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

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.