sigurdsson et al., 1996). This method reduces considerably the complexity of problem from a computational and practical point of view. However, a major problem facing international genetic evaluations is the increasing number of traits (countries), and genetic ties between countries are often weak. This situation leads to problems for the computations of the genetic correlations, and imprecise correlation estimates can affect predicted genetic values. This problem becomes worse with the addition of new countries with small populations and poor genetic connections with existing INTERBULL member countries

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Research paper thumbnail of Genetic parameters for test day measurements in Spanish Holstein-Friesian

Interbull Bulletin, 1995

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Research paper thumbnail of Morpho-Biometric Evaluation of the Genetic Diversity of Local Chicken Ecotypes in Four Regions (Centre-East, Sahel, Centre-North and South-West) of Burkina Faso

International Journal of Poultry Science, 2021

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Research paper thumbnail of Genotype by environment interaction in response to cold stress in a composite beef cattle breed

Animal, 2020

Extreme weather conditions such as cold stress influence the productivity and survivability of be... more Extreme weather conditions such as cold stress influence the productivity and survivability of beef cattle raised on pasture. The objective of this study was to identify and evaluate the extent of the impact of genotype by environment interaction due to cold stress on birth weight (BW) and weaning weight (WW) in a composite beef cattle population. The effect of cold stress was modelled as the accumulation of total cold load (TCL) calculated using the Comprehensive Climate Index units, considering three TCL classes defined based on temperature: less than −5°C (TCL5), −15°C (TCL15) and −25°C (TCL25). A total of 4221 and 4217 records for BW and WW, respectively, were used from a composite beef cattle population (50% Red Angus, 25% Charolais and 25% Tarentaise) between 2002 and 2015. For both BW and WW, a univariate model (ignoring cold stress) and a reaction norm model were implemented. As cold load increased, the direct heritability slightly increased in both BW and WW for TCL5 class;...

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Research paper thumbnail of Evaluation of extent and amount of heterogeneous variance for milk yield in Uruguayan Holsteins

Animal Science, 2001

The extent and amount of heterogeneous phenotypic variance for milk yield in the Uruguayan Holste... more The extent and amount of heterogeneous phenotypic variance for milk yield in the Uruguayan Holstein population were evaluated and a simple method of accounting for heterogeneity was developed. Lactation records (159 169) collected between 1989 and 1998 by two recording schemes were used to form 8955 herd-year-season-parity-lactation length contemporary groups. A log-linear model was used to identify factors affecting heterogeneity of phenotypic variance. The model included effects of production level, contemporary group size, recording scheme, herd, season of calving, parity number, calving year period and length of lactation and accounted for 50% of the variation in log variances. Estimates from this model were used in a Bayesian manner, to obtain posterior mean estimates of within-contemporary-group variances, which were then used to standardize records to a baseline variance. Effects of the adjustment were assessed by comparing coefficients of variation before and after correctio...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Use of phenotypic and molecular information to ascertain paternity

Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Minas Gerais, Brazil, 13-18 August, 2006., 2006

Bookmarks Related papers MentionsView impact

Research paper thumbnail of 330 Multivariate genome wide association for continuous and discrete responses using multivariate Bernoulli prior

Journal of Animal Science, Dec 1, 2018

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Genetic evaluation in the presence of uncertain additive relationships. I. Use of phenotypic information to ascertain paternity

Journal of Animal Science, Oct 1, 2007

Bookmarks Related papers MentionsView impact

Research paper thumbnail of High density marker panels, SNPs prioritizing and accuracy of genomic selection

BMC Genetics, Jan 5, 2018

Bookmarks Related papers MentionsView impact

Research paper thumbnail of National evaluation for calving ease, gestation length and birth weight by linear and threshold model methodologies

PubMed, 2002

Data included 393,097 calving ease, 129,520 gestation length, and 412,484 birth weight records on... more Data included 393,097 calving ease, 129,520 gestation length, and 412,484 birth weight records on 412,484 Gelbvieh cattle. Additionally, pedigrees were available on 72,123 animals. Included in the models were effects of sex and age of dam, treated as fixed, as well as direct, maternal genetic and permanent environmental effects and effects of contemporary group (herd-year-season), treated as random. In all analyses, birth weight and gestation length were treated as continuous traits. Calving ease (CE) was treated either as a continuous trait in a mixed linear model (LM), or as a categorical trait in linear-threshold models (LTM). Solutions in TM obtained by empirical Bayes (TMEB) and Monte Carlo (TMMC) methodologies were compared with those by LM. Due to the computational cost, only 10,000 samples were obtained for TMMC. For calving ease, correlations between LM and TMEB were 0.86 and 0.78 for direct and maternal genetic effects, respectively. The same correlations but between TMEB and TMMC were 1.00 and 0.98, respectively. The correlations between LM and TMMC were 0.85 and 0.75, respectively. The correlations for the linear traits were above.97 between LM and TMEB but as low as 0.91 between LM and TMMC, suggesting insufficient convergence of TMMC. Computing time required was about 2 hrs, 5 hrs, and 6 days for LM, TMEB and TMMC, respectively, and memory requirements were 169, 171, and 445 megabytes, respectively. Bayesian implementation of threshold model is simple, can be extended to multiple categorical traits, and allows easy calculation of accuracies; however, computing time is prohibitively long for large models.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Longitudinal multiple-trait versus cumulative single-trait analysis of male and female fertility and hatchability in chickens

Poultry Science, Jul 1, 2005

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Disease class prediction using gene expression data: dealing with potential misdiagnosis

Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Minas Gerais, Brazil, 13-18 August, 2006, 2006

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Genetic evaluation of calving to first insemination using natural and artificial insemination mating data1

Journal of Animal Science, Feb 1, 2004

Bookmarks Related papers MentionsView impact

Research paper thumbnail of SNPxGE2: a database for human SNP-coexpression associations

Bioinformatics, Nov 30, 2011

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Longitudinal random effects models for genetic analysis of binary data with application to mastitis in dairy cattle

Genetics Selection Evolution, Sep 15, 2003

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Male and female fertility and hatchability in chickens: a longitudinal mixed model approach

Poultry Science, Aug 1, 2004

The objective of the current study was to investigate different approaches for handling missing r... more The objective of the current study was to investigate different approaches for handling missing records and to develop and implement a multivariate longitudinal mixed model for the genetic evaluation of male and female fertility and hatchability in chickens. The traits recorded on a weekly basis were eggs set (E), percentage fertility (F), and percentage hatch of fertile eggs (H). Three approaches for handling missing records were investigated: 1) all records with zero weekly laid eggs were removed and remaining records with missing F and H were predicted (M1); 2) missing records, including zero weekly laid eggs, were assumed known and equal to zero (M2); and 3) zero weekly laid eggs were assumed as a valid record and missing F and H were predicted (M3). A longitudinal mixed model was used for the multiple trait analysis of E, F, and H. Fixed effects included week-flock, age of service sire (rooster in the pen at data collection), and age of hen. Unrelated service sire, additive hen, permanent environmental, and the residual term were included as random effects. Heritability estimates ranged from 0.06 to 0.13 for E, F, and H. Heritability estimates of F and H were overestimated using M2. Correlations among the 3 traits were highest using M2 and lowest using M1. Pearson correlations indicated that reranking of birds and service sires could occur when using M1. Therefore, M1 should not be used for the analysis of longitudinal data of fertility and hatchability in chickens. Furthermore, M3 seems to be the most ideal method for handling missing records.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Growth Rate Distribution and Potential Non-Linear Relationship between Body Weight and Walking Ability in Turkeys

Animals

The aim of this study was to investigate the potential non-linear relationship between growth and... more The aim of this study was to investigate the potential non-linear relationship between growth and walking ability (WA). The phenotypic data included body weights at 12 and 20 weeks and WA at 20 weeks of age measured on 276,059 male turkeys. The growth rate at three age periods (0 to 12, 12 to 20 and 0 to 20 weeks) was calculated. Each bird was assigned to one of the quartiles of the growth rate distribution for each age period. Between the first and fourth quartiles, the incidence of score 1 (bad WA) increased by 31, 18, and 33% for the first, second, and third age periods, respectively. For good WA (scores 4, 5, and 6), the incidence decreased by 55, 66, and 72% between the first and fourth quartiles for the first, second, and third age periods, respectively. Estimates of heritability of WA ranged between 0.18 and 0.26. The genetic correlations between adjacent growth rate quartiles were high and decayed as the interval between quartiles increased. The magnitude of the variation in...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of 54 Image Based Sampling to Assess Horn Fly Abundance on Cattle

Journal of Animal Science

Horn flies are a major irritant to livestock. In cattle, horn flies can cause increased heart and... more Horn flies are a major irritant to livestock. In cattle, horn flies can cause increased heart and respiratory rates, decreased feed efficiency, decreased weaning weights, and reduced milk production, resulting in substantial economic loss. Fly abundance varies within and across breeds, and genetic analyses have shown sufficient variation to permit selection of hosts for resistance to horn flies. A major limitation for selecting against horn fly abundance is the difficulty associated with measuring on-animal fly counts under pasture conditions. Traditionally, trained evaluators examine cattle in the pasture and estimate fly numbers. Fly movement and animal movements, as well as evaluator expertise are major sources of variation. Image analysis has also been proposed as a means to evaluate horn fly abundance. However, several issues related to image acquisition and processing need to be resolved before reliable estimates can be obtained. Cows (n = 752) and heifers (n = 129) were asses...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Poultry Breeding

Springer eBooks, Nov 2, 2022

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Genomic selection using Bayesian methods

Advances in poultry genetics and genomics, 2020

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Estimation of parameters of structural model for genetic covariances in international genetic evaluations

Interbull Bulletin, 1999

In international genetic evaluations, genetic correlations between countries are computed using d... more In international genetic evaluations, genetic correlations between countries are computed using deregressed proofs as dependent variables (Sigurdsson et al., 1996). This method reduces considerably the complexity of problem from a computational and practical point of view. However, a major problem facing international genetic evaluations is the increasing number of traits (countries), and genetic ties between countries are often weak. This situation leads to problems for the computations of the genetic correlations, and imprecise correlation estimates can affect predicted genetic values. This problem becomes worse with the addition of new countries with small populations and poor genetic connections with existing INTERBULL member countries

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Genetic parameters for test day measurements in Spanish Holstein-Friesian

Interbull Bulletin, 1995

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Morpho-Biometric Evaluation of the Genetic Diversity of Local Chicken Ecotypes in Four Regions (Centre-East, Sahel, Centre-North and South-West) of Burkina Faso

International Journal of Poultry Science, 2021

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Genotype by environment interaction in response to cold stress in a composite beef cattle breed

Animal, 2020

Extreme weather conditions such as cold stress influence the productivity and survivability of be... more Extreme weather conditions such as cold stress influence the productivity and survivability of beef cattle raised on pasture. The objective of this study was to identify and evaluate the extent of the impact of genotype by environment interaction due to cold stress on birth weight (BW) and weaning weight (WW) in a composite beef cattle population. The effect of cold stress was modelled as the accumulation of total cold load (TCL) calculated using the Comprehensive Climate Index units, considering three TCL classes defined based on temperature: less than −5°C (TCL5), −15°C (TCL15) and −25°C (TCL25). A total of 4221 and 4217 records for BW and WW, respectively, were used from a composite beef cattle population (50% Red Angus, 25% Charolais and 25% Tarentaise) between 2002 and 2015. For both BW and WW, a univariate model (ignoring cold stress) and a reaction norm model were implemented. As cold load increased, the direct heritability slightly increased in both BW and WW for TCL5 class;...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Evaluation of extent and amount of heterogeneous variance for milk yield in Uruguayan Holsteins

Animal Science, 2001

The extent and amount of heterogeneous phenotypic variance for milk yield in the Uruguayan Holste... more The extent and amount of heterogeneous phenotypic variance for milk yield in the Uruguayan Holstein population were evaluated and a simple method of accounting for heterogeneity was developed. Lactation records (159 169) collected between 1989 and 1998 by two recording schemes were used to form 8955 herd-year-season-parity-lactation length contemporary groups. A log-linear model was used to identify factors affecting heterogeneity of phenotypic variance. The model included effects of production level, contemporary group size, recording scheme, herd, season of calving, parity number, calving year period and length of lactation and accounted for 50% of the variation in log variances. Estimates from this model were used in a Bayesian manner, to obtain posterior mean estimates of within-contemporary-group variances, which were then used to standardize records to a baseline variance. Effects of the adjustment were assessed by comparing coefficients of variation before and after correctio...

Bookmarks Related papers MentionsView impact