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sRNA dataset of PKWxPKW banana plant (GWT-13)
No full textDeep sequencing of sRNA from PKW self pollinated plant
GWT-13 is homozygous for the non-infective allele of endogenous Banana streak Obino l'Ewai virus (eBSOLV-2), homozygous for the infective allele of endogenous Banana streak Goldfinger virus (eBSGFV-7) and homozygous for the endogenous Banana streak Imové virus (eBSIMV)
[Jeu de données : résultats d'enquêtes 2023] Diagnostic des systèmes de culture ananas à la Réunion : état des lieux des pratiques de gestion de l’enherbement
No full textCompilation de résultats d'enquêtes menées auprès de 45 agriculteurs dans le cadre d'un stage de césure dans l'UPR Geco du Cirad de la Réunion (avril 2023 - août 2023) visant à établir un diagnostic des systèmes de culture ananas à la Réunion, notamment un état des lieux des pratiques de gestion de l’enherbement.
Results of surveys conducted with 45 farmers during an internship at CIRAD's Geco unit in Réunion (April 2023 - August 2023) to assess pineapple cropping systems in Réunion, including an inventory of weed control practices
sRNA dataset of PKWxPKW banana plant (GWT-17)
No full textDeep sequencing of sRNA from self-pollinated PKW plant.
GWT-17 is homozygous for the infective allele of endogenous Banana streak Obino l'Ewai virus (eBSOLV-1), homozygous for the infective allele of endogenous Banana streak Goldfinger virus (eBSGFV-7) and homozygous for the endogenous Banana streak Imové virus (eBSIMV)
TropGene Cocoa
No full textThe data come from the TropGeneDB CIRAD information system (https://tropgenedb.cirad.fr/tropgene/JSP/index.jsp).
TropGeneDB contains data from studies on tropical and mediterranean plants for various kinds of topics such as marker, QTL, genotype, genetic, phenotype, cartography (genetic, physical and linkage disequilibrium maps), linkage disequilibrium, association and germplasm.
The plants concerned are banana, breadfruit, citrus, cocoa, coconut palm, cotton, oil palm, rice, rubber, sorghum and sugarcane.
The IS has a database per plant. The data were produced by CIRAD researchers or by CIRAD researchers and colleagues associated in research projects.
All The data have been published.
The COCOA data in this dataset produced between 2008 and 2020 were extracted from the TROPGENE_COCOA database in tabulated text format files. There is a file for each type of data which name includes the data type. Each line of a file has several columns describing the study (title, description, year, country, place, contact) it belongs to.
The tropgene_cocoa_references‧txt file contains the references of the scientific publications on these data
RNAseq dataset of PKW banana plant (GWT-18)
No full textDeep sequencing of total RNA from Pisang Klutuk Wulung (PKW) banana plan
Dataset of RGB and multispectral aerial images of cocoa agroforestry plots (Divo, Côte d'Ivoire)
No full textThis dataset contains all the raw multispectral and RGB drone-collected images from ten biodiverse cocoa agroforestry plots in Côte d'Ivoire. The plots are located in the main cocoa-growing region of the country in the neighborhood of Divo, in the central-western region, with latitudes ranging from 5°51' to 6°00' N and longitudes from 4°51' to 5°51' W. This area features a subequatorial climate, dense forests, annual rainfall between 900-1200 mm, and temperatures ranging from 24 to 27 °C.
Images were captured in May 2022 using a DJI Phantom 4 Pro drone, equipped with six cameras: one optical and five spectral (R, G, B, Rededge, NIR). The flight pattern was set at 80 meters altitude, with an overlap of 70% side and 80% front, achieving an average ground sampling distance of less than 5 cm. The entire image set covers an area of approximately 52 hectares.
The data have been collected in the frame of the Cocoa4Future European project
Genomics of white and black fonio millets : passport data, snp and kmer files.
No full textCrop evolutionary history and domestication processes are key issues for better conservation and effective use of crop genetic diversity. In Western Africa, two small indigenous grain cereals are found, black and white fonio (Digitaria exilis and Digitaria iburua respectively). The relationship between these two cultivated crops and wild Digitaria species is still unclear.
We analysed whole genome sequences of 265 accessions comprising the two cultivated species and their closely wild relatives.
We used different complementary methods and genomic approaches to unravel the domestication history of these fonio millets, which is key to support a process of valorisation of these native species while preserving the diversity necessary for future adaptations.
We provide here the passport data, the vcf files, and the kmer files used to perform the analyses. Codes can be accessed in the CIRAD GitLab repository
Two compressed VCF files are provided. They contain high quality biallelic SNPs. One is filtered for Minor Allele Frequency (MAF) at 5%. Both vcf.gz are associated to their corresponding index file .tbi
Different extensions for the kmer analysis files are provided and correspond to the 1,000,000 k-mer presence/absence table for each individual.</p
Replication Data for: Does fertilization type drive soil and mulch macroinvertebrate communities in a sugarcane agroecosystem? Evidences from a 10-year field trial
No full textMacroinvertebrates play a central role in processes supporting soil fertility. In the framework of the ecological intensification of agriculture, the choice of management practices should be guided by their ability to support these beneficial organisms supplying ecosystem services. This study aims at investigating the specific effect of partial substitution of synthetic fertilizers by locally produced organic fertilizers at a similar level of major nutrient inputs on macroinvertebrate’s abundance and diversity in sugarcane agroecosystems, on a Nitisol. Invertebrates visible to the naked eye were sampled in 2013, 2016, 2019 and 2023 using the standardized TSBF method on a long term experimental field trial in Réunion island. The individuals were identified and soil samples were analyzed for physico-chemical properties. Despite the low response of macroinvertebrates to the fertilizer type, total macroinvertebrate abundance increased over time, especially isopods and earthworms. The input of organic carbon via the return of litter to the soil surface and the root turnover after each harvest enables soil macroinvertebrates to be more abundant even after the replanting tillage. Mulching and root turnover are therefore important levers to consider for promoting macroinvertebrates in sugarcane agroecosystems
Data and code for analysis of a bi-mode network of sources and outbreaks of Avian influenza and African swine fever, identified by the PADI-web media monitoring tool
No full textThis repository contains the data and code for analysis of a bi-mode network of sources and outbreaks of Avian influenza and African swine fever identified in the news by the PADI-web media monitoring tool (https://padi-web.cirad.fr/en/) worldwide between 2018 and 2019. More precisely, for each disease, we provide the data on all sources communicating about a given outbreak identified in the online news, the data on the outbreaks communicated in the news and the network of both sources and outbreaks (bi-mode network). We further provide the Exponential random graph Model (ERGM model) code to analyse the bi-mode networks on the two diseases, respectively. The datasets and code can be useful for network modelling in epidemiology and information /communication science
TropGene Cotton
No full textThe data come from the TropGeneDB CIRAD information system (https://tropgenedb.cirad.fr/tropgene/JSP/index.jsp).
TropGeneDB contains data from studies on tropical and mediterranean plants for various kinds of topics such as marker, QTL, genotype, genetic, phenotype, cartography (genetic, physical and linkage disequilibrium maps), linkage disequilibrium, association and germplasm.
The plants concerned are banana, breadfruit, citrus, cocoa, coconut palm, cotton, oil palm, rice, rubber, sorghum and sugarcane.
The IS has a database per plant. The data were produced by CIRAD researchers or by CIRAD researchers and colleagues associated in research projects.
All The data have been published.
The COTTON data in this dataset produced between 2008 and 2012 were extracted from the TROPGENE_COTTON database in tabulated text format files. There is a file for each type of data which name includes the data type. Each line of a file has several columns describing the study (title, description, year, country, place, contact) it belongs to.
The tropgene_cotton_references‧txt file contains the references of the scientific publications on these data