• Biotechnology and Bioprocess Engineering:BBE
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• 제5권1호
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• pp.23-26
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• 2000

In order to develop the specific genetic marker for Korean native cattle (Hanwoo), randomly amplified polymorphic DNA (RAPD) analysis of 6 different cattle breeds was attempted by using 38 decamer primers. In comparison of RAPD patterns, two distinctive DNA bands specific for Hanwoo were detected. One was 296 bp of DNA fragment found to be specific only for female Hanwoo when primer GTCCACACGG was employed. In individual analysis of this RAPD marker was observed only in female individuals with the possibility of $85.3\%$. The other was 521 bp of RAPD marker amplified using TCGGCGATAG and AGCCAGCGAA primers, which showed $83.0\%$ of genetic frequency in 85 male and 68 female individuals tested. Nucleotide sequencing of these genetic markers revealed that 296 bp marker has a short micro satellite-like sequence, ACCACCACAC, and a tandem repeat sequence of microsatellite GAAAAATG in the determined sequence. Two distinctive tandem repeats of microsatellite sequences, MC and GAAGA, were also appeared in 521 bp DNA marker. In BLAST search, any gene having high homology with these markers was not found.

• Journal of Microbiology and Biotechnology
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• 제16권5호
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• pp.724-730
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• 2006

A sequence characterized amplified region (SCAR) marker, which was tightly linked with the A1 mating type locus in Phytophthora infestans, was developed. During the random amplified polymorphic DNA-based phylogenic studies of 33 isolates of P infestans collected from year 2002 to 2004, we found an A1 mating type-specific DNA fragment. This 573-bp DNA fragment was generated only in the genomic DNA of the A1 mating types, when OPC-5 primer was used. Based on the specific DNA sequence, we designed the primer sets for generating the A1 mating type-specific 569-bp DNA fragment. When 33 genomic DNAs of P. infestans were subjected to PCR amplification using different primer combinations, the A1 mating type-specific DNA was amplified, when LB-1F and LB-2R primers were used. The specific 569-bp DNA fragment was generated only from all 18 A1 strains, but not from 15 A2 mating type strains. These results corresponded to the mating type discriminating bioassay of 33 isolates of P. infestans. Therefore, the primer combination of LB-1F/LB2R was chosen as a SCAR marker. Overall, this study indicates that the SCAR marker could be developed into a useful tool for mating type determination of P. infestans.

• 한국자원식물학회지
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• 제27권3호
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• pp.236-241
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• 2014

A sex-linked random amplified polymorphic DNA (RAPD) marker was identified from Asparagus officinalis L. and was converted into a sequence-characterized amplified regions (SCAR) marker for the large-scale screening of male and female plants. A total of 100 arbitrary decamer oligonucleotide primers were used for the RAPD analysis. Among them, the primer UBC347 amplified one female-specific 400 base pair DNA. Subsequently, the amplified RAPD fragment was cloned and sequenced. The fragment was abundant in AT and shared sequence homology with retrotransposon elements. On the basis of the sequence obtained, a pair of SCAR primer was designed. The amplification product, named F400, was the same size as the respective RAPD fragment from which it was derived. The F400 SCAR marker resulted to be female-specific in the three asparagus varieties tested in this study. This SCAR marker can be used for an early and rapid identification of female and male plants during breeding programs of asparagus.

• 생명과학회지
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• 제14권3호
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• pp.521-524
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• 2004

본 연구는 short oligonucleotide primer를 이용하여 마 품종간 유전 분석을 실시 하고자 PCR증폭 기법을 확립하고, 확립된 기술을 이용하여 제주도에 사육중인 천념기념물 347호로 등록된 제주말과 경주마로 잘 알려진 더러브렛간의 유전적인 다양성을 분석한 결과 마 품종간 차이를 보이는 DNA marker는 9개의 primer에서 확인되었으며, 이중 6개의 primer에서 더러브렛 특이 밴드와 나머지 3개에서 제주 마 특이 RAPD 밴드가 확인되어 cloning과 sequencing후에 SCAR primer를 제작하여 마 품종 식별에 활용할 수 있을 것으로 사료되며, 본 연구결과 RAPD표지인자는 마 품종간의 유전 분석에 매우 유용한 것으로 판단되었다.

• Journal of Microbiology and Biotechnology
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• 제24권9호
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• pp.1189-1195
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• 2014

A strain-specific identification method is required to secure Chlorella strains with useful genetic traits, such as a fast growth rate or high lipid productivity, for application in biofuels, functional foods, and pharmaceuticals. Microsatellite markers based on simple sequence repeats can be a useful tool for this purpose. Therefore, this study developed five novel microsatellite markers (mChl-001, mChl-002, mChl-005, mChl-011, and mChl-012) using specific loci along the chloroplast genome of Chlorella vulgaris. The microsatellite markers were characterized based on their allelic diversities among nine strains of C. vulgaris with the same 18S rRNA sequence similarity. Each microsatellite marker exhibited 2~5 polymorphic allele types, and their combinations allowed discrimination between seven of the C. vulgaris strains. The two remaining strains were distinguished using one specific interspace region between the mChl-001 and mChl-005 loci, which was composed of about 27 single nucleotide polymorphisms, 13~15 specific sequence sites, and (T)n repeat sites. Thus, the polymorphic combination of the five microsatellite markers and one specific locus facilitated a clear distinction of C. vulgaris at the strain level, suggesting that the proposed microsatellite marker system can be useful for the accurate identification and classification of C. vulgaris.

• Journal of Plant Biotechnology
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• 제50권
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• pp.190-199
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• 2023

Date palm (Phoenix dactylifera L.: Arecaceae) is a dioecious species where only female trees bear fruits. In their natural state, date palms produce dates once a year. However, in Thailand, some trees were observed to produce dates during the off-season, despite no variations in morphology. The availability of such off-season fruits can significantly increase their market value. Interestingly, most female off-season date palms investigated in this study were obtained through micropropagation. Hence, there is an urgent need for genetic markers to distinguish female offseason flowering plantlets within tissue culture systems. In this study, we aimed to develop random amplification of polymorphic DNA-sequence characterized amplified region (RAPD-SCAR) markers for the identification of female off-season flowering date palms cultivated in Thailand. A total of 160 random decamer primers were employed to screen for specific RAPD markers in off-season flowering male and female populations. Out of these, only one primer, OPN-02, generated distinct genomic DNA patterns in female off-season flowering (FOFdp) individuals compared to female seasonal flowering genotypes. Based on the RAPD-specific sequence, specific SCAR primers denoted as FOFdpF and FOFdpR were developed. These SCAR primers amplified a single 517-bp DNA fragment, predominantly found in off-season flowering populations, with an accuracy rate of 60%. These findings underscore the potential of SCAR marker technology for tracking offseason flowering in date palms. Notably, a BLAST analysis revealed a substantial similarity between the SCAR marker sequence and the transcript variant mRNA from Phoenix dactylifera encoding the SET DOMAIN GROUP 40 protein. In Arabidopsis, this protein is involved in the epigenetic regulation of flowering time. The genetic potential of the off-season flowering traits warrants further elucidation.

• 한국균학회지
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• 제39권1호
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• pp.31-38
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• 2011

현재 70개 이상의 느타리 품종이 유통되어 재배되고 있다. 본 연구에서는 81개 품종을 수집하여 핵산지문법으로 분석하였다. 이중 수한과 그 유사품종에서 특이하게 나타나는 밴드를 이용하여 수한 품종에 특이적인 SCAR marker로 개발하였다. 수한 품종 특이 band에 대한 clone을 기존에 알려진 유전자 염기서열과 유사성이 있는지를 확인한 결과 POMFBO1 Pleurotus ostreatus cDNA clone MFB02-A05, mRNA sequence와 92%의 homology를 나타냈고, 등록된 아미노산 서열과의 유사성을 확인한 결과 큰졸각버섯인 Laccaria bicolor의 predicted protein과 가장 높은 sequence homology (BlastX score = 73.9, E value = $5e^{-25}$)를 보였다. 본 연구를 통하여 개발된 수한특이 마커는 정확한 품종구분이 요구되는 종균유통 과정에서 수한계통 품종을 구분하는 유용한 마커로 이용될 것으로 기대된다.

• 한국균학회지
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• 제39권1호
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• pp.22-30
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• 2011

원형느타리버섯의 자실체는 다발형성이 잘되고 갓 색깔이 회색이면서 수량성이 높은 중요한 품종이다. 저자들은 핵산 지문법을 이용하여 느타리종에 속하는 70품종을 3 그룹으로 나누고 이 중 원형품종이 속한 그룹 35개 품종 중 원형품종과 동일하거나 구별성이 인정되지 않는 4개 품종을 보고한 바 있다. 본 연구에서는 이들 품종을 구분할 수 있는 원형 품종 특이 분자마커를 개발하였다. 원형 품종 특이적인 SCAR marker로 개발한 'S-OPO5' primer는 1436 bp 에서 원형 유사품종인 2183, 2240, 2595, 2725 품종에서만 특이적으로 단일 band를 보였다. 이들 원형 유사품종들의 SCAR PCR 산물을 대상으로 염기서열 분석을 한 결과 nucleotide 염기서열은 NCBI database에서 상동성이 있는 유전자를 찾을 수 없었으며, 이들 5품종간의 nucleotide sequence는 99% 상동성을 보여 매우 유사하였다. 아미노산 서열을 분석한 결과는 NCBI database내에 존재하는 모든 유전자들 중 송이속에 속하는 Tricholoma bakamatsutake의 reverse transcriptase와 가장 상동성이 높은 것으로 나타났다. 본 연구를 통하여 개발된 원형특이 마커는 정확한 품종구분이 요구되는 종균유통 과정에서 원형계통 품종을 구분하는 유용한 마커로 이용될 것으로 기대된다.

• Molecules and Cells
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• 제21권3호
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• pp.411-417
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• 2006

We have developed a polymerase chain reactionrestriction fragment length polymorphism (PCR-RFLP) marker that can distinguish male-fertile (N) and male-sterile (S) cytoplasm in onions. The PCR-RFLP marker was located in a chloroplast psbA gene amplicon. Digesting the amplicons from different cytoplasm-containing varieties with the restriction enzyme MspI revealed that N-cytoplasm plants have a functional MspI site (CCGG), whereas the S-cytoplasm plants has a substitution in that site (CTGG), and thus no MspI target. The results obtained using this PCR-RFLP marker to distinguish between cytoplasmic male sterile factors in 35 onion varieties corresponded with those using a CMS-specific sequence-characterized amplified region (SCAR) marker. Moreover, the PCR-RFLP marker can identify N- ot S-cytoplasms in DNA sample mixtures in which they are in up to a 10-fold minority, indicating that use of the marker has high diagnostic precision. We also demonstrated the usefulness of the SNP detected in the psbA gene for high-throughput discrimination of CMS factors using Real-time PCR and a TaqMan probe assay.

• 생명과학회지
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• 제15권3호
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• pp.474-478
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• 2005

본 연구는 RAPD 기법을 이용한 종 특이 marker 개발 및 이 marker의 SCAR marker로의 개발을 목표로 수행되었다. Random primer 700개에 대하여 PCR 수행결과, 품종간, 개체간에 많은 다형성이 관찰되었으며 품종특이적인 양상을 나타내는 MG30, MG53의 primer는 각각 2.0kb, 2.3kb의 위치에서 제주말과 더러브렛종의 특이적인 RAPD 단편을 나타내었다. 이들 단편들 중 품종 특이적인 단편을 클로닝한 후 random primer가 포함된 부분의 염기서 열을 결정하였다. 10 bp의 RAPD random primer에 10bp의 염기를 추가하여 SCAR primer를 제작하였다. SCAR marker의 수행결과 RAPD marker와 같은 2.3kb, 2.0kb의 크기에서 제주마와 더러브렛종에 특이적인 하나의 밴드가 증폭되었다. 따라서 이 Cnh-SCAR marker는 보다 안정적이고 재현성 있는 marker로서 사용이 가능하여 제주말의 판별에 유용하게 사용될 수 있을 것이다.