• Title/Summary/Keyword: Population Genetics

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Identification of a Major QTL, qSTV11SG, Associated with Resistance to Rice Stripe Virus Disease Originated from Shingwangbyeo in Rice (Oryza Sativa L.) (신광벼 유래의 벼 줄무늬잎마름병 저항성 주동 QTL qSTV11SG탐색)

  • Kwak, Do-Yeon;Lee, Bong-Chun;Choi, Ilyoung;Yeo, Un-Sang;Cho, Jun-Hyun;Lee, Ji-Yoon;Song, You-Chun;Yun, Yeong-Nam;Park, Dong-Soo;Kang, Hang-Won;Nam, Min-Hee;Lee, Jong-Hee
    • Korean Journal of Breeding Science
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    • v.43 no.5
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    • pp.464-469
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    • 2011
  • Virus diseases often cause serious damage to rice production in Asia. The lack of information on virus resistance genes has been a major obstacle for the breeding of resistant varieties. In order to identify DNA marker associated with resistance against rice stripe virus (RSV), the quantitative trait locus (QTL) was carried out using advanced backcross population developed from a cross between RSV-resistant tongil type cultivar Shinkwang and susceptible japonica cultivar Ilpum. A RSV resistance QTL $qSTV11^{SG}$ explaining 44.2% of the phenotypic variation was identified on chromosome 11 of Tongil type rice cultivar 'Shingwang'. $qSTV11^{SG}$ was tightly linked to DNA marker RM6897. The RM6897 divided as resistance type allele and susceptible type alleles. Twenty seven resistant varieties showed the resistant-type allele and 23 susceptible varieties were susceptible-type allele to the marker of RM6897. This results and the molecular markers presented here may be useful in rice breeding for improving RSV resistance in japonica rice.

Determining the doses of probiotics for application in Scylla tranquebarica (Fabricius 1798) larvae to produce crablet

  • Gunarto, Gunarto;Yustian Rovi Alfiansah;Muliani Muliani;Bunga Rante Tampangalo;Herlinah Herlinah;Nurbaya Nurbaya;Rosmiati Rosmiati
    • Fisheries and Aquatic Sciences
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    • v.27 no.3
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    • pp.180-194
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    • 2024
  • Mass mortalities of mud crab Scylla spp. larvae due to pathogenic Vibrio spp. outbreaks have frequently occurred in hatcheries. To overcome this problem, probiotics containing Bacillus subtilis bacteria are applied to inhibit pathogenic ones. We tested different doses of probiotic-containing B. subtilis (108 CFU/g) on the Scylla tranquebarica larvae and investigated the microbiota population, including Vibrio. Water quality, larvae development, and crablet production were also monitored. The recently hatched larvae were grown in twelve conical fiber tanks filled with 200 L sterile seawater, with a salinity of 30 ppt at a stocking density of 80 ind/L. Four different doses of probiotics were applied in the larvae rearing, namely, A = 2.5 mg/L, B = 5 mg/L, C = 7.5 mg/L, and D = 0 mg/L, with three replicates. Next-generation sequencing analysis was used to obtain the abundance of microbes in the whole body of megalopa and the water media for larvae rearing after applying probiotics. Sixteen Raw Deoxyribonucleic Acid samples (eight from a whole body of megalopa extraction from four treatments of probiotics defined as A, B, C, D, and eight from water media extraction from four treatments of probiotic defined as E, F, G, H) were prepared. Then, they were sent to the Genetics Science Laboratory for NGS analysis. Ammonia, nitrite, total organic matter (TOM), larvae, and crablet production were monitored. Based on the Next-generation sequencing analysis data, the Vibrio spp. decreased significantly (p < 0.05) than control test (D) in megalopa-applied probiotics at the doses of 2.5 mg/L (A) and 7.5 mg/L (C) and in the water media for megalopa rearing treated with probiotics at the dosage of 5.0 mg/L (F). Ammonia in the zoea stage in B treatment and TOM in the zoea and megalopa stage in B and C treatments were decreased significantly (p < 0.05). It impacts the higher number of zoea survival in treatments B and C. Finally, it results in a significantly high crablet production in treatments B and C. Therefore, the dosage of 5 mg/L to 7.5 mg/L improves crablet S. tranquebarica production significantly.

STUDIES ON THE DIMORPHISM AND TRANSITION OF BISEXUALITY OF HETEROSTYLOUS POLYGONACEAE (여뀌과 이형경식물의 Dinorphism과 Bisexuality의 변화)

  • Harn, Chang-Yawl
    • Journal of Plant Biology
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    • v.3 no.2
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    • pp.6-18
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    • 1960
  • The present experiments were designed in order to clarify the differences between the long and short styled plants and the transgressive gradition in the degree of dimorphism among the three heterostylous species of the Polygonus, P. japonica, F. esculentum, and P. senticosa, based on investigations regarding the floral structure, ecological and physiological traits, the results of which are summarized as follows: (1) P. japonica, although it exhibits typical dimorphism, has undergone so high a differentiation between long and short styled that its long styled individuals behave as if they were female; and short styled individuals as if male. In long-styled individuals, filament, anther, and pollen grains show signs of degeneration, most of the pollen being abortive. On the other hand, in short styled individuals, the filament, anther, and pollen grains have attained remarkable development; the pollen grians are large and fertile. In short-plant the fertilized flowers readily drop off in every stage of their embryo development. This species has completely lost the self-fertile property, which is characteristic of the non-dimorphic Polygonum genus. Although this specsei typically exhibits the physiological characteristics of the non-dimorphic Polygonum genus. Although this specisei typically exhibits the physiological characteristics of dimorphism in controlled pollination, the short-styled individuals bear no seed in nature, thus misleading taxonomists to idenfity the short-styled plant as male. 2) The morphological feature of the flower organ of P. senticosa obviously indicates definite dimorphism. Physiologically, however, no differentiation towards dimorphism was observed, the species still retaining, both in long and short-individuals, the self-fertile property common to the Polygonum genus. Elaborate examinations revealed that regardless of the modes of pollination, both fertiization and seed setting flourish, no differentiation betwen legitimate and illegitimate unions being recognizable. This sort of physiological property has not been observed in the investigations of other heterostylous plants. It is assumed that this species is differentiated structurally into dimorphism, but not yet physiologically. In nature, however, this plant would have more opportunities to be cross-pollinated, i.e., legitimately combined, than self-pollinated because of the development of two forms of flowers. 3) In terms of heterostylism, the F. esculentum just occupies the intermediate position between P. japonica and P. senticosa structurally, ecologically, and physiologically. Doescription of some of the physiological behavior of the plant will suffice to demonstrate the above facts. While P. japonica has completely lost its self-fertile property, P. senticosa still retains it wolly. In F. esculentum 2-6% of self-fertility is the result in illegitimate combination. There occur occasionally hereditary self fertile individuals among some of the F. or 20 min. irradiation plot, when they reach any stage of the same bacterial population. In addition to this increase of total population in the plots with the more dose of UV light irradiation, it seems that the more dose of UV light irradiation is the more shortened the generation time of Azotobacter. Therefore, it is clear that variation of reproductive rate must be, mere or less, due to the genetic effects induced by UV light irradiation. On the other hand, the lag phase or logarithmic growth phase in nonirradiated culture is shortened prominently, and this must be due to the difference in bacterial number of the original inoculm. The generation time of Azotobacter is shortened by exogeneous treatment of nuclei acid derivatives, and the degree is greater in case of DNA derivatives than RNA dervatives. W.H. Price reported that the rate of ribose nucleic acid to protein in Staphylococcus muscae is proportional to the generation time: that is the faster the cell can form ribose nucleic acid, the more rapid its growth. This explains the shortening of generation time by exogeneous RNA derivatives in this work reasonably. On the other hand, it is well known that the desoxyribose nuclic acid content per cell is constant and independent of the generation time. A.D. Laren and W.N. Takahashi reported that the infectious RNA from TMV is 6 times as sensitive to inactivation by UV as it is in the form of intact virus, and that inactivation of infectious TMV involves onlu a local change on RNA chain. But, the effect of exogeneous DNA in this work suggests that irradiated living cell which cotain DNA bring about some change on DNA moleculs as well as RNA molecules. And if the mutagenic effects of UV take into consideration, it is very reasonable. Therefore, it is clear that the variation of the generation time by UV irradiation is, more or less, due to the genetic effects. Therefore, it seems that the shortness of the average lifewpan of Azotobacter by UV irradiation is resulted not only from the influence of the environmental conditions, but also from the variation of genetic factor of the individual.

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The Clinical and Genetic Characteristics of Three Korean Patients with Glycogen Storage Disease Type V (McArdle Disease) (세 명의 대한민국 제 V형 당원축적근육병(McArdle 병) 환자들의 유전학적 및 임상적 특성 보고)

  • Lee, Sunghee;Kang, Eungu;Kim, Yoonmyung;Lee, Beom Hee;Kim, Gu Hwan;Yoo, Han Wook
    • Journal of The Korean Society of Inherited Metabolic disease
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    • v.16 no.2
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    • pp.93-101
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    • 2016
  • Purpose: McArdle disease, glycogen storage disease type V (GSD V), is one of the most common adolescent-onset glycogen storage diseases. It is caused by recessive mutations in PYGM encoding myophosphorylase, which is critical to glycogen metabolism. Since only a few korean patients have been reported, we will observe the clinical and genetic features of three korean patients with McArdle disease. Methods: We retrospectively reviewed the medical records of three patients with genetically confirmed McArdle disease, including the results of forearm ischemic exercise test, electromyogram, nerve conduction velocity, muscle biopsy, and PYGM analysis in peripheral leukocytes. Results: All three cases were males and their age of symptom onset was 12, 5, 14 years old, respectively. A high basal level of serum creatine kinase was noted in all three patients. They experienced the recurrent episodes of rhabdomyolysis, but second wind phenomenon was not definite. In muscle biopsy, subsarcolemmal space vacuoles including periodic acid schiff stained materials were found in two patients, while no evidence of glycogen storage disease was found in the other. A total of five different mutations, $p.Arg50^*$, p.Trp798Arg, $p.Arg50^*$, p.Glu779del, $p.Asp511Thrfs^*28$ and p.Phe710del, were found in three patients. Avoidance of isometric exercise, aerobic exercise and glucose intake before each exercise were recommended for all patients. Conclusion: The three Korean patients with McArdle disease showed the typical manifestations of the condition. The most mutations were private. Therefore, identification of more cases with long-term follow-up will be required to understand the clinical and genetic features of this disease among Korean population.

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Stenotrophomonas maltophilia and Ventilator-Associated Pneumonia in Critically Ill Pediatric Patients: a Retrospective Analysis at a Single Center (소아 환자에서 Stenotrophomonas maltophilia와 인공 환기요법 관련 폐렴에 관한 연구)

  • Lee, Byung-Kee;Choi, Soo-Han;Kim, Soo Jin;Cho, Joong Bum;Ae, Hong;Yoo, So-young;Kim, Ji Hye;Lee, Nam Young;Kim, Yae-Jean
    • Pediatric Infection and Vaccine
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    • v.22 no.2
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    • pp.75-80
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    • 2015
  • Purpose: Ventilator-associated pneumonia (VAP) is a serious threat in critically ill pediatric patients. Data regarding Stenotrophomonas maltophilia VAP in pediatric population is limited. We evaluated the clinical data of S. maltophilia associated VAP in critically ill pediatric patients. Methods: A retrospective chart review was performed in pediatric patients 18 years old or younger who developed S. maltophilia associated VAP at Samsung Medical Center, Seoul Korea from January 2008 to December 2012. Results: A total of 31 patients were identified S. maltophilia associated VAP. Median age was 8 months (range, 0.5 month to 16.6 years) and 13 patients were male (40.6%). Underlying illnesses were cardiologic diseases (n=11, 34.4%), hematologic oncologic malignancies (n=7, 25%), neurologic diseases (n=4, 12.5%), pulmonary diseases (n=3, 9.4%), and others (n=4, 12.5%). The median duration of ventilator use before S. maltophilia VAP diagnosis was 14 days (range, 4-256 days). Overall mortality at 30 days was 12.5% (4/32). Conclusions: S. maltophilia should be also considered as a possible pathogen for VAP in critically ill pediatric patients. Empiric antibiotic choice should include agents that are active against S. maltophilia in patients who are deteriorating on broad spectrum beta-lactam antimicrobial agents.

Association Analysis between (AAT)n Repeats in the Cannabinoid Receptor 1 Gene and Schizophrenia in a Korean Population (한국인에서 조현병과 Cannabinoid Receptor 1 유전자의 삼핵산 반복서열의 연합에 대한 연구)

  • Kim, Ji-Won;Roh, Yang-Ho;Kim, Min-Jea;Kim, Chea-Ri;Park, Byung-Lae;Bae, Joon Seol;Shin, Hyoung Doo;Choi, Ihn-Geun;Han, Sang-Woo;Hwang, Jaeuk;Woo, Sung-Il
    • Korean Journal of Biological Psychiatry
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    • v.21 no.3
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    • pp.99-106
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    • 2014
  • Objectives Previous studies suggest that the cannabinoid receptor 1 (CNR1) gene could be an important candidate gene for schizophrenia. According to linkage studies, this gene is located on chromosome 6q14-q15, which is known to harbor the schizophrenia susceptibility locus (locus 5, SCZ5, OMIM 803175). The pharmacological agent delta-9-tetrahydrocannabinol (${\Delta}$-9-THC) seems to elicit the symptoms of schizophrenia. The association between CNR1 polymorphisms and schizophrenia is actively being investigated, and some studies have linked the AAT-trinucleotide repeats in CNR1 to the onset of schizophrenia. In this study, we have investigated the association between the AAT-trinucleotide repeats in CNR1 and schizophrenia by studying schizophrenia patients and healthy individuals from Korea. Methods DNA was extracted from the blood samples of 394 control subjects and 337 patients diagnosed with schizophrenia (as per the Diagnostic and Statistical Manual of Mental Disorders, fourth edition criteria). After polymerase chain reaction amplification, a logistic regression analysis, with age and gender as the covariates, was performed to study the variations in the AAT-repeat polymorphisms between the two groups. Results In total, 8 types of trinucleotide repeats were identified, each containing 7, 8, 10, 11, 12, 13, 14, and 15 repeats, respectively. $(AAT)_{13}$ allele was most frequently observed, with a frequency of 33.6% and 31.6% in the patient and control groups, respectively. The frequency of the other repeat alleles in the patient group (in the decreasing order) was as follows : $(AAT)_{13}$ 33.6%, $(AAT)_{14}$ 21.6%, $(AAT)_{12}$ 18.5%, and $(AAT)_{7}$ 11.1%. The frequency of the repeat alleles in the control group (in the decreasing order) was as follows : $(AAT)_{13}$ 31.6%, $(AAT)_{14}$ 24.5%, $(AAT)_{12}$ 17.2%, and $(AAT)_{7}$ 11.6%. However, there were no significant differences in the AAT-repeat polymorphisms of the CNR1 gene between the patient group and the control group. Conclusions Although our study revealed no significant association of the AAT-repeat polymorphism of the CNR1 gene with schizophrenia, it will serve as a good reference for future studies designed to examine the cannabinoid hypothesis of schizophrenia.

Incidence and Spectrum of Chromosomal Abnormalities associated with Spontaneous Abortions in Korea: 470 Products of Conception over a Period of 6 Years (2005-2010) (국내 자연유산에 의한 수태산물 핵형분석에서 관찰된 염색체 이상의 발생율과 유형: 6년(2005-2010)간 수태산물 470예 분석)

  • Han, Sung-Hee;An, Jeong-Wook;Yang, Young-Ho;Kim, Young-Jin;Cho, Han-Ik;Lee, Kyoung-Ryul
    • Journal of Genetic Medicine
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    • v.8 no.1
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    • pp.44-52
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    • 2011
  • Purpose: Cytogenetic analysis of spontaneous abortions (SABs) provides valuable information to establish the causes of fetal loss, information that is essential to provide accurate reproductive and genetic counseling couples. Such analysis also provides information on the frequencies and types of chromosomal abnormalities and associated risks of recurrence. However, there have only been a few reports of chromosomal abnormalities in small samples of SABs in the Korean population. Here, we report the incidence and spectrum of chromosomal abnormalities for cases of 470 SAB in Korea. Material and Methods: Between 2005 and 2010, a total of 470 products of conception (POC) resulting from SABs were submitted to our laboratory for cytogenetic analysis from various medical sites in Korea. The incidences and types of specific chromosomal abnormalities were determined. The abnormalities were distinguished by gestational age at the time of SAB and by maternal age. Results: The frequency of chromosomal abnormalities in POCs was 54.3% (255/470), including 228 (89.3%) numerical and 27 (10.7%: 3 balanced and 24 unbalanced) structural abnormalities. Among the numerical abnormalities, trisomy was predominant (67.0%), followed by monosomy X (12.5%), polyploidy (8.2%), triple X (0.8%), and autosomal monosomy (0.8%). The overall sex ratio (male: female) among the 470 POCs with normal and abnormal karyotypes were 0.58 and 0.65, respectively. Trisomies were identified for each autosome, with the exceptions of 1, 3, and 19. Among the 171 autosomal trisomies, trisomy 16 was the most common (19.9%), followed by trisomy 22 (13.5%), trisomy 21 (12.3 %), trisomy 15 (9.9%), and trisomies 18 and 13 (5.3%). The frequency of chromosomal abnormalities decreased with gestational age and increased with maternal age, but only because of increases in trisomies and complex abnormalities. Conclusions: We have presented a large collection of cytogenetic data for SABs collected during the past 6 years and provided a database for prenatal genetic counseling of parents who have experienced SABs in Korea.