해충저항성 Bacillus thuringiensis (Bt) 벼의 비표적곤충인 벼물바구미(Lissorhoptrus oryzophilus)에 대한 성충 전용살충제 Clothianidin 액상수화제의 살충제 감수성 시험을 실시한 결과, 72시간-LC50은 0.245 ml/L(95% 신뢰한계는 0.195~0.307 ml/L)이었으며, Bt벼의 모본으로 대조로 사용한 낙동벼의 72시간-LC50은 0.257 ml/L(95% 신뢰한계는 0.199~0.331 ml/L)이었다. 72시간-LC50은 낙동벼에서 다소 높았지만, 해충저항성 Bt벼 72시간-LC50이 낙동벼의 95% 신뢰한계 내에 포함되어, 두 품종의 LC50값에 유의성이 없는 것으로 판단된다.

해충저항성 Bt벼와 낙동벼의 미꾸리(Misgurnus anguillicaudatus) 와 잉어(Cyprinus carpio)에 대한 급성독성시험을 실시한 결과 48시간 및 96시간-LC50은 1,000mg/L 이상으로 나타났다. 48시간 및 96시간 무영향농도(NOEC)는 1,000mg/L이었다. 급성독성 시험기간 중 해충저항성 Bt벼와 낙동벼간의 pH, DO, 수온, 체중 및 전장에 대한 유의적인 결과는 나타나지 않았다.

Rice bran has been reckoned as a potential source of edible oil contained 15-20 % of oil, in its natural state, also contains several constituents of potential significance in diet and health. Interest has focused primarily upon gamma-oryzanol, tocotrienols, and tocopherols, all of which demonstrate antioxidant properties. We analyzed the transcriptome profiles for rice grain from high and low oil content lines at the early milky stage using the Illumina sequencing method. This analysis indicated that many transcripts showed different expressions level between high and low oil content rice. The functional classification of those genes indicated their connection with various metabolic pathways, oil transport, signal transduction, transcriptional regulation, and other processes. The results obtained here will enable to understand how changes in oil concentration or availability are interpreted into adaptive responses in early milky stage of rice. Based on the functional annotation of the differentially expressed genes, the possible processes that regulate these expressed transcripts in rice grain was further analyzed. The candidate transcripts may provide genetic resources that may be useful in the improvement of oil contents of rice.

Iron is an essential mineral found in every cell of the human body to make the oxygen-carrying proteins hemoglobin and myoglobin. More than 2 billion people face Fe deficiency. Rice can be a potentially valuable source to supplement that mineral since it is staple food for two-thirds of the world’s population. To bring the nutritional level of the milled product up to that of the whole grain (brown), rice should be enriched with thiamin, niacin and iron. Also iron has important role that absorption from the photosynthetic cells proceeds, chlorophyll synthesis and the growth process of the plant. Orthologous genes, which are homologous genes that diverged after a speciation event, generally maintain a similar function in different species. We applied a McDonald-Kreitman Test (MKT) to examine more than 10,000 orthologous genes between rice (Oryza sativa) and Brachypodium (outgroup) based on different phenotypic groups. This analysis was undertaken to find fast evolutionary genes in rice iron uptake. Three groups were separated based on the phenotype and each group was examined with the outgroup for MKT. Fast evolutionary genes that have a positive selection with FDR ≤ 0.05 were detected at each groups. Annotation of these genes were conducted and the predicted functions were also discussed here. And also, the association study between the candidate gene related to iron uptake phenotype was performed. These results support that using this orthologous based method, we may find some important candidate genes underlying the ion uptake in rice.

Zinc (Zn) deficiency is one of the important abiotic factors limiting rice productivity world-wide and also a widespread nutritional disorder affecting human health. Zinc is one of the most important essential micronutrient for human About thirty percentage world’s population doesn’t still get enough zinc through their diets. As a staple food of over half world’s population, rice should take the responsibility to provide much more zinc in the future. We analyzed the transcriptome profiles for rice grain from high zinc content and low zinc content lines at the early milky stage using the Illumina Sequencing method. The analysis results for the sequencing data indicated that many transcripts showed different expressions between high zinc content and low zinc content in early milky stage of rice and RT-qPCR analyses confirmed the expression patterns of selected transcripts. Functional analysis of the differentially expressed transcripts indicated that genes have functional annotation and their functions are mainly involved in oxidation-reduction, metabolic, transport , transcript regulation, defense response and photosynthetic processes. Based on the functional annotation of the differentially expressed genes, the possible process that regulates these differentially expressed transcripts in rice grain responding to Zinc at the early milky stage was further analyzed. The functional classification of those genes indicated their connection with various metabolic pathways, Zinc transport, signal transduction, transcriptional regulation, and other processes related to growth and development in early milky stage of rice. Using Illumina sequencing technology, the differences between the transcriptomes of high zinc content and low zinc content lines the early milky stage was described here for the first time. The candidate transcripts may provide genetic resources that may be useful in the improvement of Zinc concentration of rice. The model proposed here is based on differences in expression and transcription between two rice lines. In addition, the model may support future studies on the molecular mechanisms underlying plant responses to Zinc.

Rice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remain as a great challenge, it is important to establish piratical ways to manage them. A core collection, by definition, refers to a subset of entire population but preserves most of the possible genetic diversity, enhancing the efficiency for germplasm utilizations. Here we reports the whole genome resequencing of the 137 Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in Korean genebank of Rural Development Administration (RDA). We implemented the Illumna HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8x depth using Nipponbare as a reference. Comparisons of the sequences with the reference genome yield more than 15 million(M) single nucleotide polymorphisms (SNPs) and 1.3M insertion/deletion (INDELs). Phylogenetic and population analyses using 2,046,529 high quality SNPs successfully assigned each rice accessions to the relevant subgroups, suggesting those SNPs comprehensively capture evolutionary signatures accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for 4 exemplary agronomic traits from the KRIC_CORE manifest the utility of KRICE_CORE, identifying previously defined gene or novel genetic polymorphisms that potentially regulate the important phenotypes. This study provides strong evidences that the size of KRICE_CORE is small but contains such a high genetic and functional diversity across the genome. Thus those resequencing results will be useful for future breeding, functional and evolutionary studies in the post-genomic era.

An important worldwide plant source of dietary protein and oil, modern breeding and improvement of soybean is suffered from a narrow cultivated germplasm relative to other crop species likely because of underuse of wild soybeans as breeding resources. SNP genotyping array is regarded as a promising tool for dissecting wild and cultivated germplasms to find important adaptive genes by high-density genetic mapping and genome-wide association studies (GWAS). Here, we present the establishment of a large soybean SNP array and its use for diversity analysis and high density linkage mapping. More than 4 million high-quality SNPs identified from 16 high-depth and 31 low-depth soybean genome resequencing data were used to select 180,961 SNPs for the AxiomÒ SoyaSNP array. Our validation analysis for a set of 222 diverse soybean lines showed that a total of 171,161markers were of good quality for genotyping. Of the converted SNPs, 82.6% 82.6% SNPs had a marker spacing of less than 9 kb and 17.4% SNPs greater than 9 kb with the 297 inter-SNP spacings of >100 kb and with 812 kb of the largest spacing, thereby suggesting that our array is likely suitable for GWAS of soybean germplasm. This array is being used to construct high-density genetic map in populations generated from intermatings of two cultivated and two wild soybeans, with an objective to confirm large structural variations of chromosomes using the ultra-high-density maps

Bt gene derived from the B. thuringiensis has been used for developing GM crops, and corn, cotton and soybean producing B. thuringiensis toxins have been on the market for last 17 years or so creating a huge GM seed industry. One of the notorious pests in brassica crops is diamondback moth (DBM). In order to protect the insect plague of crops from DBM, 4-5 billion dollars have been wasted annually for applying integrated measures in worldwide. Major prevention is use of pesticides that may build the contamination level of chemicals in the ground and this practice threats the environment and ecosystem. An alternative is to develop GM brassica crops and therefore we have developed GM cabbages resistant DBM using bt gene. Lots of T0 cabbages were tested for resistance and independent GM cabbages resistant to DBM were selected. Molecular analysis was conducted to find if GM cabbage holds one copy transgene and intergenic insertion. We found an independent GM cabbage and it contained a singly copy of the transgene without disturbing the insertion site. This one called C95 line with an status of event have been self-crossed for two generation (T2). Also we are working the development of GM cabbage with different vector that contains bar gene as a selection marker. So far 17 T0 cabbages have been obtained by bar selection.

Mungbean (Vigna radiata) is a fast-growing, warm-season legume crop that is primarily cultivated in developing countries of Asia. We constructed a draft genome sequence of mungbean to facilitate genome research into the subgenus Ceratotropis and to enable a better understanding of the evolution of leguminous species. The draft genome sequence covers 80% of the estimated genome, of which 50.1% consists of repetitive sequences. In total, 22,427 high confidence protein-coding genes were predicted. Based on the de novo assembly of additional wild mungbean species, the divergence of what was eventually domesticated and the sampled wild mungbean species appears to have predated domestication. Moreover, the de novo assembly of a tetraploid Vigna species (Vigna reflexo-pilosa var. glabra) provided genomic evidence of a recent allopolyploid event. To further study speciation, we compared de novo RNA-seq assemblies of 22 accessions of 18 Vigna species and protein sets of Glycine max and Cajanus cajan. The species tree was constructed by a Bayesian Markov chain Monte Carlo method using highly confident orthologs shared by all 24 accessions. The present assembly of V. radiata var. radiata will facilitate genome research and accelerate molecular breeding of the subgenus Ceratotropis.

Glucosinolates of Brassica rapa collection from Korea genebank were measured to determine total glucosinolate content and their variation of diverse glucosinolates; Around 100 accessions representing the different morphotypes and geographical origin of Brassica rapa were analysed. The principal component analysis was performed to evaluate the differences among morphotypes using the profiles of 14 glucosinolates identified from the leaves. DMRT test and box plots showed the significant difference between total glucosinolates of subspecies. Most of turnip accessions had higher gluconilates compared to the other type accessions, Chinese cabbage and pak choi. These accessions will be used for GWAS study for glucosinolate. Now they are being finger-printed by genotyping by sequencing (GBS). Among these accession, we selected a turnip accession with high amount of glucosinolate, K0466 and two Chinese cabbage accession with low amount of glucosinolate, K0015 and K0621. To analyse quantitative traits loci (QTL) for glucosinolate synthesis, these three accessions were fixed through microspore culture. Finally, six homozygous lines were selected and were crossed each other to make F1 hybrids. We just harvested F2 seeds and transferred doubled haploid plants to pots. QTL analysis for glucosinolate will be performed these F2 and DH population.

Bt gene derived from the B. thuringiensis has been used for developing GM crops, and corn, cotton and soybean producing B. thuringiensis toxins have been on the market for last 16 years or so creating a huge GMO industry. One of the notorious pests in brassica crops is diamond backmoth (DBM). In order to protect the insect plague of crops from DBM, 4-5 billion dollars have been wasted annually for applying integrated measures in worldwide. Major prevention is use of pesticides that may build the contamination level of chemicals in the ground and this practice threats the environment and ecosystem. An alternative is to develop GM brassica crops and therefore we have developed GM cabbages resistant DBM using bt gene. Lots of T0 cabbages were tested for resistance and independent GM cabbages resistant to DBM were selected. Molecular analysis was conducted to find GM cabbage to hold one copy transgene and intergenic insertion. We found two independent GM cabbages as an event and those have been self-crossed for two generation. Also we are working the development of GM cabbage with different vector that contains bar gene as a selection marker.

The C-repeat/dehydration-responsive element binding transcription factors (CBF/DREBs) are involved in an important pathway for abiotic stress-response in plants. We have identified CBF/DREB1 gene family from Brassica rapa whole genome sequence and designated them as BrDREB1s. They contain conserved nucleus localization signal, AP2/EREBP domain, and CBF/DREB1 signature, as other known plant CBF/DREB1s. By comparative genomics, we found that nine of ten BrDREB1 genes were present in seven macro-synteny blocks co-linear to four Arabidopsis counterpart blocks and also genomic organizations of their flanking regions were very similar to those for co-linear Arabidopsis CBF/DREB1 genes. In particular, three genes, BrDREB1A, BrDREB1B1, and BrDREB1C1, were closely located within a 59 kb genomic sequence, which was similar to that of their Arabidopsis counterpart genes. However, the genomic regions of those BrDREB1 genes contained additional sequences, compared to their co-linear regions in A. thaliana. The expression of BrDREB1 genes under abiotic stresses were examined by searching microarray database and by RT-PCR analysis. All of eight genes tested were highly up-regulated during cold treatment and some of them were also responsive to salt, drought, and ABA treatment. Taken together, these results indicate that CBF/DREB1-mediated stress signaling pathway is also functioning in B. rapa. On the other hand, differences in genomic organization and gene number for CBF/DREB1 are thought to cause different response to stress between B. rapa and A. thaliana. In this presentation, we will introduce more detailed results for CBF/DREB1 gene family in B. rapa.

Bt gene derived from the B. thuringiensis has been used for developing GM crops and those crops are already on the market. The aim of this study is to construct a genetic transformation with peppers using CryIAc1 gene and consequently to develop GM peppers resistant to the oriental tobacco budworm. We have developed transgenic peppers using Agrobacterium-mediated transformation, and obtained 5 T0 peppers. T0 peppers were self-crossed and T1 pepper fruits were exposed to larvae to test the survival rate. The survival rate of larvae that were fed with GM fruits decreased dramatically while with non-GM fruits the rate was not changed much. In order to establish the selection and the culturing of bug through a year, an incubating system for tobacco budworm in chamber was manufactured and a selection system under the media that are mixed with GM green pepper was obtained. Using those system, T3 peppers tolerant to tobacco budworm were selected.

We have identified ATTIRTA1 transposon, a kind of mariner-type DNA transposon from Brassica rapa genome. A total of 811 inverted-terminal repeat, ITR consisting of the both terminal on ATTIRTA1 transposon were found from B. rapa v1.1 sequence. Among them 616 ITR were paired by two in each transposon, indicating three quarters of the transposon exists in original form. Around 10 percentage of the transposon, 82 ITR was located in gene, expecially only in intron. Using these ATTRRTA1, we developed a display system modified from AFLP technique and applied for this system to analyze genetic diversity of Korea Brassica rapa core collection. The collection includes 220 accessions representing the different morphotypes and geographical origin. The analysis of population structure revealed five subgroups and the clustering patterns matched well with their morphological traits. ATTIRTA1 transposon display seems useful marker system for studying genetic relationships. Presently we have profiled the components and contents of glucosinolate in the core collection to analyze genome wide association. This collection will be helpful to identify agriculturally desirable traits from other supspecies.

family in the Brassica genome sequences by computational approach. The MITE family showed a total of 264bp length including 36bp terminal inverted repeats and remained 2bp (TA) targets it eduplication by its insertion. By searching the genome database of Brassica species, 516, 227, and 15 members were identified from 470Mbp of Brassica oleraceae, 154Mbp of B.rapa and 15Mbp of B.napus, respectively, indicating that there are approximately 692, 760, 1235 copies in B.oleracea, B.rapa and B.napus genomes,respectively. A total of 225 relatively intact MITE members, 146,68, and 11 members, which showed >80% sequence similarity and sequence coverage were identified and retrieved for MITE analysis from B.oleracea, B.rapa and B.napus genomes, respectively. Out of 225 MITE family members 159 having full structure of MITE and 66 having the truncated end either in right TIR or left TIR. Insertion polymorphism due to insertion or non-insertion of MITEs showed high level of polymorphism among accessions intra and inter species of Brassica. The new MITE would provide abetter tool for study molecular breeding in Brassica species and also helpful to understand their contribution in evolution and diversification of the highly duplicated Brassica genome.

Recent studies revealed that about 240 species in the tribe Brassiceae are derived through diploidization process from an ancient hexaploid after divergence with Arabidopsis. Most triplicates in Brassica genome show sequence-level co-linearity with a counterpart Arabidopsis sequence. We have obtained 91,511 BAC end sequences (BES) and high-resolution fingerprints (SNapShot) from 99,456 BAC clones originated three BAC libraries (HindIII, BamHI, and Sau3AI). All BESs were used for comparative genome analysis with the Arabidopsis. A total of 47,748 (52%) BESs show significant hit (E-6) with at least one spot of Arabidopsis chromosomes. And a total of 4,647 BAC clones (10%) are mapped on the counterpart Arabidopsis chromosomes by directional matches of both ends (9,294 BES) within 30-500 kb interval on Arabidopsis chromosome. These 4,647 clones span 92 Mb of Arabidopsis genome. We have selected a total of 629 BACs that span 86 Mb Arabidopsis genome with minimally comparative overlap (comparative-tile). Up to now, about 600 BACs are sequenced and most show co-linearity with the counterparts. Sequence-based genetic mapping of each BAC and their FPC information will be used as step-stone for walking and construction physical map of all chromosomes. Up to now, 513 BACs are sequence-based anchored on ten B. rapa genetic linkage groups that provide successful information as seed BACs for further extending to close clone gaps between the adjacent seed BACs and thus to complete sequencing of the individual chromosome. We are sequencing cytological chromosome 1 (R9) and 2 (R3), until now we finished about 50% of each chromosome. We also analyzed 130,000 ESTs from 29 cDNA libraries made with various tissues at various developing stage and treatments. The hybridization results of 24K microarray will be presented. All information will be provided to Multinational Brassica Genome Project (MBGP) members, soon, using web-based tool from our Arabidopsis-Brassica Genome Browser (www.brassica-rapa.org).