• Proceedings of the Plant Resources Society of Korea Conference
• /
• 2022.09a
• /
• pp.66-66
• /
• 2022

속성수로 활용되는 버드나무속 식물들은 생식기관과 영양기관의 성장 시기가 달라 형태적 특성 평가를 위해 수년간의 조사 기간이 요구된다. 따라서 바이오매스 우수 버드나무속 교잡종 육성의 성공 여부를 조기 판별하기 위한 식별 기술이 필요하다. DNA 마커는 식물의 생장단계와 관련 없이 탐색할 수 있으며 환경에 영향을 받지 않는 장점이 있다. 식물의 계통 분류 시 주로 사용되는 엽록체 DNA는 유전자 염기서열의 변이가 비교적 크지 않은 장점이 있으나 대부분의 활엽수에서 모계를 통해 유전되는 특징이 있다. 하지만 종간 교잡종의 식별은 각각의 부모종과 구분할 수 있어야 하므로 본 연구는 엽록체 DNA가 아닌 핵 DNA를 대상으로 분석하였다. 본 연구의 목적은 호랑버들을 암나무로 갯버들을 수나무로 인공교배하여 육성된 종간 교잡종을 식별하는 핵 DNA 마커를 탐색하는 것이다. 이를 위해 버드나무속에서 개발된 총 35개의 nSSR (nuclear Simple Sequence Repeat) 마커를 대상으로 호랑버들과 갯버들, 종간 교잡종의 식별 가능성을 평가하였다. 분석 결과 호랑버들과 갯버들, 종간 교잡종 간 차이를 나타내는 2개의 핵 DNA 마커를 선발하였다. 따라서 선발된 핵 DNA 마커를 활용하여 호랑버들과 갯버들, 종간 교잡종의 조기 식별에 활용이 가능할 것으로 사료된다.

• Proceedings of the Plant Resources Society of Korea Conference
• /
• 2018.04a
• /
• pp.35-35
• /
• 2018

터리풀속(Filipendula)은 장미과(Rosaceae), 장미아과(Rosoideae)에 속하는 다년생 초본이며, 북반구 온대지역의 산지지역에 서식하며 15-20여 종이 보고되어 있고, 이 중 10여종이 한국, 중국, 일본, 타이완 등의 동아시아 지역에 분포한다. 본 연구의 목적은 DNA 염기서열 자료를 이용하여 터리풀속(Filipendula)내 종들간의 계통관계를 규명하기 위하여 본 연구를 수행하였다. 이를 위해서 11종 29개체의 터리풀속(Filipendula)샘플과 외군인 산딸기나무속(Rubus)에 속하는 3종 5개체의 샘플을 이용하였다. 추가로 Genbank에서 3속 10종 18개의 염기서열을 다운받아 비교분석에 이용하였다. 계통연구를 위하여 엽록체에 존재하는 atpF-atpH, psbK-psbI, psbA-trnH, matK, rbcL, 5개 마커와 핵에 존재하는 ITS, 총 6개 마커의 염기서열을 생산하였다. 총 52개의 샘플에 대하여 엽록체유전체 5개 마커지역은 염기서열 길이가 3,485bp였고 핵 ITS지역은 631bp였으며, 이들을 합한 염기서열 길이는 4,116bp였다. 계통분석결과, 터리풀속(Filipendula)은 단계통군을 이루었다. F. occidentalis와 F. vulgaris가 기저분류군을 이루었고 이들은 각각의 아속에 해당한다. 그리고 나머지 종들은 모두 하나의 단계통군을 이루었다. 위의 결과들은 1961년 시미즈가 본 속을 Hypogyna아속, Filipendula아속, Ulmaria아속으로 나눈 분류시스템과 일치한다. 나아가 분자계통수에서 Ulmaria아속은 크게 4개의 subclade로 구분되었다. 먼저 subclade I에는 F. vestita, F. kiraishiensis, F. tsuguwoi, F. multijiuga, F. purpurea 등 5개 종으로 구성되었다. Subclade II는 F. ulmaria 한 종으로만 구성되었다. Subclade III에는 F. glaberrima, F. koreana, F. formosa, F.camtschatica 로 구성되었으며 subclade III에는 한국에 서식하는 3종이 포함되었다. Subclade IV에는 F. rubra, F. angustiloba, F. palmata, F. intermedia 4종으로 구성되었다. 이번연구에서는 Ulmaria아속내에 4개의 subclade가 존재함이 처음으로 확인되었다.

• Korean Journal of Plant Taxonomy
• /
• v.44 no.1
• /
• pp.39-50
• /
• 2014

Phylogenetic positions of Sedirea and Neofinetia were addressed using the chloroplast matK and the nuclear ITS sequences. We also evaluate the usefulness of the makers for the identification of species and localities. Sedirea and Neofinetia form an independent monophyletic genus, respectively, in both matK and nuclear ITS trees. The sister genus of the Neofinetia was Vanda in both trees. In addition, our trees support the separate recognition of the Neofinetia from Vanda rather than the inclusion of Neofinetia into Vanda. The sister group of the Sedirea was (Dimorphorchis(Pteroceras(Saccolabiun+Phalaeonopsis))) clade. The Dimorphorchis was one of the most probable sister genus to the Sedirea. The sister group relationship between Sedirea and Aerides was suggested by their similar morphology, but not supported in molecular trees. The identification of species and localities of Neofinetia was possible using our two molecular markers. However, several pseudo-gene sequences are discovered from the public data base. In addition, the horizontal gene transfer of chloroplast genomes is frequent events in orchid hybrids. Therefore, we need a careful evaluation for the data prior to systematic use. Generation of sequence data from multiple accessions of a species may helpful to reduce these types of error.

• Journal of Plant Biotechnology
• /
• v.42 no.4
• /
• pp.312-325
• /
• 2015

In this review, we summarized the trends of genomics and transcriptomics research on peach, a model species of Rosaceae. Peach genome maps have been developed from various progeny groups with many next-generation sequencing (NGS) based single nucleotide polymorphism markers. Molecular markers of qualitative traits and quantitative trait loci (QTL) such as fruit characteristics, blooming date, and disease resistance have been analyzed. Among many characteristics, markers related to flesh softening and flesh adhesion are useful for marker assisted selection. Through comparative genomics, peach genome has been compared to the genome of Arabidopsis, Populus, Malus, and Fragaria species. Through transcriptomics and proteomics, fruit growth and development, and flavonoid synthesis, postharvest related transcriptomes and disease resistance related proteins have been reported. Recently, development of NGS based markers, construction of core collection of germplasm, and genotyping of various progenies have been preceded. In the near future, accurate QTL analysis and identification of useful genes are expected to establish a foundation for effective molecular breeding.

• Journal of Plant Biotechnology
• /
• v.45 no.2
• /
• pp.102-109
• /
• 2018

Thistle is a perennial plant that is widely used for medicinal purposes. Information on the genetic diversity of thistle populations are great important for their conservation and germ plasmic utilization. Although thistle is an important medicinal plant species registered in South Korea, no molecular markers are currently available to distinguish them from other similar species from different countries. In this study, we developed single nucleotide polymorphism (SNP) markers derived from the nuclear ribosomal DNA internal transcribed spacer (ITS) regions of genomic sequences to identify distinct Korean-specific thistle species via an amplification refractory mutation system (ARMS)-PCR and high resolution melting (HRM) curve analyses. We performed molecular authentication of four different kinds of thistle species from different regions using DNA sequences in the ITS intergenic region. We also developed a quantitative PCR assay using species-specific ITS primers, which allowed us to estimate the ratio of Korean-specific thistle species using varying ratios of mixed genomic DNA templates from the two species. The SNP markers developed in this study are useful for rapidly identifying specific thistle species from different countries.

• Weed & Turfgrass Science
• /
• v.4 no.1
• /
• pp.18-25
• /
• 2015

A universal DNA barcoding for agricultural noxious weeds is a powerful technique for species identification without morphological knowledge, by using short sections of DNA from a specific region of the genome. Two standard barcode markers, chloroplast rbcL and matK, and a supplementary nuclear ribosomal Internal Transcribed Spacer (ITS) region were used to examine the effectiveness of the markers for Pooideae barcoding using 163 individuals of 29 taxa across 16 genera of Korean Pooideae. The rbcL and ITS revealed a good level of amplification and sequencing success while matK did not. Barcode gaps were 78.6% for rbcL, 96.2% for matK, and 91.7% for ITS, respectively. Resolving powers were 89.3% for rbcL, 92.3% for matK, and 79.1% for ITS. The matK obtained the best both barcode gap and resolving power. However, it should be considered not to employ matK for Pooideae barcode because of low rate of PCR amplification and sequencing success. As a single DNA marker, rbcL and ITS were reasonable for Pooideae barcode. Barcode gap and resolving power were increased when ITS was incorporated into the rbcL. The barcode sequences were deposited to the National Center for Biotechnology Information (NCBI) database for public use.

• Korean Journal of Ichthyology
• /
• v.29 no.2
• /
• pp.139-145
• /
• 2017

The spontaneous color mutant, albino individuals of genus Misgurnus, are rarely discovered in Korea and there are difficult to identify morphological species due to lack melanin pigmentation. In this study, we developed a genetic identification method for the species of albino Misgurnus individuals based on phylogenetic analysis by using recombination activating gene 1 (rag1) and cytochrome b (cytb) region of mitochondrial DNA. As a result of molecular phylogenetic analysis, three clades were identified as Misgurnus mizolepis, M. anguillicaudatus and M. mohoity. The homology of the cytb sequences of M. mohoity was best match to that of M. mohoity sequences in GenBank database. As a result of species identification of 25 albino Misgurnus individuals based on the phylogenetic tree, the red-eye type was identified as 16 M. anguillicaudatus and one M. mizolepis. The remaining three individuals were identified as one M. mizolepis ♀${\times}$M. anguillicaudatus ♂, and two M. mohoity ♀${\times}$M. anguillicaudatus ♂, respectively. In addition, the five black-eye type individuals were identified as one M. anguillicaudatus, three M. mizolepis and one M. mohoity. Therefore, this genetic identification method will be an useful techniques for species or hybrid identification in genus Misgurnus.

• Journal of Plant Biotechnology
• /
• v.48 no.1
• /
• pp.26-33
• /
• 2021

Angelica is a widely used medicinal and perennial plant. Information on the genetic diversity of Angelica populations is essential for their conservation and germ plasmic utilization. Although Angelica is an important medicinal plant species registered in South Korea, no molecular markers are currently available to distinguish it from other similar species from different countries. This developed single nucleotide polymorphism (SNP) markers derived from nuclear ribosomal DNA internal transcribed spacer regions genomic sequences to identify distinct Korean-specific Angelica species via amplification refractory mutation system (ARMS)-PCR curve analyses. We performed molecular authentication of different kinds of Korean-specific Angelica species such as A. gigas Nakai and A. gigas Jiri using DNA sequences in the ITS intergenic region. The SNP markers developed in this study are useful for rapidly identifying specific Angelica species from different countr.

• Korean Journal of Plant Taxonomy
• /
• v.41 no.4
• /
• pp.299-314
• /
• 2011

The choice of molecular markers is the first step when selecting experimental plans in the field of population genetics. The popular molecular markers in population genetic studies are mainly allozyme, RAPD, RFLP, AFLP, microsatellite, SNP and ISSR. Among these, microsatellites are frequently found in nuclear, chloroplast and mitochondrial genome, showing a high level of polymorphism and nuclear microsatellites are codominant. Thus, it is a favorable molecular marker for population structure analyses and genetic diversity studies. Microsatellites are composed of tandem repeated 1~6 base pair nucleotide motifs and can be easily amplified by PCR reactions using locus specific primers. Because microsatellites have low cross-species transferability, however, they are only applicable between phylogenetically close species. In wild plants, the lack of genomic information and the high development cost of the microsatellite obstruct the wider use of microsatellites in plant population genetics research. In this review, we introduce the basis for microsatellite markers, the development process, and analytical methods as well as evolutionary models and their applications. In addition, possible genotyping errors which lead to erroneous conclusions are discussed.

• Weed & Turfgrass Science
• /
• v.4 no.1
• /
• pp.26-34
• /
• 2015

Korean Poaceae includes approximately 80 species of the agricultural weeds. Precise species identification is the first step for more effective weed management in the agricultural fields. However, the identification of species in Poaceae is not easy without the assistance of taxonomists or identification experts although they are relatively easy to distinguish from the plants of the other family by the unique characteristics of caryopsis. Thus, DNA barcode was suggested as an alternative powerful technique for species identification by using short sections of DNA from a specific region of the genome. Two standard barcode markers of vascular plants, chloroplast rbcL and matK, and a supplementary nuclear ribosomal Internal Transcribed Spacer (ITS) region were used for barcode of major Korean Poaceae weeds, 403 individuals of 84 taxa. All the barcode markers revealed a good level of sequencing success with the lowest 73.7% for matK and the highest 88.8% for rbcL. The barcode sequences were deposited to the National Center for Biotechnology Information (NCBI) database for public use. Combined matK and ITS showed very high resolving power with 92.9%. Besides the identification of weeds for weed managment, the generated DNA barcode data could be used for many other applications such as rapid biodiversity assessment and conservation prioritization.