• Korean Journal of Breeding Science
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• v.42 no.1
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• pp.11-22
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• 2010

The population structure of a domesticated species is influenced by the natural history of the populations of its pre-domesticated ancestors, as well as by the breeding system and complexity of breeding practices implemented by humans. In the genetic and population structure analysis of 122 South Asia collections using 29 simple sequence repeat (SSR) markers, 362 alleles were detected, with an average of 12.5 per locus. The average expected heterozygosity and polymorphism information content (PIC) for each SSR locus were 0.74 and 0.72,respectively. The model-based structure analysis revealed the presence of three clusters with the 91.8% (shared > 75%) membership, with 8.2% showing admixture. The genetic distances of Clusters 1-3 were 0.55, 0.56, and 0.68, respectively. Polymorphic information content followed the same trend (Cluster 3 had the highest value and Cluster 1 had smallest value), with genetic distances for each cluster of 0.52, 0.52, and 0.65, respectively. This result could be used for supporting rice breeding programs in South Asia countries.

• Mycobiology
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• v.45 no.2
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• pp.105-109
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• 2017

Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L. edodes genome sequences. The number of alleles ranged from 3-14 and the major allele frequency was distributed from 0.17-0.96. The values of observed and expected heterozygosity ranged from 0.00-0.76 and 0.07-0.90, respectively. The polymorphic information content value ranged from 0.07-0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering' method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.10a
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• pp.74-74
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• 2018

Little millet (Panicum sumatrense) is well known for its salt and drought stress tolerance and high nutritional value, but very limited knowledge of genetic variation and genomic information is available. This study was to develop highly polymorphic EST-SSR markers based on cross-species transferability of derived SSRs from switchgrass EST databases and characterize newly developed EST - SSRs to better understand the genetic diversity of collected 37 germplasm accessions of little millet. A total of 779 primer pairs were designed from the 22,961 EST sequences of switchgrass (Pancium virgatum), of which 48 EST - SSR markers were developed based on the trials of transferability of these primers in little millet. The EST - SSR amplicons showed reproducible single band polymorphism and produced a total of 160 alleles with an average of 3.3 alleles per locus in 37 accessions of little millet. T he average values of expected and observed heterozygosities were 0.266 and 0.123, respectively. T he polymorphic information content (PIC) values were observed in range of 0.026 to 0.549 with an average of 0.240. The genetic relatedness among the little millet accessions was evaluated by neighbor-joining dendrogram, which grouped all accessions into two distinct groups. The validation thus demonstrated the utility of the switchgrass EST - SSR markers in assessing genomic relationships in little millet. T he findings from this study could be useful for designing strategies for the identification of diverse germplasm for conservation and future molecular breeding programs for little millet.

• Journal of Life Science
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• v.25 no.3
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• pp.257-262
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• 2015

The genetic variability of four species of the genus Zoysia collected from South Korea was analyzed using an inter-simple sequence repeat (ISSR) marker system. Polymerase chain reactions (PCR) with eight ISSR primers generated 86 amplicons, 76 (87.1%) of which were polymorphisms. The polymorphism information content (PIC) value of the ISSR marker system was 0.848. The percentage of polymorphic loci (P_p) ranged from 41.2% to 44.7%. Nei’s gene diversity (H) ranged from 0.149 to 0.186, with an average overall value of 0.170. The mean of Shannon’s information index (I) value was 0.250. Total genetic diversity values (H_T) varied between 0.356 (ISSR-1) and 0.418 (ISSR-16), for an average overall polymorphic loci of 0.345. Interlocus variation in within-species genetic diversity (H_S) was low (0.170). On a per-locus basis, the proportion of total genetic variation due to differences among species (G_ST) was 0.601. This indicated that about 60.1% of the total variation was among species. Thus, about 39.9 of genetic variation was within species. The estimate of gene flow, based on G_ST, was very low among species of the genus Zoysia (N_m = 0.332). The phylogenic tree showed three distinct groups: Z. macrostachya and Z. tenuifolia clades and other species were formed the separated clusters. In conclusion, the ISSR assay was useful for detecting genetic variation in the genus Zoysia, and its discriminatory power was comparable to that of other genotyping tools.

• Journal of Life Science
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• v.17 no.10
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• pp.1441-1446
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• 2007

This study was conducted to establish the individual identification system and to estimate the genetic characteristic of Jeju native horse (JNH) using 13 microsatellite markers located on different horse autosomes. The markers were genotyped on 191 animals from five horse breeds including Jeju native horse (JNH). In total, 138 alleles were detected from the genotypes of 13 microsatellite markers. The average heterozygosities ranged from 0.317 to 0.902 and the polymorphic information content (PIC) ranged from 0.498 to 0.799 in JNH. We found that there were significant differences in allele frequencies in JNH when compared with other horse breeds. In ATH4 marker, there were specific allele frequence pattern that some of allele only found in JNH, Mongolian horse (MONG) and Jeju racing horse (JRH). The calculated cumulative power of discrimination (CPD) was 99.9% when nine microsatellite loci were used for analysis in the individual identification system. Also, the matching probability that two unrelated animals would show the same genotypes, was estimated to be $0.60{\times}10^{-10}$. Therefore, in the nine markers used in this study can be used for individual identification in the Jeju native horse population.

• Journal of Forest and Environmental Science
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• v.29 no.3
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• pp.200-210
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• 2013

Biochemical characteristics of 24 Pongamia pinnata genotypes (candidate plus trees) from three agroclimatic zones were estimated and molecular characterization through RAPD markers was done. Various biochemical characters viz. seed oil, total carbohydrates, protein, acid value and Iodine number recorded significant variation among different genotypes. The highest seed oil content was 41.87% while seeds of 14 genotypes recorded above average (32.11%) for the trait. Seed oil and protein content exhibited a significant positive correlation and moderate heritability. Out of the initially selected twenty-five random primers, twenty-two RAPD primers were found to be highly reproducible and produced a total of 183 loci of which 147 (80.32%) loci were polymorphic. Percentage of polymorphism varied from 44% to 100% with an average of 80.62%. High level of genetic variation was found among different genotypes of P. pinnata. Both molecular and oil content (biochemical) markers appeared useful in analyzing the extent of genetic diversity in Pongamia and the result of these analyses will help to better understand the genetic diversity and relationship among populations. Overall, the Pongamia genotypes included in the study showed a correlation with their geographical origins such that genotypes from the same region tend to have higher genetic similarity as compared to those from different regions. However, in UPGMA based Nei's analysis, some genotypes were found not to be grouped based on geographical origins possibly due to the exchange of germplasm over time between farmers across the regions. The results from oil content analyses showed that several genotypes in 'Central and Western Plateau' agroclimatic zone of Jharkhand displayed a good potential for high oil content. The study provides insight about P. pinnata populations in Jharkhand (India) and constitutes a set of useful background information that can be used as a basis for future breeding strategy and improvement of the species.

• Journal of Microbiology and Biotechnology
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• v.20 no.4
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• pp.683-692
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• 2010

Morphologically, nine different slow-growing protoclones were screened from regenerated protoplasts of heterokaryotic Agaricus bisporus. As such, the present study is the first report on differentiating homo- and heterokaryotic protoclones using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Among 80 primers tested, the seven ISSR and seven RAPD primers selected for the analysis generated a total of 94 ISSR and 52 RAPD fragments, respectively. The ISSR fingerprinting also detected more polymorphic loci (38.29%) than the RAPD fingerprinting (34.61%). A principal coordinate analysis (PCA) was employed to evaluate the resolving power of the markers as regards differentiating protoclones. As a result, the mean polymorphism information content (PIC) for each marker system (i.e., 0.787 for RAPD and 0.916 for ISSR) suggested that ISSR is more effective for determining polymorphisms. The dendrograms constructed using RAPD, ISSR, and an integrated RAPD and ISSR marker system were highly correlated with one another as revealed by a high Mantel correlation (r= 0.98). The pairwise similarity index values also ranged from 0.64 to 0.95 (RAPD), 0.67 to 0.98 (ISSR), and 0.67 to 0.98 (RAPD and ISSR), whereas the mean similarity index values of 0.82, 0.81, and 0.84 were obtained for the RAPD, ISSR, and combined data, respectively. As there was a good correspondence between the RAPD and ISSR similarity matrices, ISSR would appear to be an effective alternative to RAPD in the genetic diversity assessment and accurate differentiation of homo- and heterokaryotic protoclones of A. bisporus.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.3
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• pp.316-322
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• 2013

In order to evaluate the genetic diversity and discrimination among five Korean native chicken lines, a total of 86 individuals were genotyped using 150 microsatellite (MS) markers, and 15 highly polymorphic MS markers were selected. Based on the highest value of the number of alleles, the expected heterozygosity (He) and polymorphic information content (PIC) for the selected markers ranged from 6 to 12, 0.466 to 0.852, 0.709 to 0.882 and 0.648 to 0.865, respectively. Using these markers, the calculated genetic distance (Fst), the heterozygote deficit among chicken lines (Fit) and the heterozygote deficit within chicken line (Fis) values ranged from 0.0309 to 0.2473, 0.0013 to 0.4513 and -0.1002 to 0.271, respectively. The expected probability of identity values in random individuals (PI), random half-sib ($PI_{half-sibs}$) and random sibs ($PI_{sibs}$) were estimated at $7.98{\times}10^{-29}$, $2.88{\times}10^{-20}$ and $1.25{\times}10^{-08}$, respectively, indicating that these markers can be used for traceability systems in Korean native chickens. The unrooted phylogenetic neighbor-joining (NJ) tree was constructed using 15 MS markers that clearly differentiated among the five native chicken lines. Also, the structure was estimated by the individual clustering with the K value of 5. The selected 15 MS markers were found to be useful for the conservation, breeding plan, and traceability system in Korean native chickens.

• Korean Journal of Poultry Science
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• v.44 no.2
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• pp.75-81
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• 2017

A total of 340 individuals from seven duck populations were studied using 24 polymorphic microsatellite (MS) markers to identify plumage colors with genetic diversity. The estimated average number of alleles (Na), polymorphic information content (PIC) value, and expected heterozygosity (He) per locus of all populations were 11.5, 0.602, and 0.635, respectively. The calculated population genetic distance (Fst), inbreeding coefficient of individuals within duck populations (Fis), and total inbreeding among populations (Fit) were 0.135, 0.105, and 0.229, respectively. Statistical analyses for each population using 24 marker combinations, revealed that the estimated average number of effective alleles (Ne), observed heterozygosity (Ho), and fixation index of inbreeding within populations (F) were 3.129, 0.505, and 0.104, respectively. The results of genetic distance and phylogenetic analysis revealed that Korean native duck populations were clearly separated from all Bangladeshi duck populations. Moreover, all populations clustered well according to their genetic distance, but could not be clearly separated according to black and white plumage colors or plumage color pattern. The combination of these 24 MS markers can be used for discrimination and determination of the genetic diversity of native duck breeds in further investigations for conservation and special development purposes.

• 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.