In order to better understand the biological systems that are affected in response to cosmic ray, we conducted the weighted gene co-expression network analysis with module detection method. By using the Pearson’s correlation coefficient value, we were evaluated the complex gene-gene functional interactions between 680 CR-response probes from integrated microarray datasets, which included large-scale transcriptional profiling of 918 microarray samples. These probes were divided into 6 distinct modules that contained 20 enriched function such as oxidoreductase activity, response to stimulus and stress, and hydrolase activity. Especially, module 1 and 2 commonly showed the enriched annotation categories such as oxidoreductase activity, including the enriched cis-regulatory elements known as ROS specific regulator. These results suggest in module1 and 2 that ROS-mediated irradiation response pathway are affected by CR. We found the 243 irradiation-dependent probes, which were exhibited the similarities of differentially expressed patterns in various irradiation microarray datasets, and RT-PCR for confirmations of several irradiation-dependent genes were exhibited the similar expressed patterns in rice by CR, gamma ray and Ion beam treatments. Interestingly, these genes were differentially expressed by non-gravity. Moreover, we were identified the co-regulations between several irradiation-dependent genes and functional interacted genes in the CR-responsive network by various GA treatments such as different conditions of dose and treatment time. These results of network-based analysis might provide a clue to understanding the complex biological system of CR.

A male gametophyte, or pollen develops in the anther, and its development plays an important male reproductive process in flowering plants. A properly designed transgene construct can help to tailor transgene expression in plants by altering the expression strength, timing, and location. In this process, the promoter plays a pivotal role in controlling transgene expression. In this research, the promoter regions of rice anther/pollen-specific genes, named as OsMSP1 to OsMSP11,were selected from the microarray data sets covering 4 developmental stage of male gametophyte and then used for the construction of vector by Gateway cloning method and transformed into rice and Arabidopsis. All 11 promoters in rice and 9 in Arabidopsis were displayed as anther/pollen-specific/preferential genes by GUS assay and RT-PCR analysis. Three out of 11 promoters showed consistent results with published data. In this study, we demonstrated on eight new anther/pollen-specific or -preferential promoters (OsMSP1, OsMSP2, OsMSP3, OsMSP4, OsMSP5, OsMSP6, OsMSP8, and OsMSP9, which have not been reported before. Although the expression pattern of different genes active in pollen grains is diverse and complex, these experimental results would be helpful to understand the molecular mechanism of regulatory elements in rice microspore/pollen-specific genes.

Rice is one of the most important food crops in the world, and has been used as model monocots for genetic studies, because of its relatively small genome size. We have previously reported the different functions of several RING (Really Interesting New Gene) proteins to respond the various abiotic stresses. In order to study a regulation of RING proteins in rice under ionizing irradiation such as gamma ray (GA), we have identified the expression patterns of these genes by RT-PCR. We found Gamma-ray induced RING finger protein (OsGRP) gene, which were associated with cytosol by subcellular localization analysis. in vitro ubiquitination assay revealed that OsGRP possess E3 ligase activity. Also, we demonstrate that C196A point mutation in the RING finger domain of OsGRP can have a critical effect to the breakdown of structural integrity in RING constructs. To identify the interaction partners for OsGRP in protein-protein interactions, we found the seven genes interacted with OsGRP by Yeast Two Hybrid method. To examine the GA-influence of interaction partners by RT-PCR, two genes were specifically down-regulated in rice during GA treatment. These interaction partners were identified the reliable interactions and subcellular localizations via BiFC method. Interestingly, five genes associated with plastid, while two down-regulated genes associated with cytosol and plastid. These results of OsGRP based on genetic approach might provide a clue to understanding the GA responsive mechanism in rice.

As the market demand on functionality rice has been increasing, embryo rice in which embryo residue remains even after milling has come to comsumers’ attention because rice embryo contains several functionality components. Consequently, development of rice varieties for higher rate of embryo adhesion to grains after milling has become one of the breeding objectives for quality improvement. In this study, we observed embryo dent of 49 commercial varieties and analyzed the relationship between embryo dent and grain size and shape. Embryo dent of rice grains varied 0.27 (Keunnun)~0.59 (Daerip 1) mm. Varieties Jinbu, Jinbo, Heugseol, Obong, Unkwang, and Cheongnam showed relatively deeper embryo dent, suggesting that they will be applicable in breeding for embryo rice. Embryo dent was correlated positively with grain width (r=0.53**) and grain size(r=0.34*), and negatively with grain width/length ratio (r= -0.38**). Strategies for breeding embryo rice were discussed in relation to embryo dent, grain size and shape.

β-carotene hydroxylase (BCH) has been implicated as a key enzyme conferring a stress tolerant mechanism in plants by production of carotenoids, which serve as protectants against photoinhibition and precursor of ABA biosynthesis. We previously cloned a gene encoding a novel cytosolic form of BCH (GmBCH1) from soybean (Glycine max) whose expression increased during nodulation with Bradyrhizobium japonicum. In the present work we extended our study to three GmBCHs as soybean is an allotetraploid, and examined their possible role(s) in nodule development. In situ hybridization revealed the expression of three GmBCHs (GmBCH1, GmBCH2, and GmBCH3) in the infected cells of root nodules, and their enzymatic activities were confirmed by functional assays in E. coli. Localization of GmBCHs by transfecting Arabidopsis protoplasts with GFP fusions and by EM immunogold detection in soybean nodules indicated that GmBCH2 and GmBCH3 were present in plastids while GmBCH1 appeared to be cytosolic. RNAi of the GmBCHs severely impaired nitrogen fixation as well as nodule development. Surprisingly, we failed to detect zeaxanthin, a product of GmBCH, or any other carotenoids, in nodules. We therefore examined the possibility that most of the carotenoids in nodules are converted or cleaved to other compounds. We detected the expression of some carotenoid cleavage dioxygenases (GmCCDs) in wild-type nodules, and also a reduced amount of zeaxanthin in GmCCD8-expressing E. coli, suggesting cleavage of the carotenoid. In view of these findings we propose that carotenoids such as zeaxanthin synthesized in root nodules are cleaved by GmCCDs, and we discuss the possible roles of the carotenoid cleavage products in nodulation.

Bacterial blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), is a significant disease in most rice cultivation areas. The present study was performed to identify new BB R-gene conferring resistance to Korea Xoo isolates, derived from IR65482-7-216-1-2 and to construct a physical map of the candidate gene. An F2 population derived from a cross between 11325 and Anda was used to determine the exact position of the nearest recombination event to the target region. The position of the R-gene was delimited by flanking markers, RM1233 and RM5766, on chromosome 11. Of the 56 markers designed in the flanking region, 20 were selected as anchor markers and the R-gene was mapped to a 295kb region on chromosome 11. To narrow down the interval spanning the R-gene, an additionally SSR marker, 20 STS markers, and CAPS marker between RM27320 and ID55.05-79 were developed using rice reference genome information. From the result the gene was defined by RM27320 and ID55.WA18-5 located in the BAC clone OSJNBa0036K13. The physical distance between these two markers is approximately 80kb. In a further study, gene expression analysis against listed candidate genes was investigated using semi-quantitative transcription PCR. These results will useful for future disease breeding as well as gene function studies regarding resistance genes.

In this study, we generated and characterized the transgenic rice plant expressing a spider silk protein. A cDNA coding for the C-terminus of spider silk protein (AvMaSp) was cloned from the spider Araneus ventricosus. Analysis of the cDNA sequence shows that the C-terminus of AvMaSp consists of 165 amino acids of are petitive region and 99 amino acids of a C-terminalnon-repetitive region. The peptide motifs found in spider silk proteins, GGX and An, were conserved in the repetitive region of AvDrag. The AvMaSp cDNA was expressed as a 28kDa polypeptide in baculovirus-infected insect cells. To produce transgenic rice plant with high contents of glycine and alanine, the prolamin promoter-driven AvMaSp was introduced into rice plant via Agrobacteriumtumefaciens-mediated gene transformation. Because of seeds pecific prolamin promoter, expression of AvMaSp protein has been achieved inriceseed. The introduction and copy number of the AvMaSp gene in transgenic rice plants were determined by PCR and Southern blot analysis. AvMaSp expression in transgenic rice seeds was examined by Northern blot and Western blot analysis. Immuno fluorescence staining with the AvMaSpantiserum revealed that the recombinant AvMaSp proteins were localized in transgenic rice seeds. Furthermore, the amino acid content analysis showed that transgenic rice seeds were greatly increased in glycine and alanine as compared to controls. The present study is the first to show the expression of spider silk protein in rice seed.

Recent global warming and climate change has presented greater challenge to the global agriculture of having to cope with more severe adversaries from various abiotic stress conditions including drought, cold, and heat. As a preliminary step towards developing a heat-tolerant japonica rice variety through molecular breeding, we examined and compared expression of several genes that have been reported being expressed specifically during rice panicle development in different rice varieties after subjecting them heat stress. Although the induction of these transcripts upon heat treatment was invariably observed in all rice varieties tested, the magnitude and kinetics of the induction were found to be different among these varieties, suggesting possible functional implication of these genes in conferring heat tolerant phenotype during reproductive organ development of these plants. General protein synthesis activity as well as pollen viability incurred by the heat stress treatment were also monitored in these plants and the result showed a close correlation overall with the induction dynamic of these transcripts under heat stress. Therefore, these genes, together with the ones involved in the regulatory network for the expression of them, could serve as candidates for useful markers with which molecular breeding of heat tolerant japonica rice can be facilitated.

Doubled haploid system is a very effective tool which has been widely applied in wheat breeding programmes. Wide-hybridization, wheat X maize cross, is used for the production of wheat doubled haploids (DH). The introduction of doubled haploid (DH) approach into breeding programs has reduced the times and population sizes required for the production of pure lines. We carried out the experiment for development on effective method of producing haploid in wheat. Emasculated spikelets of wheat were pollinated with maize pollen and cultured in the solution containing 40 g/ℓ sucrose and 2,4-D, ABA and GA3 24 h after pollination, and then incubated until embryo rescue. twelve to fourteen days after pollination, the embryos are excised and cultured in half-strength MS basal medium supplemented with 20 g/ℓ sucrose and 1 ㎎/ℓ NAA. The type of plant growth regulators was found to be most significant in production of haploid plants. The application of synthetic auxins to pollinated florets, stimulates haploid embryo development to a stage where the embryos can be rescued onto nutrient media. The percentage of embryos formed was significantly affected by 100 ㎎/ℓ 2,4-D plus 50 ㎎/ℓ BAP and 100 ㎎/ℓ 2,4-D plus 50 ㎎/ℓ GA3. There was varied efficiency in embryo formation from 5.7 to 53%.

The early senescence mutant was isolated from the japonica rice Koshihikari through Ethyl-methane-sulfonate (EMS) mutagenesis. The early senescence phenotype was controlled by a single recessive gene, tentatively symbolized as es-k. Using an F2 population derived from a cross between the mutant and Milyang23 and molecular markers, we mapped the es-k locus to the long arm of chromosome 7 between STS markers 147-1 and 147-2 with a physical distance of 66-kb. The symptom of early senescence appeared even before heading, while appeared during ripening in wild-type. Physiological characteristics of the es-k mutant before initiation of senescence was similar to the wild-type. However, after heading, es-k mutants started to exhibit a significant decrease in chlorophyll and soluble protein content compared to the wild-type. The wild-type leaf color appeared normal irrespective of temperature treatment, while the leaf of es-k mutant appeared pale-green at the low temperature and dark-green at the high temperature. During dark-induced senescence, mutant did not show significant differences compared to normal type. The results show that es-k is sensitive to temperature but not to light.

Arabidopsis Fused kinase TWO-IN-ONE (TIO) controls phragmoplast expansion and interacts with the Kinesin-12 subfamily proteins that anchor the plus ends of interdigitating microtubules (MTs) in the phragmoplast midzone. Previous analyses of loss-of-function mutants and RNA interference lines revealed that TIO positively controls both somatic and gametophytic cell cytokinesis, however, knowledge of the full spectrum of TIO functions during plant development remains incomplete. In order to further characterize TIO functions, we expressed TIO and a range of TIO variants under control of its own promoter in wild type Arabidopsis plants. We discovered that TIO-overexpressing transgenic lines produce enlarged pollen grains, arising from incomplete cytokinesis during male meiosis, and showed sporophytic abnormalities indicating polyploidy. These phenotypes arose independently in TIO variants that abolished either gametophytic function or the ability of TIO to interact with Kinesin-12 subfamily proteins. Interaction assays in yeast showed TIO to bind to AtNACK2/TETRASPORE and plants doubly homozygous for kinesin-12a and kinesin-12b knockout mutations to produce enlarged pollen grains. Our results show that TIO dominantly inhibits male meiotic cytokinesis in a dosage dependent manner that may involve direct binding to acomponent of the canonical NACK-PQR cytokinesis signaling pathway.

VitE (tocotrienols and tocopherols) are micronutrients with antioxidant properties synthesized by photosynthetic bacteria and plants that play important roles in animal and human nutrition. A new mutant line, T1001-1, was isolated from in vitro mutagenized population by ionizing radiation and shown to have increased VitE contents. The total VitE content was 26% increased in the T1001-1 mutant seeds compare with cv. Dongan (wild-type). In addition, we showed that the mutant confers retarded seedling growth during the early seedling growth stage in rice. To study the molecular mechanism of VitE biosynthesis, we used the rice microarray to identify genes that are upor down-regulated in T1001-1 mutant. In addition, we identified differentially regulated pathway using MapMan analysis, which provides deep insight into changes in transcript and metabolites. Our results enhanced the transcription of genes involved in starch and lipid metabolism in T1001-1 mutant. To identify the molecular mechanisms of the events involving transcription factors in tocopherol accumulation, we compared the expression patterns of transcription factors. The AP2-EREBP, WRKY, C2H2 transcription factor were up-regulated, whereas the MYB family was down-regulated in T1001-1 mutant. Our results demonstrate change of important transcript in high level of VitE accumulating rice mutant.

Although much effort has been made to find agronomically important loci in the soybean plant, extensive linkage disequilibrium and genome duplication have limited efficient genome-wide linkage analyses that can identify important regulatory genes. In this respect, recombination block-based analysis of cultivated plant genomes is a potential critical step for molecular breeding and target locus screening. We propose a new three-step method of detecting recombination blocks and comparative genomics of bred cultivars. It utilizes typical reshuffling features of their genomes, which have been generated by the recombination processes of breeding ancestral genomes. To begin with, mutations were detected by comparing genomes to a reference genome. Next, sequence blocks were examined for likenesses and difference with respect to the reference genome. The boundaries between the blocks were taken as recombination sites. All recombination sites found in the cultivar set were used to split the genomes, and the resulting sequence fragments were named as core recombination blocks (CRBs). Finally, the genomes were compared at the CRB level, instead of at the sequence level. In the genomes of the five Korean soybean cultivars used, the CRB-based comparative genomics method produced long and distinct CRBs that are as large as 22.9 Mb. We also demonstrated efficiency in detecting functionally useful target loci by using indel markers, each of which represents a CRB. We further showed that the CRB method is generally applicable to both monocot and dicot crops, by analyzing publicly available genomes of 31 soybeans and 23 rice accessions.

Quantitative trait locus (QTL) mapping is a highly effective approach for studying genetically complex forms of plant shattering. With QTLs mapping, the shattering loci can be described. SSR marker is based on the imformation of Simple Sequence Repeat and easy to analyze using PCR and has high reproducibility. For analyzing QTLs associated with shattering, we selected 219 SSR markers from 254 SSR markers and used them for implementing Mapmaker(Ver. 3.0) and Mapchart(Ver. 2.2). Mapmaker help to calculate distances between each markers and Mapchart is a program for drawing Genetic map. This Genetic map of rice (Oryza sativa L.) covering 2082.4 cM with 9.5 cM between makers in the Kosambi function has been constructed using 120 F1 DH plants from a single cross between the indica variety Chungchung and the japonica variety Nagdong.

‘Youhan’ (Hordeum vulgare L.), a new whole crop barley cultivar, was developed by the breeding team at the Department of Rice and Winter Cereal Crop, National Institute of Crop Science, RDA in 2012. ‘Youhan’ has the growth habit of III, light green and middle size leaf, hooded and lax-type spikes. The cultivar showed 107 cm of culm length, 641 spikes per m2. Heading date of ‘Youhan’ was May 1, one day later than that of check cultivar ‘Yuyeon’ in upland, and 2 days earlier than that of check in paddy field. Maturing time was similar to check cultivar ‘Yuyeon’ as June 4 in upland and May 31 in paddy field. ‘Youhan’ also showed better winter hardiness, the resistance to lodging and disease than those of check cultivar. The average forage dry matter yield in the regional yield trial was about 12.6 and 12.0 ton ha-1 in upland and paddy field, respectively, which were 6%, 5% higher than that of the check. It also showed 7.3% of crude protein, 26.8% of ADF(Acid Detergent Fiber), 47.8% of NDF(Neutral Detergent Fiber), and 67.7% of TDN(Total Digestible Nutrients), including higher grade of silage quality for whole crop barley. Fall sowing cropping of ‘Youhan’ is recommended only in areas where average daily minimum mean temperatures in January are higher than －8°C, and it should not be cultivated in mountain areas of Korea.

In U.S.A. maize breeding, exotic germplasm is considered as high-risk and usually introduced by backcrossing specific traits into elite lines. The U.S.A. maize germplasm base is narrow. Only a few open-pollinated varieties are well represented in current programs. Currently, the barrier in using of exotic germplasm in the U.S.A is less formidable than in the 1980s. The major reason is that U.S.A materials are now used in tropical breeding to accelerate earlier maturity and lodging resistance. These exotic materials, developed with U.S.A germplasm, are being introduced back into the U.S.A.Since1994, the ARS-led Germplasm Enhancement of Maize (GEM) project has sought to help broaden the genetic base of America’s corn crop by promising exotic germplasm and crossing it with domestic lines. New hybrids derived from such crosses have provided corn researchers and the producers. These may include improved or alternative native source of resistance to insect pests such as corn rootworms and diseases like northern leaf blight. GEM’s aim is to provide source of useful genetic maize diversity to help the producers to reduce risks from new or evolving insect and disease threats or changes in the environment or respond to new marketing opportunities and demand. During the 2009 growing season, the Ames (Iowa) and Raleigh (North Carolina) locations managed or coordinated evaluations on 17,200 nursery plots as well as 14,000 yield trial plots in Ames and 12,000 in Raleigh. A new “allelicdiversity” study is devoted to exploring and capturing the genetic variation represented by over 300 exotic corn races. Since 2001, GEM has released 221 new corn lines to cooperators for further development into elite commercial new hybrids. GEM has already identified about 50%-tropical, 50%-temperate families tracing primarily to tropical hybrids that are competitive with commercial checks. In North Carolina State University program, they have examined the potential of tropical inbredand hybrids for U.S.A. breeding by crossing temperate-adapted, 100%-tropical lines to U.S.A hybrids. There should be favorably unique alleles or genomic regions in temperate germplasm that can be helpful in tropical maize improvement as well as utilization of tropical lines in temperate areas.

In this study, we examined the palatability and physicochemical properties of rice varieties in the year when there was 10% increase in yield compared to normal year due to daily temperature range and sunshine hours. The results of the analysis of rice yield over the last 20 years (1993-2012) showed 10% difference between the yield in 2000, which was normal, and that in 2001. With regard to the crop weather condition during the ripening period in 2001 compared to 2000, the daily range and sunshine hours were higher, but the mean temperature was similar. The rice yield in 2001 was 9.8% higher than that in 2000 due to the increased number of spikelets per panicles and ratio of ripened grain. In terms of chemical traits, protein, Mg, and K contents decreased in 2001 compared to 2000, but amylose content increased. Trough and final viscosity assessed with a Rapid Visco Analyser were significantly higher in 2001 than 2000. The results suggested that the palatability of cooked rice was good in that year with about 10% increase in rice yield compared to normal year due to daily temperature range and sunshine hours.

Fruit quality traits like heat, color and flavor are unique and important for pepper cuisines and industrial use. Pepper pigments include chlorophyll, carotenoids, anthocyanin and red pigments like capsanthin are unique carotenoids to capsicum spp. So developing carotenoids-rich peppers and use of red pigments extraction along with capsaicinoids are one of interest pepper breeding goals in the world. Horticultural traits of 113 germplasms introduced by international cooperative research with YASS of China were evaluated to select promissing materials for high quality peppers during the past 3 years. All of germplasms including 60 local peppers were belong to C. annuum and fruit characteristics were diverse. Especially fruit chemical compositions like ASTA color, capsaicinoids and sugars were evaluated compared with korean commercial peppers. Average contents of ASTA　color was 98±37, 55±63mg in capsaicinoids and 12±6% in total sugars. ASTA color which generally means red pigments content was over 120 in 25 germplasms including over 200 in 2 germplasms. Higher ASTA colors were observed in different fruit types. Capsaicinoids content was over 90mg/100g in 24 germplasms including 5 germpalsms over 200mg. Especially higher capsaicinoids were higher in local peppers with round and wrinkled fruit shape. And total sugar content was over 20% in 10 germplasms. Germplasms of different fruit shapes and characteristics will be useful materials for diverse fruit quality breeding.

Soybean isoflavones include daidzein, genistein and glycitein with their glycosides, and their malonated derivatives are the main polyphenolic compounds that are helpful for human health. Our research objective was to investigate the differentitation of soybean isoflavones contents of breeding populations between yellow and black soybean. Isoflavones contents in soybean are a wide range from 500 to 7000 ㎍/g. In this study, we used Ilmi (Isoflavones content, 3.612 ㎍/g) as male parent and 04GAYT-4 (Isoflavones content, 1,648 ㎍/g) as female parent. From these varieties, we obtained 94 breeding lines (yellow, 48 lines; black, 25 lines; brown, 21 lines) which have isoflavones content range from 1000 to 6000 ㎍/g. Highest isflavone contents of three different breeding lines was yellow seed coated lines (average isoflavone content, yellow 3,046 ㎍/g, brown 2,935 ㎍/g, black 2,813 ㎍/g).

In order to find new genetic sources of rice salt tolerance, we did screening with about 10,000 rice mutant lines created by Ac/Ds insertional mutagenesis. First, we raised rice seedlings with media soil on 0.7% NaCl solution and selected 71 putative salt tolerant lines and analyzed their Ds insertion sites. We tested their salt tolerance by growing seedlings on MS medium containing, 0 mM, 150 mM, and 250 mM NaCl. Also, their seedling salt tolerance were evaluated by growing on Yoshida nutritional solution containing 0.6% NaCl. Finally, we selected eight mutant lines showing increased seedling salt tolerance compared with wild type variety, Dongjin, repeatedly. We grow them in rice field and investigated their agronomic traits such as heading time, culm length, panicle length, and panicles per hill. Among them two lines which were named Salt10 and Salt23 and showed favorable agronomic characteristics were crossed with Dongjin for further genetic analysis and mapping the causative gene variation.