The coffee species Coffea canephora is commercially identified as “Conilon” when produced in Brazil, or “Robusta” when produced elsewhere in the world. It represents approximately 40 % of coffee production worldwide. While the genetic diversity of wild C. canephora has been well studied in the past, only few studies have addressed the genetic diversity of currently cultivated varieties around the globe. Vietnam is the largest Robusta producer in the world, while Mexico is the only Latin American country, besides Brazil, that has a significant Robusta production. Knowledge of the genetic origin of Robusta cultivated varieties in countries as important as Vietnam and Mexico is therefore of high interest. Through the use of Sequencing-based diversity array technology-DArTseq method-on a collection of C. canephora composed of known accessions and accessions cultivated in Vietnam and Mexico, 4,021 polymorphic SNPs were identified. We used a multivariate analysis using SNP data from reference accessions in order to confirm and further fine-tune the genetic diversity of C. canephora. Also, by interpolating the data obtained for the varieties from Vietnam and Mexico, we determined that they are closely related to each other, and identified that their genetic origin is the Robusta Congo – Uganda group. The genetic characterization based on SNP markers of the varieties grown throughout the world, increased our knowledge on the genetic diversity of C. canephora, and contributed to the understanding of the genetic background of varieties from very important coffee producers. Given the common genetic origin of the Robusta varieties cultivated in Vietnam, Mexico and Uganda, and the similar characteristics of climatic areas and relatively high altitude where they are grown, we can state that the Vietnamese and the Mexican Robusta have the same genetic potential to produce good cup quality.

Whilst it is established that almost all cultivated coffee (Coffea arabica L.) varieties originated in Yemen after some coffee seeds were introduced into Yemen from neighboring Ethiopia, the actual coffee genetic diversity in Yemen and its significance to the coffee world had never been explored. We observed five genetic clusters. The first cluster, which we named the Ethiopian-Only (EO) cluster, was made up exclusively of the Ethiopian accessions. This cluster was clearly separated from the Yemen and cultivated varieties clusters, hence confirming the genetic distance between wild Ethiopian accessions and coffee cultivated varieties around the world. The second cluster, which we named the SL-17 cluster, was a small cluster of cultivated worldwide varieties and included no Yemen samples. Two other clusters were made up of worldwide varieties and Yemen samples. We named these the Yemen Typica-Bourbon cluster and the Yemen SL-34 cluster. Finally, we observed one cluster that was unique to Yemen and was not related to any known cultivated varieties and not even to any known Ethiopian accession: we name this cluster the New-Yemen cluster. We discuss the consequences of these findings and their potential to pave the way for further comprehensive genetic improvement projects for the identification of major resilience/adaptation and cup quality genes that have been shaped through the domestication process of C. arabica.

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. 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. 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. 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. 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. 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.

The coffee species Coffea arabica is facing numerous challenges regarding climate change, pests and disease pressure. Improved varieties will be part of the solution. Making optimal use of the scarce genetic diversity of the species is hence essential. In this paper, we present the first study of C. arabica genetic diversity covering its complete native habitat in Ethiopia together with its main domestication centers: Yemen and Hararghe region in Ethiopia. All in all, 555 samples were analyzed with a set of Single Sequence Repeat markers. Through admixture genetic analysis, six clusters were identified. A total of two “Core Ethiopian” clusters did not participate in the domestication of the species. There were four clusters that were part of the “Domestication Pathway” of C. arabica. The first one was named “Ethiopian Legacy” as it represents the genetic link between “Core Ethiopia” and the “Domestication Pathway” in Yemen and Hararghe. The geographic origin of this cluster in Ethiopia was the south of Ethiopia, namely Gedio, Guji and Sidama, which hence appears as the source of coffee seeds that led to the domestication of C. arabica. In Yemen, in addition to the “Ethiopian Legacy” cluster, we confirmed the “Typica/Bourbon” and “New-Yemen” clusters. In Hararghe, the “Harrar” cluster, never described before, likely originates from a re-introduction of domesticated coffee from Yemen into this region of Ethiopia. Cultivated varieties around the world today originate from the “Ethiopian Legacy” and “Typica/Bourbon” clusters and but none are related to the “new-Yemen” and “Harrar” clusters. Implications for breeding strategies are discussed.

L'amélioration variétale de Coffea canephora représente un grand défi pour augmenter la productivité de cette espèce et assurer un meilleur revenu aux planteurs. Les opportunités sont nombreuses : la diversité génétique de cette espèce est bien documentée, les paramètres génétiques sont relativement bien établis pour les principaux caractères d'intérêt et les ressources génomiques disponibles s'accumulent. Toutefois, des contraintes sont également à considérer : en particulier, l'histoire spécifique de la mise en culture et de la sélection a conduit à une inégalité des sélectionneurs à travers le monde pour l'accès à l'ensemble de la diversité génétique de l'espèce. Ainsi, la sélection récurrente réciproque (SRR) qui représente une innovation majeure en termes d'utilisation raisonnée des ressources génétiques n'a pu être menée qu'en Côte d'Ivoire qui seule dispose d'un ensemble complet et référencé des ressources génétiques de base de C. canephora. Cette stratégie est adaptée à une sortie variétale sous la forme de semences hybrides, plus adaptées à une diffusion de masse que les boutures clonales. En dehors de la Côte d'Ivoire, une sélection massale clonale sur des populations en recombinaison plus ou moins bien décrites reste souvent l'axe des programmes de création variétale. Par ailleurs, le génome de C. canephora est sur le point d'être séquencé et les ressources génomiques sont maintenant suffisantes pour venir en appui des programmes de sélection. Les choix stratégiques qui permettront d'utiliser au mieux ces ressources au service de l'amélioration génétique doivent être l'objet d'une réflexion approfondie, tenant compte de l'expérience acquise pour d'autres plantes : les clés de ces choix sont discutées. (Résumé d'auteur

The Nagoya Protocol on Access and Benefit-sharing (ABS) of the Convention on Biological Diversity (CBD) is a fundamental international agreement that plays a crucial role in the protection and equitable utilization of plant genetic resources. While this agreement is essential for conservation and sustainable use, it presents specific challenges to coffee research and industry. One major issue is the requirement to obtain prior informed consent (PIC) from the source country or community, which can be a complex and time-consuming process, especially in regions with limited governance capacity. Additionally, the mandates of this agreement necessitate benefit-sharing with the source community, a requirement that poses implementation challenges, particularly for small businesses or individual researchers. Despite these challenges, the importance of the Nagoya Protocol in the coffee sector cannot be overstated. It contributes significantly to the conservation of coffee genetic resources and the sustainable utilization of these resources, ensuring fair distribution of benefits. To address the complexities presented by this international framework, coffee researchers and industry need to engage proactively with source countries and communities. This includes developing clear and equitable benefit-sharing and implementing strategies for compliance. This article explores the impact of the Nagoya Protocol on the coffee industry, particularly emphasizing the need for balancing scientific investigation with the ethical considerations of resource sharing. It also discusses practical strategies for navigating the complexities of this agreement, including research focused on authenticity control and the challenges in conducting large-scale coffee studies. The conclusion underscores the potential for international collaboration, particularly through platforms like the International Coffee Organization (ICO), to harmonize research activities with the ethical imperatives of the Nagoya Protocol.