• KOREAN JOURNAL OF CROP SCIENCE
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• v.49 no.1
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• pp.69-72
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• 2004

Somaclonal variation, defined as phenotypic and genetic variations among regenerated plants from a parental plant, could be caused by changes in chromosome structure, single gene mutation, cytoplasm genetic mutation, insertion of transposable elements, and DNA methylation during plant regeneration. The objective of this study was to evaluate DNA variations among somaclonal variants from the cotyledonary node culture in soybean. A total of 61 soybean somaclones including seven $\textrm{R}_1$ lines and seven $\textrm{R}_2$ lines from Iksannamulkong as well as 27 $\textrm{R}_1$ lines and 20 $\textrm{R}_2$ lines from Jinju 1 were regenerated by organogenesis from the soybean cotyledonary node culture system. Field evaluation revealed no phenotypic difference in major agronomic traits between somaclonal variants and their wild types. AFLP and SSR analyses were performed to detect variations at the DNA level among somaclonal variants of two varieties. Based on AFLP analysis using 36 primer sets, 17 of 892 bands were polymorphic between Iksannamulkong and its somaclonal variants and 11 of 887 bands were polymorphic between Jinju 1 and its somaclonal variants, indicating the presence of DNA sequence change during plant regeneration. Using 36 SSR markers, two polymorphic SSR markers were detected between Iksannamulkong and its somaclonal variants. Sequence comparison amplified with the primers flanking Satt545 showed four additional stretches of ATT repeat in the variant. This suggests that variation at the DNA level between somaclonal variants and their wild types could provide basis for inducing mutation via plant regeneration and broadening crop genetic diversity.

• Journal of Genetic Medicine
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• v.20 no.2
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• pp.39-45
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• 2023

As advanced sequencing technologies continue to uncover an increasing number of variants in genes associated with human genetic diseases, there is a growing demand for systematic approaches to assess the impact of these variants on human development, health, and disease. While in silico analyses have provided valuable insights, it is essential to complement these findings with model organism studies to determine the functional consequences of genetic variants in vivo. Drosophila melanogaster is an excellent genetic model for such functional studies due to its efficient genetic technologies, high gene conservation with humans, accessibility to mutant fly resources, short life cycles, and cost-effectiveness. The traditional GAL4-UAS system, allowing precise control of gene expression through binary regulation, is frequently employed to assess the effects of monoallelic variants. Recombinase medicated cassette exchange or CRISPR-Cas9-mediated GAL4 insertion within coding introns or substitution of gene body with Kozak-Gal4 result in the loss-of-function of the target gene. This GAL4 insertion strategy also enables the expression of reference complementary DNA (cDNA) or cDNA carrying genetic variants under the control of endogenous regulatory cis elements. Furthermore, the CRISPR-Cas9-directed tissue-specific knockout and cDNA rescue system provides the flexibility to investigate candidate variants in a tissue-specific and/or developmental-timing dependent manner. In this review, we will delve into the diverse genetic techniques available in Drosophila and their applications in diagnosing and studying numerous undiagnosed diseases over the past decade.

• BMB Reports
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• v.37 no.2
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• pp.167-176
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• 2004

Although efficient antiviral lamivudine is used for HBV-infected patients, a prolonged treatment with nucleoside analogs often results in lamivudine-resistant variants. In this study, we evaluated the fidelity of the lamivudine-resistant variants. The FLAG-tagged wild-type (FPolE) and Met550 variants (FPolE/M550A, M550V, and M550I) of HBV DNA polymerases were expressed in insect cells then purified. Like many other reverse transcriptases, no $3'{\rightarrow}5'$ exonuclease activity was detected in the HBV DNA polymerase. Since there is no proofreading activity, then the use of the site-specific nucleotide misincorporation method is beneficial. From the $f_{ins}$ value analysis, it is evident that M550I and M550V exhibit higher fidelity values than the wild-type HBV DNA polymerase, while M550A exhibits similar fidelity values. It is therefore suggested that lamivudine resistance comes from the stringency to dNTP binding and the discrimination of dCTP and lamivudine in M550V and M550I.

• Korean Journal of Plant Taxonomy
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• v.43 no.1
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• pp.63-68
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• 2013

ITS DNA sequences of two variants of Pinus spp. having single fasciculate leaf or two to three fasciculate leaves within an individual were analysed in order to determine their origin. Also, the same DNA locus of P. densiflora, P. rigida and P. koraiensis, distributed at the same region together with the OTUs having leaf variations, were analysed to compare with each other. Aligned sequences including ITS1, 5.8S and ITS2 were 580~584 bp in length. The 5.8S region was well conserved among all the OTUs we tested except for P. koraiensis, which has two nucleotide substitutions. The partial ITS1 region upstream of the 5.8S region showed relatively high sequence diversity compare to the ITS2 and has 181~185 bp in length. In this region, the sequences of the two variants were identical to that of P. densiflora. The ITS2 has identical for all OTUs in length and the two variants also have same sequences compare to that of P. densiflora. These two variants and samples of P. densiflora were grouped together in the UPGMA tree with 100% similarity level. The result strongly suggest that these two variants were originated from P. densiflora.

• Genomics & Informatics
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• v.12 no.4
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• pp.136-144
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• 2014

Besides single-nucleotide variants in the human genome, large-scale genomic variants, such as copy number variations (CNVs), are being increasingly discovered as a genetic source of human diversity and the pathogenic factors of diseases. Recent experimental findings have shed light on the links between different genome architectures and CNV mutagenesis. In this review, we summarize various genomic features and discuss their contributions to CNV formation. Genomic repeats, including both low-copy and high-copy repeats, play important roles in CNV instability, which was initially known as DNA recombination events. Furthermore, it has been found that human genomic repeats can also induce DNA replication errors and consequently result in CNV mutations. Some recent studies showed that DNA replication timing, which reflects the high-order information of genomic organization, is involved in human CNV mutations. Our review highlights that genome architecture, from DNA sequence to high-order genomic organization, is an important molecular factor in CNV mutagenesis and human genomic instability.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.3
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• pp.301-307
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• 2005

Genetic variants of Hanwoo mtDNA in the region of cytochrome oxidase subunit I, II and III complex were detected using restriction enzymes. PCR primers were designed based on the bovine mtDNA sequence, and 6 primer sets (Mt4, Mt5, Mt6, Mt7, Mt8 and Mt9) were used. A total of 20 restriction enzymes were used, and 6 restriction enzymes, which were Hinf I, Pvu II, Rsa I, Eco RI, Bgl II, and Msp I, showed genetic polymorphisms. Significant associations between genetic variants and weight traits were observed at WT15 (p<0.05) and WT18 (p<0.01) with Pvu II for Mt9, Bgl II for Mt6 and Rsa I for Mt8 segments in the region of cytochrome oxidase subunit complex. Significant associations were also observed at Mt9-Pvu II and Mt6-Bgl II segments for WT9 (p=0.01), WT12 (p=0.02), respectively. These results suggest that genetic variants of mtDNA in the region of cytochrome oxidase subunit complex may be candidate segments for improvement of animal growth as weight traits.

• Genomics & Informatics
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• v.19 no.4
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• pp.44.1-44.9
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• 2021

Autism is a complex neurodevelopmental disorder, the prevalence of which has increased drastically in India in recent years. Neuroligin is a type I transmembrane protein that plays a crucial role in synaptogenesis. Alterations in synaptic genes are most commonly implicated in autism and other cognitive disorders. The present study investigated the neuroligin 3 gene in the Indian autistic population by sequencing and in silico pathogenicity prediction of molecular changes. In total, 108 clinically described individuals with autism were included from the North Karnataka region of India, along with 150 age-, sex-, and ethnicity-matched healthy controls. Genomic DNA was extracted from peripheral blood, and exonic regions were sequenced. The functional and structural effects of variants of the neuroligin 3 protein were predicted. One coding sequence variant (a missense variant) and four non-coding variants (two 5'-untranslated region [UTR] variants and two 3'-UTR variants) were recorded. The novel missense variant was found in 25% of the autistic population. The C/C genotype of c.551T>C was significantly more common in autistic children than in controls (p = 0.001), and a significantly increased risk of autism (24.7-fold) was associated with this genotype (p = 0.001). The missense variant showed pathogenic effects and high evolutionary conservation over the functions of the neuroligin 3 protein. In the present study, we reported a novel missense variant, V184A, which causes abnormal neuroligin 3 and was found with high frequency in the Indian autistic population. Therefore, neuroligin is a candidate gene for future molecular investigations and functional analysis in the Indian autistic population.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.10
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• pp.4719-4722
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• 2016

Background: Glutathione S-transferase M1 (GSTM1) is involved in the detoxification of carcinogenic agents. DNA copy number variants of GSTM1 may be associated with cancer progression and may result in reduced survival time of various cancers. Determination of DNA copy number variants was here used to assess the association between GSTM1 copy number variant and pathological status and survival time of colorectal-cancer patients treated with 5-fluorouracil-based chemotherapy. Methods: One hundred thirteen Thai colorectal-cancer patients were investigated for GSTM1 copy number variant by real-time PCR. Relationships between gene copy number variants and clinico-pathological parameters were determined. Result: Associations were evident between GSTM1 copy number and stage of tumor (P = 0.026) and metastasis at diagnosis (P = 0.049), with odds ratio values of 0.2 and 0.3 respectively. Conclusions: GSTM1 copy number variant was here not related with reduced overall survival for the colorectal-cancer patients receiving 5-FU-based chemotherapy.

• Clinical and Experimental Pediatrics
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• v.60 no.10
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• pp.327-332
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• 2017

Purpose: Short stature affects approximately 2%-3% of children, representing one of the most frequent disorders for which clinical attention is sought during childhood. Despite assumed genetic heterogeneity, mutations or deletions in the short stature homeobox-containing gene (SHOX ) are frequently detected in subjects with short stature. Idiopathic short stature (ISS) refers to patients with short stature for various unknown reasons. The goal of this study was to screen all the exons of SHOX to identify related mutations. Methods: We screened all the exons of SHOX for mutations analysis in 105 ISS children patients (57 girls and 48 boys) living in Taif governorate, KSA using a direct DNA sequencing method. Height, arm span, and sitting height were recorded, and subischial leg length was calculated. Results: A total of 30 of 105 ISS patients (28%) contained six polymorphic variants in exons 1, 2, 4, and 6. One mutation was found in the DNA domain binding region of exon 4. Three of these polymorphic variants were novel, while the others were reported previously. There were no significant differences in anthropometric measures in ISS patients with and without identifiable polymorphic variants in SHOX. Conclusion: In Saudi Arabia ISS patients, rather than SHOX, it is possible that new genes are involved in longitudinal growth. Additional molecular analysis is required to diagnose and understand the etiology of this disease.

• Food Science of Animal Resources
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• v.26 no.1
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• pp.121-126
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• 2006

Major milk proteins have considerable variane which comes from substitution and deletions in their amino arid sequences. Variants in genes that code for milk proteins, such as ${\beta}$-lactoglobulin (${\beta}-LG$) have been established as genetic markers for milk production and milk protein composition in dairy cattle. The effect of ${\beta}-LG$ variant on milk production traits, such as milk yield. fat yield, protein yield, fat percentage and protein percentage, was estimated for 482 Holstein cows in the first lactation. The ${\beta}-LG$ variants were determined by PCR-RFLP technique at the DNA level. Single trait linear model was used for the statistical analysis of the data. Results of this study indicated that ${\beta}-LG$ variants affected significantly protein yield (p<0.05) and fat percentage (p<0.05). Animals with the AA variant produced 31kg of milk protein more than animals with the BB variant. On the contrary, cows with the BB variant had fat percentage higher by 0.35 and 0.32% compared with cows with the AA and AB variants, respectively. No associations between the ${\beta}-LG$ variants and milk yield, protein percentage and fat yield were found Therefore, milk production traits could be improved through ${\beta}-LG$ typing by increasing the frequency of A variant for protein yield or the frequency of B variant for fat content in Holstein dairy cattle population.