Expression and trans-specific polymorphism of self-incompatibility RNases in Coffea (Rubiaceae)

Self-incompatibility (SI) is widespread in the angiosperms, but identifying the biochemical components of SI mechanisms has proven to be difficult in most lineages. Coffea (coffee; Rubiaceae) is a genus of old-world tropical understory trees in which the vast majority of diploid species utilize a mechanism of gametophytic self-incompatibility (GSI). The S-RNase GSI system was one of the first SI mechanisms to be biochemically characterized, and likely represents the ancestral Eudicot condition as evidenced by its functional characterization in both asterid (Solanaceae, Plantaginaceae) and rosid (Rosaceae) lineages. The S-RNase GSI mechanism employs the activity of class III RNase T2 proteins to terminate the growth of "self" pollen tubes. Here, we investigate the mechanism of Coffea GSI and specifically examine the potential for homology to S-RNase GSI by sequencing class III RNase T2 genes in populations of 14 African and Madagascan Coffea species and the closely related self-compatible species Psilanthus ebracteolatus. Phylogenetic analyses of these sequences aligned to a diverse sample of plant RNase T2 genes show that the Coffea genome contains at least three class III RNase T2 genes. Patterns of tissue-specific gene expression identify one of these RNase T2 genes as the putative Coffea S-RNase gene. We show that populations of SI Coffea are remarkably polymorphic for putative S-RNase alleles, and exhibit a persistent pattern of trans-specific polymorphism characteristic of all S-RNase genes previously isolated from GSI Eudicot lineages. We thus conclude that Coffea GSI is most likely homologous to the classic Eudicot S-RNase system, which was retained since the divergence of the Rubiaceae lineage from an ancient SI Eudicot ancestor, nearly 90 million years ago.United States National Science Foundation [0849186]; Society of Systematic Biologists; American Society of Plant Taxonomists; Duke University Graduate Schoolinfo:eu-repo/semantics/publishedVersio

Molecular Genetic Diversity Study of Forest Coffee Tree (Coffea arabica L.) Populations in Ethiopia: Implications for Conservation and Breeding

Coffee provides one of the most widely drunk beverages in the world, and is a very important source of foreign exchange income for many countries. Coffea arabica, which contributes over 70 percent of the world's coffee productions, is characterized by a low genetic diversity, attributed to its allopolyploidy origin, reproductive biology and evolution. C. arabica has originated in the southwest rain forests of Ethiopia, where it is grown under four different systems, namely forest coffee, small holders coffee, semi plantation coffee and plantation coffee. Genetic diversity of the forest coffee (C. arabica) gene pool in Ethiopia is being lost at an alarming rate because of habitat destruction (deforestation), competition from other cash crops and replacement by invariable disease resistant coffee cultivars. This study focused on molecular genetic diversity study of forest coffee populations in Ethiopia using PCR based DNA markers such as random amplified polymorphic DNA (RAPD), inverse sequence-tagged repeat (ISTR), inter-simple sequence repeats (ISSR) and simple sequence repeat (SSR) or microsatellites. The objectives of the study are to estimate the extent and distribution of molecular genetic diversity of forest coffee and to design conservation strategies for it’s sustainable use in future coffee breeding. In this study, considerable samples of forest coffee collected from four coffee growing regions (provinces) of Ethiopia were analysed. The results indicate that moderate genetic diversity exists within and among few forest coffee populations, which need due attention from a conservation and breeding point of view. The cluster analysis revealed that most of the samples from the same region (province) were grouped together which could be attributed to presence of substantial gene flow between adjacent populations in each region in the form of young coffee plants through transplantation by man. In addition wild animals such as monkeys also play a significant role in coffee trees gene flow between adjacent populations. The overall variation of the forest coffee is found to reside in few populations from each region. Therefore, considering few populations from each region for either in situ or ex situ conservation may preserve most of the variation within the species. For instance, Welega-2, Ilubabor-2, Jima-2 and Bench Maji-2 populations should be given higher priority. In addition, some populations or genotypes have displayed unique amplification profiles particularly for RAPD and ISTR markers. Whether these unique bands are linked to any of the important agronomic traits and serve in marker assisted selections in future coffee breeding requires further investigations

Evaluation of Somatic Embryogenesis Ability in Robusta Coffee (Coffea Canephora Pierre)

Embriogenesis somatik diharapkan sebagai metode perbanyakan tanaman yang sangat efektif pada kopi. Evaluasi dua jenis proses embriogenesis somatik, yaitu proses langsung dan tidak langsung akan bermanfaat untuk menggambarkan kemampuan proliferasi sel. Penelitian untuk mengevaluasi embriogenesis somatik kopi Robusta (Coffea canephora) yang mempunyai tingkat keragaman genetik tinggi telah dilakukan di Nestlé R&D Centre Tours, Perancis. Bahan tanam menggunakan kopi Robusta koleksi Nestle Perancis dan tiga klon koleksi Pusat Penelitian Kopi dan Kakao Indonesia (Puslitkoka). Tiga aspek, yaitu proses embriogenesis, keragaman embriogenesis dan kemantapan embriogenesis dievaluasi dalam penelitian ini. Hasil penelitian menunjukkan bahwa baik embriogenesis somatik langsung maupun tidak langsung dapat diamati. Penelitian ini menunjukkan bahwa kedua proses embriogenesis somatik tersebut merupakan dua mekanisme yang berbeda. Dalam penelitian ini ditunjukkan bahwa kemampuan embriognesis somatik tergantung pada genotipe, baik antar maupun di dalam kelompok genetik kopi Robusta, yaitu Congolese,Guinean dan Conillon. Lebih lanjut diketahui bahwa kedua proses embriogenesis somatik tersebut stabil terhadap indukan sebagai sumber eksplan. Kemampuan embriogenesis somatik tidak langsung ketiga klon Puslitkoka (BP409, BP961 dan Q121) sangat beragam, sehingga memberikan harapan adanya pola segregasi yang baik berdasarkan kemampuan embriogenesis somatik tidak langsung pada populasi yang dibuat dari silangan klon tersebut

Coffea arabica und C. canephora – Kaffeestrauch (Rubiaceae)

Der Kaffeestrauch gehört zu der großen, weltweit verbreiteten Pflanzenfamilie der Rubiaceae (Rötegewächse) und hier zur Gattung Coffea. Die am häufigsten kultivierten Arten sind C. arabica (Arabica-Kaffee), ursprünglich aus Äthiopien und Sudan, und C. canephora (Robusta-Kaffee), der ursprünglich aus West- und Zentral-Afrika, Sudan, Uganda und Angola stammt

Confirmation of Transgenic Robusta Coffee (Coffea Canephora) Transformed by Chitinase-encoding Gene and Its Propagation Through Somatic Embryogenesis

Genetic engineering of Robusta coffee resistant to fungal diseases might be done by introducing a chitinase-encoding gene into genome of this plant. This research was aimed to confirm transgenic plant of BP 308 clone Robusta coffee transformed by chi gene and to evaluate its ability for the somatic embryogenesis. Confirmation of transgenic was carried out by analysis the presence of NPTII gene as a selectable marker for Canamysin resistant using PCR technique. The somatic embryo initiation and reproduction were evaluated in 11 plant accessions. Three kinds of sucrose concentration, 20%, 30% and 40% were applied in initiation stage of somatic embryo germination. The suitability of 4 medium, namely M1 (without addition by liquid medium), M2 (addition by liquid medium contained 0.25 mg/l kinetin), M3 (addition by liquid medium contained 0.25 mg/l IAA) and M4 (addition by liquid medium contained 0.25 mg/l GA3 ) was evaluated for somatic embryo maturation. The result showed that 8 out of 10 plant accessions tested were transgenic and they could be propagated through somatic embryogenesis. The ability of transgenic plant for somatic embryo initiation, reproduction and regeneration were similar with that of nontransgenic one. Germination of somatic embryo could be improved by using 40% sucrose. Maturation of somatic embryo could be improved by addition of fresh liquid medium on the ancient gelled medium that used for somatic embryos reproduction. The best result was obtained on addition of fresh medium contained 0.25 mg/l GA 3 in which 65% of the somatic embryos developed to pre-germinate somatic embryo

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma's D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors