• Title/Summary/Keyword: 분자마커

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SNP Marker Development for Purity Test of Oriental Melon and Melon (멜론 및 참외 순도 검정을 위한 SNP 마커 개발 및 F1 종자 순도 검정)

  • An, Song-Ji;Kwon, Jin-Kyung;Yang, Hee-Bum;Choi, Hye-Jeong;Jeong, Hee-Jin;Kim, Yong-Jae;Choi, Gyung-Ja;Kang, Byoung-Cheorl
    • Korean Journal of Breeding Science
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    • v.42 no.4
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    • pp.397-406
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    • 2010
  • Field screening method has been commonly used for purity test of $F_1$ hybrid seeds in melon and oriental melon. However, as this method takes a lot of time and cost, molecular marker-based purity test is necessary. To develop molecular markers for purity test, thirty pairs of SNP (single nucleotide polymorphism) primers were obtained from melon EST sequences, and 10 polymorphic markers showing HRM (high resolution melting) polymorphisms between parents of two melon cultivars and one oriental melon cultivar were selected. Blind tests were performed to validate usefulness of the selected markers for purity test. Blind test results showed that HRM genotypes were matched with the expected identity of individual sample, $F_1$ hybrid, male or female parents. Three HRM-based SNP markers were converted to CAPS markers for general use which is favor to breeders. We expect that SNP markers developed in this study will be useful for purity test of $F_1$ hybrid seeds in melon and oriental melon.

Taxonomy of Korean Calanthe species and few of its mutants based on AFLP data (AFLP에 의한 한국산 새우난초속 식물과 그의 수종 돌연변이에 대한 분류학적 연구)

  • Srikanth, Krishnamoorthy;Koo, Ja Choon;Ku, Jajung;Choi, Kyung;Park, Kwang-Woo;So, Soonku;Choi, Yong-Gook;Whang, Sung Soo
    • Korean Journal of Plant Taxonomy
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    • v.42 no.3
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    • pp.215-221
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    • 2012
  • Five Korean Calanthe species, C. discolor, C. bicolor, C. sieboldii, C. reflexa, and C. aristulifera, were studied using amplified fragment length polymorphism (AFLP) to assess their taxonomic and genetic relationships. Sixteen accessions belonging to five native Calanthe spp. and mutants with yellow tepal and white lip (YW mutants) were studied. We identified 50 putative markers using AFLP analysis. The results of AMOVA showed that genetic variance was higher between species than within species. Genetic dissimilarity when compared with the rest of the species was the lowest for individuals of the YW mutants and the highest for individuals of C. reflexa. The mutants clustered outside the major group. Calanthe bicolor clustered with C. discolor, suggesting that its genetic composition is closer to that of C. discolor. Though it is suggested to have originated as a result of natural hybridization between C. sieboldii and C. discolor, introgression is likely to have occurred in the direction of C. discolor based on the data of molecular marker, clustering and genetic dissimilarity. Calanthe reflexa and C. aristulifera were genetically the most diverse of the species studied. In conclusion, the results showed that there is genetic diversity in Korean Calanthe species, that C. bicolor introgressed in the direction of C. discolor and that the YW mutants are genetically closer to C. sieboldii.

Selection and Characterization of Horticultural Traits of Tomato leaf curl virus (TYLCV)-resistant Tomato Cultivars (토마토 황화잎말림바이러스(TYLCV) 저항성 품종 선발 및 원예특성 분석)

  • Kim, Woo-Il;Kim, Kwang-Hwan;Kim, Young-Bong;Lee, Heung-Su;Shon, Gil-Man;Park, Young-Hoon
    • Horticultural Science & Technology
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    • v.31 no.3
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    • pp.328-336
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    • 2013
  • This study was conducted to evaluate imported tomato $F_1$ cultivars as breeding materials for the resistance to Tomato yellow leaf curl virus (TYLCV) by molecular markers and bioassay. From marker genotyping and disease evaluation of 40 $F_1$ cultivars, most of the cultivars declared as TYLCV-resistance carried heterozygous marker genotype for the TYLCV resistance genes Ty-1, Ty-3, or Ty-3a, and showed low disease rates. Whereas, 4 of 5 $F_1$ cultivars declared as intermediate resistance showed marker genotype for susceptibility and disease rates ranged 18.1-33.3%. However, the xx cultivars showed inconsistency in marker genotype and disease rate. Characterization of horticultural traits of the $F_1$ cultivars with TYLCV-resistance indicated that large-size fruit cultivars were higher in yield and similar in sugar contents and solid-acid ratio compared to a control cultivar preferred in the domestic market, although hardness remained to be a problem. On the other hand, cherry tomato cultivars showed lower yield and brix, but longer internode compared to a control cultivar, indicating that breeding for TYLCV-resistance using these cultivars will require more efforts and time compared to large-sized.

Development of Solanum hougasii-specific markers using the complete chloroplast genome sequences of Solanum species (엽록체 전장유전체 정보를 이용한 Solanum hougasii 특이적 분자마커 개발)

  • Kim, Soojung;Park, Tae-Ho
    • Journal of Plant Biotechnology
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    • v.47 no.2
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    • pp.141-149
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    • 2020
  • Solanum hougasii, one of the wild Solanum species, has been widely used in potato breeding since it exhibits excellent resistance to diverse important pathogens. S. hougasii can be directly crossed with the cultivated tetraploid potato (S. tuberosum) owing to its EBN (Endosperm Balanced Number) value of 4, which is same as that of S. tuberosum although it is an allohexaploid. In this study, the complete chloroplast genome sequence of S. hougasii was obtained by next-generation sequencing technology, and compared with that of the chloroplast genome of seven other Solanum species to identify S. hougasii-specific PCR markers. The length of the complete chloroplast genome of S. hougasii was 155,549 bp. The structural organization of the chloroplast genome in S. hougasii was found to be similar to that of seven other Solanum species studied. Phylogenetic analysis of S. hougasii with ten other Solanaceae family members revealed that S. hougasii was most closely related to S. stoloniferum, followed by S. berthaultii, and S. tuberosum. Additional comparison of the chloroplast genome sequence with that of five other Solanum species revealed five InDels and 43 SNPs specific to S. hougasii. Based on these SNPs, four PCR-based markers were developed for the differentiation of S. hougasii from other Solanum species. The results obtained in this study will aid in exploring the evolutionary and breeding aspects of Solanum species.

PCR-based markers for discriminating Solanum demissum were developed by comparison of complete chloroplast genome sequences of Solanum species (가지속 식물의 엽록체 전장유전체 비교를 통한 PCR 기반의 Solanum demissum 특이적 분자마커 개발)

  • Park, Tae-Ho
    • Journal of Plant Biotechnology
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    • v.48 no.1
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    • pp.18-25
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    • 2021
  • Solanum demissum is one of the wild Solanum species originating from Mexico. It has wildly been used for potato breeding due to its resistance to Phytophthora infestans. S. demissum has an EBN value of four, which is same as that of S. tuberosum, so that it is directly crossable for breeding purposes with the cultivated tetraploid potato (S. tuberosum). In this study, the chloroplast genome sequence of S. demissum obtained by next-generation sequencing technology was described and compared with those of seven other Solanum species to develop S. demissum-specific markers. Thetotal sequence length of the chloroplast genome is 155,558 bp, and its structural organization is similar to those of other Solanum species. Phylogenetic analysis with ten other Solanaceae species revealed that S. demissum is most closely grouped with S. hougasii and S. stoloniferum followed by S. berthaultii and S. tuberosum. Additional comparison of the chloroplast genome sequence with those of seven other Solanum species revealed two InDels specific to S. demissum. Based on these InDels, two PCR-based markers for discriminating S. demissum from other Solanum species were developed. The results obtained in this study will provide an opportunity to investigate more detailed evolutionary and breeding aspects in Solanum species.

Stress Evaluation to Heavy Metal Exposure using Molecular Marker in Chironomus riparius (분자지표 유전자 발현을 통한 Chironomus riparius 중금속 노출 스트레스 평가)

  • Kim, Won-Seok;Park, Kiyun;Kwak, Ihn-Sil
    • Korean Journal of Ecology and Environment
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    • v.53 no.2
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    • pp.165-172
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    • 2020
  • Heavy metals are common pollutants in the freshwater environment and have toxicological effect in habitat organisms. The heavy metals highly accumulated in sediment and organism, and observed various physiological responses. In this study, we investigated the molecular response to heavy metal toxicity (Al, Aluminum; Cr, Chromium; Cu, copper; Mn, Manganese; Zn, Zinc) through expression of heat shock protein 40, 70, 90 (HSP40, 70, 90), cytochrome 450 (CYP450), Glutathione S-transferase (GST) and Serine-type endopeptidase (SP). HSPs showed up-regulation in Cu and Zn exposures. Furthermore, HSPs expression in treated groups tended to be higher than the control group. The tendency of CYP450 and GST mRNA expression was higher for Cr and Cu than for other exposure group. The expression of SP gene was low at Al exposure and other group were measured to be similar to control. These results suggest that heavy metal toxicity in freshwater ecosystem may affect physiological and molecular process. Also, the comprehensive gene expression in the aquatic midge Chironomus riparius give useful information to potential molecular biomarkers for assessing heavy metal toxicity.

Discrimination of Korean Agaricus bisporus cultivars using CAPS markers (CAPS 마커를 이용한 국내 개발 양송이 품종 구분)

  • Lee, Hwa-Yong;An, Hyejin;Oh, Youn-Lee;Jang, Kab-Yeul;Chung, Jong-Wook
    • Journal of Mushroom
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    • v.19 no.4
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    • pp.336-340
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    • 2021
  • The cleaved amplified polymorphic sequence (CAPS) marker uses a restriction enzyme recognition site resulting from single nucleotide polymorphisms and insertions and deletions on the DNA sequence. This technique does not require expensive equipment, the process is simple, and clear results can be obtained reliably. In this study, Agaricus bisporus cultivars SaeA, SaeDo, SaeHan, SaeYeon, SaeJeong, Dodam, Seolgang, Dahyang, Hogam, and Hadam developed in Korea were discriminated using four CAPS markers. Our results indicated that it is possible to distinguish the ten cultivars and determine the genetic diversity among them.

Molecular Phylogenetic Studies of Korean Calystegia R.Br. Based on ITS and psbA-trnH Sequences (ITS와 psbA-trnH 염기서열에 의한 한국산 메꽃속(Calystegia R.Br.)의 분류학적 연구)

  • Kim, SangJun;Park, SeonJoo
    • Korean Journal of Plant Taxonomy
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    • v.41 no.4
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    • pp.338-344
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    • 2011
  • Molecular phylogenetic studies were conducted to evaluate evolutionary trends, relationships and species identities among four species, one variety and one outgroup of the Korean Genus Calystegia. The important characteristics of Calystegia are the shape of the lamina, the length ofthe corolla and the presence of hair. However, many variations were observed as regards the characteristics of the leaf, making true identification difficult. In molecular phylogenetic studies, C. soldanella formed one clade, and it was located mostly in the base. C. hederacea and C. sepium did not form an independent clade in their ITS regions and psbA-trnH regions, and this investigation could not confirm a relationship. Therefore, a relationship between these two species is not sufficiently supported by these markers (ITS and psbA-trnH). Consequently, this research should be achieved through many samples and markers. C. sepium var. japonica and C. dahurica are closely related.

Molecular Monitoring of Plankton Diversity in the Seonakdong River and Along the Coast of Namhae (분자 모니터링을 이용한 서낙동강과 남해 연안 플랑크톤 군집 분석)

  • Kim, Bo-Kyung;Lee, Sang-Rae;Lee, Jin-Ae;Chung, Ik-Kyo
    • The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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    • v.15 no.1
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    • pp.25-35
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    • 2010
  • The biodiversity of eukaryotic plankton has commonly been used to evaluate the status of aquatic ecosystems. Therefore, an accurate and rapid method for species identification is needed to reveal the biodiversity of environmental water samples. To date, molecular methods have provided a great deal of information that has enabled identification of the hidden biodiversity in environmental samples. In this study, we utilized environmental polymerase chain reaction (PCR) and constructed the 18S nuclear ribosomal RNA clone library from environmental water samples in order to develop more efficient methods for species identification. For the molecular analysis, water samples were collected from the Seonakdong River (Gimhae Bridge) and the coast of Namhae,(Namhaedo). Colony PCR and restriction fragment length polymorphism of PCR (PCR-RFLP) were then adopted to isolate unique clones from the 18S rDNA clone library. Restriction fragment length polymorphism pattern analysis of the Gimhae Bridge sample revealed 44 unique clones from a total of 60 randomly selected clones, while analysis of the Namhae sample revealed 27 unique clones from 150 clones selected at random. A BLAST search and subsequent phylogenetic analysis conducted using the sequences of these clones revealed hidden biodiversity containing a wide range of taxonomic groups (Heterokontophyta (7), Ciliophora (23), Dinophyta (1), Chytridiomycota (1), Rotifera (1) and Arthropoda (11) in the Gimhae Bridge samples Ciliophora (4), Dinophyta (3), Cryptophyta (1), Arthropoda (19) in the Namhae samples). Therefore, the molecular monitoring method developed here can provide additional information regarding the biodiversity and community structure of eukaryotic plankton in environmental samples and helps construct a useful database of biodiversity for aquatic ecosystems.

Analysis of Genetic Relationship of Apple Varieties using Microsatellite Markers (Microsatellite 마커를 이용한 사과 품종 간 유전적 유연관계 분석)

  • Hong, Jee-Hwa;Kwon, Yong-Sham;Choi, Keun-Jin
    • Journal of Life Science
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    • v.23 no.6
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    • pp.721-727
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    • 2013
  • The objective of this study was to evaluate the suitability of microsatellite markers for variety identification in 42 apple varieties. For microsatellite analysis, 305 primer pairs were screened in 8 varieties and twenty six primer pairs showed polymorphism with clear band pattern and repetitive reproducibility. A total of 165 polymorphic amplified fragments were obtained in 42 varieties using 26 markers. Two to twelve alleles were detected for each locus with an average of 6.4 alleles per locus. A value of polymorphism information content (PIC) ranged from 0.461 to 0.849 with an average of 0.665. A total of 165 marker loci were used to calculate Jaccard's distance coefficients using unweighted pair-group method with arithmetical average (UPGMA) cluster analysis. Genetic distance of cluster ranged from 0.27 to 1.00. Analysis of genetic relationship revealed that these 26 microsatellite marker sets discriminated a total of 41 varieties except for 1 variety among 42 varieties. These markers will be utilized as molecular data in variety identification of apple.