Unveiling a unique genetic diversity of cultivated Coffea arabica L. in its main domestication center: Yemen

Abstract

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.

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.…”

“…Two other accessions of the CATIE germplasm collection had one of the two specific alleles to the South Sudan group: SL-14 (T.02747) and SL-17 (T.02745). Interestingly, these two accessions represented one specific mother population (named 'SL-17') in the study by Montagnon et al (2021). The accessions that are part of that mother population do not seem to have followed the Yemeni domestication route.…”

“…Despite the documented consumption of this coffee species as a beverage since at least the sixth century, and its contribution to the economy of many countries, it is remarkable that there was no factual data confirming native status in Ethiopia until the twentieth century (Meyer, 1965). The first documented cultivation of Arabica is in Yemen from around the fifteenth century, from where two main genetic types (Bourbon and Typica) were disseminated, giving rise to most of the commercial cultivars of Arabica grown worldwide (Anthony et al, 2002;Scalabrin et al, 2020;Krishnan et al, 2021;Montagnon et al, 2021).…”

“…Regardless, crossing global cultivars with cultivated Ethiopian accessions of wild origin has proven to bring significant crop improvement as compared to traditional cultivars (Van der Vossen, 2017; Marie et al, 2020). For example, a new genetic group of cultivated Arabica was revealed recently for Yemen (Montagnon et al, 2021). Additional genetic diversity in the species could be an opportunity for further progress.…”

Tissue-specific analysis of Coffea arabica L. transcriptome revealed potential regulatory roles of lncRNAs

“…arabica occupies 70% of the world coffee cultivation and production ( Lashermes et al, 1999 ). Growing coffee represents the sole income source for more than 12.5 million households around the world ( Montagnon et al, 2021 ). Therefore, coffee represents the most valuable tropical export crop worldwide, with an annual retail value of roughly 88 billion dollars ( Valencia-Lozano et al, 2021 ).…”