• Molecules and Cells
• /
• v.37 no.1
• /
• pp.36-42
• /
• 2014

The tomato (Solanum lycopersicum L.) is a model plant for genome research in Solanaceae, as well as for studying crop breeding. Genome-wide single nucleotide polymorphisms (SNPs) are a valuable resource in genetic research and breeding. However, to do discovery of genome-wide SNPs, most methods require expensive high-depth sequencing. Here, we describe a method for SNP calling using a modified version of SAMtools that improved its sensitivity. We analyzed 90 Gb of raw sequence data from next-generation sequencing of two resequencing and seven transcriptome data sets from several tomato accessions. Our study identified 4,812,432 non-redundant SNPs. Moreover, the workflow of SNP calling was improved by aligning the reference genome with its own raw data. Using this approach, 131,785 SNPs were discovered from transcriptome data of seven accessions. In addition, 4,680,647 SNPs were identified from the genome of S. pimpinellifolium, which are 60 times more than 71,637 of the PI212816 transcriptome. SNP distribution was compared between the whole genome and transcriptome of S. pimpinellifolium. Moreover, we surveyed the location of SNPs within genic and intergenic regions. Our results indicated that the sufficient genome-wide SNP markers and very sensitive SNP calling method allow for application of marker assisted breeding and genome-wide association studies.

• Proceedings of the Korea Information Processing Society Conference
• /
• 2011.04a
• /
• pp.1260-1263
• /
• 2011

최근 차세대 시퀀싱 (Next Generation Sequencing, NGS) 기술이 발전하면서 DNA, RNA 등의 시퀀싱 데이터를 이용한 유전체 분석 방식에 관한 연구가 활발히 이루어지고 있다. 차세대 시퀀싱 데이터를 이용한 유전체 분석 방식은 마이크로어레이 혹은 EST/cDNA 데이터를 이용한 기존의 분석 방식에 비하여 비용이 적게 들고 정확한 결과를 얻을 수 있다는 장점이 있다. 그러나 이 들 DNA, RNA 시퀀싱 데이터는 각 시퀀스의 길이가 짧고 전체 용량은 매우 커서 이 들 데이터로부터 정확한 분석 결과를 추출하는 데에 많은 어려움이 있다. 본 연구에서는 클라우드 컴퓨팅 기술을 기반으로 하여 대용량의 RNA 시퀀싱 데이터를 고속으로 처리하는 병렬 SNP 추출 알고리즘을 제안한다. 전체 게놈 데이터 중 유전자 영역만을 high coverage로 시퀀싱하여 얻어지는 RNA 시퀀싱 데이터는 유전자 변이 추출을 목적으로 분석되며, SNP(Single Nucleotide Polymorphism)와 같은 유전자 변이는 질병의 원인 규명 및 치료법 개발에 직접 이용된다. 제안된 알고리즘은 동시에 실행되는 다수의 Map/Reduce 함수에 의해서 대규모 RNA 시퀀스를 병렬로 처리하며, 레퍼런스 시퀀스에 매핑된 각 염기의 출현 빈도와 품질점수를 이용하여 SNP를 추출한다. 또한 이 들 SNP 추출 결과에 대한 시각적 분석 도구를 제공하여 SNP 추출 과정 및 근거를 시각적으로 확인/검증할 수 있도록 지원한다.

• Journal of Life Science
• /
• v.32 no.12
• /
• pp.947-955
• /
• 2022

Silkworms, which have recently shown promise as functional health foods, show functional differences between varieties; therefore, the need for variety identification is emerging. In this study, we analyzed the whole silkworm genome to identify 10 unique silkworm varieties (Baekhwang, Baekok, Daebaek, Daebak, Daehwang, Goldensilk, Hansaeng, Joohwang, Kumkang, and Kumok) using single nucleotide polymorphisms (SNP) present in the genome as biomarkers. In addition, nine SNPs were selected to discriminate between varieties by selecting SNPs specific to each variety. We subsequently created a decision tree capable of cross-verifying each variety and classifying the varieties through sequential analysis. Restriction fragment length polymorphism (RFLP) was used for SNP867 and SNP9183 to differentiate between the varieties of Daehwang and Goldensilk and between Kumkang and Daebak, respectively. A tetra-primer amplification refractory (T-ARMS) mutation was used to analyze the remaining SNPs. As a result, we could isolate the same group or select an individual variety using the nine unique SNPs from SNP780 to SNP9183. Furthermore, nucleotide sequence analysis for the region confirmed that the alleles were identical. In conclusion, our results show that combining SNP analysis of the whole silkworm genome with the decision tree is of high value as a discriminative marker for classifying silkworm varieties.

• Journal of Plant Biotechnology
• /
• v.41 no.2
• /
• pp.73-80
• /
• 2014

Pretreatment of chinese cabbage leaves with $100{\mu}M$ sodium nitroprusside (SNP), a nitric oxide (NO) donor, effectively improved their tolerance to subsequent $2{\mu}M$ paraquat (PQ)-induced oxidative damage. The fresh weight, and chlorophyll and protein contents in primary leaves treated with PQ alone were noticeably reduced over 24 h light incubation. However, these leaf injury symptoms were significantly alleviated with $100{\mu}M$ SNP pretreatment for 3 h prior to PQ exposure. In additions, the increase of the contents of malondialdehyde (MDA) and $H_2O_2$ due to PQ exposure were significantly inhibited by SNP pretreatment. Together with the protective effects of SNP against PQ toxicity in leaves, the changes of ascorbate-glutathione cycle enzymes activities were examined. In the PQ alone treatment, the activities of APX, DHAR, and GR after 6 h incubation were rapidly reduced and showed 19%, 50% and 39% respectively, compared with those of the control. However, the decreases in these enzyme activities were significantly inhibited by SNP pretreatment. As a result, their activities were higher than those of PQ alone treatment by 5 times, 2 times, and 1.5 times, respectively, at 6 h incubation. Thereafter, these enzymes decrease their activities gradually showing high levels than those of PQ alone. Based on the above results, it can be assumed that the activation of ascorbate-glutathione cycle by SNP pretreatment in chinese cabbage leaves exposed to PQ can prevent $H_2O_2$ accumulation, thereby leading to protection against PQ-induced oxidative stress. Also, these results indicate that NO acts as an protectant against PQ stress in the leaves of chinese cabbage.

• Journal of Plant Biotechnology
• /
• v.47 no.3
• /
• pp.218-226
• /
• 2020

This report describes methods for selecting informative single nucleotide polymorphisms (SNPs), and the development of an online Solanaceae genome database, using 234 tomato resequencing data entries deposited in the NCBI SRA database. The 126 accessions of Solanum lycopersicum, 68 accessions of Solanum lycopersicum var. cerasiforme, and 33 accessions of Solanum pimpinellifolium, which are frequently used for breeding, and some wild-species tomato accessions were included in the analysis. To select tag-SNPs, we identified 29,504,960 SNPs in 234 tomatoes and then separated the SNPs in the genic and intergenic regions according to gene annotation. All tag-SNP were selected from non-synonymous SNPs among the SNPs present in the gene region and, as a result, we obtained tag-SNP from 13,845 genes. When there were no non-synonymous SNPs in the gene, the genes were selected from synonymous SNPs. The total number of tag-SNPs selected was 27,539. To increase the usefulness of the information, a Solanaceae genome database website, TGsol (http://tgsol. seeders.co.kr/), was constructed to allow users to search for detailed information on resources, SNPs, haplotype, and tag-SNPs. The user can search the tag-SNP and flanking sequences for each gene by searching for a gene name or gene position through the genome browser. This website can be used to efficiently search for genes related to traits or to develop molecular markers.

• Journal of Animal Science and Technology
• /
• v.53 no.4
• /
• pp.311-317
• /
• 2011

The aim of this study was to evaluate the association between economic traits of Korean cattle (Hanwoo) and genetic variation in fatty acid binding protein 5 (FABP5) gene within QTL region of carcass weight and marbling score traits on BTA 14. We sequenced for detection of single nucleotide polymorphism (SNP) with 24 unrelated Hanwoo samples and identified four SNPs (-1141A>G, 949A>G, 969A>G and 1085C>G). Relationship between the genotypes of 583 Hanwoo individuals by PCR-RFLP and economic traits were analyzed by the mixed regression model implemented in the ASReml program. As the result of statistical analysis, SNP1 (-1141A>G) showed significant effect (p<0.003) on marbling score (MS) and SNP2 (949A>G) showed significant effect (p<0.034) on eye muscle area (EMA). Further studies are required to validate the significant SNPs in a bigger population, but the SNPs (-1141A>G and 949A>G) of FABP5 could be a genetic marker to estimate molecular breeding value (MEBV) for carcass traits in Hanwoo.

• Journal of Life Science
• /
• v.30 no.7
• /
• pp.614-624
• /
• 2020

The recent development of next-generation sequencing technology has enabled increased genomic analysis, but very few single nucleotide polymorphism (SNP) markers applicable to sweet persimmon (Diospyros kaki Thunb.) cultivars have been identified. In this study, SNP primers developed from five pollination-constant astringent (PCA) persimmons native to Korea were applied to discriminate between cultivars and verify their usability. The polymerase chain reactions of 19 SNP primers developed by Jung et al. were checked, with 11 primers finally selected. The other eight were very difficult to analyze in the agarose gel electrophoresis and QIAxcel Advanced System used in this experiment and were therefore excluded. The 11 SNP primers were applied through first and second verification to 76 cultivars and collection lines including 20 pollination-variant non-astringent (PVNA), 30 pollination-constant non-astringent (PCNA), 20 PCA, and six pollination-variant astringent (PVA). Of these, 38 were indistinguishable (eight PVNA, 18 PCNA, nine PCA, and three PVA). However, the results of applying the 11 SNP primers to new sweet persimmon cultivars, namely Gamnuri, Dannuri, Hongchoo, Jamisi, and Migamjosaeng, showed that they have the potential to be used as a unique marker for simultaneously determining between them.

• Journal of Life Science
• /
• v.33 no.12
• /
• pp.1025-1035
• /
• 2023

In this study, we analyzed SNPs that appear between Korean and Chinese Scapharca subcrenata using the nucleotide sequence data of S. subcrenata analyzed by genotyping by sequencing (GBS). To distinguish the country of origin for S. subcrenata in Korean and Chinese, we developed a primer set as single nucleotide polymorphism (SNP) markers for quantitative real-time PCR (qPCR) analysis and validated by sequencing SNPs. A total of 180 samples of S. subcrenata were analyzed by genotyping by sequencing, and 15 candidate SNPs were selected. SNP marker selection for country of origin were identified through real-time qPCR. Insertion 1 and SNP 21 markers showed the most distinct separation between the sequence types as well as the country of origin through qPCR, with the observed amplification patterns matching the expected outcomes.. Additionally, in a blind test conducted by mixing samples of S. subcrenata at random, Insertion 1 showed 74% accuracy, 52% sensitivity, and 96% specificity, and SNP 21 showed 86% accuracy, 79% sensitivity, and 93% specificity. Therefore, the two SNP markers developed are expected to be useful in verifying the authenticity of the country of origin of S. subcrenata when used independently or in combination.

• Proceedings of the Korea Information Processing Society Conference
• /
• 2010.11a
• /
• pp.1395-1398
• /
• 2010

최근 GWAS(Genome-wide association study)로 인해 수십만 개의 SNP들이 사용 가능하게 되었다. 그러나 SNP 정보의 양이 방대하여 모든 SNP 조합을 검토하는 방식은 계산 비용이 클 뿐 아니라 오버피팅의 위험이 따른다. 본 논문에서는 필터링 기반 알고리즘인 SNPHarvester의 속도를 개선하고 평가함수를 상호정보량으로 대체하여 실험한다. 기존 SNPHarvester와 비교해 속도면에서 50%가 향상되었고 평가함수 면에서는 기존 SNPHarvester와 동일한 성능을 보였다.

• Journal of Acupuncture Research
• /
• v.21 no.3
• /
• pp.107-119
• /
• 2004

Objective : The purpose of this study was to investigate the effect of Bee Venom and melittin on the lipopolysaccharide(LPS) and sodium nitroprusside(SNP)-induced expressions of Cell viability, nitric oxide(NO), inducible nitric oxide synthase(iNOS), extra-signal response kinase(ERK), jun N-terminal Kinase(JNK) and p38 kinase(p38)- mitogen activated protein kinase(MAPK) Family- in RAW 264.7 cells, a murine macrophage cell line. Methods : The expressions of cell viability by MTT assay, NO by Nitrite assay and iNOS, ERK, JNK and p38 were determined by Western blotting. Results : 1. Compared with the control group, 0.5, 1, $5{\mu}g/m{\ell}$ bee venom and 5, $10{\mu}g/m{\ell}$ melittin increased cell viability of RAW 264.7 induced by LPS and SNP significantly respectively. 2. Compared with the control group, 0.5, 1, $5{\mu}g/m{\ell}$ bee venom and 5, $10{\mu}g/m{\ell}$ melittin inhibited expression of NO induced by LPS and SNP significantly respectively. 3. Compared with the control group, 1, $5{\mu}g/m{\ell}$ bee venom and 5, $10{\mu}g/m{\ell}$ melittin inhibited expression of iNOS induced by LPS significantly and 0.5, 1, $5{\mu}g/m{\ell}$ bee venom and 5, $10{\mu}g/m{\ell}$ melittin inhibited expression of iNOS induced by SNP significantly. 4. Compared with the control group, the expression of ERK induced by LPS and SNP decreased significantly in the treatment groups of $5{\mu}g/m{\ell}$ bee venom and 5, $10{\mu}g/m{\ell}$ melittin, which of p-ERK by LPS also did in 1, $5{\mu}g/m{\ell}$ bee venom and 5, $10{\mu}g/m{\ell}$ melittin, but which of p-ERK by SNP did not decrease. 5. Compared with the control group, the. expression of JNK induced by LPS and SNP decreased significantly in the treatment groups of 5, $10{\mu}g/m{\ell}$ melittin, which of p-JNK by LPS in 5, $10{\mu}g/m{\ell}$ melittin and by SNP in $1{\mu}g/m{\ell}$ bee venom and $10{\mu}g/m{\ell}$ melittin decreased significantly. 6. Compared with the control group, the expression of p38 induced by LPS did not have significant difference, which induced by SNP decreased significantly in the treatment groups of 1, $5{\mu}g/m{\ell}$ bee venom and 5, $10{\mu}g/m{\ell}$ melittin. p-p38 induced by LPS decreased significantly in the treatment group of $10{\mu}g/m{\ell}$ of melittin, which induced by SNP also decreased significantly in 0.5, 1, $5{\mu}g/m{\ell}$ bee venom and 5, $10{\mu}g/m{\ell}$ melittin.