• Korean Journal of Breeding Science
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• v.43 no.4
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• pp.265-272
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• 2011

This study is to generate SCARs markers for identification of Perilla species. A SCAR is a genomic DNA fragment at a single genetically defined locus that is identified by PCR amplification using a pair of specific oligonucleotide primers. We derived SCARs by sequencing and cloning the both ends of the amplified products of RAPD markers. Sixteen sequence-specific primers were synthesized from eight RAPD markers, which were completely sequenced. We developed the species-specific SCAR markers which could be used successfully in detecting genetic variation in four Perilla species. These markers could be used to verify species-origins of various forms of Perilla germplasms.

• Proceedings of the Korean Society for Food Science of Animal Resources Conference
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• 2000.11a
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• pp.59-75
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• 2000

This study was carried out to develop a DNA marker for identifying between Korean cattle (Hanwoo) and other breeds. First experiment was performed to isolate Hanwoo specific DNA marker at sequence characterized amplified regions (SCARs). Five breeds of cattle including Hanwoo, Holstein, Hereford, Angus and Charolais were represented with the from 8 to 20 individuals. Fourteen primers of 300 arbitrary primers of 10 nucleotides showed reproducible polymorphism across the breeds. An amplified band of 0.9 kb in the primer MG-3 showed the specificity to Holstein breed. And MG-6 and MG-12 detected the Hereford and Hanwoo specific markers at the size of 2.0 kb and 1.0 kb, respectively. A 1.0 kb band of MG-12 was cloned and sequenced. A SCAR primer was designed based on the obtained sequences. It was possible to identify the Hanwoo from Holstein breed. Second experiment was carried out to observe the genotype frequencies of MC1R in 1,044 samples of imported beef and eight different cattle breeds including Hanwoo, Holstein, Angus, Brown-Swiss, Charolais, Limousin, Simmental and Hereford. The primers for the amplification of bovine MC1R gene were designed based on a bovine MC1R gene sequence (GenBank accession no.Y19103). A size of 350 bp was amplified by polymerase chain reaction(PCR), digested with two different restriction enzyme, BsrFI and MspA II, and electrophoresed in 2.5% Metaphore agarose gel for determination of genotypes. Genotype frequencies of Hanwoo were 0.10 in E+e and 0.90 in ee. Allele ED was shown in all of Holstein and Angus breeds tested which have black coat color phenotypes. We suggested that SCAR marker and the bovine MC1R gene could be used as a DNA marker for distinguishing beef between Hanwoo and Holstein.

• Plant Biotechnology Reports
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• v.4 no.1
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• pp.1-7
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• 2010

Definitive identification of original plant species is important for standardizing herbal medicine. The herbal medicines Cynanchi Wilfordii Radix (Baekshuoh in Korean and Beishuwu in Chinese) and Polygoni Multiflori Radix (Hashuoh in Korean and Heshuwu in Chinese) are often misidentified in the Korean herbal market due to morphological similarities and similar names. Therefore, we developed a reliable molecular marker for the identification of Cynanchi Wilfordii Radix and Polygoni Multiflori Radix. We used random amplified polymorphic DNA (RAPD) analysis of three plant species, Polygoni multiflorum, Cynanchum wilfordii, and Cynanchum auriculatum, to obtain several species-specific RAPD amplicons. From nucleotide sequences of these RAPD amplicons, we developed six sequence characterized amplification region (SCAR) markers for distinguishing Polygoni Multiflori Radix and Cynanchi Wilfordii Radix. Furthermore, we established SCAR markers for the simultaneous discrimination of the three species within a single reaction by using multiplex-PCR. These SCAR markers can be used for efficient and rapid authentication of these closely related species, and will be useful for preventing the distribution of adulterants.

• Journal of Korean Society of Forest Science
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• v.105 no.4
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• pp.422-428
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• 2016

Ginkgo (Ginkgo biloba L.) is one of the most appropriate roadside trees because of a good transplantation nature and ability to grow well in urban environment. Ginkgo is a dioecious species. Sex discrimination of ginkgo is possible through comparing morphological characters of reproductive organs. However, it needs more than about twenty years for reproductive organs to appear after sexual maturity. Until now, ginkgo trees for roadside plantation have been planted without discriminating the sex because ginkgo trees have been usually planted before sexual maturity. Ginkgo nuts from the female ginkgo trees planted along the roadside emit a foul odor, and make much pollution on the streets. Thus in this study a novel SCAR marker (SCAR-GBM) for the early sex discrimination was developed. Primers were developed on the basis of the sequence of male-specific RAPD variants reported previously. False-negative problem of SCAR marker, probably caused by dominant nature, was resolved by using multiplex PCR using primers of both the SCAR-GBM and a universal primer set of atp1 region in mitochondria DNA, which resulted in improved discrimination efficiency. The results showed that DNA bands of 1,039 bp were commonly amplified by the atp1 primer set in male and female trees, and SCAR-GBM markers of 675 bp were specifically amplified only in male trees. Reproducible and specific discrimination of the multiplex PCR was finally confirmed by applying multiple male and female individuals.

• Journal of Plant Biotechnology
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• v.31 no.1
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• pp.1-6
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• 2004

Bang-Poong and related species are an important herbal medicine. However, it is difficult to determine the commercial dry material through anatomical and chemotaxonomical characteristics. Here, we used a PCR-based technique for an accurate discrimination of Bang-Poong and related species. With the RAPD primers, 215 RAPDSs(random amplified polymorphic DNAs) were obtained, and 98% of them showed polymorphic patterns. RAPDs from the four primers were appropriate for the discrimination of S. divaricata $(T_{URCZ{\cdot}})\;S_{CHISKIN}$, those from the six primers for P. japonicum $T_{HUNBERG}$, those from the four primers for P. terebinthaceum $F_{ISHER}$, and those from the six primers for G. littoralis Fr. $S_{CHMIDT}$. The specific bands from the primer 425 were obtained and used to develop SCAR (sequence characterized amplified region) markers, based on the sequence information of the RAPD markers. The SCAR primers generated a 215 bp fragment specific to Peucedanum terebinthaceum $F_{ISHER}$, and a 177 bp and a 300 bp fragment specific to G. littoralis Fr. $S_{CHMIDT}$. As a result, the three SCAR markers were able to discriminate from two Bang-Poong related species.

• Horticultural Science & Technology
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• v.34 no.6
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• pp.912-923
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• 2016

Watermelon production is often limited by powdery mildew in areas with a large daily temperature range. Development of resistant watermelon cultivars can protect against powdery mildew; however, little is known about the characteristics of its causal agents. Here, we identified the genus and race of a causal pathogen of powdery mildew in Ansung province of South Korea, and developed molecular markers for the generation of resistant watermelon cultivars. The causal pathogen was determined to be Podosphaera xanthii based on multiple sequence alignments of internal transcribed spacers (ITS) of rDNA. The physiological race was identified as 1W, and the Ansung isolate was named P. xanthii 1W-AN. Following inoculation with the identified P. xanthii 1W-AN, we found inheritance of the resistant gene fitting a single dominant Mendelian model in a segregated population ('SBA' ${\times}$ PI 254744). To develop molecular markers linked to fungus-resistant loci, random amplified polymorphic DNA (RAPD) was accomplished between DNA pooled from eight near-isogenic lines (NILs; $BC_4F_6$), originated from PI 254744 and susceptible 'SBB' watermelon. After sequencing bands from RAPD were identified in all eight NILs and PI254744, 42 sequence-characterized amplifiedregion (SCAR) markers were developed. Overall, 107 $F_2$ plants derived from $BC_4F_6$ NIL-1 ${\times}$ 'SBB' were tested, and one SCAR marker was selected. Sequence comparison between the SCAR marker and the reference watermelon genome identified three Nco I restriction enzyme sites harboring a single nucleotide polymorphism, and codominant cleavage-amplified polymorphic site markers were subsequently developed. A CAPS marker was converted to a high-resolution melt (HRM) marker, which can discriminate C/T SNP (254PMR-HRM3). The 254PMR-HRM3 marker was evaluated in 138 $F_{2:3}$ plants of a segregating population ('SBA' ${\times}$ PI254744) and was presumed to be 4.3 cM from the resistance locus. These results could ensure P. xanthii 1W-AN resistance in watermelon germplasm and aid watermelon cultivar development in marker-assist breeding programs.

• Korean Journal of Medicinal Crop Science
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• v.12 no.1
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• pp.53-59
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• 2004

Finding a means to discriminate the commercial herb medicines when they were dried and sliced is a very important and imminent project in Korea. To differentiate plant origins and the commercial herb medicines of Atractylodes japonica and A. macrocephala, two discriminative methods using anatomical characteristics and SCAR marker were applied. It was possible to discriminate plant origins and the commercial herb medicines between A. japonica and A. macrocephala by anatomical characteristics: development of periderm, layer of stone cell, distribution of laticiferous vessels, development of xylem fiber in xylem ray, contained quantity of clustered crystals and others. While, two SCAR markers were developed from RAPD clones: SAjR2 (600 bp) from AjR2 and SAmR1 (1,200 bp) from AmR1. These two markers were enough for discrimination plant origins and the commercial herb medicines between A. japonica and A. macrocephala. The result of application of anatomical characteristics and SCAR markers to investigate current status in domestic herb market, Daegu and Kumsan herb market, it was identified to be current herb medicines of A japonica.

• The Plant Pathology Journal
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• v.22 no.1
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• pp.36-45
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• 2006

Twenty isolates of Didymella bryoniae were isolated from infected cucurbit plants in various growing areas of southern Korea in 2001 and 2002. Random Amplified Polymorphic DNA (RAPD) group [RG] I of D. bryoniae was more virulent than RG IV to watermelon. Virulence of the RG I isolate was strong to moderate to cucumber, whereas that of the RG IV varied from strong, moderate to weak. Two hundred seventy-three amplified fragments were produced with 40 primers, and were analyzed by a cluster analysis using UPGMA method with an arithmetic average program of NTSYSPC. At the distance level of 0.7, two major genomic DNA RAPD groups were differentiated among 20 isolates. The RG I included 7 isolates from watermelon and one isolate from melon, whereas the RG IV included 12 isolates from squash, cucumber, watermelon and melon. Amplification of internal transcribed spacer (ITS) region and small subunit rRNA region from the 20 isolates yielded respectively a single fragment. Restriction pattern with 12 restriction enzymes was identical for all isolates tested, suggesting that variation in the ITS and small subunit within the D. bryoniae were low. Amplification of the genomic DNAs of the tested isolates with the sequence characterized amplified regions (SCAR) primer RG IF-RG IR specific for RG I group resulted in a single band of 650bp fragment for 8 isolates out of the 20 isolates. Therefore, these 8 isolates could be assigned into RG I. The same experiments done with RG IIF-RG IIR resulted in no amplified PCR product for the 20 isolates tested. An about 1.4 kb-fragment amplified from the RG IV isolates was specifically hybridized with PCR fragments amplified from genomic DNAs of the RG IV isolates only, suggesting that this PCR product could be used for discriminating the RG IV isolates from the RG I isolates as well other fungal species.

• Journal of Life Science
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• v.20 no.12
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• pp.1764-1771
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• 2010

Carthamus tinctorius L. (Compositae) is an herb primarily distributed throughout in the world. The species is regarded as ecologically important in the world. Safflower was used for medicines, as well as making red (carthamin) and yellow dyes. We have used the RAPD technique to investigate the phylogenetic relationships and genetic diversity of C. tinctorius. We obtained 123 bands from all the 26 cultivars. The average number of bands was 9.5 per primer. The genetic diversity of safflower is found among cultivars and there is a high among-cultivar differentiation. The OPC18-01 band is the specific marker for Syria cultivar, whereas no products were detected in individuals from other country cultivars. We found seven phenetic bands for determining the specific marker of cultivars with SCAR markers. Though the number of individuals sampled for analysis was small and probably not fully representative of the total available diversity in C. tinctorius, this study demonstrates that the regions (Morocco, Syria, and Turkey) of the Mediterranean Sea were more variable than other regions with the exception of India. In this result, although only simple result of RAPD is difficult to assert the center of species diversity of C. tinctorius, the regions of the Mediterranean Sea may be the most probable candidate for the origin of safflower. India was also the candidate of the center or secondary center of species diversity of C. tinctorius. RAPD markers were effective in classifying cultivar levels of safflower.

• Korean Journal of Breeding Science
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• v.42 no.5
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• pp.495-501
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• 2010

Peaches (Prunus persica) are less popular than the fresh fruits, because their flesh gets soft faster. So many breeders focused on their aim to firmness. Other breeders focused on juiciness, flavor and aroma. Breeding requires much labor, time and money. To reduce these requirements, many scientists develop many SSR, CAPS and SCAR makers. New peach varieties bred in our National Institute of Horticultural & Herbal Science (NIHHS) such as, Cheonhong, Suhong and Harhong are yellow flesh cultivars and Yumyeong, Baekmijosaeng, Baekhyang, Jinmi, Soomee, Mihong, Misshong and Yumee are white flesh cultivars. These peach cultivars are planted in orchard of Korea. To assert breeding cultivar patents and prevent patent disputes, we detected cultivar-specific DNA fragment using 235 sets of Operon RAPD primers, analyzed 134 DNA sequences and constructed SCAR primers. To confirm the cultivar-specific SCAR markers, we applied candidate SCAR primers to 30 peach cultivars widely cultivated in Korea. These selected lines are included father and mother lines that were used to develop new varieties in NIHHS. Using fourteen SCAR primer sets, we characterized thirty cultivars selected. The SCAR marker is expected to serve as molecular evidence distinguishing different peach varieties.