Scripts and data of the genetic analysis of Syrah x Grenache progeny

R-scripts and data associated with the publication "Harnessing multivariate, penalized regression methods for genomic prediction and QTL detection of drought-related traits in grapevine". Article abstract: Viticulture has to cope with climate change and decrease pesticide inputs, while maintaining yield and wine quality. Breeding is a key lever to meet this challenge, and genomic prediction is a promising tool to accelerate breeding programs. Multivariate methods are potentially more accurate than univariate ones. Moreover, some prediction methods also provide marker selection, thus allowing quantitative trait loci (QTLs) detection and allowing the identification of positional candidate genes. To study both genomic prediction and QTL detection for drought-related traits in grapevine, we applied several methods, interval mapping as well as univariate and multivariate penalized regression, in a bi-parental progeny. We used a new denser genetic map, simulated two traits under four QTL configurations, and re-analyzed 14 traits measured in semi-controlled conditions under different watering conditions. According to our simulations, we recommend the penalized regression method Elastic Net (EN) for genomic prediction, and controlling the marginal False Discovery Rate on EN selected markers to prioritize the QTLs. Indeed, penalized methods were more powerful than interval mapping for QTL detection across various genetic architectures. Multivariate prediction did not perform better than its univariate counterpart, despite strong genetic correlation between traits. Using experimental data, penalized regression methods proved as very efficient for intra-population prediction whatever the genetic architecture of the trait, with accuracies reaching 0.68. These methods applied on the denser map found new QTLs controlling traits linked to drought tolerance and provided relevant candidate genes. Overall, these findings provide a strong evidence base for implementing genomic prediction in grapevine breeding. Scripts and data associated with the SNP genetic map of Syrah x Grenache progeny are available at: https://doi.org/10.15454/QEDX2V. Raw phenotypic data of Syrah x Grenache progeny in the phenotypic platform PhenoArch are available at: https://doi.org/10.15454/YTRKV6.

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  • get_colours.Rtext/x-r-source

    This R script contains is used to get colours associated with each method for...

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  • plot_corP_pharch_comp_xdata_mean-resp.pngPNG

    Mean predictive ability across traits according to input matrix data Mean...

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  • genetic_map_phys-gen_SxG_GBS.tabTSV

    Table file which combines information with genetic and physical positions of...

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  • cv_EN_simul.Rmdtext/x-r-markdown

    For each script "cv_xx_simul.Rmd", we apply cross-validation on simulated...

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  • SxG_Doligez-et-al-2013.mapBIN

    Text file in Joinmap format with the Syrah x Grenache consensus genetic map...

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  • find_candidate_genes.Rmdtext/x-r-markdown

    This script takes as input the tables "most_reliable_QTLs.tsv" and...

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  • SxG_GBS.quaBIN

    Text file in R/qtl format for creating the cross object of the SNP map...

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  • cv_MTV_LASSO_diff-h2.Rmdtext/x-r-markdown

    We applied genomic prediction with different methods on simulated data with...

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  • SxG_GBS.locBIN

    Text file in R/qtl format for creating the cross object of the SNP map...

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  • cv_LASSO_diff-h2.Rmdtext/x-r-markdown

    We applied genomic prediction with different methods on simulated data with...

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  • SxG.allelic-effects_SSR_add.tabTSV

    This text file is the design matrix for coding additive allelic effects with...

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  • cv_LASSO_simul.Rmdtext/x-r-markdown

    For each script "cv_xx_simul.Rmd", we apply cross-validation on simulated...

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  • cv_MTV_LASSO_simul.Rmdtext/x-r-markdown

    For each script "cv_xx_simul.Rmd", we apply cross-validation on simulated...

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  • SxG_GBS.mapBIN

    Text file in R/qtl format for creating the cross object of the SNP map...

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  • Function4GenoClass.Rtext/x-r-source

    This R script contains diverse R functions useful for the analysis, such that...

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  • cv_LASSO_RD.Rmdtext/x-r-markdown

    For each following scripts, the input files are the genetic map (SSR or GBS)...

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  • compare_SSR-GBS_mapping.Rmdtext/x-r-markdown

    Script which load physical and genetic position of markers from the SSR and...

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  • cv_MTV_LASSO_JJ.Rmdtext/x-r-markdown

    We downloaded simulated data from Jia and Jannink (2012) and applied our...

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  • cv_MTV_RR_diff-h2.Rmdtext/x-r-markdown

    We applied genomic prediction with different methods on simulated data with...

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  • cv_LASSO.GB_RD.Rmdtext/x-r-markdown

    For each following scripts, the input files are the genetic map (SSR or GBS)...

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  • list_genes_vitis_correspondencesV3_1-2.tsvTSV

    This table is the list of correspondence between v1 and v3 structural...

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  • cv_MTV_RR_RD.Rmdtext/x-r-markdown

    For each following scripts, the input files are the genetic map (SSR or GBS)...

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  • SxG.allelic-effects_dominance-removed.txtTXT

    This text file is the design matrix for coding additive allelic effects with...

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  • BLUPs_extraction_information.tabTSV

    This table contains information about the BLUPs extraction process combined...

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  • analyse_results_JJ.Rmdtext/x-r-markdown

    This script combines genomic prediction results for all predictions based on...

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  • SxG_GBS_genedose.tsvTSV

    This table is the genotyping file after map construction, with 3,961 markers,...

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  • 0_ReadMe.mdtext/markdown

    This document describes the input files, scripts and output files generated...

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  • cv_MIM_simul.Rmdtext/x-r-markdown

    For each script "cv_xx_simul.Rmd", we apply cross-validation on simulated...

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  • cv_MTV_RR_simul.Rmdtext/x-r-markdown

    For each script "cv_xx_simul.Rmd", we apply cross-validation on simulated...

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  • genetic_map_phys-gen_SxG_SSR.tabTSV

    Table which combines information with genetic and physical position of...

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  • launch_cv_RD.shapplication/x-shellscript

    Bash script for launching genomic prediction with experimental data. The bash...

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  • estimate_LD_SxG.Rmdtext/x-r-markdown

    This script takes as input the genotypic matrix SxG_GBS_genedose.tsv and...

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  • cv_spring_RD.Rmdtext/x-r-markdown

    For each following scripts, the input files are the genetic map (SSR or GBS)...

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  • conversion_table_SxG-geno-names.tabTSV

    This table contains 2 columns: "geno" with genotype names that we use for...

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  • cv_SIM_simul.Rmdtext/x-r-markdown

    For each script "cv_xx_simul.Rmd", we apply cross-validation on simulated...

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  • gather_BLUP_info.Rmdtext/x-r-markdown

    This R script is run when all BLUPs are computed, to combine them into one...

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  • pharch_explo-pheno_lme4_DeltaPsi_WW_2012-2013.Rmdtext/x-r-markdown

    This script exports for each trait a table with BLUP values, as well as model...

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  • analyse_results_simul_pred-ability-accuracy.Rmdtext/x-r-markdown

    Script which combines all genomic prediction results on simulated data, for...

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  • launch_cv_simul.shapplication/x-shellscript

    Bash script for launching data simulation and genomic prediction with default...

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  • compare_mrk-selection_RD_mapping_IM-methods.Rmdtext/x-r-markdown

    This script compares QTLs from Coupel-Ledru et al., (2014,2016) with SIM and...

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  • cv_RR_RD.Rmdtext/x-r-markdown

    For each following scripts, the input files are the genetic map (SSR or GBS)...

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  • bash_mrk_sim.shapplication/x-shellscript

    Bash script for launching data simulation and genomic prediction with default...

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  • cv_spring_diff-h2.Rmdtext/x-r-markdown

    We applied genomic prediction with different methods on simulated data with...

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  • analyse_results_real-data_pred-ability.Rmdtext/x-r-markdown

    This script combines genomic prediction results for all predictions based on...

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  • SxG.allelic-effects.txtTXT

    This text file is the design matrix for coding additive and dominance allelic...

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  • TxDb_Vvinifera_IGGP12Xv2_URGIv3-20.sqliteBIN

    This database file is generated from Canaguier et al. (2017) data, inserted...

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  • 0_ReadMe.htmlHTML

    This document describes the input files, scripts and output files generated...

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  • cv_MTV_EN_diff-h2.Rmdtext/x-r-markdown

    We applied genomic prediction with different methods on simulated data with...

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  • cv_MIM_RD.Rmdtext/x-r-markdown

    For each following scripts, the input files are the genetic map (SSR or GBS)...

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  • SxG_pharch_BLUPs.tsvTSV

    Table with fitted genotypic data for all traits (14) and for the progeny (186...

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  • SxG_Doligez-et-al-2013.locBIN

    Text file with genotypes in Joinmap format, for the 191 offsprings and the...

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  • fit_mrk-selection_simul.Rmdtext/x-r-markdown

    This script takes as input simulated genotypic values, the genetic map and...

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  • cv_RR_diff-h2.Rmdtext/x-r-markdown

    We applied genomic prediction with different methods on simulated data with...

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  • cv_MTV_EN_simul.Rmdtext/x-r-markdown

    For each script "cv_xx_simul.Rmd", we apply cross-validation on simulated...

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  • cv_LASSO.GB_simul.Rmdtext/x-r-markdown

    For each script "cv_xx_simul.Rmd", we apply cross-validation on simulated...

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  • fit_mrk-selection_RDpharch_SSR.Rmdtext/x-r-markdown

    This script applies marker selection for all traits and Interval Mapping...

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  • fit_mrk-selection_RDpharch_GBS.Rmdtext/x-r-markdown

    This script applies marker selection for all traits and methods on...

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  • cv_MTV_LASSO_RD.Rmdtext/x-r-markdown

    For each following scripts, the input files are the genetic map (SSR or GBS)...

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  • MapGBS_CIM.SSR_MIM.SSR_MIM.GBS.pdfPDF

    This figure has been generated in...

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  • cv_MTV_RR_JJ.Rmdtext/x-r-markdown

    We downloaded simulated data from Jia and Jannink (2012) and applied our...

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  • prediction_and_selection_quality.Rmdtext/x-r-markdown

    This script takes as input classification results (the table...

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  • cv_spring_JJ.Rmdtext/x-r-markdown

    We downloaded simulated data from Jia and Jannink (2012) and applied our...

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  • cv_EN_JJ.Rmdtext/x-r-markdown

    We downloaded simulated data from Jia and Jannink (2012) and applied our...

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  • SxG_Doligez-et-al-2013.quaBIN

    Text file with genotype names and a single fake phenotype in Joinmap format,...

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  • compare_mrk-selection_RDpharch_GBS_LD.Rmdtext/x-r-markdown

    This script compares marker selection for all methods. It characterizes...

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  • cv_simul-data.Rmdtext/x-r-markdown

    This script creates simulated phenotypic values for two traits for the Syrah...

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  • cv_EN_diff-h2.Rmdtext/x-r-markdown

    We applied genomic prediction with different methods on simulated data with...

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  • SxG_Doligez2013_ordered-genos-design-mat.tabTSV

    This text file is the design matrix for coding additive and dominance...

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  • create_diffX_GP.Rmdtext/x-r-markdown

    This script takes as input SNP or SSR genotypic data and genetic maps and...

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  • cv_RR_JJ.Rmdtext/x-r-markdown

    We downloaded simulated data from Jia and Jannink (2012) and applied our...

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  • cv_MTV_EN_RD.Rmdtext/x-r-markdown

    For each following scripts, the input files are the genetic map (SSR or GBS)...

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  • cv_MTV_EN_JJ.Rmdtext/x-r-markdown

    We downloaded simulated data from Jia and Jannink (2012) and applied our...

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  • cv_SIM_RD.Rmdtext/x-r-markdown

    For each following scripts, the input files are the genetic map (SSR or GBS)...

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  • cv_spring_simul.Rmdtext/x-r-markdown

    For each script "cv_xx_simul.Rmd", we apply cross-validation on simulated...

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  • cv_simul-data_diff-h2_JJ.Rmdtext/x-r-markdown

    This script creates simulated phenotypic values for the Syrah x Grenache...

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  • cv_RR_simul.Rmdtext/x-r-markdown

    For each script "cv_xx_simul.Rmd", we apply cross-validation on simulated...

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  • SxG.gendose.imputed_mean.txtTXT

    This text file is the design matrix of gene dose from SNP markers, extracted...

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  • compare_maps_SSR-GBS.pngPNG

    Comparison of SSR and SNP consensus genetic maps of a pseudo-F1 V. vinifera...

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  • classify_mrk-selection_simul.Rmdtext/x-r-markdown

    This script loads the selected markers, generated in...

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  • boxplot_perc.var_CIM_MIM_common-QTLs.pngPNG

    This figure has been generated in...

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  • compare_mrk-selection_RD_most_reliable.Rmdtext/x-r-markdown

    This script takes the 25 most reliable QTLs ("most_reliable_QTLs.tsv" table)...

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  • cv_EN_RD.Rmdtext/x-r-markdown

    For each following scripts, the input files are the genetic map (SSR or GBS)...

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  • launch_cv_diff-h2.shapplication/x-shellscript

    Bash script for launching data simulation and genomic prediction with Jia and...

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  • cv_LASSO_JJ.Rmdtext/x-r-markdown

    We downloaded simulated data from Jia and Jannink (2012) and applied our...

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Additional Info
Field Value
access_rights https://f2ds.eosc-pillar.eu/dataset/f11cc95d-8f47-470a-ad36-6c5af9dda779#accessRights
catalogue_title inrae
Conforms to ["https://f2ds.eosc-pillar.eu/profile/2f08228e-1789-40f8-84cd-28e3288c3604"]
has_version ["1"]
Identifier doi:10.15454/NOUQY2
Issued 2021-05-25T00:00:00+00:00
Language ["http://id.loc.gov/vocabulary/iso639-1/en"]
Modified 2021-06-09T12:53:16+00:00
Publisher name Portail Data INRAE
system:type F2DSItem
URI https://f2ds.eosc-pillar.eu/dataset/f11cc95d-8f47-470a-ad36-6c5af9dda779
Management Info
Field Value
Source https://doi.org/10.15454/NOUQY2
Author D4Science Jarvis
Maintainer D4Science Jarvis
Last Updated 12 December 2022, 01:10 (CET)
Created 2 March 2022, 12:02 (CET)