Abstract
Coffee is one of the most economically important agricultural commodities in the world. Labeling accuracy and conservation efficiency are essential for coffee germplasm management and for the exchange and utilization in breeding new varieties. However, due to its homogenous genetic background, accurate identification of Coffea arabica germplasm has not been fully achieved. Specifically, data comparison across different laboratories and genotyping platforms has not been available. Here, we report the screening of 672 candidate SNPs using Nano-Fluidic Array genotyping. Based on call rate, Minor Allele Frequency and Linkage Disequilibrium, a set of 96 SNPs were selected for genotyping C. arabica. This validated panel is suitable for use in coffee germplasm conservation and crop improvement, including varietal identification, seeds and nursery accreditation, and coffee bean authentication.
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Acknowledgements
This work was supported by the United States Department of Agriculture (USDA) /Agricultural Research Service (ARS). Any mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer.
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Zhang, D., Vega, F.E., Solano, W. et al. Selecting a core set of nuclear SNP markers for molecular characterization of Arabica coffee (Coffea arabica L.) genetic resources. Conservation Genet Resour 13, 329–335 (2021). https://doi.org/10.1007/s12686-021-01201-y
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DOI: https://doi.org/10.1007/s12686-021-01201-y