• Title/Summary/Keyword: DNA length

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Present and Prospect of Plant Genomics in Japan (일본의 식물유전체 연구현황 및 전망)

  • Yoon, Ung-Han;Lee, Jeonghwa;Lee, Gang-Seob;Kim, Young-Mi;Ji, Hyeon-So;Kim, Tae-Ho
    • Journal of the Korean Society of International Agriculture
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    • v.23 no.5
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    • pp.560-569
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    • 2011
  • In Japan, plant genomics research is mainly leaded by the national research institutes. The various structural studies such as rice genome has allowed researchers to analyze useful traits, and to focus their commercialization. With aims to facilitate structural and functional study in plant genome, NIAS (National Institute of Agrobiological Sciences) constructed Poaceae genome DB and RIKEN (Rikagaku Kenkyusho) built DB for Arabidopsis genome and plant full-length cDNA. NIG (National Institute of Genetics) constructed a national biological resources DB (National Bio Resource Project). This compiling DB provides a variety of genome-related research materials for researchers in the field. Recently, as an effort to resolve global issues of food supply and environmental problems, New Agri-genome Project has been performed aiming to develop an innovative agricultural technologies for the quantity, disease resistance and identifying useful genes related to environmental problems. In addition, in order to improve agricultural productivity in developing countries, JIRCAS assisted technical supports for the plant genome research and developed NERICA rice, which is suitable for African area. Such these approaches are expected to contribute to solving the global issues about food, energy and environment in the world.

Development of PCR-based markers for selecting plastid genotypes of Solanum hjertingii (Solanum hjertingii 색소체 유전자형 선발을 위한 PCR 기반 분자마커 개발)

  • Tae-Ho Park
    • Journal of Plant Biotechnology
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    • v.50
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    • pp.34-44
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    • 2023
  • The tetraploid Solanum hjertingii, a wild tuber-bearing species from Mexico is a relative of potato, S. tuberosum. The species has been identified as a potential source of resistance to blackening for potato breeding. It does not exhibit enzymatic browning nor blackspot which are physiological disorders. However, due to their sexual incompatibility, somatic hybridization between S. hjertingii and S. tuberosum must be used to introduce various traits from this wild species into potato. After somatic hybridization, molecular markers are essential for selecting fusion products. In this study, the chloroplast genome of S. hjertingii was sequenced by next-generation sequencing technology and compared with those of other Solanum species to develop specific markers for S. hjertingii. The chloroplast genome has a total sequence length of 155,545 bp, and its size, gene content, order and orientation are similar to those of the other Solanum species. Phylogenic analysis including 15 other Solanaceae species grouped S. hjertingii with S. demissum, S. hougasii, and S. stoloniferum. After detailed comparisons of the chloroplast genome sequence with eight other Solanum species, we identified one InDel and seven SNPs specific to S. hjertingii. Based on these, five PCR-based markers were developed for discriminating S. hjertingii from other Solanum species. The results obtained in this study will aid in exploring the evolutionary aspects of Solanum species and accelerating breeding using S. hjertingii.

Chloroplast genome sequence and PCR-based markers for S. cardiophyllum (감자 근연야생종 Solanum cardiophyllum의 엽록체 전장유전체 구명 및 이를 이용한 S. cardiophyllum 특이적 분자마커의 개발)

  • Tae-Ho Park
    • Journal of Plant Biotechnology
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    • v.50
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    • pp.45-55
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    • 2023
  • The diploid Solanum cardiophyllum, a wild tuberbearing species from Mexico is one of the relatives to potato, S. tuberosum. It has been identified as a source of resistance to crucial pathogens and insects such as Phytophthora infestans, Potato virus Y, Colorado potato beetle, etc. and is widely used for potato breeding. However, the sexual hybridization between S. cardiophyllum and S. tuberosum is limited due to their incompatibility. Therefore, somatic hybridization can introduce beneficial traits from this wild species into the potato. After somatic hybridization, selecting fusion products using molecular markers is essential. In the current study, the chloroplast genome of S. cardiophyllum was sequenced by next-generation sequencing technology and compared with those of other Solanum species to develop S. cardiophyllum-specific markers. The total length of the S. cardiophyllum chloroplast genome was 155,570 bp and its size, gene content, order and orientation were similar to those of the other Solanum species. Phylogenic analysis with 32 other Solanaceae species revealed that S. cardiophyllum was expectedly grouped with other Solanum species and most closely located with S. bulbocastanum. Through detailed comparisons of the chloroplast genome sequences of eight Solanum species, we identified 13 SNPs specific to S. cardiophyllum. Further, four SNP-specific PCR markers were developed for discriminating S. cardiophyllum from other Solanum species. The results obtained in this study would help to explore the evolutionary aspects of Solanum species and accelerate breeding using S. cardiophyllum.

Amelioration of colitis progression by ginseng-derived exosome-like nanoparticles through suppression of inflammatory cytokines

  • Jisu Kim;Shuya Zhang ;Ying Zhu;Ruirui Wang;Jianxin Wang
    • Journal of Ginseng Research
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    • v.47 no.5
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    • pp.627-637
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    • 2023
  • Background: Damage to the healthy intestinal epithelial layer and regulation of the intestinal immune system, closely interrelated, are considered pivotal parts of the curative treatment for inflammatory bowel disease (IBD). Plant-based diets and phytochemicals can support the immune microenvironment in the intestinal epithelial barrier for a balanced immune system by improving the intestinal microecological balance and may have therapeutic potential in colitis. However, there have been only a few reports on the therapeutic potential of plant-derived exosome-like nanoparticles (PENs) and the underlying mechanism in colitis. This study aimed to assess the therapeutic effect of PENs from Panax ginseng, ginseng-derived exosome-like nanoparticles (GENs), in a mouse model of IBD, with a focus on the intestinal immune microenvironment. Method: To evaluate the anti-inflammatory effect of GENs on acute colitis, we treated GENs in Caco2 and lipopolysaccharide (LPS) -induced RAW 264.7 macrophages and analyzed the gene expression of proinflammatory cytokines and anti-inflammatory cytokines such as TNF-α, IL-6, and IL-10 by real-time PCR (RT-PCR). Furthermore, we further examined bacterial DNA from feces and determined the alteration of gut microbiota composition in DSS-induced colitis mice after administration of GENs through 16S rRNA gene sequencing analysis. Result: GENs with low toxicity showed a long-lasting intestinal retention effect for 48 h, which could lead to effective suppression of pro-inflammatory cytokines such as TNF-α and IL-6 production through inhibition of NF-κB in DSS-induced colitis. As a result, it showed longer colon length and suppressed thickening of the colon wall in the mice treated with GENs. Due to the amelioration of the progression of DSS-induced colitis with GENs treatment, the prolonged survival rate was observed for 17 days compared to 9 days in the PBS-treated group. In the gut microbiota analysis, the ratio of Firmicutes/Bacteroidota was decreased, which means GENs have therapeutic effectiveness against IBD. Ingesting GENs would be expected to slow colitis progression, strengthen the gut microbiota, and maintain gut homeostasis by preventing bacterial dysbiosis. Conclusion: GENs have a therapeutic effect on colitis through modulation of the intestinal microbiota and immune microenvironment. GENs not only ameliorate the inflammation in the damaged intestine by downregulating pro-inflammatory cytokines but also help balance the microbiota on the intestinal barrier and thereby improve the digestive system.

The Association of Neonatal Hyperbilirubinemia with UGT1A1 and CYP1A2 Gene Polymorphism in Korean Neonates (한국인의 신생아 황달과 UGT1A1 및 CYP1A2 유전자 다형성과의 연관성)

  • Kang, Hoon;Lim, Jun Ho;Kim, Ji Sook;Kim, Eun Ryoung;Kim, Sung Do;Lee, Hee Jae;Chung, Joo Ho
    • Clinical and Experimental Pediatrics
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    • v.48 no.4
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    • pp.380-386
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    • 2005
  • Purpose : The incidence of nonphysiologic neonatal hyperbilirubinemia is twice as high in East Asians as in whites. Recently, UGT1A1 mutation was found to be a risk factor for neonatal hyperbilirubinemia. In congenitally-jaundiced Gunn rats, which lack expression of UDP-glucuronosyltransferase, alternative pathways can be stimulated by inducers of CYP1A1 and CYP1A2 enzymes. CYP1A2 plays a major role in bilirubin degradation of the alternate pathway. We studied the relationship between UGT1A1 and CYP1A2 gene polymorphism of neonatal hyperbilirubinemia in Koreans. Methods : Seventy-nine Korean full term neonates who had hyperbilirubinemia(serum bilirubin >12 mg/dL) without obvious causes of jaundice, were analyzed for UGT1A1 and CYP1A2 gene polymorphism; the control group was sixty-eight. We detected the polymorphism of Gly71Arg of UGT1A1 gene by direct sequencing and T2698G of CYP1A2 by polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP) using MboII and direct sequencing. Results : Allele frequency of Gly71Arg mutation in the hyperbilirubinemia group was 32 percent, which was significantly higher than 11 percent in the control group(P<0.0001). Mutant gene frequency of T2698G was 41.8 percent in patients and 32.3 percent in the control group(P=0.015), but allele frequency was 21 percent in patients and 19 percent in the control group, which was not significantly higher(P=0.706). There was no relationship between mutations of two genes(P=0.635). Conclusion : The polymorphism of UGT1A1 gene(Gly71Arg) and CYP1A2 gene(T2698G) was detected in Korean neonatal hyperbilirubinemia. Only polymorphisms of Gly71Arg in UGT1A1 were significantly higher than control group.

Estimation of Genetic Parameters for Growth-related Traits of Two Korean Abalone Subspecies, Haliotis discus hannai and H. discus discus, by using Multiple Traits of Animal Model in Early Growth Period (다형질 Animal Model에 의한 한국산 전복 2 아종의 초기 치패의 성장관련 형질에 대한 유전모수 추정)

  • Choe, Mi-Kyung;Han, Seock-Jung;Yang, Sang-Geun;Won, Seung-Hwan;Park, Choul-Ji;Yeo, In-Kyu
    • The Korean Journal of Malacology
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    • v.23 no.2
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    • pp.217-225
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    • 2007
  • This study was conducted to estimate the general genetic parameters, heritabilities, and genetic and phenotypic correlations on growth-related traits by studying multiple trait animal model in two Korean abalone species, Haliotis discus hannai and H. discus discus. The data was collected from the records of 3,795 individuals produced from 54 sires and 74 dams in Haliotis discus hannai and 399 individuals produced from 7 sires and 7 dams in Haliotis discus discus. The data was evaluated by the Genetics and Breeding Research Center, National Fisheries Research & Development Institute (NFRDI). Genetic parameters were estimated for two abalone species raised in Bukjeju branch, NFRDI, from May 20 to November 1, 2004. The heritability estimates for growth traits of shell length, shell width and body weight obtained from restricted maximum likelihood (REML) were ranging from 0.73 to 0.78 in Haliotis discus hannai, and from 0.87 to 0.89 in H. discus discus. The heritabilities for shell shape and condition factor were ranging from 0.17 to 0.20 in Haliotis discus hannai, and from 0.01 to 0.45 in H. discus discus. Genetic and phenotypic correlations were over than 0.96 between shell parameters and weight in both of abalone subspecies, indicating that breeding for weight gains could successfully be achieved by selecting for shell length.

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Effect of Dietary Siberian Ginseng and Eucommia on Broiler Performance, Serum Biochemical Profiles and Telomere Length (가시오갈피와 두충의 첨가 급여가 브로일러의 생산 능력, 혈장 생화학 지표 및 텔로미어 함량에 미치는 영향)

  • Sohn, S.H.;Jang, I.S.;Moon, Y.S.;Kim, Y.J.;Lee, S.H.;Ko, Y.H.;Kang, S.Y.;Kang, H.K.
    • Korean Journal of Poultry Science
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    • v.35 no.3
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    • pp.283-290
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    • 2008
  • The Siberian ginseng and Eucommia are a kind of medicinal plant with powerful anti-oxidant activity. An experiment was conducted to investigate the effect of Siberian ginseng leaf and Eucommia leaf at level of 0.5% and 1% per feed in Ross commercial broiler for 4 to 35 days of age on performance, organ weight, blood biochemical profiles and telomere quantity. Chickens consuming diets containing 1% Siberian ginseng had higher feed conversion ratio than the other treated chicken during experimental period whereas no significant differences were detected in body weight, weight gain and feed intake. The weight of bursa of fabricius was significantly increased in chickens with dietary supplementation compared with chickens fed control but this was not seen in liver, spleen and thymus. In blood biochemical profiles, chickens with dietary supplementation had higher concentration than chickens fed control in triglyceride, cholesterol and glucose. The concentration of aspartate aminotransferase, alanine aminotransferase, albumin and total protein, however, was not significantly different between dietary supplemented chickens and control chickens. The relative amount of telomeric DNA of lymphocytes in chickens with dietary supplementation was significantly higher than that of control chickens but the difference was not found in liver, heart and testis tissues. In conclusion, dietary supplementation of Siberian ginseng and Eucommia in broiler improved immune activity and telomere length without decreasing chicken growth performance.

Studies on the Bacteriophages of Brevibacterium lactofermentum (L-글루타민산 생산균 Brevibacterium lactofermentum의 Bacteriophag에 관한 연구)

  • 이태우
    • Korean Journal of Microbiology
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    • v.17 no.3
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    • pp.97-130
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    • 1979
  • Many industrial processes those employ bacteria are subjected to phage infestations. In L-glutamic acid fermentions using acetic acid, the phage infestations of the organisms have been recently recognized. In efforts to elucidate the sources of phage contamination involved in the abnormal fermentation, a series of study was conducted to isolate the phages both from the contents of abnormally fermented tanks and the soil or sewage samples from the surroundings of a fermentation factory, to define major charateristics of the phage isolates, and finally to determine the correlation between the phage isolates and temperate phages originating from the miscellaneous bacterial species isolated from the soil or sewage samples. The results are summarized as follows; 1) All phages were isolated from the irregular fermentation tanks and soil or sewage samples, and they were designated as phage PR-1, PR-2, PR-3, PR-4, PR-5, PR-6, and PR-7, in the order of isolation. These PR-series phages were proved to be highly specific for the variant strains of Br. lactofermentum only, namely, phage PR-1 and PR-2 for Br. lactofermentum No. 468-5 and phage PR-3~PR-7 for Br. lactofemrentum No. 2256. By cross-neutralization test, the 7 phagescould be subdivided into 3 groups, i. e., phage PR-I and PR-2 the first, phage PR-3, PR-4, PR-5, PR-6 the second, and the phage PR-7 the third. 2) The 7 phages were virulent under the experimental conditions. They produced plaques with clear and relatively sharp margins without distinct halo. The mean sizes of plaques were 1.5mm in diameter for phage PR-1 and PR-2, and 1. Omm for phages PR-3~PR-7. Double layer technique modified by Hongo and described by Adams, was applied to assay of the PR-series phages. The factors influencing the plaques were as follows;young age cells of host bacteria cultured for 3-6 hours represented the largest number and size, optimum was pH 7.0, incubation temperature was $30^{\circ}C$, and agar concentration and amount of overlayer medium were 0.6% and 0.2ml, respectively. 3) PR-series phages were stable in 0.05M tris buffer and 0.1M ammonium acetate buffer solution. The addition of $5{\times}10^{-3}M$ magnesium ion effectively increased the stability. Thermostability experiments indicated that PR-series phages were stable at the teinperture between $50^{\circ}{\sim}55^{\circ}C$ in nutrient medium, $45^{\circ}{\sim}50^{\circ}C$ in buffer solution. However, the phages mere completely inactivated at 603C and 65$^{\circ}$C within 10 minutes. The phages were stable at the range of pH6~9 in nutrient medium and of pH 8-9 in buffer solution, respectively. Exposure of the phages to UV for 25, 60 and 100 seconds resulted in the complete loss of infectivily, respectively. 4) Electron microscopy showed that PR-series phage particles exhibited rather similar morphology, differing in the size All of PR-series phages had a multilateral head and had a simple long tiil about three to five times long as compared with head. By the size, phage PR-1 and PR-2, PR-3, PR-4, PR-5, and PR-6 and PR-7 were classified into same groups, respectively. The head and tail size of phage PR-1, PR-5, PR-5(T) and PR-7 were 85nm, 74nm and 235nm and 350mm, and 72nm and 210nm, respectively. 5) Nucleic acids of PR-series phages were double stranded DNA. The G+C contents of phage PR-1, PR-5 and PR-7 were 56.1, 52.9 and 53.7, respectively. The values of G+C contents derived from the $T_m$ were in agreement with the chemically determined values. 6) PR-series phages effectively adsorbed on their host bacteria at the rate of more than 90% during 5 min. K value for phage PR-1, PR-5 and PR-7 were calculated to be $6{\times}10^9 ml$ per minute, respectiveky. The pH of the medium did effect adsorption rate, but both temperature and age of host cells did not. Generally, optimum adsorption condition of phages seemed to be almost same as optimum growth conditions of host bacteria. 7) In one-step growth experiments, the latent periods at $30^{\circ}C$ for PR-1, and PR-7 were about 70, 50 and 55 min, respectively. The corresponding average burst size was 200, 70 and 90, respectively. Lpsis period according to the multiplicity of infection and a phage series. In case of m. o. i. 100, strain No. 2256 (PR-5) and No. 468-5(PR-1) failed to grow and turbidity decreased after 50 and 70min, respectively. 8) In the lysate of a plaque purified phage PR-5 infected bacteria, there observed 2 types ofphage particles, i. e., phage PR-5 and PR-5 (T) of similar morphology but differing at the length of phage tail, and phage tail like particles. The phage taillike particles could be divided into 4 types by the length. Induction experiments of Br. lactofermentum with UV irradiation, mitomycin C or bacitracin treatment produced neither phage PR-5 (T) or phage tail-like particles. 9) No lysis occured when the growth of 7 strains of miscellaneous bacteria, isolated from soil and sewage samples, were inoculated with either phage PR-5 (T) or phage tail-like particles the inoculation of phage PR-5 pellet resulted in the growth inhibition of the orgainsms in the spot test. The lysates obtained from 3 miscellaneous soil derived bacteria following mitomycin C treatment the growth of Br. lactofermentum, but did not lyze the bacterium.

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Estimation of Genetic Parameters for Growth-Related Traits in 1-Year Old of Two Korean Abalone Subspecies, Haliotis discus hannai and H. discus discus, by Using Multiple Traits of Animal Model (다형질 Animal Model에 의한 12개월령 한국산 전북 2 아종의 성장관련형질에 대한 유전모수 추정)

  • Choe, Mi-Kyung;Han, Seock-Jung;Yang, Sang-Geun;Won, Seung-Hwan;Park, Choul-Ji;Yeo, In-Kyu
    • The Korean Journal of Malacology
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    • v.24 no.2
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    • pp.121-130
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    • 2008
  • In other aquaculture species, large improvements in growth have been achieved through selective breeding. Ezo abalone(Haliotis discus hannai) and disk abalone(H. discus discus) are major aquatic animals cultured in Asia, but selective breeding for the promotion of growth with these abalones has not been actively pursued. Recently significant efforts are being made to promote production of these species through selective breeding in Korea. The aims of this work were to estimate the general genetic parameters, heritabilities, and genetic and phenotypic correlations on growth-related traits at 1-year old in two Korean abalone subspecies, H. discus hannai and H. discus discus, by using multiple trait animal model. The data were collected from the records of 1,504 individuals produced from 22 sires and 26 dams in H. discus hannai and 297 individuals produced from 5 sires and 6 dams in H. discus discus, which evaluated by the Genetics and Breeding Research Center, National Fisheries Research & Development Institute(NFRDI). Genetic parameters were estimated for these abalone subspecies raised in Bukjeju branch, NFRDI, from May 20, 2004 to May 16, 2005, respectively. The heritability estimates obtained from restricted maximum likelihood(REML) were higher than expected, ranging from 0.40 to 0.43 for growth traits shell length, shell width and body weight in H. discus hannai and from 0.26 to 0.51 in H. discus discus, respectively. The heritabilities for shell shape and condition factor were lower than others of growth traits such as ranging from 0.09 to 0.19 in H. discus hannai and from 0.10 to 0.23 in H. discus discus, respectively. Genetic and phenotypic were > 0.93 between shell parameters and weight in two abalone species, respectively, indicating that breeding for weight gains could be successfully achieved by selecting for shell length.

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Characterization of Traits Related to Grain Shape in Korean Rice Varieties (국내 육성 벼 품종 입형 관련 특성 분석)

  • Lee, Chang-Min;Lee, Keon-Mi;Baek, Man-Kee;Kim, Woo-Jae;Suh, Jung-Pil;Jeong, Oh-Young;Cho, Young-Chan;Park, Hyun-Su;Kim, Suk-Man
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.65 no.3
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    • pp.199-213
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    • 2020
  • Grain size and shape are the two important components contributing to rice yield and quality. To analyze traits related to grain-shape, a total of 272 varieties derived from japonica, japonica black and Tongil-type rice accession in Korea were evaluated in this study. The traits, grain length (GL), grain width (GW), grain thickness (GT), length to width ratio (RLW), and 1000-grain weight (TGW) were measured and replicated 10 times. Genes (GW2, GS3, qGL3, qSW5, GS5, TGW6, GW7, and GW8) related to grain-shape were validated in the accessions using specific DNA marker sets. K-mean clustering of the accession based on phenotypic data revealed three groups: group 1 was classified by GW and GT and included most of japonica type, group 2 was classified by RLW and GL reached a medium size and possessed a half spindle-shaped type, and group 3 was classified by TGW, reached a long size and possessed a semi-round shape. In validation tests using the marker sets, both gw2 and tgw6 were validated in less than 1% of the tested accessions and two allelic types, qgl3 and gw8, were only verified in Tongil-type accessions. For GW8 and GW2, any different amplicons were not amplified in any japonica or Tongil-type accessions, respectively. In order to suggest the representative grain-shape gene combinations for each ecotype, the allelic combinations were evaluated by PCR analysis. Cj1 and 2 in japonica (Cj1-7), Cj_b1 and 2 in japonica-black (Cj_b1-3), and CT3 in Tongil-type (CT1-13) turned out to be the dominant combination in each ecotype, respectively. In addition, the results revealed that introgression of four genes (gw2, gs3, qSW5, and GS5) would expand the diversity of grain shape in Korean japonica varieties. The gene combinations information could be utilized practically to understand or enhance grain shape in japonica rice breeding program.