• Title, Summary, Keyword: molecular markers

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General properties and phylogenetic utilities of nuclear ribosomal DNA and mitochondrial DNA commonly used in molecular systematics

  • Hwang, Ui-Wook;Kim, Won
    • The Korean Journal of Parasitology
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    • v.37 no.4
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    • pp.215-228
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    • 1999
  • To choose one or more appropriate molecular markers or gene regions for resolving a particular systematic question among the organisms at a certain categorical level is still a very difficult process. The primary goal of this review, therefore, is to provide a theoretical information in choosing one or more molecular markers or gene regions by illustrating general properties and phylogenetic utilities of nuclear ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA) that have been most commonly used for phylogenetic researches. The highly conserved molecular markers and/or gene regions are useful for investigating phylogenetic relationships at higher categorical levels (deep branches of evolutionary history). On the other hand, the hypervariable molecular markers and/or gene regions are useful for elucidating phylogenetic relationships at lower categorical levels (recently diverged branches). In summary, different selective forces have led to the evolution of various molecular markers or gene regions with varying degrees of sequence conservation. Thus, appropriate molecular markers or gene regions should be chosen with even greater caution to deduce true phylogenetic relationships over a broad taxonomic spectrum.

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An Overview for Molecular Markers in Plants (식물에서 분자 마커의 동향)

  • Huh, Man Kyu
    • Journal of Life Science
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    • v.25 no.7
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    • pp.839-848
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    • 2015
  • A molecular marker is a molecule contained within a sample taken from an organism or other matter. The development of molecular techniques for genetic analysis has led to a great contribution to our knowledge of plant genetics and our understanding of the structure and behavior of various genomes in plants. Recently, functional molecular markers have been developed to detect the presence of major genes from the analysis of pedigreed data in absence of molecular information. DNA markers have developed into many systems based on different polymorphism-detecting techniques or methods such as RFLP, AFLP, RAPD, SSR, SNP, etc. A new class of very useful DNA markers called genic molecular markers utilizing the ever-increasing archives of gene sequence information being accumulated under the EST sequencing projects on a large number of plant species. Functional markers are derived from polymorphic sequences, and are more likely to be involved in phenotypic trait variation. Based on this conceptual framework, the marker systems discussed below are all (gene)-targeted markers, which have the potential to become functional. These markers being part of the cDNA/EST-sequences, are expected to represent the functional component of the genome i.e., gene(s), in contrast to all other random DNA based markers that are developed/generated from the anonymous genomic DNA sequences/domains irrespective of their genic content/information. Especially I sited Poczai et al’ reviews, advances in plant gene-targeted and functional markers. Their reviews may be some useful information to study molecular markers in plants.

Combined Genome Mapping of RFLP-AFLP-SSR in Pepper

  • Lee, Je Min;Kim, Byung-Dong
    • Genomics & Informatics
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    • v.1 no.2
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    • pp.108-112
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    • 2003
  • We have constructed a molecular linkage map of pepper (Capsicum spp.) in an interspecific $F_2$ population of 107 plants with 320 RFLP, 136 AFLP, and 46 SSR markers. The resulting linkage map consists of 15 linkage groups covering 1,720 cM with an average map distance of 3.7 cM between framework markers. Most RFLP markers ($80\%$) were pepper-derived clones and these markers were evenly distributed all over the genome. Genes for defense and biosynthesis of carotenoids and capsaicinoids were mapped on this linkage map. By using 30 primer combinations, AFLP markers were generated in the $F_2$ population. For development of SSR markers in Capsicum, microsatellites were isolated from two small-insert genomic libraries and the GenBank database. This combined map provides a starting point for high-resolution QTL analysis, gene isolation, and molecular breeding.

Linkage Map Construction and Molecular Genetic Approach in Capsicum spp.

  • Kim, Byung-Dong
    • Korean Journal of Plant Tissue Culture
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    • v.27 no.5
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    • pp.367-373
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    • 2000
  • We have constructed a molecular linkage map of chili pepper (Capsicum spp.) in an interspecific (C. annuum cv. TF68 x C. chinense cv. Habanero) F$_2$ population of 107 plants with 150 RFLP and 430 AFLP markers. The resulting linkage map consists of 11 large (206-60.3 cM) and 5 small (32.6- 10.3 cM) linkage groups cover-ing 1,320 cM with an average map distance between framework markers of 7.5 cM. Most (80%) of the RFLP markers were pepper-derived clones and these markers were evenly distributed across the genome. By using 30 primer combinations, 444 AFLP markers were generated in the F$_2$population. The majority of the AFLP markers clustered in each linkage group, although PstI/MseI markers were more evenly distributed than Eco RI/MseI markers within the linkage groups. Genes for biosynthesis of carotenoids and capsaicinoids were mapped on our linkage map. This map will provide the basis of studying secondary metabolites in pepper.

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Characterization of Pyrenophora graminea Markers Associated with a Locus Conferring Virulence on Barley

  • Mokrani, Lubna;Jawhar, Mohammad;Shoaib, Amina;Arabi, Mohammad Imad Eddin
    • The Plant Pathology Journal
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    • v.28 no.3
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    • pp.290-294
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    • 2012
  • The fungus Pyrenophora graminea is the causal agent of barley leaf stripe disease. Two leaf stripe isolates PgSy3 (exhibiting high virulence on the barley cultivar 'Arabi Abiad') and PgSy1 (exhibiting low virulence on Arabi Abiad), were mated and 63 progeny were isolated and phenotyped for the reaction on Arabi Abiad. The population segregated in a 1:1 ratio, 32 virulent to 31 avirulent (${\chi}^2$ = 0.05, P = 0.36), indicating single gene control of PgSy3 virulence on Arabi Abiad. Among 96 AFLP markers identified, three AFLP markers, E37M50-400, E35M59-100 and E38M47-800 were linked to the virulence locus VHv1 in isolate PgSy3. The results of this study indicate that (the three markers) are closely linked to VHv1 and are unique to isolates carrying the virulence locus. This work represents an initial step towards map-based cloning of VHv1 in P. graminea.

Molecular Immunological Markers for the Toxicological Investigation: Experiences from Lead-Induced Immunotoxicities

  • Yong Heo;David A. Lawrence;Kim, Hyoung-Ah
    • Proceedings of the Korean Society of Toxicology Conference
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    • pp.15-20
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    • 2003
  • Molecular immunological methods are extensively applied to toxicological investigations. Furthermore, various immunological markers have been developed to substantiate molecular mechanisms of xenobiotics-mediated immunotoxicities. We discuss molecular immunological approach to evaluate lead (Pb)-induced immune alteration resulting in suppression of IFN${\gamma}$ production, and its value for establishing useful immunotoxicological markers.(omitted)

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Applications of molecular markers in the discrimination of Panax species and Korean ginseng cultivars (Panax ginseng)

  • Jo, Ick Hyun;Kim, Young Chang;Kim, Dong Hwi;Kim, Kee Hong;Hyun, Tae Kyung;Ryu, Hojin;Bang, Kyong Hwan
    • Journal of Ginseng Research
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    • v.41 no.4
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    • pp.444-449
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    • 2017
  • The development of molecular markers is one of the most useful methods for molecular breeding and marker-based molecular associated selections. Even though there is less information on the reference genome, molecular markers are indispensable tools for determination of genetic variation and identification of species with high levels of accuracy and reproducibility. The demand for molecular approaches for marker-based breeding and genetic discriminations in Panax species has greatly increased in recent times and has been successfully applied for various purposes. However, owing to the existence of diverse molecular techniques and differences in their principles and applications, there should be careful consideration while selecting appropriate marker types. In this review, we outline the recent status of different molecular marker applications in ginseng research and industrial fields. In addition, we discuss the basic principles, requirements, and advantages and disadvantages of the most widely used molecular markers, including restriction fragment length polymorphism, random amplified polymorphic DNA, sequence tag sites, simple sequence repeats, and single nucleotide polymorphisms.

Genetic Diversity Analysis of Maintaining Lines for Kenyan Sunflower (Helianthus annus L.) Using Allele Specific SSR Markers

  • Mwangi, Esther W.;Lee, Myung-Chul;Sung, Jung Suk;Marzougui, Salem;Bwalya, Ernest C.
    • Proceedings of the Plant Resources Society of Korea Conference
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    • pp.61-61
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    • 2019
  • In any crop breeding program Selection and use of genetically diverse genotypes to develop cultivars with a broad genetic base is important. Molecular markers play a major role in selecting diverse genotypes. Molecular breeding programs of the crop can be made more efficient by use of molecular markers. The present study was done with an aim of analyzing genetic diversity and the population structure in 24 accessions of sunflower (Helianthus annus L.) from Kenya genetic diversity using 35 EST-SSR and gSSR primers.Out of the 35 markers 3 were not polymorphic as they indicated Polymorphic Information content( PIC) of value 0.00 and so the data analysis was done using 32 markers . The 32 set of markers used produced 29 alleles ranging from 2 to 7with a mean of 3.0 alleles per locus.The average value of polymorphic information contents(PIC) were 0.3 .Genetic diversity analysis using these markers revealed 3 major clusters. This result could be useful for designing strategies to make elite hybrid and inbreeding of crossing block for breeding and future molecular breeding programs to make elite variety.

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Utility of taxon-specific molecular markers for the species identification of herbarium specimens: an example from Desmarestia japonica (Phaeophyceae, Desmarestiales) in Korea

  • Lee, Sang-Rae;Lee, Eun-Young
    • Fisheries and aquatic sciences
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    • v.21 no.3
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    • pp.8.1-8.6
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    • 2018
  • Desmarestia japonica (Phaeophyceae, Desmarestiales) was recently established from the Japanese ligulate Desmarestia and is morphologically similar to D. ligulata. This species has been reported only from Japan. However, the taxonomic reports based on additional regional distributions are needed to clarify this taxonomic entity and its species boundaries. Because Desmarestia species have restricted distributions in Korea, we reexamined herbarium specimens of D. ligulata deposited at the National Institute of Biological Resources (South Korea). To improve the amplification efficiency of the polymerase chain reaction and avoid contamination by the DNA of other organisms, we developed taxon-specific molecular markers suitable for DNA barcoding of Desmarestia species. Nuclear ribosomal small subunit RNA (18S rDNA) and mitochondrial cytochrome c oxidase 1 (cox1) regions were selected as target DNA. As a result, both were successfully isolated from herbarium specimens of D. japonica acquired over 10 years. These molecular markers provide useful genetic information for herbarium specimens for which conventional molecular analysis is challenging.

Estimation of Genetic Variation of Korean Isolates of Phytophthora capsici by Using Molecular Markers

  • Chee, Hee-Youn;Jee, Hyeong-Jin
    • Mycobiology
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    • v.29 no.1
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    • pp.43-47
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    • 2001
  • Genetic diversity of 21 Korean Phytophthora capsici isolates was analyzed by using several molecular markers such as random amplified polymorphic DNA(RAPD), M-13, microsatellite and random amplified microsatellite sequences(RAMS). The overall average similarity coefficient among the isolates was 86% based on the combined data obtained by the molecular markers. No molecular markers were found to be associated with hosts or geographic regions. In addition to RAPD, analysis based on repeated sequences such as $(GTG)_5$, M-13 and RAMS could be used to assess population structure of P. capsici.

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