Magnesium is important not only for the growth of rice itself, but also as an essential micronutrient component of half of the world population who are supported by rice. Here, we performed genome-wide association study (GWAS) with high-resolution density SNPs to identify natural allelic variation in Mg2+ increase from rice set, which is derived from a total 24,368 rice germplasms. The range of the concentration and distribution of Mg2+ in 295 core accessions of brown rice grain were wide, from 18.17mg/L to 57.11mg/L, with mean 39.71mg/L. In particular, GWAS result shows that the high peak found on chromosomes 3 and 11. 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.

‘Hyowon 4’, a new medium maturing glutinous rice variety was developed by the rice breeding team of Pusan National University in 2013. This cultivar was derived from a cross between ‘Boseokchal’ and ‘Donna’ with good glutinous property. During F3~F8 generation, breeding lines were selected by a pedigree breeding method. As a result, the promising line (JS23-4-39-14-5-1-1-1) with good glutinous property was advanced and designated as the name of ‘SP 106’ in 2012. This variety headed on Aug. 15, which is 2 days later than ‘Dongjinchal’ in middle plane. The culm length and panicle length of this variety was 82.4 cm and 21.1 cm, respectively. This variety has about 13.9 tillers per a hill and 100 spikelets per a panicle. The ratio of ripened grain is about 92.0% and 1000-grain weight was 20.9 g in brown rice. The yield performance was 5.03 MT/ha in local adaptability test.

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 5’, a new aromatic rice variety with high yield was derived from a cross between 'Dasan’ as a high yield source and ‘IR841-1-1-2’ as a donor for aroma. A general pedigree breeding method was applied to develop Hyowon 5. In F8 generation, a promising line, JS14-12-36-8-5-3-1-1-1, was selected and designated as the name of ‘SP 102’ in 2012. This variety headed on Aug. 14 , which is 3 days later than ‘Hwayoung’ in middle plane. The brown rice of this aromatic variety ‘Hyowon 5’ exhibited 51 odor-active volatiles including a pop corn-flavoring 2-acetyl-1-pyrroline which is exclusively detected in aroma rice varieties. The Culm length and panicle length of this variety was 83.2 cm and 26.4 cm, respectively. This variety has about 14.9 tillers per hill and 124.5 spikelet numbers per panicle. The 1000-grain weight was 20.9 g in brown rice. The yield performance of brown rice was 6.27 MT/ha in local adaptability test.

'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.

본 논문에서는 어선원 및 일반인들이 해상에서 조난을 당하였을 경우 구조를 위해 조난신호 및 위치정보를 송신할 수 있으면서, 팽창식 구명조끼에 장착이 가능한 유연한 다중대역 안테나를 제안한다. 이 안테나는 VHF-DSC 대역(156MHz), COSPAS-SARSAT 대역 (406MHz) 및 GPS대역(1,575MHz) 에서 동작하는 3중대역 안테나이다. GPS대역은 사각형 슬롯 링(square slot-ring) 형태의 평판 구조로 구 현하였고, COSPAS-SARSAT 대역과 VHF-DSC 대역은 모노폴 구조로 구현을 하였다. 또한 기판은 구명조끼 장착을 위한 유연성 확보를 위 해 0.2mm 두께를 가지는 FR4-epoxy 기판을 사용하였다. 제작된 안테나는 최종적으로 사람이 구명조끼를 장착한 상태에서 VHF-DSC, COSPAS-SARSAT, GPS 대역에서 각각 –8.8dB, -20.4dB, -10.7dB의 반사손실 특성을 나타내었다.

By the strengthening of sewage treated quality law and the amount of sewage sludge every year is increasing in Korea. However, it is difficult to disposal of sewage sludge due to ocean dumping restriction. As an alternative to this, drying, incineration, anaerobic digestion etc. is applied, which is uneconomical in most be processed by the consumption of energy. In particular, anaerobic digestion technology has been installed in the sewage treatment 65 plats in Korea’s STP(sewage treatment plant). It is most of the digestion efficiency requires the application of improved technology to less than 50%. As an improvement technology for most anaerobic digester, ultrasonic, electronic beam, ozone etc. solubilization method using has been mainly used. Therefore, in this study, after the wet milling particles of sludge to subject the sludge that has not been decomposed in the digested sludge circulating fluid of anaerobic digestion, was let examine the characteristic at the time of ozonation. The size of the particles before and after the wet milling, which is the measurement at each 105.26 μm and 77.18 μm, solubilization rate is increased to 23.5%. When ozonation after wet milling using sludge is determined as possible to improve the efficiency.

In order to breakthrough upcoming challenges for the food production, the efficient use of rice germplasm would be a indispensible. These rice germplasm, adapted from diverse eco-systems, are undiscovered treasures for rice breeders/researchers, potentially providing a broad array of useful alleles that enrich gene pools of current cultivated rice varieties. Although growing ex-situ conservation efforts are an important for preserving diverse rice genetic resources, the activity on finding the novel and favorable genetic variants from the vast genebank collection is greatly challenging, requiring extensive screening processes. Therefore, rice core collection is a powerful solution to accelerate utilizations of the exotic germplasm of the entire population. In addition, The application of whole genome re-sequencing technology would establish a potent platform for fast forward genetic study, such as genome wide association study (GWAS). The GWAS has been implemented to efficiently identify candidate genes related to various useful agricultural traits in many crop species including rice. Given the significant associations between genetic variations and phenotypic diversity does not require prior knowledge, GWAS using high genome coverage of SNP markers provides a genomics platform to dissect previously unknown adaptive or other useful genetic variation accumulated in plant germplasm resources over the times. Once pinpointing candidate genes, GWAS allows informed choice of parents for QTL analysis based on the haplotype information, along with suggesting targets for following mutagenesis and transgenics. Here, we are to report our current achievements and perspectives from GWAS and post-GWAS undertaken to dissect and exploit useful alleles underlying many agricultural traits from Rice core set, including PHS (Pre-Harvest Sprouting), salt tolerance and disease resistance and so forth. Also, we will introduce the integrated Omics based GWAS case study using transcriptomes, proteomes, metabolomes and ionomes of our rice core set.

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.

Rice (Oryza sativa L.) is one of the most important staple crops in the world, providing main energy source for more than half of the world’s population. It is even closely associated with economic and political stability in many developing countries of Asia and Africa. These days, moreover, amount of land suitable for the agriculture is shrinking due to a variety factors, such as rapid climate changes and industrializations, while rice eating human populations keeps growing. To meet the nutritional and socio-economic demands worldwide, dedicated efforts in developing superior rice varieties need to be reinforced, accumulating and combining beneficial alleles as much as possible from rice germplams. Here, we propose a pipeline for genome assisted breeding where new genomic technologies including GWAS, omics and evolutionary studies together with follow-up breeding programs are integrated. Once pinpointing candidates genes, the integrated genomics approach allows informed choice of parents for the following breeding program based on the haplotype information, in addition to providing precise molecular marker information. We also conducted proof-of-concept analysis, using various agriculturally important phenotypes for rice improvements.

Salt is the major factor limiting crop productivity in saline soils. Development of genetic basis of high salt-tolerant rice is necessary to satisfy urgent needs in rice breeding. In this study, 295 rice accessions from a Korean authentic core set were used to identify the evolution associated genes regarding salt tolerance. By using McDonald-Kreitman Test (MKT), we detected orthologous genes in rice (Oryza sativa) using Brachypodium as an outgroup to investigate fast evolved genes that express differentially based on distinct phenotypic groups. Three groups which represented the salt sensitive (group 1), salt medium tolerant (group 2) and salt tolerant (group 3) were separated and each group was examined with the outgroup in neutral and non-neutral polymorphism together with the divergence levels. Total 53 fast evolutionary genes that have a positive selection with FDR ≤ 0.05 were found in the three groups. Among them, 15, 31 and 7 genes were included exclusively in group 1, 2 and 3, respectively. Annotation of these genes showing the predicted functions were checked. Two genes were found to be related to high salt tolerance based on the previous studies. Besides, association study of the candidate gene alleles and salt tolerance phenotype was carried out, indicating that these genes were correlated with salt tolerance. All these result support that using this type of evolution study, we may find some important candidate genes which are related to important traits in rice, such as the salt tolerance, providing important information for future gene based molecular breeding and functional analysis in rice.

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.

We report the C language implementation of a program that merges SNP data from all samples and estimates various statistical quantities related to SNP. The software combines the SNP information from different samples according to the SNP position in the nucleotide sequence. The combined SNP information is converted into HapMap format that can be used as an input for genome-wide association analysis for quantitative traits. The software additionally provides estimates of the minor allele frequency, the heterozygosity ratio, and the In/Del frequency. The software is prepared as a stand-alone program and is downloadable from http://info.kongju.ac.kr/snpmerge/.

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.

Pre-harvest sprouting (PHS) results in lower yields for rice and other crops, especially in rainy season before harvest. By using gene based functional studies to reveal the mechanism of PHS related pathways can be a good way in breeding for more PHS resistant accessions. Orthologous genes, which are homologous genes that diverged after a speciation event, generally maintain a similar function in different species to that of the ancestral gene in which they evolved from. Applied 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 in order to find some fast evolutionary genes in rice PHS. Three groups which represented the PHS susceptible (group 1), PHS medium (group 2) and PHS resistant (group 3) were separated based on the phenotype and each group was examined with the outgroup for MKT. Total 60 fast evolutionary genes that have a positive selection with FDR ≤ 0.05 were found in the three groups, and 19, 5 and 8 genes were specific existed in group 1, 2 and 3, respectively. Annotation of these genes were conducted and the predicted functions were investigated, leading that one Ethylene receptor-like gene that may related to PHS based on the previous studies, which need to be validated later, however. In addition, network analysis of these characterized genes were also investigated, which could reveal the connection of genes between each other. Moreover, the association study between the candidate gene ethylene receptor and the PHS phenotype was performed and indicated that this gene is significantly correlated with PHS in rice. All these above indicated that with this orthologous based method, we can find some important candidate genes that may play an important role in some traits.

Aroma in rice (Oryza sativa L.) results from the loss of function of the betaine aldehyde dehydrogenase (Badh2) gene on chromosome 8. An 8-bp deletion in exon 7 of Badh2 was reported to be the main allele functionally associated with fragrance. The discovery of new functional alleles will provide additional genetic resources to improve fragrant rice. In this study, we sequenced the Badh2 gene in 30 rice accessions and filtered the Badh2 polymorphisms from whole genome re-sequence data of 295 rice accessions. Seven alleles were detected from the sequence data. Six of the seven were known alleles and one was a novel allele (badh2-E12). The novel allele was a 3-bp deletion in exon 12. Five functional markers, targeting six of the seven alleles, were identified. Fourteen accessions were selected to test the utility of these markers. The five molecular markers reliably distinguishing this fragrant rice from other fragrant or non-fragrant rice accessions. Analysis of two F2 rice population validated the genetic markers FME12-3 and FME14I as functional markers. These two markers co-segregated with the fragrance phenotype. These markers will be used in a Badh2 diversity study and to breed improved fragrant rice accessions via marker-assisted selection.

BADH1 and BADH2 are two homology genes, encoding betaine aldehyde dehydrogenase in rice. In the present study, we scanned BADHs sequences of 295 rice cultivars, and 10 wild rice accessions to determine the polymorphisms, gene functions and domestication of these two genes. A total of 16 alleles for BADH1 and 10 alleles for BADH2 were detected in transcription region of cultivars and wild species. Association study showed that BADH1 has significant correlation with salt tolerance in rice during germination stage, the SNP P11483(T/A)ishighlycorrelatedwithsalttoleranceindex(STI)(P<10-4). While, BADH2 was only responsible for rice fragrance, of which two BADH2 alleles (P23036, P25390) explain 97% of aroma variation in our germplasm. It indicated that there are no overlapping functions between the two homology genes. In addition, a large LD block was detected in BADH2 region, however, no large LD blocks in a 4-Mb region of BADH1. Only BADH2 region shown significant bias Tajima’s D value from the balance. Extended haplotype homozygosity study revealed fragrant accessions had a large LD block that extended around the mutation site (P23036) of BADH2, while both of the BADH1 alleles (SNP P11483(T/A)) did not show large extended LDblock. All these results suggested that BADH2 was identified as a domesticated gene during rice evolution, while BADH1 was not selected by human beings.

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.

Ratio of functional changes from orthologous genes is being widely used for detecting the signature for natural selection between species. However, one to one orthologous genes allows only for the analysis due to methodological limitation. A number of genes have in-paralogs as a result of gene expansion in crops. Here, we report a new approach for detecting accelerated evolution, which includes in-paralogs as well as one to one orthologs. This new approach can detect many novel accelerated genes among rice in-paralogs, which have not been investigated yet.