• Title/Summary/Keyword: RAPD-SCAR marker

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Development of RAPD-Derived SCAR Markers and Multiplex-PCR for Authentication of the Schisandrae Fructus (오미자 (五味子) 종 감별을 위한 RAPD 유래 SCAR Marker 및 Multiplex-PCR 기법 개발)

  • Lee, Young Mi;Moon, Byeong Cheol;Ji, Yunui;Seo, Hyeong Seok;Kim, Ho Kyoung
    • Korean Journal of Medicinal Crop Science
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    • v.21 no.3
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    • pp.165-173
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    • 2013
  • The fruits of Schisandra chinensis have been used as an edible ingredient and traditional medicine in Korea. Due to morphological similarities of dried mature fruits, the correct identification of S. chinensis from other closely related Schisandrae species is very difficult. Therefore, molecular biological tools based on genetic analysis are required to identify authentic Schisandrae Fructus. Random amplifed polymorphic DNA (RAPD) and Sequence Characterized Amplified Region (SCAR) were used to develop an easy, reliable and reproducible method for the authentication of these four species. In this paper, we developed several RAPD-derived species specific SCAR markers and established a multiplex-PCR condition suitable to discriminate each species. These genetic markers will be useful to distinguish and authenticate Schisandrae Fructus and four medicinal plants, S. chinensis, S. sphenanthera, S. repanda and K. japonica, in species level.

Development of a Female-associated SCAR Marker in Schisandra nigra Max. (Schisandra nigra Max.에서 암그루에 연관된 SCAR 마커의 개발)

  • Han, Hyo Shim;Jung, Jae Sung
    • Journal of Life Science
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    • v.31 no.6
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    • pp.537-542
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    • 2021
  • Schisandra nigra Max., a dioecious plant native to Jeju Island in Korea, is cultivated on a small scale for fruit production. As fruit-producing female individuals are generally considered to be more valuable than male, early identification of plant sex at the seedling stage is important. In this study, a sequence-characterized amplified region (SCAR) marker associated with a female-specific region in the genome of S. nigra was investigated. Of 120 randomly amplified polymorphic DNA (RAPD) primers, one primer (OPB-03) consistently amplified a 749 bp band in female plants. The female-specific PCR product was isolated and cloned, and the nucleotide sequences were then determined. Southern hybridization performed using the female-specific fragment as a probe produced positive signals only in genomic DNA from the female plants. This result revealed that the 749 bp segment of DNA was present in the genome of female plants but absent in the genome of male plants. A SCAR primer pair was designed based on the RAPD marker to amplify a 436 bp fragment in the genomic DNA of female plants. This primer pair amplified the expected size of DNA fragment in female plants and four monoecious individuals collected from a natural population. The SCAR marker identified in this study can be used to distinguish female-flowering individuals at the seedling stage.

Development of RAPD-SCAR Molecular Marker Related to Seed-hair Characteristic in Carrot (당근(Daucus carota var. sativa) 종자모 형질 관련 RAPD-SCAR 분자표지 개발)

  • Shim, Eun-Jo;Park, Sung-Kwan;Oh, Gyu-Dong;Jun, Sang-Jin;Park, Young-Doo
    • Horticultural Science & Technology
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    • v.31 no.6
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    • pp.756-763
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    • 2013
  • Mechanical hair removal of carrot seed causes seed injuries and suppresses the germination in carrot cultivation. This study was performed to develop molecular markers for breeding high quality cultivars with short-hair seed. To meet this objective, random amplified polymorphic DNA (RAPD)-sequence characterized amplified region (SCAR) markers specifically linked to seed-hair characteristic were identified using CT-SMR 616 OP 389-1 line with short-haired seed and CT-SMR 616 OP 616-33 line with long-haired seed, bred by self-pollination for 6 years from 2008 to 2013, as parents. After seed hair lengths of these lines were analyzed using microscope, next generations were advanced and compared with the molecular markers polymorphism. From RAPD analysis using fixed lines in 2011, twelve RAPD primers showing polymorphic bands specific between the two lines were identified from 80 random primers. To develop RAPD-SACR marker, SCAR primers were designed based on sequence analysis of these specific RAPD bands and more than three combinations of primers were tested. As a result, it was found that the $SCA2_{1.2}$ amplified single polymorphic band from short-haired seed line. To confirm this result, $SCA2_{1.2}$ marker was retested by applying to the 2012 and 2013 progenies. Finally, it was concluded that the developed $SCA2_{1.2}$ marker distinguished short-haired line from long-haired seed line. Therefore, SCAR marker, $SCA2_{1.2}$ is expected to be utilized for breeding of the short-haired seed cultivars.

Development and Application of Weonhyeong Strain-specific SCAR Marker in Pleurotus ostreatus (느타리 버섯에서 원형 품종 특이 SCAR marker 개발)

  • Seo, Kyoung-In;Jang, Kab-Yeul;Yoo, Young-Bok;Park, Soon-Young;Kim, Kwang-Ho;Kong, Won-Sik
    • The Korean Journal of Mycology
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    • v.39 no.1
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    • pp.22-30
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    • 2011
  • Weonhyeong is one of important commercial strains. It has good characteristics of bundle formation, grey colored pilei and high productivity. We previously reported grouping of 70 strains of Pleurotus ostreatus in which one group contained 35 strains including Weonhyeong. Four strains in that group showed same profiles implicating no variety distinction for mushroom cultivation. Now we developed a specific marker for identification of Weonhyeong. Sequence Characterized Amplified Region (SCAR) marker was developed from the RAPD amplicon. SCAR marker 'S-OPO5' produced only one band specific to 2183, 2240, 2595 and 2725 strains showing similar banding patterns to Weonhyeong in RAPD-PCR results. The sequence of 'S-OPO5' marker was unknown when compared with the data in the Genbank using BLASTN. BLASTX results indicated that the marker showed significant alignment with the protein sequences in Tricholoma bakamatsutake reverse transcriptase. The results indicate that this new SCAR marker ('S-OPO5') will be valuable to distinguish the Weonhyeong similar strains from Pleurotus spp.

Development of a psychrophilic-SCAR marker for Pleurotus eryngii (큰느타리버섯의 저온적응성 형질에 관련된 SCAR Marker 개발)

  • Kim, Su Chul;Hwang, Hye Sung;Cho, Yun Jun;Kim, Hye Su;Ryu, Jae-San;Cho, Soo Jeong
    • Journal of Mushroom
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    • v.11 no.3
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    • pp.171-176
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    • 2013
  • Genomic DNAs of psychrophilic strains of Pleurotus eryngii were analyzed by randomly amplified polymorphic DNA (RAPD) using OP-A, OP-B, OP-L, OP-P, OP-R and OP-S3 primers to develop the strain-specific DNA marker. A unique DNA fragment with the size of 480 bp was yielded by OP-S3 primer from the psychrophilic strain. A sequence characterized amplified region (SCAR) marker, designated as OP-S3-1, was designed on the basis of the determined sequence. The PCR analysis with the OP-S3-1 primer showed that this SCAR marker can clearly distinguish the psychrophilic strains from the control strains.

Identification of Mating Type Loci and Development of SCAR Marker Genetically Linked to the B3 Locus in Pleurotus eryngii

  • Ryu, Jae-San;Kim, Min Keun;Ro, Hyeon-Su;Kang, Young Min;Kwon, Jin-Hyeuk;Kong, Won-Sik;Lee, Hyun-Sook
    • Journal of Microbiology and Biotechnology
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    • v.22 no.9
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    • pp.1177-1184
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    • 2012
  • In order to estimate how diverse the mating types in Pleurotus eryngii from different regions are, pairings between monokaryons derived from inter- and intra-groups were done. Sixteen and 15 alleles were identified at loci A and B from the 12 strains. In the P. eryngii KNR2312, widely used for commercial production, four mating loci, A3, A4, B3, and B4, were determined. Those loci, except A3, were found in 4 strains out of 12 strains. To improve breeding efficiency, especially in mating type determination, RAPD and BSA were performed to screen for a mating type specific marker. The SCAR marker 13-$2_{2100}$ was developed based on the RAPD-derived sequence typing B3 locus. The sequence analysis of 13-$2_{2100}$ revealed that it contained a conserved domain, the STE3 super-family, and consensus sequences like the TATA box and GC box. It seems likely that the SCAR marker region is a part of the pheromone receptor gene.

Development of SCAR Markers for the Authentication of Acori Rhizoma Based on the Analysis of RAPD and Multiplex-PCR (RAPD 분석과 multiplex-PCR을 이용한 석창포 감별용 SCAR 마커 개발)

  • Moon, Byeong-Cheol;Ji, Yun-Ui;Lee, Young-Mi;Chun, Jin-Mi;Lee, A-Yeong;Choo, Byung-Kil;Kim, Ho-Kyoung
    • Korean Journal of Medicinal Crop Science
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    • v.19 no.3
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    • pp.162-169
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    • 2011
  • The rhizomes and herbal medicines originating from Acorus gramineus, A. calamus, A. tatarinowii, and A. gramineus var. pusilus, show significant similarity, and the correct identification of species is very difficult. Random Amplified Polymorphic DNA (RAPD) and Sequence Characterized Amplified Region (SCAR) were used to develop a reliable method for identification of these four species. Several distinct SCAR markers were developed from species-specific RAPD amplicons for each species. Furthermore, a useful molecular marker was established for multiplex-PCR, in order to the four species could be distinguished concurrently. These markers allow efficient and rapid identification of closely-related Acorus species and will be useful for standardization of herbal medicines.

Development of SCAR Markers for the Discrimination of Rhei Radix et Rhizoma and Rhei Undulatai Rhizoma based on the RAPD (RAPD 분석을 통한 대황(大黃)과 종대황(種大黃) 감별용 SCAR 유전자 마커 개발)

  • Moon, Byeong-Cheol;Lee, Young-Mi;Chun, Jin-Mi;Lee, A-Young;Yoon, Tae-Sook;Cheon, Myeong-Sook;Choo, Byung-Kil;Kim, Ho-Kyoung
    • The Korea Journal of Herbology
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    • v.24 no.4
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    • pp.115-120
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    • 2009
  • Objectives : Due to the morphological similarity and frequent occurrence of intermediate forms as well as morphological variations of aerial part, the correct identification between Rhei Radix et Rhizoma and Rhei Undulatai Rhizoma is very difficult. To develop a reliable method for correct identification and improving the quality standards of Rhei Radix et Rhizoma and Rhei Undulatai Rhizoma, we analyzed RAPD and developed SCAR marker. Methods : To amplify target DNA at the genomic level, 32 Operon 10-mer random primers were applied with four Rheum species, R. officinale, R. palmatum, R. tanguticum and R. undulatum. The nucleotide sequences were determined and species-specific primers were prepared depending on the species-specific RAPD amplicons after subcloned into the pGEM-Teasy vector. To develop the SCAR markers, species-specific PCR amplification and multiplex-PCR were carried out using the single species-specific primer pairs and combinations of them, respectively. Results : We used RAPD analysis of four Rheum plant species to obtain several species-specific RAPD amplicons. From nucleotide sequences of these RAPD amplicons, we developed two SCAR markers that amplified 314 bp and 390 bp DNA fragments in only R. undulatum but not in R. officinale, R. palmatum, R. tanguticum and R. undulatum, for distinguishing Rhei Undulatai Rhizoma and Rhei Radix et Rhizoma. Furthermore, we established SCAR markers for the simultaneous discrimination of the three species within a single reaction by using multiplex-PCR. Conclusions : These genetic markers can be used for the efficient discrimination of plants species and commercial herbal medicines between Rhei Undulatai Rhizoma and Rhei Radix et Rhizoma, to ultimately prevent indiscriminate distribution and prescription of these herbal medicines.

Development of SCAR Marker for Discriminating between Violet Flowered Lines and White Flowered Lines in Chinese Bellflower (Platycodon grandiflorum A.) (청도라지와 백도라지의 구분을 위한 SCAR 마커 개발)

  • Park, Chun-Geon;Bang, Kyong-Hwan;Kim, Ok-Tae;Jin, Dong-Chun;Kim, Dong-Hwi;Sung, Jung-Sook;Seong, Nak-Sul;Park, Hee-Woon;Lee, Sang-Chul
    • Korean Journal of Medicinal Crop Science
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    • v.15 no.1
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    • pp.1-5
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    • 2007
  • To develop a convenient method for discriminating between violet flowered lines and white flowered lines in Chinese bellflower, RAPD analysis was carried out and SCAR markers were generated. Eighteen specific RAPD bands were obtained from 6 OPERON primer sets. Two out of eighteen RAPD bands were cloned into pGEM-T-Easy vectors and then subjected to the nucleotide sequence analysis. PgR1 and PgR2 DNA fragment, each specific for violet and white flowered lines, consist of 887 bp and 863 bp sequences, respectively. Two SCAR markers were developed from RAPD clones: SPgR1 (355 bp) from PgR1 and SPgR2 (493 bp) from PgR2. One (SPgR2) of these two markers was useful to differentiate between violet flowered lines and white flowered lines in Chinese bellflower.

SCAR markers were developed to identify zoysiagrass mutants exhibiting fine leaf characteristics (세엽 한국들잔디 변이체 식별을 위한 SCAR 마커 개발)

  • Chung, Sung Jin;Park, Su Jeong;Choi, Young In;Kim, In-Kyung;Lee, Ka-Yeon;Kim, Hun-Joong;Lee, Geung-Joo
    • Korean Journal of Agricultural Science
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    • v.40 no.2
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    • pp.115-121
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    • 2013
  • Polymorphic bands of two fine-leaf zoysiagrass mutants (CNU 70-1, CNU 70-2) induced via a gamma-ray irradiation on seeds of Zoysia japonica were obtained by using randomly amplified polymorphic DNA (RAPD) primers. The genotype-specific fragments were then converted into PCR-based sequence characterized amplified region (SCAR) markers, which are now amenable to detecting them among other zoysiagrass species widely noticeable in Korea. The CNU 70-1-specific primer set amplified about 900 bp successfully, while the CNU 70-6 marker produced the expected 1,500 bp band, by which those markers were nominated by CNU 70-1_900 and CNU 70-6_1500 SCARs, respectively. The developed SCAR markers can be an applicable tool in sod industry where illegal appropriation hampers breeder's right and profits due to the turfgrass plant vegetatively propagating.