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 purpose of this study was to develop the cost-effective and efficiency seed longevity prediction method of rice (Oryza sativa L.) germplasm for viability monitoring. To find an optimum predicting method for rice seed longevity at genebank, an accelerated ageing (AA) test, a controlled deterioration (CD) test and a dry-heat treatment (DHT) were conducted to the four groups of rice germplasm based on ecotype, such as Indica, Japonica, Javanica and Tongil type. Among the three artificial aging treatments, the dry-heat treatment of 36 hours at 90°C is suggested as a routine predictive test method of rice germplasm longevity at a genebank. The distribution of germination rate on 3,066 accessions which conserved 26.5 years at 4°C showed similar trend with the result of distribution by dry-heat treatment at 90°C on 36 hours using 106 accessions of rice selected samples which composed four ecotype groups. The results show that the dry-heat treatment affect not only predicting the rice seed longevity but also determining effective interval for monitoring germination of rice germplasm in genebanks.

Rice is the staple food for more than half the world’s population. It is known that 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. Here, we performed Genome-Wide Association Study(GWAS) with high-resolution density SNPs and InDels to identify natural allelic variation in zinc increase from Heuristic or core rice set, which is derived from a total 24,368 rice germplasms. The range of the concentration and distribution of zinc in 137 core accessions of brown rice grain were wide, from 7.86ppm to 31.76ppm, with mean 18.97ppm. In particular, GWAS result show that the high peak found in Chromosomes (1, 4, 6, 8). The new natural variants identified through haplotyping analysis would be useful to develop new rice varieties with improved storage ability of the valuable mineral through the future molecular breeding.

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.

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

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.

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.

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.

Rice (Oryza sativa L.) is one of the most important staple foods that feed more than 50% of the world’s population. With the improving of people’s living standard, eating quality of rice become the most important aims in current breeding programs. Amylose content (AC) and gelatinization temperature (GT) are the two main measures to estimate the rice grain quality. In rice, a total of 27 genes directly involved the rice starch biosynthesis effecting on the rice eating quality. It clearly identified chromosome 6 to be rich in the genes related to AC and GT properties (GBSS I, SSIIa and SBE I) along with other genomic regions scattered in rice genome. Rice blast, caused by the fungal pathogen M. oryzae, is the most devastating disease of rice and severely affects crop stability and sustainability worldwide. Many fungal genes involved in pathogenicity and rice genes involved in effector recognition and defense responses have been identified over the past decade. A total of 99 and 22 blast resistance genes have been identified and cloned; in which 45% were found in japonica cultivars, 51% in indica cultivars, and the rest 4% in wild rice species. Among them, three major resistance gene clusters have been characeterized: the Pik locus on Chromosome 11, and the Pita locus on Chromosome 12, the Piz locus on Chromosome 6 closely to the starch synthesis-related genes. These results could be important clues for studying the relationship between resistance / susceptible materials and eating quality.

One of the biotic stresses in rice production is rice blast disease caused by Magnaporthe oryzae, which is one of the most destructive fungal diseases in rice. We outlined an approach towards genome wide association study for the blast disease resistance in rice. In total, 295 rice accessions including 137 Heuristic Set accessions (HS) and 158 Korean Bred varieties (KB) were screened for the rice blast disease resistance. Firstly, Magnaporthe oryzae were inoculated to the rice seedlings of two weeks after germinations. Then, evaluation of the disease symptoms and checking the crossing point (CP) value were conducted one week after inoculation. To quantify the CP value, real-time polymerase chain reaction (PCR) was employed in combination with the primer pair and Taqman probe specific to Magnaporthe oryzae HYDROPHOBIN class 1 (MHP1) which is an indispensable unigene encoding HYDROPHOBIN for normal virulence expression. Based on these CP values from the PCR reactions containing a series of increasing concentration of cloned amplicon or fungal genomic DNA, correlation among the template’s copy number or its amount and amplification pattern was calculated. Reliability of this equation was further confirmed using the DNA samples from the rice leaves infected with compatible or incompatible strains of M. oryzae. These steps are still being undertaken, and after the complete process of disease resistance phenotyping for the whole population containing 295 accessions, GWAS will be performed to examine the associated genes involving in blast resistance mechanism using the whole genome resequencing data of 295 accessions. This approach would be a useful technique for identifying genetic loci responsible for natural variation in rice blast disease resistance and ultimately, new R genes which can improve the blast resistance in rice.

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.

‘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.