• Journal of Ginseng Research
• /
• 제35권4호
• /
• pp.399-412
• /
• 2011

Little is known about the genetics or genomics of Panax ginseng. In this study, we developed 70 expressed sequence tagderived polymorphic simple sequence repeat markers by trials of 140 primer pairs. All of the 70 markers showed reproducible polymorphism among four Panax species and 19 of them were polymorphic in six P. ginseng cultivars. These markers segregated 1:2:1 manner of Mendelian inheritance in an $F_2$ population of a cross between two P. ginseng cultivars, 'Yunpoong' and 'Chunpoong', indicating that these are reproducible and inheritable mappable markers. A phylogenetic analysis using the genotype data showed three distinctive groups: a P. ginseng-P. japonicus clade, P. notoginseng and P. quinquefolius, with similarity coefficients of 0.70. P. japonicus was intermingled with P. ginseng cultivars, indicating that both species have similar genetic backgrounds. P. ginseng cultivars were subdivided into three minor groups: an independent cultivar 'Chunpoong', a subgroup with three accessions including two cultivars, 'Gumpoong' and 'Yunpoong' and one landrace 'Hwangsook' and another subgroup with two accessions including one cultivar, 'Gopoong' and one landrace 'Jakyung'. Each primer pair produced 1 to 4 bands, indicating that the ginseng genome has a highly replicated paleopolyploid genome structure.

• The Plant Pathology Journal
• /
• 제28권1호
• /
• pp.20-31
• /
• 2012

Endophytic bacterial communities of tidal flat plants antagonistic to oomycete plant pathogens were studied by the isolation of 256 root colonizing endophytic bacteria from surface-disinfected root tissues of six plants ($Rosa$ $rugosa$, $Suaeda$ $maritima$, $Vitex$ $rotundifolia$, $Carex$ $scabrifolia$, $Glehnia$ $littoralis$ and $Elymus$ $mollis$) growing in a tidal flat area of Namhae Island, Korea. To understand the antagonistic potential, an $in$ $vitro$ antagonistic assay was performed to characterize and identify strains that were antagonistic to the oomycete plant pathogens $Phytophthora$ $capsici$ and $Pythium$ $ultimum$ from the total population. Nine percent of the total number of isolated bacteria exhibited in vitro inhibitory activity against target plant pathogenic oomycetes. Taxonomic and phylogenetic placement of the antagonistic bacteria was investigated by analysis of the 16S rRNA gene sequences. The sequence analysis classified the antagonistic strains into four major classes of the domain bacteria ($Firmicutes$, ${\alpha}-Proteobacteria$, ${\gamma}-Proteobacteria$ and $Actinomycetes$) and 10 different genera. Further production of secondary metabolites, hydrolytic enzymes and plant growth promoting traits were determined for the putative new species of antagonistic endophytic bacteria. These new strains could not be identified as known species of ${\alpha}-Proteobacteria$, and so may represent novel bacterial taxa. The unexpected high antagonistic bacterial diversity associated with the tidal flat plants may be indicative of their importance in tidal flat plants as a promising source of novel antimicrobial compounds and biocontrol agents.

• 식물병연구
• /
• 제19권2호
• /
• pp.77-83
• /
• 2013

Bean yellow mosaic virus (BYMV; genus Potyvirus, family Potyviridae) causes severe losses to various legume species and a number of non-legume species, particularly freesia plants. In a survey of virus diseases in Gyeonggi province, Korea, BYMV isolates were identified from many cultivated freesia species. Here, we determined the complete nucleotide sequences of a BYMV freesia isolate (BYMV-Fr; accession number FJ492961). BYMV-Fr genome consists of 9,545 nucleotides (nt) excluding the poly (A) tail and encodes 3,057 amino acid (aa), with an AUG start and UAG stop codon, containing one open reading frame typical of a potyvirus polyprotein. The polyprotein of BYMV-Fr was divided to ten proteins and the cleavage sites of each protein were determined. The coat protein (CP) and polyprotein of BYMV-Fr were compared at the aa level with those of the previously reported 4 BYMV isolates. BYMV-Fr shared 90.1 to 97.1 and 91.0 to 92.5% at the CP and polyprotein homology. Interestingly, BYMV-Fr showed identities of a lower level at the nt level of 5' noncoding region (61.4 to 67.6%) and at the aa level of P1 (71.4 to 72.8%), comparing with four BYMV isolates. Based on the aa sequence diversity of CP and polyprotein, phylogenetic analysis with the four BYMV isolates showed two distinct groups and BYMV-Fr and most BYMV isolates were most closely related to the clover yellow vein virus among 52 potyviruses. To our knowledge, this is the first report of the complete genome sequence of BYMV freesia strain.

• Asian-Australasian Journal of Animal Sciences
• /
• 제31권9호
• /
• pp.1393-1400
• /
• 2018

Objective: This study was carried out to assess the haplotype diversity and population dynamics in cattle populations of Ethiopia. Methods: We sequenced the complete mitochondrial cytochrome b gene of 76 animals from five indigenous and one Holstein Friesian${\times}$Barka cross bred cattle populations. Results: In the sequence analysis, 18 haplotypes were generated from 18 segregating sites and the average haplotype and nucleotide diversities were $0.7540{\pm}0.043$ and $0.0010{\pm}0.000$, respectively. The population differentiation analysis shows a weak population structure (4.55%) among the populations studied. Majority of the variation (95.45%) is observed by within populations. The overall average pair-wise distance ($F_{ST}$) was 0.049539 with the highest ($F_{ST}=0.1245$) and the lowest ($F_{ST}=0.011$) $F_{ST}$ distances observed between Boran and Abigar, and Sheko and Abigar from the indigenous cattle, respectively. The phylogenetic network analysis revealed that all the haplotypes detected clustered together with the Bos taurus cattle and converged to a haplogroup. No haplotype in Ethiopian cattle was observed clustered with the reference Bos indicus group. The mismatch distribution analysis indicates a single population expansion event among the cattle populations. Conclusion: Overall, high haplotype variability was observed among Ethiopian cattle populations and they share a common ancestor with Bos taurus.

• Asian-Australasian Journal of Animal Sciences
• /
• 제26권3호
• /
• pp.316-322
• /
• 2013

In order to evaluate the genetic diversity and discrimination among five Korean native chicken lines, a total of 86 individuals were genotyped using 150 microsatellite (MS) markers, and 15 highly polymorphic MS markers were selected. Based on the highest value of the number of alleles, the expected heterozygosity (He) and polymorphic information content (PIC) for the selected markers ranged from 6 to 12, 0.466 to 0.852, 0.709 to 0.882 and 0.648 to 0.865, respectively. Using these markers, the calculated genetic distance (Fst), the heterozygote deficit among chicken lines (Fit) and the heterozygote deficit within chicken line (Fis) values ranged from 0.0309 to 0.2473, 0.0013 to 0.4513 and -0.1002 to 0.271, respectively. The expected probability of identity values in random individuals (PI), random half-sib ($PI_{half-sibs}$) and random sibs ($PI_{sibs}$) were estimated at $7.98{\times}10^{-29}$, $2.88{\times}10^{-20}$ and $1.25{\times}10^{-08}$, respectively, indicating that these markers can be used for traceability systems in Korean native chickens. The unrooted phylogenetic neighbor-joining (NJ) tree was constructed using 15 MS markers that clearly differentiated among the five native chicken lines. Also, the structure was estimated by the individual clustering with the K value of 5. The selected 15 MS markers were found to be useful for the conservation, breeding plan, and traceability system in Korean native chickens.

• Asian-Australasian Journal of Animal Sciences
• /
• 제28권4호
• /
• pp.457-466
• /
• 2015

Taoyuan pig is a native Taiwan breed. According to the historical record, the breed was first introduced to Taiwan from Guangdong province, Southern China, around 1877. The breed played an important role in Taiwan's early swine industry. It was classified as an indigenous breed in 1986. After 1987, a conserved population of Taoyuan pig was collected and reared in isolation. In this study, mitochondrial DNA sequences and 18 microsatellite markers were used to investigate maternal lineage and genetic diversity within the Taoyuan pig population. Population differentiation among Taoyuan, Asian type, and European type pig breeds was also evaluated using differentiation indices. Only one D-loop haplotype of the Taoyuan pig was found. It clustered with Lower Changjiang River Basin and Central China Type pig breeds. Based on the polymorphism of microsatellite markers, a positive fixation index value ($F_{IS}$) indicates that the conserved Taoyuan population suffers from inbreeding. In addition, high $F_{ST}$ values (>0.2105) were obtained, revealing high differentiation among these breeds. Non-metric multi-dimensional scaling showed a clear geometric structure among 7 breeds. Together these results indicate that maternally Taoyuan pig originated in the Lower Changjiang River Basin and Central China; however, since being introduced to Taiwan differentiation has occurred. In addition, Taoyuan pig has lost genetic diversity in both its mitochondrial and nuclear genomes.

• Journal of Microbiology and Biotechnology
• /
• 제18권12호
• /
• pp.1874-1883
• /
• 2008

Bacterial diversity and the composition of individual communities during the composting process of swine and mushroom cultural wastes in a field-scale composter (Hazaka system) were examined using a PCR-based approach. The composting process was divided into six stages based on recorded temperature changes. Phylogenetic analysis of eighty 16S rRNA sequences from uncultured composting bacterial groups revealed the presence of representatives from three divisions, including plant pathogenic bacteria, high-molecule-degrading bacteria and spore-forming bacteria. The plant pathogen A. tumefaciens gradually decreased in abundance during the composting process and eventually disappeared during the thermophilic and cooling stage. A bacterium homologous to Bacillus humi first appeared at the early thermophilic stage and was established at the intermediate thermophilic, post-thermophilic, and cooling stages. It was not possible to isolate the B. humi during any of the stages using general culture techniques.

• Journal of Microbiology and Biotechnology
• /
• 제22권1호
• /
• pp.1-12
• /
• 2012

The present study examines the effects of 30 mg/kg butachlor on the cyanobacterial diversity of rice fields in Eastern Uttar Pradesh and Western Bihar in India. A total of 40 samples were grouped into three classes [(i) acidic, (ii) neutral, and (iii) alkaline soils], based on physicochemical and principle component analyses. Acidic soils mainly harbored Westillopsis, Trichormus, Anabaenopsis, and unicellular cyanobacteria; whereas Nostoc, Anabaena, Calothrix, Tolypothrix, and Aulosira were found in neutral and alkaline soils. Molecular characterization using 16S rRNA PCR and DGGE revealed the presence of 13 different phylotypes of cyanobacteria in these samples. Butachlor treatment of the soil samples led to the disappearance of 5 and the emergence of 2 additional phylotypes. A total of 40 DGGE bands showed significant reproducible changes upon treatment with butachlor. Phylogenetic analyses divided the phylotypes into five major clusters exhibiting interesting links with soil pH. Aulosira, Anabaena, Trichormus, and Anabaenopsis were sensitive to butachlor treatment, whereas uncultured cyanobacteria, a chroococcalean member, Westillopsis, Nostoc, Calothrix, Tolypothrix, Rivularia, Gloeotrichia, Fischerella, Leptolyngbya, and Cylindrospermum, appeared to be tolerant against butachlor at their native soil pH. Butachlor-induced inhibition of nitrogen fixation was found to be 65% (maximum) and 33% (minimum) in the soil samples of pH 9.23 and 5.20, respectively. In conclusion, low butachlor doses may prove beneficial in paddy fields having a neutral to alkaline soil pH.

• The Plant Pathology Journal
• /
• 제29권3호
• /
• pp.274-284
• /
• 2013

The incidence of Broad bean wilt virus 2 (BBWV2) on red pepper was investigated using the samples obtained from 24 areas of 8 provinces in Korea. Two hundred and five samples (79%) out of 260 collected samples were found to be infected with BBWV2. While the single infection rate of BBWV2 was 21.5%, the co-infection rate of BBWV2 with Cucumber mosaic virus, Pepper mottle virus, Pepper mild mottle virus and/or Potato virus Y was 78.5%. To characterize the genetic diversity of BBWV2 Korean isolates, 7 isolates were fully sequenced and analyzed. Phylogenetic analyses revealed that BBWV2 isolates could be divided largely into two groups as Group I and Group II. Based on the partial sequence analyses, 153 selected BBWV2 isolates were subgrouped into GS-I (21.6%), GS-II (3.9%) and GS-III (56.9%). BBWV2 GS-III, which was predominant in Korea, appears to be a new combination between Group I RNA-1 and Group II RNA-2. Viral disease incidence of BBWV2 on red pepper was under 2% before 2004. However, the incidence was increased abruptly to 41.3% in 2005, 58.2% in 2006 and 79% in 2007. These rapid increases might be related with the emergence of new combinations between BBWV2 groups.

• 생명과학회지
• /
• 제17권1호
• /
• pp.24-30
• /
• 2007

꽃치자(Gardenia jasminoides var. radicans)와 열매치자(C. jasminoides for. grandiflora)는 Gardenia속으로는 우리나라에 두 분류군밖에 없으며 열매치자는 약용, 식용, 꽃치자는 방향제로 쓰인다. 그런데 꽃이 지고 나면 형태적으로 구분이 거의 되지 않는다 ISSR분석으로 이들 종의 유전적 다양도와 집단구조를 실시하였다. 88개의 DNA 분절에서 한 분류군에만 나타나는 특이밴드가 탐지되었다. 한국의 세 야생 집단은 분리되어 있고 패치 분포를 보이지만 재배종에 비해 높은 유전적 다양성을 유지하친 있었다. 열매치자가 꽃치자보다 유전적 다양성이 높았으며 ISSR 마커로 이들 분류군이 잘 분리되었다. 또한 야생 집단이 재배 집단보다 다양성이 약간 높으나 유의성은 없었다. 이는 재배화과정에서 유전적 다양성의 일부 상실이 있었으나 인위적인 채취와 식재로 야생 집단과 재배 집단의 유전적 교류가 존재하였음을 시사한다.