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.

尽管面临着诸多挑战，海地农业林业系统中种植的咖啡（阿拉伯咖啡，Coffea arabica）对于农村生计和提供多种生态系统服务具有重要意义。关于其遗传多样性和所使用的品种混合的研究工作甚少，因此有必要对海地咖啡的多样性进行表征，以助力该行业的复兴。我们在海地北部和南部历史上重要的咖啡种植区域采样了28个农业林业系统。我们对样本进行了Hi-Plex靶向多重扩增子测序和KASP基因分型SNP标记，以及来自国际收藏的几个埃塞俄比亚和商业品种。在此，我们提供了此研究获得的数据，包含四个文件：Millet23_coffee_1_reference_info：此文件包含了研究中使用的各种咖啡参考样本的国际收藏信息，包括登录号、物种和产地（如有）。部分参考数据适用于KASP基因分型方法，但HiPlex靶向测序数据则不适用，已注明。Millet23_coffee_2_field_sample_info：此文件包含了在哈特伊收集的咖啡田间样本信息，包括地理位置、采集日期和当地标识。Millet23_coffee_3_kasp_genotypes：此文件包含了由LGC生物搜索技术（英国米德尔塞克斯）进行的KASP靶向基因分型数据，编码为A/B的双等位基因标记，并过滤掉了在30%以下样本中存在缺失数据的位点，以及具有30%以下缺失基因型数据的个体，最终得到87个基因型。此外，还提供了样本的来源和身份的附加信息。Millet23_coffee_4_hiplex_haplotypes：此文件包含了从HiPlex多重扩增子测序中获得的单倍型数据，由Yves Bawin开发的定制生物信息学管道生成，可在GitLab（https://gitlab.com/ybawin/sequence-data-processing-tetraploids）上获取。此外，还提供了一个Readme文件，其中包含本描述中的信息以及关于HiPlex单倍型数据解释的附加细节。这四个文件还合并为一个.xlsx文档，以便于使用。