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The complete chloroplast genome of Zoysia macrostachya Franch. & Sav. isolated in Korea is 135,902 bp long (GC ratio is 38.4%) and has four subregions; 81,546 bp of large single-copy (36.3%) and 12,586 bp of small single-copy (32.7%) regions are separated by 20,885 bp of inverted repeat (44.1%) regions, including 130 genes (83 protein-coding genes, eight rRNAs, and 39 tRNAs). Thirty-nine single nucleotide polymorphisms and 11 insertions and deletion (INDEL) regions were identified from two Z. macrostachya chloroplast genomes, the smallest among other Zoysia species. Phylogenetic trees show that two Z. macrostachya chloroplast genomes are clustered into a single clade. However, we found some incongruency with regard to the phylogenetic position of the Z. macrostachya clade. Our chloroplast genome provides insights into intraspecific variations and species delimitation issues pertaining to the Zoysia species.

A drought-tolerant transgenic rice (Agb0103) was developed using a pepper methionine sulfoxide reductase (CaMsrB2) under the control of rice Rab21 promoter with a selection marker, the phosphinothricin acetyltransferase (PAT) gene. Commercialization of genetically modified (GM) crops will require the evaluation of risks associated with the release of GM crops. With the potential problems associated to GM crops safety testing, the investigation of their effects on non-target organisms is necessary for environmental risk research. This study was carried out to assess acute toxicity of a GM crop using the water flea (Daphnia magna) for non-target organism risk evaluation. The effect of acute toxicity on Daphnia magna of Agb0103 rice and a non-GM rice, Ilmibyeo, were investigated at different concentrations (0, 625, 1,250, 2,500, 5,000, and 10,000 ㎎/L). The Agb0103 rice used for the test was confirmed to express the CaMsrB2/PAT gene by the PCR and ELISA. Daphnia magna feeding tests showed no significant differences in cumulative immobility or abnormal response with either Agb0103 rice or non-GM rice. The 48hr-EC 50 values showed no difference between Agb0103 rice (2243 ㎎/L) and non-GM rice (2694 ㎎/L). These results suggest that there is no significant difference in toxicity to Daphnia magna between Agb0103 rice and its non-GM counterpart.

This study was conducted to investigate the effect of Psy-2A-CrtI (PAC), a genetically modified (GM) rice with enhanced β-carotene, on the soil microbial community. The soil used to cultivate GM rice and its wild-type, Nakdong, was analyzed for population density, denaturing gradient gel electrophoresis (DGGE), and pyrosequencing. It was found that the bacterial, fungal and actinomycetes population densities of the PAC soils were within the range of those of the non-GM rice cultivar, Nakdong. The DGGE banding patterns of the GM and non-GM soils were also similar, suggesting that the bacterial community structures were stable within a given month and were unaffected by the presence of a GM plant. The pyrosequencing result showed a temporal difference in microorganism taxon and distribution ratio, but no significant difference between GM and non-GM was found. The persistence of the transgene DNA in the plant and surrounding soil were investigated for different time periods. There were differences in the persistence within the plant depending on the gene, but they could not be detected after 5 weeks. Also the transgenes were not detected in the surrounding soil. These results indicate that soil microbial communities are unaffected by the cultivation of a PAC rice within the experimental time frame.

Background Rice is one of the most important food crops for humans. To improve the agronomical traits of rice, the functions of more than 1,000 rice genes have been recently characterized and summarized. The completed, map-based sequence of the rice genome has significantly accelerated the functional characterization of rice genes, but progress remains limited in assigning functions to all predicted non-transposable element (non-TE) genes, estimated to number 37,000–41,000. Results The International Rice Functional Genomics Consortium (IRFGC) has generated a huge number of gene-indexed mutants by using mutagens such as T-DNA, Tos17 and Ds/dSpm. These mutants have been identified by 246,566 flanking sequence tags (FSTs) and cover 65 % (25,275 of 38,869) of the non-TE genes in rice, while the mutation ratio of TE genes is 25.7 %. In addition, almost 80 % of highly expressed non-TE genes have insertion mutations, indicating that highly expressed genes in rice chromosomes are more likely to have mutations by mutagens such as T-DNA, Ds, dSpm and Tos17. The functions of around 2.5 % of rice genes have been characterized, and studies have mainly focused on transcriptional and post-transcriptional regulation. Slow progress in characterizing the function of rice genes is mainly due to a lack of clues to guide functional studies or functional redundancy. These limitations can be partially solved by a well-categorized functional classification of FST genes. To create this classification, we used the diverse overviews installed in the MapMan toolkit. Gene Ontology (GO) assignment to FST genes supplemented the limitation of MapMan overviews. Conclusion The functions of 863 of 1,022 known genes can be evaluated by current FST lines, indicating that FST genes are useful resources for functional genomic studies. We assigned 16,169 out of 29,624 FST genes to 34 MapMan classes, including major three categories such as DNA, RNA and protein. To demonstrate the MapMan application on FST genes, transcriptome analysis was done from a rice mutant of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) gene with FST. Mapping of 756 down-regulated genes in dxr mutants and their annotation in terms of various MapMan overviews revealed candidate genes downstream of DXR-mediating light signaling pathway in diverse functional classes such as the methyl-D-erythritol 4-phosphatepathway (MEP) pathway overview, photosynthesis, secondary metabolism and regulatory overview. This report provides a useful guide for systematic phenomics and further applications to enhance the key agronomic traits of rice. Electronic supplementary material The online version of this article (doi:10.1186/s12284-016-0089-2) contains supplementary material, which is available to authorized users.

Although susceptibility to seed shattering causes severe yield loss during cereal crop harvest, it is an adaptive trait for seed dispersal in wild plants. We previously identified a recessive shattering locus, sh-h, from the rice shattering mutant line Hsh that carries an enhanced abscission layer. Here, we further mapped sh-h to a 34-kb region on chromosome 7 by analyzing 240 F(2) plants and five F(3) lines from the cross between Hsh and Blue&Gundil. Hsh had a point mutation at the 3' splice site of the seventh intron within LOC_Os07g10690, causing a 15-bp deletion of its mRNA as a result of altered splicing. Two transferred DNA (T-DNA) insertion mutants and one point mutant exhibited the enhanced shattering phenotype, confirming that LOC_Os07g10690 is indeed the sh-h gene. RNA interference (RNAi) transgenic lines with suppressed expression of this gene exhibited greater shattering. This gene, which encodes a protein containing a conserved carboxy-terminal domain (CTD) phosphatase domain, was named Oryza sativa CTD phosphatase-like 1 (OsCPL1). Subcellular localization and biochemical analysis revealed that the OsCPL1 protein is a nuclear phosphatase, a common characteristic of metazoan CTD phosphatases involved in cell differentiation. These results demonstrate that OsCPL1 represses differentiation of the abscission layer during panicle development.

Seed germination is the important stage to ex-press many genes for regulation of energy metabolism, starch degradation and cell division from seed dormancy state. For the functional analysis of seed germination mech-anisms, we were analyzed the rice cDNA clones ( Oryza sativa cultivar Ilpum ) obtained from seed imbibition during 48 hours. Total number of 18,101 Expressed Sequence Tags (ESTs) were clustered using SeqMan program. Among them, 8,836 clones were identified as unique clones. We identified the chitinase gene specifically expressed in seed germination and amylase gene involved to starch degradation from the full length cDNA analysis, and several genes were registered to NCBI GeneBank. To analyzed the commonly expressed genes between inmature seed and germinated seed, 25,668 inmature ESTs and 18,101 germinated ESTs were clustered using SeqMan program and identified 2,514 clones as com-monly expressed unigene. Among them, alpha-glubulin and alcohol dehydrogenase I were supposed to LEA genes only expressed in the immature and germinated seed stages.For the clustering of orthologous group genes, we further analyzed the 8,836 EST clones from germinating seeds using NCBI clusters of orthologous groups database. Among the clones, 5,076 clones were categorized into information storage and processing, cellular processes and signaling, metabolism and poorly characterized genes, proportioning 783 (14.29%), 1,484 (27%), 1,363 (24.8%) and 1,869 (34%) clones to the previous four categories, respectively.

A gene detection strategy using two-component Ac/Ds construct, with the mobile Ds transposon, has been developed to better understand gene functions in crops. Currently, 115,000 Ds insertion lines have been generated through the Ac/Ds gene trap system in Korea using japonica rice Dongjin as donor. Four hundred and thirty-seven mutants from 12,162 Ds-tagged lines were catalogued, including physiological and agronomic traits. Different traits were identified with distinct characteristics in terms of tillers, panicles, leaves, flowers, seed, chlorophyll content, and height. Culm and panicle length, number of panicles, and days to flowering of the Dongjin Ds population revealed high standard deviations compared with the donor cultivar. An evaluation of the Ds distribution on the chromosome revealed that 74.5% of the Ds were reinserted into gene-rich regions, making this Ac/Ds-mediated gene trap system useful in helping to gain an understanding of the function of genes and thus improve the gene-tagging system in rice.

Transposon-mediated insertional mutagenesis is one of powerful strategy for assessing functions of genes in higher plants. In this report, we have selected highly susceptible and tolerance plant by screening about high salt (3% NaCl) and cold stresses () from F2 seeds of 30,000 Ac/Ds insertional mutagenesis lines in rice (Oryza sativa L. cv. Dongjin). In order to identify the gene tagging, insertion of Ds element was analyzed by Southern blot and these results revealed that 19 lines were matched genotype of selected lines with phenotype from the first selected 212 lines, and 13 lines have one copy of Ds elements. The Franking Sequence Tags (FSTs) of selected mutant lines showed high similarities with the following known function genes: signal transduction and regulation of gene expression (transpoter, protease family protein and apical meristem family protein), osmotic stress response (heat shock protein, O-methyltransferase, glyceraldehyde-3-phosphate dehydrogenase and drought stress induce protein), vesicle trafficking (SYP 5 family protein) and senescence associated protein. The expression pattern of 19 genes were analyzed using RT-PCR under the abiotic stresses of 9 class; 250mM NaCl, osmotic, drought, 3% , ABA, IAA, 0.1 ppm 2,4-D, cold and high temperature. Isolated knock-out genes showed the positive response about 250 mM NaCl, drought, , PEG, IAA, 2,4-D, ABA treatment and low () and high temperature (). The results from this study indicate that function of selected knock-out genes could be useful in improving of tolerance to abiotic stresses as an important transcriptional activators in rice.

본 연구는 동진벼 유래의 Ac/Ds 삽입변이집단의 GUS 분석을 통하여 뿌리 및 미숙종자에서 강하게 GUS가 발현한 개체를 선발하여 FST(flanking sequence tag) 분석 한 결과 Ds 전이 인자가 3번 염색체 zinc finger RING-H2 관련 Oszinc626 유전자의 첫 번째 exon 부위에 single copy로 삽입되어 있었으며, 선발변이체는 뿌리 및 종자 발달이 정상인 동진벼에 비해 매우 낮은 것으로 나타났다. Oszinc626 유전자는 RING-H2 type(C3-H2-C3)으로 $Cys-X_2-Cys-X_{28}-Cys-X-His-X_2-His-X_2-Cys-X_{14}-Cys-X_2-Cys$ 배열이 C-terminus 가장 말단에 위치하며, 49 kDa의 분자량을 가지고 있다. 또한 Southern blot 분석에서 Oszinc626 유전자는 벼 게놈상에 single copy로 존재하였다. RT-PCR을 통한 돌연변이 유전자의 발현분석 결과 250 mM의 염과, $4^{\circ}C$ 저온등과 같은abiotic stress에 의해 발현이 증가함을 보였고, 호르몬처리에 있어서 ABA와 IAA의 식물호르몬을 처리했을 경우 24시간까지 계속해서 발현양이 증가하는 것을 보이는 반면, 2,4-D 처리의 경우 30분 후에 발현이 일시적으로 증가되었으나 이후 발현이 급속히 감소한 것을 보였다. 벼의 조직 별 발현 검정에서 미성숙한 종자, 뿌리 분열조직 및 신초 등 주로 생장점 부위에서 강하게 발현되는 것을 보임에 따라 Oszinc626 유전자의 경우 식물의 생장에 관여하는 주동 유전자의 하나로 판단된다. 【Ac/Ds mutant lines of this study were transgenic rice plants, each of which harbored the maize transposable element Ds together with a GUS coding sequence under the control of a promoterless(Ds-GUS). We selected the mutants that were GUS expressed lines, because the GUS positive lines will be useful for identifying gene function in rice. One of these mutants was identified knock-out at Oszinc626(NP_001049991) gene, encoding a RING-H2 zinc-finger protein, by Ds insertion. In this mutant, while primary root development is normal, secondary root development from lateral root was very poor and seed development was incomplete compare with normal plant. RING zinc-finger proteins play important roles in the regulation of development in a variety of organisms. In the plant kingdom, a few genes encoding RING zinc-finger proteins have been documented with visible effects on plant growth and development. The consensus of the RING-H2(C3-H2-C3 type) domain for this group of protein is $Cys-X_2-Cys-X_{28}-Cys-X-His-X_2-His-X_2-Cys-X_{14}-Cys-X_2-Cys$ . Oszinc626 encodes a predicted protein product of 445 amino acids residues with a molecular mass of 49 kDa, with a RING-zinc-finger motif located at the extreme end of the C-terminus. RT-PCR analysis indicated that the expression of Oszinc626 gene was induced by IAA, cold, dehydration, high-salinity and abscisic acid, but not by 2,4-D, and the transcription of Oszinc626 gene accumulated primarily in rice immature seeds, root meristem and shoots. The gene accumulation patterns were corresponded with GUS expression.】

The Korean Rice Ds-tagging lines Database (KRDD) is designed to provide information about Ac/Ds insertion lines and activation tagging lines using japonica rice. This database has provided information on 18,158 Ds lines, which includes the ID, description, photo image, sequence information, and gene characteristics. The KRDD is visualized using a web-based graphical view, and anonymous users can query and browse the data using the search function. It has four major menus of web pages: (i) a Blast Search menu of a mutant line; Blast from rice Ds-tagging mutant lines; (ii) a primer de-sign tool to identify genotypes of Ds insertion lines; (iii) a Phenotype menu for Ds lines, searching by identi-fication name and phenotype characteristics; and (iv) a Management menu for Ds lines. Availability: The KRDD can be accessed at the web site of the National Institute of Agricultural Biotechnology (http://www. niab.go.kr/RDS/) Keywords: Ac/Ds database, Ds phenotype, Ds-tagging line, insertion line, KRDD

We used a multiple screening process to identify genes involved in salt tolerance–specific biosynthesis and metabolism in rice (Oryza sativa L.). We selected 8,275 salt tolerance–related candidate genes using expression profiles generated across four stages on a microarray containing 135,000 probes (135 K microarray) in Oryza sativa. Using our method, we screened 342 ortholog genes, and 74 pathway genes associated with salt –response–related biosynthesis. Finally, we identified six genes by comparison of pathway-network genes and orthologous genes. The six genes were anchored to the chromosomes of rice to characterize their genetic-map positions and were used to construct the phylogenetic tree. The results were verified by reverse transcription–polymerase chain reaction.

OSH6 (Oryza sativa Homeobox6) is an ortholog of lg3 (Liguleless3) in maize. We generated a novel allele, termed OSH6-Ds, by inserting a defective Ds element into the third exon of OSH6, which resulted in a truncated OSH6 mRNA. The truncated mRNA was expressed ectopically in leaf tissues and encoded the N-terminal region of OSH6, which includes the KNOX1 and partial KNOX2 subdomains. This recessive mutant showed outgrowth of bracts or produced leaves at the basal node of the panicle. These phenotypes distinguished it from the OSH6 transgene whose ectopic expression led to a "blade to sheath transformation" phenotype at the midrib region of leaves, similar to that seen in dominant Lg3 mutants. Expression of a similar truncated OSH6 cDNA from the 35S promoter (35S::DeltaOSH6) confirmed that the ectopic expression of this product was responsible for the aberrant bract development. These data suggest that OSH6-Ds interferes with a developmental mechanism involved in bract differentiation, especially at the basal nodes of panicles.

Insertional mutagen-mediated gene tagging populations have been essential resources for analyzing the function of plant genes. In rice, maize transposable elements have been successfully utilized to produce transposant populations. However, many generations and substantial field space are required to obtain a sufficiently sized transposant population. In rice, the japonica and indica subspecies are phenotypically and genetically divergent. Here, callus cultures with seeds carrying Ac and Ds were used to produce 89,700 lines of Dongjin, a japonica cultivar, and 6,200 lines of MGRI079, whose genome is composed of a mixture of the genetic backgrounds of japonica and indica. Of the more than 3,000 lines examined, 67% had Ds elements. Among the Ds-carrying lines, 81% of Dongjin and 63% of MGRI079 contained transposed Ds, with an average of around 2.0 copies. By examining more than 15,000 lines, it was found that 12% expressed the reporter gene GUS during the early-seedling stage. GUS was expressed in root hairs and crown root initials at estimated frequencies of 0.78% and 0.34%, respectively. The 5,271 analyzed Ds loci were found to be randomly distributed over all of the rice chromosomes.

Using a population of recombinant inbred lines of the 164 genotypes derived from a cross between ‘Milyang 23’ (indica) and ‘Gihobyeo’ (japonica) in rice (Oryza sativa L.), salt tolerance was evaluated at a young seedling stage in concentrations of 0.5% and 0.7% NaCl. Mapping quantitative trait loci (QTLs) related to salt tolerance was carried out by interval mapping using Qgene 3.0. Two QTLs (qST1 and qST3) conferring salt tolerance at young seedling stage were mapped on chromosome 1 and 3, respectively, and explained 35.5–36.9% of the total phenotypic variation in 0.5% and 0.7% NaCl. The favourable allele of qST1 was contributed by ‘Gihobyeo’, and that of qST3 by ‘Milyang 23’. The results obtained in 0.5% and 0.7% NaCl for 2 years were similar in flanked markers and phenotypic variation.

Rapid, large-scale generation of a Ds transposant population was achieved using a regeneration procedure involving tissue culture of seed-derived calli carrying Ac and inactive Ds elements. In the F(2) progeny from genetic crosses between the same Ds and Ac starter lines, most of the crosses produced an independent germinal transposition frequency of 10-20%. Also, many Ds elements underwent immobilization even though Ac was expressed. By comparison, in a callus-derived regenerated population, over 70% of plants carried independent Ds insertions, indicating transposition early in callus formation. In the remaining population, the majority of plants carried only Ac. Most of the new Ds insertions were stably transmitted to a subsequent generation. An exceptionally high proportion of independent transposants in the regenerated population means that selection markers for transposed Ds and continual monitoring of Ac/Ds activities may not necessarily be required. By analyzing 1297 Ds-flanking DNA sequences, a genetic map of 1072 Ds insertion sites was developed. The map showed that Ds elements were transposed onto all of the rice chromosomes, with preference not only near donor sites (36%) but also on certain physically unlinked arms. Populations from both genetic crossing and tissue culture showed the same distribution patterns of Ds insertion sites. The information of these mapped Ds insertion sites was deposited in GenBank. Among them, 55% of Ds elements were on predicted open-reading frame (ORF) regions. Thus, we propose an optimal strategy for the rapid generation of a large population of Ds transposants in rice.

To mutagenize rice genomes, a two-element system is utilized. This system comprises an immobile Ac element driven by the CaMV 35S promoter, and a gene trap Ds carrying a partial intron with alternative splice acceptors fused to the GUS coding region. Rapid, large-scale generation of a Ds transposant population was achieved using a plant regeneration procedure involving the tissue culture of seed-derived calli carrying Ac and Ds elements. During tissue cultures, Ds mobility accompanies changes in methylation patterns of a terminal region of Ds, where over 70% of plants contained independent Ds insertions. In the transposon population, around 12% of plants expressed GUS at the early seedling stage. A flanking-sequence-tag (FST) database has been established by cloning over 19,968 Ds insertion sites and the Ds map shows relatively uniform distribution across the rice chromosomes.

To characterize genes involved in fruit body development, two complementary DNA (cDNA) libraries were constructed from RNA isolated from liquid-cultured mycelia and fruit bodies of Pleurotus ostreatus. Using single-pass sequencing of cDNA clones, 952 and 1069 expressed sequence tags (ESTs) were generated from liquid-cultured mycelia and fruit body cDNA library, respectively. A BLASTX search revealed that 390 of the liquid-cultured mycelia ESTs (41%) and 531 of the fruit body ESTs (50%) showed significant similarity to protein sequences described in the nonredudant database (E values < or =1 x 10(-5)). When liquid-cultured mycelia and fruit body ESTs were compared by the SeqMan II program, among the total of 2021 ESTs, 1256 ESTs were unigenes, and 66 unigenes (5.3%) were commonly expressed during both stages. The functional catalogs of the ESTs were made by comparison with functionally identified Saccharomyces cerevisiae genes. Liquid-cultured mycelium ESTs were compared with fruit body ESTs and changes of the expressed genes during fruit body development were analyzed.