DNA barcoding of Orchidaceae in Korea

Abstract

Species of Orchidaceae are under severe threat of extinction mainly due to overcollection and habitat destruction; accurate identification of orchid species is critical in conservation biology and sustainable utilization of orchids as plant resources. We examined 647 sequences of the cpDNA regions rbcL, matK, atpF-atpH IGS, psbK-psbI IGS and trnH-psbA IGS from 89 orchid species (95 taxa) and four outgroup taxa to develop an efficient DNA barcode for Orchidaceae in Korea. The five cpDNA barcode regions were successfully amplified and sequenced for all chlorophyllous taxa, but the amplification and sequencing of the same regions in achlorophyllous taxa produced variable results. psbK-psbI IGS showed the highest mean interspecific K2P distance (0.1192), followed by matK (0.0803), atpF-atpH IGS (0.0648), trnH-psbA IGS (0.0460) and rbcL (0.0248). The degree of species resolution for individual barcode regions ranged from 60.5% (rbcL) to 83.5% (trnH-psbA IGS). The degree of species resolution was significantly enhanced in multiregion combinations of the five barcode regions. Of the 26 possible combinations of the five regions, six provided the highest degree of species resolution (98.8%). Among these, a combination of atpF-atpH IGS, psbK-psbI IGS and trnH-psbA IGS, which comprises the least number of DNA regions, is the best option for barcoding of the Korean orchid species.

<b>DNA barcode regions for differentiating <i>Cattleya walkeriana</i> and <i>C. loddigesii</i>

“…Although some methods have been proposed for the Orchidaceae, our work showed that it is possible to discriminate between C. walkeriana and C. loddigesii based only on ITS region, but the inclusion of other high variable markers could be valuable to discriminate all of the other species, as found by Kim et al (2014).Therefore, taking into account the current economic importance and conservation status of both species, such region provides a rapid identification method to differentiate the species C. walkeriana and C. loddigesii, with a great power of discrimination and precise identification of these two orchid species.…”

“…These were successfully implemented in barcoding species of the orchid genus Dendrobium. For other genus of Orchidaceae from Korea, Kim et al (2014) used another combination of DNA barcodes, based on four regions combined, and reached a 98.8% species resolution…”

“…However, DNA barcoding in Orchidaceae is very recent. Consequently, several studies have proposed a new system to discriminate between species based on infrageneric taxonomy, within few genus (Kim, Oh, Bhandari, Kim, & Park, 2014;van den Berg, 2014).…”

DNA marker techniques in study and selection of plant

“…Trình tự các chuỗi vùng đệm giữa các gen hay trình tự các chuỗi không mã của các gen hoặc giữa hai gen (trnL (UAA), rbcL-atpB cũng được sử dụng [130,208]. Trình tự các vùng gen rbcL, matK, atpF-atpH IGS, psbK-psbI IGS và trnH-psbA IGS còn được dùng cho mã vạch (barcode) ở các loài lan [87].…”

Review on molecular markers for identification of Orchids

“…Besides this, the species can be transported in a vegetative state, as seeds or as fragments [3]. Accurate authentication of orchid species is critical for biodiversity conservation and effective utilisation of orchids as plant resources [4].…”