Short Communication: Genetic variation of Coelogyne pandurate, C. rumphii and their hybrids based on RAPD markers

Hartati, Sri; Muliawati, Endang Setia

doi:10.13057/biodiv/d211033

Cited by 8 publications

(4 citation statements)

References 10 publications

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“…The phylogenetic tree (Figure 3) also showed that all Coelogyne from Indonesia such as C. mayeriana from Kalimantan, C. asperata from West Kalimantan have close evolutionary relationship then followed with C. pandurata from East Kalimantan that classified in the same subclade. This result is in agreement with phenetic taxonomy that has been done previosly in morphology comparison of each species from Indonesia (Hartati et al 2019;Hartati & Muliawati 2020). However, the tree are not representative for the separation of orchids originating from Asia, such as C. fimbriata and C. ovalis which should have close relationship (Jiang et al 2020) but located far apart in the phylogenetic tree constructed with rbcL.…”

Section: Resultssupporting

confidence: 84%

In Silico Approach for DNA Barcoding using Phylogenetic Analysis of Coelogyne spp. based on the matK, rpoC1, rbcL and nrDNA Markers

Pratiwi,

Kinasih,

Meidianing

et al. 2023

J.Tropical Biodiversity Biotechnology

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In silico biology is considered as an effective and applicable approach to initiate various research, such as biodiversity taxonomical conservation. Phylogenetic analysis using in silico taxonomy method for orchid species can provide data on genetic diversity and evolutionary relationships. One particular method that can be used to evaluate specific targets of gene loci in the taxonomic study is DNA barcoding. This research was conducted to determine the specific target locus gene using matK, rbcL, rpoC1, and nrDNA markers for DNA barcoding of the Coelogyne genus with in silico approach using phylogenetic analysis. All marker sequences were collected from the NCBI website and analysed using several softwares and methods, namely Clustal X for sample sequence alignment and MEGA 11 for phylogenetic tree construction and analysis. The results showed that the gene locus in Coelogyne recommended was the nrDNA gene locus. Phylogenetic analysis revealed that the use of the nrDNA gene locus was able to separate 17 Coelogyne species with two outgroup species, namely Cymbidium and Vanilla, then followed with ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) while the other gene loci, namely maturase K (matK) and polymerase beta' subunit (rpoC1) provided a visual phylogenetic tree in which the two outgroup species entered into the same clade as the Coelogyne species. Thus, the results of this study can be used as a reference to support the Coelogyne breeding and conservation program.

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Section: Resultssupporting

confidence: 84%

In Silico Approach for DNA Barcoding using Phylogenetic Analysis of Coelogyne spp. based on the matK, rpoC1, rbcL and nrDNA Markers

Pratiwi,

Kinasih,

Meidianing

et al. 2023

J.Tropical Biodiversity Biotechnology

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“…Further research to determine the molecular characteristics using RAPD (Random Amplified Polymorphic DNA) showed that analysis has successfully detected genetic variation of ♀ C. rumphii, ♂ C. pandurata, and their F1 hybrids. The orchid parents and their F1 hybrid have a similarity range of 16-100 % (Hartati and Muliawati 2020).…”

Section: Morphological Characterization Of Phaius Orchidsmentioning

confidence: 99%

Morphological characteristics of Phaius spp. orchids from Indonesia

et al. 2021

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Abstract. Hartati S, Samanhudi, Manurung IR, Cahyono O. 2021. Morphological characteristics of Phaius spp. orchids from Indonesia. Biodiversitas 22: 1991-1995. Orchid is one of the ornamental plants with great economic value in various communities. Characterization and grouping of several orchid species can be used in breeding efforts to obtain hybrid with the desired traits. This study is aimed to characterize the morphological appearance of Phaius orchids and to cluster the species based on their similarity in morphological characteristics. Five species of Phaius (P. tankervilleae, P. indigoferus, P. montanus, P. amboinensis, and P. callosus) of the collection of the Bogor Botanical Garden were observed based on 30 morphological characters including the characters of stems, pseudobulbs, leaves and flowers. The data obtained were converted into binary data and computed using the Numerical Taxonomy and Multivariate Analysis System (NTSYS) Spc 2.02 program to produce dendrogram. The results show that based on the morphological characterization of the five species of Phaius spp., they have similarities from 63% to 80%. Among the five Phaius species, P. amboinensis, P. tankervilleae, and P. montanus had 80% similarity and can be used as parents for crossing.

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“…The first contained only C. pandurata as the male parent, while the second comprised both C. rumphii as the female parents and all the ten hybrids. This indicated that maternal inheritance in the intergeneric hybridization between both orchid species occurred (Hartati & Muliawati, 2020).…”

Section: Resultsmentioning

confidence: 93%

RAPD Profiles of Rhynchostylis gigantea (Lindl.) Ridl. Collected from Puspa Nirmala Orchids Banyumas, Central Java

Susanto

Romadhoni

Dwiati

2022

molekul

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Rhynchostylis gigantea (Lindl.) Ridl. is an orchid species spread over Southeast Asia countries. This species is very popular among ornamental plant collectors, especially due to its densely pack inflorescences. Hence, it is commercially found in many ornamental plant nursuries, such as Puspa Nirmala Orchids Banyumas, Central Java. Further development of the species should be supported by scientific data, particularly regarding the genetic variation. One of the molecular markers commonly used to study genetic variation is Random Amplified Polymorphic DNA (RAPD). This study aims to assess genetic variation of R. gigantea cultivars of Puspa Nirmala Orchids Banyumas collection by RAPD profiles. Genomic DNAs were extracted from leaf samples of eight R. gigantea individuals, while RAPD markers were amplified using five random primers (OPA-15, OPK-16, OPP-15, OPP-08 and OPO-08). Descriptive analysis was employed on the data obtained. It was revealed that all of the primers resulted in a 100% monomorphism. This indicates an extremely low genetic variation among R. gigantea population of Puspa Nirmala Orchids collection, which is probably due to the same origin from a selected hybrid of the same crosses.

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Short Communication: Genetic variation of Coelogyne pandurate, C. rumphii and their hybrids based on RAPD markers

Cited by 8 publications

References 10 publications

<i>In Silico</i> Approach for DNA Barcoding using Phylogenetic Analysis of <i>Coelogyne</i> spp. based on the <i>mat</i>K, <i>rpo</i>C1, <i>rbc</i>L and nrDNA Markers

<i>In Silico</i> Approach for DNA Barcoding using Phylogenetic Analysis of <i>Coelogyne</i> spp. based on the <i>mat</i>K, <i>rpo</i>C1, <i>rbc</i>L and nrDNA Markers

Morphological characteristics of Phaius spp. orchids from Indonesia

RAPD Profiles of Rhynchostylis gigantea (Lindl.) Ridl. Collected from Puspa Nirmala Orchids Banyumas, Central Java

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