Showing papers in "Genes & Genomics in 2009"

Analysis of genetic diversity and population structure of rice cultivars from Korea, China, and Japan using SSR markers

Abstract: A total of 29 simple sequence repeat (SSR) markers were used to analyze the genetic diversity of 150 accessions of cultivated rice (Oryza sativa L.) from Korea, China, and Japan. A total of 375 alleles were detected with an average of 12.9 per locus. The averaged values of gene diversity and polymorphism information content (PIC) for each SSR locus were 0.7001 and 0.6683, respectively. Alleles per locus in Korean rice were 8.8, whereas 8.1 and 7.2 alleles per locus were found in Chinese and Japanese rice, respectively. The mean gene diversity in Korean, Chinese, and Japanese rice was 0.6058, 0.6457, and 0.5174, respectively, whereas the mean PIC values for each SSR locus were 0.5759, 0.6138, and 0.4881, respectively. The genetic diversity of the Korean and Chinese cultivars was higher than that of the Japanese cultivars, and the genetic diversity ofjaponica was higher than that ofindica. The model-based structure analysis revealed the presence of three subpopulations, which was basically consistent with clustering based on genetic distance. An AMOVA analysis showed that the between-population component of genetic variance was less than 22% in contrast to 78% for the within-population component. The overallFST value was 0.2180, indicating a moderate differentiation among groups. The results could be used for designing effective breeding programs aimed at broadening the genetic bases of commercially grown varieties.

A genetic linkage map construction for sesame (Sesamum indicum L.)

Abstract: Sesame (Sesamum indicum L.) is one of the oldest oilseed crops with high seed oil quality. The first sesame genetic linkage map based on F2 segregating population of an intraspecific cross between two cultivars was constructed. Using three types of PCR-based markers, 284 polymorphic loci including 10 EST-SSR marker, 30 AFLP marker and 244 RSAMPL marker, respectively, had been screened. Subsequently, a total of 220 molecular markers were mapped in 30 linkage groups covering a genetic length of 936.72 cM, and the average distance between markers was 4.93 cM. In this map, the linkage groups contained from 2 to 33 loci each and ranged in distance from 6.44 cM to 74.52 cM. Based on map information, sesame genome length was estimated to be approximately 1,232.53 cM, and genome coverage of this map was about 76.0%. As a starting point of sesame genome study, the genetic linkage map will be hopeful to tag traits of breeding interest and further aid in the sesame molecular breeding. Furthermore, RSAMPL marker had been also appreciated in this paper, for its first usage in genetic map construction and higher utilization potential in some crop species lacking much genome information.

QTLs of cold tolerance-related traits at the booting stage for NIL-RILs in rice revealed by SSR

Abstract: QTLs for cold tolerance-related traits at the booting stage using balanced population for 1525 recombinant inbred lines of near-isogenic lines (viz.NIL-RILs for BC5F3 and BC5F4 and BC5F5) over 3 years and two locations by backcrossing the strongly cold-tolerant landrace (Kunmingxiaobaigu) and a cold-sensitive cultivar (Towada) was analyzed. In this study, 676 microsatellite markers were employed to identify QTLs conferring cold tolerance at booting stage. Single marker analysis revealed that 12 markers associated with cold tolerance on chromosome 1, 4 and 5. Using a LOD significance threshold of 3.0,compositive interval mapping based on a mixed linear model revealed eight QTLs for 10 cold tolerance-related traits on chromosomes 1, 4, and 5. They were tentatively designatedqCTB-1-1, qCTB-4-1, qCTB-4-2, qCTB-4-3, qCTB-4-4, qCTB-4-5, qCTB-4-6, andqCTB-5-1. The marker intervals of them were narrowed to 0.3-6.8 cM. Genetic distances between the peaks of the QTL and nearest markers varied from 0 to 0.04 cM. We were noticed in some traits associated cold tolerance, such asqCTB-1-1 for 5 traits (plant height, panicle exsertion, spike length, blighted grains per spike and spikelet fertility),qCTB-4-1 for 8 traits (plant height, node length under spike, leaf length, leaf width, spike length, full grains per spike, total grains per spike and spikelet fertility),qCTB-4-2 for 3 traits (spike length, full grains per spike and spikelet fertility),qCTB-5-1 for 5 traits (plant height, panicle exsertion, blighted grains per spike, full grains per spike and spikelet fertility). The variance explained by a single QTL ranged from 0.80 to 16.80%. Three QTLs (qCTB-1-1, qCTB-4-1, qCTB-4-2) were detected in two or more trials. Our study sets a foundation for cloning cold-tolerance genes and provides opportunities to understand the mechanism of cold tolerance at the booting stage.

Comparison of base composition and codon usage in insect mitochondrial genomes

Abstract: Insects, the most biodiverse taxonomic group, have high AT content in their mitochondrial genomes. Although codon usage tends to be AT-rich, base composition and codon usage of mitochondrial genomes may vary among taxa. Thus, we compare base composition and codon usage patterns of 49 insect mitochondrial genomes. For protein coding genes, AT content is as high as 80% in the Hymenoptera and Lepidoptera and as low as 72% in the Orthopotera. The AT content is high at positions 1 and 3, but A content is low at position 2. A close correlation occurs between codon usage and tRNA abundance in nuclear genomes. Optimal codons can pair well with the antr codons of the most abundant tRNAs. One tRNA gene translates a synonymous codon family in vertebrate mitochondrial genomes and these tRNA anticodons can pair with optimal codons. However, optimal codons cannot pair with anticodons in mtDNA ofCochiiomyia hominivorax (Dipteral: CaLliphoridae). Ten optimal codons cannot pair with tRNA anticodons in all 49 insect mitochondrial genomes; non-optimal codon-anticodon usage is common and codon usage is not influenced by tRNA abundance.

Assessment of Genetic Variation among Commercial Tomato (Solanum lycopersicum L.) Varieties Using SSR Markers and Morphological Characteristics

Abstract: Simple sequence repeats (SSR) is one of the most suitable markers for variety identification as it has great discrimination power for varieties with limited genetic variation. Genetic characterization of commercial tomato varieties was investigated using 33 SSR markers and 22 morphological traits. Thirty three SSR primer pairs were screened for 63 tomato varieties. A total of 132 polymorphic amplified fragments were obtained by using 33 SSR markers. The average polymorphism information content (PIC) was 0.628 ranging from 0.210 to 0.880. One hundred thirty two SSR loci were used to calculate Jaccard's distance coefficients for UPGMA cluster analysis. A clustering group of varieties, based on the results of SSR analysis, were categorized into cherry and classic fruit type varieties. Almost all of the varieties were discriminated by SSR marker genotypes. The relationship between morphological and molecular data for 33 varieties out of 63 varieties was analyzed using Mantel matrix correspondence test. The correlation value between two methods was 0.644. However, SSR based dendrogram topology showed some similar form with morphological traits at the two main groups. Therefore, these markers may be used wide range of practical application in variety identification and pre-screening for distinctiveness test of tomato varieties.

Regulatory mechanisms of polyamine biosynthesis in plants

Abstract: Polyamines are small positively charged molecules with a widespread presence in all living organisms. In plants they modulate several aspects of growth and differentiation, and they also participate in the response to abiotic stress. Here we review the molecular mechanisms involved in the regulation of polyamine biosynthesis, which is exerted at different levels including gene expression, protein synthesis, and formation of multienzyme complexes. The importance of polyamines both in development and in stress resistance is also subtended by the phenotype of loss-of-function mutants and of overexpressing lines affecting the different genes that encode polyamine metabolism enzymes.

Molecular Characterization and Physico-Chemical Analysis of a New Giant Embryo Mutant Allele (get) in Rice (Oryza sativa L.)

Abstract: The rice embryo is rich in lipid and protein bodies, bioactive chemicals such as dietary fiber, phytic acids, vitamin B and E, and gamma aminobutyric acid (GABA) than the endosperm. In this paper, we report a new giant embryo mutant,get, induced from somaclonal variation derived by anther culture in rice. Sequence analysis of Cytochrome P450 of the get mutant revealed thatget is a new allele of theGE gene with a single point mutation with substitution of amino acid, W395 to L395. The weight of theget mutant embryo was 3.7 times higher than normal embryo. Tocopherol and mineral content were also higher than the previously reported giant embryo rice variety, Keunnun. These results indicated that this new giant embryo rice (get) offers a promising source of genetic material in improving nutritional quality of rice especially tocopherol, essential minerals, and GABA.

Population genetic structure of three major river Populations of rohu,Labeo rohita (Cyprinidae: Cypriniformes) using microsatellite DNA markers

Abstract: Determining the genetic structure is essential for developing conservation and stock improvement plans. Four dinucleotide microsatellite loci were analysed to reveal population genetic structure of the Indian major carp,Labeo rohita collected from three major rivers namely the Halda, the Jamuna, and the Padma in Bangladesh. The four loci were polymorphic (P 95) in all the populations. The populations varied in the number and frequencies of alleles as well as heterozygosities in the loci analyzed. Population differentiation (F ST) value between the Halda and the Jamuna population was significant (P<0.05). Relatively high level of gene flow and low level ofF ST values were found between the Padma and the Jamuna population. The unweighted pair group method with averages (UPGMA) dendrogram based on genetic distance resulted in two clusters: the Halda population was alone in one cluster whereas the Jamuna and the Padma made another cluster. The results revealed a relatively low level of genetic variability in the river populations ofL. rohita in Bangladesh.

Mitochondrial genome of the eurasian otterLutra lutra (Mammalia, Carnivora, Mustelidae)

Abstract: We determined the complete mitochondrial genome of the Eurasian otterLutra lutra, which is an endangered species in Korea. The circle genome (16,536 bp in size) consists of 13 protein-coding, 22 tRNA, and 2 rRNA genes, and a control region, as found in other metazoan animals. Out of the 37 genes, 28 are encoded on the H-strand, and the nine (ND6 and 8 tRNA genes) on the L-strand. Three overlaps among the 13 protein-coding genes were found: ATP8-ATP6, ND4L-ND4, and ND5-ND6. A control region (1090 bp) including the origin of H-strand replication (OH), TAS (a conserved motif TACAT-16bp-ATGTA) and CSB (CSB-1, CSB-2. and CSB-3) was observed between tRNA-Pro and tRNA-Phe genes, and OL, with 36 highly conserved nucleotides between tRNA-Asn (N) and tRNA-Cys (C) within a cluster of five tRNA genes (WANCY), as typically found in vertebrates. The other important characteristics of theL. lutra mitochondrial genome were described in detail. In addition, a maximum likelihood and Bayesian trees of 9 mustelid species and 1 outgroup were reconstructed based on the nucleotide sequences of 11 protein-coding genes excluding ATP8 and ND6. It showed that Lutrinae formed a monophyletic group with Mustelinae that is not monophyletic. Within the subfamily Lutrinae,L. lutra andEnhydra lutris were grouped together and thenLontra canadentis placed as a sister of the clade. The present result is the first complete mitochondrial genome sequence reported from the genusLutra, and is applicable to molecular phylogenetic, phylogeographic, conservation biological studies for mustelid members. In particular, exploration of sequence variations of the control region may be helpful for analyzing inter-and intra-species variations in the genusLutra.

Sequence diversity at cytochrome oxidase 1 (Co-1) gene among sculpins (Scorpaeniformes, Cottidae) and some other scorpionfish of Russia Far East with phylogenetic and taxonomic insights

Abstract: Mitochondrial DNA (mtDNA) atCo-1 gene region was sequenced for 7 scorpion fish species (in total, 16 sequences of at least 552 bp) from the Far East of Russia and compared with 15 other sequences of Scorpaeniformes comprising altogether 29 scorpion-like fish sequences and two outgroup sequences (Cypriniformes). The analysis of the protein-codingCo-1 gene revealed statistically substantiated bias in the (T+C) ∶ (A+G) content, proving basic findings. The average scores ofp-distances for different scales of the evolutionary history atCo-1 gene revealed a clear pattern of increased nucleotide diversity at four different levels: (1) intraspecies, (2) intragenus, (3) intrafamily, and (4) intraorder. The scores of averagep-distances for the compared fish groups were: (1) 1.00±0.20%, (2) 3.80±0.20%, (3) 12.40±1.20%, and (4) 18.00±0.38%, respectively (mean±SE). These data support the concept that speciation in the order Scorpaeniformes, in most cases, follows a geographic mode through accumulation of numerous small genetic changes over a long period of time. However, intraspecies diversity was surprisingly high among scorpionfish. Phylogenetic trees for 29 sequences of scorpionfish and 2 other fishes belonging to ray-finned fishes (Actinopterigii) were developed usingCo-1 gene and four different analytical approaches: Bayesian (BA), maximum likelihood (ML), neighbour-joining (NJ), and maximum parsimony (MP). The analysis revealed a monophyletic origin for the representatives of Cottidae, which is the principal scorpionfish family investigated (100, 96, 98% support level in our BA, MP, and NJ analyses). Similarly, the monophyletic origin of up to the three compared scorpion-like fish genera was supported by molecular phylogenetic data. Species identification on individual basis (barcoding tagging) was high. A few taxonomic complications arose during the analysis and they are discussed here in.

ITS2 Ribosomal DNA Sequence Variation of the Bumblebee, Bombus ardens (Hymenoptera: Apidae)

Abstract: The bumblebee species,Bombus, is an invaluable natural resource for greenhouse pollination. Low levels of genetic variation ofBombus ardens have been reported in a previous mitochondrial (mt) gene study. In this study, we sequenced the complete internal transcribed spacer 2 (ITS2) of the nuclear rDNA obtained from 100B. ardens individuals collected from several Korean localities, in an effort to assess its usefulness in characterizing the genetic diversity and relationships among populations of B. ardens. The ITS2 sequences ofB. ardens were shown to be longest among known insects, ranging in size from 1,971–1,984 bp. The sequences harbor four duplicated repeats-≈27 bp repeats, ≈20 bp repeats, ≈33 bp repeats, and ≈34 bp repeats-which have never before been reported in other insect ITS2 rDNA. The maximum sequence divergence of 1.01% among 96 sequence types confirmed the applicability of this molecule to the study of intraspecific variation, revealing higher sequence variation as compared to the previously studied mt COI gene. Overall, a very high per generation migration ratio (Nm = 5.83 ≈ infinite) and a very low level of genetic fixation (FST =0 –0.08) were noted to exist among populations ofB. ardens. The high estimation of gene flow among most populations-in particular, between the remote island Ulleungdo and several inland populations-suggest that historical events may be more responsible for the contemporary population structure of B. ardens. The finding of the lowest genetic diversity (π) in the population on Ulleungdo Island (π = 0.007434) may be reflective of a relatively small population size and the geographical isolation of the population as compared with other inland populations.

AGHR polymorphism and its associations with carcass traits in Harrwoo cattle

Abstract: The growth hormone receptor (GHR) is a membrane transmitter for the growth hormone signal transduction pathway that regulates various metabolic activities, including cell growth and expressions of cytokine genes. The presence or absence of a genetic polymorphism for the LINE-1 retroposon in the PI promoter, which specifically regulates theGHR gene expression in the liver, was screened by a novel detection method and examined for its relationships with carcass traits in Hanwoo cattle. Han woo cattle had taurine type LINE-1 present (alleleI) as well as incidine type LINE-1 absent (alleleA) promoter sequences. Three genotypes,I/I, I/A andA/A, showed frequencies of 49.1, 36.7 and 14.2%, respectively. The effects of allele A were significant on mean differences for final weight, eye muscle area, marbling score and fat color (p 0.05). Most 30-month old Hanwoo steers bearing the LINE-1 absent promoter had whiter fat color, heavier live weight and higher marbling score, reflecting intramuscular fat deposition inM. longissimus dorsi, compared to animals bearing a LINE-1 present promoter. This suggests that aGHR polymorphism could be a potential genetic marker for improving beef production of Hanwoo cattle.

Characterization of polymorphic microsatellite loci in cultivated and wildPanax ginseng

Abstract: Ginseng (Panax ginseng) is one of the most important herbal remedies used in East Asia. The present study investigated six polymorphic microsatellite markers (PG29, PG281, PG287, PG668, PG1319, and PG1481) in samples of cultivated and wildP. ginseng collected in Korea. Total allelic number observed in this study was 27 (average allelic numbers per locus: 4.5). All examined loci exhibited deviation from the Hardy-Weinberg equilibrium and deficiency of heterozygosity in both cultivated and wild groups. Although the wild ginseng group exhibited slightly more polymorphic behavior (mean PIC=0.392, GD=0.454 and Hobs=0.129), compared with the cultivated group (mean PIC=0.383, GD=0.438 and Hobs=0.105), no significant differences of allele frequencies and genotype distributions were revealed. By combined analysis of six loci in 100 cultivated ginsengs, 71 different types were observed. The analyzed microsatellite loci in this study will be helpful for understanding genetic variation, QTL mapping and phylogenic studies inPanax species.

Alu tandem sequences inhibit GFP gene expression by triggering chromatin wrapping

Abstract: Alu elements belonging to the short interspersed nuclear elements (SINE) of repetitive elements are present in more than one million copies which altogether represent 10% of the whole human genome. In this study, the roles ofAlu tandem sequences in the process of GFP gene (GFP) expression and packing into chromatin of its DNA were studied. To detect the effect ofAlu repeats on gene expression, different copies ofAlus were insertedGFP downstream respectively in pEGFP-C1 vector. We found thatAlu sequences decreased the amount ofGFP transcription, the percentage of GFP positive cells and the accessibility to DNase I in length-dependent manner. InsertingAlu caused the production of higher-molecular-mass RNA, indicatingAlu sequence did not induce premature transcriptional termination. Tight packing chromatins keep silent and resist to DNase I digestion, which is a general phenomenon. We suggested that head and tail tandemAlu sequences suppressedGFP expression in length dependent manner by triggering chromatin packing.

FISH and GISH Analysis of the Genomic Relationships among Panax Species

Abstract: Ginseng is a well-known medicinal plant that has been used as an anti-aging agent for many years in East Asia. In the genusPanax, only three species,P. ginseng (Oriental ginseng),P. quinquefolius (American ginseng) andP. notoginseng (Chinese ginseng), are currently considered to be important medicinal herbs. Despite the increase in their breeding value, molecular cytogenetic information on the species is not available. To analyze the genomic relationships among thePanax species, FISH (fluorescencein situ hybridization) and GISH (genomicin situ hybridization) techniques were applied. FISH analysis revealed that the 45S and 5S rRNA genes ofP. notoginseng (2n=2x=24) andP. ginseng (2n=4x=48) cluster on a single locus on different chromosomes, whileP. quinquefolius (2n=4x=48),P. japonicus (2n=4x=48), and Korean wild ginseng (2n =4x= 48) had one locus of the 45S rRNA gene and two loci of the 5S rRNA gene, respectively. GISH analysis using genomic DNA as a probe detected strong cross-hybridization of genomes betweenP. ginseng andP. quinquefolius. GISH analysis of other species showed weak or no distinct signals on the chromosomes. Our data revealed thatP. ginseng andP. quinquefolius showed the highest degree of homology, indicating that these species diverged in most recent years.

The mitochondrial DNA control region comparison studies of four hinged turtles and its phylogentic significance of the genusCuora sensu lato (Testudinata: Geoemydidae)

Abstract: The complete sequences of the mitochondrial DNA (mtDNA) control region (CR) ofCistoclemmys flavomarginata, Cistoclemmys galbinifrons, Cuora aurocapitata andCyclemys atripons were amplified by long-polymerase chain reaction (Long-PCR). The lengths were 1207 bp, 1722 bp, 1379 bp and 980 bp, respectively. Combining with the CR sequence ofPyxidea mouhotii (DQ659152), we compared the CR structure, and identified three functional domains (TAS, CD and CSB) in which the conservation sequences (TAS, CSB-F, CSB-1, CSB-2 and CSB-3) were also successfully identified according to their homology to those of other turtles. These 5 turtles have the identical CSB-2 and CSB-3 sequences, and 4 of them have the same CSB-1 sequence while there is one base transversion (T → A) inCy. atripons. We analyzed the variable number of tandem repeat (VNTR) sequences or microsatellites at the 3′ end of CR. The motifs of tandem repeats (7 types) are made up of 2–8 nucleotides, and the copy numbers are from 4 to 48. All of the 5 turtles exceptCy. atripons have the “TATTATAT” repeats and are ended by TA. The results of CR structure analysis displayed that theCuora, Cistoclemmys, andPyxidea have many similarities, but differ fromCyclemys. WithIndotestudo elongate (DQ080043) andIndotestudo forstenii (DQ080044) as outgroups, using the CR sequences (1123bp) excluded the microsatellites at the 3′ end of CR, we constructed the molecular phylogenetic trees using the MP, ML and BI methods. The results showed that there was a strong support to the monophyly of theCuora group consisting ofCuora,Cistoclemmys andPyxidea, which has a close relationship withMauremys andChinemys but far fromCyclemys, which are consistent with the analysis of the CR structure of the 5 turtles.

The Glucosamine-Mediated Induction of CHOP Reduces the Expression of Inflammatory Cytokines by Modulating JNK and NF-κB in LPS-Stimulated RAW264.7 Cells

Abstract: Macrophages secrete inflammatory cytokines and mono-nitrogen oxide (NO), and play crucial roles in inflammation in early-stage rheumatoid arthritis (RA). This study investigated whether glucosamine hydrochloride (GlcN), a nonsteroidal anti-inflammatory agent (NSAID) widely used to treat arthritis, affects the expression of inflammatory cytokines via the unfolded protein response (UPR) in lipopolysaccharide (LPS)-stimulated mouse macrophages (RAW264.7 cells). Pretreatment with GlcN reduced the expression of inflammatory cytokines and inhibited cell differentiation. Moreover, GlcN treatment increased the expression of CHOP and BiP/Grp78, the UPR target genes, in the presence or absence of LPS. Indeed, knockdown of CHOP using siRNAs prevented the GlcN-mediated reduction of inflammatory cytokines in LPS-stimulated RAW264.7 cells. Finally, we found that GlcN-mediated induction of CHOP reduced the phosphorylation of JNK and NF-?B in LPS-stimulated RAW264.7 cells. Combined, these results suggest that the GlcN-mediated induction of CHOP negatively regulates the inflammatory response by modulating JNK and NF-?B in LPS-stimulated RAW264.7 cells.

QTL analysis of floral traits of rice (Oryza Sativa L.) under well-watered and drought stress conditions

Abstract: Three floral traits, spikelet number per panicle (SNP), percentage of single exserted stigma (PSES) and dual exserted stigma (PDES) of a RI population with 185 lines under water stress and non-stress conditions for two years were investigated in a drought tolerance screening facility. ANOVA results showed high significance between years, lines, and water stress treatments, together with interactions among them in pairs. High phenotypic correlation was found between PSES and PDES (r=0.5424***). Based on a linkage map of 203 SSR markers, when under well-watered condition, six QTLs (qSNP-3b, qSNP-4, qSNP-11 qSNP-2, qSNP-5 andqSNP-9) were detected for SNP. Half of them had significant Q × E interactions. Three QTLs (qPSES-1, qPSES-2, qPSES-5) were found to influence PSES, including one locus (qPSES-2) having Q × E interaction. And three QTLs (qPDES-2, qPDES-5 andqPDES-8) were also detected to influence PDES.qPDES-5 was found to have Q × E interaction. The contribution rate of a single QTL varied from 0.80% to 8.83% for additive effect, and 1.86% to 15.25% for Q × E interactions. Under drought stress, six QTLs (qSNP-3a, qSNP-4, qSNP-7a, qSNP-7b, qSNP-8 andqSNP-9) were associated with SNP, includingqSNP-3a andqSNP-4 with Q × E interaction. Three QTLs (qPSES-1, qPSES-10 andqPSES-12) were located on rice chromosome 1, 10 and 12 for PSES. Four QTLs (qPDES-1a, qPDES-1b, qPDES-4 andqPDES-9) were detected for PDES, includingqPDES-9 with Q × E interaction. The additive effect of single QTL can only explain 1.16% to 5.84% of total variance while Q × E interaction of four loci can explain 4.25% to 11.54% of total variance for each locus. There were one to nine pairs of epistatic QTLs influencing SNP and stigma exsertion. The contribution rates of additive and epistatic effects seemed to be in a low magnitude for most cases (0.76%≈9.92%) while a few QTLs or QTL pairs explained more than 10% of total variance. Some main effect QTL and epistasis were commonly detected among PSES and PDES, explaining the high positive correlation between them. Few QTLs were detected under both water stress and non-stress conditions, indicating that drought had severe impact on the genetic behaviors of both spikelet number and stigma exsertion.

Molecular evidence for the hybridity ofIlex × wandoensis and the phylogenetic study of KoreanIlex based on ITS sequence data

Abstract: In this study, internal transcribed spacer (ITS) regions within the nuclear ribosomal DNA of KoreanIlex were analyzed in order to investigate any molecular evidence thatI. × wandoensis could serve as a putative hybrid betweenI. cornuta andI. integra. We also sought to clearly identify taxonomic relationships and problems caused by consecutive external morphological characters among taxa in the genus. We sequenced 20 clones fromI. × wandoensis and found these individuals displayed intra-genomic polymorphisms within ITS regions. The analysis of the clones clearly demonstrated the presence of discrete sequences from bothI. cornuta andI. integra, thereby confirmingI. × wandoensis is a species that was formed by crossingI. cornuta andI. integra. Lastly, the subgenusIlex, which contains the evergreen species, failed to form a monophyletic group in a strict consensus tree that was prepared based upon ITS regions.I. crenata var.microphylla in the subgenus KoreaIlex, which has presented taxonomic problems previously, formed an independent clade within the consensus tree, thereby showing distinction fromI. crenata.) Genetic discontinuity ofI. macropoda andI. Macropoda for.pseudo-macropoda individuals couldn't be confirmed.

Genetic Analysis and QTL Mapping for Grain Chalkiness Characteristics of Brown Rice (Oryza sativa L.)

Abstract: Grain chalkiness is one of the important appearance qualities in rice marketing. But it is a complex trait, controlled by polygenes and easily influenced by the environment. Genetic analysis and QTL detection was carried out on six characteristics of grain chalkiness consisting of the percentage of chalkiness (PGC), white belly (PWB) and white core grains (PWC), and the area of chalkiness (CA), white belly (WBA) and white core (WCA) in brown rice. A total of 16 main-effect QTLs associated with chalkiness characteristics of brown rice were mapped on seven chromosomes over two years. Among them,qPGC7.1 andqPWB7.2 were simultaneously located on chromosome 7 flanked by 7038 and 7042 at LOD scores 4.34 and 3.76, whileqPWC2.1 andqWCA2.1 were simultaneously located on chromosome 2 flanked by RM492 and RM324 with LOD scores of 2.50 and 3.39. Twelve epistatic combinations were detected for five chalkiness characteristics except for CA. Results indicated that WBA was mainly influenced by the additive effects of main-effect QTLs. PGC and PWC were affected by the effects of epistatic QTLs and the interactions between additive-by-additive effects and the environment. The effects of epistatic QTLs and the main-effect QTLs played important roles on CA, PWB and WCA. For the genetic improvement of grain chalkiness in breeding system, more attention should be paid to epistatic effects and the additive effects of main-effect QTLs.

Gene mapping related to yellow green leaf in a mutant line in rice (Oryza sativa L.)

Abstract: A mutant, which derived from the restorer line Jinhui10 treated with EMS, showed completely yellow green leaves, and it had low chlorophyll content and poor agronomic characteristics during the growing stage. The F1 plants from the cross between normal × the mutant showed normal green leaves, and the segregation ratio of normal to yellow green leaves was 3 : 1 in F2 population. It indicated that the trait was controlled by a single recessive nuclear gene, temporarily designated asygl3. The geneygl3 was mapped between RM468 and RM3684 with genetic distances 8.4 cM and 1.8 cM on chromosome 3. This result would be used as genetic information for fine mapping and map-based cloning ofygl3 gene.

Molecular characterization of mungbean peroxisomal alanine glyoxylate aminotransferase gene induced by low temperature stress

Abstract: Photorespiration reduces carbon fixation rate, but it is an essential process in plant. Photorespiration involves reactions in chloroplasts, peroxisomes, and mitochondria. In photorepiratory peroxisome, alanine glyoxylate aminotransferase (AGT) catalyzes the conversion of alanine and glyoxylate into glycine and pyruvate, respectively. We isolated a low temperature-inducible cDNA encoding AGT from mungbean leaves. The full-length cDNA, designated asMLT92, contains an open reading frame of 1,203 nucleotides coding for a protein of 401 amino acids. Genomic DNA blotting showed that the mungbean genome has one copy ofMLT92. MLT92 mRNA was induced by low temperature and its RNA expression was not much increased by drought stress. ABA and NaCl did not induce RNA expression ofMLT92. Based on GFP/RFP targeting experiment, GFP-MLT92 fusion protein and SKL-RFP, a peroxisome marker, were colocalized to peroxisome in tobacco protoplasts. This suggests that peroxisomalMLT92 is involved in molecular response to low temperature stress.

Molecular Cloning and Characterization of Two Brassica napus TTG1 Genes Reveal Genus-Specific Nucleotide Preference, Extreme Protein-Level Conservation and Fast Divergence of Organ-Specificity

Abstract: Encoding a WD40 protein,Arabidopsis thaliana TRANSPARENT TESTA GLABRA1 (AtTTG1) regulates trichome and root hair differentiation as well as flavonoids and seed mucilage deposition in plants. Here, twoBrassica napus TTG1 (BnTTG1) genes were isolated, and Southern hybridization also generated only two bands. The 1511-bpBnTTG1-1 and the 1555-bpBnTTG1-2 both have one intron, and show alternative sites for transcription start, polyadenylation and intron right border splicing. EST and GSS tags suggested thatBnTTG1-1 was derived from B. rapa, whileBnTTG1-2 from B. oleracea. Evidence implies that TTG1 was possibly triplicated in Brassiceae, but some triplicated members were lost soon, which might involve fragmental rearrangements.BnTTG1-1 shares 88.7% genomic and 95.7% mRNA identities withBnTTG1-2. Deduced BnTTG1-1 and BnTTG1-2 proteins both are 337 aa, differed only by substitution of a similar residue. They resemble AtTTG1 in WD40 domain and all conserved motifs. TTG1 / AN11-type WD40 proteins are extremely conserved even across kingdoms. Homological and structural characterizations identifiedBnTTG1-1 andBnTTG1-2 to be orthologs of AtTTG1. Several non-coding motifs are conserved between AtTTG1 and BnTTG1. BnTTG1 coding regions tend to evolve high GC contents through T/A→C/G substitutions especially T→C transition, butAtTTG1 shows opposite base preference.BnTTG1 genes also evolve a GA-stretch in the leader sequence. RT-PCR detected complementation in organ-specificity betweenBnTTG1-1 andBnTTG1-2.BnTTG1-2 is more like AtTTG1 and is expressed in all major organs.BnTTG1-1 is more organ-specific with lower expression in seed and root, possibly withdrawing from regulating seed coat pigment /mucilage deposition and root hair formation.

Effect of Mild Hypothermia on Blood Brain Barrier Disruption Induced by Oleic Acid in Rats

Abstract: The blood-brain barrier (BBB) is essential for the normal function of the central nervous system The pathological conditions induced by brain diseases including cerebral ischemia result in the alteration of BBB integrity This alteration of BBB is relieved by mild hypothermia that has been regarded as an effective therapy for brain injury Experimental fat embolism by intra-arterial administration of fatty acid induces reversible dysfunction of BBB and is considered as a beneficial method for the research on BBB disruption However, the implication of hypothermia on the fatty acid-induced BBB disruption is not clear yet In this study, we aim to investigate the effect of mild hypothermia on BBB disruption by comparing the changes of brain inflammation, free radical production, and matrix metalloproteinases (MMPs) caused by cerebral fatty acid infusion between normothermic (37°C) and hypothermic (33°C) groups Oleic acid infusion into the carotid artery induced the increase of BBB permeability, which was inhibited by mild hypothermia Neutrophils were infiltrated and intercellular adhesion molecule-1 (ICAM-1) expression was increased in the vascular structures in the affected brain tissue of normothermic rats at 24 hrs following oleic acid administration Inducible nitric oxide synthase (iNOS) and nitro-tyrosine immunoreactivities were also observed in the normothermic group The expression of matrix metalloproteinase (MMP)-2, 3, and 13 were upregulated predominantly in the oleic acid-treated brain of the normothermic rats In mild hypothermic condition, neutrophil infiltration and ICAM-1 expression were attenuated, whereas the inductions of iNOS, nitrotyrosine and MMPs except MMP3 were not affected Therefore, we suggest that mild hypothermia contributes to the protective effect on oleic acid-induced BBB damage via reducing neutrophil infiltration and brain inflammation

Organization and analysis of the histidine biosynthetic genes fromCorynebacterium glutamicum

Abstract: Corynebacterium glutamicum, a Gram-positive bacterium, has been widely used for industrial amino acid production. In addition to our previously clonedhisEG andhisHA-impA-hisFI genes, the remaininghisDCB genes were cloned in this study. The entireC. glutamicum histidine biosynthesis genes, when compared with those of other microorganisms, showed high degree of similarities in deduced amino acid sequences but also significant differences in gene organization. Transcription analysis by RT-PCR revealed thatC. glutamicum his genes are located and transcribed in two unlinked loci,hisEG andhisDCB-orf1-orf2-hisHA-impA-hisFI. The primer extension analysis showed that the latterhis operon starts the transcription at C residue localized 196-bp upstream of thehisD ATG start codon. Genetic analysis inhisD promoter region showed the putative Pribnow boxes, TTTAAT and CAGTAT at 7 and 31 upstream ofhisD gene transcription start site. Further analysis revealed Shine-Dalgarno sequence, AGGGAG, at 10-bp upstream ofhisD translational start codon. Our result also suggests that the histidine biosynthesis inC. glutamicum is negatively regulated by their end-product, histidine, suggesting the histidine-dependent regulation ofhis gene transcription.

The inheritance of seed color in a resynthesizedBrassica napus line No. 2127-17 including a new epistatic locus

Abstract: Yellow seed is an important trait inBrassica napus. To know the genet ic basis of yellow seed color inBrassica napus, we carried out genetic studies by using conventional genetics analyses. The conventional genetics was studied in generations (F1 F2 reciprocal F2, BC1, and F23) ofB. napus derived from crosses between a yellow-seeded (No. 2127-17) and nine different black-seeded parents. The results indicated that seed color was mainly controlled by the maternal genotype but influenced by the interact ion between the maternal and endosperm and/or embryonic genotypes. In the combinations which included black-seeded lines SW0780, 94560, 94545 and 1141B, the yellow seed is partially dominant over black with two or three dominance epistasis ratio. A dominant yellow-seeded gene Y which exhibits epistatic effects on the two independent dominant black-seeded genes B and C was ident ified in DH line No. 2127-17. These observations are in agreement with our previous reports. But in the rests, including the crosses with HS No.4, HS No. 3, XY No. 15, 94570 and ZS No. 10, the black seed color was dominant over yellow seed color. The inheritance of this trait in the segregating populations fits the model of a digenic dominance epistasis or triplicate dominance epistasis. A new locus was identified and designated as D: the dominant gene D for black seed color inhibits the dominant gene Y. Therefore, in combination with the Y, B and C, we found that the seed color was influenced by at least four genes. Identifying seed color genes and defining their inheritance should further our understanding of yellow seed color trait and facilitate development of new and better yellow-seeded cult ivars ofBrassics napus.

Polymorphisms of Alcohol Metabolizing Enzyme and Cytochrome P4502E1 Genes in Mongolian Population

Abstract: Although the genetic polymorphism of the alcohol-metabolizing enzymes was extensively studied at the molecular level by many investigators, the genetic polymorphism studies for ethanolmetabolizing enzymes in Mongolians are very rare. The present study was therefore performed to determine the genetic distribution of various forms of alcohol-metabolizing enzymes such as alcohol dehydrogenase 2 (ADH2, currently accepted nomenclature ADH1B), ADH3 (ADH1C), aldehyde dehydrogenase 2 (ALDH2) and cytochrome P4502E1 (CYP2E1) in 300 healthy Mongolian males. Genetic polymorphisms were determined by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) methods. The allele frequencies ofADH2 *1 andADH2 *2 were 0.24 and 0.76;ADH3 *1 andADH3 *2 were 0.92 and 0.08;ALDH2 *1 andALDH2 *2 were 0.96 and 0.04; andCYP2E1 *C andCYP2E1 *D were 0.15 and 0.85, respectively. Compared to the results reported by other investigators, the allele frequencies ofALDH2 *2 andCYP2E1 *C among Mongolian subjects were much lower than among East Asians (Korean, Japanese, and/or Han-Chinese), while those ofADH2 andADH3 were more similar. Interestingly, this study shows that the ineffectiveALDH2 gene (ALDH2*2 allele) among Mongolians is not as common as among East Asians.

Y-STR genetic structure of the most common surnames in Korea

Abstract: The genetic pattern of the Y-chromosomal short tandem repeat (Y-STR) haplotypes of 542 unrelated males having the five most common surnames was analyzed to evaluate their usefulness for Korean forensic science and to provide the basic information for Korean genetic genealogy. We identified 439 Y-STR haplotypes, with 385 (87.7%) being found once. Each of the most common Korean surnames examined here showed high haplotype diversity (>0.9949), indicating that Y-STR haplotypes are very heterogeneous within each surname. Population genetic analysis showed that there are little genetic difference among five surnames due to the genetic heterogeneity within each surname and the various kinds of non surname-specific haplotypes (33.6%: 182/542) distributed among five surnames. Surname prediction may not be adequate for narrowing down the suspect list in Korean forensic science, and additional Y-STR haplotype data of thebon-gwans are needed.

Antibacterial activity of novel naphthoquiones derivatives

Abstract: l,4-naphthoquinone moiety is Known to confer numerous molecules with distinct-hiological activities including anti -mycobacterial, anticancer and anti-inflammatory activities. Vitamin K2, doxorubicin and mitomycin are among the few examples of this class of chemicals used in the treatment of bleeding, lymphoma and carcinoma respectively. Although the exact action mechanism of these molecules is still under investigation, proposed mechanisms include their interact ion with DNA inhibition of topoisomerase II, and production of ROS, contributing individually or in combination with DNA damage and cell death . In the present study, 6 naphthoquinones were synthesized and assayed for their antimicrobial activity againstStaphylococcus aureus by disc diffusion assay and spectrophotometric analys is. DNA topoisomerase II activity was also measured to investigate the degreee of conformation change of a test plasmid DNA affected by the naphthoquinone deriva tives.

Microsatellite markers for population-genetic studies of shiitake (Lentinula edodes) strains

Abstract: In order to analyze the genotyping of shiitake (Lentinula edodes, Berk.), one of commercially and widely grown edible mushrooms, we examined group of total 89 strains that are registered in Korea, Japan, and China respectively, using five microsatellite markers (Led A2, Led A8, Led B2, Led B6, and Led D6) registered in NCBI (National Center for Biotechnology Information). After we prepared synthesis of primers modified with 5′-FAM fluorescent dye and conducted PCR program, we obtained reasonable products. And then we performed microsatellite genotyping analysis using an ABI 3730xl Genetic Analyzer. According to genotyping analysis, the number of alleles of each microsatellite marker ranged from 5 to 14 with the average value of 8.2. The expected and the observed heterozygosity over all microsatellite ranged from 0.27–0.83 and 0.14–0.61. Among 5 microsatellite markers PIC (Polymorphism Information Content) values of Led A8, Led D6, and Led B6 resulted 0.82, 0.60, and 0.57 respectively. We observed that these values showed relatively high values discriminating from other values of microsatellite marker. The average of total values of Led A8, Led D6, and Led B6 came out 0.53 as result, which is higher than 0.5. As a result, this average can be subject to significant value to be used as marker. By using microsatellite marker we can analogically establish population relationships among shiitake (L. edodes) strains grown in East Asian region, develop new varieties, and propose discriminative criteria for different breeding and variety classification. Moreover, microsatellite markers enable us to obtain the genetic inheritance and information that can be used for protection of intellectual property rights.