• 한국육종학회지
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• 제42권2호
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• pp.144-150
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• 2010

The objective of this study was to map gene/QTL for photoblastism in a weedy rice (photoblastic rice: PBR) using DNA markers. Light-induced effect on germination of seeds was compared among three accessions (Oryza sativa L.), PBR, Milyang 23 and Ilpum. Results showed that PBR seeds started to show photoblastism during seed development, different from Ilpum and Milyang 23. Frequency distribution of germination in the F4 lines from crosses between Ilpum and PBR and, Milyang 23 and PBR revealed bimodal distributions suggesting that photoblastism was controlled by a few genes. Bulked segregant analysis using $F_4$ populations derived from the above two crosses was conducted to identify gene/QTL for photoblastism. Two QTL were identified on chromosomes 1 and 12 explaining 11.2 and 12.8% of the phenotypic variance, respectively. Two QTL were further mapped between two SSR markers, RM8260 and RM246 on chromosome 1, and between RM270 and 1103 on chromosome 12. It is noteworthy that two QTL for photoblastism were colocalized with the QTL for seed dormancy reported in the previous QTL studies. The clustering of two genes for photoblastism and dormancy possibly indicates that these regions constitute rice phytochrome gene clusters related to germination. Because PBR has a low degree of dormancy, a pleiotropic effect of a single gene controlling dormancy and photoblastism can be ruled out. The linked markers will provide the foundation for positional cloning of the gene.

• 대한의생명과학회지
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• 제24권2호
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• pp.64-75
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• 2018

CCN3 (also known as NOV, Nephroblastoma overexpressed) proteins are involved in various pathologies during different developmental stages. We have previously shown that intracellular levels and normal extracellular secretion of CCN3 are important for neuronal differentiation. Furthermore, we demonstrated that a single amino acid in the CCN3 TSP-1 domain is important for extracellular secretion and that palmitoylation of CCN3 is required in this process. However, the effect of abnormal CCN3 accumulation on cells remains to be studied. Here, we found mutations in the TSP-1 domain of CCN3 that led to intracellular accumulation and abnormal aggregation of CCN3. It was observed that this mutation resulted in a phenomenon similar to neurodegeneration when overexpressed in the developing mouse cortex. This mutation also confirmed the activation of apoptotic gene expression in Neuro2a cells. In addition, we confirmed the in vivo transcriptional changes induced by this mutation using microarray analysis. We observed a significant increase in the expression of Anp32a, an apoptosis-related gene. Collectively, these results indicate that a single mutation in CCN3 can lead to abnormal cell death if it shows intracellular accumulation and abnormal aggregation.

• 미생물학회지
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• 제20권4호
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• pp.173-182
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• 1982

From FGSC 159 strain of Aspergillus nidulans, temperature sensitive mutants that are defective in growth and differentiation have been isolated by N-methyl-N'-nitroN-nitrosoguanidine (NTG) treatment. The optimum concentration of NTG and incubation time to get the highest mutation frequency was $100{\mu}g$ per ml and 1 hour, respectively. The survival frequency was 1%. Among the isolated mutants, five strains that were affected in early steps of differentiation were selected for further studies and named smK, smY, smB, smF, and smZ. The execution point of each mutant was determined and the growing pattern of each mutant at the restrictive temperature was observed under the microscope. Growth of mutant was arrested near at the execution point. From genetic analysis, each temperature-sensitive mutants was thought to have a single recessive gene. The genes of smK, smY, smB, smF, and smZ are linked to the chromosome VII, IV, VIII, I, and VI, respectively. It can be concluded that the genes controlling the differentiation are widely dispersed in the genome. From the results of mutant, smK, it is considered that a single gene can affect a function (functions) which act(s) at two different steps during differentiation.

• The Plant Pathology Journal
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• 제15권3호
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• pp.131-136
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• 1999

In fungi known as ascomycetes, ability to mate is controlled by a single mating type (MAT) locus with two dissimilar sequences called idiomorphs carrying genes encoding transcription factors that are unrelated to each other. Fungi requiring strains with different MAT genes to complete the sexual process are heterothallic (self-sterile); species in which as single strain is able to undergo sexual reproduction are homothallic (self-fertile). Previous analysis of sequences from several heterothallic and homothallic species of the ascomycete genus Cochliobolus showed that homothallics evolve from heterothallics and that each known Cochliobolus homothallic species arose independently, from a different heterothallic ancestral species. Here we report detailed comparative analyses of MAT sequences ad their flanking regions, and show that: (1) The level of MAT gene similarity is not correlated with reproductive life style; (2) MAT proteins from all Cochliobolus species are conserved within the transcription factor signature sequences; they are not conserved in the carboxy terminal half of MAT-1, or third of MAT-2, except in those from very closely related species; (3) A gene (ORF1) of unknown function, consistently found on the MAT flank, is more conserved than are the MAT genes themselves; (4) The intergenic sequences diverge sharply among species.

• 한국동물생명공학회지
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• 제36권3호
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• pp.129-136
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• 2021

This study identified single nucleotide polymorphisms (SNPs) that affect the body weight of chickens. Analysis of body weight showed that the Cornish breed had the highest body weight, and the Korean native chicken (Gray Brown) had the lowest body weight. TSH is composed of an α-subunit and a β-subunit, and the TSH-β gene encoding the β-subunit has been reported to be associated with obesity. In chickens, it is located on chromosome 26 and is reported to be associated with growth. The calcium-sensing receptor gene (CaSR) plays a role in the regulation of extracellular calcium homeostasis and is responsible for calcium absorption in the urinary tract, which affects the eggshell quality in poultry. It was shown that TSH-β was strongly correlated with weight in Cornish and Korean native (Gray Brown) chickens, particularly in those with the CC trait. However, CaSR showed no association with body weight in poultry; it was associated with calcium and the eggshell. Thus, selection for TSH-β can be used to produce individuals with more favorable traits in terms of body weight.

• Communications for Statistical Applications and Methods
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• 제26권1호
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• pp.1-9
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• 2019

Various probabilistic methods have been proposed for using interpopulation allele frequency differences to infer the ethnic group of a DNA specimen. The selection of the statistical method is critical because the accuracy of the statistical classification results vary. For the ancestry classification, we proposed a new ancestry evaluation method that estimate the combined ethnicity index as well as compared its performance with various classical classification methods using two real data sets. We selected 13 SNPs that are useful for the inference of ethnic origin. These single nucleotide polymorphisms (SNPs) were analyzed by restriction fragment mass polymorphism assay and followed by classification among ethnic groups. We genotyped 400 individuals from four ethnic groups (100 African-American, 100 Caucasian, 100 Korean, and 100 Mexican-American) for 13 SNPs and allele frequencies that differed among the four ethnic groups. Additionally, we applied our new method to HapMap SNP genotypes for 1,011 samples from 4 populations (African, European, East Asian, and Central-South Asian). Our proposed method yielded the highest accuracy among statistical classification methods. Our ethnic group classification system based on the analysis of ancestry informative SNP markers can provide a useful statistical tool to identify ethnic groups.

• Asian Pacific Journal of Cancer Prevention
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• 제13권12호
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• pp.6121-6128
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• 2012

Radiation-induced side effects on normal tissue are determined largely by the capacity of cells to repair radiation-induced DNA damage. X-ray repair cross-complementing group 1 (XRCC1) plays an important role in the repair of DNA single-strand breaks. Studies have shown conflicting results regarding the association between XRCC1 gene polymorphisms (Arg399Gln, Arg194Trp, -77T>C and Arg280His) and radiation-induced side effects in patients undergoing whole breast radiotherapy. Therefore, we conducted a meta-analysis to determine the predictive value of XRCC1 gene polymorphisms in this regard. Analysis of the 11 eligible studies comprising 2,199 cases showed that carriers of the XRCC1 399 Gln allele had a higher risk of radiation-induced toxicity than those with the 399 ArgArg genotype in studies based on high-quality genotyping methods [Gln vs. ArgArg: OR, 1.85; 95% CI, 1.20-2.86] or in studies with mixed treatment regimens of radiotherapy alone and in combination with chemotherapy [Gln vs. ArgArg: OR, 1.60; 95% CI, 1.09-2.23]. The XRCC1 Arg399Gln variant allele was associated with mixed acute and late adverse reactions when studies on late toxicity only were excluded [Gln allele vs. Arg allele: OR, 1.22; 95% CI, 1.00-1.49]. In contrast, the XRCC1 Arg280His variant allele was protective against radiation-induced toxicity in studies including patients treated by radiotherapy alone [His allele vs. Arg allele: OR, 0.58; 95% CI, 0.35-0.96]. Our results suggest that XRCC1 399Gln and XRCC1 280Arg may be independent predictors of radiation-induced toxicity in post-surgical breast cancer patients, and the selection of genotyping method is an important factor in determining risk factors. No evidence for any predictive value of XRCC1 Arg194Trp and XRCC1 -77T>C was found. So, larger and well-designed studies might be required to further evaluate the predictive value of XRCC1 gene variation on radiation-induced side effects in patients undergoing whole breast radiotherapy.

• 한국발생생물학회지:발생과생식
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• 제18권4호
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• pp.275-286
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• 2014

To successful molecular breeding, identification and functional characterization of breeding related genes and development of molecular breeding techniques using DNA markers are essential. Although the development of a useful marker is difficult in the aspect of time, cost and effort, many markers are being developed to be used in molecular breeding and developed markers have been used in many fields. Single nucleotide polymorphisms (SNPs) markers were widely used for genomic research and breeding, but has hardly been validated for screening functional genes in olive flounder. We identified single nucleotide polymorphisms (SNPs) from expressed sequence tag (EST) database in olive flounder; out of a total 4,327 ESTs, 693 contigs and 514 SNPs were detected in total EST, and these substitutions include 297 transitions and 217 transversions. As a result, 144 SNP markers were developed on the basis of 514 SNP to selection of useful gene region, and then applied to each of eight wild and culture olive flounder (total 16 samples). In our experimental result, only 32 markers had detected polymorphism in sample, also identified 21 transitions and 11 transversions, whereas indel was not detected in polymorphic SNPs. Heterozygosity of wild and cultured olive flounder using the 32 SNP markers is 0.34 and 0.29, respectively. In conclusion, we identified SNP and polymorphism in olive flounder using newly designed marker, it supports that developed markers are suitable for SNP detection and diversity analysis in olive flounder. The outcome of this study can be basic data for researches for immunity gene and characteristic with SNP.

• 한국작물학회지
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• 제49권5호
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• pp.429-433
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• 2004

A single recessive gene, rxp, controls the bacterial leaf pustule (BLP) resistance in soybean and in our previous article, it has been mapped on linkage group (LG) D2 of molecular genetic map of soybean. A total of 130 recombinant inbred lines (RILs) from a cross between BLP-resistant SS2-2 and BLP-susceptible Jangyeobkong were used to identify molecular markers linked to rxp. Fifteen simple sequence repeat (SSR) markers on LG D2 were screened to construct a genetic map of rxp locus. Only four SSR markers, Satt135, Satt372, Satt448, and Satt486, showed parental polymorphisms. Using these markers, genetic scaffold map was constructed covering 26.2cM. Based on the single analysis of variance, Satt372 among these four SSR markers was the most significantly associated with the resistance to BLP. To develop new amplified fragment length polymorphism (AFLP) marker linked to the resistance gene, bulked segregant analysis (BSA) was employed. Resistance and susceptible bulks were made by pooling equal amount of genomic DNAs from ten of each in the segregating population. A total of 192 primer combinations were used to identify specific bands to the resistance, selecting three putative AFLP markers. These AFLP markers produced the fragment present in SS2-2 and the resistant bulk, and not in Jangyeobkong and the susceptible bulk. Linkage analysis revealed that McctEact97 $(P=0.0004,\;R^2=14.67\%)$ was more significant than Satt372, previously reported as the most closely linked marker.

• 한국동물생명공학회지
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• 제39권2호
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• pp.138-144
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• 2024

Background: As the number of households raising companion dogs increases, the pet genetic analysis market also continues to grow. However, most studies have focused on specific purposes or native breeds. This study aimed to collect genomic data through single nucleotide polymorphism (SNP) chip analysis of companion dogs in South Korea and perform genetic diversity analysis and SNP annotation. Methods: We collected samples from 95 dogs belonging to 26 breeds, including mixed breeds, in South Korea. The SNP genotypes were obtained for each sample using an Axiom^TM Canine HD Array. Quality control (QC) was performed to enhance the accuracy of the analysis. A genetic diversity analysis was performed for each SNP. Results: QC initially selected SNPs, and after excluding non-diverse ones, 621,672 SNPs were identified. Genetic diversity analysis revealed minor allele frequencies, polymorphism information content, expected heterozygosity, and observed heterozygosity values of 0.220, 0.244, 0.301, and 0.261, respectively. The SNP annotation indicated that most variations had an uncertain or minimal impact on gene function. However, approximately 16,000 non-synonymous SNPs (nsSNPs) have been found to significantly alter gene function or affect exons by changing translated amino acids. Conclusions: This study obtained data on SNP genetic diversity and functional SNPs in companion dogs raised in South Korea. The results suggest that establishing an SNP set for individual identification could enable a gene-based registration system. Furthermore, identifying and researching nsSNPs related to behavior and diseases could improve dog care and prevent abandonment.