Notch signaling plays fundamental roles in various animal development. It has been suggested that Hr-Notch, a Notch homologue in the ascidian Halocynthia roretzi, is involved in the formation of peripheral neurons by suppressing the neural fates and promoting the epidermal differentiation. However, roles of Notch signaling remain controversial in the formation of nervous system in ascidian embryos. To precisely investigate functions of Notch signaling, we have isolated and characterized Hr-Numb, a Numb homologue which is a negative regulator of Notch signaling, in H. roretzi. Maternal expression of Hr-Numb mRNAs was detected in egg cytoplasm and the transcripts were inherited by the animal blastomeres. Its zygotic expression became evident by the early neurula stage and the transcripts were detected in dorsal neural precursor cells. Suppression of Hr-Numb function by an antisense morpholino oligonucleotide resulted in larvae with defect in brain vesicle and palps formation. Similar results have been obtained by overexpression of the constitutively activated Hr-Notch forms. Therefore, these results suggest that Hr-Numb is involved in Notch signaling during ascidian embryogenesis.

Spikelets per panicle (SPP) is one of the most important traits associated with rice yield. In this study, IL28, a near isogenic line (NIL) developed by introgressing chromosomal segments from ‘Moroberekan’ into ‘Ilpumbyeo’ showed significantly higher number of spikelets per panicle than the recurrent parent, ‘Ilpumbyeo’. Quantitative trait locus (QTL) analysis in 243 F2 plants derived from a cross between IL28 and Ilpumbyeo indicated that a QTL for spikelets per panicle, qSPP6 was located in the interval RM3430 - RM20580. The Moroberekan allele increased SPP. The fact that QTLs for panicle length and the number of secondary branches were mapped in the same interval as qSPP6 appears to indicate that this locus was associated with panicle structure. To map the QTL more precisely, substitution mapping of qSPP6 using F3 lines was conducted. Substitution mapping with 41 F3 lines further narrowed the interval containing not only qSPP6 for spikelets per panicle but also qNDW6 for node width to about 680-kb between markers RM20521 and RM20572 based on Nipponbare genome sequence. The locus, qSPP6 is of particular interest because of its independence from undesirable height and flowering time. SSR markers tightly linked to the qSPP6 will facilitate cloning of the gene underlying this QTL as well as marker assisted selection for variation in SPP in the breeding program.

In direct-seeding cultivation of rice, the emergence and establishment of seedlings are important for determining the actual yield. These traits depend principally upon elongation of both the mesocotyl and coleoptile. Mesocotyl elongation in rice is controlled by several genetic factors and is also affected by environmental factors. In this study, we mapped QTL for mesocotyl elongation using F8 lines from a cross between the cultivated rice, Ilpumbyeo and a weedy rice, PBR. One of the Korean weedy rice, PBR showed the long mesocotyl length than that of cultivars, Ilpumebyeo under soil and agar media conditions. This weedy rice showed long mesocotyl than the elite japonica cultivars. After a phenotyping of 150 F7 lines for mesocotyl length, a subset of 20 lines selected from the two extreme phenotypic tails was used for the bulked segregant analysis. Two QTL were identified on chromosomes 1 and 3. These two QTL were confirmed using 120 F8 lines. Two QTL, qMel-1 and qMel-3 on chromosomes 1 and 3 accounted for 37.3% and 6.5% of the phenotypic variance, respectively. The PBR alleles were associated with an increase in mesocotyl elongation at both loci. It is noteworthy that two QTL for mesocotyl elongation were colocalized with the QTL for mesocotyl length reported in the previous QTL reports. These QTLs can be introgressed into cultivar background using marker assisted backcrossing in an effort to enhance the level of mesocotyl elongation.

Brown leaf spot, caused by necrotrophic Cochliobolus miyabeanus (imperfect; Bipolaris oryzae), is one of the devastating disease in rice (Oryza sativa). Especially, recommended agricultural system such as diminishing fertilizer and environmental alteration like temperature increment result in the favorable conditions for the outbreak of this disease. Lack of water supply also requires drought-tolerant rice cultivar. We hypothesized that regulation of programmed cell death (PCD) should be a common solution conferring resistance and tolerance against above biotic and abiotic stresses at the same time. Among 17 CYCLIC NUCLEOTIDE-GATED ION CHANNEL in rice (OsCNGCs), over expression of a CNGC resulted in lesion mimic phenotypes in Dongjin background. Further, knock out of a CNGC resulted in enhanced resistance against rice brown spot in the field. These results indicate that selected OsCNGC should be involved in the PCD regulation and fungal infection-specific regulation of OsCNGC expression might induce resistance against rice brown spot because of pathogen’s necrotrophic nature. Vitamin E, tocopherol, is involved in the accumulation inhibition of reactive oxygen species involving superoxide and hydrogen peroxide. Tocopherol cyclase in Nicotiana benthamiana (NtTC), which is included in tocopherol systhesis, conferred tolerance against drought stress to rice. We already have settled down the recombination system effectively removing selection markers in vector. Based on these systems, we will define fungal secretome and genome, confirmation of PAMPs/effectors, identification of rice pattern recognition receptor, and functional characterization of these rice genes in the respect of PCD and disease resistance. We will also develop marker-free transgenic rice tolerant to drought and/or salinity stresses. These works should give us a bundle of rice genes conferring resistance and tolerance against biotic and abiotic stresses and amount of information useful for the analyses of common cross talk points between disease resistance and stress-tolerance.

The objective of this study were to identify QTLs for agronomic traits using a set of introgression lines carrying wild rice (Oryza rufipogon) segment in cultivated rice (ssp. japonica cv. Hwaseongbyeo). Ninety-six ILs were evaluated for seven agronomic traits, amylose and protein contents. The proportion of the recurrent genome in ILs ranged from 87.8 to 100%, with an average of 96.7%. The mean number of homozygous and heterozygous donor segments were 2 (ranging 0-7) and 1.7 (ranging 0-6), respectively, and the majority of these segments had size less than 10 cM. A total of 22 quantitative trait loci were identified for 9 traits and each QTL explained 7.2% to 56.6% of the phenotypic variance. Some QTLs were clustered in a few chromosomal regions. A first cluster was located near RM527 on chromosome 6 with QTLs for culm length, panicle length, days to heading, 1000-grain weight and protein content. Three ILs with high spikelets per panicle compared to the recurrent parent were selected to detect and fine map the wild segments responsible for this variation. The results will be discussed.

Spikelets per panicle is one of the most important trait associated with rice yield component. In this study, IL28, near isogenic line (NIL) developed by introgressing chromosomal segments from Moroberekan into Ilpumbyeo, showed significantly higher number of spikelets per panicle than the recurrent parent Ilpumbyeo. Quantitative trait locus (QTL) analysis in 243 F2 plants derived from a cross between IL28 and Ilpumbyeo, indicated that a QTL for spikelets per panicle, qspp6, located in the interval RM3430 – RM20580. The fact that QTLs for panicle length and secondary branch number were mapped in the same interval as that for qspp6 indicated that this locus was associated with panicle structure. To map the QTL more precisely, substitution mapping of qspp6 using F4 lines was conducted. As a result, substitution mapping with ten F4 lines further narrowed the interval containing qspp6 to about 429kb between marker RM20521 and RM20562 based on the japonica genome sequence. The locus, qspp6 is of particular interest because of its independence from undesirable height and flowering time. SSR markers tightly linked to the qspp6 will facilitate cloning of the gene underlying this QTL as well as marker assisted selection for variation in SPP in an applied breeding program.

The cereal grain crops have strong flexibility against adverse environment and they have various functional compounds. The objective of the present study was to screen phenolic compounds in sorghum [Sorghum bicolor (L.) Moench], foxtail millet (Setaria italica), common millet (Panicum miliaceum L.) by high performance liquid chromatography (HPLC) with photodiode array (PDA) detector. Sorghum contained the highest amount of phenolic compounds among three different crops (sorghum, foxtail millet, common millet). Especially Moktaksusu showed the highest amount of phenolic compounds concentrations and biggest regional differences. The comparison of average phenolic compounds in sorghums by regions showed order to Milyang (963.3~;~mug~cdotg-1 ), Yeongyang (923.1~;~mug~cdotg-1 ), Gijang (831.3~;~mug~cdotg-1 ) and Bonghwa (735.6~;~mug~cdotg-1 ). Among the sorghum cultivars, Moktaksusu (1407.9~;~mug~cdotg-1 ) had the highest concentration of phenolic compounds. The average phenolic compounds of foxtail millets showed similar amount among Milyang (319.0~;~mug~cdotg-1 ), Gijang (288.1~;~mug~cdotg-1 ) and Bonghwa (281.9~;~mug~cdotg-1 ) areas. The phenolic compounds of Yeongyang (246.6~;~mug~cdotg-1 ) slightly low and that showed similar concentrations among three different regions. The concentration of phenolic compounds in foxtail millets, Chungchajo (335.6~;~mug~cdotg-1 ) showed the highest concentrations. The average phenolic compounds of common millets showed the highest concentrations in Milyang (305.5~;~mug~cdotg-1 ), Bonghwa (262.0~;~mug~cdotg-1 ), Gijang (195.1~;~mug~cdotg-1 ), Yeongyang (237.2~;~mug~cdotg-1 ) in decreasing order. The concentration of phenolic compounds of common millets was the highest in the Norangchalgijang (337.0~;~mug~cdotg-1 ), Hwanggumgijang (250.0~;~mug~cdotg-1 ) was also relatively higher than others. The results of this study will provide basic information for breeding sorghums, foxtail millets and common millets with higher phenolic compound concentrations.

MicroRNAs (miRNAs) function as a key regulator of diverse cellular functions. To find out novel miRNAs that promote the differentiation of mouse embryonic stem cells (mESCs), we compared the miRNAs expression profiles of mESCs under self-renewal vs. differentiation states. We noticed that miR-222 was highly expressed during the differentiation of mESCs. Quantitative RT-PCR analysis revealed that expression of miR-222 was up-regulated during the embryonic bodies formation and retinoic acid -dependent differentiation. When miR-222 was suppressed by antogomiR-222, the differentiation of mESCs was delayed compared to control. Self-renewal marker expression or cell proliferation was not affected but the expression of lineage specific marker was suppressed by the treatment of miR-222 inhibitor during the differentiation of mESCs. Taken together, these results suggest that miR-222 functions to promote the differentiation of mESCs by regulating expression of differentiation related genes.

Beta-carotene producing transformants were produced in the background of 'Nagdongbyeo', a Japonica rice cultivar. Introgression of the carotenoid locus in the transformant, PAC4-2 into the elite cultivar 'Ilpumbyeo' was started. To initiate a backcrossing program, we surveyed 220 SSR markers and found that 38% of them were polymorphic between 'Ilpumbyeo' as a recurrent parent and the PAC4-2 as a recipient parent. The selection strategy comprising foreground and background selection was employed. First, foreground selection was practiced in BC1, BC2, and BC3 generations using the transgene specific PCR-based marker in addition to visual scoring of the seed color. Marker-based background selection combined with phenotypic selection was employed from BC3F2 to BC3F4 generations. Blast search indicated that the transgene PAC4-2 was located between SSR markers, RM6 and RM482. 240 BC3F3 and 63 BC3F4 lines were evaluated for four agronomic traits including days to heading. Most of the lines were similar to Ilpumbyeo in agronomic traits evaluated. The percentage of PAC4-2 genome ranged from 4% to 21% with a mean of 12.5%, which was higher than the expected for an unselected BC3 backcross population. This could be explained by the fact that two genes for beta-carotene and the stripe virus resistance were targeted in this study. We selected 10 representative BC3F5 lines from 63 BC3F4 lines based on agronomic traits and carotenoids content. The selection strategy would be appropriate for the introgression of beta-carotene gene in a breeding program.

The objectives of this study were to identify QTLs for agronomic traits using introgression lines from a cross between a japonica weedy rice and a Tongil-type rice. A total of 75 introgression lines developed in the Tongil-type rice were characterized. A total of 368 introgressed segments including 285 homozygous and 83 heterozygous loci were detected on 12 chromosomes based on the genotypes of 136 SSR markers. Each of 75 introgression lines contained 0-9 homozygous and 0-8 heterozygous introgressed segments with an average of 5.8 segments per line. A total of 31 quantitative and 2 qualitative loci were identified for 14 agronomic traits and each QTL explained 4.1% to 76.6% of the phenotypic variance. Some QTLs were clustered in a few chromosomal regions. A first cluster was located near RM315 and RM472 on chromosome 1 with QTLs for 1,000 grain weight, culm length, grain width and thickness. Another cluster was detected with four QTLs for 1,000 grain weight, grain length, grain width and grain length/width ratio near the SSR marker RM249 on chromosome 5. Among the 31 QTLs, 9 (28.1%) Hapcheonaengmi3 alleles were beneficial in the Milyang23 background. ILs would be useful to confirm QTLs putatively detected in a primary mapping population for complex traits and serve as a starting point for map-based cloning of the QTLs. Additional backcrosses are being made to purify nearly isogenic lines (NILs) harboring a few favorable Hapcheonaengmi3 alleles in Milyang23 background.

In a previous study, we mapped 12 QTLs for 1,000 grain weight (TGW) in the 172 BC2F2 lines derived from a cross between Oryza sativa ssp. Japonica cv. Hwaseongbyeo and O. rufipogon. These QTLs explained 5.4 – 11.4% of the phenotypic variance for TGW. Marker-aided selection combined with backcrosses was employed to develop QTL-NILs for each QTL. BC2F2 lines with each target QTL were backcrossed to Hwaseongbyeo twice and then allowed to self to produce BC4F5 populations. SSR markers linked to TGW were employed to select QTL-NILs with the respective target QTL. Six QTL-NILs with the recurrent parent, Hwaseongbyeo were evaluated for nine traits for three years from 2007 and 2009. Differences were observed between each of the 6 QTL-NILs and Hwaseongbyeo in TGW. In addition to TGW, these QTL-NILs displayed differences in other agronomic traits possibly indicating a tight linkage of genes controlling these traits. The direction of the QTL for TGW in 6 QTL-NILs was consistent as in the BC2F2 lines from the same cross. Difference in TGW between each of the QTL-NILs and Hwaseongbyeo was associated with the difference in one or two grain shape traits; grain length, grain width, and grain thickness. SSR markers linked to the QTL for TGW will facilitate selection of the grain shape character in a breeding program to diversify grain shape and provide the foundation for map-based gene isolation. Also, the QTL-NILs developed in this report and the progenies from crosses between the QTL-NILs will be useful in clarifying epistatic interactions among QTLs for TGW.