• Asian-Australasian Journal of Animal Sciences
• /
• v.23 no.9
• /
• pp.1145-1151
• /
• 2010

The objective of this work was to analyze the relationship between ovine major histocompatibility complex (MHC) DRB1 gene polymorphism and genetic resistance to hydatidosis in Kazakh sheep. The Ovar (ovine MHC) class II DRB1 second exon was amplified by polymerase chain reaction (PCR) from DNA samples of 702 Kazakh sheep, including 302 sheep with hydatidosis and 400 health controls. PCR products were characterized by the restriction fragment length polymorphism (RFLP) technique using five restriction enzymes, i.e., MvaI, HaeIII, SacI, SacII and Hin1I, yielding 14 alleles and 28 genotypes. Comparing the frequency of genotypes in hydatidosis sheep with the control group, it was found that the genotype frequencies of MvaIbc, Hin1Iab, SacIIab, HaeIIIde, HaeIIIdf and HaeIIIdd in control sheep were significantly (p<0.01) higher than in hydatidosis sheep, indicating that a significant correlation existed between these genotypes and resistance to hydatidosis. Genotype frequencies of MvaIbb, SacIIaa, Hin1Ibb and HaeIIIef in sheep with hydatidosis were extremely significantly (p<0.01) higher than in the control group, and the genotype frequency of HaeIIIab was significantly higher (p<0.05), indicating that a marked correlation existed between these genotypes and susceptibility to hydatidosis. By way of analyzing haplotype with these resistant genotypes, the hydatidosis resistant haplotype MvaIbc-SacIIab-Hin1Iab of Kazakh sheep was screened out, and then verified through artificial hydatid infection in sheep. The results indicated that the infection rate of sheep with the resistant haplotype of hydatidosis was significantly lower (p<0.01) than without this resistant haplotype. It showed that the genic haplotype MvaIbc-SacIIab-Hin1Iab of Ovar-DRB1 exon 2 was the resistant haplotype of hydatidosis in Kazakh sheep.

• Korean Journal of Ichthyology
• /
• v.22 no.2
• /
• pp.115-120
• /
• 2010

Genetic variation and population structure of the slender bitterling Acheilognathus lanceolatus of Korea (the Han, Geum, Dongjin, Seomjin and Nakdong Rivers) and Japan (the Katsura River) were assessed by amplified fragment length polymorphism (AFLP) analysis. Five combinations of selective primers generated 345~374 DNA fragments, of which 55~131 were polymorphic. The Nakdong River population had the highest genetic diversity and the Han River population had the lowest genetic diversity. Dendrogram based on the distance matrix revealed that individuals from each population consistently clustered together and bifurcated into two distinct clades (or population groups) composed of the Han, Geum, Dongjin and Seomjin River populations and of the Nakdong and Katsura River populations, supported with high bootstrap values. The pairwise genetic differentiation ($F_{ST}$) estimates showed that the six populations were genetically well differentiated (P<0.01). The analysis of molecular variance (AMOVA) after partitioning the six populations into two population groups revealed very strong biogeographic structuring between them with 25.49% of total variance (P<0.01). Taken together, the AFLP markers clearly divided six A. lanceolatus populations into two population groups.

• Korean Journal of Plant Taxonomy
• /
• v.34 no.1
• /
• pp.43-61
• /
• 2004

Molecular taxonomic studies were conducted to evaluate interspecific relationships in Korean Viola 34 taxa including two Japanese populations using RAPD(randornly amplified polymorphic DNA), ISSR(inter simple sequence repeat) and PCR-RFLP(restriction fragment length polymorphism) analysis. Only six and four primers out of 40 arbitrary and 12 ISSR primers were screened for 34 taxa, and were revealed 70 (98.6%) and 28 (96.6%) polymorphic bands, respectively. Fifteen restriction endonucleases produced 80 restriction sites and size variations from the large single copy region of cpDNA, 16 (20%) of which were polymorphic. The separate analyses from the RAPD, ISSR and PCR-RFLP data were incongruent in the relationships among 34 taxa, but combined data was in accordance with previous infrageneric classification system based on morphological characters, especially the subsection and series level. Section Chamaemelanium placed between subsect. Patellares and Vagimtae of section Nomimium was not formed as a distinct group. Viola alb ida complex including three very closely related taxa was recognized independent group within subsect. Patellares in combined data tree. This result strongly suggested that they should be treated to series Pinmtae. RAPD analysis was very useful to clarify the interspecific relationships among the species of Korean Viola than ISSH and PCR-RFLP analyses.

• KOREAN JOURNAL OF CROP SCIENCE
• /
• v.51 no.3
• /
• pp.259-268
• /
• 2006

Miniature inverted transposable elements (MITEs) are abundant genomic components in plant including rice. MITE-transposon display (MITE-TD) is an Amplified Fragment Length Polymorphism (AFLP)-related technique based on MITE sequence. In this study, we used the MITE-AFLP for the analysis of diversity and relation-ship of the 114 japonica accessions. Of the several MITEs, the mPing family was applied to detect polymorphisms based on PCR amplification. The BfaI adaptor primer and the specific primer derived from mPing terminal inverted repeat (TIR) region were used to PCR amplification of 114 accessions. Nine primer pairs produced a total of 160 polymorphic bands. PIC values of the polymorphic bands generated by nine primer pairs ranged from 0.269 (BfaI + ACT) to 0.426 (BfaI + T). Each accession revealed a distinct fingerprint with two primer combinations, BfaI + G and BfaI + C. Cluster analysis using marker-based genetic similarity classified 114 accessions into five groups. MITE-AFLP markers were genetically mapped using a population of 80 BILs (BC1F7) derived from a cross between the rice accessions, Milyang 23 and Hapcheonaengmi 3. Eight of the markers produced with the primer pair BfaI + 0 were mapped on chromosomes 1, 2, 4, 5, 7, and 9. Considering that one MITE-AFLP marker on chromosome 7 was tightly linked to the Rc gene, the MITE-AFLP markers will be useful for gene tagging and molecular cloning.

• Biomedical Science Letters
• /
• v.19 no.3
• /
• pp.275-279
• /
• 2013

Etiological agents of extended spectrum ${\beta}$-lactamase (ESBL) producing uropathogenic Escherichia coli (UPEC) have become a major problem in urinary tract infections. The purpose of this study was to compare the molecular characteristics of ESBL producing UPEC strains isolated from 1989 and 2010. A total of 301 strains of UPEC clinical isolates was collected from Korean healthcare facility in 1989 (126 strains) and in 2010 (175 strains). UPEC clinical isolates were analyzed by multiplex polymerase chain reaction method (ESBL related bla genes and phylogenetic groups) and amplified fragment length polymorphism (AFLP). Among 301 isolates, ESBL producing UPEC were 8 strains (6.3%) in 1989 isolates and 35 strains (20%) in 2010 isolates. The rate of bla genes in ESBL producing UPEC from 1989 isolates and 2010 isolates were $bla_{TEM}$ (75% and 85.7%), $bla_{CTX-M}$ (0% and 91.4%), $bla_{OXA}$ (25% and 20%), $bla_{PER}$ (0% and 2.9%). The distribution of phylogenetic groups in 1989 isolates and 2010 isolates were A (37.5% and 11.4%), B2 (12.5% and 51.4%), and D (50% and 37.1%). The most prevalent ESBL related bla gene and phylogenetic group were $bla_{CTX-M}$ (91.4%) and B2 (51.4%) in 2010 isolates, while $bla_{CTX-M}$ was not detected in 1989 isolates. Among 43 ESBL producing UPEC were grouped into 12 clusters up to 76% of genetic similarities by AFLP analysis. During past twenty one years, the rate of the ESBL producing UPEC strains in 2010 isolates was increased than that of in 1989 isolates. Also, the most prevalent ESBL related bla gene has been changed from $bla_{TEM}$ to $bla_{CTX-M}$.

• Korean Journal of Microbiology
• /
• v.40 no.3
• /
• pp.244-247
• /
• 2004

To investigate the effects of elevated $CO_2$ on the denitrifying bacterial community structure in a wetland soil, dynamics of bacterial community structure was explored in an artificial wetland ecosystem with one of three plant species (T. latifolia, S. lacustris, and 1. effusus) under two levels of $CO_2$(370 ppm or 740 ppm) after 110day incubation. For the analysis of bacterial community structure, functional genes such as nitrite reductase genes (nirS) were PCR-amplified followed by cloning of PCR products and screening by restriction fragment length polymorphism (RFLP). nirS gene fragments were amplified in all analyzed soil samples. Species richness estimated by the number of distinct phylotypes were 83 and 95 in the ambient $CO_2$ treatment and the elevated treatment, respectively. Two phylotypes (type 1 and type 2) were dominant in both of the treatments. Elevated $CO_2$ treatment increased species richness of denitrifying as well as changed a large proportion of denitrifier phylotypes compared to those of the ambient treatment. Overall, the data in this study suggested that the denitrifying communities in the wetland soil are diverse and that the richness of denitrifying bacterial community might be affected by elevated $CO_2$ treatment.

• Korean Journal of Environment and Ecology
• /
• v.25 no.4
• /
• pp.470-478
• /
• 2011

Aster altaicus var. uchiyamae is on the list of endangered species in Korea. Using amplified fragment length polymorphism (AFLP) markers, we investigated the genetic diversity within and among four populations (Guram, Dori Island, Samhap, and Danyang) of A. altaicus var. uchiyamae. We also present the collecting strategies that most efficiently capture the genetic diversity of A. altaicus var. uchiyamae. Four AFLP primer combinations produced a total of 936 bands, of which 934 (99.8%) were polymorphic. A high level of genetic diversity (PPB = 45.3%, h = 0.104, I = 0.168, hs = 0.108) was recognized within the populations of A. altaicus var. uchiyamae. A low degree of genetic differentiation ($G_{ST}$ = 0.075, ${\theta}^B$ = 0.079) was detected among the populations. In addition, analysis of molecular variance (AMOVA) showed that genetic variation was greater within populations (91%) than among populations (9%). These results indicate that the high rate of gene flow has played an important role in forming the present populations of A. altaicus var. uchiyamae. According to maximization strategy, 17, 16, and 11 individuals captured all of the genetic variation in Dori Island, Samhap, and Guram population, respectively. The determination the minimum population size of A. altaicus var. uchiyamae in terms of the genetic information is critical and thereby gain reliable decision support for ex situ conservation of the endangered species, A. altaicus var. uchiyamae.

• Korean Journal of Ecology and Environment
• /
• v.41 no.1
• /
• pp.98-103
• /
• 2008

Genetic diversity and population genetic structure within or among three stream populations (Gab, Baekgok and Ji streams) of Korean endangered natural monument fish, Iksookimia choii, were assessed by amplified fragment length polymorphism (AFLP). AFLP analysis using three primer combinations generated 104 to 106 AFLP bands, and percent polymorphic bands were similar in those three populations ranging 21.5 to 24.5%. Heterozygosity and genetic diversity within or among populations were quite low for all of these populations with average values ranging from 0.067 to 0.084 and from 0.076 to 0.087, respectively. Analyses of pairwise distance and genetic similarity among three populations of I. choii also revealed the similar results with very low genetic differentiation one another. Although pairwise Fst values were very low, our data clearly indicated distinct genetic differentiation among the three populations. This is the first report concerning the genetic diversity and differentiation of this species, and provides basic genetic information that should facilitate attempts to conserve this species.

• Korean Journal of Plant Taxonomy
• /
• v.39 no.2
• /
• pp.63-73
• /
• 2009

$Iso{\ddot{e}}tes$ L. ($Iso{\ddot{e}}taceae$) is difficult to identify among the infrageneric taxa because of morphological simplicity. Since two species (I. japonica and I. coreana) had been reported, I. jejuensis and I. hallasanensis were described as two new species from Jeju Island, South Korea. The habitats of all species were confirmed by current studies except for I. japonica. We compared the morphological and anatomical characters of seven species, three domestic species and four species in adjacent regions (I. taiwanensis, I. sinensis, I. japonica, and I. asiatica). I. asiatica differs from other species in the lobe number of corm, spreading sporophylls, lack of stomata and degree of velum development. All of the seven species were identified by the characteristics of their mega- and microspores. Especially, it was possible to identify the four species in South Korea by the types of ornamentation on their megaspores. Each species has a specific type of megaspore ornamentation: I. coreana - cristate, I. jejuensis - rugulate, I. hallasanensis - echinate, and I. japonica - reticulate. We also discussed the phylogeny of the genus in East Asia in relation to recent studies based on the second intron of LEAFY sequence and amplified fragment length polymorphism (AFLP) analysis. We suggest strategies for the conservation of the endangered $Iso{\ddot{e}}tes$ species in South Korea.

• Asian-Australasian Journal of Animal Sciences
• /
• v.25 no.7
• /
• pp.1045-1054
• /
• 2012

The phylogenetic diversity of the bacteria in hot composting samples collected from three spatial locations was investigated by molecular tools in order to determine the influence of gradient effect on bacterial communities during the thermophilic phase of composting swine manure with rice straw. Total microbial DNA was extracted and bacterial near full-length 16S rRNA genes were subsequently amplified, cloned, restriction fragment length polymorphism-screened and sequenced. The superstratum sample had the highest microbial diversity among the three samples which was possibly related to the surrounding conditions of the sample resulting from the location. The results showed that the sequences related to Bacillus sp. were most common in the composts. In superstratum sample, 45 clones (33%) and 36 clones (27%) were affiliated with the Bacillus sp. and Clostridium sp., respectively; 74 clones (58%) were affiliated with the Clostridium sp. in the middle-level sample; 52 clones (40%) and 29 clones (23%) were affiliated with the Clostridium sp. and Bacillus sp. in substrate sample, respectively. It indicated that the microbial diversity and community in the samples were different for each sampling site, and different locations of the same pile often contained distinct and different microbial communities.