Investigation of the genetic diversity of jewel orchid in Vietnam using RAPD and ISSR markers

Abstract

Abstract. Tran TKP, Pham MH, Trinh TH, Widiarsih S, Ho VT. 2022. Investigation of the genetic diversity of jewel orchid in Vietnam using RAPD and ISSR markers. Biodiversitas 23: 4816-4825. Jewel orchid is a general name for several genera belonging to the Orchidaceae family, namely Anoectochilus, Doddinia, Goodyera, Ludisia, and Macodes. These plants are generally used as medicinal herbal for common diseases in Vietnam. Due to over-exploitation, the natural resources of jewel orchids are gradually depleted. Therefore, genetic resource research for proper development of this medicinal plant is necessary. This study aimed to investigate the genetic diversity of jewel orchids in Vietnam using RAPD and ISSR markers to provide basic data conservation of genetic resources and the development of this medicinal plant. A total of 20 jewel orchid samples were genetically characterized by using 10 RAPD and 10 ISSR primers. The amplified bands were binary coded and used to construct phylogenetic trees with NTSYSpc 2.1 software. Each RAPD primer produced 5-11 bands with an average of 8.0, and similarity coefficients ranged from 0.52 to 0.81. Each ISSR primer produced 5-10 bands with an average of 7.6, and the similarity coefficients ranged from 0.54 to 0.87. Combined RAPD and ISSR markers produced similarity coefficients ranging from 0.53 to 0.83. Based on the PIC values, the primers used by both markers are highly informative. However, the topology of cluster analysis of 20 jewel orchid accessions does not correspond to the taxa studied. The findings could be potential to employ in future classification, conservation, and development of this plant.

Revealing genetic diversity of wild Phalaenopsis orchids in Thailand through Random Amplified Polymorphic DNA markers

“…Furthermore, genetic relationship evaluation using RAPD markers is in good agreement with pedigree and RFLP data (Babu et al 2021). RAPDs have been successfully applied in genetic relatedness or diversity estimation of several orchids, such as Cymbidium (Obara-Okeyo and Kako 1998), Phalaenopsis (Been et al 2002;Goh et al 2005;Niknejad et al 2009, Mursyidin et al 2022, Vanilla (Besse et al 2004), and jewel orchid (Tran et al 2022).…”

“…In contrast, molecular markers detect varietal differences based on DNA polymorphism and offer informative, abundant, and environment-independent information throughout the genome (Nadeem et al 2018). Among DNA markers used in plant conservation research, random amplified polymorphic DNA (RAPD) has been widely employed to reveal genetic diversity and population structure in Phalaenopsis (Been et al 2002;Goh et al 2005;Mursyidin et al 2022), jewel orchid (Tran et al 2022), and several medicinal plants like Cichorium spinosum (Shidfar et al 2018), edible honeysuckle (Lonicera kamtschatica) (Cehula et al 2019), and Curcuma comosa (Boonsrangsom 2020). RAPD markers are amplification products of anonymous DNA sequences using a single, arbitrary deca-oligonucleotide primer, and thus do not require prior knowledge of DNA sequences.…”

The Jewel Orchids of Crocker Range Park, Sabah, Malaysia: A Review

“…Globally, jewel orchids are categorised as an endangered species. For example, in Vietnam, jewel orchids have been included in the Vietnam Red Book of endangered species (Tran et al, 2022), while Anoectochilus koshunensis is categorised as an endangered species by CITES checklist (https://checklist.cites.org). This situation is alarming as it may lead to the global extinction of jewel orchids, not only in Malaysia.…”

Complete chloroplast genome of the Jewel Orchid, Anoectochilus formosanus (Orchidaceae) and its relatives

“…approach has limitations, particularly when closely related species share similar morphological characteristics (Suetsugu et al, 2022;Tran et al, 2022). Certain orchid species exhibit comparable leaf colors and patterns, creating challenges for differentiation.…”