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

Abstract

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.

Genetic diversity among 24 clones of robusta coffee in Lampung based on RAPD markers

“…Since these selected local clones were derived from genetically limited germplasms, they understandably displayed high genetic similarity as shown in our study. Syafaruddin et al (2014) also reported high genetic similarity (60%) of farmerselected Robusta coffee in Bengkulu Province (also in Sumatra island). They did not mention where the Robusta coffee plants in Bengkulu came from, but Kristian (2019) stated that Robusta coffee in Bengkulu was also introduced from Java.…”

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

“…Klon-klon terseleksi tersebut dikembangkan secara luas melalui teknik sambung tunas plagiotrop (tak-ent) dengan batang bawah berupa tanaman kopi Robusta yang sudah berumur tua dan tidak produktif. Hasil analisis keragaman genetik yang telah dilakukan sebelumnya menggunakan penanda molekuler SSR terhadap beberapa klon lokal yang dikembangkan di wilayah Bengkulu menunjukkan keragaman genetik antar klon yang relatif sempit (Syafaruddin, Randriani, Dani, Sulistyorini, & Pabendon, 2014). Hal ini diduga karena klon-klon tersebut merupakan hasil seleksi petani dari populasi sibling yang sama.…”

“…Amplifikasi PCR dilakukan dengan menggunakan 34 marka SSR yang telah digunakan sebelumnya oleh Missio et al (2010) dan Syafaruddin et al (2014) (Tabel 1). Proses amplifikasi dilakukan dengan total volume 10,0 μl, terdiri atas 1,0 μl DNA genomik dengan konsentrasi 10 ng/μl, 0,5 μl primer SSR forward dan reverse (konsentrasi 0,5 μM), 6,25 μl PCR mix yang mengandung 0,2 mM masing-masing dNTP dan 1,5 mM MgCl 2 (KAPA2G Fast ReadyMix), dan 2,25 μl air ultrapure steril.…”

“…Pada tingkat kemiripan genetik 0,53, 19 klon kopi Robusta lokal terbagi menjadi 4 klaster utama, yaitu klaster I (klon KPA23, KPA30, KPA31, KPA34, KPA37, KPA38, KPA39, dan KPA40), klaster II (KPA24, KPA25, KPA26, KPA27, KPA28, KPA29, dan KPA32), klaster III (klon KPA33, KPA35, dan KPA36), dan klaster IV (KPA41). Munculnya klaster dengan anggota tunggal juga ditunjukkan pada hasil analisis keragaman genetik antar klon kopi Robusta lokal Bengkulu yang juga dikembangkan oleh petani menggunakan teknik sambung tunas plagiotrop (Syafaruddin et al, 2014).…”

Superior morphological characteristics of Kobura promising Robusta coffee clones from South Sumatera Province

“…The most widely grown species in Indonesia is Robusta coffee, especially in Bengkulu Province. Robusta coffee was introduced to farmers to replace the Arabica and Liberica species because it has a higher resistance to leaf rust disease and higher yield [4].…”