• Korean Journal of Breeding Science
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• v.43 no.2
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• pp.133-138
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• 2011

The groundnut or cultivated peanut (Arachis hypogaea L.) in Korea consists of 36 domestic varieties which have been developed and registered as cultivars for the public during last 25 years. To screen and identify of Korean peanut varieties and genetic resources, we present a simple and reliable method. A methodology based on simple sequence repeat (SSR) markers developed and widely used for prominent gene identification and variety discrimination. For identification of those 36 Korean peanut varieties, 238 unique peanut SSR markers were selected from some previously reported results, synthesized and used for polymerase chain reaction (PCR). Data were taken through acryl amide gel electrophoresis and changed into proper formats for application of data mining analysis using Biomine (all-in-one functional genomics data mining program). Consequently, twelve SSR primers were investigated and revealed the differences between those 36 varieties. These primer pairs amplified 27 alleles with an average of 2.3 allele per primer pair. In addition, those results showed genetic relationship by classification method within 36 varieties. The approach described here could be applied to monitoring of our varieties and adapting to peanut breeding program.

• International Journal of Industrial Entomology and Biomaterials
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• v.45 no.1
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• pp.29-34
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• 2022

Silkworms have recently attracted attention as healthy functional foods. Different varieties of silkworms have functional differences; thus, there is an emerging need for variety identification. In this study, we sequenced complete mitochondrial genomes (mitogenomes) of ten government-recommended silkworm varieties (BaekHwang, BaekOk, DaeBaek, DaeBak, DaeHwang, GoldenSilk, HanSaeng, JooHwang, KumKang, and KumOk). Comparison of these sequences allowed us to select the single nucleotide polymorphisms (SNPs) in 34 sites that are specific to six silkworm varieties: 13 in DaeBak, 8 in GoldenSilk, 9 in KumKang, 2 in BaekHwang, 1 in BaekOk, and 1 in DaeHwang. Among these each one SNP per variety was amplified by preparing variety-specific primers and then using tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR). As a result, it was possible to identify these six varieties among the ten silkworm varieties, evidencing that SNPs developed from mitogenomes are useful marker for the discrimination of genetically closer silkworm varieties.

• Journal of Plant Biotechnology
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• v.33 no.4
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• pp.289-295
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• 2006

This study was carried out to evaluate the suitability of simple sequence repeat (SSR) markers for varietal identification and genetic diversity in 28 commercial tomato varieties. The relationship between marker genotypes and 28 varieties was analyzed. Of the 219 pairs of SSR primers screened against ten tomato varieties, 18 pairs were highly polymorphic with polymorphism information content (PIC) ranging from 0.467 to 0.800. Among the polymorphic loci, two to nine SSR alleles were detected for each locus with an average of 3.3 alleles per locus. Genetic distances were estimated according to Jaccard's methods based on the probability that the amplified fragment from one genotype would be present in another genotype. These varieties were categorized into cherry and classic fruit groups corresponding to varietal types and genetic distance of cluster ranging from 0.35 to 0.97. The phonogram discriminated all varieties by marker genotypes. The SSR markers proved to be useful variety identification and genetic resource analysis of tomato.

• Journal of Plant Biotechnology
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• v.43 no.4
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• pp.457-465
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• 2016

Microsatellites are one of the most suitable markers for identification of variety, as they have the capability to discriminate between narrow genetic variations. The polymorphism level between 120 microsatellite primer pairs and 148 soybean varieties was investigated through the fluorescence based automatic detection system. A set of 16 primer pairs showed highly reproducible polymorphism in these varieties. A total of 204 alleles were detected using the 16 microsatellite markers. The number of alleles per locus ranged from 6 to 28, with an average of 12.75 alleles per locus. The average polymorphism information content (PIC) was 0.86, ranging from 0.75 to 0.95. The unweighted pair group method using the arithmetic averages (UPGMA) cluster analysis for 148 varieties were divided into five distinctive groups, reflecting the varietal types and pedigree information. All the varieties were perfectly discriminated by marker genotypes. These markers may be useful to complement a morphological assessment of candidate varieties in the DUS (distinctness, uniformity and stability) test, intervening of seed disputes relating to variety authentication, and testing of genetic purity in soybean varieties.

• Korean Journal of Breeding Science
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• v.43 no.4
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• pp.322-329
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• 2011

Microsatellite markers were utilized to investigate genetic diversity among 70 Korean barley varieties (Hordeum vulgare). Ninety nine microsatellite primer pairs were screened for 9 varieties. Twenty primer pairs showed highly polymorphic. The relationship between markers genotypes and 70 varieties was analyzed. A total of 124 polymorphic amplified fragments were obtained by using 20 microsatellite markers. Two to nine SSR alleles were detected for each locus with an average of 6.2 alleles per locus. Average polymorphism information content (PIC) was 0.734, ranging from 0.498 to 0.882. A total of 124 marker loci were used to calculate Jaccard's distance coefficients for cluster analysis using UPGMA. Clustering group was divided 2 groups corresponding to 2-rowed and 6-rowed barley varieties. The phenogram was discriminated all varieties by markers genotypes. These markers may be used wide range of practical application in variety identification and genetic purity assessment of barley.

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

• Plant Resources
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• v.1 no.2
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• pp.81-91
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• 1998

Fifty-nine Korean soybean (Glycine max L. Merr.) landrace accessions were tested for genotype fingerprinting, differentiation and association between morphological traits and SSR profile. Using 8 SSR loci, 59 varieties were divided into 55 groups, and only 4 pairs of varieties were not uniquely identified. The resolving power of SSR for soybean genotyping was much higher than that of the morphological traits that were studied. Identification efficiency also differed among SSR loci. Those loci with higher numbers of alleles distinguished varieties more effectively. Genetic differentiation values of the soybean landraces varied from 0.57 to 0.82 with a mean of 0.68. The number of alleles detected by the 8 loci ranged from 3 to 8. and the effective number of alleles ranged from 2.3 to 5.1. In a study of the association of SSR alleles with morphological traits, some alleles seemed to be related with some specific morphological traits. Comparison of two kinds of dendrograms which were derived from SSR markers and quantitative traits indicated that the dendrograms were not consistent. Considering the correlation between single SSR locus and qualitative traits governed by major genes, the data suggest that alleles of microsatellite loci be more closely related to some traits determined by major genes than those determined by minor genes.

• 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.

• Journal of Plant Biotechnology
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• v.47 no.2
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• pp.124-130
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• 2020

The sweet potato (Ipomoea batatas [L.] Lam.) is the sixth-most important crop in the world following rice, wheat, potato, maize, and cassava. Four varieties ('Beniharuka', 'Annobeni', 'Pungwonmi', 'Hogammi') and their Japanese cultivars are broadly distributed in South Korea. In the Korean marketplace, sweet potatoes are classified by color and shape, not by variety, making it necessary to differentiate varieties for uniform production and consumption. In this study, molecular markers were developed to distinguish the four varieties of sweet potato using SNPs and genotyping-by-sequencing (GBS) analysis via a tetra-primer amplification refractory mutation system (ARMS)-PCR. The results revealed that three variety-specific fragments (164 bp and 241 bp of SNP 04-27457768 and 292 bp of SNP 03-16195623) were amplified in the 'Beniharuka', 'Pungwonmi', and 'Annobeni' sweet potato varieties. There were instances where some varieties produced three bands within the gel electrophoresis, indicating heterozygosity at the given SNPs loci. DNA sequencing analysis also confirmed the results of electrophoresis at the SNPs loci. Overall, these molecular markers would provide a useful, rapid, and, simple evaluation method for the Korean sweet potato marketplace, where the mixing of varieties is a serious issue.

• Applied Biological Chemistry
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• v.41 no.2
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• pp.160-165
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• 1998

Current discriminating technique of rice variety is known to be not objective till this time because of depending on naked eye of well trained inspector. DNA finger print method based on genetic character of rice has been indicated inappropriate for on-site application, because the method need much labor and skilled expert. The purpose of this study was to develops the identification technique of polished rice varieties using CCD camera images. To minimize the noise of the captured image, thresholding and median filtering were carried out, and edge was extracted from the image data. Image data after pretreatment of normalize and FFT(fast fourier transform) were used for library model and feedforward backpropagation neural network model. Image processing technique using CCD camera could discriminate the variety of rice with high accuracy in case of quite different rice of shape, but the accuracy was reached at 85% in the similar shape of rice.