• Journal of Life Science
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• v.30 no.3
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• pp.291-297
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• 2020

This study was conducted to develop microsatellite markers in Seriola quinqueradiata using next-generation sequencing. A total of 28,873,374 reads were generated on an Illumina Hiseq2500 system, yielding 7,247,216,874 bp sequences. The de novo assembly resulted in 466,359 contigs. A total of 132 contigs (0.43%), including 60 microsatellite loci, were derived from 30,729 contigs longer than 518 bp. A total of 60 primer sets were designed from the 132 microsatellite loci. A total of 15 polymorphic nuclear microsatellite loci were chosen to evaluate population genetic parameters in the parents and offspring. The mean number of effective alleles was 18.5, ranging from 11 to 30. The observed heterozygosity (H_O) and expected heterozygosity (H_E) ranged between 0.431 and 0.972 with an average of 0.812 and from 0.782 to 0.949 with an average of 0.896, respectively. No significant linkage disequilibrium was observed after Bonferroni revision in any loci. The results show that the 15 polymorphic nuclear microsatellite markers can be used to study the population and conservation genetics of S. quinqueradiata in Korea. To ensure the success of artificial seedling production technology, genetic variations between the parent and offspring populations should be monitored, and inbreeding should be controlled.

• Horticultural Science & Technology
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• v.31 no.5
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• pp.580-589
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• 2013

This study was carried out to evaluate the suitability of microsatellite markers for varietal identification and genetic relationship of 170 commercial pepper cultivars. The relationship between marker genotypes and 11 pepper cultivars with different morphological traits was also analyzed. Of the 302 pairs of microsatellite primers screened against 11 pepper cultivars, 24 pairs were highly polymorphic in terms of number of alleles. These markers were applied for the construction of DNA profile data base for 170 commercial pepper cultivars. A total of 164 polymorphic amplified fragments were obtained from 24 microsatellite primers. The average polymorphism information content was 0.673 ranging from 0.324 to 0.824. One hundred and sixty four microsatellite alleles were used to calculate Jaccard's distance coefficients using unweighted pair group method. A clustering group of varieties, based on the results of microsatellite analysis, were categorized into 3 major groups corresponding to morphological traits. The phenogram discriminated all varieties by markers genotypes. These microsatellite markers will be useful as a tool for protection of plant breeders' intellectual property rights through variety identification in distinctness, uniformity and stability test.

• Journal of Life Science
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• v.33 no.8
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• pp.623-631
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• 2023

This study was conducted to develop microsatellite markers in Parapristipoma trilineatum using next-generation sequencing. A total of 402,244,934 reads were generated on the Illumina Hiseq X Ten System, yielding 60,738,985,034 bp of sequences. The de novo assembly resulted in 1,320,995 contigs. A total of 952,326 contigs (0.016%) including 151 microsatellite loci were derived from the 1,320,995 contigs longer than 640 bp. A total of 34 primer sets were designed from the 151 microsatellite loci. As a result, 15 microsatellite loci were chosen and used for assuming population genetic parameters in the wild and farmed populations. The mean number of effective alleles was 12, ranging from 6 to 25. The observed heterozygosity (H_O) and the expected heterozygosity (H_E) ranged between 0.530 and 0.873, with an average of 0.750, and from 0.647 to 0.895, with an average of 0.793, respectively. According to these results, the developed set of 15 microsatellite markers is expected to be useful for the analysis of genetic characteristics in the population of P. trilineatum in Korea. There are requirements now for further genetic information, fishery resource management, breeding guidelines, support with the selection of breeds and studies on the effects of release, all of which will improve species conservation, and through future research, we aim to offer genetic foundational data with that goal.

• Horticultural Science & Technology
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• v.31 no.3
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• pp.344-351
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• 2013

Microsatellite is one of the most suitable marker for cultivar identification as it has great discrimination power for cultivars with narrow genetic variation. The polymorphism level between 358 microsatellite primer pairs and 11 commercial cucumber cultivars was investigated. Thirty-one primer pairs showed high polymorphism within cucumber cultivars with different fruit types. These markers were applied for the constructing DNA profile data base of 110 commercial cucumber cultivars through multiplex PCR and fluorescence based automatic detection system. A total of 139 polymorphic amplified fragments were obtained by using 31 microsatellite markers. The average of PIC value was 0.610 ranging from 0.253 to 0.873. One hundred and thirty nine microsatellite loci were used to calculate Jaccard's distance coefficients for UPGMA cluster analysis. A clustering group of varieties, based on the results of microsatellite analysis, were categorized into plant shape and fruit type. Almost the cultivars were discriminated by marker genotypes. This information may be useful to compare through genetic relationship analysis between existing variety and candidate varieties in distinctive tests and protection of plant breeders' intellectual property rights through variety identification.

• Horticultural Science & Technology
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• v.33 no.5
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• pp.737-750
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• 2015

This study was carried out to construct a DNA profile database for 102 watermelon cultivars through the comparison of polymorphism level and genetic relatedness using genomic microsatellite (gMS) and expressed sequence tag (EST)-microsatellite (eMS) markers. Sixteen gMS and 10 eMS primers showed hyper-variability and were able to represent the genetic variation within 102 watermelon cultivars. With gMS markers, an average of 3.63 alleles per marker were detected with a polymorphism information content (PIC) value of 0.479, whereas with eMS markers, the average number of alleles per marker was 2.50 and the PIC value was 0.425, indicating that eMS detects a lower polymorphism level compared to gMS. Cluster analysis and Jaccard's genetic distance coefficients using the unweighted pair group method with arithmetic average (UPGMA) based on the gMS, eMS, and combined data sets showed that 102 commercial watermelon cultivars could be categorized into 6 to 8 major groups corresponding to phenotypic traits. Moreover, this method was sufficient to identify 78 out of 102 cultivars. Correlation analysis with Mantel tests for those clusters using 3 data sets showed high correlation ($r{\geq}0.80$). Therefore, the microsatellite markers used in this study may serve as a useful tool for germplasm evaluation, genetic purity assessment, and fingerprinting of watermelon cultivars.

• Horticultural Science & Technology
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• v.32 no.6
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• pp.853-863
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• 2014

This study was carried out to construct a DNA profile database of 100 strawberry cultivars using microsatellite markers. Two hundred seventy four microsatellite primer pairs were screened with a set of 21 strawberry cultivars with different morphological traits. Twenty five primer pairs were selected because they produced reliable and reproducible fingerprints. These primer pairs were used to develop DNA profiles of 100 strawberry cultivars. Three to thirteen alleles were detected by each marker with an average of 7.50. The average polymorphism information content varied from 0.331 to 841 (average 0.706). Cluster analysis showed that the 100 cultivars were divided into 7 major groups reflecting geographic origin and pedigree information. Moreover, most of the cultivars could be discriminated by marker genotypes. These markers will be useful as a tool for the protection of plant breeders' intellectual property rights in addition to providing the means to intervene seed disputes relating to variety authentication.

• Journal of Ginseng Research
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• v.33 no.3
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• pp.199-205
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• 2009

Ginseng (Panax ginseng C.A. Meyer) is one of the most important medicinal plants in East Asia. Microsatellite or simple sequence repeat (SSR) markers are used in obtaining genetic analysis and authentication in many plants. The present study examined five microsatellites in conjunction with P. ginseng in Korea. The total observed allelic number was 17 (mean = 3.4), and gene diversities varied from 0.078 to 0.543 with an average of 0.314. Through a combined analysis of five loci in 100 ginseng samples, 44 different combined genotypes were observed. Expected and observed heterozygosites ranged from 0.077 to 0.541 (mean = 0.313) and 0.040 to 0.130 (0.083), respectively. All examined loci exhibited deficiency of heterozygosity and deviation from the Hardy-Weinberg equilibrium. Such results may be explained by the non-random mating and inbreeding that has occurred for several hundred years. These microsatellite markers could be used for the study of molecular genetics and the establishment of DNA marker database, as well as authentication of ginseng species and chromosomal mapping of QTL loci in P. ginseng.

• Horticultural Science & Technology
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• v.35 no.1
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• pp.98-107
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• 2017

A DNA profile database was constructed to investigate the genetic relatedness of 72 germplasm samples of Pyrus and related cultivars using microsatellite markers. Three P. pyrifolia, four P. commus, and one P. betulifolia cultivars with different morphological traits were screened using 387 pairs of microsatellite primers. A core set of 11 primer pairs was selected to obtain 133 polymorphic amplified fragments meeting three criteria: high polymorphism information contents (PIC), high repeatability, and distinct allele patterns. The number of alleles per locus ranged between 4 and 22. Average PIC was 0.743 (range: 0.557 - 0.879). Cluster analysis using the unweighted pair - group method with arithmetical average (UPGMA) separated the 72 pear cultivars and germplasm samples into four major groups: Chinese, European pears, and a cluster of 55 Asian pears that could be reclassify into two subcluster, I - $1^{st}$ and II - $2^{nd}$, according to pedigree information. Almost all of the cultivars were discriminated by 11 microsatellite marker genotypes. The microsatellite DNA profile database may be utilized as tool to verify distinctness, uniformity, and stability between candidate cultivar, and to verify in the distinctness of existing cultivars.

• 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.

• Korean Journal of Plant Taxonomy
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• v.41 no.4
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• pp.299-314
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• 2011

The choice of molecular markers is the first step when selecting experimental plans in the field of population genetics. The popular molecular markers in population genetic studies are mainly allozyme, RAPD, RFLP, AFLP, microsatellite, SNP and ISSR. Among these, microsatellites are frequently found in nuclear, chloroplast and mitochondrial genome, showing a high level of polymorphism and nuclear microsatellites are codominant. Thus, it is a favorable molecular marker for population structure analyses and genetic diversity studies. Microsatellites are composed of tandem repeated 1~6 base pair nucleotide motifs and can be easily amplified by PCR reactions using locus specific primers. Because microsatellites have low cross-species transferability, however, they are only applicable between phylogenetically close species. In wild plants, the lack of genomic information and the high development cost of the microsatellite obstruct the wider use of microsatellites in plant population genetics research. In this review, we introduce the basis for microsatellite markers, the development process, and analytical methods as well as evolutionary models and their applications. In addition, possible genotyping errors which lead to erroneous conclusions are discussed.