• Title/Summary/Keyword: Specific markers

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Development of SSR Markers for Identification of Korean Ginseng (Panax ginseng C. A. Meyer) Cultivars (SSR 마커를 이용한 고려인삼 품종 판별기술 개발)

  • Bang, Kyong-Hwan;Chung, Jong-Wook;Kim, Young-Chang;Lee, Jei-Wan;Jo, Ick-Hyun;Seo, A-Yeon;Kim, Ok-Tae;Hyun, Dong-Yun;Kim, Dong-Hwi;Cha, Seon-Woo
    • Korean Journal of Medicinal Crop Science
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    • v.19 no.3
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    • pp.185-190
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    • 2011
  • The principal objective of this study was to develop a discrimination method using SSR markers in Korean ginseng cultivars. Five cultivars--Chunpoong, Yunpoong, Gopoong, Sunpoong, and Kumpoong--were evaluated by nine markers out of 22 SSR markers. A total of 23 alleles were detected, ranging from 1 to 4, with an average of 2.6 alleles per locus, and an averages of gene diversity (GD) of 0.480. Nine markers were tested in order to distinguish among five Korean ginseng cultivars. Two markers out of nine SSR markers, GB-PG-065 and GB-PG-142, were selected as key markers for discrimination among Korean ginseng cultivars. Two genotypes were detected in GB-PG-065. Chunpoong and Kumpoong shared the same allele type, and Yunpoong, Gopoong, and Sunpoong shared another identical allele type. In the case of GB-PG-142, a specific allele type differentiated from those of other four cultivars was observed only in Sunpoong cultivar. Consequently, the SSR markers developed in this study may prove useful for the identification of Korean ginseng cultivars and the development of ginseng seed management systems, as well as tests to guarantee the purity of ginseng seeds.

Identification of tobacco Burley species specific marker in several tobacco species by AFLP (AFLP 방법을 이용한 담배 버어리종 특이 프라이머의 개발)

  • Lee, Yung-Gi;Jung, Suk-Hun;Keum, Wan-Soo;Lee, Jeong-Heon;Lee, Cheong-Ho;Rhee, Moon-Soo
    • Journal of the Korean Society of Tobacco Science
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    • v.28 no.2
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    • pp.94-99
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    • 2006
  • AFLP(Amplified Fragment Length Polymorphism) analysis was conducted to cultivars of tobacco, Nicotiana tabacum in order to select the cultivar-specific markers. AFLP results using 12 primer sets revealed genetic diversity among 12 field grown tobacco cultivars. Polymorphic fragments amplified by PCR was purified and cloned to identify their nucleotide sequences. From the sequences of them, 40 primer sets were designed to select cultivar-specific markers. When genomic DNA isolated from tobacco were used as PCR template, a set of primers, BrSF/BrSR showed Burley-specific band patterns. The results indicate that AFLP technique used in this experiments is useful for identifying tobacco cultivars in a rapid manner.

Characterization of Indian Riverine Buffaloes by Microsatellite Markers

  • Sukla, Soumi;Yadav, B.R.;Bhattacharya, T.K.
    • Asian-Australasian Journal of Animal Sciences
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    • v.19 no.11
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    • pp.1556-1560
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    • 2006
  • Six breeds of riverine buffalo viz. Murrah, Mehsana, Jaffrabadi, Nagpuri, Nili-Ravi and Bhadawari were characterized using FAO-recommended cattle specific microsatellite markers. Among the total of twenty microsatellite markers screened to explore genomic variability of six buffalo breeds, only ten were polymorphic in nature. Four out of ten polymorphic microsatellite loci were rated as informative. The numbers of alleles detected ranged from 2 to 7, with a mean of $5.5{\pm}0.07$ per microsatellite marker. The most polymorphic marker was BM1818 with a total of 7 alleles present at this locus. One breed specific marker was found in each of Mehsana (BM1818) and Bhadawari (ILSTS030) and four were found in Jaffarabadi (BM1818, ILSTS030, ILSTS054 and ILSTS011). Genetic distance (Ds) between the Mehsana and Bhadawari breed was the maximum (0.29), followed by Murrah and Mehsana (0.27), and Nili-Ravi and Bhadawari (0.26). The lowest Ds was found between the Jaffrabadi and Nagpuri breeds which was only 0.05. The highest divergence time of 1318 years was established between Mehsana and Bhadawari breeds whereas it was found to be lowest (272 years) between the Jaffrabadi and Nagpuri breeds.

Proteomic analysis of porcine pancreas development

  • Choi, Jong-Soon;Cho, Young-Keun;Yoon, Sung-Ho;Kwon, Sang-Oh;Koo, Deog-Bon;Yu, Kweon
    • BMB Reports
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    • v.42 no.10
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    • pp.661-666
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    • 2009
  • Porcine pancreas development is not well studied at the molecular level despite being a therapeutic resource for diabetic patients. In this study, we investigated expression of lineage markers and performed proteomic analysis. Expression of the early lineage markers Pdx1 and Ptf1a was developmentally conserved between mice and pigs, whereas expression of the islet differentiation marker Pax4 was delayed in porcine compared with murine pancreas development. Proteomic analysis found that expression levels of chymotrypsinogen were down-regulated during porcine pancreas development while those of digestive enzymes like lipases, elastase and serine protease were up-regulated. In addition, specific isoforms of protein folding assistants such as protein disulfide isomerase and prefoldin were expressed at specific stages during the maturation of digestive enzymes. Taken together, these results show that development of the porcine pancreas is regulated by a concerted interplay of pancreas lineage marker proteins and other specified proteins, resulting in a functional endocrine and exocrine organ.

Genetic Differences and Variation of Ascidians, Halocynthia roretzi von Drasche and H. hilgendorfi Oka Identified by PCR Analysis

  • Yoon, Jong-Man;Kim, Jong-Yeon
    • Development and Reproduction
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    • v.15 no.4
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    • pp.359-364
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    • 2011
  • The seven selected primers OPA-02, OPA-04, OPA-18, OPD-07, OPD-08, OPD-15 and OPD-16 were used to generate unique shared loci to each species and shared loci by the two species. The hierarchical dendrogram indicates three main branches: cluster 1 (RORETZI 01~RORETZI 11) and cluster 2 (HILGENDORF 12~HILGENDORF 22) from two geographic populations of ascidians, Halocynthia roretzi and H. hilgendorfi. The shortest genetic distance displaying significant molecular difference was between individuals' HILGENDORF no. 14~HILGENDORF no. 19 (genetic distance =0.008). Ultimately, individual no. 02 of the RORETZI ascidian was most distantly related to HILGENDORF no. 21 (genetic distance=0.781). These results demonstrate that the H. roretzi population is genetically different from the H. hilgendorfi population. From what has been said above, the potential of PCR analysis to identify diagnostic markers for the identification of two ascidian populations has been demonstrated. Generally speaking, using a variety of decamer primers, this PCR method has been applied to identify specific markers particular to line, species and geographical population, as well as genetic diversity/polymorphism in diverse species of organisms.

Use of Cattle Microsatellite Markers to Assess Genetic Diversity of Thai Swamp Buffalo (Bubalus bubalis)

  • Sraphet, Supajit;Moolmuang, Benchamart;Na-Chiangmai, Ancharlie;Panyim, Sakol;Smith, Duncan R.;Triwitayakorn, Kanokporn
    • Asian-Australasian Journal of Animal Sciences
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    • v.21 no.2
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    • pp.177-180
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    • 2008
  • In this study, cattle microsatellite markers recommended for diversity studies of cattle by the EU AIRE 2066 Concerted Action Group were used to study the genetic diversity of 105 Thai swamp buffalo which were randomly selected from eight different research stations of the Department of Livestock Development, Thailand. Of 34 primer pairs, 16 were successfully amplified while the rest showed non-specific amplification. The lowest number of alleles was two while the highest was nine, with an average of 4.7 alleles per locus. The average unbiased heterozygosity for all eight populations was 0.5233, with a low of 0.4772 (Samui) and a high of 0.5616 (Burirum). The genetic distance ranged from 0.0574 to 0.2575. Populations from Lopburi and Burirum showed the closest relationship, whereas Srisagat and Samui were the most divergent. The results generated with the primers recommended by the EU AIRE 2066 Concerted Action Group are at a slight variance from our previous study, possibly as a result of the number of specific amplification products obtained, suggesting that cattle markers may not be optimal for studies of the genetic diversity of the Thai swamp buffalo.

Capillary Gel Electrophoretic Analysis of Cattle Breeds Based on Difference of DNA Mobility of Microsatellite Markers

  • Lee, Mi-Ji;Yoon, Du-Hak;Jeon, Jin-Tae;Eo, Seong-Kug;Kang, Seong-Ho
    • Bulletin of the Korean Chemical Society
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    • v.30 no.11
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    • pp.2655-2660
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    • 2009
  • A breed of cattle, i.e., Korean cattle (Hanwoo), was identified based on the DNA mobilities of their microsatellites (MSs) by capillary gel electrophoresis (CGE) with a laser-induced fluorescence (LIF) detector. The MS markers were used for the accurate identification of species-specific genes. The DNA mobilities of the MS markers of Hanwoo and Holstein were measured using a CGE system with a fused-silica capillary (inner diameter of 75 ${\mu}m$, outer diameter of 365 ${\mu}m$, and total length of 50 cm). The capillary was dynamically coated with 1.0% (w/v) polyvinylpyrrolidone ($M_r$ = 1,000,000) and then filled with a mixture of 1.3% (w/v) poly(ethylene oxide) ($M_r$ = 600,000) and 1.9% (w/v) poly(ethylene oxide) (Mr = 8,000,000) as a sieving gel matrix. The species-specific genes of Hanwoo and Holstein were clearly distinguished within 33 min. This CGE assay technique is expected to be a useful analytical method for the fast and accurate identification of breeds of cattle.

Genetic information analysis for the development of an event-specific PCR marker for herbicide tolerance LM crops

  • Do Yu, Kang;Myung Ho, Lim;Soo In, Sohn;Hyun Jung, Kang;Tae Sung, Park
    • Korean Journal of Agricultural Science
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    • v.48 no.4
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    • pp.1051-1065
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    • 2021
  • Recent times have seen sustained increases in genetically modified (GM) crops not only for cultivation but also for the utility of food and feed worldwide. Domestically, commercial planting and the accidental or unintentional release of living modified (LM) crops into the environment are not approved. Many detection methods had been devised in an effort to realize effective management of the safety of agricultural genetic resources. In order to develop event-specific polymerase chain reaction (PCR) markers for LM crops, we analyzed the genetic information of LM crops. Genetic components introduced into crops are of key importance to provide a basis for the development of detection methods for LM crops. To this end, a total of 18 varieties from four major LM crop species (maize, canola, cotton, and soybeans) were subjected to an analysis. The genetic components included introduced genes, promoters, terminators and selection markers. Thus, if proper monitoring techniques and single or multiplex PCR strategies that rely on selection markers can be established, such an accomplishment can be regarded as a feasible solution for the safe management of staple crop resources.

Forensic Body Fluid Identification by Analysis of Multiple RNA Markers Using NanoString Technology

  • Park, Jong-Lyul;Park, Seong-Min;Kim, Jeong-Hwan;Lee, Han-Chul;Lee, Seung-Hwan;Woo, Kwang-Man;Kim, Seon-Young
    • Genomics & Informatics
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    • v.11 no.4
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    • pp.277-281
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    • 2013
  • RNA analysis has become a reliable method of body fluid identification for forensic use. Previously, we developed a combination of four multiplex quantitative PCR (qRT-PCR) probes to discriminate four different body fluids (blood, semen, saliva, and vaginal secretion). While those makers successfully identified most body fluid samples, there were some cases of false positive and negative identification. To improve the accuracy of the identification further, we tried to use multiple markers per body fluid and adopted the NanoString nCounter system instead of a multiplex qRT-PCR system. After measuring tens of RNA markers, we evaluated the accuracy of each marker for body fluid identification. For body fluids, such as blood and semen, each body fluid-specific marker was accurate enough for perfect identification. However, for saliva and vaginal secretion, no single marker was perfect. Thus, we designed a logistic regression model with multiple markers for saliva and vaginal secretion and achieved almost perfect identification. In conclusion, the NanoString nCounter is an efficient platform for measuring multiple RNA markers per body fluid and will be useful for forensic RNA analysis.

Single nucleotide polymorphism marker combinations for classifying Yeonsan Ogye chicken using a machine learning approach

  • Eunjin, Cho;Sunghyun, Cho;Minjun, Kim;Thisarani Kalhari, Ediriweera;Dongwon, Seo;Seung-Sook, Lee;Jihye, Cha;Daehyeok, Jin;Young-Kuk, Kim;Jun Heon, Lee
    • Journal of Animal Science and Technology
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    • v.64 no.5
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    • pp.830-841
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    • 2022
  • Genetic analysis has great potential as a tool to differentiate between different species and breeds of livestock. In this study, the optimal combinations of single nucleotide polymorphism (SNP) markers for discriminating the Yeonsan Ogye chicken (Gallus gallus domesticus) breed were identified using high-density 600K SNP array data. In 3,904 individuals from 198 chicken breeds, SNP markers specific to the target population were discovered through a case-control genome-wide association study (GWAS) and filtered out based on the linkage disequilibrium blocks. Significant SNP markers were selected by feature selection applying two machine learning algorithms: Random Forest (RF) and AdaBoost (AB). Using a machine learning approach, the 38 (RF) and 43 (AB) optimal SNP marker combinations for the Yeonsan Ogye chicken population demonstrated 100% accuracy. Hence, the GWAS and machine learning models used in this study can be efficiently utilized to identify the optimal combination of markers for discriminating target populations using multiple SNP markers.