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Song S.Y.,Korea Research Institute of Bioscience and Biotechnology | Song S.Y.,Jeju National University | Ha T.J.,Research Policy Bureau | Jang K.C.,South Korean National Institute of Crop Science | And 2 more authors.
Journal of Plant Biotechnology | Year: 2012

To determine whether FT-IR spectroscopy combined with multivariate analysis for whole cell extracts can be used to discriminate major leguminous plant at metabolic level, seed extracts of six leguminous plants were subjected to Fourier transform infrared spectroscopy (FT-IR). FT-IR spectral data from seed extracts were analyzed by principal component analysis (PCA), partial least square discriminant analysis (PLS-DA) and hierarchical clustering analysis (HCA). The PCA could not fully discriminate six leguminous plants, however PLS-DA could successfully discriminate six leguminous plants. The hierarchical dendrogram based on PLS-DA separated the six leguminous plants into four branches. The first branch was consisted of all three Vigna species including Vigna radiata var. radiate, Vigna angularis var. angularis and Vigna unguiculata subsp. Unguiculata. Whereas Pisum sativum var. sativum, Glycine max L and Phaseolus vulgaris var. vulgaris were clustered into a separate branch respectively. The overall results showed that metabolic discrimination system were in accordance with known phylogenic taxonomy. Thus we suggested that the hierarchical dendrogram based on PLS-DA of FT-IR spectral data from seed extracts represented the most probable chemotaxonomical relationship between six leguminous plants. © Korean Society for Plant Biotechnology.

Hur Y.-J.,South Korean National Institute of Crop Science | Cho J.-H.,South Korean National Institute of Crop Science | Park H.-S.,South Korean National Institute of Crop Science | Noh T.-H.,South Korean National Institute of Crop Science | And 7 more authors.
Theoretical and Applied Genetics | Year: 2016

Key message: We fine mapped the Xa4 locus and developed a pyramided rice line containing Xa3 and Xa4 R-alleles and a cold-tolerance QTL. This line will be valuable in rice breeding.Abstract: Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a destructive disease of cultivated rice. Pyramiding BB resistance genes is an essential approach for increasing the resistance level of rice varieties. We selected an advanced backcross recombinant inbred line 132 (ABL132) from the BC3F7 population derived from a cross between cultivars Junam and IR72 by K3a inoculation and constructed the mapping population (BC4F6) to locate the Xa4 locus. The Xa4 locus was found to be delimited within a 60-kb interval between InDel markers InDel1 and InDel2 and tightly linked with the Xa3 gene on chromosome 11. After cold (4 °C) treatment, ABL132 with introgressions of IR72 in chromosome 11 showed lower survival rate, chlorophyll content, and relative water content compared to Junam. Genetic analysis showed that the cold stress-related quantitative trait locus (QTL) qCT11 was located in a 1.3-Mb interval close to the Xa4 locus. One line, ABL132-36, containing the Xa3 resistance allele from Junam, the Xa4 resistance allele from IR72, and the cold-tolerance QTL from Junam (qCT11), was developed from a BC4F6 population of 250 plants. This is the first report on the pyramiding of Xa3 and Xa4 genes with a cold-tolerance QTL. This region could provide a potential tool for improving resistance against BB and low-temperature stress in rice-breeding programs. © 2016 Springer-Verlag Berlin Heidelberg

Chandran A.K.N.,Kyung Hee University | Lee G.-S.,National Academy of Agricultural Science | Yoo Y.-H.,Kyung Hee University | Yoon U.-H.,National Academy of Agricultural Science | And 7 more authors.
Rice | Year: 2016

Background: Rice is one of the most important food crops for humans. To improve the agronomical traits of rice, the functions of more than 1,000 rice genes have been recently characterized and summarized. The completed, map-based sequence of the rice genome has significantly accelerated the functional characterization of rice genes, but progress remains limited in assigning functions to all predicted non-transposable element (non-TE) genes, estimated to number 37,000–41,000. Results: The International Rice Functional Genomics Consortium (IRFGC) has generated a huge number of gene-indexed mutants by using mutagens such as T-DNA, Tos17 and Ds/dSpm. These mutants have been identified by 246,566 flanking sequence tags (FSTs) and cover 65 % (25,275 of 38,869) of the non-TE genes in rice, while the mutation ratio of TE genes is 25.7 %. In addition, almost 80 % of highly expressed non-TE genes have insertion mutations, indicating that highly expressed genes in rice chromosomes are more likely to have mutations by mutagens such as T-DNA, Ds, dSpm and Tos17. The functions of around 2.5 % of rice genes have been characterized, and studies have mainly focused on transcriptional and post-transcriptional regulation. Slow progress in characterizing the function of rice genes is mainly due to a lack of clues to guide functional studies or functional redundancy. These limitations can be partially solved by a well-categorized functional classification of FST genes. To create this classification, we used the diverse overviews installed in the MapMan toolkit. Gene Ontology (GO) assignment to FST genes supplemented the limitation of MapMan overviews. Conclusion: The functions of 863 of 1,022 known genes can be evaluated by current FST lines, indicating that FST genes are useful resources for functional genomic studies. We assigned 16,169 out of 29,624 FST genes to 34 MapMan classes, including major three categories such as DNA, RNA and protein. To demonstrate the MapMan application on FST genes, transcriptome analysis was done from a rice mutant of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) gene with FST. Mapping of 756 down-regulated genes in dxr mutants and their annotation in terms of various MapMan overviews revealed candidate genes downstream of DXR-mediating light signaling pathway in diverse functional classes such as the methyl-D-erythritol 4-phosphatepathway (MEP) pathway overview, photosynthesis, secondary metabolism and regulatory overview. This report provides a useful guide for systematic phenomics and further applications to enhance the key agronomic traits of rice. © 2016, Chandran et al.

Alam I.,Gyeongsang National University | Lee D.-G.,Gyeongsang National University | Kim K.-H.,Gyeongsang National University | Park C.-H.,Gyeongsang National University | And 5 more authors.
Journal of Biosciences | Year: 2010

To gain better insight into how soybean roots respond to waterlogging stress, we carried out proteomic profiling combined with physiological analysis at two time points for soybean seedlings in their early vegetative stage. Seedlings at the V2 stage were subjected to 3 and 7 days of waterlogging treatments. Waterlogging stress resulted in a gradual increase of lipid peroxidation and in vivo H2O2 level in roots. Total proteins were extracted from root samples and separated by two-dimensional gel electrophoresis (2-DE). A total of 24 reproducibly resolved, differentially expressed protein spots visualized by Coomassie brilliant blue (CBB) staining were identified by matrix assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry or electrospray ionization tandem mass spectrometry (ESI-MS/MS) analysis. Of these, 14 proteins were upregulated; 5 proteins were decreased; and 5 were newly induced in waterlogged roots. The identified proteins include well-known classical anaerobically induced proteins as well as novel waterlogging-responsive proteins that were not known previously as being waterlogging responsive. The novel proteins are involved in several processes, i.e. signal transduction, programmed cell death, RNA processing, redox homeostasis and metabolisms of energy. An increase in abundance of several typical anaerobically induced proteins, such as glycolysis and fermentation pathway enzymes, suggests that plants meet energy requirement via the fermentation pathway due to lack of oxygen. Additionally, the impact of waterlogging on the several programmed cell death- and signal transduction-related proteins suggest that they have a role to play during stress. RNA gel blot analysis for three programmed cell death-related genes also revealed a differential mRNA level but did not correlate well with the protein level. These results demonstrate that the soybean plant can cope with waterlogging through the management of carbohydrate consumption and by regulating programmed cell death. The identification of novel proteins such as a translation initiation factor, apyrase, auxin-amidohydrolase and coproporphyrinogen oxidase in response to waterlogging stress may provide new insight into the molecular basis of the waterlogging-stress response of soybean. © 2010 Indian Academy of Sciences.

Park H.H.,Research Policy Bureau | Park C.-G.,National Academy of Agricultural Science | Choi B.-R.,National Academy of Agricultural Science | Lee S.-G.,National Academy of Agricultural Science | Ahn J.J.,Research Institute of Climate Change and Agriculture
Journal of Asia-Pacific Entomology | Year: 2015

Naranga aenescens Moore is an important insect pest found in rice paddy field. We investigated the development periods of N. aenescens egg, larva, pupa, and total immature insects at eight constant temperatures: 15.0. °C, 17.5. °C, 20.0. °C, 22.5. °C, 25.0. °C, 27.5. °C, 30.0. °C, and 32.5. °C. N. aenescens developed successfully from the egg stage to the adult stage at all the tested temperatures except 15.0. °C. The developmental time of each life stage was significantly influenced by temperatures. The developmental rate of N. aenescens increased as the temperature increased from 15.0. °C to 30.0. °C but declined at 32.5. °C, except in the pupa stage. The lower developmental threshold (LDT) and the thermal constant (K) was estimated using linear regression. The higher temperature threshold and the lower temperature threshold were calculated using two nonlinear functions. LDT and K from egg to adult emergence were 12.01. °C and 330.84 degree days, respectively. The temperature range of N. aenescens from the lower developmental threshold to the higher developmental threshold using a performance model (24.03) was wider than that determined using the Sharpe-Schoolfield-Ikemoto model (19.77). Developmental completion of N. aenescens was described using a two-parameter Weibull distribution model. Adult emergence frequency of N. aenescens over a full range of constant temperatures was simulated using developmental rate functions and the Weibull function. Biological characteristics of N. aenescens populations from different geographic areas were discussed. © 2015 Korean Society of Applied Entomology, Taiwan Entomological Society and Malaysian Plant Protection Society..

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