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1.
Plant Pathol J ; 40(3): 329-335, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38835304

ABSTRACT

Phytophthora root and stem rot (PRR), caused by Phytophthora sojae, can occur at any growth stage under poorly drained and humid conditions. The expansion of soybean cultivation in South Korean paddy fields has increased the frequency of PRR outbreaks. This study aimed to identify four P. sojae isolates newly collected from domestic fields and evaluate race-specific resistance using the hypocotyl inoculation technique. The four isolates exhibited various pathotypes, with GJ3053 exhibiting the highest virulence complexity. Two isolates, GJ3053 and AD3617, were screened from 205 soybeans, and 182 and 190 genotypes (88.8 and 92.7%, respectively) were susceptible to each isolate. Among these accessions, five genotypes resistant to both isolates were selected. These promising genotypes are candidates for the development of resistant soybean cultivars that can effectively control PRR through gene stacking.

2.
Plants (Basel) ; 12(20)2023 Oct 16.
Article in English | MEDLINE | ID: mdl-37896053

ABSTRACT

This study aimed to discover the quantitative trait loci (QTL) associated with a high seed protein content in soybean and unravel the potential candidate genes. We developed two recombinant inbred line populations: YS and SI, by crossing Saedanbaek (high protein) with YS2035-B-91-1-B-1 (low protein) and Saedanbaek with Ilmi (low protein), respectively, and evaluated the protein content for three consecutive years. Using single-nucleotide polymorphism (SNP)-marker-based linkage maps, four QTLs were located on chromosomes 15, 18, and 20 with high logarithm of odds values (5.9-55.0), contributing 5.5-66.0% phenotypic variance. In all three experimental years, qPSD20-1 and qPSD20-2 were stable and identified in overlapping positions in the YS and SI populations, respectively. Additionally, novel QTLs were identified on chromosomes 15 and 18. Considering the allelic sequence variation between parental lines, 28 annotated genes related to soybean seed protein-including starch, lipid, and fatty acid biosynthesis-related genes-were identified within the QTL regions. These genes could potentially affect protein accumulation during seed development, as well as sucrose and oil metabolism. Overall, this study offers insights into the genetic mechanisms underlying a high soybean protein content. The identified potential candidate genes can aid marker-assisted selection for developing soybean lines with an increased protein content.

3.
Plants (Basel) ; 12(8)2023 Apr 16.
Article in English | MEDLINE | ID: mdl-37111888

ABSTRACT

Soybean (Glycine max L.) is a globally important source of plant proteins, oils, and amino acids for both humans and livestock. Wild soybean (Glycine soja Sieb. and Zucc.), the ancestor of cultivated soybean, could be a useful genetic source for increasing these components in soybean crops. In this study, 96,432 single-nucleotide polymorphisms (SNPs) across 203 wild soybean accessions from the 180K Axiom® Soya SNP array were investigated using an association analysis. Protein and oil content exhibited a highly significant negative correlation, while the 17 amino acids exhibited a highly significant positive correlation with each other. A genome-wide association study (GWAS) was conducted on the protein, oil, and amino acid content using the 203 wild soybean accessions. A total of 44 significant SNPs were associated with protein, oil, and amino acid content. Glyma.11g015500 and Glyma.20g050300, which contained SNPs detected from the GWAS, were selected as novel candidate genes for the protein and oil content, respectively. In addition, Glyma.01g053200 and Glyma.03g239700 were selected as novel candidate genes for nine of the amino acids (Ala, Asp, Glu, Gly, Leu, Lys, Pro, Ser, and Thr). The identification of the SNP markers related to protein, oil, and amino acid content reported in the present study is expected to help improve the quality of selective breeding programs for soybeans.

4.
Int J Mol Sci ; 24(4)2023 Feb 17.
Article in English | MEDLINE | ID: mdl-36835486

ABSTRACT

Soybean seeds consist of approximately 40% protein and 20% oil, making them one of the world's most important cultivated legumes. However, the levels of these compounds are negatively correlated with each other and regulated by quantitative trait loci (QTL) that are controlled by several genes. In this study, a total of 190 F2 and 90 BC1F2 plants derived from a cross of Daepung (Glycine max) with GWS-1887 (G. soja, a source of high protein), were used for the QTL analysis of protein and oil content. In the F2:3 populations, the average protein and oil content was 45.52% and 11.59%, respectively. A QTL associated with protein levels was detected at Gm20_29512680 on chr. 20 with a likelihood of odds (LOD) of 9.57 and an R2 of 17.2%. A QTL associated with oil levels was also detected at Gm15_3621773 on chr. 15 (LOD: 5.80; R2: 12.2%). In the BC1F2:3 populations, the average protein and oil content was 44.25% and 12.14%, respectively. A QTL associated with both protein and oil content was detected at Gm20_27578013 on chr. 20 (LOD: 3.77 and 3.06; R2 15.8% and 10.7%, respectively). The crossover to the protein content of BC1F3:4 population was identified by SNP marker Gm20_32603292. Based on these results, two genes, Glyma.20g088000 (S-adenosyl-l-methionine-dependent methyltransferases) and Glyma.20g088400 (oxidoreductase, 2-oxoglutarate-Fe(II) oxygenase family protein), in which the amino acid sequence had changed and a stop codon was generated due to an InDel in the exon region, were identified.


Subject(s)
Glycine max , Quantitative Trait Loci , Glycine max/genetics , Plant Proteins/genetics , Seeds/metabolism , Glycine/metabolism
5.
Biomed Pharmacother ; 156: 113780, 2022 Dec.
Article in English | MEDLINE | ID: mdl-36228379

ABSTRACT

Influenza viruses cause respiratory infections in humans with high morbidity and mortality rates. Neuraminidase inhibitors such as oseltamivir and peramivir are the most commonly used drugs for influenza virus infections. However, the emergence of resistant viruses necessitates the urgent need to develop next-generation anti-influenza drugs. Soybean (Glycine max L. Merr.) is widely cultivated and used as food worldwide. In addition, soybean has long been used as a nutritional supplement and herbal medicine. However, the potential anti-influenza properties of the soybean cultivar "GL 2626/96″ (SG2626) are yet to be investigated. Herein, we determined whether the ethanolic extract of SG2626 (SG2626E) has anti-viral activity through performing SG2626E pre-, co-, and post-treatment assays, using the influenza green fluorescent protein (GFP)-tagged influenza A/PR/8/34 (A/PR/8/34-GFP) virus. SG2626E showed anti-influenza virus activity in pre- and co-treated cells in a dose-dependent manner, but not in post-treated cells. SG2626E imparted a considerable inhibitory effect on influenza A virus (IAV) infection through blocking viral attachment. SG2626E inhibited the activity of viral hemagglutinin, but not viral neuraminidase of the IAV. SG2626E inhibited IAV infection by reducing intracellular calcium levels in infected human lung epithelial A549 cells. Additionally, SG2626E reduced body weight loss, decreased mortality, and increased the survival rate through reducing viral replication in the lungs of IAV-infected mice. Overall, these results suggest that SG2626E inhibits IAV infection and is a potential novel anti-influenza agent.


Subject(s)
Influenza A Virus, H1N1 Subtype , Influenza A virus , Influenza, Human , Humans , Mice , Animals , Antiviral Agents/pharmacology , Neuraminidase , Glycine max , Influenza, Human/drug therapy , Virus Replication , Plant Extracts/pharmacology , Plant Extracts/therapeutic use
6.
Genomics ; 114(4): 110432, 2022 07.
Article in English | MEDLINE | ID: mdl-35843383

ABSTRACT

Soyasaponin is a type of glycoside such as steroids, steroidal alkaloids or triterpenes, which enhance the body immunity. In order to efficiently identify genes and markers related to the soyasaponin, we used a 180K Axiom® SoyaSNP array and whole genome resequencing data from the Korean soybean core collection. As a result of conducting GWAS for group A soyasaponin (Aa and Ab derivatives), 16 significant common markers associated with Aa and Ab derivatives were mapped to chromosome 7, and three candidate genes including Glyma.07g254600 were detected. The functional haplotypes for candidate genes showed that Aa and Ab contents were mainly determined by alleles of AX-90322128, the marker of Glyma.07g254600. In addition, 14 novel SNPs variants closely associated with Aa and Ab derivatives were discovered for Glyma.07g254600. Therefore, the results of this study that identified soyasaponin-associated markers and useful genes utilizing various genomic information could provide insight into functional soybean breeding.


Subject(s)
Glycine max , Polymorphism, Single Nucleotide , Genome-Wide Association Study/methods , Plant Breeding , Quantitative Trait Loci , Glycine max/genetics
7.
Article in English | MEDLINE | ID: mdl-35130136

ABSTRACT

A Gram-stain-negative, facultatively anaerobic, motile by gliding, rod-shaped, oxidase- and catalase-positive bacterial strain, designated BB8T, was isolated from the stems of a Korean soybean cultivar (Glycine max L. cv. Gwangan). The strain produced a yellow pigment on tryptic soy agar. Growth of strain BB8T occurred at pH 5.0-8.0 (optimum, pH 7.0), at 10-35 °C (optimum, 25-30 °C) and in the presence of 0-1 % (w/v) NaCl (optimum, 0.5%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BB8T formed a lineage within the genus Flavobacterium and was most closely related to Flavobacterium artemisiae SYP-B1015T (96.9 % 16S rRNA gene sequence similarity) and Flavobacterium ustbae T13T (96.8%). The complete genome sequence of strain BB8T was 5 513 159 bp long with a G+C content of 34.1 mol%. The major fatty acids (>10 %) of strain BB8T were iso-C15 : 0 (21 %), summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c, 20.3%) and iso-C16 : 0 3-OH (13.7%). The predominant polar lipids were phosphatidylethanolamine and unidentified aminolipids, and the major respiratory quinone was menaquinone-6. Based on these phenotypic, genotypic and chemotaxonomic characteristics, strain BB8T is considered to represent a novel species of the genus Flavobacterium, for which the name Flavobacterium endoglycinae sp. nov. is proposed. The type strain is BB8T (=KCTC 82167T=CCTCC AB 2020070T).


Subject(s)
Flavobacterium , Glycine max , Phylogeny , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Flavobacterium/classification , Flavobacterium/isolation & purification , Phospholipids/chemistry , Plant Stems/microbiology , RNA, Ribosomal, 16S/genetics , Republic of Korea , Sequence Analysis, DNA , Glycine max/microbiology , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
8.
PLoS One ; 16(1): e0245446, 2021.
Article in English | MEDLINE | ID: mdl-33444365

ABSTRACT

The resveratrol-producing rice (Oryza sativa L.) inbred lines, Iksan 515 (I.515) and Iksan 526 (I.526), developed by the expression of the groundnut (Arachis hypogaea) resveratrol synthase 3 (AhRS3) gene in the japonica rice cultivar Dongjin, accumulated both resveratrol and its glucoside, piceid, in seeds. Here, we investigated the effect of the AhRS3 transgene on the expression of endogenous piceid biosynthesis genes (UGTs) in the developing seeds of the resveratrol-producing rice inbred lines. Ultra-performance liquid chromatography (UPLC) analysis revealed that I.526 accumulates significantly higher resveratrol and piceid in seeds than those in I.515 seeds and, in I.526 seeds, the biosynthesis of resveratrol and piceid reached peak levels at 41 days after heading (DAH) and 20 DAH, respectively. Furthermore, RNA-seq analysis showed that the expression patterns of UGT genes differed significantly between the 20 DAH seeds of I.526 and those of Dongjin. Quantitative real-time PCR (RT-qPCR) analyses confirmed the data from RNA-seq analysis in seeds of Dongjin, I.515 and I.526, respectively, at 9 DAH, and in seeds of Dongjin and I.526, respectively, at 20 DAH. A total of 245 UGTs, classified into 31 UGT families, showed differential expression between Dongjin and I.526 seeds at 20 DAH. Of these, 43 UGTs showed more than 2-fold higher expression in I.526 seeds than in Dongjin seeds. In addition, the expression of resveratrol biosynthesis genes (PAL, C4H and 4CL) was also differentially expressed between Dongjin and I.526 developing seeds. Collectively, these data suggest that AhRS3 altered the expression pattern of UGT genes, and PAL, C4H and 4CL in developing rice seeds.


Subject(s)
Acyltransferases/metabolism , Arachis/enzymology , Glycosyltransferases/metabolism , Oryza/metabolism , Plant Proteins/metabolism , Resveratrol/metabolism , Uridine Diphosphate/metabolism , Acyltransferases/genetics , Glycosyltransferases/genetics , Oryza/genetics , Oryza/growth & development , Plant Proteins/genetics , Seeds/genetics , Seeds/growth & development , Seeds/metabolism , Transgenes
9.
Nat Commun ; 12(1): 97, 2021 01 04.
Article in English | MEDLINE | ID: mdl-33397978

ABSTRACT

Globally, soybean is a major protein and oil crop. Enhancing our understanding of the soybean domestication and improvement process helps boost genomics-assisted breeding efforts. Here we present a genome-wide variation map of 10.6 million single-nucleotide polymorphisms and 1.4 million indels for 781 soybean individuals which includes 418 domesticated (Glycine max), 345 wild (Glycine soja), and 18 natural hybrid (G. max/G. soja) accessions. We describe the enhanced detection of 183 domestication-selective sweeps and the patterns of putative deleterious mutations during domestication and improvement. This predominantly selfing species shows 7.1% reduction of overall deleterious mutations in domesticated soybean relative to wild soybean and a further 1.4% reduction from landrace to improved accessions. The detected domestication-selective sweeps also show reduced levels of deleterious alleles. Importantly, genotype imputation with this resource increases the mapping resolution of genome-wide association studies for seed protein and oil traits in a soybean diversity panel.


Subject(s)
Domestication , Glycine max/genetics , Mutation/genetics , Chromosomes, Plant/genetics , Databases, Genetic , Genetic Variation , Genetics, Population , Genome, Plant , Genome-Wide Association Study , Haplotypes/genetics , Phylogeny , Selection, Genetic
10.
RSC Adv ; 11(3): 1841-1849, 2021 Jan 04.
Article in English | MEDLINE | ID: mdl-35424110

ABSTRACT

The stabilization of decontamination foams containing a chemical reagent is a crucial requirement for their use in the decontamination of nuclear power plants. We have investigated the effects on decontamination foam stability of adding silica nanoparticles (NPs) modified with various functional groups, namely propyl (-CH3), amine (-NH2), and thiol (-SH) groups. The surface properties of these silica NPs were characterized with ATR-FTIR, solid NMR, and TGA analyses. We also established that the agglomeration in such foams of the amine-modified silica NPs is weaker than that of the other modified silica NPs due to their thorough dispersion in the liquid film. Further, the foam containing amine-modified silica NPs was found to be stable for 60 min at a pH of 2, i.e. under decontamination conditions. The bubble structure analysis showed that this decontamination foam has a bubble count that is approximately 5-8 times higher than the foams containing NPs modified with the other functional groups, which indicates that the decontamination foam with amine-modified silica NPs has the best foam structure of the three investigated foams. The well-dispersed and smaller amine-modified silica NPs enhance the foam stability by providing a barrier between the gas bubbles and delaying their coalescence. In contrast, the thiol- and propyl-modified silica NPs form aggregates with large diameters that reduce the maximum capillary pressure of coalescence and hence decrease the foam stability.

11.
Plants (Basel) ; 9(9)2020 Sep 08.
Article in English | MEDLINE | ID: mdl-32911865

ABSTRACT

Pod shattering is an important reproductive process in many wild species. However, pod shattering at the maturing stage can result in severe yield loss. The objectives of this study were to discover quantitative trait loci (QTLs) for pod shattering using two recombinant inbred line (RIL) populations derived from an elite cultivar having pod shattering tolerance, namely "Daewonkong", and to predict novel candidate QTL/genes involved in pod shattering based on their allele patterns. We found several QTLs with more than 10% phenotypic variance explained (PVE) on seven different chromosomes and found a novel candidate QTL on chromosome 16 (qPS-DS16-1) from the allele patterns in the QTL region. Out of the 41 annotated genes in the QTL region, six were found to contain SNP (single-nucleotide polymorphism)/indel variations in the coding sequence of the parents compared to the soybean reference genome. Among the six potential candidate genes, Glyma.16g076600, one of the genes with known function, showed a highly differential expression levels between the tolerant and susceptible parents in the growth stages R3 to R6. Further, Glyma.16g076600 is a homolog of AT4G19230 in Arabidopsis, whose function is related to abscisic acid catabolism. The results provide useful information to understand the genetic mechanism of pod shattering and could be used for improving the efficiency of marker-assisted selection for developing varieties of soybeans tolerant to pod shattering.

12.
Sensors (Basel) ; 20(1)2020 Jan 01.
Article in English | MEDLINE | ID: mdl-31906262

ABSTRACT

Data phenotyping traits on soybean seeds such as shape and color has been obscure because it is difficult to define them clearly. Further, it takes too much time and effort to have sufficient number of samplings especially length and width. These difficulties prevented seed morphology to be incorporated into efficient breeding program. Here, we propose methods for an image acquisition, a data processing, and analysis for the morphology and color of soybean seeds by high-throughput method using images analysis. As results, quantitative values for colors and various types of morphological traits could be screened to create a standard for subsequent evaluation of the genotype. Phenotyping method in the current study could define the morphology and color of soybean seeds in highly accurate and reliable manner. Further, this method enables the measurement and analysis of large amounts of plant seed phenotype data in a short time, which was not possible before. Fast and precise phenotype data obtained here may facilitate Genome Wide Association Study for the gene function analysis as well as for development of the elite varieties having desirable seed traits.


Subject(s)
Biosensing Techniques , Glycine max/anatomy & histology , High-Throughput Screening Assays , Seeds/anatomy & histology , Breeding , Genotype , Humans , Phenotype , Quantitative Trait Loci/genetics , Seeds/genetics , Glycine max/genetics
13.
PLoS One ; 14(10): e0224074, 2019.
Article in English | MEDLINE | ID: mdl-31639154

ABSTRACT

A core collection is a subset that represents genetic diversity of the total collection. Soybean (Glycine max (L.) Merr.) is one of major food and feed crops. It is the world's most cultivated annual herbaceous legume. Constructing a core collection for soybean could play a pivotal role in conserving and utilizing its genetic variability for research and breeding programs. To construct and evaluate a Korean soybean core collection, genotypic and phenotypic data as well as population structure, were analyzed. The Korean soybean core collection consisted of 430 accessions selected from 2,872 collections based on Affymetrix Axiom® 180k SoyaSNP array data. The core collection represented 99% of genotypic diversity of the total collection. Analysis of population structure clustered the core collection into five subpopulations. Accessions from South Korea and North Korea were distributed across five subpopulations. Analysis of molecular variance indicated that only 2.01% of genetic variation could be explained by geographic origins while 16.18% of genetic variation was accounted for by subpopulations. Genome-wide association study (GWAS) for days to flowering, flower color, pubescent color, and growth habit confirmed that the core collection had the same genetic diversity for tested traits as the total collection. The Korean soybean core collection was constructed based on genotypic information of the 180k SNP data. Size and phenotypic diversity of the core collection accounted for approximately 14.9% and 18.1% of the total collection, respectively. GWAS of core and total collections successfully confirmed loci associated with tested traits. Consequently, the present study showed that the Korean soybean core collection could provide fundamental and practical material and information for both soybean genetic research and breeding programs.


Subject(s)
Genome, Plant , Genome-Wide Association Study/methods , Glycine max/classification , Glycine max/genetics , Plant Breeding , Plant Proteins/genetics , Polymorphism, Single Nucleotide , Genotype , Humans , Phenotype , Republic of Korea
14.
Int J Mol Sci ; 20(1)2019 Jan 01.
Article in English | MEDLINE | ID: mdl-30609682

ABSTRACT

Branch number is one of the main factors affecting the yield of soybean (Glycine max (L.)). In this study, we conducted a genome-wide association study combined with linkage analysis for the identification of a candidate gene controlling soybean branching. Five quantitative trait nucleotides (QTNs) were associated with branch numbers in a soybean core collection. Among these QTNs, a linkage disequilibrium (LD) block qtnBR6-1 spanning 20 genes was found to overlap a previously identified major quantitative trait locus qBR6-1. To validate and narrow down qtnBR6-1, we developed a set of near-isogenic lines (NILs) harboring high-branching (HB) and low-branching (LB) alleles of qBR6-1, with 99.96% isogenicity and different branch numbers. A cluster of single nucleotide polymorphisms (SNPs) segregating between NIL-HB and NIL-LB was located within the qtnBR6-1 LD block. Among the five genes showing differential expression between NIL-HB and NIL-LB, BRANCHED1 (BRC1; Glyma.06G210600) was down-regulated in the shoot apex of NIL-HB, and one missense mutation and two SNPs upstream of BRC1 were associated with branch numbers in 59 additional soybean accessions. BRC1 encodes TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTORS 1 and 2 transcription factor and functions as a regulatory repressor of branching. On the basis of these results, we propose BRC1 as a candidate gene for branching in soybean.


Subject(s)
Crops, Agricultural/genetics , Glycine max/genetics , Plant Proteins/genetics , Polymorphism, Single Nucleotide , Quantitative Trait Loci , Transcription Factors/genetics , Crops, Agricultural/growth & development , Linkage Disequilibrium , Plant Proteins/metabolism , Quantitative Trait, Heritable , Glycine max/growth & development , Transcription Factors/metabolism
15.
Theor Appl Genet ; 132(4): 1179-1193, 2019 Apr.
Article in English | MEDLINE | ID: mdl-30588539

ABSTRACT

KEY MESSAGE: Genotyping data of a comprehensive Korean soybean collection obtained using a large SNP array were used to clarify global distribution patterns of soybean and address the evolutionary history of soybean. Understanding diversity and evolution of a crop is an essential step to implement a strategy to expand its germplasm base for crop improvement research. Accessions intensively collected from Korea, which is a small but central region in the distribution geography of soybean, were genotyped to provide sufficient data to underpin population genetic questions. After removing natural hybrids and duplicated or redundant accessions, we obtained a non-redundant set comprising 1957 domesticated and 1079 wild accessions to perform population structure analyses. Our analysis demonstrates that while wild soybean germplasm will require additional sampling from diverse indigenous areas to expand the germplasm base, the current domesticated soybean germplasm is saturated in terms of genetic diversity. We then showed that our genome-wide polymorphism map enabled us to detect genetic loci underlying flower color, seed-coat color, and domestication syndrome. A representative soybean set consisting of 194 accessions was divided into one domesticated subpopulation and four wild subpopulations that could be traced back to their geographic collection areas. Population genomics analyses suggested that the monophyletic group of domesticated soybeans was likely originated at a Japanese region. The results were further substantiated by a phylogenetic tree constructed from domestication-associated single nucleotide polymorphisms identified in this study.


Subject(s)
Domestication , Genetic Variation , Glycine max/genetics , Ecotype , Genetics, Population , Genome-Wide Association Study , Genotype , Polymorphism, Single Nucleotide/genetics , Seeds/genetics
16.
J Nanosci Nanotechnol ; 15(11): 8937-42, 2015 Nov.
Article in English | MEDLINE | ID: mdl-26726622

ABSTRACT

The NASICON (sodium super ionic conductor) based Na3V2(PO4)3/Ag + graphene (NVP/Ag + G) was successfully synthesized through a sol-gel route using a silver nitrate and graphene as a raw material. The effects of the physical and electrochemical properties of the NVP/Ag + G composites have been evaluated with X-ray diffraction (XRD), scanning electron microscopy (SEM), Raman spectroscopy, and electrochemical measurements. The graphene and Ag significantly influenced the morphology, structure and electrochemical performance of the Na3V2(PO4)3 material. In the electrochemical measurement, the (NVP/Ag + G) electrode showed the discharge capacity of 102 mAh g(-1) at 0.1 C rate, which was higher than the pristine Na3V2(PO4). At a current rate of 5 C, it still exhibits the discharge capacity of 73 mAh g(-1) and the capacity retention of 71.6%. The results of higher electrochemical performance of the NVP/Ag + G composites are mainly attributed to the synergetic effect of the graphene and the silver particles.

17.
BMC Genomics ; 15: 477, 2014 Jun 15.
Article in English | MEDLINE | ID: mdl-24929792

ABSTRACT

BACKGROUND: In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for the screening of target loci for agricultural traits. RESULTS: We propose the variation block method, which is a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing the short-read DNA sequences of the cultivar to the reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in the cultivar set are used to split the genomes, and the resulting sequence regions are termed variation blocks. Finally, the genomes are compared using the variation blocks. The variation block method identified recurring recombination blocks accurately and successfully represented block-level diversities in the publicly available genomes of 31 soybean and 23 rice accessions. The practicality of this approach was demonstrated by the identification of a putative locus determining soybean hilum color. CONCLUSIONS: We suggest that the variation block method is an efficient genomics method for the recombination block-level comparison of crop genomes. We expect that this method will facilitate the development of crop genomics by bringing genomics technologies to the field of crop breeding.


Subject(s)
Crops, Agricultural/genetics , Genome, Plant , Glycine max/genetics , Base Sequence , Chromosome Mapping , Plant Proteins/genetics , Polymorphism, Single Nucleotide , Promoter Regions, Genetic , Sequence Analysis, DNA
18.
J Nanosci Nanotechnol ; 14(10): 7718-22, 2014 Oct.
Article in English | MEDLINE | ID: mdl-25942854

ABSTRACT

The 0.3Li2MnO3 x 0.7LiMn0.60Ni0.25Co0.15O2 cathode materials were synthesized using a coprecipitation method at a various heat-treatment temperature. From XRD pattern analysis, pure layered structure without impurities was confirmed from all samples and the peak intensity of Li2MnO3 was increased as the heat-treatment temperature increased. The primary particle size increased approximately from 100 nm to 500 nm with increasing heat-treatment temperature. The initial discharge capacity of the materials obtained at 950 degrees C was 235 mA h/g at 0.1 C rate, but then decreased down to 228 mA h/g with further increasing heat-treatment temperature. And, in the voltage range of 2.0-4.6 V, the electrode heat-treated at 900 degrees C showed the highest capacity retention of 68% at 5 C rate against to 0.1 C rate.

19.
Mol Cells ; 34(5): 463-71, 2012 Nov.
Article in English | MEDLINE | ID: mdl-23124383

ABSTRACT

Nitric oxide (NO) is known for its role in the activation of plant defense responses. To examine the involvement and mode of action of NO in plant defense responses, we introduced calmodulin-dependent mammalian neuronal nitric oxide synthase (nNOS), which controls the CaMV35S promoter, into wild-type and NahG tobacco plants. Constitutive expression of nNOS led to NO production and triggered spontaneous induction of leaf lesions. Transgenic plants accumulated high amounts of H(2)O(2), with catalase activity lower than that in the wild type. nNOS transgenic plants contained high levels of salicylic acid (SA), and they induced an array of SA-, jasmonic acid (JA)-, and/or ethylene (ET)-related genes. Consequently, NahG co-expression blocked the induction of systemic acquired resistance (SAR)-associated genes in transgenic plants, implying SA is involved in NO-mediated induction of SAR genes. The transgenic plants exhibited enhanced resistance to a spectrum of pathogens, including bacteria, fungi, and viruses. Our results suggest a highly ranked regulatory role for NO in SA-, JA-, and/or ET-dependent pathways that lead to disease resistance.


Subject(s)
Disease Resistance/genetics , Nicotiana/microbiology , Nitric Oxide Synthase/genetics , Pseudomonas/physiology , Animals , Cyclopentanes/metabolism , Gene Expression Regulation, Plant , Hydrogen Peroxide/metabolism , Nitric Oxide Synthase/metabolism , Oxylipins/metabolism , Plants, Genetically Modified/genetics , Plants, Genetically Modified/metabolism , Plants, Genetically Modified/microbiology , Pseudomonas/genetics , Rats , Salicylic Acid/metabolism , Nicotiana/genetics , Nicotiana/metabolism
20.
Mol Cells ; 33(1): 43-51, 2012 Jan.
Article in English | MEDLINE | ID: mdl-22134721

ABSTRACT

Rice stripe virus (RSV) is a viral disease that seriously impacts rice production in East Asia, most notably in Korea, China, and Japan. Highly RSV-resistant transgenic japonica rice plants were generated using a dsRNAi construct designed to silence the entire sequence region of the RSV-CP gene. Transgenic rice plants were inoculated with a population of viruliferous insects, small brown planthoppers (SBPH), and their resistance was evaluated using ELISA and an infection rate assay. A correlation between the expression of the RSV-CP homologous small RNAs and the RSV resistance of the transgenic rice lines was discovered. These plants were also analyzed by comparing the expression pattern of invading viral genes, small RNA production and the stable transmission of the RSV resistance trait to the T3 generation. Furthermore, the agronomic trait was stably transmitted to the T4 generation of transgenic plants.


Subject(s)
Capsid Proteins/genetics , Oryza/genetics , Plant Diseases/prevention & control , Tenuivirus/genetics , Viral Nonstructural Proteins/genetics , Gene Silencing , Genes, Viral , Genetic Predisposition to Disease , Plant Diseases/genetics , Plant Diseases/virology , Plants, Genetically Modified , RNA Interference , RNA, Plant/genetics , RNA, Small Interfering/genetics , Tenuivirus/metabolism
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