Genotyping data for field samples from Haitian coffee agroforestry systems and international collection accessions

Version 1.1
Genotyping data for field samples from Haitian coffee agroforestry systems and international collection accessions
Millet, Claude Patrick; Allinne, Clémentine; Vi, Tram; Marraccini, Pierre; Verleysen, Lauren; Couderc, Marie; Ruttink, Tom; Zhang, Dapeng; Solano Sánchez, William; Christine, Tranchant-Dubreuil; Jeune, Wesly; Poncet, Valérie, 2023, "Genotyping data for field samples from Haitian coffee agroforestry systems and international collection accessions", https://doi.org/10.23708/T6YZML, DataSuds, V1, UNF:6:4wzzOYlt0nsxd5jgI0e5Eg== [fileUNF]
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Description

Though facing significant challenges, Coffee (Coffea arabica) grown in Haitian agroforestry systems are important contributors to rural livelihoods and provide several ecosystem services. There has been little work done on their genetic diversity and the variety mixtures used, and there is a need to characterize Haitian coffee diversity to help inform revitalization of this sector. We sampled 28 agroforestry systems in historically important coffee growing regions of Northern and Southern Haiti. We performed Hi-Plex targeted multiplex amplicon sequencing and KASP-genotyping of SNP markers on our samples, as well as several Ethiopian and commercial accessions from international collections.
Here we provide the data acquired from this work, in four files:

Millet23_coffee_1_reference_info: This file contains information about the various Coffea reference samples from international collections used in the study, including the accession information, species , and origin (where applicable). Some reference data are available for the KASP genotyping assay method, but not for HiPlex targeted sequencing. These are noted.

Millet23_coffee_2_field_sample_info: This file contains information about the Coffee field samples collected in Haiti, including the geographic location, date of collection and local identification.

Millet23_coffee_3_kasp_genotypes: This file contains the data from KASP targeted genotyping conducted by LGC BioSearch Technologies (Middlesex, UK), coded as A/B, biallelic markers, and filtered to exclude loci with missing data in <30% of samples, then individuals with <30% missing genotype data, leaving 87 genotypes. Additional information on the sample's origin and identity are also provided.

Millet23_coffee_4_hiplex_haplotypes: This file contains the Haplotype data obtained from HiPlex multiplex amplicon sequencing, output from a custom bioinformatics pipeline by Yves Bawin, available on GitLab (https://gitlab.com/ybawin/sequence-data-processing-tetraploids).

In addition, a Readme file is provided, containing the information present in this description as well as additional details regarding the interpretation of the HiPlex Haplotype data. These fours files are also combined in a .xlsx document for ease.
Subject Agricultural Sciences
Keyword coffee, arabica, genotyping data, Haiti, field samples, Germplasm collection
Related Publication Millet CP, Allinne C, Vi T, Marraccini P, Verleysen L, Couderc M, Ruttink T, Zhang D, Sanchéz WS, Tranchant-Dubreuil C, Jeune W, Poncet V. (2024) Haitian coffee agroforestry systems harbor complex arabica variety mixtures and under-recognized genetic diversity. PLoS One. 2024 Apr 16;19(4):e0299493. doi: 10.1371/journal.pone.0299493
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Millet23_coffee_0_Readme.pdf
Millet23_coffee_0_Readme.pdf
Millet23_coffee/Adobe PDF - 84.6 KB
Published Nov 29, 2023
6 Downloads
MD5: 68c9886481656da24e8f4044b5d68a76
Data documentation
Documentation
Millet23_coffee_1_references_info.tab
Millet23_coffee/Tabular Data - 9.9 KB
Published Nov 29, 2023
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8 Variables, 128 Observations UNF:6:cnk88qwuB9aou3ACaJVW5A==
This file contains information about the various Coffea reference samples from international collections used in the study
Data
Millet23_coffee_2_field_sample_info.tab
Millet23_coffee/Tabular Data - 60.5 KB
Published Nov 29, 2023
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10 Variables, 610 Observations UNF:6:RxSTcnFSQOxeLTRcDf4VVw==
This file contains information about the Coffee field samples collected in Haiti
DataGeospatial
Millet23_coffee_3_kasp_genotypes.tab
Millet23_coffee/Tabular Data - 408.1 KB
Published Nov 29, 2023
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93 Variables, 733 Observations UNF:6:v6l2QsJcVY795JaocXLe+Q==
This file contains the data from KASP targeted genotyping (87 loci)
Data
Millet23_coffee_4_hiplex_haplotypes.tab
Millet23_coffee/Tabular Data - 2.2 MB
Published Nov 29, 2023
1 Download
725 Variables, 771 Observations UNF:6:6R27Yo4iGEvbuknJjRX4FQ==
This file contains the Haplotype data obtained from HiPlex multiplex amplicon sequencing
Data
Millet23_coffee_alldatasets.xlsx
Millet23_coffee/MS Excel Spreadsheet - 1.9 MB
Published Nov 29, 2023
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MD5: 2373559d3f310e747529fb876755bbb3
This file combines all data tables in Excel (.xlsx) format
Data
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In order to comply with agreements with Haitian authorities, the data are available upon request. Please contact Valérie Poncet (valerie.poncet@ird.fr) and inform us of intended use for the data.
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