• Journal of Plant Biotechnology
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• v.37 no.2
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• pp.125-132
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• 2010

Rice is the staple food of more than 50% of the worlds population. Cultivated rice has the AA genome (diploid, 2n=24) and small genome size of only 430 megabase (haploid genome). As the sequencing of rice genome was completed by the International Rice Genome Sequencing Project (IRGSP), many researchers in the world have been working to explore the gene function on rice genome. Insertional mutagenesis has been a powerful strategy for assessing gene function. In maize, well characterized transposable elements have traditionally been used to clone genes for which only phenotypic information is available. In rice endogenous mobile elements such as MITE and Tos (Hirochika. 1997) have been used to generate gene-tagged populations. To date T-DNA and maize transposable element systems has been utilized as main insertional mutagens in rice. A main drawback of a T-DNA scheme is that Agrobacteria-mediated transformation in rice requires extensive facilities, time, and labor. In contrast, the Ac/Ds system offers the advantage of generating new mutants by secondary transposition from a single tagged gene. Revertants can be utilized to correlate phenotype with genotype. To enhance the efficiency of gene detection, advanced gene-tagging systems (i.e. activation, gene or enhancer trap) have been employed for functional genomic studies in rice. Internationally, there have been many projects to develop large scales of insertionally mutagenized populations and databases of insertion sites has been established. Ultimate goals of these projects are to supply genetic materials and informations essential for functional analysis of rice genes and for breeding using agronomically important genes. In this report, we summarize the current status of Ac/Ds-mediated gene tagging systems that has been launched by collaborative works from 2001 in Korea.

• Journal of Crop Science and Biotechnology
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• v.10 no.4
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• pp.265-276
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• 2007

The 13 major blast resistance(R) genes against Magnaporthe grisea were screened in a number of Korean rice varieties using molecular markers. Of the 98 rice varieties tested, 28 were found to contain the Pia gene originating from Japanese japonica rice genotypes. The Pib gene from BL1 and BL7 was incorporated into 39 Korean japonica varieties, whereas this same gene from the IRRI-bred indica varieties was detected in all Tongil-type varieties. We also found that 17 of the japonica varieties contained the Pii gene. The Pii gene in Korean rice varieties originates from the Korean japonica variety Nongbaeg, and Japanese japonica varieties Hitomebore, Inabawase, and Todorokiwase. The Pi5 gene, which clusters with Pii on chromosome 9, was identified only in Taebaeg. Thirty-four varieties were found to contain alleles of the resistance gene Pita or Pita-2. The Pita gene in japonica varieties was found to be inherited from the Japanese japonica genotype Shimokita, and the Pita-2 gene was from Fuji280 and Sadominori. Seventeen japonica and one Tongil-type varieties contained the Piz gene, which in the japonica varieties originates from Fukuhikari and 54BC-68. The Piz-t gene contained in three Tongil-type varieties was derived from IRRI-bred indica rice varieties. The Pi9(t) gene locus that is present in Korean japonica and Tongil-type varieties was not inherited from the original Pi9 gene from wild rice Oryza minuta. The Pik-multiple allele genes Pik, Pik-m, and Pik-p were identified in 24 of the varieties tested. In addition, the Pit gene inherited from the indica rice K59 strain was not found in any of the Korean japonica or Tongil-type varieties tested.

• Korean Journal of Breeding Science
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• v.40 no.4
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• pp.387-393
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• 2008

Over 7 individual rice (Oryza sativa L.) plants per a line were sowed and sampled by pooled sampling method for genomic DNA extraction. The 5,400 flanking sequence tags (FSTs) were analysed by adaptor PCR and direct sequencing. FST analysis showed that the intragenic FSTs, the intergenic FSTs, and the original insertional sequences including hot spot covered 48.1% (2,597), 25.6% (1,383), and 25% (1,350), respectively. The 2,597 intragenic FSTs were used for genotyping to determine whether they are heterozygous or homozygous, and 1,393 core lines were selected. Among them, 422 knockout genes were distributed on chromosome 3, while 56 - 157 intragenic FSTs scattered on other chromosomes. Among 1,393 FSTs, known genes such as transcription factor covered 59.4% (827), while unknown genes such as expressed protein covered 40.6% (566). RT-PCR indicated that some core lines had no expression or decreased expression level in their knockout genes. It means that core lines are very useful knockout lines for functional genomic studies.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.47 no.5
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• pp.335-340
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• 2002

To evaluate the efficiency of anther floating culture according to the maturing group, the varietal difference and classification of fifty varieties was conducted in N6 liquid medium containing 1mg $l^{-1}$ NAA, 0.25 mg $l^{-1}$ kinetin. The efficiency of callus induction was widely ranged from 0 to 113.4%, but the mean callus induction was not significantly different among maturing groups. The efficiency of anther floating culture showed the highest variation in early-maturing group among three maturing groups. The varieties with the best callus induction were Sambaegbyeo and Jinbuolbyeo, while the recalcitrant variety was Obongbyeo in early-maturing group. The efficiency of plant regeneration showed the highest trends in late-maturing group among three maturing groups. The fifty varieties were classified into three groups (distance=0.78) by cluster analysis based on the callus formation and plant regeneration. Group including only two varieties, Shinunbongbyeo and Sambaegbyeo had the excellent androgenic efficiency, and the medium efficiency of Group was included thirty-six varieties. Whereas twelve varieties, including three Tongil varieties were fell into the bad efficiency of Group. Especially, Tongil varieties containing Japonica rice, Obongbyeo were the recalcitrant genotypes for the anther floating culture.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.46 no.6
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• pp.453-458
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• 2001

The Rural Development Administration (RDA) of Korea now operates a system called Rice Variety Selection Tests (RVST), which are now being implemented in eight Agricultural Research and Extension Services located in eight province RVST's objective is to provide accurate yield estimates and to select well-adapted varieties to each province. Systematic evaluation of entries included in RVST is a highly important task to select the best-adapted varieties to specific location and to observe the performance of entries across a wide range of test sites within a region. The rice yield data in RVST for ordinary transplanting in Kangwon province during 1997-2000 were analyzed. The experiments were carried out in three replications of a random complete block design with eleven entries across five locations. Additive Main effects and Multiplicative Interaction (AMMI) model was employed to examine the interaction between genotype and environment (G$\times$E) in the biplot form. It was found that genotype variability was as high as 66％, followed by G$\times$E interaction variability, 21％, and variability by environment, 13％. G$\times$E interaction was partitioned into two significant (P＜0.05) principal components. Pattern analysis was used for interpretation on G$\times$E interaction and adaptibility. Major determinants among the meteorological factors on G$\times$E matrix were canopy minimum temperature, minimum relative humidity, sunshine hours, precipitation and mean cloud amount. Odaebyeo, Obongbyeo and Jinbubyeo were relatively stable varieties in all the regions. Furthermore, the most adapted varieties in each region, in terms of productivity, were evaluated.

• Journal of Radiation Industry
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• v.4 no.4
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• pp.325-334
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• 2010

Transcriptional regulation in response to salt in mutant lines was investigated using oligonucleotide microarrays. In order to characterize the salt-responsive genes in rice, the expression profiles of transcripts that responded to salt-treatment were monitored using the microarrays. In the microarray analysis, among 37,299 reliable genes, 5,101, 2,758 and 2,277 genes were up-regulated by more than 2-fold using the salt treatment, while the numbers of down-regulated genes were 4,619, 3,234, and 1,878 in the WT, ST-495, and ST-532, respectively. From genotype changes induced by gamma ray mutagenesis, 3,345 and 2,397 genes were up-regulated, while 2,745 and 2,075 genes were down-regulated more than 2-fold in the two untreated mutants lines compared with untreated WT, respectively. A total of 3,108 and 2,731 genes were up-regulated more than 2-fold, while 3,987 and 3,660 genes were down-regulated by more than 2-fold in the salt treatment of the two mutants lines compared with the salt treated WT, respectively. The expressions of membrane transporter genes such as OsAKT1, OsKUP, and OsNAC increased more severely in ST-495 and ST-532 than in the WT. The expressions of the proline accumulation related genes such as OsP5CS and OsP5CR were also markedly increased in the salt tolerant mutants when compared to the WT plant.

• Journal of Life Science
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• v.16 no.6
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• pp.1001-1005
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• 2006

The objective of this study was carried out to evaluate the suitability of simple sequence repeat (SSR) markers for genetic diversity assessment and identification of rice varieties. The 23 primers selected from 50 SSR primers showed polymorphisms in the 21 rice varieties. The 2 to 9 SSR alleles were detected for each locus with an average of 3.00 alleles per locus. The polymorphism information content (PIC) ranged form 0.091 to 0.839. Based on band patterns, UPGMA cluster analysis was conducted. These varieties were separate into 4 groups corresponding to rice ecotype and pedigree information and genetic distance of cluster ranging from 0.59 to 0.92. The 4 SSR primer sets (RM206, RM225, RM418, RM478) selected form 23 polymorphic primers were differentiated all the rice variety from each other by markers genotypes. These markers may be used wide range of practical application in variety identification of rice.

• Journal of Applied Biological Chemistry
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• v.65 no.4
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• pp.429-438
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• 2022

The composition of crops reveal natural variation according to genetic characteristics and environmental factors such as the cultivated regions. For comparative investigation of the impact of genetic difference and environmental influence on the levels of bioactive components in rice seeds, 23 cultivars including indica, japonica, and tongil rice were grown in two location in Korea (Jeonju and Cheonan) for two years (2015 and 2016). Sixteen compounds consisting of tocopherols, tocotrienols, phytosterols, and policosanols were identified from 368 rice samples and the compositional data were subjected to data mining processes including principal component analysis and Pearson's correlation analysis. Under 4 different environmental conditions (Jeonju in 2015, Cheonan in 2015, Jeonju in 2016, Cheonan in 2016), the natural variability of rice seeds showed that the genetic background (indica vs japonica vs tongil) had more impact on the compositional changes of bioactive components compared to the environments. Especially, the results of correlation analysis revealed negative correlation between α-, β-tocopherols and γ-, δ-tocopherols as a representative genetic effect that did not changed by the environmental influence.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.12
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• pp.1726-1733
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• 2012

The effect of genotype, fibre level and fibre source on gut morphology, environment and microflora was studied using 18 Mong Cai (MC) and 18 Landrace${\times}$Yorkshire (LY) pigs, aged around 60 d. The diets were based on maize, rice bran, soybean meal, fish meal and soybean oil, and cassava residue (CR) or brewer's grain (BG) as fibrous ingredient sources in the high-fibre diets (HF). A low-fibre diet (LF), containing around 200 g NDF/kg dry matter (DM), was formulated without CR and BG as feed ingredients. The HF diets (HF-CR and HF-BG) were formulated to contain around 270 g NDF/kg DM. The experiment was arranged according to a $2{\times}3$ factorial completely randomized design with six replications, and lasted 30 d. Crypt density in ileum was lowest (p<0.05) and villus height in jejunum and ileum were the greatest (p<0.05) in pigs fed diet HF-BG. Villus width in ileum was greatest in pigs fed diets HF-CR and HF-BG (p<0.05). Lactic acid bacteria (LAB) counts in stomach were greatest (p<0.05) and E. coli counts in ileum and colon were lowest (p<0.05) in pigs fed diet HF-CR. The concentration of total organic acids in ileum, caecum and colon were greatest (p<0.05), and pH in ileum and colon were lowest (p<0.05) in pigs fed diet HF-CR. Crypt density in ileum was lowest, and villus height in ileum and villus width in jejunum and ileum was greatest in LY pigs (p<0.05). LAB counts in stomach and ileum were greatest, and E. coli counts in ileum were lowest in MC pigs (p<0.05). The concentration of total organic acids in ileum, caecum and colon were greatest (p<0.05) and pH lowest (p<0.05) in MC pigs.

• Korean Journal of Agricultural Science
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• v.45 no.4
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• pp.575-582
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• 2018

Bacterial fruit blotch (BFB) caused by Acidovorax citrulli is a devastating disease found in many cucurbits cultivation fields. The genetic diversity for 29 strains of A. citrulli collected from various cucurbits in South Korea was determined by DNA fingerprinting with a pathogenicity test, multi locus analysis, Rep-PCR (repetitive sequence polymerase chain reaction), and URP (universal rice primers) PCR bands. Two distinct groups (Korean Clonal Complex, KCC1 and KCC2) in the population were identified based on group specific genetic variation in the multi locus phylogeny using six conserved loci and showed a very high similarity with DNA sequences for representative foreign groups [the group I (CC1-1 type) and the group II (CC2-5 type)] widely distributed worldwide, respectively. Additionally, in the case of phaC, a new genotype was found within each Korean group. The KCC1 was more heterogeneous compared to the KCC2. The KCC1 recovered mainly from melons and watermelons (ratio of 6 : 3) and 15 of the 20 KCC2 strains recovered from watermelons were dominant in the pathogen population. Accordingly, this study found that two distinct groups of differentiated A. citrulli exist in South Korea, genetically very similar to representative foreign groups, with a new genotype in each group resulting in their genetic diversity.