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

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High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)
Barnaud, Adeline; Veltman, Margaretha; Kaczmarek, Thomas; Argout, Xavier; Vigouroux, Yves; Berthouly-Salazar, Cecile; Billot, Claire, 2024, "High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)", https://doi.org/10.23708/ETC16I, DataSuds, V1, UNF:6:ON0wb/ZYjxl4qqjnr8NEPA== [fileUNF]
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Description

Marginal land is land that is of little agricultural value because crops produced there would be worth less than any rent paid for access to the area. Helping to develop such zones in Africa is a key goal for the EU-funded EWA-BELT project. The aim is to promote the sustainable intensification of agricultural production in organic, agroforestry and mixed crop and livestock farming systems in 38 study areas of six countries belonging to East and West Africa. The project will enhance current scientific knowledge on the adaptation of new and improved traditional crops in different agroecosystems and the impacts of traditional agricultural practices on soil health.

This initiation to genomic data analysis with R was designed within the EWA-BELT H2020 EU project (grant agreement ID 862848).

The training module introduced to a variety of population genomics analyses for genotyping by sequencing (GBS) datasets. It included an introduction to single-nucleotide polymorphism (SNP) calling and filtering options, experimental design and various applications, population genomics statistics (genetic diversity and structure, Fst-based analyses) and genome-wide association studies (GWAS).

The majority of the course consisted of practical R sessions to give hands-on experience of these analyses.

Main topic and contents treated during the courses :
Session 1. Passport data and Bioinformatics analysis
Session 2. VCF filtering
Session 3. Genetic diversity and structure
Session 4. Genome-Wide Association Studies (GWAS)

Each session includes a short introduction outlining the core concepts (PDF), R scripts (HTLM/PDF) and associated datasets.

(2024-02-22)
Subject Agricultural Sciences; Medicine, Health and Life Sciences
Keyword population genomics, crop diversity, GBS
Related Publication Berthouly-Salazar C, Mariac C, Couderc M, Pouzadoux J, Floc’h J-B and Vigouroux Y (2016) Genotyping-by-Sequencing SNP Identification for Crops without a Reference Genome: Using Transcriptome Based Mapping as an Alternative Strategy. Front. Plant Sci. 7:777. doi: 10.3389/fpls.2016.00777
Notes This course content is distributed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND). Genomic data delivered were extracted from Berthouly-Salazar et al. (2016) and Varshney et al. (2017). These dataset are subsets of the original data. They should not be distributed independently of this course.
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0_ReadMe.txt
General_information/Plain Text - 2.1 KB
Published May 16, 2024
2 Downloads
MD5: 0ad59fd46069aaec2008347fc45ec2ce
Dataset citation, description and terms of use.
Documentation
chr5_5association.txt
Session4_GWASbasic/Plain Text - 382.2 MB
Published May 16, 2024
2 Downloads
MD5: 5888c01657ff5624ad88b8200d103076
This file contains the data for the GWAS analysis to be used with 'S4_script_GWAS_basic_Rcode.pdf' (Varshney et al. 2017).
Data
GBS-chr2_raw.vcf.gz
Session2_VCFfiltering/Gzip Archive - 53.7 MB
Published May 16, 2024
2 Downloads
MD5: 7ac07ce9f286e974d6c5c572c40f78d8
VCF file containing the raw genomic data of pearl millet. This data file is associated with the script "S2_filter_VCF.html".These data are published in Berthouly-Salazar et al. (2016).
Data
Introduction.pdf
Introduction.pdf
General_information/Adobe PDF - 1.8 MB
Published May 16, 2024
6 Downloads
MD5: fdde654296e7c56ad70fd3ee0a2ea070
This file presents the course, its objectives and the context in which it was implemented.
Documentation
millet_filtered.vcf
Session3_GeneticDiversityStructure/text/vcard - 34.5 MB
Published May 16, 2024
2 Downloads
MD5: 6eab73245746d73169f90b8141511fa0
VCF file containing the genomic data of the pearl millet. This data file is associated with the script "S3_Genetic_diversity+structure.html".These data are published in Berthouly-Salazar et al. (2016).
Data
millet_metadata.tab
Session3_GeneticDiversityStructure/Tabular Data - 2.5 KB
Published May 16, 2024
2 Downloads
5 Variables, 55 Observations UNF:6:LNg1C4IBq05VUN9bbZDOeQ==
Table containing the passport data of the pearl millet accessions in the VCF file. This data file is associated with the script "S3_Genetic_diversity+structure.html". These data are published in Berthouly-Salazar et al. (2016).
Data
S1-IntroductionToGBS.pdf
S1-IntroductionToGBS.pdf
Session1_IntroductionToGBS/Adobe PDF - 3.3 MB
Published May 16, 2024
6 Downloads
MD5: 09f0c52d9219dd372cf0f3c3eff8b2f5
Documentation
S1_Download_R.pdf
S1_Download_R.pdf
Session1_IntroductionToGBS/Adobe PDF - 288.7 KB
Published May 16, 2024
5 Downloads
MD5: dbbdb9df803c84725df9ff5b4abc42f7
This file is a tutorial for installing R and RStudio.
Documentation
S1_example.fastq
Session1_IntroductionToGBS/Unknown - 3.6 KB
Published May 16, 2024
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MD5: 3bc9d9f537ea4d956c4dc7f7970e7956
Data
S1_example.txt
Session1_IntroductionToGBS/Plain Text - 3.6 KB
Published May 16, 2024
2 Downloads
MD5: 3bc9d9f537ea4d956c4dc7f7970e7956
Documentation
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