Rice is the major food for half of the world population. The nutrition component in rice is critical for improvement of people’s health. Vitamin E serves as important antioxidant by quenching the free radical intermediates and thus protects the cell membrane. Because of the high nutritional value and the benefits of vitamin E in human health, increasing the tocochromanol content of major agricultural crops has long been in the focus of breeding programs and genetic engineering approaches. The key genes involved in tocopherol biosynthesis have been elucidated in Arabidopsis and other model organisms. Quantitative trait locus (QTL) study performed in Arabidopsis suggested that some of these key genes and a few additional loci contribute to natural tocopherol variations. Identifying such genetic variations in rice, enrich our understanding of the genetic mechanisms controlling tocopherol variation, which can be directly applied to rice breeding programs. In this study, we used genome-wide association mapping with high-resolution density SNPs of rice core set to identify natural allelic variations, which contribute to tocopherol increase in rice

Chloroplast (cp) DNA sequence data are a versatile tool for plant identification, barcoding and establishing genetic relationships among plant species. Different chloroplast loci have been utilized to infer evolutionary relationship of plant species. Although the overall structure of the chloroplast genome is generally well conserved, a number of mutations have been observed. Thus, documentation of chloroplast sequence variation has also been an valuable asset in plant population and evolutionary studies for over two decades. Recently, advance in chloroplast genome assembly from whole genome NGS data has become available. In the present study, chloroplast variations among 295 diverse origin accessions were detected based on Oryza rufipogon, which thought to be the progenitor of cultivated rice.. Variation calling was carried out using the whole genome re-sequencing data of those accessions along with the five rice reference cp genomes. Phylogenetic and evolution analysis of the six references and 295 accessions were performed using the whole reference genome sequence and the variation data, respectively. Also, nucleotide polymorphisms of 295 rice accessions were validated by using previously characterized 50 ecotypes. Differential SNP frequency across the rice cp genome suggests a regional dependent preferential high variation occurrence during the evolution of chloroplast

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.

2-acetyl-1-pyrroline (2AP) was widely known as the principal aroma compound, it development in rice has been reported due to the loss of function of betaine aldehyde dehydrogenase gene (badh2) on chromosome 8. In previous study, a lot of haplotypes have been found of this gene, while only limited haplotypes have been proved as functional mutations. A total of 137 core set accessions, and additional 45 germplasms have been employed in this study. Finally, two new mutations have been found (3bp deletion in exon12 and C/A SNP in exon 10), and 23 haplotypes have been detected, most of them had strong relations with aroma formation. According to the sequence results, five functional markers have been developed, the markers showed a highly efficient in discriminating the special aromatic rice varieties, and displayed perfect co-segregation with the trait of fragrance in F2 population. Those new markers developed in the present study would be useful in molecular breeding of fragrant rice varieties. Based on the haplotypes, the further research is in progress.

Salt toxicity is the major factor limiting crop productivity in saline soils. Rice is an important staple food crop of nearly half of the world population and is well known to be a salt sensitive crop. The completion and enhanced annotations of rice genome sequence has provided the opportunity to study functional genomics of rice. With the rapid development of the biotechnology techniques, we can use more accurate and reliable methods to study the mechanism and function in different stress conditions. In present study, 295 rice accessions of diverse origin were re-sequenced and used for genome-wide association study (GWAS) with several germination-related traits, including germination percentage (GP), germination energy (GE), germination rate (GR), germination index (GI), salt tolerance index (STI) in salt tolerant germination stage. Phenotyping of the rice accessions were carried out at 200mM NaCl to screen salt tolerance levels. GWAS was applied to detect the associated genes related to salt tolerance in rice germination stage. Variations and haplotypes of the associated genes were detected and correlation between the phenotypes and genotypes were validated using qRT-PCR.

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.

Genetic resources play a great role in crop breeding because of containing a broad array of useful genes. Currently, the harder are rice breeders trying to develop new rice cultivars with the improved traits, they are more often handicapped by the limited availability of germplasm resources. Thus, a desirable core or heuristic (HS) set of germplasm with maximum genetic diversity can be usefully exploited to breakthrough the present and future challenges of the rice breeding. As such we previously developed the rice HS sets of 166 diverse accessions out of a total 24,368 rice germplasms. Here, we report a large-scale analysis of the patterns of genome-wide genetic variations accumulated in the HS as well as Korean rice over the time. We characterized a total of about 11.8 millions of single nucleotide polymorphisms (SNPs) across the rice genome from resequencing a total of 295 rice genomes including 137 HS and 158 KB rice sets, with an average of approximately 10x depth and > 90% coverage. Using about 460,000 high-quality SNPs (HQSNPs), we specified the population structure, confirming our HS set covers all the rice sub-populations. We further traced the relative nucleotide variabilities of HQSNPs and found the level of the diversity was dynamically changing across the KB genome, which reveals the selection history of KB lines in the past and present. In addition, the results of our genome wide association study (GWAS) suggests that our HS can be also a good reservoir of valuable alleles, pinpointing those alleles underlying the important rice agronomical traits. Overall, the resequencing of our HS set re-illuminates the past, present of the germplasm utilization, which will support the Korean rice breeding in the future.

Most eukaryotic organisms, including plants, display specialized cellular and behavioral rhythms with a period of approximately 24 hours. The circadian clock generates this rhythm to convey daily or seasonal basis of temporal information, coordinating the proper phasing of many important cellular processes. Temperature compensation (TC) is one of the defining features of the clock mechanism. Under this function, the speed of the clock or period remains relatively constant over physiologically relevant temperatures, unlike the biochemical reactions. Thus, TC allows organisms to sustain their life ordinarily in various thermal environments by providing an accurate measure of the passage of time regardless of surrounding temperatures. Previously, Edward and his colleagues performed a quantitative trait loci (QTL) study to find TC related natural variations in the recombinant inbred line (RIL) population from two Arabidopsis ecotypes, which are adapted to different thermal environments; one parent is Cvi accession (Cvi) which originates from the warm climate, Cape Verde Island, and the other is Ler accession (Ler) from Northern Europe. For the two most significant QTLs, the core clock components in Arabidopsis clock, GIGANTEA (GI) and ZEITLUPE (ZTL) are proposed as strong candidates. Moreover, the amino acid substitution leading to GICvi and ZTLCvi (Ler to Cvi) are suggested to be the causal factors for the TC QTLs respectively. However, precise molecular mechanisms of these natural variations on TC are still not understood well. Here, we elucidate the molecular impact of the natural variation shaping GICvi and ZTLCvi on TC function. GICvi and ZTLCvi post-translationally regulate ZTL stability in antagonistic way, resulting in the opposite period/clock effects mediated by ZTL protein abundance. However, if both GICvi and ZTLCvi are present, they mutually balance their own effect on ZTL, which in turn supports TC capacity of Cvi especially at high temperatures. Considering the amino acid residues in GI and ZTL, where the natural variations arise, are highly conserved across many important crop species including rice, corn, cabbage and etc., this research will give valuable insights into the TC related thermal adaptive processes in Arabidopsis as well as those important crop plants.