• Title/Summary/Keyword: Genome analysis

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Rapid prenatal diagnosis of Down syndrome and Edward syndrome by fluorescence In situ hybridization : Clinical experience with 309 cases (FISH를 이용한 다운증후군과 에드워드증후군의 신속한 산전확인 : 309예의 임상적 고찰)

  • Kang, Jin-Hee;Lee, Sook-Hwan;Park, Sang-Hee;Park, Ji-Hyun;Kim, Ji-Youn;Han, Won-Bo;Kim, In-Hyun;Park, Sang-Won;Jang, Jin-Beum;Lee, Kyoung-Jin;Park, Hee-Jin;Jun, Hye-Sun;Lee, Kyung-Ju;Shin, Joong-Sik;Cha, Dong-Hyun
    • Journal of Genetic Medicine
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    • v.4 no.1
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    • pp.64-71
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    • 2007
  • Purpose : The purpose of this study was to evaluate the clinical utility of rapid detection of Down syndrome and Edward syndrome by Interphase Fluorescence in Situ Hybridization (FISH) analysis. Methods : Aretrospective study in 309 cases of amniotic fluid samples, analysed by interphase FISH with DNA probes specific to chromosome 18 and 21, was performed. All FISH results w ere compared with conventional cytogenetic karyotypings. Results : The results were considered as informative and they were obtained within 48 hrs. A case of Down syndrome and a case of Edward syndrome were diagnosed by FISH and confirmed by subsequent cytogenetic analysis. In 12 cases with normal FISH results, the cytogenetic analysis showed a case of partial trisomy 22, three cases of sex chromosomal aneuploidy, two cases of mosaicism, two cases of microdeletion, and four cases of structural rearrangement. Conclusion : FISH is a rapid and effective diagnostic method, which can be used as an adjunctive test to cytogenetic analysis, for prenatal identification of chromosome aneuploidies. For the more genome-wide screening with variety of probes, the technique of FISH is both expensive and labor-intensive.

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SSR Marker Related to Major Characteristics Affected Kernel Quality in Waxy Corn Inbred Lines (찰옥수수 자식계통의 주요 품질특성과 관련된 SSR마커)

  • Jung, Tae-Wook;Moon, Hyeon-Gui;Son, Beom-Young;Kim, Sun-Lim;Kim, Soon-Kwon
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.51 no.spc1
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    • pp.185-192
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    • 2006
  • This experiment was conducted to assess genetic diversity of waxy corn inbred lines and to identify SSR markers related to major characteristics affected kernel quality for improving waxy corn $F_1$ hybrid with good quality. Diversity of 64 waxy com inbred lines was evaluated using 30 microsatellite markers. The 30 microsatellite markers representing 30 loci in the maize genome detected polymorphisms among the 64 inbred lines and revealed 225 alleles with a mean of 7.5 alleles per primer. The polymorphism Information content (PIC) value ranged from 0.14 to 0.87, with an average of 0.69. Based on Nei's genetic distances, the 64 inbred lines were classified into 9 groups by the cluster analysis. The group I included 26 inbred lines (41%), other groups included 3 to 9 inbred lines. One-way analysis of variance was conducted to identify significant relationship between individual markers and major characteristics that affect kernel quality. The analysis showed that umc1019 was related to amylopectin and crude protein content, me 1020 to amylopectin content and peak viscosity, and bnlg1537 to 100-kernel weight, kernel length, and kernel width.

Transgenic tobacco culture cells expressing spike protein gene of porcine epidemic diarrhea virus (돼지 유행성 설사병 바이러스 스파크 단백질 유전자 발현 형질전환 담배 배양세포)

  • Yang, Kyoung-Sil;Kim, Hyeon-Soo;Kwon, Suk-Yoon;Kwak, Sang-Soo;Lee, Haeng-Soon
    • Journal of Plant Biotechnology
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    • v.35 no.1
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    • pp.87-94
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    • 2008
  • Porcine epidemic diarrhea virus (PEDV) is an infectious and highly contagious virus of swine. In order to develop the transgenic tobacco culture cells producing PEDV antigen protein, four vectors expressing PEDV spike protein (SP) gene under the control of a CaMV 35S promoter were constructed. Four fragments of the SP region of PEDV, SP1 (444 bp, 1487-1930 bp), SP2 (1.7 kb, 2300-3987 bp), SP3 (1.4 kb, 1559-2950 bp), and SP4 (2.6 kb, 9-2643 bp) were amplified by PCR and then C-MYC tag was fused to the end of each SP gene, respectively. These cassettes are inserted into the pCAMBIA2300 (named as 35S::SP1-M, 35S::SP2-M 35S::SP3-M, and 35S::SP4-M, respectively). Tobacco (cv. BY-2) cultured cells were transformed by co-cultivation with Agrobacterium tumefaciens harboring expression vector. We selected kanamycin-resistant calli and checked for the presence of the introduced SP gene using PCR, resulting 70% of them showed the foreign gene. We selected the lines with high-level expression of PEDV antigen protein based on dot blot analysis. Southern blot analysis confirmed that the PEDV SP gene was integrated into the genome of the tobacco cultured cells. Northern blot analysis showed that the introduced gene was highly expressed in transgenic cultured cells. Transgenic tobacco cultured cells-derived antigen induced immunogenicity in mice as determined by a plaque reduction neutralization assay. These results suggest that the vectors expressing PEDV spike protein gene in this study will be useful for the development of transgenic plants and cultured cells producing PEDV antigene protein.

Chromosomal Localization and Mutation Detection of the Porcine APM1 Gene Encoding Adiponectin (Adiponectin을 암호화하는 돼지 APM1 유전자의 염색체상 위치파악과 돌연변이 탐색)

  • Park, E.W.;Kim, J.H.;Seo, B.Y.;Jung, K.C.;Yu, S.L.;Cho, I.C.;Lee, J.G.;Oh, S.J.;Jeon, J.T.;Lee, J.H.
    • Journal of Animal Science and Technology
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    • v.46 no.4
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    • pp.537-546
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    • 2004
  • Adiponectin is adipocyte complement-related protein which is highly specialized to play important roles in metabolic and honnonal processes. This protein, called GBP-28, AdipoQ, and Acrp30, is encoded by the adipose most abundant gene transcript 1 (APM1) which locates on human chromosome 3q27 and mouse chromosome 16. In order to determine chromosomal localization of the porcine APM1, we carried out PCR analysis using somatic cell hybrid panel as well as porcine whole genome radiation hybrid (RH) panel. The result showed that the porcine APM1 located on chromosome 13q41 or 13q46-49. These locations were further investigated with the two point analysis of RH panel, revealed the most significant linked marker (LOD score 20.29) being SIAT1 (8 cRs away), where the fat-related QTL located. From the SSCP analysis of APM1 using 8 pig breeds, two distinct SSCP types were detected from K~ native and Korean wild pigs. The determined sequences in Korean native and Korean wild pigs showed that two nucleotide positions (T672C and C705G) were substituted. The primary sequence of the porcine APM1 has 79 to 87% identity with those of human, mouse, and bovine APM1. The domain structures of the porcine APM1 such as signal sequence, hypervariable region, collagenous region. and globular domain are also similar to those of mammalian genes.

Effect of methyl jasmonate on the glucosinolate contents and whole genome expression in Brassica oleracea (유묘기 양배추류에서 메틸자스모네이트에 의한 글루코시놀레이트 함량 변화 및 전사체 발현 분석)

  • Lee, Jeongyeo;Min, Sung Ran;Jung, Jaeeun;Kim, HyeRan
    • Journal of Plant Biotechnology
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    • v.46 no.3
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    • pp.189-204
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    • 2019
  • In this study, we analyzed the changes in glucosinolate content and gene expression in TO1000DH3 and Early big seedling upon methyl jasmonate (MeJA) treatment. Analysis of glucosinolate contents after MeJA treatment at $200{\mu}M$ concentration showed that the total glucosinolate content increased by 1.3-1.5 fold in TO1000DH3 and 1.3-3.8 fold in Early big compared to those before treatment. Aliphatic glucosinolates, progoitrin and gluconapin, were detected only in TO1000DH3, and the changes in the content of neoglucobrassicin were the greatest at 48 hours after MeJA treatment in TO1000DH3 and Early big. The transcriptomic analysis showed that transcripts involved in stress or defense reactions, or those related to growth were specifically expressed in TO1000DH3, while transcripts related to nucleosides or ATP biosynthesis were specifically expressed in Early big. GO analysis on transcripts with more than two-fold change in expression upon MeJA treatment, corresponding to 12,020 transcripts in TO1000DH3 and 13,510 transcripts in Early big, showed that the expression of transcripts that react to stimulus and chemical increased in TO1000DH3 and Early big, while those related to single-organism and ribosome synthesis decreased. In particular, the expression increased for all transcripts related to indole glucosinolate biosynthesis, which is associated with increase in glucobrassicin and neoglucobrassicin contents. Upon MeJA treatment, the expression of AOP3 (Bo9g006220, Bo9g006240), TGG1 (Bo14804s010) increased only in TO1000DH3, while the expression of Dof1.1 (Bo5g008360), UGT74C1 (Bo4g177540), and GSL-OH (Bo4g173560, Bo4g173550, Bo4g173530) increased specifically in Early big.

Transcriptomic Analysis of Triticum aestivum under Salt Stress Reveals Change of Gene Expression (RNA sequencing을 이용한 염 스트레스 처리 밀(Triticum aestivum)의 유전자 발현 차이 확인 및 후보 유전자 선발)

  • Jeon, Donghyun;Lim, Yoonho;Kang, Yuna;Park, Chulsoo;Lee, Donghoon;Park, Junchan;Choi, Uchan;Kim, Kyeonghoon;Kim, Changsoo
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.67 no.1
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    • pp.41-52
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    • 2022
  • As a cultivar of Korean wheat, 'Keumgang' wheat variety has a fast growth period and can be grown stably. Hexaploid wheat (Triticum aestivum) has moderately high salt tolerance compared to tetraploid wheat (Triticum turgidum L.). However, the molecular mechanisms related to salt tolerance of hexaploid wheat have not been elucidated yet. In this study, the candidate genes related to salt tolerance were identified by investigating the genes that are differently expressed in Keumgang variety and examining salt tolerant mutation '2020-s1340.'. A total of 85,771,537 reads were obtained after quality filtering using NextSeq 500 Illumina sequencing technology. A total of 23,634,438 reads were aligned with the NCBI Campala Lr22a pseudomolecule v5 reference genome (Triticum aestivum). A total of 282 differentially expressed genes (DEGs) were identified in the two Triticum aestivum materials. These DEGs have functions, including salt tolerance related traits such as 'wall-associated receptor kinase-like 8', 'cytochrome P450', '6-phosphofructokinase 2'. In addition, the identified DEGs were classified into three categories, including biological process, molecular function, cellular component using gene ontology analysis. These DEGs were enriched significantly for terms such as the 'copper ion transport', 'oxidation-reduction process', 'alternative oxidase activity'. These results, which were obtained using RNA-seq analysis, will improve our understanding of salt tolerance of wheat. Moreover, this study will be a useful resource for breeding wheat varieties with improved salt tolerance using molecular breeding technology.

cSNP Identification and Genotyping from C4B and BAT2 Assigned to the SLA Class III Region (돼지 SLA class III 영역 내 C4B 및 BAT2의 cSNP 동정 및 이를 이용한 유전자형 분석)

  • Kim, J.H.;Lim, H.T.;Seo, B.Y.;Lee, S.H.;Lee, J.B.;Yoo, C.K.;Jung, E.J.;Jeon, J.T.
    • Journal of Animal Science and Technology
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    • v.49 no.5
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    • pp.549-558
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    • 2007
  • C4B and BAT2, assigned to the SLA class III region, were recently reported on relation with human diseases. The primers for RT-PCR and RACE-PCR for CDS analysis of these genes of pig were designed by aligning the CDSs of humans and mice from GenBank. After we amplified and sequenced with these primers and cDNAs, the full-length CDSs of pig were determined. The CDS lengths of C4B and BAT2 were shown as 5226 bp and 6501 bp. In addition, the identities of nucleotide sequences with human and mouse were 76% to 87%, and the identities of amino acids were 72% to 90%. After we carried out the alignment with determined CDSs in this study and pig genomic sequences from GenBank, the primers for cSNP detection in genome were designed in intron regions that flanked one or more exons. Then, we amplified and directly sequenced with genomic DNAs of six pig breeds. Four cSNPs from C4B and three 3 cSNPs from BAT2 were identified. In addition, amino acid substitution occurred in six cSNP positions except for C4248T of C4B. By the Multiplex-ARMS method, we genotyped seven cSNPs with DNA samples used for direct sequencing. We verified that this result was the same as that analyzed using direct sequencing. To demonstrate recrudescence, we performed both direct sequencing and Multiplex-ARMS on two randomly selected DNA samples. The genotype of each sample showed the same result from both methods. Therefore, seven cSNPs were identified from C4B and BAT2 and could be used as the basic data for haplotype analysis of SLA class III region. Moreover, the Multiplex-ARMS method should be powerful for genotyping of genes assigned to the whole SLA region for the xenograft study.

Development of a Window Program for Searching CpG Island (CpG Island 검색용 윈도우 프로그램 개발)

  • Kim, Ki-Bong
    • Journal of Life Science
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    • v.18 no.8
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    • pp.1132-1139
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    • 2008
  • A CpG island is a short stretch of DNA in which the frequency of the CG dinucleotide is higher than other regions. CpG islands are present in the promoters and exonic regions of approximately $30{\sim}60$% of mammalian genes so they are useful markers for genes in organisms containing 5-methylcytosine in their genomes. Recent evidence supports the notion that the hypermethylation of CpG island, by silencing tumor suppressor genes, plays a major causal role in cancer, which has been described in almost every tumor types. In this respect, CpG island search by computational methods is very helpful for cancer research and computational promoter and gene predictions. I therefore developed a window program (called CpGi) on the basis of CpG island criteria defined by D. Takai and P. A. Jones. The program 'CpGi' was implemented in Visual C++ 6.0 and can determine the locations of CpG islands using diverse parameters (%GC, Obs (CpG)/Exp (CpG), window size, step size, gap value, # of CpG, length) specified by user. The analysis result of CpGi provides a graphical map of CpG islands and G+C% plot, where more detailed information on CpG island can be obtained through pop-up window. Two human contigs, i.e. AP00524 (from chromosome 22) and NT_029490.3 (from chromosome 21), were used to compare the performance of CpGi and two other public programs for the accuracy of search results. The two other programs used in the performance comparison are Emboss-CpGPlot and CpG Island Searcher that are web-based public CpG island search programs. The comparison result showed that CpGi is on a level with or outperforms Emboss-CpGPlot and CpG Island Searcher. Having a simple and easy-to-use user interface, CpGi would be a very useful tool for genome analysis and CpG island research. To obtain a copy of CpGi for academic use only, contact corresponding author.

Construction of a Transgenic Tobacco Expressing a Polydnaviral Cystatin (폴리드나바이러스 유래 시스타틴 유전자 발현 형질전환 담배 제작)

  • Kim, Yeongtae;Kim, Eunsung;Park, Youngjin;Kim, Yonggyun
    • Korean journal of applied entomology
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    • v.54 no.1
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    • pp.7-15
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    • 2015
  • CpBV (Cotesia plutellae bracovirus) is a polydnavirus and encodes a cystatin (CpBV-CST1) gene. Its overexpression suppresses insect immunity and alters insect developmental processes. This study aimed to construct a genetically modified (GM) tobacco to further explore the physiological function of the viral cystatin and to apply to control insect pests. To this end, the transgenic tobacco lines were screened in expression of the target gene and assessed in insecticidal activity. A recombinant vector (pBI121-CST) was prepared and used to transform a bacterium, Agrobacterium tumefasciens. The transformed bacteria were used to generate transgenic tobacco lines, which were induced to grow callus and resulted in about 92% of shoot regeneration. The regenerated plants were screened by PCR analysis to confirm the insertion of the target gene in the plant genome. In addition, the expression of the target gene was assessed in the regenerated plants by quantitative real-time PCR (qRT-PCR). The qRT-PCR analysis showed that the transgenic line plant expressed the target gene about 17 times more than the control tobacco, indicating a stable insertion and expression of the target gene in the transgenic tobacco line. The insecticidal activity was then analyzed using the screened transgenic tobacco lines against the teneral 1st instar larvae of the oriental tobacco budworm, Helicoverpa assulta. Though there was a variation in the insecticidal efficacy among transgenic lines, T9 and T12 lines exhibited more than 95% mortality at 7 days after feeding treatment. These results suggest that CpBV-CST1 is a useful genetic resource to be used to generate GM crop against insect pests.

Development of dry milling suitable rice cultivar to invigorate rice processing products

  • Jeung, Ji-Ung
    • Proceedings of the Korean Society of Crop Science Conference
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    • 2017.06a
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    • pp.10-10
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    • 2017
  • Rice consumption has been continuously decreasing as the eating habits of Koreans have become westernized and diversified. The per capita annual rice consumption in Korea has dropped sharply from 136.4 kg in 1970 to 61.9 kg in 2016. The Korean government, therefore, has been trying to promote rice consumption by invigorating the processed food industry using rice flour. To facilitate the market for processed rice foods, it is essential to develop proper milling technology in terms of flour particle size and damaged starch content to produce high quality rice flour at competitive cost. Dry milling and wet milling are the two major processes used to produce rice flour. Although the dry milling process is relatively simple with a lower production cost, damaged starch content increases because of the high grain hardness of rice. In wet milling, the quality of rice flour is improved by reducing flour particle size as well as damaged starch content through soaking procedures. However, the production costs are high because of the additional expenses associated with the disposal of waste water, sterilization and drying of the wet flour. Recently developed technologies such as jet milling and cryogenic milling also require expensive investment and production. Therefore, developing new rice cultivars with dry milling adaptability as well as good processing properties is an important goal of rice breeding in Korea. 'Suweon 542' is a floury endosperm mutant line derived from sodium azide treatment on a high-yield, early maturing, and non-glutinous japonica rice cultivar, 'Namil'. Compared with the wild type, after dry milling process, the grain hardness of 'Suweon 542' was significantly lower because of its round and loosely packed starch granules. Also, the flour of 'Suweon 542' had significantly smaller particles and less damaged starch than 'Namil' and other rice cultivars and its particle size distribution was similar to a commercial wheat cultivar. Recently, through collaborations with nine universities and food companies, a total of 21 kinds of processed prototypes, using the dry milling flour of 'Suweon 542', were evaluated. In the production of major rice processing products, there was no significant quality difference between the flours prepared by wet milling and dry milling. Although the amount of water added to the dough was slightly increased, it was confirmed that the recipe applying the wet flour could be used without significant change. To efficiently transfer the floury endosperm characteristics of 'Suweon 542' to other commercial rice cultivars, it is essential to develop DNA marker tightly linked to the target gene. Association analysis using 70 genome-wide SSR markers and 94 F2 plants derived from 'Suweon 542'/'Milyang 23' showed that markers on chromosome 5 explained a large portion of the variation in floury grains percentage (FGP). Further analysis with an increased number of SSR markers revealed that the floury endosperm of 'Suweon 542' was directed by a major recessive locus, flo7(t), located in the 19.33-19.86 Mbp region of chromosome 5, with RM18639 explaining 92.2% of FGP variation in the F2 population. Through further physical mapping, a co-segregate and co-dominant DNA marker with the locus, flo7(t) was successfully developed, by which, thereby, breeding efficiency of rice cultivars having proper dry milling adaptability with high yield potential or useful functional materials would be improved. 'Suweon 542' maintained the early maturity of the wild type, Namil, which can be used in rice-wheat double cropping systems in Korea not only for improved arable land but also for sharing flour production facilities. In addition to the high susceptibility against major rice diseases, nevertheless, another possible drawback of 'Suweon 542' is the high rate of viviparous under prolonged rainfall during the harvesting season. To overcome susceptibility and vivipary of 'Suweon 542', the progeny lines, derived from the crosses 'Suweon 542' and 'Jopyeong', an early maturing rice cultivar with multiple resistance against rice blast, bacterial blight, and rice strip virus, and 'Heugjinju', a anthocyanin pigment containing black rice cultivar, were intensively evaluated. As the outputs, three dry milling suitable rice elite lines, 'Jeonju614', 'Jeonju615', and 'Jeonju616' were developed.

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