Do-Yeon Kwak

Single nucleotide polymorphisms in a gene for translation initiation factor (eIF4G) of rice (Oryza sativa) associated with resistance to Rice tungro spherical virus.

Rice tungro disease (RTD) is a serious constraint to rice production in South and Southeast Asia. RTD is caused by Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus. Rice cv. Utri Merah is resistant to RTSV. To identify the gene or genes involved in RTSV resistance, the association of genotypic and phenotypic variations for RTSV resistance was examined in backcross populations derived from Utri Merah and rice germplasm with known RTSV resistance. Genetic analysis revealed that resistance to RTSV in Utri Merah was controlled by a single recessive gene (tsv1) mapped within an approximately 200-kb region between 22.05 and 22.25 Mb of chromosome 7. A gene for putative translation initiation factor 4G (eIF4G(tsv1)) was found in the tsv1 region. Comparison of eIF4G(tsv1) gene sequences among susceptible and resistant plants suggested the association of RTSV resistance with one of the single nucleotide polymorphism (SNP) sites found in exon 9 of the gene. Examination of the SNP site in the eIF4G(tsv1) gene among various rice plants resistant and susceptible to RTSV corroborated the association of SNP or deletions in codons for Val(1060-1061) of the predicted eIF4G(tsv1) with RTSV resistance in rice.

The identification of candidate rice genes that confer resistance to the brown planthopper (Nilaparvata lugens) through representational difference analysis

The development of rice varieties (Oryza sativa L.) that are resistant to the brown planthopper (BPH; Nilaparvata lugens Stål) is an important objective in current breeding programs. In this study, we generated 132 BC5F5 near-isogenic rice lines (NILs) by five backcrosses of Samgangbyeo, a BPH resistant indica variety carrying the Bph1 locus, with Nagdongbyeo, a BPH susceptible japonica variety. To identify genes that confer BPH resistance, we employed representational difference analysis (RDA) to detect transcripts that were exclusively expressed in one of our BPH resistant NIL, SNBC61, during insect feeding. The chromosomal mapping of the RDA clones that we subsequently isolated revealed that they are located in close proximity either to known quantitative trait loci or to an introgressed SSR marker from the BPH resistant donor parent Samgangbyeo. Genomic DNA gel-blot analysis further revealed that loci of all RDA clones in SNBC61 correspond to the alleles of Samgangbyeo. Most of the RDA clones were found to be exclusively expressed in SNBC61 and could be assigned to functional groups involved in plant defense. These RDA clones therefore represent candidate defense genes for BPH resistance.

Suppression of Two Tungro Viruses in Rice by Separable Traits Originating from Cultivar Utri Merah

Rice tungro disease (RTD) is caused by Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus (RTBV) transmitted by green leafhoppers. Rice cv. Utri Merah is highly resistant to RTD. To define the RTD resistance of Utri Merah, near-isogenic lines (NIL, BC(5) or BC(6)) developed from Utri Merah and susceptible cv. Taichung Native 1 (TN1) were evaluated for reactions to RTSV and RTBV. TW16 is an NIL (BC(5)) resistant to RTD. RTBV was able to infect both TN1 and TW16 but the levels of RTBV were usually significantly lower in TW16 than in TN1. Infection of RTSV was confirmed in TN1 by a serological test but not in TW16. However, the global gene-expression pattern in an RTSV-resistant NIL (BC(6)), TW16-69, inoculated with RTSV indicated that RTSV can also infect the resistant NIL. Infection of RTSV in TW16 was later confirmed by reverse-transcription polymerase chain reaction but the level of RTSV was considerably lower in TW16 than in TN1. Examination for virus accumulation in another NIL (BC(6)), TW16-1029, indicated that all plants of TW16-1029 were resistant to RTSV, whereas the resistance to RTBV and symptom severity were segregating among the individual plants of TW16-1029. Collectively, these results suggest that RTD resistance of Utri Merah involves suppression of interacting RTSV and RTBV but the suppression trait for RTSV and for RTBV is inherited separately.

Suppression of NS3 and MP is important for the stable inheritance of RNAi-mediated Rice Stripe Virus (RSV) resistance obtained by targeting the fully complementary RSV-CP gene

Rice stripe virus (RSV) is a viral disease that seriously impacts rice production in East Asia, most notably in Korea, China, and Japan. Highly RSV-resistant transgenic japonica rice plants were generated using a dsRNAi construct designed to silence the entire sequence region of the RSV-CP gene. Transgenic rice plants were inoculated with a population of viruliferous insects, small brown planthoppers (SBPH), and their resistance was evaluated using ELISA and an infection rate assay. A correlation between the expression of the RSV-CP homologous small RNAs and the RSV resistance of the transgenic rice lines was discovered. These plants were also analyzed by comparing the expression pattern of invading viral genes, small RNA production and the stable transmission of the RSV resistance trait to the T3 generation. Furthermore, the agronomic trait was stably transmitted to the T4 generation of transgenic plants.

Antioxidant Compounds and Antioxidant Activities of Different Varieties of Foxtail Millet and Proso Millet according to Cultivation Time

Effects of cultivation time on the antioxidant contents and activities of foxtail millet and proso millet were determined. The cultivation times were early-season (ES), normal-season (NS), and late-season (LS), and the cultivated varieties were Hwanggeum-cho (HGC), Cheongcha-cho (CCC), Samdamae (SDM), Gyeongkwan 1 (GK 1), Gyeongkwan 2 (GK 2), Ganghae-cho (GHC), Hwanggeum-gijang (HGG), Manhongchal-gijang (MHCG), Byeoruk-gijang (BRG), Norangchal-gijang (NRG), and Whin-gijang (WG). The total polyphenol, flavonoid, tannin content, and DPPH and ABTS radical scavenging activities of the methanolic extracts of foxtail millet and proso millet showed significant differences according to cultivation variety and time. The highest total polyphenol content of foxtail millet was 29.33 mg of gallic acid equivalent (GAE)/g of sample in GK 1 at LS, whereas that of proso millet was 23.48 mg of GAE/g of sample in BRG at LS. The highest total flavonoid content of foxtail millet was 2.12 mg of catechin equivalent (CE)/g of sample in CCC at ES, whereas that of proso millet was 4.49 mg of CE/g of sample in BRG at LS. The highest total tannin content of foxtail millet was 14.07 mg of tannic acid equivalent (TAE)/g of sample in SDM at LS, whereas that of proso millet was 15.59 mg of TAE/g of sample in BRG at LS. The highest DPPH radical scavenging activity of foxtail millet was 7.71 mg of TE/g of sample in CCC at NS, whereas that of proso millet was 12.66 mg of TE/g of sample in BRG at LS. The highest ABTS radical scavenging activity of foxtail millet was 8.05 mg of TE/g of sample in GK 1 at LS, whereas that of proso millet was 34.46 mg of TE/g of sample in BRG at LS. Generally, HGC, GK 1, and GHC had more beneficial effects at LS than ES or NS, whereas CCC, SDM, and GK 2 had more beneficial effects at NS than ES or LS, and proso millet had more beneficial effects at LS than ES or NS.

A systems approach for identifying resistance factors to Rice stripe virus.

Rice stripe virus (RSV) causes disease that can severely affect the productivity of rice (Oryza sativa). Several RSV-resistant cultivars have been developed. However, host factors conferring RSV resistance in these cultivars are still elusive. Here, we present a systems approach for identifying potential rice resistance factors. We developed two near-isogenic lines (NIL), RSV-resistant NIL22 and RSV-susceptible NIL37, and performed gene expression profiling of the two lines in RSV-infected and RSV-uninfected conditions. We identified 237 differentially expressed genes (DEG) between NIL22 and NIL37. By integrating with known quantitative trait loci (QTL), we selected 11 DEG located within the RSV resistance QTL as RSV resistance factor candidates. Furthermore, we identified 417 DEG between RSV-infected and RSV-uninfected conditions. Using an interaction network-based method, we selected 20 DEG highly interacting with the two sets of DEG as RSV resistance factor candidates. Among the 31 candidates, we selected the final set of 21 potential RSV resistance factors whose differential expression was confirmed in the independent samples using real-time reverse-transcription polymerase chain reaction. Finally, we reconstructed a network model delineating potential association of the 21 selected factors with resistance-related processes. In summary, our approach, based on gene expression profiling, revealed potential host resistance factors and a network model describing their relationships with resistance-related processes, which can be further validated in detailed experiments.

Evaluation of Optimum Rice Heading Period under Recent Climatic Change in Yeongnam Area

This study was conducted to analyze the optimum heading period according to the recent climatic change for improvement of rice yield and grain quality in the Yeongnam area. We analyzed climatic elements including daily mean air temperature, daily range of air temperature, sunshine hours, and amount of precipitation from 1996 to 2005 in comparison with those of the 1971 to 2000 normal. Daily mean air temperature and amount of precipitation in the recent 10 years increased, but daily range of air temperature and sunshine hours decreased in comparison with the norm. Also, monthly mean air temperature was lowered remarkably in July and August. The monthly amount of precipitation largely increased in August and September. The daily range of air temperature and sunshine hours were greatly decreased from August to October, Possible cultivation periods for rice in the recent 10 years ranged from 171 days in Boughwa to 228 days in Busan and was expanded about days in comparison with the normal. Optimum heading date by local regions for the maximum climatic yield potential was estimated as July 31 at Bonghwa to September 7 at Busan, Masan, and Tongyeong in the recent 10 years. There was a wide difference in optimum heading date according to local legions of the Yeongnam area. Compared to the normal, optimum heading date in the recent 10 years was delayed about I~8 days in most local regions except Bonghwa, Mungyeong, and Yeongdeok. These results suggested that it is necessary to develop late maturity rice cultivars for producing high yield and quality rice grain due to the recent climatic change. Moreover, it is still more important to select the most suitable cultivation period appropriate to the changed climate of each local region in Yeongnam area.

Effects of Soil Organic Matter Contents, Paddy Types and Agricultural Climatic Zone on CH 4 Emissions from Rice Paddy Field

To evaluate the effects of abiotic factors of paddy fields on greenhouse gases (GHGs) emissions from rice paddy fields, CH4 emission amounts were investigated from rice paddy fields by different soil organic matter contents, paddy types, and agricultural climatic zone in Yeongnam area during 3 years. CH4 emission amounts according to soil organic matter contents in paddy field were conducted at having different contents of 5 soil organic matters fields (23.6, 28.7, 31.0, 34.5, and 38.0 g kg -1 ), The highest CH4 emission amount was recorded in the highest soil organic matters plot of 38.0 g kg -1 . High correlation coefficient (r=0.963 ** ) was obtained between CH4 emissions from paddy fields and their soil organic matter contents. According to paddy field types, CH4 emission amounts were investigated at 4 different paddy fields as wet paddy, sandy paddy, immature paddy, and mature paddy. The highest CH4 emissions was recorded in wet paddy (100%) and followed as immature paddy 64.0%, mature paddy 46.8%, and sandy paddy 23.8%, respectively. For the effects of temperature on CH4 emissions from paddy fields, 4 agricultural climatic zones were investigated, which were Yeongnam inland zone (YIZ), eastern coast of central zone (ECZ), plain area of Yeongnam inland mountainous zone (PMZ), and mountainous area of Yeongnam inland mountainous zone (MMZ). The order of CH4 emission amounts from paddy fields by agricultural climatic zone were YIZ (100%) > ECZ (94.6%) > PMZ (91.6%) > MMZ (78.9%). The regression equation between CH4 emission amounts from paddy fields and average air temperature of Jul. to Sep. of agricultural climatic zone was y = 389.7x–4,287 (x means average temperature of Jul. to Sep. of agricultural climatic zone, R 2 =0.906 * )

Viruliferous Rate of the Small Brown Planthopper in the Maize Field Infected with Rice black-streaked dwarf virus

The Rice black-streaked dwarf virus (RBSDV) infected 99-100% of a -maize field in Mungyeong City in 2007. Adjacent to the area is a Persimmon orchard where barley crops were grown under the trees as green manure crops and for soil amendments. The barley acted as winter host to the small brown plant hoppers (SBPH) enabling the insects to survive and pass the winter season. The existence of RBSDV was detected and confirmed by RT-PCR using S9 specific primer. Samples of the insect vector SBPH were collected in the area on May 3, June 7 and, August 4 and the results of the RT-PCR analysis revealed viruliferous insect rates of 2.9, 4.8, and 4.4%, respectively. These observed viruliferous insect rates were similar with those detected in RBSDV infected rice fields.

Detection of Rice Stripe Virus using RT-PCR

Until now, occurrence of rice stripe virus (RSV) is limitted in southern part of Korea. However, recently the occurrence of RSV is increased and spreaded in central part of Korea including Chungcheong and Kyonggi province. It is very difficult to distinguish RSV symptoms on virus symptom physiological damage of rice. We detected RSV viral RNA from infected rice and its insect vector Laodelphax striatellus using specific primer of RSV-polymerase and coat protein gene with reverse transcription (RT)-PCR. The result of RT-PCR, we observed specific band including RSV-polymerase (1,,023 bp) and CP (969 bp) in both host of rice and insect vector.