• The Plant Pathology Journal
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• v.31 no.1
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• pp.33-40
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• 2015

Pigeonpea Sterility Mosaic Disease (PSMD) is an important foliar disease caused by Pigeonpea sterility mosaic virus (PPSMV) which is transmitted by eriophyid mites (Aceria cajani Channabasavanna). In present study, a F2 mapping population comprising 325 individuals was developed by crossing PSMD susceptible genotype (Gullyal white) and PSMD resistant genotype (BSMR 736). We identified a set of 32 out of 300 short decamer random DNA markers that showed polymorphism between Gullyal white and BSMR 736 parents. Among them, eleven DNA markers showed polymorphism including coupling and repulsion phase type of polymorphism across the parents. Bulked Segregant Analysis (BSA), revealed that the DNA marker, IABTPPN7, produced a single coupling phase marker (IABTPPN $7_{414}$) and a repulsion phase marker (IABTPPN $7_{983}$) co-segregating with PSMD reaction. Screening of 325 F2 population using IABTPPN7 revealed that the repulsion phase marker, IABTPPN $7_{983}$, was co-segregating with the PSMD responsive SV1 at a distance of 23.9 cM for Bidar PPSMV isolate. On the other hand, the coupling phase marker IABTPPN $7_{414}$ did not show any linkage with PSMD resistance. Additionally, single marker analysis both IABTPPN $7_{983}$ (P<0.0001) and IABTPPN $7_{414}$ (P<0.0001) recorded a significant association with the PSMD resistance and explained a phenotypic variance of 31 and 36% respectively in $F_2$ population. The repulsion phase marker, IABTPPN7983, could be of use in Marker-Assisted Selection (MAS) in the PPSMV resistance breeding programmes of pigeonpea.

• Journal of Microbiology and Biotechnology
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• v.27 no.7
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• pp.1223-1232
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• 2017

Cordyceps militaris, a member of Ascomycota, a mushroom referred to as caterpillar Dong-chung-ha-cho, is commercially valuable because of its high content of bioactive substances, including cordycepin, and its potential for artificial cultivation. Cordycepin (3'-deoxyadenosine) is highly associated with the pharmacological effects of C. militaris. C. militaris is heterothallic in that two mating-type loci, idiomorph MAT1-1 and MAT1-2, exist discretely in two different spores. In this study, nine C. militaris strains were mated with each other to prepare newly bred strains that produced a larger amount of cordycepin than the parent strains. Nine strains of C. militaris were identified by comparing the internal transcribed spacer sequence, and a total of 12 single spores were isolated from the nine strains of C. militaris. After the MAT idiomorph was confirmed by PCR, 36 mating combinations were performed with six single spores with MAT1-1 and the others with MAT1-2. Eight mating combinations were successfully mated, producing stroma with perithecia. Cordycepin content analysis of all strains by high-performance liquid chromatography revealed that the KASP4-bred strain produced the maximum cordycepin among all strains, regardless of the medium and stroma parts. Finally, universal rice primer-PCR was performed to demonstrate that the bred strains were genetically different from the parental strains and new C. militaris strains. These results may be related to the recombination of genes during mating. The newly produced strains can be used to meet the industrial demand for cordycepin. In addition, breeding through mating suggests the possibility of producing numerous cordycepin-producing C. militaris strains.

• Journal of Genetic Medicine
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• v.15 no.2
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• pp.64-71
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• 2018

Purpose: Overgrowth syndromes are conditions that involve generalized or localized areas of excess growth. In this study, the clinical, molecular, and genetic characteristics of Korean patients with overgrowth syndrome were analyzed. Materials and Methods: We recruited 13 patients who presented with overgrowth syndrome. All patients fulfilled inclusion criteria of overgrowth syndrome. Analysis of the clinical and molecular investigations of patients with overgrowth syndrome was performed retrospectively. Results: Among the 13 patients with overgrowth syndrome, 9 patients (69.2%) were found to have molecular and genetic causes. Among the seven patients with Sotos syndrome (SS), two had a 5q35microdeletion that was confirmed by fluorescent in situ hybridization. In two patients with SS, intragenic mutations including a novel mutation, c.5993T>A (p.M1998L), were found by Sanger sequencing. One patient had one copy deletion of NDS1 gene which was confirmed by multiplex ligation-dependent probe amplification. Among five patients with Beckwith-Wiedemann syndrome, three had aberrant imprinting control regions; 2 hypermethylation of the differentially methylated region of H19, 1 hypomethylation of the differentially methylated region of Kv. In one patient displaying overlapping clinical features of SS, a de novo heterozygous deletion in the chromosomal region 7q22.1-22.3 was found by single nucleotide polymorphism-based microarray. Conclusion: Considering high detection rate of molecular and genetic abnormalities in this study, rigorous investigations of overgrowth syndrome may be an important tool for the early diagnosis and genetic counseling. A detailed molecular analysis of the rearranged regions may supply the clues for the identification of genes involved in growth regulation.

• Journal of Crop Science and Biotechnology
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• v.11 no.1
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• pp.17-22
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• 2008

Aromatic rice has become popular owing to its aroma. Growing demand for aromatic rice has spurred interest in the development of domestic cultivars that offer similar combinations of grain attributes such as texture, cooking characteristics, aroma, and taste. In this study, the most important agronomic attributes and aroma of 26 cultivars from Afghanistan, Iran, and Uzbekistan, and controls from Japan, Thailand, and India were characterized. Also $F_2$ populations derived from the cross between(Jasmine 85 aromatic$\times$Nipponbare non-aromatic) and(Jasmine 85$\times$Basmati 370 aromatic) were obtained. Tasting individual grains, cooking test, 1.7% KOH sensory test, and molecular marker analysis have been applied to distinguish between aromatic and non-aromatic rice. Diversity for some traits of agronomic importance, such as plant height was detected among countries, e.g. Afghan cultivars classified as tall, and Iranian and Uzbek intermediate and short, respectively. Differentiations of panicle, grain, leaf, basal internode, and culm dimension among rice cultivars, indicating the source of rice diversity in Central Asia. According to the results, 6 of 10, 2 of 7, and 0 of 6 of Afghan, Iranian, and Uzbek rice cultivars were scored as aromatic, respectively. Therefore, Afghan cultivars are a good source of aromatic rice germplasm for Central Asia. The expression between aromatic and non-aromatic, and aromatic and aromatic combinations has been evaluated. The observed segregation ratio of these crosses in the $F_2$ populations was tested by $x^2$ analysis against the expected ratio for a single gene. A segregation ratio of 3:1 between non-aromatic and aromatic combination has been detected, while segregation has not been detected between the aromatic and aromatic combinations. Also, parallel results were obtained from the tested aromatic rice cultivars. Thus, our results suggest that a single recessive gene controls aroma in all aromatic rice cultivars.

• Journal of Plant Biotechnology
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• v.35 no.3
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• pp.177-183
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• 2008

Ac/Ds mutant lines of this study were transgenic rice plants, each of which harbored the maize transposable element Ds together with a GUS coding sequence under the control of a promoterless(Ds-GUS). We selected the mutants that were GUS expressed lines, because the GUS positive lines will be useful for identifying gene function in rice. One of these mutants was identified knock-out at Oszinc626(NP_001049991) gene, encoding a RING-H2 zinc-finger protein, by Ds insertion. In this mutant, while primary root development is normal, secondary root development from lateral root was very poor and seed development was incomplete compare with normal plant. RING zinc-finger proteins play important roles in the regulation of development in a variety of organisms. In the plant kingdom, a few genes encoding RING zinc-finger proteins have been documented with visible effects on plant growth and development. The consensus of the RING-H2(C3-H2-C3 type) domain for this group of protein is $Cys-X_2-Cys-X_{28}-Cys-X-His-X_2-His-X_2-Cys-X_{14}-Cys-X_2-Cys$. Oszinc626 encodes a predicted protein product of 445 amino acids residues with a molecular mass of 49 kDa, with a RING-zinc-finger motif located at the extreme end of the C-terminus. RT-PCR analysis indicated that the expression of Oszinc626 gene was induced by IAA, cold, dehydration, high-salinity and abscisic acid, but not by 2,4-D, and the transcription of Oszinc626 gene accumulated primarily in rice immature seeds, root meristem and shoots. The gene accumulation patterns were corresponded with GUS expression.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.86-86
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• 2003

Phytophthora capsici is a pathogen on several economically important crops including pepper. In pepper growing areas in Korea, Phytophthora blight caused by p. capsici has been considered as the most serious problem in pepper production. The Oomycete attacks the roots, stems, leaves and fruits of the plant. To understand the molecular mechanisms involved in the disease development, the genes expressed doting pepper p. capsici interaction were explored by analyzing expressed sequence tags (ESTs). A complementary DNA (cDNA) library was constructed from total RNA extracted from pepper leaves challenged with p. capsici for 3 days resulting in early stage of symptom development. The comprehensive analysis on the single pass sequencing of over 4000 randomly selected cDNA clones with contig assembly, unique gene extraction, sequence comparison, and functional categorizing will be presented with an emphasis on the genes involved in plant defense and pathogenicity during disease development of the pepper Phytophthora blight.

• Journal of Life Science
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• v.12 no.4
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• pp.399-406
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• 2002

The Arabidopsis mutants involved in chloroplast development were induced by seed treatment of diepoxybutane which was rarely known mutagenic compound in plant mutagenesis. Three kinds of mutants designated as iml, gev, and yev were represented by the characteristics of variegated leaves, green vein with yellow leaves, and yellow green vein with green leaves respectively. We investigated the ultrastructure of chloroplast in mutated regions using transmission electron microscopy. The ultrastructure of chroloplast in wildtype showed regularly stacked grana thylakoid and stroma thylakoid while iml, gev and yev mutants displayed different shapes of grana stacking and stroma stacking of chloroplasts. Genetic analysis of three chloroplast mutants exhibit that divergent traits were ruled by a single recessive nuclear gene.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.6
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• pp.893-899
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• 2009

Few studies have reported the existence of imprinted genes in cattle compared to the human and mouse. Genomic imprinting is expressed in monoallelic form and it depends on a single parent-specific form of the allele. Comparative analysis of mammals other than the human is a valuable tool for explaining the genomic basis of imprinted genes. In this study, we investigated 34 common imprinted genes in the human and mouse as well as 35 known non-imprinted genes in the human. We found short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINEs), and long terminal repeats (LTRs) in imprinted (human and mouse) and control (cattle) genes. Pair-wise comparisons for the three species were conducted using SINEs, LINEs, and LTRs. We also calculated 95% confidence intervals of frequencies of repetitive sequences for the three species. As a result, most genes had a similar interval between species. We found 11 genes with conserved SINEs, LINEs, and LTRs in the human, mouse, and cattle. In conclusion, eleven genes (CALCR, Grb10, HTR2A, KCNK9, Kcnq1, MEST, OSBPL5, PPP1R9A, Sgce, SLC22A18, and UBE3A) were identified as candidate imprinted genes in cattle.

• Mycobiology
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• v.31 no.1
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• pp.19-22
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• 2003

The primary objective of the current research was to detect genetic variations within the Indonesian isolates of Cochliobolus heterostrophus collected from ecologically different places of the country at molecular level using PCR-RFLP analyses. The primer pair of NS3 and NS6 produced amplification fragment in all of the isolates tested. A single fragment of estimated 907 bp was observed in the PCR product pattern. RFLP analysis of the PCR product employing three restriction enzymes, HaeIII, HhaI, and RsaI, respectively, did not reveal intraspecific variations within the fungus. Similarly, nucleotide sequences of portion of small subunit of the ribosomal DNA gene of two of the isolates collected showed no appreciable differences, indicating the absence of genetic diversities among the isolates tested. A phylogenetic tree was constructed and the Indonesian C. heterostrophus, represented by SM-1 isolate, was found to be phylogenetically located near C. sativus, a closely related species.

• BMB Reports
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• v.44 no.9
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• pp.578-583
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• 2011

Aspartate aminotransferase (AST) and alanine aminotransferase (ALT) are biochemical markers used to test for liver diseases. Copy number variation (CNV) plays an important role in determining complex traits and is an emerging area in the study various diseases. We performed a genome-wide association study with liver function biomarkers AST and ALT in 407 unrelated Koreans. We assayed the genome-wide variations on an Affymetrix Genome-Wide 6.0 array, and CNVs were analyzed using HelixTree. Using single linear regression, 32 and 42 CNVs showed significance for AST and ALT, respectively (P value < 0.05). We compared CNV-based genes between the current study (KARE2; AST-140, ALT-172) and KARE1 (AST-1885, ALT-773) using NetBox. Results showed 9 genes (CIDEB, DFFA, PSMA3, PSMC5, PSMC6, PSMD12, PSMF1, SDC4, and SIAH1) were overlapped for AST, but no overlapped genes were found for ALT. Functional gene annotation analysis shown the proteasome pathway, Wnt signaling pathway, programmed cell death, and protein binding.