• Korean Journal of Veterinary Service
• /
• v.41 no.4
• /
• pp.257-262
• /
• 2018

Avian pathogenic E. coli (APEC) causes severe economic losses in the poultry farms, due to systemic infections leading to lethal colisepticemia. It causes a variety of diseases from air sac infection to systemic spread leading to septicemia. Secondary infection contains opportunistic infections due to immunosuppression disease. Collibacillosis causes the great problems in the poultry industry in Korea. Thus, it is necessary to identify and classify the characteristics of E. coli isolate of chicken origin to confirm the diversity of symptoms and whether they are transmitted among the farms. Fragment analysis is identify the difference in the number of Variable-Number Tandem-Repeats (VNTRs) for genotyping. VNTRs have repeating structure (Microsatellite, Short tandem repeats; STR, Simple sequence repeats; SSR) in the chromosome. This region can be used as a genetic marker because of its high mutation rate. And various lengths of the amplified DNA fragment cause the difference in the number of repetition of the DNA specific site. The number of repetition sequences indicates the separated size of fragments, so the each fragments can be distinguished by specific samples. The results of the sample show that there is no difference in six microsatellite loci (yjiD, aidB, molR_1, ftsZ, b1668, yibA). There are differences among the farms in relation of the number of repetitions of other six microsatellite loci (ycgW, yaiN, yiaB, mhpR, b0829, caiF). Four (ycgW, yiaB, b0829, caiF) of these six microsatellite loci show statistically significant differences (P<0.05). It means that the analysis using four microsatellite loci including ycgW, yiaB, b0829, and caiF can confirm among the farms. Five E. coli samples in one farm have same SSR repetition at all markers. But, there are significant differences from other farms at Four (ycgW, yiaB, b0829, caiF) microsatellite loci. These results emphasize again that the four microsatellite loci makes a difference in the amplified DNA fragments, enabling it to be used for E. coli genotyping.

• Molecules and Cells
• /
• v.24 no.1
• /
• pp.60-68
• /
• 2007

Microsatellites, also called simple sequence repeats (SSR), are very useful molecular genetic markers commonly used in crop breeding, species identification and linkage analysis. In the present study, we constructed a microsatellite-enriched genomic library of Panax ginseng, and identified 251 novel microsatellite sequences. Tri-nt repeat units were the most abundant (46.6%), followed by di-nt repeats (35.5%). The $(AG)_n$ motif was most common (23.1%), followed by the $(AAC)_n$ motif (22.3%). From the genotyping of 94 microsatellites using marker-specific primer sets, we identified 11 intraspecific polymorphic markers as well as 14 possible interspecific polymorphic markers differing between P. ginseng and P. quinquefolius. The exact allele structures of the polymorphic markers were determined and the alleles were named. This study represents the first report of the bulk isolation of microsatellites by screening a microsatellite-enriched genomic library in P. ginseng. The microsatellite markers could be useful for linkage analysis, genetic breeding and authentication of Panax species.

• Proceedings of the Plant Resources Society of Korea Conference
• /
• 2018.04a
• /
• pp.38-38
• /
• 2018

The genus Carduus (Asteraceae), containing ca. 90 species, is mainly distributed in Eurasia and Africa. Carduus species are one of the most hazardous invasive species, which causes serious environmental threats and biodiversity damages in North America. Thus, the member of Carduus are targeted for classical biological control in this region. Here, we provide the complete cp genome of Carduus crispus using next-generation sequencing technology. The size of cp genomes of C. crispus is 152,342 bp. It shows a typical quadripartite structure, consisting of the large single copy (LSC; 83,254 bp), small single copy (SSC; 18,706 bp), separated by a pair of inverted repeats (IRs; 25,191 bp). It contains 115 unique genes of which 21 genes duplicated in the IR regions. The cpSSR regions of Carduus species were searched through the complete chloroplast genome sequence using a tandem repeat search tool in Geneious with the parameters set to ${\geq}7$ mononucleotide repeats, ${\geq}4$ di- and trinucleotide repeats, and ${\geq}3$ tetra-, penta-, and hexanucleotide repeats. A total of 22 repeat motifs were identified, which may be useful for molecular identification of Korean Carduus species (C. cripus), and providing a guideline for its conservation.

• Journal of Plant Biotechnology
• /
• v.43 no.3
• /
• pp.311-316
• /
• 2016

The efficacy of plant breeding has been enhanced by application of molecular markers in population screening and selection. Pepper (Capsicum annuum L.) is a major staple crop that is economically important with worldwide distribution. It is valued for its spicy taste and medicinal effect. The aim of this study was to discover single nucleotide polymorphisms (SNPs), microsatellite markers information, and percentage sharing through orthologous analysis of pepper-specific pungency-related genes. Here, we report the results of transcriptome analysis and microsatellite markers for four pepper varieties that possess a pungency-related gene. Orthologous analyses was performed to identify species-specific pungency-related genes in pepper, Arabidopsis thaliana L., potato (Solanum tuberosum L.), and tomato (Solanum lycopersicum L.). Advancements in next-generation sequencing technologies enabled us to quickly and cost-effectively assemble and characterize genes to select molecular markers in various organisms, including pepper. We identified a total of 9762, 7302, 8596, and 6886 SNPs for the four pepper cultivars Blackcluster, Mandarine, Saengryeg 211, and Saengryeg 213, respectively. We used 454 GS-FLX pyrosequencing to identify microsatellite markers and tri-nucleotide repeats (54.4%), the most common repeats, followed by di-, hexa-, tetra-, and penta-nucleotide repeats. A total of 5156 (15.9%) pepper-specific pungency-related genes were discovered as a result of orthologous analysis.

• Journal of Life Science
• /
• v.32 no.9
• /
• pp.690-697
• /
• 2022

This study was conducted to analyze genome of red sea cucumber and to use it as basic data for the development of genetic markers for red sea cucumber. Microsatellite marker analysis of Ulleungdo_normal and Ulleungdo_native red sea cucumbers revealed that dinucleotide simple sequence repeats (SSRs) had the highest ratio, at 81.3~81.4%, and the number of the detected SSRs tended to decrease as the number of repeating sequence units in SSRs increased. In general, microsatellites with between 5 and 10 iterations were most common. As the size of the SSR repeating sequence units increased, the SSR iterations gradually decreased. The di-, tri-, and tetra-nucleotides in SSRs were detected in the highest numbers as (AT)₅, (AAT)₅, and (AAAT)₅, respectively. (CG) and (CCG) had very low frequencies compared to the numbers of other repeating SSR units. The numbers of di-and tri-nucleotide repeats were up to 35 and 32, respectively, and then increased discontinuously up to 44 and 43 repeats, respectively. Tetra-, penta-, and hexa-nucleotides in SSRs occurred in numbers up to 25, 21 and 14, respectively. This analysis of red sea cucumber indicated that it maintains its own repetition sequence and repetition number; therefore, we suggest that using it as basic data for molecular marker will be possible in future research.

• Asian-Australasian Journal of Animal Sciences
• /
• v.21 no.5
• /
• pp.624-627
• /
• 2008

An enrichment library of GATA-repeats from genomic DNA was constructed in this study to isolate and characterize microsatellite loci in Tsaiya duck (Anas platyrhynchos). Thirty-three microsatellite markers were developed and used to detect polymorphisms in 30 Tsaiya ducks. A total of 177 alleles were observed and all loci except APT022 were polymorphic. The number of alleles ranged from 2 to 9 with an average of 5.5 per microsatellite locus. The observed and expected heterozygosity of these polymorphic markers ranged from 0.07 to 0.93 with an average number of 0.60 and 0.10 to 0.86 with an average number of 0.61, respectively. Among the polymorphic markers, the observed heterozygosities of 23 loci were higher than 0.50 (69.70%). The polymorphism information content (PIC) in the 32 loci ranged from 0.09 to 0.83 with an average of 0.57. Seven of the 33 duck microsatellite loci had orthologs in the chicken genome, but only APT004 had a similar core repeat to chickens. These microsatellite markers will be useful in constructing a genetic linkage map for the duck and a comparative mapping with the chicken can also provide a valuable tool for studies related to biodiversity and population genetics in this duck species.

• Molecules and Cells
• /
• v.26 no.3
• /
• pp.250-257
• /
• 2008

Microsatellites or simple sequence repeats (SSR) are widely distributed in eukaryotic genomes and are informative genetic markers. Despite many advantages of SSR markers such as a high degree of allelic polymorphisms, co-dominant inheritance, multi-allelism, and genome-wide coverage in various plant species, they also have shortcomings such as low polymorphic rates between genetically close lines, especially in Capsicum annuum. We developed an alternative technique to SSR by normalizing and alternating anchored primers in random amplified microsatellite polymorphisms (RAMP). This technique, designated reverse random amplified microsatellite polymorphism (rRAMP), allows the detection of nucleotide variation in the 3' region flanking an SSR using normalized anchored and random primer combinations. The reproducibility and frequency of polymorphic loci in rRAMP was vigorously enhanced by translocation of the 5' anchor of repeat sequences to the 3' end position and selective use of moderate arbitrary primers. In our study, the PCR banding pattern of rRAMP was highly dependent on the frequency of repeat motifs and primer combinations with random primers. Linkage analysis showed that rRAMP markers were well scattered on an intra-specific pepper map. Based on these results, we suggest that this technique is useful for studying genetic diversity, molecular fingerprinting, and rapidly constructing molecular maps for diverse plant species.

• KOREAN JOURNAL OF CROP SCIENCE
• /
• v.44 no.2
• /
• pp.112-116
• /
• 1999

Genetic diversity of 31 rice varieties including 25 japonica and 6 indica varieties was evaluated using a combination of 19 microsatellite or simple sequence repeats (SSRs) and 28 random decamer oligonucle-otide primers. All 19 microsatellite primer sets representing 19 loci in the rice genome showed polymorphisms among the 31 varieties and revealed 91 alleles with an average of 4.80 bands per primer. Also all 28 random decamer primers used were informative and generated 114 non-redundant bands with a mean of 4.07 bands. Microsatellite markers detected higher number of alleles than random primers .although the mean difference was not statistically significant. A cluster analysis based on Nei＇s genetic distances calculated from the 205 bands resolved the 31 varieties into two major groups that correspond to indica and japonica subspecies, which is consistent with the genealogical information. As few as six random decamer primers or a combination of one microsatellite and four random decamer primers were sufficient to uniquely differentiate all 31 varieties. These combinations would be potentially useful in rice variety protection and identification considering that 25 out of 31 varieties used in this study are japonica rices with high grain quality and have close make up.

• Korean Journal of Plant Taxonomy
• /
• v.47 no.1
• /
• pp.6-10
• /
• 2017

Microsatellite markers were isolated for Daphne kiusiana var. kiusiana (Thymelaeaceae), an evergreen broad-leaved shrub endemic to Korea and Japan. Because its populations in Jeju Island are morphologically controversial, and consistently threatened by anthropogenic pressures, taxonomic delimitation and conservation effort are required at the genetic level. We developed 21 polymorphic microsatellite loci from Next Generation Sequencing data. The primer set included di-, tri-, and tetra-nucleotide repeats. Variability in the markers was tested for 80 individuals of D. kiusiana from three natural populations in Jeju Island and Japan. Among the 21 loci, three were unavailable for population JKJU of Japan. The Neighbor-Joining tree based on microsatellite markers described here classified the three populations into two groups according to geographical or morphological traits. These will be a powerful genetics tool for determining the taxonomic boundary and establishing suitable conservation strategies for D. kiusiana in Jeju Island.

• Journal of Microbiology and Biotechnology
• /
• v.24 no.9
• /
• pp.1189-1195
• /
• 2014

A strain-specific identification method is required to secure Chlorella strains with useful genetic traits, such as a fast growth rate or high lipid productivity, for application in biofuels, functional foods, and pharmaceuticals. Microsatellite markers based on simple sequence repeats can be a useful tool for this purpose. Therefore, this study developed five novel microsatellite markers (mChl-001, mChl-002, mChl-005, mChl-011, and mChl-012) using specific loci along the chloroplast genome of Chlorella vulgaris. The microsatellite markers were characterized based on their allelic diversities among nine strains of C. vulgaris with the same 18S rRNA sequence similarity. Each microsatellite marker exhibited 2~5 polymorphic allele types, and their combinations allowed discrimination between seven of the C. vulgaris strains. The two remaining strains were distinguished using one specific interspace region between the mChl-001 and mChl-005 loci, which was composed of about 27 single nucleotide polymorphisms, 13~15 specific sequence sites, and (T)n repeat sites. Thus, the polymorphic combination of the five microsatellite markers and one specific locus facilitated a clear distinction of C. vulgaris at the strain level, suggesting that the proposed microsatellite marker system can be useful for the accurate identification and classification of C. vulgaris.