Development of microsatellite markers of vandaceous orchids for species and variety identification

Genetic diversity based on SSR markers of 30 Aeridinae sub-tribe orchid genetic resources of Indonesian Ornamental Crop Research Institute, Cianjur, Indonesia

“…The number of amplified DNA fragments per primer ranged from five (VMJ09 primer pairs) to 33 (MOK26) (Table 2) and with an average number of 14.1 amplified DNA fragments. The number of amplified DNA fragments obtained using the evaluated SSR primer pairs in this study is higher than those reported by Lim et al (2007), Phuekvilai et al (2009), andPeyachoknagul et al (2014).…”

“…A total of 17 SSR primer pairs, previously used for Aeridinae genetic characterization (Lim et al 2007, Phuekhvilai et al 2009, Peyachoknagul et al 2014 were used for genotyping the IOCRI's Aeridinae accessions (Table 2). The final volume of the PCR reaction was 25 µL, consisting of DNA template (2 µL), DreamTaq PCR master mix (12.5 µL) (Thermo Scientific, USA), forward and reverse primer (1 µL of 0.4 M), and 8.5 µL ddH2O.…”

“…The final volume of the PCR reaction was 25 µL, consisting of DNA template (2 µL), DreamTaq PCR master mix (12.5 µL) (Thermo Scientific, USA), forward and reverse primer (1 µL of 0.4 M), and 8.5 µL ddH2O. The PCR amplification was carried out in a Gradient PCR Thermal Cycler (SensoQuest, Germany) using the following settings 94ºC for 3 minutes of initial denaturation, 35 cycles of denaturation at 94ºC for 30 seconds, annealing at appropriate temperatures (depending on the primers used) for 1 minute, and primer extension at 72ºC for 30 seconds, followed by a final primer extension cycle at 72ºC for 5 minutes (Peyachoknagul et al 2014). The PCR amplified DNA products were fractionated using the Automated Parallel Capillary Electrophoresis (CE) System (QIAxcel Advanced, Qiagen, Germany) Fragment Analyzer.…”

“…However, molecular markers used to evaluate the genetic relationship and diversity of the Aeridinae subtribe have been limited (Lim et al 2007, Phuekhvilai et al 2009, Hidayat et al 2012, Peyachoknagul et al 2014, Zou et al 2015. The SSR markers have been used in orchid research for the characterization of microsatellites in Mokara and the intergeneric hybrid from 3 genera (Vanda, Ascocentrum, and Arachnis); genetic diversity of endangered Neofinetia falcata; genetic diversity of the Cymbidium goeringii; and genetic diversity of the endangered orchid Pelatantheria scolopendrifolia (Peyachoknagul et al 2014;Han et al 2018;Noh et al 2020;Yun et al 2020). Research conducted by Hidayat et al (2012) used DNA sequences of ITS region of nrDNA and matK of cpDNA to determine the phylogenetic relationship of the subtribe Aeridinae.…”

Identification of Vietnamese native Dendrobium species based on ribosomal DNA internal transcribed spacer sequence

“…The advantages of molecular techniques are capable to identify the diversity at molecular level, providing the basis for assessing the conservation value of species, identification of cultivars, selection of parents for breeding, and conservation of genetic resources such as: Restriction Fragment Length Polymorphism (RFLP); Amplified Fragment Length Polymorphism (AFLP); Random Amplified Polymorphic DNA (RAPD); Microsatellite or Simple Sequence Repeats (SSR); Inter-simple sequence repeats (ISSRs); and Internal transcribed spacer (ITS) sequencing. The molecular markers have been widely used for the identification of numberous orchids species: Dendro-Identification of Vietnamese native Dendrobium species … 3 bium [4], Cymbidium [5], Vanda [6], Paphiopedilum [7], Phalaenopsis [8]. Particularly, ITS technique has been frequently used to identify Orchidaceae using biological molecular markers [9].…”