UMR DIADE

DIversity - Adaptation - plant DEvelopment

The DIADE Research Unit aims to understand the diversification of tropical plants, one of the main original reservoirs of biodiversity, and for which conservation, management and exploitation are an important issue for Sustainable Development.

The nine teams forming the Unit belong to IRD, University of Montpellier, CIRAD, and CNRS.

CERES Team

DYNADIV Team

PANEEC Team

EVOGEC Team

ADvENS Team

AgroLD

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351 to 360 of 991 Results

S3_Structure.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 3.8 MB - MD5: f5d2b43e2d5a5eefd051c29b2c68833e Documentation Introduction to Population Genetics for analysing the genetic structure of crops.
S4_Introduction_GenomeWideAssociationStudy_GWAS.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 912.5 KB - MD5: da9c01bfb9ae62fefc2a5b288cc9889d Documentation Introduction to the core concept of genome wide association studies.
S4_script_GWAS_basic_Rcode.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 73.2 KB - MD5: 17bd3bb83031e7349c5d4730581569e8 Documentation This file comments on the R script for GWAS analysis.
S4_Script_GWAS_Introduction.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 574.9 KB - MD5: b3bd4b806a6968e50f665cd4e34e832b Documentation This file presents a script for GWAS analysis using R. We used a dataset of pearl millet accessions (Varshney et al. 2017).
sample_metadata.tab May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Tabular Data - 2.5 KB - 5 Variables, 55 Observations - UNF:6:LNg1C4IBq05VUN9bbZDOeQ== Data Table containing the passport data of the pearl millet accessions. This data file is associated with the script "S1_Introduction_to_R_Passport.html". These data are published in Berthouly-Salazar et al. (2016).
DiscriminantSitesOnly_biallelic_freebayes_bcftools_snps_on_AZUwithOrganelles_chr01.vcf.gz Apr 29, 2024 - Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population Gzip Archive - 206.7 MB - MD5: 161bb7f90f38757bd830bc5e005cd453 Data Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population
ReadMe.txt Apr 29, 2024 - Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population Plain Text - 1.0 KB - MD5: 91fe283277eff5f80f7fb8e3703d8c40 Documentation ReadMe file - data citation, description and terms of use.
Fonio_Genotype_Senegal_2013_2015.tab Dec 6, 2023 - Supplementary data for: Ethnolinguistic and genetic diversity of fonio (Digitaria exilis - Kippist - Stapf) in Senegal Tabular Data - 26.1 KB - 20 Variables, 158 Observations - UNF:6:NeauNrptcRyq6NeGtIhJqg== Data This dataset is the most comprehensive collection on fonio in Senegal. It includes the individuals, regions, villages, ethnic groups of the farmers interviewed, their linguistic group, the cycle of fonio accessions reported by the farmers and SSR data.
Millet23_coffee_0_Readme.pdf Nov 29, 2023 - Genotyping data for field samples from Haitian coffee agroforestry systems and international collection accessions Adobe PDF - 84.6 KB - MD5: 68c9886481656da24e8f4044b5d68a76 Documentation Data documentation
Millet23_coffee_1_references_info.tab Nov 29, 2023 - Genotyping data for field samples from Haitian coffee agroforestry systems and international collection accessions Tabular Data - 9.9 KB - 8 Variables, 128 Observations - UNF:6:cnk88qwuB9aou3ACaJVW5A== Data This file contains information about the various Coffea reference samples from international collections used in the study

S3_Structure.pdf

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Adobe PDF - 3.8 MB -

Documentation

Introduction to Population Genetics for analysing the genetic structure of crops.

S4_Introduction_GenomeWideAssociationStudy_GWAS.pdf

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Adobe PDF - 912.5 KB -

Documentation

Introduction to the core concept of genome wide association studies.

S4_script_GWAS_basic_Rcode.pdf

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Adobe PDF - 73.2 KB -

Documentation

This file comments on the R script for GWAS analysis.

S4_Script_GWAS_Introduction.pdf

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Adobe PDF - 574.9 KB -

Documentation

This file presents a script for GWAS analysis using R. We used a dataset of pearl millet accessions (Varshney et al. 2017).

sample_metadata.tab

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Tabular Data - 2.5 KB - 5 Variables, 55 Observations -

Data

Table containing the passport data of the pearl millet accessions. This data file is associated with the script "S1_Introduction_to_R_Passport.html". These data are published in Berthouly-Salazar et al. (2016).

DiscriminantSitesOnly_biallelic_freebayes_bcftools_snps_on_AZUwithOrganelles_chr01.vcf.gz

Apr 29, 2024 - Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population

Gzip Archive - 206.7 MB -

Data

Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population

ReadMe.txt

Apr 29, 2024 - Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population

Plain Text - 1.0 KB -

Documentation

ReadMe file - data citation, description and terms of use.

Fonio_Genotype_Senegal_2013_2015.tab

Dec 6, 2023 - Supplementary data for: Ethnolinguistic and genetic diversity of fonio (Digitaria exilis - Kippist - Stapf) in Senegal

Tabular Data - 26.1 KB - 20 Variables, 158 Observations -

Data

This dataset is the most comprehensive collection on fonio in Senegal. It includes the individuals, regions, villages, ethnic groups of the farmers interviewed, their linguistic group, the cycle of fonio accessions reported by the farmers and SSR data.

Millet23_coffee_0_Readme.pdf

Nov 29, 2023 - Genotyping data for field samples from Haitian coffee agroforestry systems and international collection accessions

Adobe PDF - 84.6 KB -

Documentation

Data documentation

Millet23_coffee_1_references_info.tab

Nov 29, 2023 - Genotyping data for field samples from Haitian coffee agroforestry systems and international collection accessions

Tabular Data - 9.9 KB - 8 Variables, 128 Observations -

Data

This file contains information about the various Coffea reference samples from international collections used in the study

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