• 제목/요약/키워드: Marker nucleotide

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Nuclear rDNA characteristics for DNA taxonomy of the centric diatom Chaetoceros (Bacillariophyceae)

  • Oh, Hye-Young;Cheon, Ju-Yong;Lee, Jin-Hwan;Hur, Sung-Bum;Ki, Jang-Seu
    • ALGAE
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    • v.25 no.2
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    • pp.65-70
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    • 2010
  • The genus Chaetoceros provides highly diversified diatoms in marine systems. Morphological descriptions of the genus are well-documented, yet the DNA taxonomy of Chaetoceros has not been satisfactorily established. Here, the molecular divergences of the 18S-28S rDNA of Chaetoceros were assessed. DNA similarities were relatively low in both 18S (93.1 $\pm$ 3.9%) and 28S rDNA (81.0 $\pm$ 4.6%). Phylogenies of the 18S, 28S rDNAs showed that Chaetoceros was divided according to individual species, clustering the same species into single clades. Statistical analysis with corrected genetic (p-) distance scores showed that nucleotide divergence of Chaetoceros 28S rDNA significantly differed from that of 18S rDNA (Student's t-test, p < 0.05). This finding suggests that the 28S rDNA may be treated as a more suitable marker for species-level taxonomic distinctions of Chaetoceros.

Molecular Variation and Distribution of Anopheles fluviatilis (Diptera: Culicidae) Complex in Iran

  • Naddaf, Saied Reza;Razavi, Mohammad Reza;Bahramali, Golnaz
    • Parasites, Hosts and Diseases
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    • v.48 no.3
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    • pp.231-236
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    • 2010
  • Anopheles fluviatilis James (Oiptera: Culicidae) is one of the known malaria vectors in south and southeastern Iran. Earlier ITS2 sequences analysis of specimens from Iran demonstrated only a single genotype that was identical to species Y in India, which is also the same as species T. We identified 2 haplotypes in the An. fluviatilis populations of Iran based on differences in nucleotide sequences of D3 domain of the 28S locus of ribosomal DNA (rDNA). Comparison of sequence data from 44 Iranian specimens with those publicly available in the Genbank database showed that all of the 288-D3 sequences from Kazeroun and Khesht regions in Fars Province were identical to the database entry representing species U in India. In other regions, all the individuals showed heterozygosity at the single nucleotide position, which identifies species U and T. It is argued that the 2 species may co-occur in some regions and hybridize; however, the heterozygosity in the 288-D3 locus was not reflected in ITS2 sequences and this locus for all individuals was identical to species T. This study shows that in a newly diverged species, like members of An. fluviatilis complex, a single molecular marker may not be sufficiently discriminatory to identify all the taxa over a vast geographical area. In addition, other molecular markers may provide more reliable information for species discrimination.

Genome-Wide SNP Calling Using Next Generation Sequencing Data in Tomato

  • Kim, Ji-Eun;Oh, Sang-Keun;Lee, Jeong-Hee;Lee, Bo-Mi;Jo, Sung-Hwan
    • Molecules and Cells
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    • v.37 no.1
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    • pp.36-42
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    • 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.

The SNP of WBP1 is associated with heifer reproductive performance in the Korean native cattle Hanwoo

  • Jeong, Jiyeon;Lee, Seung-Hwan;Choi, Inchul
    • Korean Journal of Agricultural Science
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    • v.46 no.1
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    • pp.27-31
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    • 2019
  • It is well documented that intensive selection in dairy cattle for economic value such as increased milk yield led to a decline in reproductive performance. Recent studies using genome-wide association studies (GWASs) discovered candidate genes involved in the lower fertility including embryo development and conception rates. However, the information, which showed a lower reproductive performance, is limited to dairy cattle, especially Holstein, and the candidate genes were not examined in the Korean native cattle Hanwoo which has been intensively selected and bred for meat in the last few decades. We selected the candidate genes WBP1 and PARM1 reported to be associated with cow and/or heifer conception in dairy cattle and analyzed the genotype because those genes have non-synonymous single nucleotide polymorphisms (SNPs). To determine the single base change, we used the high resolution melting (HRM) assay which is rapid and cost-effective for a small number of genes. We found that most heifers with higher conception (1: service per conception) have the AA genotype coding Threonine rather than Proline in the WBP1 gene. We did not detect an association for a SNP in PARM1 in our analysis. In conclusion, the genetic variation of WBP1 can be used as a selective marker gene to improve reproductive performance, and HRM assay can be used to identify common SNP genotypes rapidly and cost effectively.

Development of HRM Markers for Discrimination of Pyogo (Lentinula edodes) Cultivars Sanjo 701 and Chamaram

  • Suyun Moon;Hojin Ryu
    • The Korean Journal of Mycology
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    • v.50 no.3
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    • pp.225-233
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    • 2022
  • Pyogo (Shiitake, Lentinula edodes) is one of the most important edible mushrooms because of its outstanding nutritive and medicinal value. In the registration and protection procedure for newly developed mushroom cultivars, the application of molecular markers that can supplement the morphological characteristic-based distinction has been strongly requested. Sanjo 701 and Chamaram, newly developed at the Federation Forest Mushroom Research Center of Korea, have been characterized as innovative cultivars suitable for customer demands because of their high yields and cultivation rates. However, no technical tools can protect the rights to these important cultivars. In this study, using comparative genomic information from 23 commercially available pyogo cultivars, we identified single nucleotide polymorphisms (SNPs) that accurately differentiated Sanjo701 and Chamaram from the other cultivars. We also developed high-resolution melting analysis (HRM)-based SNP markers that discriminate among the tested 23 pyogo cultivars. The developed SNP markers can be utilized for rapid, accurate identification of pyogo cultivars with low genetic diversity and to prevent cultivar contamination caused by illegally distributed inocula. In addition, these markers can serve as a crucial scientific basis for securing the right to conserve new cultivars in international markets.

Development of Cleaved Amplified Polymorphic Sequence Markers for the Identification of Lentinula edodes Cultivars Sanmaru 1ho and Chunjang 3ho (표고버섯 품종 산마루1호, 천장3호를 구분할 수 있는 CAPS Marker 개발)

  • Moon, Suyun;Lee, Hwa-Yong;Kim, Myungkil;Ka, Kang-Hyeon;Ko, Han Kyu;Chung, Jong-Wook;Koo, Chang-Duck;Ryu, Hojin
    • The Korean Journal of Mycology
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    • v.45 no.2
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    • pp.114-120
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    • 2017
  • Lentinula edodes is an edible mushroom that is mainly cultivated in Asian countries. Recently, new cultivars of this mushroom have been developed in Korea; variety protection is very important, so the development of efficient molecular markers that can distinguish each variety is required. In this study, we developed cleaved amplified polymorphic sequence (CAPS) markers for the identification of L. edodes cultivars (Sanmaru 1ho and Chunjang 3ho). These markers were developed from whole genomic sequencing data from L. edodes monokaryon strain B17 and resequencing data from 10 dikaryon strains. A single nucleotide polymorphism changed in scaffold 9 POS 1630048 in Sanmaru 1ho($G{\rightarrow}T$), and in scaffold 13 POS 920681 in Chunjang 3ho ($G{\rightarrow}A$). The restriction enzymes TspR I and Xho I distinguished Sanmaru 1ho and Chunjang 3ho, respectively, from other strains. Thus, we developed 2 CAPS markers for the identification of the L. edodes cultivars Sanmaru 1ho and Chunjang 3ho.

Investigation of Single Nucleotide Polymorphisms in the Adipocyte Fatty-Acid Binding Protein (FABP4) Gene (FABP4 유전자의 단일염기 다형성에 관한 연구)

  • Kim, Sang-Wook;Jung, Ji-Hye;Kim, Kwan-Suk;Lee, Cheol-Koo;Kim, Jong-Joo;Choi, Bong-Hwan;Kim, Tae-Hun;Song, Ki-Duk;Cho, Byung-Wook
    • Journal of Life Science
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    • v.17 no.11
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    • pp.1505-1510
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    • 2007
  • We found 8 single nucleotide polymorphisms (SNPs) in adipocyte fatty acid bonding protein (FABP4) gene as candidate gene of FAT1 locus on pig chromosome 4. With over 800 heads of major commercial pig breeds including Duroc, Landrace, Berkshire and Yorkshire, we analyzed SNPs of FABP4 gene to determine possible effects of FABP4 genotype to economically important traits. $400{\sim}800\;bp$ amplicons in FABP4 gene were used PCR-RFLP for each SNPs and we found that the frequency of some SNPs of this gene was different among the breeds. According to the statistical analyses to determine possible associations of each genotype with economic traits, it was found that subgroup with different genotypes showed significant differences in daily gain, backfat thickness, lean percentage and feed conversion ratio (P<0.05). Thus, as a Part of enhancing the selection competence related to swine growth rate and lean percentage, it is expected that FABP4 gene markers verified in this study will be useful to use for Korean commercial pig industry.

Molecular Authentication and Phylogenetic Relationship of Bupleurum Species by the rDNA-ITS Sequences (rDNA-ITS 염기서열 분석을 통한 시호 종 감별용 유전자 마커 개발 및 유연관계 분석)

  • Moon, Byeong-Cheol;Choo, Byeong-Kil;Ji, Yun-I;Yoon, Tae-Sook;Lee, A-Young;Cheon, Myeong-Sook;Kim, Bo-Bae;Kim, Ho-Kyoung
    • The Korea Journal of Herbology
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    • v.24 no.3
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    • pp.59-68
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    • 2009
  • Objectives : Bupleuri Radix (Siho) is prescribed as the root of different Bupleurum species on the pharmarcopoeia in Korea and China. Moreover, other species and varieties of the genus Bupleurum have been also distributed on the herbal market as Bupleuri Radix. However, due to the morphological similarity and frequent occurrence of intermediate forms, the correct identification of this radix is very difficult. To develop a reliable method for correct identification and improving the quality standards of official Bupleuri Radix, we analyzed sequences of the ribosomal RNA gene and internal transcribed spacer (rDNA-ITS) region. Methods : PCR amplification of rDNA-ITS region was performed using ITS1 and ITS4 primer from 6 Bupleurum species and 1 variety, B. falcatum L. (Siho), an improved breed of B. falcatum L. (Samdo-Siho), B. chinense DC. (Buk-Siho), B. scorzonerifolium Willd. (Nam-Siho), B. longiadiatum Turcz. (Gae-Siho), B. euphorbiodes Nakai (Deungdae-Siho) and B. latissimum Nakai (Seom-Siho), and nucleotide sequence was determined after sub-cloning into the pGEM-Teasy vector. Authentic marker nucleotides were estimated by the analysis of ClastalW using entire rDNA-ITS sequence of three samples per species. Results : In comparative analysis of the rDNA-ITS sequences, we found specific nucleotides to distinguish Korean (B. falcatum L. and its variety) and Chinese official species (B. chinense DC. and B. scorzonerifolium Willd.) from others at positions 411 and 447, and positions 89, 101, 415 and 599, respectively. Futhermore, we also found nucleotide indels (insertion and/or deletion) and substitutions to identify each of different Bupleurum species, 2 positions for B. falcatum L. and its variety, 6 positions for B. chinense DC., 49 positions for B. scorzonerifolium Willd., 8 positions for B. euphorbioides Nakai, 7 positions for B. longiradiatum Nakai and 9 positions for B. latissimum Nakai. These sequence differences at corresponding positions are avaliable nucleotide markers to determine the botanical origins of Bupleuri Radix. Moreover, we confirmed the phylogenetic relationship of B. latissimum Nakai, a Korean endemic speices, among Bupleurum species based on the rDNA-ITS sequence. Conclusions : These marker nucleotides would be useful to identify the official herbal medicines by the providing of definitive information that can identify each plant species and distinguish it from unauthentic adulterant Bupleurum species.

Examination of Improved Tetracycline Inducible Gene Expression System In Vitro (새로운 Tetracycline 유도적 유전자 발현 System의 In Vitro 검정)

  • Kwon, Mo Sun;Kim, Teoan;Koo, Bon Chul
    • Reproductive and Developmental Biology
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    • v.37 no.3
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    • pp.109-115
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    • 2013
  • Until recently the most popular tetracycline-inducible gene expression system has been the one developed by Gossen and Bujard. In this study, we tested the latest version of same system and the results are summarized as follows: Compared with previous one, the difference of new system are minor changes of nucleotide sequences in transactivator and tetracycline response element (TRE) regions. Sensitivity to the doxycycline (a tetracycline derivative) was improved. Leakiness of GFP marker gene expression in non-inducible condition was significantly decreased. Higher expression of the marker gene was observed when the cells were fed with doxycycline-containing medium. Optimal insertion site of woodchuck posttranscriptional regulatory element (WPRE) sequence which was known to increase gene expression was different depending on the origin of cells. In chicken embryonic fibroblast, location of WPRE sequence at 3' end of TRE resulted in the highest GFP expression. In bovine embryonic fibroblasts, 3' end of transactivator was the best site for the GFP expression.

Restricted partition method and gene-gene interaction analysis with Hanwoo economic traits (제한된 분할방법과 한우 경제형질에서 유전자들간의 상호작용)

  • Lee, Jea-Young;Kim, Dong-Chul
    • Journal of the Korean Data and Information Science Society
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    • v.20 no.1
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    • pp.171-178
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    • 2009
  • In order to make the high quality Korean cattle, it has been identified the gene which influence to various economic characters. In this paper, we introduce Restricted Partition Method for gene-gene interaction analysis. Further, economic traits, longissimus muscle dorsi area (LMA), carcass cold weight (CWT) and average daily gain (ADG) are applied with Restricted Partition Method (RPM). The SNP (19_1)$^*$SNP (28_2) was selected and was best marker on Single nucleotide polymorphisms (SNPs). It also influenced SNP (19_1)$^*$SNP (28_2) was an very important marker for economic character and to make the thing know it became.

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