scholarly journals Genetic diversity of Coffea canephora Pierre ex A. Froehner in Temanggung District, Indonesia based on molecular marker RAPD

2021 ◽  
Vol 22 (11) ◽  
Author(s):  
Intan Widya Pangestika ◽  
Ari Susilowati ◽  
Edi Purwanto
Keyword(s):  
Genetic Diversity ◽  
Molecular Marker ◽  
Species Identification ◽  
Morphological Traits ◽  
Coffea Canephora ◽  
Global Market ◽  
Trunk Diameter ◽  
Robusta Coffee ◽  
Coffee Yield ◽  
Biochemical Compositions

Abstract. Authors. 2021. Genetic diversity of Coffea canephora Pierre ex A. Froehner in Temanggung District, Indonesia based on molecular marker RAPD. Biodiversitas 22: 4775-4783. Temanggung District in Central Java Province, Indonesia is one of robusta coffee production centers. The condition of coffee plantations in Temanggung shows variations in some morphological traits. Variations in coffee phenotypes are considered less profitable for farmers because they produce yields of undesirable quality in the global market. This study aimed to evaluate the genetic diversity of robusta coffee in Temanggung. The coffee plants were derived from six villages located at two levels of altitude. The morphological traits were observed from canopy width, trunk diameter, plant height, cherry volume, and bean volume, while the biochemical compositions were determined by caffeine content and brew’s pH value. The molecular assays were performed using PCR-RAPD with ten primers and species identification was based on the ITS rDNA. Our finding showed a variation in all morphological characters and biochemical compositions based on the LSD test 5%. The molecular marker RAPD revealed the genetic diversity by showing the DNA polymorphism levels of 95%, with the genetic similarity coefficient ranged from 0.35 to 0.86. The species identification also demonstrated that our robusta coffee was 97.11-99.70% similar to robusta coffee MK615737.1 from Philippines and robusta coffee DQ153593.1 from Cameroon. Thus, genetic diversity on six populations of robusta coffee was found, along with its variations on phenotypes which might lead the coffee yield quality to become uneven.

scholarly journals Genetic diversity of native and cultivated Ugandan Robusta coffee (Coffea canephora Pierre ex A. Froehner): Climate influences, breeding potential and diversity conservation

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0245965
Author(s):  
Catherine Kiwuka ◽  
Eva Goudsmit ◽  
Rémi Tournebize ◽  
Sinara Oliveira de Aquino ◽  
Jacob C. Douma ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Allelic Variation ◽  
Coffea Canephora ◽  
Ex Situ ◽  
Negative Effects ◽  
Robusta Coffee ◽  
Genetic Diversity And Structure ◽  
Adaptive Diversity ◽  
Southern Central

Wild genetic resources and their ability to adapt to environmental change are critically important in light of the projected climate change, while constituting the foundation of agricultural sustainability. To address the expected negative effects of climate change on Robusta coffee trees (Coffea canephora), collecting missions were conducted to explore its current native distribution in Uganda over a broad climatic range. Wild material from seven forests could thus be collected. We used 19 microsatellite (SSR) markers to assess genetic diversity and structure of this material as well as material from two ex-situ collections and a feral population. The Ugandan C. canephora diversity was then positioned relative to the species’ global diversity structure. Twenty-two climatic variables were used to explore variations in climatic zones across the sampled forests. Overall, Uganda’s native C. canephora diversity differs from other known genetic groups of this species. In northwestern (NW) Uganda, four distinct genetic clusters were distinguished being from Zoka, Budongo, Itwara and Kibale forests A large southern-central (SC) cluster included Malabigambo, Mabira, and Kalangala forest accessions, as well as feral and cultivated accessions, suggesting similarity in genetic origin and strong gene flow between wild and cultivated compartments. We also confirmed the introduction of Congolese varieties into the SC region where most Robusta coffee production takes place. Identified populations occurred in divergent environmental conditions and 12 environmental variables significantly explained 16.3% of the total allelic variation across populations. The substantial genetic variation within and between Ugandan populations with different climatic envelopes might contain adaptive diversity to cope with climate change. The accessions that we collected have substantially enriched the diversity hosted in the Ugandan collections and thus contribute to ex situ conservation of this vital genetic resource. However, there is an urgent need to develop strategies to enhance complementary in-situ conservation of Coffea canephora in native forests in northwestern Uganda.

Analysis of genetic diversity in Indian robusta coffee genepool (Coffea canephora) in comparison with a representative core collection using SSRs and AFLPs

2005 ◽  
Vol 52 (3) ◽  
pp. 333-343 ◽  
Author(s):  
Nayani Surya Prakash ◽  
Marie-Christine Combes ◽  
Stéphane Dussert ◽  
Somanna Naveen ◽  
Philippe Lashermes
Keyword(s):  
Genetic Diversity ◽  
Core Collection ◽  
Coffea Canephora ◽  
Robusta Coffee

scholarly journals Genetic diversity and variability among pigmented rice germplasm using molecular marker and morphological traits

2020 ◽  
Vol 34 (1) ◽  
pp. 747-762 ◽  
Author(s):  
Hamidah Mohd Sarif ◽  
Mohd Y. Rafii ◽  
Asfaliza Ramli ◽  
Yusuff Oladosu ◽  
Hanafi M. Musa ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Marker ◽  
Morphological Traits ◽  
Pigmented Rice ◽  
Rice Germplasm

scholarly journals Genetic diversity of wild and cultivated Coffea canephora in northeastern DR Congo and the implications for conservation.

2021 ◽  
Author(s):  
Samuel Vanden Abeele ◽  
Steven B. Janssens ◽  
Justin Asimonyio Anio ◽  
Yves Bawin ◽  
Jonas Depecker ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Coffea Canephora ◽  
Congo Basin ◽  
Ex Situ ◽  
Gene Pools ◽  
Wild Populations ◽  
Genetic Composition ◽  
Robusta Coffee ◽  
Republic Of The Congo

Premise: Many cultivated coffee varieties descend from Coffea canephora, commonly known as Robusta coffee. The Congo Basin has a century long history of Robusta coffee cultivation and breeding, and is hypothesized to be the region of origin of many of the cultivated Robusta varieties. Since little is known about the genetic composition of C. canephora in this region, we assessed the genetic diversity of wild and cultivated C. canephora shrubs in the Democratic Republic of the Congo. Methods: Using 18 microsatellite markers, we studied the genetic composition of wild and backyard-grown C. canephora shrubs in the Tshopo and Ituri provinces, and from the INERA Yangambi Coffee Collection. We assessed genetic clustering patterns, genetic diversity, and genetic differentiation between populations. Key results: Genetic differentiation was relatively strong between wild and cultivated C. canephora shrubs, and both gene pools harbored multiple unique alleles. Strong genetic differentiation was also observed between wild populations. The level of genetic diversity in wild populations was similar to that of the INERA Yangambi Coffee Collection, but local wild genotypes were mostly missing from that collection. Shrubs grown in the backyards were genetically similar to the breeding material from INERA Yangambi. Conclusions: Most C. canephora that is grown in local backyards originated from INERA breeding programs, while a few shrubs were obtained directly from surrounding forests. The INERA Yangambi Coffee Collection could benefit from an enrichment with local wild genotypes, to increase the genetic resources available for breeding purposes, as well as to support ex situ conservation.

scholarly journals Genetic Variability of 15 Robusta Coffee Genotypes Selected by Farmer Based on SSRs Markers

2014 ◽  
Vol 1 (2) ◽  
pp. 87
Author(s):  
Syafaruddin Syafaruddin ◽  
Enny Randriani ◽  
Dani Dani ◽  
Indah Sulistyorini ◽  
M. B. Pabendon
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Coffea Canephora ◽  
Coffee Plantations ◽  
Robusta Coffee ◽  
Allele Number ◽  
Grafting Technique ◽  
Ssrs Markers ◽  
Biology Laboratory ◽  
Research Institute

<p>Robusta coffee (Coffea canephora) has been grown widely in Indonesia, especially in Bengkulu Province. For the last few decades, some farmers have been selected and developed several Robusta clones through plagiotropic shoot grafting technique to replace earlier coffee populations which were derived from seed. Hence, it would reduce the genetic diversity of Robusta coffee at farmer’s field. To understand the genetic variability among 15 Robusta coffee genotypes selected by farmer, it is important to perform molecular analysis. Leaf samples of 15 Robusta coffee genotypes selected by farmer were collected from smallholder Robusta coffee plantations in Bengkulu Province. Genetic diversity analysis was conducted in the Germplasm, Breeding, and Biotechnology Laboratory of Indonesian Industrial and Beverage Crops Research Institute (IIBCRI), and Molecular Biology Laboratory, Indonesian Cereals Research Institute (ICERI). DNA samples were amplified using 34 SSRs markers. The result showed that 23 out of 34 SSRs markers had high polymorphism levels. Allele number per locus ranged from 2-8 with an average of 4 alleles per locus. Dendrogram analysis based on genetic similarity was obtained with score of about 0,44-0,79, and r score = 0,92 (good fit). Based on cluster analysis as well as PCoA analysis, there are three distinct groups of genotypes. Those three groups can be distinguished by specific character of leaf morphotype. Nevertheless, the majority of genotypes were clustered together into the single group. This indicates narrow genetic diversity among Robusta genotypes that selected by farmer.</p><p>Kopi Robusta telah dikembangkan secara luas di Indonesia, khususnya di Provinsi Bengkulu. Beberapa dekade terakhir sebagian petani telah menyeleksi dan mengembangkan beberapa genotipe dengan teknik sambung tunas plagiotrop untuk merehabilitasi populasi kopi Robusta asal biji. Oleh sebab itu, terdapat peluang terjadinya penurunan keragaman genetik kopi Robusta di lahan petani. Analisis molekuler perlu dilakukan untuk mengevaluasi keragaman genetik antar 15 genotipe kopi Robusta hasil seleksi petani. Kegiatan analisis keragaman genetik dilaksanakan di Laboratorium Plasma Nutfah, Pemuliaan, dan Bioteknologi, Balai Penelitian Tanaman Industri dan Penyegar (Balittri), Sukabumi dan Laboratorium Biologi Molekuler, Balai Penelitian Tanaman Serealia (Balitsereal), Maros. DNA diamplifikasi dengan menggunakan 34 marka SSR. Hasil penelitian menunjukkan bahwa 23 dari 34 marka SSR yang digunakan mampu menghasilkan tingkat polimorfisme yang tinggi. Jumlah alel berada pada kisaran 2-8 alel per lokus dengan rata-rata 4 alel per lokus SSR. Analisis dendrogram berdasarkan kemiripan genetik diperoleh dengan skor sekitar 0,44-0,79 dan skor r = 0,92 (good fit). Berdasarkan hasil analisis gerombol dan analisis komponen utama diketahui bahwa terdapat tiga kelompok genotipe. Masing-masing kelompok dapat dibedakan berdasarkan karakter morfotipe daun. Meskipun demikian, sebagian besar genotipe diklasifikasikan ke dalam satu kelompok. Ini menandakan bahwa keragaman genetik klon-klon kopi Robusta hasil seleksi petani cenderung rendah.</p><p>Keywords: Coffea canephora, klon plagiotropik, kehilangan genetik</p>

scholarly journals Keragaman Genetik antar Klon Kopi Robusta Lokal Pagar Alam berdasarkan Analisis Marka SSR

2017 ◽  
Vol 4 (3) ◽  
pp. 133
Author(s):  
Syafaruddin Syafaruddin ◽  
Dani Dani ◽  
Marcia Bunga Pabendon
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Binary Data ◽  
Clonal Selection ◽  
Coffea Canephora ◽  
Robusta Coffee ◽  
Long Period ◽  
Ssr Loci ◽  
Biology Laboratory

<em>Robusta coffee (</em>Coffea canephora <em>var. robusta) is the most extensive developed in Indonesia, including Pagar Alam, South Sumatra. In the last few decades, many farmers in Pagar Alam conducted clonal selection and rehabilitation of Robusta coffee trees that generated indigenous clonal populations. This pattern in the long period can damage important alleles and reduce the genetic diversity of indigenous Robusta coffee in farmland. The research aimed to know the genetic diversity among indigenous Robusta coffee clones developed in Pagar Alam based on SSR markers. The study was conducted at Molecular Biology Laboratory, Cereals Research Institute, Maros, from February to April 2017. Molecular characterization of 19 indigenous Robusta coffee clones was conducted using 33 polymorphic SSR markers. The resulting binary data was then analyzed using PowerMarker program to determine polymorphism value (PIC), number and diversity of alleles, and heterozygosity values. The results showed that 33 polymorphic SSR loci produced 134 alleles with an average of 4.06 alleles/locus, whereas PIC values </em><em>ranged from 0.09</em>–<em>0.77 with an average of 0.48. Of the 33 SSR loci, 19 loci (57.58%) exhibited very informative PIC value (&gt; 0.55). Dendrogram generated using NTSYS program divided 19 indigenous Robusta coffee clones into 4 clusters at 0.53 similarity coefficient. KPA41clone was separated in its own cluster, potentially crossed with other clones. Based on genetic distance values &gt;0.55, could arrange 14 combinations of interclonal crosses that potentially increase the genetic variability of indigenous Robusta coffee from Pagar Alam.</em>

scholarly journals New insights on spatial genetic structure and diversity of Coffea canephora (Rubiaceae) in Upper Guinea based on old herbaria

2020 ◽  
Vol 153 (1) ◽  
pp. 82-100
Author(s):  
Jean-Pierre Labouisse ◽  
Philippe Cubry ◽  
Frédéric Austerlitz ◽  
Ronan Rivallan ◽  
Hong Anh Nguyen
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
Coffea Canephora ◽  
Ex Situ ◽  
Herbarium Specimens ◽  
Robusta Coffee ◽  
Forest Remnants ◽  
History Of ◽  
Genetic Structure And Diversity

Backgrounds and aims – Previous studies showed that robusta coffee (Coffea canephora Pierre ex A.Froehner), one of the two cultivated coffee species worldwide, can be classified in two genetic groups: the Guinean group originating in Upper Guinea and the Congolese group in Lower Guinea and Congolia. Although C. canephora of the Guinean group is an important resource for genetic improvement of robusta coffee, its germplasm is under-represented in ex situ gene banks and its genetic diversity and population structure have not yet been investigated. Methods – To overcome the limitations of living collections, we explored old herbarium specimens collected in Guinea and Côte d’Ivoire and conserved at the Muséum National d’Histoire Naturelle, Paris. First, we reviewed the history of collection missions in both countries and how the C. canephora herbaria from the Muséum were assembled. Then, using 23 nuclear microsatellite markers, factorial and model-based Bayesian analyses, we investigated the genetic diversity of 126 specimens and 36 controls, analysed their distribution among the Congolese and Guinean groups, and estimated admixture proportions for each individual.Key results – For the first time, we detected population genetic structure within the Guinean group of C. canephora. The Guinean genotypes can be assigned to five sub-groups with distinct geographic distribution, especially in Guinea where two sub-groups (Maclaudii and Gamé) are characterized by a low level of admixture due to geographical isolation.Conclusions – We showed how combining a literature review and genetic data from old herbarium specimens can shed light on previous observations made by botanists and guide further actions to better preserve native coffee plants in forest remnants of West Africa.

Sign in / Sign up

Export Citation Format

Share Document