'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.

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.

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.

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.

‘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.

Rice blast disease caused by the fungal pathogen Magnaporthe oryzae is one of the most destructive rice diseases worldwide. Resistance to rice blast pathogen mostly shows a quantitative trait controlled by several genes. A total of 13 major blast resistance (R) genes were reported in a number of Korean rice varieties using molecular markers. The Pi-ta gene, which locates near to the centromere of chromosome 12, was haplotyping using 1790 accessions including cultivated and wild varieties in previous research. However, the genetic variations of other R genes in rice still not clear. Three R genes, Pi9, Pia, and Pib on chromosome 6, 11 and 2 respectively, were resequenced among 84 accessions of rice core set. Different types of halotype among the 84 accessions were detected. Some new SNPs and InDels found in exon part of R genes were expected to result into amino acid changes following analysis of the genetic code variations, and the germplam in this rice core set which are resistance to blast were explored. We are expecting to develop the new functional markers and incorporate of resistance genes into existing rice cultivars and finally these apply outcomes in breeding rice resistance to blast diseases.

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.

Allele mining in starch synthesis-related genes (SSRGs) has facilitated the discovery of desired natural sequence variations for eating quality in rice. This study investigated the sequence variations from 10 SSRGs, and further evaluated their relationship with the amylose content (AC) and rapid viscosity analysis profiles in a global collection of rice accessions by association mapping (AM). In total, 83 sequence variations were found in 10 sequenced amplicons, including 73 single nucleotide polymorphisms (SNPs), eight insertion-deletions (InDels) and two polymorphic simple sequence repeats (SSRs). Four subpopulations were identified by population structure analysis based on 170 genome-wide SSR genotypes. AM revealed 11 significant associations between three phenotypic indices and three sequence variations. One SNP with a g/c transversion at the 63rd nucleotide downstream of the OsBEIIb gene termination codon on rice chromosome 2 was significantly associated with multiple trait indices in both the general linear and mixed linear models (GLM and MLM), including the final viscosity (p < 0.001, R2 = 23.87%) in both 2009 and 2010, and AC (p < 0.01, R2 = 11.25%) and trough viscosity (p < 0.01, R2 = 20.43) in 2010. This study provides a new perspective of allele mining for breeding strategies based on marker-assisted selection.

Anther derived double haploids (DHs) from sweet pepper genotypes ('Special', 'Derby', 'Bossanova', 'Fiesta', 'Debora' and 'Minipaprika') were used to study the agronomic variation in 2006. Ninety-nine successful DHs regenerants (32 from 'Special', 25 from 'Derby', 23 from 'Bossanova', 10 from 'Fiesta', 6 from 'Debora' and 3 from 'Minipaprika') were transplanted at plastic house and studied on their agronomic characters. Variation in agronomic characters was observed within the DHs of each genotype. DHs obtained from 'Derby' and 'Fiesta' exhibited wide variation in fruit yield plant-1 whereas averaged fruit yield plant-1 was highest in 'Derby' (1608 g) and less variation was observed in DHs of 'Bossanova'. Based on the agronomic characters expressed in DHs population at this environment, SP55, SP56, SP60, and SP116 from 'Special', SP8, SP10, SP14, SP16, and SP34 from 'Derby', SP115, SP119, SP142, SP143, SP196, and SP199 from 'Bossanova', SP41, SP45, and SP114 from 'Fiesta', SP21 from 'Debora' and SP91 from 'Minipaprika' identified as elite inbred lines and these DH lines could be used for commercial hybrids production in sweet pepper. Genetic relationship among the selected inbred lines using molecular markers and their response to diseases are further recommended to study.

This experiment was conducted on rice (cv. 2005 Thaoi) seeds to study whether priming with deep sea water (DSW) results in enhancement of seed emergence and seedling growth and to identify the optimum concentration of Deep Sea Water (DSW) for priming. Two experiments were conducted subsequently. In experiment 1, four concentrations of the DSW (10%, 20%, 30% and 40%), and in experiment 2, five concentrations of DSW (10%, 15%, 20%, 25% and 30%) were prepared and seeds were primed for 24 hours duration at 25℃. Beside this, hydro priming with plain water was also included as a control. Experiments were laid out in Completely Randomized Design (CRD) with three replications. Result showed that 20% DSW seed priming treatment had improved the emergence, seedling height, number of roots and root length as compare to other with DSW or without DSW treatments. Beyond 20% DSW priming (i.e. 25%, 30% and 40%) were not suitable for priming the seed. On the basis of seedlings growth parameters; emergence, seedling height, root number and length, and shoot root ratio, 20% DSW priming was the best priming treatment.

This experiment was conducted on wild vegetables; Gondalbi (Cirsium setidens), Deoduck (Codonopsis lanceolata Trautv.), and Jandae (Adenophora triphylla var. Joponica Hara) seed to study whether priming with deep sea water results in enhancement of seed germination and identify the optimum concentration of the priming solution, and duration of priming. Seeds were primed with 5 various concentrations (5%, 10%, 15%, 20% and 30%) of deep sea water (DSW) in 12 hours, 24 hours, and 48 hours at 24℃. Since Jandae had seed dormancy, it was kept for four weeks in refrigerator at 2℃ after priming treatment. In Deoduck, 5 percentage DSW priming significantly improved the early germination percentage, radicle length, and plumule emergence percentage. Among the priming period of treatments, 24 hours priming showed better performance in this treatment whereas, in Jandae, 12 hours priming with 10 percentages DSW significantly improved the germination percentage and germination rate. This treatment had increased the final germination percentage by 54%, 15% and 40% compared with control, plain water and KNO3 priming respectively. But in Gondalbi, priming did not improve the germination of seed. However, among the priming treatments, 12 hours priming with 3% KNO3 and 20% DSW gave better performance. In both the wild vegetables; Deoduck and Jandae, priming in deep sea water had improved the germination percentage and germination rate as compare to plain water, KNO3, and without priming treatment. Hence the best seed priming treatment on Deoduck and Jandae are 24 hours with 5% DSW and 12 hours with 10% DSW respectively.

This experiment was conducted to study whether priming with deep sea water results in enhancement of seed germination and to identify the optimum concentration of the priming solution, and duration of priming using sweet pepper (Cv. California wonder), rice (Cv. Ilpum) and ginseng seed. Sweet pepper and rice seeds were primed with 5 various concentrations (5%, 10%, 15%, 20% and 30%) for deep sea water for 48 hours, 24 hours and 12 hours at 25℃ and ginseng seeds in 5%, 10%, 15%, 20%, 25% and 30%, and 2,4,6, and 8 electrical conductivity (EC) which were made by desalinating deep sea water. Priming in deep sea water (DSW) improved the early and final germination percentage, mean germinal on rate, emergence percentage and root and shoot length, compared with plain water, KNO3 and without priming treatments. In sweet pepper, 24 hours priming with 5 percentage DSW significantly improved the early germination percentage and radical length. It has also improved the mean germination and emergence days and early emergence percentage, compared with KNO3 and control. Whereas, in rice, 48 hours priming with 10 percent DSW significantly improved the early germination percentage, plumule emergence percentage, root length and shoot height. Hence the best seed priming treatment on sweet pepper and Rice are 24 hours with 5 percentage DSW and 48 hours with 10 percentage DSW, respectively, whereas in ginseng, priming with EC4, EC8 and 25% DSW had shown better germination.