• Molecules and Cells
• /
• 제25권1호
• /
• pp.20-29
• /
• 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.

• Parasites, Hosts and Diseases
• /
• 제51권4호
• /
• pp.401-412
• /
• 2013

Because of an increased number of Acanthamoeba keratitis (AK) along with associated disease burdens, medical professionals have become more aware of this pathogen in recent years. In this study, by analyzing both the nuclear 18S small subunit ribosomal RNA (18S rRNA) and mitochondrial 16S rRNA gene loci, 27 clinical Acanthamoeba strains that caused AK in Japan were classified into 3 genotypes, T3 (3 strains), T4 (23 strains), and T5 (one strain). Most haplotypes were identical to the reference haplotypes reported from all over the world, and thus no specificity of the haplotype distribution in Japan was found. The T4 sub-genotype analysis using the 16S rRNA gene locus also revealed a clear subconformation within the T4 cluster, and lead to the recognition of a new sub-genotype T4i, in addition to the previously reported sub-genotypes T4a-T4h. Furthermore, 9 out of 23 strains in the T4 genotype were identified to a specific haplotype (AF479533), which seems to be a causal haplotype of AK. While heterozygous nuclear haplotypes were observed from 2 strains, the mitochondrial haplotypes were homozygous as T4 genotype in the both strains, and suggested a possibility of nuclear hybridization (mating reproduction) between different strains in Acanthamoeba. The nuclear 18S rRNA gene and mitochondrial 16S rRNA gene loci of Acanthamoeba spp. possess different unique characteristics usable for the genotyping analyses, and those specific features could contribute to the establishment of molecular taxonomy for the species complex of Acanthamoeba.

• The Korean Journal of Physiology and Pharmacology
• /
• 제21권1호
• /
• pp.11-17
• /
• 2017

Crohn's disease (CD) is a chronic inflammatory bowel disease with multifactorial causes including environmental and genetic factors. Several studies have demonstrated that the organic cation/carnitine transporter 1 (OCTN1) non-synonymous variant L503F is associated with susceptibility to CD. However, it was reported that L503F is absent in Asian populations. Previously, we identified and functionally characterized genetic variants of the OCTN1 promoter region in Koreans. In that study, four variants demonstrated significant changes in promoter activity. In the present study, we determined whether four functional variants of the OCTN1 promoter play a role in the susceptibility to or clinical course of CD in Koreans. To examine it, the frequencies of the four variants of the OCTN1 promoter were determined by genotyping using DNA samples from 194 patients with CD and 287 healthy controls. Then, associations between genetic variants and the susceptibility to CD or clinical course of CD were evaluated. We found that susceptibility to CD was not associated with OCTN1 functional promoter variants or haplotypes showing altered promoter activities in in vitro assays. However, OCTN1 functional promoter haplotypes showing decreased promoter activities were significantly associated with a penetrating behavior in CD patients (HR=2.428, p=0.009). Our results suggest that the OCTN1 functional promoter haplotypes can influence the CD phenotype, although these might not be associated with susceptibility to this disease.

• 응용통계연구
• /
• 제18권2호
• /
• pp.297-310
• /
• 2005

본 연구에서는 강화연구(서일, 2004)를 통해 수집된 277명의 환자-대조군 자료와 40개의 가계 자료를 이용하여 ACE(angiotensin-I converting enzyme) 유전자 내에 있는 4개의 단일염기다형성(single nucleotide polymorphism; SNP)으로 이루어진 일배체형(haplotype)과 고혈압의 관련성을 알아보고자 한다. 이를 위해 일배체형에 기초한 환자-대조군의 우도비 검정과 가계 자료의 TDT(transmission/disequilibrium test) 연구를 수행하고자 한다. 또한 이 일배체형을 동정(identification)할 수 있는 tag-SNPs에 기초하여 동일한 연구를 하고자 하며, Seltman 등(2003)이 제안한 분기도(cladogram) 분석 방법을 써서 일배체형의 진화 과정에서 가깝게 위치하고 질병 발생 위험이 비슷한 클레이드(clade)를 찾아내고 이 클레이드와 고혈압의 연관성을 살펴보고자 한다.

• International Journal of Industrial Entomology and Biomaterials
• /
• 제35권1호
• /
• pp.51-57
• /
• 2017

The tiny dragonfly, Nannophya pygmaea (Odonata: Libellulidae), is an endangered insect in South Korea. Previously, a partial mitochondrial DNA sequence that corresponded to a DNA barcoding region has been used to infer genetic diversity and gene flow. In this study, we additionally sequenced the barcoding region from N. pygmaea that had been collected from three previously sampled populations (40 individuals) and these sequences were combined with the preexisting data. We also selected and sequenced an additional mitochondrial gene (ND5) to find further variable gene regions in the mitochondrial genome. DNA barcoding sequences of 108 individuals from five South Korean localities showed that genetic diversity was highest in Gangjin, Jeollanam-do Province. Muuido, which was previously occupied by a single haplotype, was also found to have an identical haplotype, which confirmed the low genetic diversity on this islet. Gene flow among populations is highly limited, and no clear distance- or region-based geographic partitioning was observed. Phylogenetic relationships among haplotypes showed that there were no discernable haplotypes in South Korea. ND5 provided slightly more haplotypes compared to the barcoding region in 40 individuals (14 vs. 10 haplotypes in the COI gene). It also had a slightly higher within-locality diversity estimate, which suggested that ND5 had potential as mitochondrial DNA-based marker for population genetic analysis.

• 한국가금학회지
• /
• 제39권4호
• /
• pp.311-315
• /
• 2012

The increasing demand for Korean native chicken meat indicates that the discovery of haplotypes is very important from both economic and conservation points of view. In this study, mtDNA D-loop sequences from two crossbred Korean native chicken populations of 138 individuals were investigated. Twenty six nucleotide substitutions were identified from sequence analysis and were classified into 12 haplotypes. The haplotype H_8 represents 73.47% of Woorimatdag (chicken population) sequences, which were identified in all five Woorimatdag chicken populations investigated. The H_7 haplotype (Dhap1) for D population covers 45% sequences, which indicate maternal inheritance from black Korean native chicken. On the other hand, Chap3 and Chap4 for C population are specific haplotypes, as H_5 and H_2, respectively. Based on the network profiles, six SNPs (C199T, A239G, G242A, A291G, T330C and C391A) of the D-loop region are effective markers for discrimination between Woorimatdag and Hanhyup chicken populations. Also, the phylogenetic analyses of Woorimatdag and Hanhyup chicken populations were used to identify the genetic relationships among the haplotypes. The results presented here can be used for developing molecular markers to discriminate between two commercial Korean native chickens.

• Asian-Australasian Journal of Animal Sciences
• /
• 제31권10호
• /
• pp.1558-1564
• /
• 2018

Objective: We report monitoring conservation effect for a Chinese indigenous chicken (Langshan) breed using major histocompatibility complex (MHC) and DNA barcords. Methods: The full length of MHC B-G gene and mitochondrial cytochrome oxidase I (COI) gene in generations 0, 5, 10, 15, 16, and 17 was measured using re-sequencing and sequencing procedures, respectively. Results: There were 292 single nucleotide polymorphisms of MHC B-G gene identified in six generations. Heterozygosity (He) and polymorphic information content (PIC) of MHC B-G gene in generations 10, 15, 16, and 17 remained stable. He and PIC of MHC B-G gene were different in six generations, with G10, G15, G16, G17 >G5>G0 (p<0.05). For the COI gene, there were five haplotypes in generations 0, 5, 10, 15, 16, and 17. Where Hap2 and Hap4 were the shared haplotypes, 164 individuals shared Hap2 haplotypes, while Hap1 and Hap3 were the shared haplotypes in generations 0 and 5 and Hap5 was a shared haplotype in generations 10, 15, 16, and 17. The sequence of COI gene in 6 generations was tested by Tajima's and D value, and the results were not significant, which were consistent with neutral mutation. There were no differences in generations 10, 15, 16, and 17for measured phenotypic traits. In other generations, for annual egg production, with G5, G10, G15, G16, G17>G0 (p<0.05). For age at the first egg and age at sexual maturity, with G10, G15, G16, G17>G5>G0 (p<0.05). Conclusion: Combined with the results of COI gene DNA barcodes, MHC B-G gene, and phenotypic traits we can see that genetic diversity remained stable from generations 10 to 17 and the equimultiple random matching pedigrees conservation population conservation effect of Langshan chicken was effective as measured by these criteria.

• International Journal of Industrial Entomology and Biomaterials
• /
• 제14권2호
• /
• pp.107-112
• /
• 2007

The mole crickets, Gryllotalpa, are insect pest distributed in the world. In Korea, G. orientalis was reported to occur, but previous ecological studies suggested the presence of two ecological types. To test this hypothesis, we sequenced a portion of mitochondrial (mt) genome from 48 G. orientali individuals collected over five Korean localities: Busan, Suwon, Okchon, Wonju, and Gangneung. From the sequence analysis, only two haplotypes were obtained, but the sequence divergence between the two haplotypes was 11 %, suggesting the presence of two distinct genetic groups in Korea. Although the population of Busan, Okchon, Wonju, and Gangneung was identified as a single haplotype, but that of Suwon was occupied by both hapotypes. Considering sequence divergence of other insect species occurring in Korea, the divergence estimate found between the two haplotypes seems to be too large to be considered as identical species. This result may suggest that the two differentiated haplotypes found in this study may reflect the previously reported two ecological types found in Suwon, Korea. To further understand the genetic divergence of the two phylogenetic groups, analysis of more variable regions of G. orientalis genome is required.

• 한국육종학회지
• /
• 제41권4호
• /
• pp.397-402
• /
• 2009

Self-incompatibility (SI) prevents self-fertilization by inhibiting the pollen tube growth of self-pollen. Molecular analysis has revealed that the S locus comprises a number of genes, such as the S-locus glycoprotein (SLG), the S-locus receptor kinase (SRK), and SP11 (SCR). Although molecular markers related to those genes have been developed, a simple S-haplotype detecting method has not been reported due to the highly polymorphic and relatively small coding regions. In this study, the sequence characterized amplified region (SCAR) markers were used to establish an efficient radish genotyping method. We identified the S-haplotypes of 192 radish accessions using 19 different markers, which proved to be highly reliable. The accessions were assigned to 17 types of S-haplotypes, including 8 types of SRKs and 9 types of SLGs. Since the developed SCAR markers are based on their gene sequences, we could easily identify the S-haplotypes by a single specific band, with the highest frequencies detected for SLG 5, SRK 1, and SLG 1, in order. Among the tested markers, the SLG 1, SRK 1, and SRK 5 markers exhibited high reliability, compared to phenotypic results. Furthermore, we identified the seven types of unreported SLGs using SLG Class -I and -II specific markers. Although the developed SCAR markers still need to be improved for the genotyping of all S-haplotypes, these markers could be helpful for monitoring inbred lines, and for developing the MAS in radish breeding programs.

• Parasites, Hosts and Diseases
• /
• 제58권6호
• /
• pp.661-668
• /
• 2020

In Europe, 5 Lipoptena species have been recorded, including Lipoptena fortisetosa. This species, native to Asian countries, was described as a parasite of sika deer and its appearance in Europe dates back to more than 50 years ago. Lipoptena fortisetosa has been recently reported in Italy, sharing its hosts with Lipoptena cervi. A morpho-molecular approach was developed to determine the phylogenetic interrelationship of Italian and Asian CO1 haplotypes sequenced from Lipoptena fly individuals collected in Italy, and their DNA sequences were compared with conspecifics available in GenBank; morphological key-characters (terminalia) of L. fortisetosa were compared with the original description. Two haplotypes were recorded from Italy and assigned to L. cervi and L. fortisetosa, respectively. The latter was part of the monophyletic clade L. fortisetosa, along with 2 Central European and 2 Korean haplotypes (100% identical to one of the Korean haplotypes); moreover, Italian L. fortisetosa female terminalia were consistent with the original description of Asian individuals. Pending more in-depth investigations, this study provides a first answer to the hypothesis of the recent colonization of Italy by L. fortisetosa from Asia as we did not detect any obvious and stable morphological and molecular differences in specimens from the 2 geographical areas. The presence of the sika deer in Europe was retraced and the possible route traveled by the parasite from Asia and the eco-biological factors that may have enhanced its settlement are discussed.