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.

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.

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.

Rice is the most important staple food crop of almost half of the world`s population. In rice, seed longevity is major factor for production and storage potential of seeds. But it is faced with grain degradation and loss of seed viability. Lipoxygenases(LOX) are a family of enzymes related to the seed longevity. LOX activity in rice grain is present in a bran-milling fraction. It is also observed that rice embryos contains three isozymes activites, Lox1, Lox2 and Lox3. Among those, the Lox3 isozyme is known as the major component in the embryonic tissue. In this study, genetic structure variability of three seed longevity related genes, Lox1, Lox2 and Lox3 were examined by using whole-genome resequencing data of 137 accessions of rice core set. The new SNPs and InDels in the exon regions identified through haplotyping analysis would be useful to develop new varieties with improved storage ability of rice in the future molecular breeding.

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.

Amaranth (Amaranthus sp. L.) is an important group of plants that includes grain, vegetable, and ornamental types. Centers of diversity for Amaranths are Central and South America, India, and South East Asia, with secondary centers of diversity in West and East Africa. The present study was performed to determine the genetic diversity and population structure of 75 amaranth accessions: 65 from South America and 10 from South Asia as controls using 14 SSR markers. Ninety-nine alleles were detected at an average of seven alleles per SSR locus. Model-based structure analysis revealed the presence of two subpopulations and 3 admixtures, which was consistent with clustering based on the genetic distance. The average major allele frequency and polymorphic information content (PIC) were 0.42 and 0.39, respectively. According to the model-based structure analysis based on genetic distance, 75 accessions (96%) were classified into two clusters, and only three accessions (4%) were admixtures. Cluster 1 had a higher allele number and PIC values than Cluster 2. Model-based structure analysis revealed the presence of two subpopulations and three admixtures in the 75 accessions. The results of this study provide effective information for future germplasm conservation and improvement programs in Amaranthus.

Direct seeding of rice is increasingly being practiced in both rainfed and irrigated areas because of labor shortage for transplanting and opportunities for crop intensification. However, slow seed germination and delayed seedling establishment will become a major problem for rice production in flood-prone lowland areas as sowing method shifts from transplanting to direct seeding. Identification of anoxia-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, genetic structure variability of three AG related genes, Sub1 (Sub1A, Sub1B, Sub1C), Sub2 (OsGAPPH) and Ramy3D were examined by using whole-genome resequencing data of 84 accessions of rice core set. Some new SNPs and InDels found in exon part of anaerobic germination related genes in the present study would be useful in developing markers to identify the submergence resistant varieties in the future molecular breeding.

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.