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

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.6
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• pp.2747-2751
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• 2014

Background: DNA repair pathways play a crucial role in maintaining the human genome. Previous studies associated DNA repair gene polymorphisms (XPD Lys751Gln, XRCC1 Arg280His and XRCC1 Arg399Gln) with nasopharyngeal carcinoma. These non-synonymous polymorphisms may alter DNA repair capacity and thus increase or decrease susceptibility. The present study aimed to determine the genotype distribution of XPD codon 751, XRCC1 codon 280 and codon 399 polymorphisms and haplotype associations among NPC cases and controls in the Malaysian population. Materials and Methods: We selected 157 NPC cases and 136 controls from two hospitals in Kuala Lumpur, Malaysia for this study. The polymorphisms studied were genotyped by PCR-RFLP assay and allele and genotype frequenci es, haplotype and linkage disequilibrium were determined using SNPstat software. Results: For the XPD Lys751Gln polymorphism, the frequency of the Lys allele was higher in cases than in controls (94.5% versus 85.0%). For the XRCC1 Arg280His polymorphism, the frequency of Arg allele was 90.0% and 89.0% in cases and controls, respectively and for XRCC1 Arg399Gln the frequency of the Arg allele was 72.0% and 72.8% in cases and controls respectively. All three polymorphisms were in linkage disequilibrium. The odds ratio from haplotype analysis for these three polymorphisms and their association with NPC was 1.93 (95%CI: 0.90-4.16) for haplotype CGC vs AGC allele combinations. The global haplotypte association with NPC gave a p-value of 0.054. Conclusions: Our study provides an estimate of allele and genotype frequencies of XRCC1Arg280His, XRCC1 Arg399Gln and XPD Lys751Gln polymorphisms in the Malaysian population and showed no association with nasopharyngeal cancer.

• Korean Journal of Plant Taxonomy
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• v.45 no.3
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• pp.213-220
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• 2015

To elucidate the origin and patterns of establishment of insular plants on Ulleungdo Island, maternally inherited chloroplast DNA, which is useful for tracing seed movements, was used. Fagus multinervis, an endemic species that dominated broadleaf deciduous forests on Ulleungdo Island, is an excellent model for such a study. To understand the diversity and spatial distribution of the chloroplast haplotypes of F. multinervis, nucleotide sequences of the psbA-trnH region were determined from 144 individuals sampled throughout the island. Results of a phylogenetic analysis of the region with close relatives of F. multinervis suggest that F. multinervis is sister to a clade of F. japonica and F. engleriana. No haplotype variation was found within F. multinervis. This remarkably low cpDNA haplotype diversity is in contrast to the findings of previous allozyme studies of F. multinervis populations that showed high genetic diversity on Ulleungdo Island. Repeated colonization during the early stage of establishment via birds that migrated from a source area where the F. multinervis cpDNA haplotype was geographically structured may have resulted in the observed pattern of haplotype diversity. Alternatively, long-distance dispersal of seeds of the progenitor of F. multinervis via birds or typhoons to Ulleungdo may have been a single event, whereas the immigration of pollen from the mainland likely occurred frequently. Comparative phylogeographic studies of other species endemic to Ulleungdo Island and their close relatives on the neighboring mainland are necessary for a more complete understanding of the evolution of the island's native species.

• Journal of Korean Society of Forest Science
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• v.94 no.3 s.160
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• pp.178-182
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• 2005

To identify the seedlings from controlled pollination between one paternal tree and three maternal trees of Japanese red pine, cpSSR markers of the paternally inherited haploid genome were analyzed in two year old 114 seedlings of full sib families. Individual specific DNA fingerprint like haplotypes of the parental trees were determined by PCR with three cpSSR primers. Haplotypes of the 114 seedlings were also identified by PCR with the same primers. On the basis of the comparison of cpDNA haplotypes of the 114 seedlings with those of the parental trees, 14 seedlings revealed to have distinguished haplotypes from those of the paternal tree. It was tentatively concluded that they were generated via pollination with the non-paternal trees. A seedling of Gangwon30 revealing non-paternal haplotype might have been generated via self pollination with the pollens of maternal tree through improper emasculation or contamination during artificial pollination. DNA fingerprint like cpSSR profiles observed in this study could be successfully applied to the various plant forensic analyses, such as identification of siblings of individual trees, asexually reproduced ramets of a specific clone, vegetatively propagated individuals via tissue culture, and pure full sib progenies.

• Journal of Life Science
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• v.19 no.6
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• pp.711-719
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• 2009

We determined a portion of mitochondrial 16S rRNA gene sequences (416 bp) to investigate the genetic structure of the octopus (Octopus minor Ssaki) population in Korea and China. Samples were obtained from Korea (Yeosu, Namhae, Jindo, Muan, Geomundo and Seosan) and China (Sandong) during the period of August 2006 to September 2007. Sequence analyses of 28 individual specimens collected from 7 localities revealed 11 haplotypes, ranging in a sequence divergence of 0.2% - 1.2%. Phylogenetic analyses using PHYLIP and networks subdivided the octopus into two clades (termed clade A and B) and the nucleotide divergence between them was 0.4%. This haplotype subdivision was in accordance with geographic separation: one at Yeosu, Namhae, Muan and Jindo, and the other at Seosan, Geomundo and Sandong. On the basis of hierarchial genetic analysis, genetic distance between localities in Korea and China were also found, but a significant population differentiation was not shown in this study (p>0.05). Consequently, most of the octopus populations in Korea had considerable distribution due to the mitochondrial gene flow that resulted in a formation of a genetically homogenous structure, whereas some of the Korean and Chinese populations had different genetic structures. Gene flow among populations may be restricted due to impassable geographic barriers that promote genetic differentiation.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.18 no.3
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• pp.131-141
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• 2013

Stock identification of Todarodes pacificus collected in the East Sea, Yellow Sea and East China Sea during the period from September to December in 2011 was analyzed by morphometric characters and mitochondrial DNA (mtDNA) cytochrome oxidase subunit I (COI) gene nucleotide variations. Frequency distributions of mantle length was analyzed by morphological method with measuring size of T. pacificus. Then each stock was estimated to confirm their maturation for mean mantle length comparing with mean mature mantle length 20-22 cm. According to morphologic stock identification, it is estimated that the northern part of East Sea is categorized as summer stock and the rest parts, including mid /southern part of the East Sea, northern part of the East China Sea and northern part of the West Sea were autumn stock. For genetic analysis, a total 49 haplotypes were defined by 33 variable nucleotide sites. From the extensive haplotype diversity, limited nucleotide diversity and star-like shape of haplotype network, T. pacificus appears to have undergone rapid population expansion from an ancestral population with a small effective population size. Although pair-wise Fst estimates which represent genetic difference among groups were low, there are relatively remarkable difference of Fst between middle and southern part of the East Sea. Although middle part of the East Sea and southern part of the East Sea were situated at the East Sea, genetically separated groups were appeared.

• Journal of Animal Science and Technology
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• v.54 no.4
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• pp.241-246
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• 2012

The goal of this study was to verify the phylogenetic status of the Korean native goats (KNG). We determined the complete sequence of the mitochondrial cytochrome b gene in 48 goats among four populations. We also analyzed genetic variability within goats, and a phylogenetic analysis was performed by comparison with other country's goats. Three nucleotide substitutions were detected, and two of these were missense mutations that occurred due to a substitution of amino acid. Four haplotypes were defined from KNG. Three of these haplotypes were only found in the Chinese goat. However, the other haplotype was KNG-specific. In the phylogenetic analysis, four clades (A~D) were classified among domestic goats, and the KNG was classified into clade 1 that estimated as lineage A based on the D-loop sequence. Each haplotype from the KNG was clustered closely with that of the Chinese goat. The results of haplotype distribution and phylogenetic location suggest that strong gene flow occurred from China to the Korean Peninsula.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.28 no.5
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• pp.649-658
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• 1995

In order to estimate the level of genetic differences among the pleuronectid species, mitochondrial DNAs were isolated from four species: brown sole, Limanda herensteini; marbled sole, Limanda Yokohamae; stone flounder, Kareius bicoloratus; starry flounder, Platichthys stellatus, and the number of nucleotide substitutions was calculated by the restriction fragment length polymorphisms (RFIPs) generated by f4 sin base recognition restriction endonucleases. Total lengths of the mitochondrial DNA were measured as about 17.6 kbp in all species. Ten different composite genotypes were observed in brown sole, four different genotypes in marbled sole, and two different genotypes in starry flounder. However, only one genotype was observed in stone flounder. The calculated haplotypic diversity value of brown sole was higher than that of marbled sole. The average number of nucleotide substitutions per sites in four species was estimated to be 0.0045 in the intraspecies, 0.0344 in the interspecies, and 0.0457 in the genera, respectively. From these results, we could estimate that the genetic differences among interspecies were not influenced by nucleotide substitutions but genetical discontinuous.

• Proceedings of the Korean Society of Crop Science Conference
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• 2021.04a
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• pp.119-119
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• 2021

• Molecules and Cells
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• v.25 no.1
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• pp.20-29
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• 2008

Cytoplasmic male sterility (CMS), one of the most important traits in crop breeding, has been used for commercial seed production by $F_1$ hybrid cultivars of pepper (Capsicum annuum L.). To develop reliable molecular markers for allelic selection of the Restorer-of-fertility (Rf) gene, which is known to be a major determinant of pollen fertility restoration in peppers, a sequence of approximately 10 kb flanking an RAPD fragment closely linked to the Rf locus was obtained by genome walking. A homology search revealed that this sequence contained an LTR retrotransposon and a non-LTR LINE-like retrotransposon. Sequencing of this Rf-linked region to search for polymorphisms between a dominant and recessive allele revealed 98% nucleotide sequence identity between them. A third polymorphic haplotype of the Rf-linked sequence, which has 94-96% nucleotide sequence identity with the two previously isolated haplotypes, was identified among a large number of breeding lines. Utilizing polymorphic sequences in the haplotypes, PCR markers were developed for selection of particular haplotypes and used to examine the distribution of the haplotypes in diverse breeding lines, cultivars, and C. annuum germplasms. Surprisingly, the third haplotype was the predominant type in C. annuum germplasms, while its frequency in $F_1$ hybrid cultivars was relatively low. Meanwhile, analysis of breeding lines whose Rf allele genotypes and male-sterility phenotypes were already known revealed that the third haplotype was mainly present in exotic breeding lines that cause unstable male-sterility when combined with sterile cytoplasms.