식물에서 분자 마커의 동향

허만규(Man Kyu Huh) 한국생명과학회 2015 생명과학회지 Vol.25 No.7

분자 마커는 유기체에서 다른 유기체와 분자적 수준에서 식별하는 마커이다. 유전적 분석을 위한 분자 마커의 발달은 식물 유전학, 다양한 구조와 가능을 이해하는데 기여하였다. DNA 마커는 임의유전자 증폭에서 다형성을 탐지하는 기법이나 방법(예를 들면 서든 블로팅, 핵산 교잡법, PCR을 이용한 중합효소 연쇄 증폭 반응, DNA 서열화)으로 RFLP, AFLP, RAPD, SSR, SNP 등을 이용하였고 현재에도 이용하고 있다. 최근 기능성 유전자를 이용한 기능성 마커가 각광을 받고 있다. 기능성 마커는 다형성 서열에서 유래한 것으로 표현형 변이를 내포하고 있다. 이런 개념에서 출발한 기능성 마커는 모든 유전자를 타깃으로 할 수 있으나 식물에서는 P450, 튜블린 형성 유전자의 다형성(TBPs), 전이요소 마커(TEMs), 병원균 저항성 유전자 마커(RGMs), RNA를 기반으로 한 마커(RBMs) 등이 널리 이용되고 있다. 본 연구는 Poczai 등의 총설을 기반으로 구성하였다. 식물에서 이런 분자 마커의 이용은 식물의 분화, 진화, 생리적 기능성 유전자의 변화 등 생물학 전반에 관한 정보 획득에 도움을 될 것이다. 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.

NABIC marker database: A molecular markers information network of agricultural crops

Kim, Chang-Kug,Seol, Young-Joo,Lee, Dong-Jun,Jeong, In-Seon,Yoon, Ung-Han,Lee, Gang-Seob,Hahn, Jang-Ho,Park, Dong-Suk Biomedical Informatics 2013 Bioinformation Vol.9 No.17

<P>In 2013, National Agricultural Biotechnology Information Center (NABIC) reconstructs a molecular marker database for useful genetic resources. The web-based marker database consists of three major functional categories: map viewer, RSN marker and gene annotation. It provides 7250 marker locations, 3301 RSN marker property, 3280 molecular marker annotation information in agricultural plants. The individual molecular marker provides information such as marker name, expressed sequence tag number, gene definition and general marker information. This updated marker-based database provides useful information through a user-friendly web interface that assisted in tracing any new structures of the chromosomes and gene positional functions using specific molecular markers.</P><P><B>Availability</B></P><P>The database is available for free at http://nabic.rda.go.kr/gere/rice/molecularMarkers/</P>

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

Ick Hyun Jo,Young Chang Kim,Dong Hwi Kim,Kee Hong Kim,Tae Kyung Hyun,Hojin Ryu,Kyong Hwan Bang 고려인삼학회 2017 Journal of Ginseng Research Vol.41 No.4

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.

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 The Korean Society of Ginseng 2017 Journal of Ginseng Research Vol.41 No.4

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.

식물신품종분쟁 사례 분석으로 본 품종판별기술로써 분자표지의 적용 전망

권순호,강규석 한국국제농업개발학회 2018 韓國國際農業開發學會誌 Vol.30 No.1

New varieties of various plants are being developed, and disputes related to plant genetic resources are increasing. The sovereignty of genetic resources and developmental interests are expected to become complicated due to the pursuit of breed conservation policies and economic interests. The breed dispute has been judged on the basis of cultivation adaptation test, substance analysis and molecular marker. Among them, research on genetic analysis techniques and functional molecular markers is actively applied as the rapidity and reproducibility in comparison with the development of technology and other techniques. Therefore, it would be more efficient and objective to improve discrimination technology using molecular markers. The purposes of this study were to identify the position of varieties discrimination technology using molecular markers in disputes based on the case study, and to suggest directions for future varieties discrimination techniques by comparing and analyzing dispute of the domestic and overseas varieties of crop plants. This study analyzed seven domestic and foreign cases. As a result, technology such as molecular markers has not yet been adopted as a crucial evidence in the dispute. On the other hand, the statistical data of the cultivation test on the phenotypic difference of the target traits were adopted as more definitive evidence. Therefore, molecular markers should be developed in the gene linked to the trait, and gene expression markers in quantitative traits should be developed. if also the breeders could develop molecular markers from the early stage of breed development, and if the dispute regulatory agency could apply the improved molecular markers to judge the verdict of new variety dispute, more efficient and objective judgment of breed disputes would be possible. 1. 전세계에서 식량문제 해결을 위해 다양한 식물 신품종들이 개발되고 있다. 이에 따라 식물 유전자원과 관련된 국내외 분쟁 또한 증가하고 있다. 2. 품종 분쟁 판결에 있어 재배시험, 물질분석 및 분자표지들이 근거로 제시되어 왔다. 그 중에서 유전적 분석 기법과 기능성 분자표지에 대한 연구가 신속성, 재현성, 기술 발달 등의 이유로 활발하게 적용되고 있다. 3. 국내외 7개의 분쟁 사례를 분석한 결과, 결정적인 증거자료로써 분자표지를 이용한 판별기술이 채택되고 있지는 않았다. 반면 목표 형질의 표현형 차이에 대한 재배시험의 통계적자료가 더욱 결정적인 증거자료로 채택되고 있었다. 분자표지가 충분한 증거로써 채택되지 못하는 원인은 분자표지 제공자의 객관성과 증거로 제시된 표지가 품종의 결정적 차이를 보이는 목적 형질과 연결되지 않았기 때문이었다. 4. 형질과 연결되지 않는 분자표지 대신 유전자 발현표지나 기능성 분자표지를 개발하여 적용하는 것이 더 효율적이고 합리적이라 판단한다. 5. 분쟁에서 근거로써 분자표지의 단점을 보완하여 분쟁에 적용한다면 품종 분쟁에 있어 보다 효율적이고 객관적인 판정이 이루어질 수 있을 것이다.

Distribution of MITE Transposons in a Rice Genetic Map

박경철,이주경,권순재,신지현,이점호,양찬인,김남수 한국육종학회 2004 한국육종학회지 Vol.36 No.2

Molecular genetic markers have wide applicability for a various genetic analyses, and genetic mapping with PCR-based markers has identified many loci in the rice genome. This study was conducted to develop a genetic map of rice based on SSR and MITE-AFLP markers. The F2 mapping population was established from a cross between Oryza sativa var. Ilpoombyeo (Japonica type variety) and O. rufipogon W259. A total of 334 markers, including 54 SSR and 280 MITE-AFLP markers, were mapped on rice chromosomes using an F2 population. Of these, 280 markers, including 226 MITE-AFLP and 54 SSR markers were found to be genetically linked to form 12 linkage groups. The size of framework map spanned 2899.7 cM of the 12 linkage groups. The average linkage distance between markers among all linkage groups was 10.4 cM. The number of markers per linkage group ranged from 15 to 37. Most of MITE-AFLP markers were well distributed through the twelve rice chromosomes. In this study, we have exploited the MITE-AFLP markers to develop a new class of molecular markers for rice genome study. These new markers are expected to provide valuable resources for map-based studies, such as marker-assisted selection, gene tagging, and the analysis of quantitative trait loci (QTLs) in rice genome research program.

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

조익현,김영창,김동휘,김기홍,현태경,류호진,방경환 고려인삼학회 2017 Journal of Ginseng Research Vol.41 No.4

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.

Research advances and prospects of molecular markers in sesame: a review

Weldemichael Micheale Yifter,Gebremedhn Hailay Mehari 한국식물생명공학회 2023 Plant biotechnology reports Vol.17 No.5

Sesame (Sesamum indicum L, 2n = 2x = 26) is one of the ancient and most important oilseed crops, extensively cultivated in tropical and sub-tropical countries. Due to its high oil quality and content, rich in vitamins and minerals, ingredients of medical products, antioxidant resistance as well as the main component in the production of soaps, cosmetics, perfumes, and insecticides, sesame is considered as the queen of oilseeds. In spite of its industrial, economical, medicinal and nutritional importance, sesame is considered as an orphan crop as very limited attention has been given from science, academia, industry and policy-makers. In recent years, the situation has substantially changed due to significant development in molecular markers. In this regard, numerous studies have been conducted on molecular markers and their importance in marker-assisted breeding, genetic conservation and genetic diversity. This paper, therefore, aims to review research advances and prospects of molecular markers employed so far for sesame genetic diversity and conservation studies. In this section, we present a review on different molecular techniques which were developed and used for sesame genetic improvement. We also pinpoint the progress of different molecular markers targeted for genetic diversity studies, germplasm conservation, cultivar identification, determination of genetic variation, construction of genetic linkage maps, identification of QTLs/genes and discovery of molecular markers using freely available online databases. Finally, this review identifies hot topics and upcoming directions for future sesame improvement programs.

Efficiency of Some Molecular Markers Linked to Rhizomania Resistance Gene (Rz1) for MarkerAssisted Selection in Sugar Beet

Peyman Norouzi,Mohammad Sabzehzari,Hasan Zeinali 한국작물학회 2015 Journal of crop science and biotechnology Vol.18 No.5

Sugar beet (Beta vulgaris L.) is one of the two major products supplying sugar (sucroses) in the world. Rhizomania is one of the most destructive diseases of sugar beet world-wide. Holly is the major source of resistance to rhizomania. The objectives of this study were to identify the dominant homozygous genotypes resistant to rhizomania using ZN1 molecular marker, to field evaluate S1 progenies of plants already proved to be containing the marker and also to determine the relationship of this and other SCAR (sequence characterized amplified region) markers with SNP1 (single nucleotide polymorphism) marker associated with the Rz1 gene. Molecular analysis was carried out on 27 O-type populations (consisting of 13 susceptible and 6 resistant genotypes). Field evaluation and scoring of the phenotypic traits including greenness, growth, uniformity and disease score of 12 O-type populations were carried out on a rhizomania-infested field. The percent agreement of coupling marker ZN1 and repulsion marker ZN8 with disease score was 0.91 and 0.93, respectively. Although all O-types had the Rz1 resistance gene but the phenotypic differences were observed due to the effect of different genetic backgrounds and modifier genes. Overall, the results showed that the selected markers can be used for marker-assisted selection (MAS) to reduce the time and cost of breeding programs and increase the efficiency of selection.

Analysis of Molecular Variance and Population Structure in Southern Indian Finger Millet Genotypes Using Three Different Molecular Markers

Host Antony David Rajendran,Ramakrishnan Muthusamy,Antony Caesar Stanislaus,Thirugnanasambantham Krishnaraj,Sivasankaran Kuppusamy,Savarimuthu Ignacimuthu,Naif Abdullah Al-Dhabi 한국작물학회 2016 Journal of crop science and biotechnology Vol.19 No.4

The genetic relationship among 42 genotypes of finger millet collected from different geographical regions of southern India was investigated using random amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR), and simple sequence repeats (SSR) markers. Ten RAPD primers produced 111 polymorphic bands. Five ISSR primers produced a total of 61 bands. Of these, 23 bands were polymorphic. The RAPD and ISSR fingerprints revealed 71.3 and 37.4% polymorphic banding patterns, respectively. Thirty-six SSR primers yielded 83 scorable alleles in which 62 were found to be polymorphic. Out of 36 SSR primers used, 14 primers (46.6%) produced polymorphic bands. The SSR primer UGEP7 produced a maximum number of six alleles. Mean polymorphic information content (PIC) of RAPD, ISSR and SSR were 0.44, 0.28, and 0.14, respectively. Molecular variances among the population were 2, 11, and 1% for RAPD, ISSR, and SSR markers, respectively. SSR produced 99% molecular variance within individuals. RAPD and ISSR markers produced a low level of molecular variance within individuals. The STRUCTURE (model-based program) analysis revealed that the 42 finger millet genotypes could be divided into a maximum of four subpopulations. Based on the Bayesian statistics, each RAPD and SSR marker produced three subpopulations (K=3), while ISSR marker showed four subpopulations (K=4). This study revealed that RAPD and SSR markers could narrow down the analysis of population structure and it may form the basis for finger millet breeding and improvement programs in the future.