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TropGeneDB specifications

Information


Unique identifier OMICS_03259
Name TropGeneDB
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Publications for TropGeneDB

TropGeneDB citations

 (4)
call_split

Tolerance to mild salinity stress in japonica rice: A genome wide association mapping study highlights calcium signaling and metabolism genes

2018
PLoS One
PMCID: 5771603
PMID: 29342194
DOI: 10.1371/journal.pone.0190964
call_split See protocol

[…] onverted to missing data. The missing data were imputed using Beagle v4.0 []. The final resulting matrix involves 235 individuals and 30 314 markers and can be downloaded in HapMap format from http://tropgenedb.cirad.fr/tropgene/JSP/interface.jsp?module=RICE study “Genotypes”, study type “GreenRice_panel_GBS_data”. […]

call_split

Rice diversity panel provides accurate genomic predictions for complex traits in the progenies of biparental crosses involving members of the panel

2017
PMCID: 5787227
PMID: 29138904
DOI: 10.1007/s00122-017-3011-4
call_split See protocol

[…] a minor allele frequency (MAF, threshold of 2.5%) among the RP accessions and PP lines, considered together, led to a final working set of 43,686 SNP loci. The genotypic data are available at http://tropgenedb.cirad.fr/tropgene/JSP/interface.jsp?module=RICE, (Choose Tab Studies) as GS-Ruse_CREA_GBSgenotype_RP&PP. […]

library_books

Genome wide association analysis for heat tolerance at flowering detected a large set of genes involved in adaptation to thermal and other stresses

2017
PLoS One
PMCID: 5289576
PMID: 28152098
DOI: 10.1371/journal.pone.0171254

[…] ing Beagle v3.3.2 []. Finally, when the distance between two consecutive markers was below 1 kb, the marker with the lowest MAF was discarded.The phenotypic and genotypic data are available at http://tropgenedb.cirad.fr/tropgene/JSP/interface.jsp?module=RICE, (Choose Tab Studies) as “ORYTAGE_indica_Heat-tolerance_167-accessions_21-traits”, and “ORYTAGE_indica_GBS-genotype_167-accessions_13160-SNP” […]

library_books

A first genetic map of date palm (Phoenix dactylifera) reveals long range genome structure conservation in the palms

2014
BMC Genomics
PMCID: 4023600
PMID: 24735434
DOI: 10.1186/1471-2164-15-285

[…] www.ncbi.nlm.nih.gov) selecting only microsatellite DNA markers with significant (~500 bp) surrounding sequence. Location of the downloaded markers on the coconut genetic map was obtained from http://tropgenedb.cirad.fr/.Fifty six coconut markers were associated with genomic sequence. BLASTN with an e-value cutoff of 10e-05 was used to identify homologous regions on the oil palm chromosomes for th […]

Citations

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TropGeneDB institution(s)
UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, TA A-108/03, Montpellier, France; UMR Intertryp, CIRAD, Campus International de Baillarguet, Montpellier, France; UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, TA A-108/03, Montpellier, France

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