본 연구는 효율적인 자원보존과 유전자원의 작물육종 활용 성 제고를 위한 기초정보제공을 목적으로, 29개 SSR marker 를 이용하여 아시아지역의 10개 국가에서 수집된 벼 유전자원 에 대해 유전적 다양성 및 집단 구조 분석을 수행하였다. 1. 총 85점의 벼 유전자원이 수집되었으며, 29개 SSR 마커 에 의해 증폭된 allele 수는 총 342개 였다. Allele 수는 2 개에서 28개 범위로 나타났으며, 마커당 평균 allele 수는 11.8 개 였다. 유전적 다양성을 나타내는 genetic diversity와 PIC 값의 범위는 각각 0.12-0.93과 0.11-0.93으로 나타났고, 평균은 각각 0.73과 0.71로 나타났다. 2. 국가별 벼 자원의 유전적 거리를 기초로 유연관계를 분 석한 결과 2개 그룹으로 구분되었다. BⅠ 그룹에는 남아시아 지역에 속하는 스리랑카, 인도, 방글라데시, 파키스탄이 포함 되었고, BII 그룹에는 라오스를 제외한 동남아시아 지역인 미 얀마, 부탄, 베트남, 필리핀, 태국이 포함되었다. 3. 수집 국가별 마커당 평균 allele 수는 미얀마가 1.28개로 가장 낮았고, 필리핀이 7.03개로 가장 높았으며, PIC 값 역시 필리핀이 0.64로 가장 높은 값을 보였고, 미얀마는 가장 낮은 0.15로 관찰됐다. 4. 유전적 거리와 Structure ver2.2를 이용하여 집단의 구조 를 분석한 결과, 75%의 확률에서 85개 자원 중 80개 자원 (64.1%)는 3개의 subpopulation으로 나눌 수 있었으며, 5개 자원(5.9%)은 유전적으로 혼입된 형태를 나타냈다. 5. 각각의 subpopulation은 수집 국가의 특성과 일치하지 않 았으며, 대부분 자원은 각각의 subpopulation에 불규칙적으로 분포되었다.

종실 돌연변이를 유기하여 미질개선을 위한 육종으로의 적극적인 활용을 목적으로 얻어진 신동진벼 돌연변이 계통의 작물학적 특성과 종실 저장단백질을 변이모본과 비교 분석을 검토하여 얻은 결과를 요약하면 다음과 같다. 1. 종실 변이계통의 작물학적 특성은 변이모본보다 생태특성의 출수기에서는 대부분 조생의 경향을 보였고, 간장 및 수장은 짧은 경향을 나타냈고, 또한 종실특성의 현미 길이, 현미폭 및 천립중에서도 변이모본보다 짧거나 낮은 정도를 나타냈다. 2. SDS-PAGE 분석결과 opaque 군의 SM-22와 giant embryo 군의 SM-34는 글루테린 폴리펩타이드에서 높은 농도를 보였고, floury 군의 SM-23, shrunken 군의 SM-26, sugary 군의 SM-31은 전단백질 농도패턴은 낮게 보이면서 55kDa 이상의 고분자 band에서 다양성을 나타냈다.

Object : This study is designed to evaluate the clinical therapy of acupuncture by the data of DITI(Digital Infrared Thermographic Imaging) and FNT(Facial Nerve stimulation Test) examination and the changes of clinical symptoms after the therapy of acupuncture in the patients with Bell's palsy. Contents : The conservative therapy with acupuncture was performed during 1-8weeks. The acupuncture points of S4, S6, G14, S2, BL2, SI18, TE23, LI4 and S36 were used. In the pre- and post therapy, DITI examinations was performed in patients who had Bell's palsy and were treated by acupuncture, and then tried to correlate the results of clinical symptoms with the difference of thermographic findings. And FNT examinations were performed in the same patients above, and then tried to correlate the results of clinical symptoms with the difference of nerve response findings. Setting : The standard routine thermographic examination with thermography (DITI) and nerve response with FNT(Facial Nerve Stimulation Test) were performed in the 16 patients with Bell's palsy at pre- and post acupuncture. Patients : Thermographic imaging of 16cases was analyzed. They had diagnosed Bell's palsy. They were treated by acupuncture and moxibustion therapy in Wonkwang Oriental Hospital from Jauary, 1999 to February, 2000. Results : 1) The results of treatment showes that 56.25% of patients achieved clinical excellent recovery and 31.25% achieved good recovery. After compairing the DITI results before and after treatment, we found 43.75% of patients achieved excellent recovery and 43.75% achieved good recovery. 2) After compairing the FNT results before and after treatment, we found 25% of patients achieved excellent recovery and 56.25% achieved good recovery. Conclusion : 1) Acupuncture showed good results over 87.5% in clinical evaluation and 87.5% in DITI. Thermographic examination showes terapeutic effect of acupuncture treatment. 2) Acupuncture showed good results over 87.5% in clinical evaluation and 81.25% in FNT. FNT showes nerve response recovery effect of acupuncture treatment.

Objective of this study was to investigate the difference of cadmium (Cd) levels in rice grains from non-polluted fields and to define the gene associated with Cd uptake for producing safety food. Cd was analyzed by Inductively Coupled Plasma Mass Spectrometer (ICP-MS). The average concentration of Cd in rice grains was 0.943 μg/kg and Cd levels ranged from 0.050 to 5.699 μg/kg. Genome-Wide Association study (GWAS) based on phenotype data for Cd levels was performed. However, results of GWAS were affected by subpopulation structure and caused false positive. Therefore, GWAS for rice ecotypes (temperate Japonica, tropical Japonica, Indica, Aus, Aromatic, and Admixture) was performed to minimize false positive. GWAS results showed that Os01g0611300, Os01g0611900, Os01g0611950, Os01g0612000, Os01g0612200, Os11g0444400, Os11g0444700, Os11g0444800, and Os11g0444900 genes have significant correlation with Cd levels in rice grains. The sequences of these genes were compared to sequence positions of each other gene (haplotype analysis). According to the results of haplotype analysis, Cd levels of non-synonymous group were higher than other groups and sequence of non-synonymous group was similar to that of Indica. These results were corresponding to the previous research result that Cd levels of Indica were higher than Japonica. Therefore, candidate genes detected through GWAS need to be examined by knock-out or cross breeding.

'Hyowon 2’, a new medium-late maturing glutinous rice variety with short clum and lodging tolerance was developed by the rice breeding team of Pusan National University in 2013. This cultivar was derived from a cross between 'Junam’ as a short clum source and ‘Donna’ with a good glutinous properties. During selected by the pedigree breeding method, until F8 generation. As a result, a promising line, JS22-3-24-1-6-2-1-1-1, was advanced and designated as the name of ‘SP 105’ in 2012. This variety headed on Aug. 22 is 9 days later than ‘Dongjinchal’ in middle plane. The Culm length and panicle length of this variety was 65.6 cm and 22.5 cm, respectively. This variety has about 14.4 tillers per hill and 113 spikelet numbers per panicle. The ratio of ripened grain is about 93.0% and 1000-grain weight was 18.4 g in brown rice. This variety has higher α-tocotrienol content compared to that of ‘Hwasunchal’. The yield performance of brown rice was 4.81 MT/ha in local adaptability test.

In rice (Oryza sativa L.), there is a diversity in flowering time that is strictly genetically regulated by plenty of genes. The floral transition from vegetative to reproductive development is a very important step in the life cycle of a flowering plant. Orthologous genes, which are homologous genes that diverged after a speciation event, generally maintain a similar function in different species. with a McDonald-Kreitman Test (MKT), we examined more than 10,000 orthologous genes between rice (Oryza sativa) and Brachypodium (outgroup), based on different phenotypic groups, to find some fast evolutionary genes of rice flowering time. Three groups with early flowering time (group 1), midium flowering time (group 2) and late flowering time (group 3) were separated and each group was examined for McDonald-Kreitman Test (MKT). Total 70 fast evolutionary genes under a positive selection were found in the three groups, and 14, 42 and 14 genes were specific existed in group 1, 2 and 3, respectively. Annotation of these genes were conducted and the predicted functions were also surveyed. In addition, network analysis of these characterized genes were also investigated to infer related pathways. And also, the association study between the one early flowering factor and the flowering time phenotype was performed and indicated that this gene is significantly correlated with flowering time in rice. These results suggest that using this orthologous based method, we could find some important candidate genes underlying flowering time regulations.

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.

Although the overall structure of the chloroplast genome is generally conserved, a number of sequence variations have been identified, which are valuable for plant population and evolutionary studies. Here, we constructed a chloroplast variation map of 30 landrace rice strains of Korean origin, using the Oryza rufipogon chloroplast genome (Genbank: NC_017835) as a reference. Differential distribution of single nucleotide polymorphisms (SNPs) and indels across the rice chloroplast genome is suggestive of a region-specific variation. Population structure clustering revealed the existence of two clear subgroups (indica and japonica) and an admixture group (aus). Phylogenetic analysis of the 30 landrace rice strains and six rice chloroplast references suggested and supported independent evolution of O. sativa indica and japonica. Interestingly, two “aus” type accessions, which were thought to be indica type, shared a closer relationship with the japonica type. One hypothesis is that “Korean aus” was intentionally introduced and may have obtained japonica chloroplasts during cultivation. We also calculated the nucleotide diversity of 30 accessions and compared to six rice chloroplast references, which shown a higher diversity in the indica and aus groups than in the japonica group in lower level substitution diversity.

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.

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. Thus we searched a possible allelic source from Heuristic or core rice set, which is derived from a total 24,368 rice germplasms, to increase the mineral content in rice varieties. The concentration and distribution of Fe in 137 accessions of core set of brown rice grain flour sample were determined by ICP-OES. The range of the concentration and distribution of Fe in 137 core accessions of brown rice grain were wide, from 0.088mg/L to 1.205mg/L, with mean 0.292mg/L. To examine Fe related genes, whole-genome resequencing data of 137 accessions of rice core set were analyzed by Genome Wide Associations Study (GWAS). Our result suggests that Fe determined by ICP-OES facilitates the evaluation of the differences in Fe composition for future rice breeding program

In rice (Oryza sativa L.), there is a diversity in flowering time that is strictly genetically regulated. The floral transition from vegetative to reproductive development is a very important step in the life cycle of a flowering plant. Although the genetic pathway for short-day flowering in rice is relatively well understood, the naturally occurring molecular mechanisms underlying flowering time diversity of the cultivated rice are still not clear. Resequencing of 295 rice accessions including 137 HS and 158 KB rice accessions, was recently finished with an average of approximately 10x depth and > 90% coverage. A wide range of variation in flowering time was observed within a diversity research set of 295 accessions ranging from 28 to 72 days. GWAS was performed using the resequencing data to investigate the candidate genes associated with flowering time in rice. Our GWAS result suggests that two SNPs in the promoter or 3’ UTR of the ‘Arabidopsis CO’ homolog FBH1 are potentially associated with early flowering. The new SNPs found in the FBH1 locus would be useful in developing markers to screen the varieties with early flowering time in the future molecular breeding.

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.

Anaerobic germination (AG) is plays important role in submergence resistance which is an important trait for rice production in flood-prone lowland areas. Slow seed germination and delayed seedling establishment due to flooding become major problem for modern sowing methods such as direct seeding and environmental friendly good agricultural practices especially using young seedling age. In total, 137 diverse rice accessions were evaluated for anerobic germination ability. Submergence 1 (SUB1) which is induced ethylene response factors is suggestive because genes belonging to this gene family play a crucial role in rice tolerance to submergence. In this study, haplotype variations of three AG related genes, SUB1 (SUB1A, SUB1B, SUB1C) were examined using whole-genome resequencing data of 137 accessions of rice core set. The new SNPs and InDels found in the exon of the sub1 loci would be useful in developing markers to screen the varieties with strong anaerobic germination ability in the future molecular breeding

As one of the most important crop, rice is not only a staple food of half world’s population but a wonderful model plant, which has been leading the evolution and functional genomics study. The next-generation sequencing technology are expediting rice genomic study, by providing a simple but powerful way. In this study, we re-sequenced a core collection of 137 rice accessions from all over the world along with 158 Korean breeding varieties. Finally, 6.3G uniquely mapped reads were obtained, and about 10 million SNPs and ~1.2 million InDels were identified with average sequencing depth of 7.5X. These will help us to maximize our germplasm utilization and assists all the deep research in population dynamics and functional studies. Here, we’d like to show the approaches applied to resequencing data mining and on-going activities.

A sugary mutant with low total starch and high sugar content was compared with its wild type Sindongjin for grain-filling caryopses. In the present study, developing seeds of Sindongjin and sugary mutant from the 11th day after flowering (DAF) were subjected to RNA sequencing (RNA-Seq). A total of 30,385 and 32,243 genes were identified in Sindongjin and sugary mutant. Transcriptomic changes analysis showed that 7,713 differentially expressed genes (DEGs) (log2 Fold change ≥1, false discovery rate (FDR) ≤ 0.001) were identified based on our RNA-Seq data, with 7,239 genes up-regulated and 474 down-regulated in the sugary mutant. A large number of DEGs were found related to metabolic, biosynthesis of secondary metabolites, plant-pathogen interaction, plant hormone signal transduction and starch/sugar metabolism. Detailed pathway dissection and quantitative real time PCR (qRT-PCR) demonstrated that most genes involved in sucrose to starch synthesis are up-regulated, whereas the expression of the ADP-glucose pyrophosphorylase small subunit (OsAGPS2b) catalyzing the first committed step of starch biosynthesis was specifically inhibited during the grain-filling stage in sugary mutant. Further analysis suggested that the OsAGPS2b is a considerable candidate gene responsible for phenotype of sugary mutant.

Preharvest sprouting resistance (PHS) causes the reduction of grain yield and also affects the quality of grains, resulting significant economic losses. PHS and its related traits were evaluated and observed in wide range among the 137 diverse rice accessions. To mine the associated signals for PHS resistance, genome wide association study (GWAS) was performed using phenotype data and whole genome resequencing data of 137 diverse rice accessions. This study not only could detect the previously identified dormancy and PHS associated genes but also explore the new candidate genes associated with the PHS and related traits. An example of them is seed dormancy 4 (Sdr4) gene which was found to be associated with germination % at day 14 (D14). This study provided the potential associated candidate genes which might be very useful to improve the PHS resistance in future rice breeding.

‘진상’은 공주대학교에서 2013년도에 육성한 고품질 저아밀로스 품종으로 주요특성과 수량성을 요약하면 다음과 같다. 1.‘진상’은 중서부평야 보통기 보비재배에서 출수기가 8월 11일로 ‘추청’보다 약 11일 빠른 중생종으로, 이삭길이는 19 cm로 ‘추청’과 비슷한 수준이었으나, 간장은 75.2 cm로 ‘추청’보다 짧다. 2.‘진상’의 정현비율은 81.2%로 ‘추청’과 비슷한 수준이며 현미길이와 폭이 각각 4.86 mm, 2.91 mm로 ‘추청’에 비해 약간 길고, 넓은 단원형 품종이다. 현미 천립중은 20.91 g 수준이며, 수량성은 457 kg/10a로 ‘추청’과 비슷하였다. 3.‘진상’은 중간찰벼로서 투명도가 중간 정도의 불투명 배유 특성이고, 알칼리 붕괴도는 6.4 정도이며, 아밀로스함량은 11.9%로 대조품종 19.1%보다 낮고, 도요 식미기로 측정한 밥 윤기치는 대조품종인 ‘추청’보다 높게 나타났다.

Rice (Oryza sativa) is an excellent model monocot with a known genome sequence for studying developmental seeds. In the study, the seeds of 10th day after flowering (DAF) were conducted RNA-Seq of the variety Shindongjin and Sugary mutant using RNA-seq technique. Approximately 202 and 214 million high-quality paired-end reads (101-bp in size) were generated in Shindongjin and Sugary mutant, respectively. Comprehensive analysis on the transcript levels of genes which encode starch-synthesis enzymes is fundamental for the assessment of the function of each enzyme and the regulatory mechanism of starch biosynthesis in seeds. Quantitative real-time PCR was also used to validate the expression profiles of 28 rice genes encoding six classes of enzymes, viz., ADPglucose pyrophosphorylase (AGPase), starch synthase, starch branching enzyme, starch debranching enzyme, starch phosphorylase, and disproportionating enzyme at different developmental grain- filling stages (DAF 1-14) between Shindongjin and Sugary mutant. The results showed that the expression of most of starch synthesis genes were up-regulated except the cytosolic AGPase small subunit2b (AGPS2b), which sharply decreased at grain-filling stages in Sugary mutant. These results will expand our understanding of the complex molecular and cellular events in rice grain-filling stages and provide a fundamental understanding of future studies on developmental endosperm in rice and other cereal crops.

AGenome-wide association studies (GWAS) have proven a useful technique for identifying genetic loci responsible for natural variation in rice. With the fast developed next-generation sequencing technology, it is possible for people to carry out GWAS by phenotyping different traits. However, how to make full use of huge data, abandon unnecessary data, and solve the problem of data application effectively seems still an obstacle for many researchers. Taking the case of whole-genome resequencing of Korean authentic rice core set, here we present a general technological path of GWAS including: 1) a schematic view of sequencing-based GWAS in rice; 2) a user-friendly and interactive web application for GWAS in rice by the aid of experience from Arabidopsis; 3) Haplotype and association analysis of candidate genes in a certain mechanism pathway, giving 10 starch synthesis genes as example; and 4) functional validation by Trans- and Mata-Omics analysis.