Authentication of Coffea arabica Varieties through DNA Fingerprinting and its Significance for the Coffee Sector

Abstract

Background Locating the optimal varieties for coffee cultivation is increasingly considered a key condition for sustainable production and marketing. Variety performance varies when it comes to susceptibility to coffee leaf rust and other diseases, adaptation to climate change and high cup quality for specialty markets. But because of poor organization and the lack of a professional coffee seed sector, most existing coffee farms (and even seed lots and nurseries) do not know which varieties they are using. DNA fingerprinting of coffee planting material will contribute to professionalize the coffee seed sector. Objective The objective of this paper is i) to check in a large scale the robustness of the existing coffee DNA fingerprinting method based on eight Single Sequence Repeats markers (SRR) and ii) to describe how it can help in moving the needle towards a more professional seed sector. Method 2533 samples representing all possible genetic background of Arabica varieties were DNA fingerprinted with 8 SRR markers. The genetic diversity was analyzed and the genetic conformity to varietal references was assessed. Results The DNA fingerprinting method proved to be robust in authenticating varieties and trace back the history of C. arabica breeding and of the movement of C. arabica varieties. The genetic conformity of two important coffee varieties, Marseillesa and Gesha, proved to be 91% and 39% respectively. Conclusions DNA fingerprinting provides different actors in the coffee sector with a powerful new tool—farmers can verify the identity of their cultivated varieties, coffee roasters can be assured that marketing claims related to varieties are correct, and most of all, those looking to establish the a more professional and reliable coffee seed sector have a reliable new monitoring tool to establish and check genetic purity of seed stock and nursery plants. Highlights While C. arabica is primarily self-pollinating, even fixed line varieties appear to be drifting away from their original genetic reference due to uncontrolled cross pollination. A set of 8 SSR markers applied to the largest possible genetically diverse set of samples prove to discriminate between a wide range of varieties Figures confirm that genetic non conformity of coffee varieties can represent up to 61% of checked samples.

Validating South Sudan as a Center of Origin for Coffea arabica: Implications for Conservation and Coffee Crop Improvement

“…The wild Arabica populations in the forest of western Wellega, northern Illubabor, western Bench Maji and Bale (Davis et al, 2018) will no doubt be found to represent key centers of diversity using molecular data and may help to elucidate the geneticgeographical structure of wild Arabica in Ethiopia. Consistent with other studies (Pruvot-Woehl et al, 2020;Scalabrin et al, 2020;Montagnon et al, 2021), SL-06 was found to be included in an Ethiopian cluster. We therefore suggest to include this accession in the Ethiopian Landrace accessions, instead of in the Worldwide Cultivars.…”

“…Former studies (Anthony et al, 2002;da Silva et al, 2019;Benti et al, 2020) had proven the efficiency of SSR markers to study the genetic diversity of Arabica. In our study, we confirm that the reduced set of SSR markers established by Pruvot-Woehl et al (2020) are efficient to describe a new genetic group in Yemen (Montagnon et al, 2021) is again efficient to describe a new genetic group in this species: the South Sudan group. Scalabrin et al (2020) found the vast majority of the SNPs found were of low-frequency alleles.…”

“…Eight SSR primer pairs (Table 4) selected after Combes et al (2000) and whose wide discrimination power was confirmed by Pruvot-Woehl et al (2020) were used. This reduced set of markers were demonstrated to be efficient.…”

Genetic Diversity of Coffea arabica L.: A Genomic Approach

“…The only allotetraploid is C. arabica L. with 2n = 4x = 44 [12], which was originated from the natural cross between Coffea eugenioides S. Moore and C. canephora Pierre ex A. Froehner [13], C. arabica is the only self-fertile among the other cultivated species. This specie is genetically less diverse when compared to the diploid species [14,15], a situation that has been associated with its susceptibility to the common coffee diseases [16].…”

Genetic Variation

“…A broader study of the diversity and fingerprinting of Arabica coffee accessions from various producing regions of the world was done in 2533 genotypes [107]. These genotypes corresponding to the Core Collection of the germplasm of the Tropical Agricultural Research and Higher Education Center, accessions from Southern Sudan, and cultivars/germplasm from North, Central, and South America as well as Africa and Asia.…”