SNP Genotyping data for Guadeloupean and Haitian coffee trees

Version 1.1
SNP Genotyping data for Guadeloupean and Haitian coffee trees
Millet, Claude Patrick; Delahaie, Boris; Georget, Frederic; Allinne, Clémentine; Solano Sánchez, William; Zhang, Dapeng; Jeune, Wesly; Toniutti, Lucile; Poncet, Valérie, 2024, "SNP Genotyping data for Guadeloupean and Haitian coffee trees", https://doi.org/10.23708/MRPVHL, DataSuds, V1, UNF:6:TVDscn+pMTNyylMj+Q8dqA== [fileUNF]
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Description

The West Indies, particularly former French colonies like Haiti and Guadeloupe, were central to the spread of coffee in the Americas. The histories of these Islands are shared until the XIXth century, where they diverged significantly. Still, both Islands experienced a strong decline in their coffee sector.

Characterizing the genetic and varietal diversity of their coffee resources and understanding historical factors shaping them can help support revitalization efforts. To that end, we performed KASP-genotyping of 80 informative SNP markers on field samples from across main coffee-growing region of Guadeloupe, and two historically important ones in Haiti, as well as 146 reference accessions from international collections, and acquired data from published sources.

While most samples are Coffea arabica, other species are represented, namely C. canephora, C. liberia, and C. congensis

(2024-09-02)
Subject Agricultural Sciences
Keyword Agrobiodiversity, Haiti, Guadeloupe, Coffee
Related Publication Millet, C.P., Delahaie, B., Georget, F., Allinne, C., Solano-Sánchez, W., Zhang, D., Jeune, W., Toniutti, L., Poncet, V. (2024) Guadeloupe and Haiti’s coffee genetic resources reflect the crop’s regional and global history. Plants, People, Planet. doi: 10.1002/ppp3.10584
Notes Type de données: Analysis data
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ReadMe.txt
SNP_genotyping_Guadeloupe_Haiti/Plain Text - 1.4 KB
Published Sep 9, 2024
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MD5: d8868d8097c2c42550aea89348ffff81
Data citation, description and terms of use.
Documentation
SNP_genotyping_1_ref_info-1.tab
SNP_genotyping_Guadeloupe_Haiti/Tabular Data - 7.0 KB
Published Sep 9, 2024
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5 Variables, 142 Observations UNF:6:5GHf/oRRquAFeU8gbioPxw==
Contains information about the various Coffea reference samples from international collections used in the study, including the accession code , the species or accession name and origin, as well as the institution that hosts the collection
Documentation
SNP_genotyping_2_kaspdata_80markers_26pind-1.tab
SNP_genotyping_Guadeloupe_Haiti/Tabular Data - 460.6 KB
Published Sep 9, 2024
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86 Variables, 866 Observations UNF:6:MU5AtJxYZNQIemBR43/J8Q==
Contains data from KASP genotyping of 80 core SNP for Haitian, Guadeloupean and reference samples of Coffee trees
Data
SNP_genotyping_3_canephora_dataset-1.tab
SNP_genotyping_Guadeloupe_Haiti/Tabular Data - 13.7 KB
Published Sep 9, 2024
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63 Variables, 34 Observations UNF:6:f+HXClTn/TUJ3oj+JiQGlA==
Contains data from Haitian and Guadeloupe canephora field samples (KASP targeted genotyping) and from wild C. canephora (DNA chip array, published by Mérot-l'Anthoëne et al, 2019)
Data
SNP_genotyping_4_liberica_dataset-1.tab
SNP_genotyping_Guadeloupe_Haiti/Tabular Data - 4.5 KB
Published Sep 9, 2024
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46 Variables, 15 Observations UNF:6:wqailoQGx0VAgAOPOWhA5A==
Contains data from KASP targeted genotyping of reference and Guadeloupean field samples of Coffea liberica, as well as two reference samples from each other species
Data
SNP_genotyping_data_dictionary.pdf
SNP_genotyping_Guadeloupe_Haiti/Adobe PDF - 48.2 KB
Published Sep 9, 2024
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MD5: 103fa04d275ad12beafa60cc3ed0b2b8
Data dictionary and referenties
Documentation
SNP_genotyping_htglcoffeedata-2.tab
SNP_genotyping_Guadeloupe_Haiti/Tabular Data - 5.8 KB
Published Sep 9, 2024
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2 Variables, 9 Observations UNF:6:C+8gMYcWK/8iPVutLCKujw==
Original xls file with data and documentation
DataDocumentation
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