• International Journal of Industrial Entomology and Biomaterials
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• 제41권2호
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• pp.56-62
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• 2020

Mulberry (Morus spp. family: Moraceae) has prime importance in the sericulture industry, and its foliage is the only natural feed of the silkworm Bombyx mori L. Traditional classification methods using morphological traits were largely unsuccessful in assessing the diversity and relationships among different mulberry species because of environmental influences on the traits of interest. For these reasons, it is difficult to differentiate between the varieties and cultivars of Morus spp. In the present study, inter-simple sequence repeat (ISSR) markers were used to investigate the genetic diversity of 48 mulberry samples genotyped using nine ISSR primers. The ISSR markers exhibited polymorphisms (53.2%) among mulberry genotypes. Furthermore, similarity coefficient estimated for these ISSR markers was found to vary between 0.67 and 0.99 for the combined pooled data. The phenogram drawn using the UPGMA cluster method based on combined pooled data of the ISSR markers divided the 48 mulberry genotypes into seven major groups. No genetic association was found in the collection area, and there was a mixed pattern between the mulberry lines. The hybridization between different mulberry species is highly likely to be homogenized due to natural hybridization.

• Plant Resources
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• 제6권1호
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• pp.16-26
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• 2003

Molecular markers are useful tools for evaluating genetic diversity and determining cultivar identity. Present study was conducted to evaluate the genetic diversity within a diverse collection of rice accessions used for Korean breeding programs. Two hundred eighty-seven rice cultivars, composed of temperate japonica, tropical japonica, indica, and Tongil-type of Korean crossing parents were evaluated by means of 15 simple sequence repeat (SSR) markers. A total of 99 alleles were detected, and the number of alleles per marker ranged from 4 to 11, with an average of 6.6 per locus. Polymorphism information content (PIC) for each of the SSR markers ranged from 0.2924 to 0.8102 with an average of 0.5785. These results, with the result that use of only 15 SSR markers made all rice cultivars examined could be uniquely distinguished, imply the efficiency of SSR markers for analysis of genetic diversity in rice. Cluster analysis was performed on similar coefficient matrics calculated from SSR markers to generate a dendogram in which two major groups corresponding to japonica (Group I) and indica and Tongil type rice (group II) with additional subclasses within both major groups. The narrowness of the Korean breeding germplasm was revealed by the fact that most of the Korean-bred and Japan-bred temperate japonica cultivars were concentrated into only 2 of the sub-group I-1 (143 cultivars) and I-2 (58 cultivars) among six sub-groups in major group of japonica. This is because of the japonica accessions used in this study was a very closely related ones because of frequent sharing of the crossing parents with similar genetic background with synergy effect of the inherited genetic difference between indica and japonica. A rice breeding strategy with the use of molecular markers was discussed for overcoming of genetic vulnerability owing to this genetic narrowness.

• Parasites, Hosts and Diseases
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• 제56권2호
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• pp.175-181
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• 2018

The giant roundworm Ascaris infects pigs and people worldwide and causes serious diseases. The taxonomic relationship between Ascaris suum and Ascaris lumbricoides is still unclear. The purpose of the present study was to investigate the genetic diversity and population genetic structure of 258 Ascaris specimens from humans and pigs from 6 sympatric regions in Ascaris-endemic regions of China using existing simple sequence repeat data. The microsatellite markers showed a high level of allelic richness and genetic diversity in the samples. Each of the populations demonstrated excess homozygosity (Ho0). According to a genetic differentiation index (Fst=0.0593), there was a high-level of gene flow in the Ascaris populations. A hierarchical analysis on molecular variance revealed remarkably high levels of variation within the populations. Moreover, a population structure analysis indicated that Ascaris populations fell into 3 main genetic clusters, interpreted as A. suum, A. lumbricoides, and a hybrid of the species. We speculated that humans can be infected with A. lumbricoides, A. suum, and the hybrid, but pigs were mainly infected with A. suum. This study provided new information on the genetic diversity and population structure of Ascaris from human and pigs in China, which can be used for designing Ascaris control strategies. It can also be beneficial to understand the introgression of host affiliation.

• Plant Breeding and Biotechnology
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• 제5권2호
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• pp.134-142
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• 2017

Resource plants are important and have strong potential for a variety of utilities as crops or pharmaceutical materials. However, most resource plants remain wild and thus their utility for breeding and biotechnology is limited. Molecular markers are useful to initiate genetic study and molecular breeding for these understudied resource plants. We collected various wild collections of Peucedanum japonicum which is indigenous resource plants utilized as oriental medicine and leafy vegetables in Korea. In this study, we produced two independent whole genome sequences (WGSs) from two collections and identified large scale polymorphic simple sequence repeat (pSSR) based on our pipeline to develop SSR markers based on comparison of two WGSs. We identified a total of 452 candidate pSSR contigs. To confirm the accuracy and utility of pSSR, we designed ten SSR primer pairs and successfully applied those to seven collections of P. japonicum. The WGS and pSSR candidates identified in this study will be useful resource for genetic research and breeding purpose for the valuable resource plant, P. japonicum.

• International Journal of Industrial Entomology and Biomaterials
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• 제10권2호
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• pp.79-86
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• 2005

Molecular markers have increasingly been used in plant genetic analysis, due to their obvious advantages over conventional phenotypic markers, as they are highly polymorphic, more in number, stable across different developmental stages, neutral to selection and least influenced by environmental factors. Among the PCR based marker techniques, ISSR is one of the simplest and widely used techniques, which involves amplification of DNA segment present at an amplifiable distance in between two identical microsatellite repeat regions oriented in opposite direction. Though ISSR markers are dominant like RAPD, they are more stable and reproducible. Because of these properties ISSR markers have recently been found using extensively for finger printing, pohylogenetic analysis, population structure analysis, varietal/line identification, genetic mapping, marker-assisted selection, etc. In mulberry (Morus spp.), ISSR markers were used for analyzing phylogenetic relationship among cultivated varieties, between tropical and temperate mulberry, for solving the vexed problem of identifying taxonomic positions of genotypes, for identifying markers associated with leaf yield attributing characters. As ISSR markers are one of the cheapest and easiest marker systems with high efficiency in generating polymorphism among closely related varieties, they would play a major role in mulberry genome analysis in the future.

• Genomics & Informatics
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• 제9권4호
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• pp.189-193
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• 2011

Simple sequence repeats (SSRs) are ubiquitous short tandem duplications found within eukaryotic genomes. Their length variability and abundance throughout the genome has led them to be widely used as molecular markers for crop-breeding programs, facilitating the use of marker-assisted selection as well as estimation of genetic population structure. Here, we report a software application, "SSR-Primer Generator " for SSR discovery, SSR-primer design, and homology-based search of in silico amplicons from a DNA sequence dataset. On submission of multiple FASTA-format DNA sequences, those analyses are batch processed in a Java runtime environment (JRE) platform, in a pipeline, and the resulting data are visualized in HTML tabular format. This application will be a useful tool for reducing the time and costs associated with the development and application of SSR markers.

• 한국약용작물학회지
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• 제24권4호
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• pp.317-322
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• 2016

Background: In the herbal medicine market, Angelica gigas, Angelica sinensis, and Angelica acutiloba are all called "Danggui" and used confusingly. We aimed to assess the genetic diversity and relationships among 14 Angelica species collected from different global seed companies. Toward this aim we developed DNA markers to differentiate the Angelica species. Methods and Results: A total of 14 Angelica species, A. gigas, A. acutiloba, A. sinensis, A. pachycarpa, A. hendersonii, A. arguta, A. keiskei, A. atropurpurea, A. dahurica, A. genuflexa, A. tenuissima, A. archangelica, A. taiwaniana, and A. hispanica were collected. The genetic diversity of all 14 species was analyzed by using five chloroplast DNA-based simple sequence repeat (SSR) markers and employing the DNA fragment analysis method. Each primer amplified 3 - 12 bands, with an average of 6.6 bands. Based on the genetic diversity analysis, these species were classified into specific species groups. The cluster dendrogram showed that the similarity coefficients ranged from 0.77 to 1.00. Conclusions: These findings could be used for further research on cultivar development by using molecular breeding techniques and for conservation of the genetic diversity of Angelica species. The analysis of polymorphic SSRs could provide an important experimental tool for examining a range of issues in plant genetics.

• Journal of Plant Biotechnology
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• 제33권4호
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• pp.289-295
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• 2006

국내에서 유통되고 있는 토마토 품종의 판별 방법에 SSR marker의 이용 가능성에 대한 연구를 수행하여 얻어진 결과를 요약하면 다음과 같다. 토마토 28품종을 18개의 SSR marker를 이용하여 분석하였을 때 대립유전자의 수는 $2{\sim}9$개로 비교적 다양한 분포를 나타내었으며 전체 60개의 대립유전자가 분석되었다. PIC 값은 $0.476 {\sim}0.800$ 범위에 속하였으며 평균값은 0.607로 나타났다. SSR marker를 이용하여 작성된 토마토 28품종의 품종간 유전적 거리는 $0.35{\sim}0.97$의 범위로 나타났고, 유사도 지수 0.36을 기준으로 할 때 28개 품종은 체리형 토마토 그룹과 일반형 토마토 그룹으로 나눌 수 있었으며, 공시 품종 모두 SSR marker의 genotype에 의해 뚜렷이 구분되었다. 이 연구결과는 토마토의 품종식별에 기초 자료로 유용하게 이용될 수 있는 것으로 나타났다.

• Journal of Plant Biotechnology
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• 제43권2호
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• pp.181-188
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• 2016

In this study, we developed 15 novel polymorphic simple sequence repeat (SSR) markers by SSR-enriched genomic library construction from Codonopsis lanceolata. We obtained a total of 226 non-redundant contig sequences from the assembly process and designed primer sets. These markers were applied to 53 accessions representing the cultivated C. lanceolata in South Korea. Fifteen markers were sufficiently polymorphic, and were used to analyze the genetic relationships between the cultivated C. lanceolata. One hundred three alleles of the 15 SSR markers ranged from 3 to 19 alleles at each locus, with an average of 6.87. By cluster analysis, we detected clear genetic differences in most of the accessions, with genetic distance varying from 0.73 to 0.93. Phylogenic analysis indicated that the accessions that were collected from the same area were distributed evenly in the phylogenetic tree. These results indicate that there is no correlative genetic relationship between geographic areas. These markers will be useful in differentiating C. lanceolata genetic resources and in selecting suitable lines for a systemic breeding program.

• 한국버섯학회지
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• 제15권3호
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• pp.139-144
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• 2017

양송이(Agaricus bisporus)는 국내에서 2015년 약 10,757톤이 생산되어 5번째로 많이 생산되는 버섯이다. 본 연구에서는 ISSR 마커를 사용하여 국내 수집균주와 상업품종간의 유전적 다양성을 분석하였다. 이를 위해 우선, 다양한 마커 중 양송이 속 내 비교 분석이 가능다고 알려진 ISSR마커를 선발하였다. 분석한 마커는 ISSR 807, 808, 809, 810, 811, 834, 835, 836, 841, 842, P3, P8, P17, P22, P30, P38 and P39 총 16종이였고 이들 중 육종에서 모본선발을 위한 효율적인 마커를 선발하기 위하여 양송이 수집균주 ASI 1110, 1114, 1115, 1238, 1246, 1365, 1366, 1369 등 8종을 선발하여 수행하였다. 그 결과 ISSR P31, P38, P39 마커에서 종내 구분이 가능한 다양한 밴드가 나타났다. 이를 바탕으로 선발된 3종의 마커를 이용하여 국내 수집균주와 새아, 새연 등의 상업품종이 포함된 39균주를 UPGMA 프로그램을 통하여 유연관계를 분석하였다. 국내 수집균주와 상업품종간의 계통도를 분석한 결과, 국내 수집균주와 상업품종들이 다른 그룹을 형성하는 것을 확인하였다. 이 결과를 근거로 ISSR P31, P38, P39가 상업품종을 구분할 수 있는 마커로 활용될 것이라 기대된다.