Selecting a core set of nuclear SNP markers for molecular characterization of Arabica coffee (Coffea arabica L.) genetic resources

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.

Automated summary

The study screened 672 candidate SNPs using Nano-Fluidic Array genotyping and selected a panel of 96 SNPs for genotyping Coffea arabica based on call rate, Minor Allele Frequency, and Linkage Disequilibrium. This validated panel is suitable for coffee germplasm conservation, crop improvement, varietal identification, seed and nursery accreditation, and coffee bean authentication.