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Genetic Characterization of Coffea arabica ‘Geisha' from Panama and Ethiopia

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Coffee is an important agricultural commodity contributing significantly to the economies of many developing countries. Of the 125 species of Coffea, the two main commercial species used in the production of the beverage are C. arabica L. (Arabica coffee) and C. canephora A. Froehner (robusta coffee). Arabica coffee accounts for about 70% of the total coffee production. The Geisha variety (C. arabica var. Geisha) was first discovered in the forested mountains of western Ethiopia in 1930s in the provinces of Maji and Goldija. It was first brought to Panama from Costa Rica in 1963 after journeying through Tanzania, Kenya and Costa Rica. Displaying unique flavor profiles, larger bean size and other phenotypic differences from other C. arabica varieties, this variety also exhibits resistance to coffee leaf rust (Hemileia vastatrix Berkeley and Broome). The specific research objective of this study was to understand the genetic differences between the Geisha coffee grown in Panama and that from the original forests in Ethiopia using Inter Simple Sequence Repeats (ISSRs).
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Thesis
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The genus Coffea L. (Rubiaceae) consists of two economically important species for the production of the beverage coffee: Coffea arabica and C. canephora. Madagascar has 59 described species of which 42 are listed as Critically Endangered, Endangered or Vulnerable by criteria of the Red List Category system of the World Conservation Union (IUCN). The National Center of Applied Research and Rural Development (FOFIFA), the main agricultural research agency in Madagascar, manages and operates the Kianjavato Coffee Research Station which has a vast ex situ collection of various Madagascan coffee species. In an attempt to understand the genetic diversity of Madagascan coffee species, this study was undertaken using the collections maintained at the Kianjavato Coffee Research Station‟s ex situ field genebank and extant, natural in situ populations. As part of my dissertation, I studied four species: C. kianjavatensis, C. montis-sacri, C. vatovavyensis, and C. commersoniana. Parentage analysis of ex situ propagated offspring of C. kianjavatensis and C. montis-sacri was performed to understand if outcrossing with other Coffea species maintained in the field genebank is compromising the genetic integrity of the collection. I found the overall genetic diversity of wild Madagascan coffee species to be similar to or even higher than other cultivated and wild Coffea species. For the three species endemic to the Kianjavato region, C. kianjavatensis, C. montis-sacri, and C. vatovavyensis, higher genetic diversity was observed in the ex situ populations than in in situ populations. For C. commersoniana, an endemic species of the littoral forests of southeastern Madagascar and soon to be impacted by mining activities in that region, the in situ populations showed higher genetic diversity than the ex situ population. Parentage analysis of seed-propagated offspring of C. kianjavatensis and C. montis-sacri revealed that cross contamination with pollen from other Coffea species in the ex situ field genebank is occurring. These results have significant implications for the conservation management of wild Coffea species. The higher genetic diversity of the ex situ collections which were originally made in the early 1960‟s could be indicative of a sampling of what was present at that time and as a result of collection from multiple origins. It could also be a result of cross contamination from pollen transfer from another species resulting in hybridization when seedlings are used in replanting lost plant collections. The genetic partitioning among the two in situ populations of C. commersoniana was high enough to warrant that these two populations be kept separate for restoration purposes. Based on these findings, recommendations for conservation management are made. This dissertation research is the first study to characterize the genetic diversity of Madagascan Coffea held at the ex situ field genebank and comparing this with extant wild populations. The parentage study is also the first to quantify the extent of cross-species contamination of collections held in this or any other Coffea genebank. This study has fundamental implications for the future of ex situ and in situ conservation of Coffea and provides a framework for future conservation research for Madagascan and other Coffea species.
Chapter
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The taxonomic position of some Coffea species is controversial. Many of the known species have been discovered along harvests made in the tropical forests of Africa since 1940. The literature suggests that the true Coffea species are those from central and equatorial regions of Africa, including Madagascar and the neighbouring islands close to Indian Ocean. The other species from Asian regions, previously described as being part of the genus Coffea, are no longer considered true Coffea species. Chevalier (1947) in his classification, considered 65 species from which 24 belonged to other genera. Cramer (1957), however, suggested the existence of at least 100 species. Purseglove (1968), cited by Wrigley (1988) referred to 50 species of the Coffea genus, from which 33 were from Tropical Africa, 14 from Madagascar and 3 from Mauritius and Reunion Islands. As these species are studied, divergences are noticed as for the number of true species from Madagascar. New Coffea species were described by Bridson (1982), especially in Eastern parts of Africa, although some of them have not been thoroughly characterized. Leroy (1980) recognized three genera of coffee plants: Coffea, Psilanthus and Nostolachma. The latter is restricted to Asia and Indonesia. He also distinguished three subgenera of Coffea and two of Psilanthus.
Article
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Inter-simple sequence repeat (ISSR) markers were used to evaluate genetic divergence among eight Coffea species and to identify the parentage of six interspecific hybrids. A total of 14 primers which contained different simple sequence repeats (SSR) were used as single primers or combined in pairs and tested for PCR amplifications. Two hundred and thirty highly reproducible fragments were amplified, which were then used to estimate the genetic similarity and to cluster the Coffea species and hybrids. High levels of interspecific genetic variation were revealed. The dinucleotide motif (GA)9T combined with other di- tri- and tetra-nucleotides produced a greater number of DNA fragments, mostly polymorphics, suggesting a high frequency of the poly GA microsatellite motifs in the Coffea genomes. The genetic similarity ranged from 0.25 between C. racemosa and C. liberica var. dewevrei to 0.86 between C. arabica var. arabica and Hybrid N. 2. The C. arabica species shared most of its markers with five of the six hybrids suggesting that it is the most likely candidate as one of the progenitors of those hybrids. These results revealed that ISSR markers could be efficiently used for genetic differentiation of the Coffea species and to identify the parentage of Coffea interspecific hybrids.
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The International Coffee Agreement 1994Conclusions Statistical InformationReference
Chapter
The cultivated coffee Coffea arabica L. (2n=4x=44) is an allotetraploid species native to Africa, containing two diploid genomes that originated from two different diploid wild ancestors (2n=2x=22), C. canephora and C. eugenioides or ecotypes related to those species (Lashermes et al., 1999). It is the only polyploid species in the genus and is self-fertile while other Coffea species are diploid and generally self-incompatible. C. arabica is characterised by a very low genetic diversity (Fig. 1), which is attributable to its origin, reproductive biology, and evolution. In addition, most cultivars are derived from the few trees which survived various efforts to spread arabica growing world-wide (Van der Vossen, 1985; Lashermes et al., 1996a). It is believed that the encountered agro-morphological variation which gave rise to so many named varieties, results from few major-gene spontaneous mutations conditioning plant, fruit and seed characters (Carvalho, 1988). The cultivars, therefore, present a homogeneous agronomic behaviour characterised by a high susceptibility to many pests and diseases, and very low adaptability (Bertrand et al., 1999).
Article
GENALEX is a user-friendly cross-platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data. Allele frequency-based analyses include heterozygosity, F statistics, Nei's genetic distance, population assignment, probabilities of identity and pairwise relatedness. Distance-based calculations include AMOVA, principal coordinates analysis (PCA), Mantel tests, multivariate and 2D spatial autocorrelation and TWOGENER. More than 20 different graphs summarize data and aid exploration. Sequence and genotype data can be imported from automated sequencers, and exported to other software. Initially designed as tool for teaching, GENALEX 6 now offers features for researchers as well. Documentation and the program are available at http://www.anu.edu.au/BoZo/GenAlEx/