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INTRODUCTION
Coffee as a crop and wild species
Coffee (Coffea L.) is one of the most consumed beverages in the world, supporting a multi-billion dollar sector (1) that crosses a long chain of values from the farmer to the consumer. Because coffee production is largely in the hands of small farmers, the value of livelihood is immense, with about 100 million coffee growers worldwide (2). Global coffee trade is based on two species: Arabica (Coffea arabica) comprising c. 60% of the exchanged coffee and the robust (Coffea canephora), the remaining 40% (1). Caffè Liberica (Coffea liberica), a third species of beverage, is grown all over the world (and used as a graft graft for Arabica and Robusta), but is insignificant in terms of global trade (1). C. arabica, a product of the ancient hybridization of C. canephora is Coffea eugenioides (3, 4) occurs naturally in Ethiopia and South Sudan (5); C. liberica is C. canephora occur wild in large parts of humid tropical Africa (6).
Arabica coffee has been grown for at least several hundred years and may have been harvested for thousands of years, first as food and then as a drink (7). Robust breeding was recorded for the first time in Africa between the first half and the mid 1800s (8) but probably precedes the records of hundreds of years. The cultivation of Liberica coffee was first documented in the early 1870s, but despite the high hopes, its cup qualities failed to satisfy the tastes of the consumer, and therefore the aspirations of growers and coffee merchants, in particular in Sri Lanka (9). Arabica and robust are unusual among the main crops, as the period of time when domestication occurs is short and their level of domestication (ie variance from wild types) is variable and the least, except in cases of interspecies hybrids. The wild variants of both species can be harvested and processed to produce coffee with sensory qualities similar or indistinguishable from the cultivated and domesticated types.
Robusta gains ground on Arabica
Despite the first records of the production of robust coffee, this species was not recognized by science until 1897, based on material from West Africa (Gabon) (10). Cultivation outside of Africa developed rapidly from the early 1900s onwards (11), in many cases replacing the widely cultivated Arabica and the recently sown Liberica coffee. Robusta has gained market share against Arabica because of its resistance to coffee leaf rust (CLR; Emileia vastatrix Berk. & Broome) (8), a broader agroecological envelope (6), higher productivity (12) and a lower market price (1). Although the robust has some negative sensory qualities (eg, notes of taste of wood and tobacco), it is favored in some cases for its taste, high content of caffeine and ability to add body to espresso coffee and coffee based espresso; it is now the sort of choice for instant coffee. Robusta coffee has been transformed from a little known African crop to a major global product in just c. 150 years. Today, robust includes c. 40% of global coffee trade (1), although its true proportion in the global market is probably higher, since it is used to adulterate Arabica coffee (13). In addition, the robust was vital for the breeding of cultivars resistant to the CLR of Arabica coffee, through the re-crossing with Arabica-robusta hybrids (14the most notable of these is the Timor hybrid (15). Robusta coffee was therefore responsible for overcoming most of the key problems for the sustainability of the coffee sector, both through direct substitution and through the use of new cultivars, making development and redundancy superfluous. Use of other species of coffee. Robust coffee provides a good example of how a newly discovered (relatively) wild has turned a globally important crop.
The species of wild coffee as a resource for the sustainability of the coffee industry
Despite the overwhelming agronomic and economic success of Arabica and Robusta, a myriad of new threats are now evident for the global coffee industry. These include climate change (16), in particular the increasing incidence and duration of drought, the spread and the intensification of the severity of devastating fungal pathogens, in particular CLR for Arabica in Central and South America (14) and coffee disease (CWD; Gibberella xylarioides R. Heim and Sacca) for robust in Africa (17), the emergence and / or spread of other diseases and parasites (18), and social, economic and market-based factors. Addressing these challenges will require a clear vision, a wide range of interventions and good governance. There will also be a growing demand for germplasm: the raw material of crop development. Wild variants of Arabica and Robusta will be of primary importance, but other species of wild coffee [crop wild relatives (CWRs)] they are probably required Even the species of wild coffee are coming back into focus (19, 20), revitalizing the considerable interest that existed during the first coffee research ages (12, 21, 22).
Most consumers, as well as many representatives of the coffee industry, are unaware that there are more than two or three species of coffee. There are 124 species of coffee known to science (6, 23), which occur naturally (wild) in tropical Africa, on the islands of the Indian Ocean (Madagascar, Comoros Islands and Mascarene), in Asia and Australasia (Figure S1) (24). All Coffea species have the characteristic morphology of coffee beans (seed)25) and many of the non-commercial species are (or have been) used on a local or regional scale as a substitute for Arabica coffee (12, 21, 22, 26, 27). These species have characteristics useful for the development of coffee, such as climatic tolerance (6) and in particular the tolerance to drought, resistance to pests and diseases (21, 28–31), low or no caffeine content (32), and sensory improvement (taste) (12, 22).
Given the importance of coffee CWRs for the sustainability of the coffee sector, two critical questions are highlighted: what is the risk of extinction of wild coffee species? And which species should be a priority for crop conservation and development? To answer these questions, we report here a global assessment of the risk of extinction for all known species of coffee by strictly applying Categories and Criteria of the Red List International Union for the Conservation of Nature (IUCN) (33); a priority system for coffee CWRs, based on phylogenetic data and information on plant selection; and an analysis of the gap of ex situ conservation in germplasm collections and in situ conservation in protected areas.
RESULTS
At least 60% of coffee species are threatened with extinction
The application of the IUCN red list categories and criteria (33) determined the evaluation of 75 species of coffee (60%) at risk of extinction, including 13 species at critical risk (CR), 40 at risk (EN) and 22 vulnerable (VU); 35 species were evaluated as not threatened [Near Threatened (NT) or Least Concern (LC)]and 14 species were lacking in data (DD) (Figure 1). Information on individual species, including the distribution interval, habitat and ecology, threats, conservation actions and assessment information, can be accessed via the IUCN Red List of Threatened portal. Species Plant (34); a summary of species is provided in Table S1 and regional and area summaries in Tables S2 and S3. Madagascar has the highest number of endangered species (43 species) (Figure 2), but the proportions of threatened species in Madagascar (72%) were similar to those of Tanzania (12 species: 71%) (Table S3).
Pod diagram, showing the proportion and number of threatened, undermined and DD coffee species in the main blocks and the proportion and number of coffee species assigned to each category of risk of extinction of IUCN. The total number of species is 124 [CR, 10.5% (13 species); EN, 32.3% (40 species); VU, 17.7% (22 species); NT, 8% (10 species); LC, 21% (26 species); DD, 11.3% (14 species)]. Each square is equal to one species.
Map showing the species of coffee threatened by the TDWG level 3 areas (countries or subdivisions of countries, see Materials and methods for the definition of TDWG level 3). See fig. S1 by number of coffee species by area.
The 14 species (11.3%) evaluated as DD were distributed in the interval of distribution of wild coffees (Figure S2). A taxon is assessed as DD when there is inadequate information to make a direct or indirect assessment of its risk of extinction based on its distribution and / or population status (35). The inadequacy of information is attributable to one or more factors including uncertain provenance, taxonomic uncertainty, old documents and uncertain threats. Thirteen species of coffee have been classified as DD due to the scarcity of basic data records (occurrence); a fourteenth species of coffee, Coffea rhamnifolia (Northern Kenya and Somalia), lacking the recent knowledge of population trends or threats. The lack of recent data on the point of contact stems from the lack of research observations of these species in nature for several decades, due to the inaccessibility generated by conflicts in a particular region (for example, in Angola, for Coffea carrisoi, Coffea kapakata, is Coffea melanocarpa), or perhaps a lack of rigorous and targeted field work (eg in Asia, for Coffea fragrans, Coffea horsfieldiana, is Coffea madurensis). Nine of the DD species have not been observed since 1940 and five of them (all Asian) are known only by three or less herbarium records made before 1900 (Coffea cochinchinensis, Coffea floresiana, C. fragrans, C. horsfieldiana, and Coffea malabarica). Some of these species are likely to be threatened (36) and some may be extinct.
Preliminary assessments of risk of extinction reported in Davis et al. (6) suggest a higher percentage (69%) of threatened wild coffee species compared to what is reported here and, for many species, the category applied subsequently (in 2006) differs significantly from that of the full evaluation reported here. However, these previous assessments were extremely provisional, being mainly based on an approximation of the size of the geographical range, without a detailed consideration of the threats; the categories and criteria of the IUCN red list (33) have not been rigorously applied and the evaluations have not been peer-reviewed and have been (or ratified) by the IUCN Red List (34). Thus, the differences between the Davis evaluations et al. (6) and those reported here should not be interpreted as indicators of trends in the risk of extinction of wild coffee species.
Coffee priority CWRs have a high risk of extinction
Three CWR priority groups have been recognized; the assignment of the species is indicated in table S1. The CWR I priority group is composed of four species, including the bred and wild variants of each crop species (C. arabica, C. canephora, is C. liberica) is C. eugenioides, a parental species of C. arabica (3, 4). wild C. arabica is the only endangered species (EN) in Group I (37). The CWR II priority group is composed of 38 species and includes all African and African clades (24, 32) except species previously placed in Psilanthus (see additional materials). In group II, 23 species (61%) are threatened (table 1). Priority Group III of the CWR contains 82 species, including all species of Madagascar, Comoros and the Mascarene Islands and their respective clades (4, 24, 32) and all the species (African and Asian) previously inserted Psilanthus (Additional materials). In group III, 51 species (62%) are threatened.
The numbers in brackets represent the percentage for each CWR priority group or each IUCN category. n / a, not applicable.
The threatened species are inadequately represented ex situ and in situ
Our gap analysis shows that just over half of all coffee species (55%) are contained in ex situ germplasm collections (Table 1 and Table S4). The most endangered species are poorly represented, with only 23% of CR species held ex situ; The species EN and VU have better coverage, respectively at 58 and 59% (table S4). The ex situ representation of the CWR priority groups is as follows: 4 species (100%) for group I, 16 species (42%) for group II and 48 species (59%) for group III (Table 1).
About two thirds of the species (89; 72%) occur in at least one protected area (in situ); 22 species (18%) do not have in situ protection and the coverage of 13 protected species is unknown (including 11 species DD). The in situ representation for each CWR priority group is as follows: 4 species (100%) for group I, 30 species (79%) for group II and 55 species (67%) for group III (Table 1).
Overall, in situ coverage is greater than ex situ: 72% versus 55%, respectively. This difference is particularly marked in the CWR II priority group (79% in situ versus 42% ex situ), while the proportions in group III vary less (67% against 59%). Twelve species (10%) do not have ex situ or in situ representations, including seven CR species (four in the CWR II priority group) and four EN species.
DISCUSSION
At 60%, the proportion of endangered coffee species is high compared to a global percentage of 22% for all plants (38) and one of the highest levels registered for a group of plants. For the palm genus of Madagascar almost endemic Dypsis (Arecaceae), 73.8% of its species are threatened (34, 39), which is comparable to the percentage of threatened species of coffee from the island of Madagascar and the Indian Ocean (71.4%). Other examples include 66% of species threatened for Encephalartos (Zamiaceae), 58% for Parody (Cactaceae) and 48.7% per Magnolia (Magnoliaceae) (34). To date, the complete gender-risk assessment for CWRs, including wood representatives, is poor. A recent and complete evaluation of tea relatives (Camellia; Theaceae) has reported a species (<1%) extinct (EX), 45.4% in danger and 21% DD (40). Other woody CWR examples include hazelnut (Corylus; Betulaceae), with 6.2% of threatened species; pistachio (Pistacia; Anacardiacae), with 9% in danger; and mango (Mangifera; Anacardiacae), with 52.4% in danger (34). The percentage of threatened species of coffee could ultimately prove to be higher than the values given here, since it has been shown that DD species with old and / or few records (as in the case of at least five coffee species) tend to have high levels of risk expected extinction (36).
C. arabica has the most accurate assessment of the risk of extinction of any kind of coffee (37), due to the abundant amount of high quality data, a rigorous review of the land and the inclusion of climate change projections (5, 16). Moat et al. (37) show that when the projections on climate change are incorporated into the assessment of the risk of extinction, C. arabica moves three categories, from LC to EN. While it may take some time to generate enough data to treat all sorts of coffee in this way, these results (37) indicate a considerable additional concern for the fate of coffee species when climate change projections are included in endangering risk assessments.
The percentage of CWR (priority groups I and II) deficient in ex situ collections is 52% (45% for all coffee species), much higher than that reported for other CWRs, for example 29.1% for 313 taxa associated with 63 crops (41). In general, coffee species are difficult, costly and risk-prone for ex situ conservation (42, 43). Unlike many other CWRs, coffee seeds are recalcitrant, ie not conserved by conventional methods (low humidity and low temperatures) (43). Keeping living coffee collections is particularly expensive (42–44) and the genetic integrity of the species is susceptible due to open pollination (45). Seed cryopreservation and the slow growth of in vitro methods provide better options and can be cost-effective, but so far these methods are largely limited to the main coffee crop species (44).
Coffee species of the CWR I priority group (C. arabica, C. eugenioides, C. canephora, and C. liberica) would appear to be in a safer position than other CWR priority groups, since each species is included in at least one protected area and is present in germplasm collections. However, there is a basic issue of inadequate coverage of diversity in both ex situ and in situ environments, including those of C. arabica is C. canephora (see discussion in additional materials). Due to the rapid deforestation (37, 46), climate change (5, 37) and genetic erosion (47), options for collecting additional game material C. arabica for conservation and ex situ use (eg plant breeding) are decreasing. In Ethiopia, low-intensity farming practices in native wetland forests and wild coffee harvesting offer a good measure of in-situ protection for wild Arabica populations (7, 16, 48, 49); the income generated by the production of coffee means that the forest has an immediate and tangible value and is thus preserved. The parameters for the CWR II priority group are more worrying: 61% of the species in this group are threatened, 58% are not represented ex situ and four (11%) CR species have neither ex situ or in situ representation (Table 1). ).
At nominal value, the number and percentage of species (89: 72%) occurring within protected areas (in situ) may seem encouraging, but the coverage of diversity within species is one important concern. Looking at the example of C. arabica, only c. 4% (1681 km2) of the potential forest area for this species is contained in the protected areas of Ethiopia and South Sudan (37). Furthermore, a large percentage of the protected area is threatened by human pressure (50) and global environmental change (51). It should also be clarified that our definition of in situ conservation is limited to the occurrence of a protected area, such as the nature reserve or national park. Many protected areas fail to conserve the diversity within their borders and feasible management plans are needed to ensure that the target species are effectively stored (52).
The main factors that determine the risk of extinction of coffee species are the reduced size of distribution (table S5) and the low number of locations (34), that is "a geographically or ecologically distinct area in which a single threatening event will affect all individuals" (33), in conjunction with ongoing threats, in particular habitat loss (Figure S3). For almost all species, there is a continuing decline in the quality, surface and extension of the available habitat (34). The loss of habitat is mainly due to land use change, in particular the loss of forests, mainly due to agriculture (general), breeding and settlement. and development, mostly associated with agriculture (Figure S3). Timber harvesting is also a threat to many species of coffee; The coffee wood is often straight, hard and resistant to termites and often collected for minor construction purposes (Figure S3) and firewood. Based on the research undertaken for this contribution, along with other research on coffee and after more than twenty years of field research, we propose that coffee species are sensitive to extinction. Wild coffee species typically have narrow climate envelopes with limited habitat specificity (niche) (5, 6, 16, 37), have a low potential for adaptation (5), and are mostly forest dwellings (6). As with other members of the family of coffee (Rubiaceae), they also require a good quality habitat, have a limited capacity for regeneration unless conditions are optimal and do not act as a pioneer species (53). There are, undoubtedly, other reasons for the prevalence of gamma limitation, including perhaps the presence of crossings between quasi-universal obligatory neighbors, due to the strong self-incompatibility of gametophytes (54).
At a time when attention is focused on food security and income shortfalls for farm subsidies, it is of great concern that raw materials for possible solutions are highly threatened. Coffee CWRs have provided important sustainability solutions for the global coffee industry over the past 400 years and up to the present day. It is very likely that similar resources will be recalled again to deal with production problems, especially those related to diseases, pests and worsening of climatic suitability, in particular because the global demand for coffee increases (1). This situation is particularly acute for Arabica coffee, given its climatic inflexibility (5, 16) and susceptibility to CLR (14) and other diseases and pests (17). Robusta coffee is also vulnerable to climatic conditions that do not fall under the climatic requirements of the species, as recent media reports on crop failure and plant death due to drought conditions in Brazil demonstrate. Furthermore, despite resistance to CLR, the robust is highly susceptible to specific fungal pathogens, such as CWD (17).
Ultimately, we need to conserve the existing species of wild coffee in situ to ensure the conservation of the remaining genetic diversity. This goal requires a lot of effort and would require the participation of several stakeholders, from the host countries and from the outside. Large protected areas under strict control have a lower impact on man and, consequently, a lower loss of biodiversity (52) but they are not immune to other pressures, such as climate change and natural events. In the case of coffee, however, better solutions could be found where the potential for human commitment exists for the benefit of both livelihoods and biodiversity, as in the case of wild Arabica forests in Ethiopia (7, 16, 48, 49). For ex situ collections, we need to improve the quantity and quality of coffee germplasm inventories (including plant identification and reduction of genetic redundancy), improve management (including storage and dissemination of data) and ensure long-term viability, especially for CWR coffee, priority species and essential collections required for breeding purposes. The global conservation strategy for coffee genetic resources, which focuses on the ex situ conservation of the main coffee crop species, develops the requirements for effective germplasm management and governance, including specific recommendations and priority actions (42). It has been argued that the use and conservation of wild coffee species outside their countries of origin are hampered by the lack of access mechanisms and sharing of the benefits that are rigorous and mutually usable for germplasm (42), an obstacle also reported to other crops and CWR (55). African countries that grow coffee and host wild coffee species in natural environments are well positioned to develop and conserve their wild coffee resources. They should be supported to do so by the international development and conservation communities.
MATERIALS AND METHODS
Ground point and field observation data
For the IUCN extinction risk assessments of the 124 coffee species, we used a data set of 5434 records of terrestrial points, including 3798 records of herbarium samples, consulted by over 40 herbaria; BM, BR, BRLU, BZ, C, COI, DSM, EA, ETH, G, K, L, LISC, P, SCA, TAN, TEF, UPS, VNM, WAG and YA[Codicidell'erbariosecondoleabbreviazionistandard([Herbariumcodesfollowingstandardabbreviations([codicidell'erbariosecondoleabbreviazionistandard([herbariumcodesfollowingstandardabbreviations(56, 57)]provided most of the recordings. A total of 162 data points were purchased online, via Tropicos (104 records) (58), Global Biodiversity Information Facility (43 registrations) (59), and the Natural History Museum, Paris (3 records) (60); 12 photographic documents were consulted through iNaturalist (61). We also used field 1624 and plot observations for wild arabica from previous studies (5, 16). Herbal registers are verifiable in space (location), time (when collected) and form (species identification) and are therefore suitable for the purposes of the study. All ground point data were georeferenced (if not already available), manually verified for geolocation accuracy and correct if necessary. We used a 2 km error radius for data points, except in cases where we needed a reference point for general mapping purposes and for poor data species (including DD species). Extensive field research has been undertaken in areas with a high diversity of coffee species, in Africa (Cameroon, Kenya, Tanzania, South Sudan and Uganda), in Madagascar (11 field expeditions) and in the Indian Ocean islands ( Mauritius). Particular attention was paid to the two main species of crops, Arabica and Robusta coffee, including field research in Ethiopia and South Sudan for the previous species, and a complete survey on the subject. Herbarium for this last one. The observations made during fieldwork were mostly accompanied by the production of good herbariums, in addition to the numerous observations recorded on Arabica coffee made in Ethiopia (1624 documents) (5, 16). The checks of the samples were performed by A.P.D.
Production of the amplitude of the event and of the area of employment metrics
The size of occurrence (EOO) and the area of employment (AOO) are key measures for the application of the IUCN Red List Categories and Criteria (33). EOO is defined as the area containing all known, inferred or projected sites of the present presence of a taxon (ie a species) within the shortest continuous imaginary boundary, which can be designed to understand the sites; EOO can often be measured with a minimal convex polygon. For convenience, EOO can be defined as the geographical radius. AOO is defined as the area within its "extent of occurrence", which is occupied by a taxon (33), excluding cases of wandering; the dimension of AOO "will be a function of the scale at which it is measured and should be on a scale appropriate to the relevant biological aspects of the taxon, the nature of the threats and the available data" (33). For the AOO calculations, the IUCN standard 2 km by 2 km standard grid cell was used. The calculations for the AOO and EOO of each coffee species were made using GeoCAT (62) and rCAT (63).
AOO was in all but a case calculated from observation data. C. arabica it was the exception, as the evaluation used the planned niche (37) rather than AOO. We expect the AOO values to be accurate at lower thresholds (eg <10 km2); it is unlikely that those for larger species are accurate, since the basic data are largely subject to species.
Evaluation of the risk of extinction (application of the categories and criteria of the IUCN red list)
Extinction risk assessments have been completed for all 124 coffee species, following the IUCN Red List categories and criteria (33). The assessments have been documented and managed in the IUCN Species Information Service (SIS) through their web application (64), following the explicit documentation and consistency standards (33, 65). After applying the criteria, each coffee species was assigned to one of the six categories of the IUCN endangering risk assessment system: (i) threatened: CR, EN or VU; (ii) not threatened: NT or LC; or (iii) DD. No species has been included in the EX, Extinct in the Wild (EW) or Unrated (NE) categories. Species with pre-existing IUCN extinction risk assessments that did not require updating were maintained for our analyzes (only two species: Coffea schliebenii is Coffea ligustroides). The reports for each species were generated via SIS (64), reviewed internally by the authors, and then externally by national / regional / group specialists, in groups, by region (West Africa, East Africa, Madagascar, Mascarene Islands and Asia / Australasia) or group, as part of the formal IUCN system revision. Dati dell'etichetta dei campioni di erbario, osservazioni sul campo (1997-2017) e fonti di letteratura (comprese le informazioni basate sul web) sono stati utilizzati come supporto aggiuntivo basato sull'evidenza per l'applicazione delle Categorie e dei criteri della lista rossa IUCN (35), ad esempio, per comprendere le minacce, il declino della popolazione, la qualità e l'idoneità dell'habitat. Immagini satellitari visualizzate tramite Google Earth Pro (66) è stato utilizzato per valutare ulteriormente lo stato dell'habitat (ad esempio, la deforestazione) e le minacce visibili dallo spazio (ad esempio, lo sviluppo agricolo e minerario). Le immagini storiche sono state accessibili in Google Earth utilizzando la funzione di immagini storiche e lo strumento di scorrimento temporale per spostarsi tra le date di acquisizione delle immagini satellitari. Per le località di specie selvatiche di caffè, l'intervallo di date più comune è stato dai primi anni 1980 al 2016, anche se le date di acquisizione per una singola scena possono risalire alla metà del 20 ° secolo (fotografia aerea).
Mappatura e analisi statistica
Le metriche di valutazione del rischio di estinzione dell'IUCN sono state esportate dal SIS di IUCN (64) e utilizzato come base per la mappatura e l'analisi statistica. Per mappare le specie di caffè a livello di paese, i dati delle specie dalla World Checklist delle famiglie di piante selezionate (67) sono stati abbinati alla geografia di livello 3 dello schema geografico del gruppo di lavoro dei database tassativi (TDWG) (68). Il livello 3 del TDWG denota un "paese botanico", in cui la maggior parte delle regioni sono suddivise in unità generalmente equivalenti a un paese politico, ma i grandi paesi possono essere divisi o le aree periferiche omesse. Questi risultati hanno fornito totali e percentuali di specie rispetto alla categoria di valutazione del rischio di estinzione (CR, EN, VU, NT, LC e DD) per ciascun paese. I dati sono stati visualizzati in ArcGIS 10.5 (69) utilizzando la proiezione Winkel I orientata attorno al 45 ° meridiano orientale (attraverso il Madagascar). I colori della mappa per la Fig. 1 e le figg. S1 e S2 sono derivati dalla versione 2 di ColorBrewer (70) per evidenziare la rappresentazione del colore (ad esempio, consentire la differenziazione delle classi e la riproducibilità in stampa e online).
Costruzione di gruppi prioritari CWR
Una definizione ampiamente utilizzata di CWR è "un taxon di piante selvatiche che ha un uso indiretto derivato dalla sua relazione genetica relativamente stretta con una coltura" e "questa relazione è definita in termini di CWR appartenenti a Gene Pools 1 o 2, o Taxon Groups Da 1 a 4 del raccolto "(71). Assegnare una specie a un pool genetico si basa sulla presenza di informazioni sulla diversità genetica e / o sui dati di impollinazione incrociata, mentre l'assegnazione a un gruppo di taxon richiede il riferimento a una classificazione tassonomica. L'approccio del pool genetico di Harlan e de Wet (72) possono essere riassunti come segue: pool genico primario (GP-1), all'interno del quale GP-1A sono le forme coltivate e GP-1B sono le forme selvatiche o erbacee del raccolto; il pool genico secondario (GP-2) comprende le coenospecie (specie meno strettamente correlate) da cui è possibile il trasferimento genico alla coltura ma difficile utilizzando le tecniche di allevamento convenzionali; e il pool genico terziario (GP-3) include le specie da cui il trasferimento genico alla coltura è impossibile o, se possibile, richiede tecniche sofisticate, come il salvataggio embrionale, la fusione somatica o l'ingegneria genetica. Maxted et al. (71) ha sottolineato la difficoltà di applicare una classificazione del pool genico (72) e, in assenza dei dati richiesti, ha proposto il concetto di gruppo taxon, basato sulla gerarchia tassonomica (71): gruppo di taxon 1a (la coltura), gruppo di taxon 1b (la stessa specie della coltura), gruppo di taxon 2 (stessa serie o sezione della coltura), gruppo di taxon 3 (lo stesso sottogenere del raccolto), gruppo di taxon 4 (stesso genere), e taxon gruppo 5 (la stessa tribù ma genere diverso da ritagliare). Sottogenere, sezione e serie sono divisioni tassonomiche gerarchiche di un genere, in ordine di inclusione tassonomica decrescente.
Vi sono ampi dati sulla diversità molecolare per il caffè, sia a livello di specie (4, 24, 32, 73) e a livello di genere (74, 75). Queste opere hanno sfidato la storica circoscrizione tassonomica del genere caffè (Coffea) e le divisioni al suo interno (6, 25), sostituendoli con un sistema stabile e praticabile per dividere il genere in gruppi di specie correlate (clade), che possono essere utilizzati per assistere la costruzione di gruppi prioritari della CWR. There are also several studies reporting the results of crossing experiments between coffee species and taxa (27, 76–78). Crossing refers to conventional breeding methods, although we recognize that more sophisticated methods are available (e.g., embryo rescue, somatic fusion, or genetic engineering) and that this is a developing area of research. In general, coffee suffers from low postcrossing fertility (flowers, pollen, and seeds), although pre- and postcrossing chromosome duplication and restoration of fertility via backcrossing can increase and restore fertility, respectively (29, 77).
Using the available data, we constructed a CWR priority group classification system for coffee, based on a combination of the gene pool approach (72), which includes crossing data, and the taxon group method (71), but using molecular systematic data (clades) rather than a formal taxonomy. Our proposed criteria for coffee CWR priority groups are as follows: CWR priority group I (to include the cultivated and wild variants of the main coffee crop species, and hybrid progenitor species), CWR priority group II (to include species closely related to the crop species, from which gene transfer to the crop is proven or assumed, with low to high postcrossing fertility rates), and CWR priority group III[toincludespeciesmoredistantlyrelatedtothecropspecies(withinthegenus[toincludespeciesmoredistantlyrelatedtothecropspecies(withinthegenus[toincludespeciesmoredistantlyrelatedtothecropspecies(withinthegenus[toincludespeciesmoredistantlyrelatedtothecropspecies(withinthegenusCoffea), including species from which gene transfer to the crop is demonstrated or assumed to be difficult or impossible without laboratory procedures, with low (or unknown) postcrossing fertility rates]. Our combined classification system for CWR priority ranking is similar to that proposed by Wiersema et al. (79), both being based on breeding information and relatedness; their terms primary, secondary, and tertiary overlap with our CWR priority groups I, II, and III, respectively. Our overall approach differs because we use phylogenetic data (clades) rather than taxonomic information (a classification system), and our CWR priority group I diverges from the primary status category (79) by including only the main crop species and their progenitors.
Gap analysis for germplasm collections (ex situ) and protected areas (in situ)
To ascertain whether a coffee species is held within a coffee germplasm collection (ex situ), we surveyed literature sources (32, 42, 43, 73, 80–86) and herbarium collections [which often house herbarium vouchers for germplasm collections (for recording and verification purposes)]. Site visits were made to the living collections at the Kianjavato Coffee Research Station in Madagascar (in 2000, 2006, and 2011) and to the L’Institut de recherche pour le développement (IRD), Montpellier, France (in 2001). For our first-pass assessment of in situ occurrences, we used the coffee data collated within SIS (64). We then compared ground point data for all species, against the World Database on Protected Areas (WDPA), accessed via Protected Planet (87) and GeoCat (62).
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