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.

Soybean (Glycine max (L.) Merr) is a short day plant and has been adapted to various climates and environments during cultivation. However, the cultivation area is restricted to a very narrow range of latitudes. To date, nine major genes (E1 to E8 and J) have been reported to control the flowering time and maturity. Here, we evaluated the role of E2, E3, E4, and their paralogue genes in late flowering soybean cultivars under long day (LD) conditions using Soybean yellow common mosaic virus (SYCMV)-based virus-induced gene silencing (VIGS) system. A total of nine VIGS constructs were infiltrated into two fully expanded cotyledons and primary leaves. After inoculation with these VIGS constructs on Jangyeobkong, which is a late-flowering cultivar, phenotypic traits were evaluated for the first flowering dates (FFDs) and pod maturities under LD conditions. The FFDs of the silenced plants occurred 50-56 days after sowing (das), while the non-silenced plants bloomed on 60-61 days. We found that the E3 paralogue-silenced plants flowered the fastest and responsive genes were identified to be associated with the promotion of flowering time. As the knock-down of E3 paralogue, expression of E1 was up-regulated, E2 was no difference, E3 and E4 genes were down-regulated in the silenced plants. Expression of GmFT2a and GmFT5a is known to be controlled by E3 and E4. Interestingly, GmFT5a were highly expressed in SYCMV:E3 paralogue-silenced plants, whereas the expression of GmFT2a was not significant. These results support that GmFT5a is able to independently promote flowering under LD conditions.

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.

The amount of carbon dioxide emission is continuously increasing and many researchers are concerned about climate change caused by its emission. Hence, some technologies which can reduce its emission have been developed and commercialized in many industries. These technologies are commonly called Carbon Capture and Storage (CCS) technology. In conventional CCS technology, carbon dioxide gas produced from industrial processes was usually captured by basic liquid absorbent such as monoethanolamine(MEA) and so on. After it is captured by those absorbents, they was flown to desorption step and was compressed at high pressure and transported to suitable places such as deep ocean or deep underground. However, there exist some problems when carbon dioxide is stored in such places. For instance, leak into the atmosphere can occur. Also, some nations including Korea may have difficulty finding suitable places for its storage since area of the nations is not that large and the ground is not stable. So, the method that can utilize captured carbon dioxide has been developed. When carbon dioxide is combined with metal cation such as calcium ion, it becomes calcium carbonate (CaCO3) which can be used for various purposes like construction materials, pharmaceutical manufacture, additives and so on. This is called Carbon Capture and Utilization (CCU) technology. In this research, seawater was used to supply calcium ions. There contained much amount of calcium component in seawater and amount of seawater is virtually limitless. MEA was used as absorbents and saturated by simulated flue gas. Pretreated seawater was then added to saturated absorbent. When carbon dioxide gas is dissolved to MEA, it exist in forms of ions and they can easily produce precipitated calcium carbonate (PCC) salts by reacting with calcium ions contained in seawater.

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.

Anthocyanins are the primary pigments in black, blue, and purple cereal grains. Recently, anthocyanins have been recognized as health-enhancing substances due to their antioxidant activity. Anthocyanin-pigmented barley grains can be a stable source of anthocyanins as well as β-glucan. Cloered barley as purple, blue and black barley consumptions are rapidlly growing presently due to their healthy functional food ingredients in Korea. Color barley cultivars accumulate purple pigments in the stem, awn, lemma, palea, and pericarp during seed maturation. The large consumption of barley in human foods is almost pearled products. Here we investigated composition of pearled barley and pearling by-products of korean colored barley varieties by degree of pearling. Barley grains from four hull-less colored barley varieties, Zasoojeongchal, Boseokchal Ganghochung and Huknarae were pearled to various degrees(5-50%). The composition (β -glucan, total phenol, proanthocyanidin and total anthocyanin) of pearled barley fractions flour and pearled barley grain was determined. β-glucan content was not changed seriously in pearled barley grain according to increasing pearling degree. Total phenol and proanthocyanidin content was decreased. β-glucan content was increased in pearling by-products according to increasing pearling degree and total phenol and proanthocyanidin content was decreased. Total anthocyanin content also was decreased in pearled barley fractions flour by the degree of pearling.

Current consumers have interest in nutrition and health. So, the interest in barley for other food and industrial applications is increasing. Noodles, which have been consumed largely in korea, are usually made from wheat flour, salt and appropriate amount of water. A New Six-rowed Naked Barley Cultivar “Dahan” was developed in 2012, have high winter hardness, lodging tolerance and good noodle property. It was crossed in 2001, and an elit line was selected in 2010 and designated as ‘Iksan 106’. It showed good agronomic performance in the regional yield trials (RYT) from 2010 to 2012. The average heading and maturing dates of “Dahan” were April 29 and June 3 in paddy field, which were two day earlier than those of the check cultivar ‘Saessalbori’ respectively. The new cultivar, “Dahan”, had 92cm of culm length and 3.9cm of spike length. It showed 625 spikes per m2, 54 grains per spike, 31.3 g of 1,000-grain weight, and 815 g of test weight. “Dahan” showed better resistance to BaYMV (Barley yellow mosaic virus) than those of the check cultivar. Its average yield of the pearled grain in the regional yield trial was 4.32 MT/ha in paddy field, which were 16% higher than those of the check cultivar. It showed higher breakdown and setback than those of the check cultivar. Texture properties of noodle was better in hardness, adhesiveness, chewiness. This cultivar would be suitable for the industrial application as noodle and bread.

We report on a unique case of diffuse large B-cell lymphoma of the cecum, which presented as a subepithelial tumor. A 62- year-old woman with abdominal pain underwent a colonoscopy, resulting in detection of a subepithelial tumor measuring 2 cm in the cecum. We performed a right hemicolectomy with diagnostic and curative intent; histological examination and immunohistochemical staining of the resected tumor indicated a diagnosis of diffuse large B-cell lymphoma. The patient achieved complete remission with combination chemotherapy.

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.

Amaranths (Amaranthus sp.) are cosmopolitan and include grain, vegetable, ornamental and weed types. Forteen simple sequence repeat (SSR) markers were used to analyze the genetic diversity of 59 accessions of cultivated amaranth from Asian countries. A total of 63 alleles were detected with an average of 4.5 per locus. The averaged values of gene diversity and polymorphism information content (PIC) were 0.35 and 0.33, respectively. Alleles per locus in accessions from South Asia was 4.35, whereas 2.93 and 3.79 alleles per locus were found in Nepal and India, respectively. The mean gene diversity in Central Asia and East Asia was 0.36 and 0.28, respectively, whereas the mean PIC values were 0.27 and 0.22, respectively. The genetic diversity and PIC of the India amaranths were higher than that of other Asian countries. The model-based structure analysis revealed the presence of three subpopulations, which was basically consistent with clustering based on genetic distance. An AMOVA analysis showed that the between-population component of genetic variance was less than 56.16% in contrast to 43.84% for the within-population component. The overall FST value was 0.56, reflecting genetic differentiation within Asian amaranths. These findings could be used for designing effective breeding programs aimed at broadening the genetic bases of commercially grown varieties.

Vitamin E and phytosterols are both valuable nutrients that act as antioxidants in human bodies. Understanding the genetic basis of these traits is necessary for the improvement of nutritional quality by breeding. In this study, 119 rice accessions of diverse origin were genotyped using 232 SSR markers to identify marker–trait associations with Vitamin E and phytosterols in rice. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r2 value for all intra-chromosomal loci pairs was 0.3361. LD between linked markers decreased with distance. Marker–trait associations were investigated using the unified mixed-model approach, considering both population structure (Q) and kinship (K). In total, 81 marker–trait associations were identified using 232 different SSR markers covering 12 chromosomes. The results suggest that association mapping in rice is a viable alternative to quantitative trait loci mapping. The results from this association mapping study will be the basis for improving rice nutritional quality.