• Journal of Convergence for Information Technology
• /
• v.8 no.6
• /
• pp.201-207
• /
• 2018

A genome contains all genetic information of an organism. Within a specific species, unique traits appear for each individual, which can be identified by analyzing nucleotide sequences. Many Genome-Wide Associations Studies have been carried out to find genetic associations and cause of diseases from slightly different base among the individuals. It is important to identify occurrence of slight variations for polymorphisms of individuals. In this paper, we introduce an analysis and visualization tool for specific variation pattern identification of polymorphisms in nucleotide sequences and show the validity of the tool by applying it to analyzing nucleotide sequences of subcultured pOka strain of varicella-zoster virus. The tool is expected to help efficiently explore allele frequency variations and genetic factors within a species.

• Molecules and Cells
• /
• v.42 no.1
• /
• pp.87-95
• /
• 2019

Long interspersed element-1 (LINE-1 or L1) is an autonomous retrotransposon, which is capable of inserting into a new region of genome. Previous studies have reported that these elements lead to genomic variations and altered functions by affecting gene expression and genetic networks. Mounting evidence strongly indicates that genetic diseases or various cancers can occur as a result of retrotransposition events that involve L1s. Therefore, the development of methodologies to study the structural variations and interpersonal insertion polymorphisms by L1 element-associated changes in an individual genome is invaluable. In this study, we applied a systematic approach to identify human-specific L1s (i.e., L1Hs) through the bioinformatics analysis of high-throughput next-generation sequencing data. We identified 525 candidates that could be inferred to carry non-reference L1Hs in a Korean individual genome (KPGP9). Among them, we randomly selected 40 candidates and validated that approximately 92.5% of non-reference L1Hs were inserted into a KPGP9 genome. In addition, unlike conventional methods, our relatively simple and expedited approach was highly reproducible in confirming the L1 insertions. Taken together, our findings strongly support that the identification of non-reference L1Hs by our novel target enrichment method demonstrates its future application to genomic variation studies on the risk of cancer and genetic disorders.

• KOREAN JOURNAL OF CROP SCIENCE
• /
• v.68 no.1
• /
• pp.8-19
• /
• 2023

Adzuki beans have gained popularity in recent years due to their health benefits. Breeding of Adzuki beans is less favorable than with other legumes due to low genetic diversity. This study aimed to evaluate the genetic diversity of 252 adzuki bean germplasms from China, Japan, and Korea using 18 agro-morphological parameters and comparing their performance to three prominent Korean cultivars: Geomguseul, Arari, and Chungjupat. Leaf shape, pod color, and seed coat color were among the qualitative traits that showed wide variations. The quantitative variables also showed wide variations among adzuki bean germplasms. Although there was no significant difference (p < 0.05), the average rate of germination declined in the order of Korean (91.44%) > Chinese (91.31%) > Japanese (87.47%) adzuki beans. Chinese adzuki beans needed fewer days to flower (DF, 58.22 days) and days to mature (DM, 107.13 days), which varied significantly compared to the Korean and Japanese adzuki beans (p < 0.05). The average number of pods per plant (PPP) and one-hundred seeds weight (HSW) were higher in Japanese adzuki beans compared to the Korean and Chinese adzuki beans although the variation of each was not significant. Almost 29.76% of the accessions had early-blooming flowers, 3.97% were premature, 21.43% produced more PPP, and 3.97% yielded more SPP compared to control cultivars. Results of hierarchical cluster and principal component analyses revealed three clusters with significant variation in all quantitative variables except for RG (p < 0.05). The key factors in multivariate analyses were DF, DM, and HSW. Our study investigated the genetic diversity of adzuki bean accessions and identified ten early maturing and ten high PPP-yielding accessions. Our findings would help farmers and breeders to select the top-performing accessions that can provide them with various options.

• Animal cells and systems
• /
• v.1 no.2
• /
• pp.247-257
• /
• 1997

Genetic and morphological variations of Korean Hynobius leechii were surveyed. Starch gel electrophoresis was used to study genetic variation at 23 loci. H. leechii is genetically divided into three groups, each of which is named as Form-A, Form-B, and Form-C. These forms are clearly separated with 4-5 fixed or nearly fixed allelic differences. At a sympatry near Jangseong, Jollanam-do, a significant deviation from random mating between Form-A and Form-B was observed. Therefore, they are considered as two distinct taxi of specific rank. Form-A is widely distributed in the inland of Korea, whereas Form-B is distributed in the islands or near the coastal regions of Western and Southern Korea. Form-B had, in addition, a significant morphological difference from Form-A. On the other hand, Form-C was restricted to an area near Kori atomic power plant, Kyongsangnam-do, and the genetic similarities between this form and Form-A and Form-B were 0.742 and 0.736, respectively. Moreover, Form-C had a unique color pattern, short body and small coccyx. Thus, it seems reasonable to assign this form as another new species.

• Asian-Australasian Journal of Animal Sciences
• /
• v.20 no.4
• /
• pp.477-481
• /
• 2007

Korean Ogol chicken has been registered as a natural monument in Korea and regarded as a valuable genetic resource for the world. As an initial step to investigate the genetic structures of this breed, phylogenetic analysis and calculation of genetic diversities have been performed using mitochondrial DNA (mtDNA) sequence variations. A total of 31 Korean Ogol chicken was grouped into four haplotypes and the large haplotype was represented in 12 individuals. The unrooted neighbor-joining tree indicates that the Korean Ogol chicken shared three (A to C) major chicken lineages representing the high genetic variability of this breed. These results can be used for making the breeding and conservation strategies for the Korean Ogol chicken.

• Asian-Australasian Journal of Animal Sciences
• /
• v.6 no.1
• /
• pp.27-35
• /
• 1993

In an attempt to reveal the interrelationship between fowls of jungle and native origin, their gene constitutions were compared using gene frequencies at the 16 loci controlling blood protein variations. Of the 16 loci analysed by electrophoresis, polymorphism was detected at following seven loci: Es-1, Amy-1, Akp-akp, Akp-2, Alb, Tf and 6-PGD. The other nine loci: Amy-3, Es-D, PGM, PHI, MDH, To, LDH, Hb-1 and Hb-2, were noted to be monomorphic. Genetic distance between pairs of native fowl and jungle fowls was estimated by a numerical taxonomic method. The Indonesian native fowl was genetically close to the Indonesian red jungle fowl, and the grey jungle fowl was genetically similar to the Ceylonese jungle fowl. It was also suggested that the green jungle fowl was genetically remote from the other jungle fowls and from the Indonesian native flow. The proportion of polymorphic loci (Ppoly), the expected average heterozygosity per individual $\bar{H}$, and the effective number of alleles per locus (Ne) were calculated to evaluate the genetic variabilities in the native and jungle fowls. The Indonesian native fowl exhibited slightly higher the proportion of polymorphic loci than the jungle fowls.

• Ocean and Polar Research
• /
• v.36 no.2
• /
• pp.189-197
• /
• 2014

The pearl-spot damsel, Chromis notata, is one of the important fishery species in Korea. While C. notata has been commonly harvested in southern Korea, the increasing number of C. notata in higher latitudes has crucial ecological, economic and evolutionary implications under conditions where the climate is rapidly changing. Here we examined the morphological and genetic characteristics of C. notata to assess patterns of geographical variations among the groups from three different sites. The groups were clearly distinguishable in the analysis of morphological characteristics. On the other hand, the groups were genetically indistinguishable. All individuals fell within a single clade in the neighbor-joining tree but appeared scattered in the haplotype network. Several haplotypes are shared among the sampling sites (Jejudo-Ulleungdo; Hap 9, Wangdolcho-Ulleungdo; Hap 28, Hap 33, Hap 34). Although control region markers did not elucidate the spatial patterns in genetic characteristics, Wangdolcho and Ulleungdo groups appear to exhibit a more robust gene flow between the two groups than with Jejudo group. Integrative approaches such as those combining morphological and genetic analyses minimize potential errors caused by limited perspectives of each analysis and can provide useful information for discovering functional DNA regions attributable to morphological characteristics expressions.

• Animal cells and systems
• /
• v.4 no.3
• /
• pp.267-272
• /
• 2000

Partial sequence of the mitochondrial cytochrome b gene was analyzed to investigate genetic variation from 10 geographic populations of Granulilittorina exigua in Korea. The sequence of 282 base pairs was determined by PCR-directed silver sequencing method. The sequences of two species within the genus Littorina reserved in NIH blast search were utilized to determine geographic variations of species referred. The levels of mtDNA sequence differences were 0.00-2.54% within populations and 0.71-4.43% between populations. There were four amino acid differences between representative species of the genera Granulilittorina and Littorina, but no differences within populations of the genus Granulilittorina. The UPGMA and the N-J trees based on Tamura-Nei genetic distance matrix were constructed, which showed that the genus Granulilittorina was divided into three groups such as eastern (even exception for Tokdo population), southern, and western regional populations. The degrees of genetic divergence within populations of each group were p=0.021, p=0.019, and p=0.018, respectively. The divergence between the eastern and southern populations was p=0.032, showing closer relationship than with the western populations (p=0.052). Based on the diverged time estimation, the eastern and southern populations of Granulilittorina exigua in Korea diverged from the western populations about 2.1 MYBP, and the eastern and southern populations diverged from each other about 1.3 MYBP.

• Plant Resources
• /
• v.8 no.2
• /
• pp.135-144
• /
• 2005

RAPD analysis was performed to discuss the taxonomic status and phylogenetic relationships among the tribe Forsythieae and related groups. Two hundred and eighteen scorable polymorphic bands were detected from fourteen oligonucleotide primers. From the results of RAPD analysis by Nei and Li's genetic distance, each individuals of Abeliophyllum distichum showed high genetic relationships with ranging from 0.085 to 0.301, also the genus Forsythia showed from 0.042 to 0.655 among the species and populations. But, Abeliophyllum and Forsythia showed distinct dissimilarity, ranging from 0.610 to 1.258. And genetic differences among the population of Forsythia were 0.042 in F. koreana, 0.275 in F. saxatilis, 0.275 in F. ovata, 0.279 in F. nakaii, and 0.249 in F. viridissima. The UPGMA phenogram of tribe Forsythieae based on the results of RAPD analysis were presented that Abeliophyllum is distinct genus different from Forsythia. NJ tree which applied as the outgroups Fontanesia and Jasminum was derived, and it showed that tribe Forsythieae might be a monophyletic group. The genus Fontanesia was showed as sister group of tribe Forsythieae. Among the populations of taxa in Forsythia, F. koreana and F. saxatilis were more closely related, and F. ovata and F. nakaii were very closely related to F.japonica. And Fontanesia was the sister group of tribe Forsythieae.

• KOREAN JOURNAL OF CROP SCIENCE
• /
• v.21 no.1
• /
• pp.92-96
• /
• 1976

Considerably large phenotypic and genotypic variations for the important agronomic traits were found in a soybean population consisted with 825 local lines collected in Korea. Genetic coefficient of variation, heritability, and genetic gain for seed weight, plant height. and number of pods per plant were relatively high. Maturity showed a high heritability value with a low genetic gain and the result may be due to the narrow range of maturity date of the population studied.