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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Sustainable Perennial Crops Laboratory » Research » Publications at this Location » Publication #322188

Title: Developing Single Nucleotide Polymorphism markers for the identification of Coffee germplasm

item ZHOU, LIN - Nanjing Agricultural University
item Vega, Fernando
item TAN, HUAWEI - Nanjing Agricultural University
item RAMIREZ LLUCH, AIXA - University Of Puerto Rico
item Meinhardt, Lyndel
item FANG, WANPING - Nanjing Agricultural University
item Mischke, Barbara
item Irish, Brian
item Zhang, Dapeng

Submitted to: Tropical Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/8/2016
Publication Date: 6/2/2016
Citation: Zhou, L., Vega, F.E., Tan, H., Ramirez Lluch, A., Meinhardt, L.W., Fang, W., Mischke, B.S., Irish, B.M., Zhang, D. 2016. Developing Single Nucleotide Polymorphism markers for the identification of Coffee germplasm. Tropical Plant Biology. 9:82-95.

Interpretive Summary: Coffee is an economically important perennial crop cultivated in more than 80 countries. With an annual production of seven million tons, coffee represents a $70 billion-a-year global market. Globally over 20,000 coffee accessions have been collected and maintained in various repositories in different countries. But records and labels of the accessions have not always been properly maintained and accessions often arrive bearing limited information about their correct identity. In the present study, we developed a set of single nucleotide polymorphism (SNP) markers and tested their ability to identify and separate coffee germplasm, including both Coffea canephora (robusta) and C. arabica cultivars. The validation led to the designation of 56 SNP markers that unambiguously identified all tested samples. This method provides a powerful tool for the management of coffee genetic resources and breeding, where accurate and efficient cultivar identification is essential. This information will be used by researchers, coffee producers and coffee industry to accurately determine cultivar authenticity.

Technical Abstract: Coffee is one of the most widely consumed beverages that represent a multibillion dollar global industry. Accurate identification of coffee cultivars is essential for efficient management, exchange and use of coffee genetic resources. So far a universal platform that can allow data comparison across different laboratories and genotyping platforms has not been available for the coffee research community. Using expressed sequence tags of Coffea arabica and C. canephora from public databases; we developed 7,538 single nucleotide polymorphism (SNP) markers and selected 180 for validation using 25 C. arabica and C. canephora accessions from Puerto Rico. Based on the validation result, we designated a panel of 56 SNP markers that are polymorphic across the two species. The average minor allele frequency and information index of this SNP panel are 0.281 and 0.690, respectively. This panel enabled the differentiation of all tested accession of C. canephora, which account for 79.2% of the total polymorphism in the samples. Only 21.8% of the polymorphic SNPs were detected in the 12 C. arabica cultivars, which nonetheless, was able to unambiguously differentiate the 12 Arabica cultivars into ten unique genotypes, including two mutant groups. Several local Puerto Rican cultivars, including ‘Limani’, ‘Fronton’ and ‘TARS 18087’, showed substantial genetic difference from the other commonly cultivated Arabica cultivars in Latin America. This coffee SNP panel provides a robust and universally comparable DNA fingerprints, thus can serve as a genotyping tool to assist coffee germplasm management, propagation of planting material, and coffee varietal authentication.