• Journal of Life Science
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• v.24 no.7
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• pp.707-712
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• 2014

We evaluated the phenetic relationships within six taxa of genus Oxalis L. in Korea with random amplified polymorphic DNA (RAPD) markers. Ten primers produced 125 bands for six taxa, and the mean number of bands per primer was 12.5. Across the six taxa, 121 (96.8%) bands were polymorphic, and only four were monomorphic. The mean number of RAPD phenotypes across the six taxa varied from 3.6 (O. stricta and O. corymbosa) to 4.8 (O. corniculata for. rubrifolia). In a simple measure of intraspecies variability according to the percentage of polymorphic bands, O. stricta and O. corymbosa exhibited the lowest variation (28.8%), and O. corniculata for. rubrifolia showed the highest (38.4%). A mean of 32.7% of the loci was polymorphic within taxa. The total interspecies genetic diversity ($H_T$) and intraspecies genetic diversity ($H_S$) was 0.362 and 0.122, respectively. On a per-locus basis, the proportion of total genetic variation due to differences among species ($G_{ST}$) was 0.663. This indicates that about 66.3% of the total variation was among species. The node of O. stricta and O. corniculata for. rubrifolia was strongly supported, with a high bootstrap value in the NJ tree and sistered with O. corniculata. According to RAPD analysis, the number of chromosomes was not congruent with a phenetic relationship.

• Journal of Life Science
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• v.19 no.10
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• pp.1382-1388
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• 2009

Rubus crataegifolius is a shrub species and is primarily distributed throughout Asia and Europe. We collected 550 representative samples of the eleven populations in Korea to estimate leaf variation within species. The 35 morphological characteristics allowed us to resolve well-supported fixed characteristics and variable characteristics. Sixteen of twenty-three quantitative characteristics and five of twelve qualitative characteristics showed significant differences among populations. We argued that the population differentiation can accounted for the variation in phenetic characteristics such as spine in this species, but were less successful in accounting for variation in other traits. Within a polystatistic leaf structure, their morphological differences could be modulated by ecological pressure such as temperature, altitude, duration of sunshine, and solar radiation. The phenogram showed two distinct clades. One was a group in central Korea and the other was a group in the southern regions of Korea. If morphological characteristics in R. crataegifolius populations reflect their ecological niche, morphology should be regarded with caution as the main criterion for population studies in R. crataegifolius.

• Korean Journal of Microbiology
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• v.23 no.3
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• pp.235-240
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• 1985

A total of 10 main characters of 16 species of family Rhodospirllaceae were phenetically and cladistically analyzed by Farris' method. The obtained phenogram and cladistic tree were compared with Bergey's manual and other papers. The results supported that the system of 5 subgroups (genera) is available in family Rhodospirllaceae and indicated that close affinities between Rhodospirllum tenue and Rhodopseudomonas gelatinosa and between Rhodomicrobium vannielii and other species of genus Rhodopseudomonas were proved.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.55 no.4
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• pp.319-326
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• 2010

Safflower (Carthamus tinctorius L.) is a herb primarily distributed throughout in the world. We have used the inter-simple sequence repeats (ISSR) technique to investigate the phylogenetic relationships and genetic diversity of C. tinctorius. Of all germplasms, 88.7% were polymorphic among all germplasms. Mean genetic diversity within germplasms was very low (0.048). The Turkey germplasm had the highest expected diversity (0.082) and Australia germplasm was the lowest (0.020). These values indicate that most of the genetic diversity of safflower is found among germplasms and there is a high among-germplasm differentiation. We found eight phenetic bands for determining the specific marker of germplasm with SCAR markers. The regions of the Mediterranean Sea and India may be the most probable candidates for the origin of safflower. The tree showed four major clades: (1) European germplasms, (2) Azerbaijan, Egypt, and Ethiopia, (3) Australia, and (4) America.

• Journal of Life Science
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• v.24 no.6
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• pp.612-617
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• 2014

The phenetic relationships among six natural populations of Equisetum pratense in Korea were investigated at the population level by constructing a tree based on Random Amplified Polymorphic DNA (RAPD) markers. RAPD analysis was also conducted to estimate genetic diversity and the population structure of E. pratense. A mean of 26.7% at the six population levels indicated polymorphism. E. pratense was found to have fewer alleles per locus (1.267) and fewer effective alleles per locus (1.176). Genetic diversity (0.102) in E. pratense is lower than the average for species with similar life history traits. Total genetic diversity values (HT) varied between 0.112 (OPD-07) and 0.445 (OPD-16), for an average overall polymorphic locus of 0.141. Inter-locus variation in the within-population genetic diversity ($H_S$) was low (0.102). Asexual reproduction, small population size, and the colonization process are proposed as possible factors contributing to the observed low genetic diversity in E. pratense. On a per-locus basis, the proportion of total genetic variation due to differences among populations ($G_{ST}$) ranged from 0.129 for OPD-07 to 0.455 for OPD-09, with a mean of 0.277. This indicated that about 27.7% of the total variation was among populations. Thus, genetic variation (72.3%) resided within populations. This study contributes new information for research on the taxonomy and population genetics of E. pratense.

• Journal of Life Science
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• v.16 no.5
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• pp.740-745
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• 2006

Inter simple sequence repeat (ISSR) markers were performed in order to analyse the phylogenetic relationships of four taxa of Castor-aralia (Kalopanax pictus): K. pictus, K. pictus var. magnificus, K. pictus var. maximowiczii, and thornless K. pictus. The 11 primers were produced 64 reproducible ISSR bands. Analysis of ISSR from individual plants of Korean K. pictus resulted in 41 polymorphic bands with 64.1%. When species were grouped by four taxa, within group diversity was 0.115 $(H_S)$, while among group diversity was 0.467 $(G_{ST})$ on a per locus basis. The estimated gene flow (Nm) for K. pictus var. maximowiczii and K. pictus var. magnificus were very higher than K. pictus. It is suggested that the isolation of geographical distance and reproductive isolation among K. pictus populations may have played roles in shaping the population structure of this species. In phenetic tree, ISSR markers are very effective in classifying natural populations as well as taxon levels of genus Kalopanax in Korea.

• Horticultural Science & Technology
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• v.35 no.1
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• pp.108-120
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• 2017

Modern watermelon cultivars (Citrullus lanatus [Thunb.] Matsum.& Nakai var. lanatus) have fruits with diverse phenotypes, including fruit shape, rind patterns, and flesh color. Molecular markers enable efficient selection of plants harboring desirable phenotypes. In the present study, publicly available DNA markers tightly linked to fruit shape, rind stripe pattern, and flesh color were evaluated using 85 watermelon accessions with diverse fruit phenotypes. For fruit shape, the dCAPS SUN - Cla011257 marker revealed an 81% of marker - trait match for accessions with elongated or round fruits. For rind stripe pattern, the SCAR wsb6-11marker was effective for selecting Jubilee-type rind pattern from other rind patterns. For flesh color, the Clcyb.600 and Lcyb markers derived from a mutation in the Lycopene ${\beta}$ - cyclase (Lcyb) gene, were effective at selecting red or yellow flesh. Forty-eight accessions possessing diverse fruit - related traits were selected as a reference array and their genetic relationships assessed using 16 SSR markers. At a coefficient of 0.11, the 48 accessions grouped into two major clades: Clade I and Clade II. Clade I subdivided further into subclades I - 1 and I - 2 at a coefficient of 0.39. All accessions with colored flesh were classified into Clade I, whereas those with white - flesh were classified into Clade II. Differences in fruit traits between subclades I - 1 and I - 2 were observed for rind pattern and fruit color; a majority of the accessions with Crimson-type striped or non-striped rind were grouped together in subclade I - 1, while most accessions in subclade I - 2 had a Jubilee - type rind stripe pattern. These results imply that reference array watermelon accessions possess distinguishable genetic structure based on rind stripe pattern. However, no significant grouping pattern was observed based on other fruit-related traits.

• Journal of Life Science
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• v.23 no.11
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• pp.1305-1310
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• 2013

Dill (Anethum graveolens L.) is an annual herb with a long history and it is mainly used as a spice and as a medicine that is effective as a digestive aid, a sedative, and a narcotic, and that helps remove bad breath. Dill grows wild in the districts along the shores of the Mediterranean Sea, West Asia, China, and Korea. An estimate of the phylogenetic relationships within dill accessions in 20 countries was inferred using data from the rps16-trnK3-intergenic spacer. The aligned data sets for dill ranged from 747 to 779 nucleotides (bp) as a result of the differences in the insert/delete nucleotides. The sequence variation within the dill accessions was mostly due to nucleotide substitutions, although several small insertions and deletions can be found. Among 100 accessions from 20 countries, the Eastern Asia accessions were more closely related to the North American accessions than to the Central Asia and European accessions. Although some accessions were not congruent completely with geographical locations, the dill accessions with rps16-trnK analysis resulted in plants with better-resolved clades.

• Horticultural Science & Technology
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• v.33 no.4
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• pp.566-574
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• 2015

Yellow or transparent fruit peel color is caused by the accumulation or lack of naringenin chalcone (NG, C) in fruit peel and determines the red or pink appearance of tomato fruit, respectively. NGC biosynthesis is regulated by the SlMYB12 gene of the Y locus on chromosome 1, and DNA markers derived from SlMYB12 would be useful for marker-assisted selection (MAS) of tomato fruit color. To develop a gene-based marker, 4.9 kb of the SlMYB12 gene including a potential promoter region was sequenced from the red-fruited (YY) line 'FCR' and pink-fruited (yy) line 'FCP'. Sequence alignment of these SlMYB12 alleles revealed no sequence variations between 'FCR' and 'FCP'. To identify SlMYB12-linked single nucleotide polymorphisms (SNPs), 'FCR' and 'FCP' were genotyped using a SolCAP Tomato SNP array and CAPS markers (CAPS-456, 531, 13762, and 38123) were developed from the four SNPs (solcap_snp_sl_456, 531, 13762, and 38123) most closely flanking the SlMYB12. These CAPS markers were mapped using $F_2$ plants derived from 'FCR' ${\times}$ 'FCP'. The map positions of the fruit peel color locus (Y) were CAPS-13762 (0 cM) - 456 (11.09 cM) - Y (15.71 cM) - 38123 (17.82 cM) - 531 (30.86 cM), and the DNA sequence of SlMYB12 was physically anchored in the middle of CAPS-456 and CAPS-38123, indicating that fruit peel color in domesticated tomato is controlled by SlMYB12. A total of 64 SolCAP tomato germplasms were evaluated for their fruit peel color and SNPs located between solcap_snp_sl_456 and 38123. Seven SNPs that were detected in this interval were highly conserved for pink-fruited accessions and specific to transparent fruit peel traits, as depicted by a phenetic tree of 64 accessions based on the seven SNPs.