1,721,005 research outputs found
Data, R scripts and ASReml scripts
No full text################################################################################################
# OBJECTIVE: Procedure to perform the data handling and the analyses + details about the files #
# AUTHOR: Nicolas Bedere ([email protected]) #
# LICENCE: CC0 1.0 Universal (CC0 1.0), Public Domain Dedication #
# LAST UPDATE: 2023-01-06 #
# PLATFORM: x86_64-pc-linux-gnu (64-bit) #
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#### INTRODUCTION ####
This text files aims to explain the procedure to perform both the data handling and the analyses
in the paper:
#### Description of the files:
#1. Datasets
PhenoAsreml.txt contains the observed values for the phenotypes described in the paper
PhenoAsreml_scaled.txt contains the scaled (mean of zero and standard deviation of one) of the same phenotypes. THIS DATASET IS USED FOR BIVARIATE ANALYSES WITH 2x2 STRATA
PhenoAsreml_scaledLong.txt contains the same information, organized differently because the dataset is reshaped from wide to long format.
PhenoAsreml_scaledLong_3x3strata.txt contains the information for BackFat and BodyWeight, THIS DATASET IS USED FOR BIVARIATE ANALYSES WITH 3x3 STRATA
PhenoAsreml_scaledLong_3x2strata.txt contains the information for BackFat and Adiponectin, THIS DATASET IS USED FOR BIVARIATE ANALYSES WITH 3x2 STRATA. It is only an example of dataset that needs to be generated in order to obtain all the results presented in the paper
BEDERE_2023_Data_PedigreeHens.txt is the pedigree file (individual/sire/dam) traced back over 5 generations
#2. Codes and parameter files
BEDERE_2023_RScript_handlingdata_Long.R is an R code to reshape PhenoAsreml_scaled into PhenoAsreml_scaledLong and to subset it to generate PhenoAsreml_scaledLong_3x3strata for instance
BEDERE_2023_ASREMLScript_bivariate_2x2strata.as (as well as ...3x2strata.as and ...3x3strata.as) are ASReml parameter files used to state the data, model specification and post-hoc calculation to ASReml
Please, note that some variance components have been fixed in some analyses when the algorithm was struggling to converge.
BEDERE_2023_RScript_BartlettTest.R is an R code to perform the Bartlett test.
#2. Results examples
Some output files of ASReml are provided to give an example of results for each type of bivariate analysis.
The .asr file is the log of the program, explaining how the program ran
The .res file is describing the residuals
The .pvc file describes the variance components and provides the genetic parameters with their associated standard errors.<br
Le_Cozler_2019_biorxiv760082
No full textData used in: Le Cozler Y., Jurquet J. and Bedere N. Effects of feeding treatment on growth rate and performance of primiparous Holstein dairy heifers. bioRxiv 760082, ver. 3 peer-reviewed and recommended by PCI Animal Science (2019).
/!\ French language in the dat
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sophisticated methods
Aptitude des vaches laitières à se reproduire dans des systèmes pâturants contrastés : quelle vache pour quel système ?
No full textLes performances de reproduction des vaches laitières se sont dégradées parallèlement à l’augmentation de leurs performances de production. L’intense sélection réalisée sur la production laitière est tenue responsable de cela. Chaque étape du processus de reproduction a été affecté : les anomalies de cyclicité ovarienne sont plus fréquentes dans la population actuelle, la durée et l’intensité des chaleurs a diminué drastiquement, et les échecs de gestation sont plus fréquents. La littérature s’accorde sur le fait que la reproduction est affectée parce que la majeure partie des ressources est investie dans la production laitière. L’objectif de cette thèse de doctorat est d’étudier l’intérêt d’une stratégie de sélection alternative basée sur un fort potentiel génétique de taux butyreux et protéique sur la robustesse des vaches laitières. Les hypothèses testées étaient que par rapport aux vaches à fort potentiel de production laitières, celles à fort potentiel de taux butyreux et protéique (i) exportent moins d’énergie dans le lait et donc préserves leur réserves corporelles, (ii) ont de meilleures aptitudes à se reproduire. Nos résultats montrent que les vaches à fort potentiel de taux butyreux et protéiques ont un retour de cyclicité plus précoce, une expression des chaleurs similaire mais plus d’échecs de gestation que celles à fort potentiel de production laitière. Ces résultats intrigants suggèrent que les étapes de la reproduction sont partiellement découplées sur le plan génétique. Sélectionner les vaches laitières sur les taux butyreux et protéique dans le but d’améliorer les performances de reproduction n’apparaît pas comme une alternative pertinente
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