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Unveiling a Unique Genetic Diversity of Cultivated Coffea Arabica L. in Its Main Domestication Center: Yemen

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Unveiling a Unique Genetic Diversity of Cultivated Coffea Arabica L. in Its Main Domestication Center: Yemen Genet Resour Crop Evol https://doi.org/10.1007/s10722-021-01139-y (0123456789().,-volV)( 0123456789().,-volV) RESEARCH ARTICLE Unveiling a unique genetic diversity of cultivated Coffea arabica L. in its main domestication center: Yemen C. Montagnon . A. Mahyoub . W. Solano . F. Sheibani Received: 21 July 2020 / Accepted: 15 January 2021 Ó The Author(s) 2021 Abstract Whilst it is established that almost all varieties and included no Yemen samples. Two other cultivated coffee (Coffea arabica L.) varieties origi- clusters were made up of worldwide varieties and nated in Yemen after some coffee seeds were intro- Yemen samples. We named these the Yemen Typica- duced into Yemen from neighboring Ethiopia, the Bourbon cluster and the Yemen SL-34 cluster. Finally, actual coffee genetic diversity in Yemen and its we observed one cluster that was unique to Yemen and significance to the coffee world had never been was not related to any known cultivated varieties and explored. We observed five genetic clusters. The first not even to any known Ethiopian accession: we name cluster, which we named the Ethiopian-Only (EO) this cluster the New-Yemen cluster. We discuss the cluster, was made up exclusively of the Ethiopian consequences of these findings and their potential to accessions. This cluster was clearly separated from the pave the way for further comprehensive genetic Yemen and cultivated varieties clusters, hence con- improvement projects for the identification of major firming the genetic distance between wild Ethiopian resilience/adaptation and cup quality genes that have accessions and coffee cultivated varieties around the been shaped through the domestication process of C. world. The second cluster, which we named the SL-17 arabica. cluster, was a small cluster of cultivated worldwide Keywords Coffea arabica Á Genetic diversity Á Yemen Á Domestication Supplementary Information The online version contains supplementary material available at https://doi.org/10.1007/ s10722-021-01139-y. & C. Montagnon ( ) Introduction RD2 Vision, 60 rue du Carignan, 34270 Valflaunes, France e-mail: [email protected] 12.5 million households around the world receive an income from coffee growing (Browning 2018). Coffee A. Mahyoub is mainly produced by two species:: Coffea arabica L. Qima Coffee, Asir, Sana’a, Yemen producing Arabica coffee and Coffea canephora W. Solano Pierre ex A.Froehner producing the coffee known as CATIE, Centro Agrono´mico Tropical de Investigacio´ny Conilon when produced in Brazil, and Robusta Ensen˜anza, Turrialba, Cartago 7170, Costa Rica anywhere else in the world. Arabica coffee production F. Sheibani is facing multiple challenges such as climate change Qima Coffee, 21 Warren Street, London W1T 5LT, UK 123 Genet Resour Crop Evol (Bunn et al. 2015) and serious diseases such as coffee (Alkimim et al. 2020). Scalabrin et al. (2020) demon- leaf rust caused by Hemileia vastatrix (Avelino et al. strated the recent unique polyploidization event by 2015), and Coffee Berry Disease caused by Col- sequencing the C. arabica genome using SNPs from letotrichum kahawae (Van der Vossen et al. 2015). the two sub-genomes of this tetraploid species. Whilst there is no single solution to such complex However, when the objective is fingerprinting or a challenges, the study of genetics and the breeding of genetic diversity study, the high level of polymor- improved varieties is a critical area of investigation for phism in SSRs renders it a reliable, practical and cost potential solutions. The search for genetically superior effective choice (Hodel et al. 2016). In grapes, the first quality coffee varieties has become a central issue for approach to characterize a Vitis germplasm collec- the specialty market (Montagnon et al. 2019). Unfor- tions with ten SSRs proved a high discriminating tunately, the genetic diversity of C. arabica is among capacity for grapevine varieties (Emmanuelli et al. the lowest in the cultivated crop, due to a recent single 2013). In the same study, SSRs proved as efficient as event of polyploidization (Scalabrin et al. 2020). SNPs to establish the genetic diversity of grapevine. Furthermore, the major part of this low genetic Singh et al. (2013) found that SSR markers were more diversity is found mainly in Ethiopia and to a lesser efficient than SNP markers when the objective was degree in South Sudan (Chevalier 1929; Harlan 1969; strictly the study of genetic diversity. Anthony et al. Sylvain 1958; Thomas 1942). (2002) found that 6 SSR markers were efficient to Whilst Ethiopia and South Sudan are the center of confirm the origin of cultivated C. arabica varieties, origin of C. arabica, Yemen has been its key center of spreading from Yemen after an early introduction domestication. Both historical records (de la Roque from Ethiopia. More recently, da Silva et al. (2019) 1716; Ukers 1922; Chevalier 1929; Cramer 1957; used 30 markers to efficiently discriminate between C. Haarer 1958; Meyer 1965; Koehler 2017) and past arabica varieties and three diploid Coffea species. phenotypic (Montagnon and Bouharmont 1996)or Benti et al. (2020) used 14 SSR markers to efficiently genetic studies (Lashermes et al. 1996; Anthony et al. discriminate between 40 cultivated C. arabica vari- 2002; Silvestrini et al. 2007; Pruvot-Woehl et al. 2020; eties in Ethiopia. Finally, Pruvot-Woehl et al. (2020) Scalabrin et al. 2020) indicate that all the Arabica demonstrated that a set 8 SSR markers—used in the varieties cultivated outside Ethiopia transited through present study-used to genotype 2533 samples repre- the Yemen domestication center. Still, while all the senting the largest known genetic diversity of C. previous genetic studies were using Yemeni coffee arabica was efficient in discriminating between vari- samples to check the Yemeni stop-over between eties and could be used for varietal authentication, and Ethiopia and the spread of Arabica coffee varieties hence for genetic diversity studies. to the world, none has revealed the Yemeni genetic Over the past half-decade, Qima Coffee (www. diversity. The few genetic studies focusing on Yemeni qimacoffee.com)—a coffee company working at the coffees (Al-Murish et al. 2013; Hussein et al. 2017) ground level in Yemen- has developed research indicated the genetic heterogeneity of varieties as activities in order to better understand the genetic identified by Yemeni farmers. Neither Ethiopian landscape of Yemeni coffee. A breeding population accessions nor worldwide cultivated varieties were made of 45 individuals representing various coffee included in these studies. morphotypes observed in Yemen has been gathered. Various molecular markers are available to geneti- Using this breeding population, together with Ethio- cists and breeders for genetic studies and genome pian accessions and cultivars as well as a representa- analysis, namely Single Nucleotide Polymorphism tion of the cultivated varieties worldwide, we present (SNPs) and Single Sequence Repeats (SSRs) (re- here the first global study aiming at describing the C. viewed by Adhikari et al. 2017). Genotyping by arabica coffee genetic diversity in Yemen. The main Sequencing (GBS) technique which provides thou- questions addressed in the study are as follows: What sands of SNPs for a dense coverage of the genome is is the magnitude and the structure of the genetic no doubt the ideal method to study the relationship diversity in Yemen? How does the genetic diversity of between genotype and phenotype, namely in poly- Yemen compare with the known genetic diversity of ploids (Clevenger et al. 2015). SNP’s are often used in coffee in Ethiopia and that of the cultivated C. arabica coffee for genome wide selection in C. canephora varieties worldwide? And finally, does Yemen’s 123 Genet Resour Crop Evol genetic diversity offer opportunities for genetic DNA extraction and SSR marker analysis improvement of C. arabica? All the operation of DNA extraction and SSR marker analysis were performed by the ADNiD laboratory of Material and methods the Qualtech company in the South of France (http:// www.qualtech-groupe.com/en/). Plant material Genomic DNA was extracted from approximately 20 mg of dried tissue according a homemade protocol 137 samples of C. arabica were studied. They belong with SDS buffer. DNA was then purified with to the following three categories (Table 1). magnetic bead (Agencourt AMPure XP, Beckman Coulter, Brea, California, USA) followed by elution in Ethiopian accessions (EA) Tris Edta (TE) buffer. The DNA concentration was estimated with a 72 accessions are representing the Ethiopian acces- Enspire spectrofluorimeter (Perkin Elmer) with a sions collected in 1966 and 1968 by the FAO and bisbenzimide DNA intercalator (Hoechst 33,258) Orstom survey, respectively (FAO 1968; Charrier and by comparison with known standards of DNA. 1978). Those 72 accessions were selected as they are Eight SSR primer pairs (Table 2) selected after part of the core collection defined by World Coffee Combes et al. (2000) and whose wide discrimination Research and the Centro Agrono´mico Tropical de power was confirmed by Pruvot-Woehl et al. (2020) Investigacio´n y Ensen˜anza (CATIE) in 2014 (Solano, have been used. personal communication). PCR was performed in a 15 lL final volume comprising 30 ng genomic DNA and 7.5 lLof Worldwide cultivars (WWC) 2 9 PCR buffer (Type-it Microsatellite PCR Kit, Qiagen), 1.0 lM each of forward and reverse primer 20 samples represent main cultivated varieties grown (10 lM). Amplifications were carried out in thermal worldwide outside Ethiopia. This includes Bourbon cycler (Eppendorf) programmed at 94 °C for 5 min and Typica, but also East African and Indian varieties for initial denaturation, followed by 94 °C for 30 s, that have been shown to have transited through Yemen annealing temperature depending on the primer used from Ethiopia before being introduced in all present for 30 s and 72 °C for 1 min for 35 cycles followed by coffee producing countries (reviewed in Pruvot- a final step of extension at 72 °C for 5 min.
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