You-Chun Song

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.

Comparative analysis of physicochemicals and antioxidative properties of new giant embryo mutant, YR23517Acp79, in rice (Oryza sativa L.)

Nutritional and physicochemical properties of new giant embryo mutant rice (YR23517Acp79, YR) were analyzed. YR exhibited increased total protein (9.3±0.3%), lipid (3.7±1.1%), amino acid (663.28±1.9 mg/g), and mineral contents (Ca=284.0±6.2, Mg=1417.5±13.6 mg/kg). In YR brown rice four major physicochemicals, including gamma-aminobutyric acid (brown rice= 0.46±0.014 mg/g), γ-oryzanol (0.43±0.021 mg/g), vitamin B1 (6.42±0.3 mg/kg), and tocopherols (alpha= 2.68±0.1, beta=0.11±0.01, gamma=0.05±0.001 mg/100 g) increased in comparison to reported giant embryo (Keunnunbyeo, KB) and normal embryo rice (Ilmibyeo, IB). YR showed higher scavenging activities against 1,1-diphenyl-2-picrylhydrazyl (0.2 g/mL=57.1±2.25) and 2,2′-Azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (0.2 g/mL=50.2±1.45) radicals but also inhibited lipopolysaccharide-induced nitric oxide production without cytotoxicity. These results indicate YR is a high quality functional rice due to its high nutrition content and antioxidant effects of physicochemicals.

Large-scale screening of rice accessions to evaluate resistance to bakanae disease

Bakanae disease is an important fungal disease in the world. No rice (Oryza sativa L.) varieties have been found to be completely resistant to this disease. To facilitate accurate, uniform and simultaneous screening of many rice accessions, we developed an inoculation method for microconidia of Fusarium fujikuroi using a tissue embedding cassette and seedling tray. Standards for evaluating the inoculated rice seedlings as healthy or unhealthy were also established. The method was fast and reproducible for accurately evaluating resistance to bakanae disease in rice.

A Waxy Black Giant Embryo Earley Maturing Rice Variety ‘Nunkeunheugchal’

Nunkeunheugchal (registration No. 01-0001-2014-4), a black waxy giant embryo rice cultivar, was developed by the rice breeding team of National Institute of Crop Science (NICS), RDA in 2012. This cultivar was derived from the cross between ge and Josaengheugchal in 2004/2005 winter season, and selected by a promising line, YR25277-B-B-314-2, was selected and designated as the line of Milyang263 in 2009. The local adaptability test of Milyang263 was carried out at four locations from 2010 to 2012 and it was named as Nunkeunheugchal. This variety is a early maturity cultivar. It has 65 cm in culm length and 72 spikelets per panicle, and 1,000 grain-weight of brown rice is 17.8 g which is less than that of Josaengheugchal. This variety is resistant to leaf blast, but susceptible to bacterial blight, neck blast, virus disease and insect pest. The yield potential of Nunkeunheugchal was about 3.54 MT/ha as brown rice at ordinary fertilizer level in local adaptability test for three years. Nunkeunheugchal possesses benefits to rice consumers because of high amounts of GABA, anthocyanin, calcium and iron. This variety would be adaptable to the paddy field of middle and southern plain region of Korea.

Comparative analysis of physicochemicals and antioxidative properties in new red rice (Oryza sativa L. cv. Gunganghongmi)

The main objectives of this study were to investigate physicochemicals and antioxidant activities of new red rice (Oryza sativa cv. Gunganghongmi (GH)) by comparing normal brown (Nampyeongbyeo, NB) and reported red rice (Jukjinjubyeo, JB) in Korea. The nutritional constituents, including protein, oil, sugar, fatty acid, GABA, and γ-oryzanol were not significantly different between normal brown and colored rice. However, the ethanol extract of GH showed the highest phenolic content (24.7 ± 1.3 mg g−1). The ethanol extracts of GH showed higher scavenging activities against DPPH (0.2 mg mL−1 = 62.1 ± 2.5%) and ABTS (0.2 mg mL−1 = 63.2 ± 3.5%) radicals. Moreover, GH more inhibited LPS-induced nitric oxide (NO) production (13.2 ± 1.4 μM) than JB (18.3 ± 2.3 μM) and NB (22.1 ± 1.4 μM) at the same concentration (0.2 mg mL−1) without cytotoxicity. These results suggest that new red rice (GH) would be considered to be new functional rice due to its anti-oxidative effect and high nutrition.

Differential Tolerance of Rice Cultivars to Mesotrione-Contained Herbicides

Greenhouse experiment was conducted to evaluate tolerance of six rice cultivars, three IndicaJaponica rice (long grain, cv. Dasanbyeo, Segejinmi and Hanareumbyeo) and three Japonica rice (short grain, Nampyung, Ilpumbyeo and Junamjosaeng) cultivars, to mesotrione+pretilachlor (MP) and bensulfuron-methyl+mesotrione+pretilachlor+pyriftalid (BMPP) in transplanting rice. Two herbicides were applied at 90 g and 180 g a.i. to three to four leaf stage rice at 5 and 15 days after transplanting, respectively. Related study was also conducted to compare for IndicaJaponica and Japonica rice cultivars at different MP rates. Response to two herbicides varied with respect to rice cultivars and herbicide rates. All IndicaJaponica rice cultivars exhibited susceptible to both MP and BMPP as reflected by increased visual injury, shorter plant height and higher plant dry matter reduction when compared with nontreated rice cutlivars. The degree of foliar chlorosis by MP at 90 g a.i. was 5~6 at 7 days after treatment(DAT) but it was decreased to 3~6 at 14DAT. The degree of leaf chlorosis treated with 180 g a.i. MP was 6~7 at 7DAT and it was also decreased to 3~8 at 14 DAT. The plant hight of IndicaJaponica rices was inhibited by 18~43% at application of 90 g a.i. MP and 30~50% at 180 g a.i. MP. The dry matter reduction was greater than that of plant height inhibition, showing 46~73% at 90 g a.i. MP and 65~82% at 180 g a.i. MP. Similar leaf chlorosis injury and growth inhibition of rice cultivars was observed in the BMPP treatment. The injury and growth inhibition by MP and BMPP increased with increase in herbicide rate from 90 g a.i. to 180 g a.i. . However, most of the Japonica cultivars are tolerant to MP and BMPP at both rates. There was no visible leaf chlorosis but plant height and dry matter production were slightly reduced at 180 g a.i. . Based on value determined in reduction of shoot dry weight for MP, the IndicaJaponica rice showed 12.9 fold lower compared with the Japonica rice. The result indicates that rice cultivars vary in tolerance to herbicides of MP and BMPP and IndicaJaponica rices were more susceptible than the Japonica rices to the MP and BMPP.

Comparative studies on major nutritional components of black waxy rice with giant embryos and its rice bran

The concentration of nutrients in brown rice is mainly associated with embryo size. Various beneficial components have been purified from rice bran. Recently developed black waxy rice with a giant embryo (‘Milyang 263’, BGE), which is the get mutant of the GE gene, was selected and analyzed to produce high quality nutritional components. γ-Aminobutyric acid (GABA) content in BGE rice bran, one of the most important nutritional compounds in rice, showed a 10.6-fold increase (2.66±0.48 mg/g) compared to that of BGE brown rice (0.25±0.01 mg/g). In addition, brown rice and BGE rice bran showed enriched amylopectin (94.5±0.5 and 97.0±0.0%) and bioactive anthocyanin [Cy-3-G: 75.15±4.18 (brown rice), 82.97±0.81 (rice bran) and Pn-3-G: 1.52±0.50 (brown rice), 4.33±0.20 (rice bran); mg/100 g] contents. These results suggest that BGE rice bran can be used as an excellent raw material to efficiently produce high quality essential amino acids, cyanidin-3 glycoside-enriched anthocyanins, and GABA.

Identification of quantitative trait loci associated with drought tolerance traits in rice ( Oryza sativa L.) under PEG and field drought stress

Two recombinant inbred line F10 rice populations (IAPAR-9/Akihikari and IAPAR-9/Liaoyan241) were used to identify quantitative trait loci (QTLs) for ten drought tolerance traits at the budding and early seedling stage under polyethylene glycol-induced drought stress, and two traits of leaf rolling index (LRI) and leaf withering degree (LWD) under field drought stress. The results showed that the drought-tolerance capacity of IAPAR-9 was stronger than that of Akihikari and Liaoyan241. Thirty-four QTLs for 12 drought tolerance traits were detected, and among them, in the IAPAR-9/Akihikari population, qLRI9-1 and qLRI10-1 for LRI were repeatedly detected in RM3600-RM553 on chromosome 9 and in RM6100-RM3773 on chromosome 10, respectively, at two times points of July 31 and August 13 in 2014. The two QTLs are stable against the environmental impact, and qLRI9-1 and qLRI10-1 explained 6.77–13.66% and 5.01–8.32% of the phenotypic variance, respectively, at the two times points. qLWD9-2 for LWD in the IAPAR-9/Liaoyan241 population contributed 8.73% of variation was detected in the same marker interval with the qLRI9-1, and qLRI1-1 for LRI and qLWD1-1 for LWD were located in the same marker interval RM11054-RM5646 on chromosome 1, which contributed 18.82 and 5.78% of phenotype variation respectively. qGV3 for germination vigor and qRGV3 for relative germination vigor at the budding stage were detected in the same marker interval RM426-RM570 on chromosome 3, which explained 14.98 and 16.30% of the observed phenotypic variation respectively, representing major QTLs. The above-mentioned stable or major QTLs regions could be useful for molecular marker assisted selection breeding, fine mapping, and cloning.

Drought-tolerant QTL qVDT11 leads to stable tiller formation under drought stress conditions in rice

Drought is an important limiting factor for rice production, but the genetic mechanisms of drought tolerance is poorly understood. Here, we screened 218 rice varieties to identify 32 drought-tolerant varieties. The variety Samgang exhibited strong drought tolerance and stable yield in rain-fed conditions and was selected for further study. To identify QTLs for drought tolerance, we examined visual drought tolerance (VDT) and relative water content (RWC) phenotypes in a doubled haploid (DH) population of 101 individuals derived from a cross between Samgang and Nagdong (a drought-sensitive variety). Three QTLs from Samgang were identified for VDT and explained 41.8% of the phenotypic variance. In particular, qVDT11 contributed 20.3% of the phenotypic variance for RWC. To determine QTL effects on drought tolerance in rain-fed paddy conditions, seven DH lines were selected according to the number of QTLs they contained. Of the drought-tolerance-associated QTLs, qVDT2 and qVDT6 did not affect tiller formation, but qVDT11 increased tiller number. Tiller formation was most stable when qVDT2 and qVDT11 were combined. DH lines with both of these drought-tolerance-associated QTLs exhibited the most stable tiller formation. Together, these results suggest that qVDT11 is important for drought tolerance and stable tiller formation in rain-fed paddy fields.

Genotype analysis of genes involved in increasing grain number per panicle in rice germplasm

벼 수량성 증진을 위하여 수당립수 증진 유전자로 보고된 5종의 유전자에 대한 분자표지를 검정하고 유전자원 479점에서 이들의 유전자에 대한 유전형을 검정하였다. 판독이 용이한 Gn1a 및 DEP1, Apo1 유전자의 In/del 분자표지를 각각 개발하였고 Ghd7과 Nal1 유전자에 대하여서는 기존 보고된 SNP 분자표지를 이용하여 편리성을 검정하였다. 이들 분자표지는 아가로즈젤에서 각각의 유전형 판독이 용이하기에 벼 수량성 향상을 위한 분자육종에 적용이 가능할 것으로 기대되었다. 유전자원 479점에서 수당립수 증진 유전자 5종의 유전형을 분석하였을 때 총 13개의 haplogype으로 분류되었다. 대부분의 Indica 품종과 Japonica 품종은 haploptype 1과 haplotype 13에 속하였다. 나머지 haplotype에 속한 55점의 유전자원은 수당립수 증진 유전자에 대한 유전다양성을 보유한 자원으로 유전체 분석 등을 위한 핵심집단으로 활용할 수 있을 것으로 판단되었다. 유전자원 396점의 수량구성요소를 비교하였을 때, Nal1을 제외한 4종의 수당립수 증진 유전자의 수량증진 대립유전자형에서 이삭 수가 0.6 ~ 0.8개/주 감소하였으나 수당립수는 이삭당 27 ~ 29개 증진되었다. Nal1 유전자는 유전적 배경에 따라 효과가 다르게 나타나며, Nal1-japonica 대립유전자형의 수당립수 증진 효과보다 Nal1-indica 대립유전자형이 감소효과가 큰 것으로 추측되었다. 앞으로 본 논문에서 검정된 수당립수 증진 분자표지 5종과 유전자원의 유전형을 정보를 바탕으로 벼 수량성 증진 육종에 활용하고자 한다.