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PubMed1998

Isolation of a cDNA for tryptophan synthase beta from rice and studies of its expression in a 5-methyltryptophan-resistant mutant of rice.

A cDNA clone encoding rice tryptophan synthase beta (TSB) was isolated and its transcript level was examined in TR-No. 73, a derivative of a previously isolated rice mutant (TR-1) that is resistant to 5-methyltryptophan. The cDNA sequence of the rice gene for TSB was very similar to that of genes for TSB from other plants. Northern blotting analysis revealed that the steady-state level of TSB mRNA in the 5MT-resistant mutant TR-No. 73 was 1.3 times higher than the level of TSB mRNA in control rice plants under standard conditions. The level of TSB mRNA in control rice plants decreased after treatment of plants with 5MT. Similarly, the level of TSB mRNA in TR-No. 73 initially decreased, although less so than in control rice. However, after 12 h of treatment with 5MT, the level of the transcript in TR-No. 73 returned to the level under standard conditions. The activity of tryptophan synthase (TS) in seedlings of TR-No. 73 was about 2.3 times higher than that in seedlings of control rice under standard conditions.

Amino Acid Sequence↗
PubMed1999

The distribution and copy number of copia-like retrotransposons in rice (Oryza sativa L.) and their implications in the organization and evolution of the rice genome.

We used 22 fragments corresponding to the reverse transcriptase domain of copia-like retrotransposons as representatives to study the organization and distribution of these elements in the rice genome. The loci detected by these 22 fragments were assigned to 47 locations in the molecular-linkage map involving all 12 chromosomes. The distributional features of copia-like retrotransposons found in the rice genome indicated that (i) the loci detected were located mainly in one arm of each chromosome; (ii) one fragment usually detected several loci that were mapped to similar locations of different chromosomes; (iii) retrotransposons sharing high identity in nucleotide sequences were usually assigned to similar locations of the chromosomes; and (iv) concurrences of multiple loci, detected by different fragments, in similar locations or stretches of different chromosomes were common in the rice genome. We also determined that the copy number of copia-like retrotransposons in rice genome may be as low as approximately 100 per haploid genome. The restricted distribution, along with low copy number, suggested that copia-like retrotransposons in rice were relatively inactive during evolution compared with those in other plants. The distributional features of the copia-like retrotransposons suggested the existence of possible lineages among the rice chromosomes, which in turn suggested that chromosome duplication and diversification may be a mechanism for the origin and evolution of the rice chromosomes. The information provided by fine mapping of the retroelements in the genetic linkage map may also be useful for gene tagging and molecular cloning.

Journal Article↗
PubMed2003

Rice proteomics: a step toward functional analysis of the rice genome.

The technique of proteome analysis with two-dimensional PAGE has the power to monitor global changes that occur in the protein expression of tissues and organisms and/or expression that occurs under stresses. In this study, the catalogues of the rice proteome were constructed, and a functional characterization of some of these proteins was examined. Proteins extracted from tissues of rice and proteins extracted from rice under various kinds of stress were separated by two-dimensional PAGE. An image analyzer was used to reveal a total of 10,589 protein spots on 10 kinds of two-dimensional PAGE gels stained by Coomassie Brilliant Blue. The separated proteins were electroblotted onto a polyvinylidene difluoride membrane, and the N-terminal amino acid sequences of 272 of 905 proteins were determined. The internal amino acid sequences of 633 proteins were determined using a protein sequencer or mass spectrometry after enzyme digestion of the proteins. Finally, a data file of rice proteins that included information on amino acid sequences and sequence homologies was constructed. The major proteins involved in the growth and development of rice can be identified using the proteome approach. Some of these proteins, including a calcium-binding protein that turned out to be calreticulin and a gibberellin-binding protein, which is ribulose-1,5-bisphosphate carboxylase/oxygenase activase in rice, have functions in the signal transduction pathway. The information thus obtained from the rice proteome will be helpful in predicting the function of the unknown proteins and will aid in their molecular cloning.

Agrobacterium tumefaciens↗
PubMed1995

Effect of rice culturing practices on seasonal occurrence of Culex tritaeniorhynchus (Diptera: Culicidae) immatures in three different types of rice-growing areas in central Japan.

Seasonal occurrence of Culex tritaeniorhynchus Giles immatures was surveyed, together with detailed observations on the rice cultivation practices, weekly in three different types of rice field habitat from 1982 to 1985. Despite early water introduction and seedling transplantation, a late seasonal peak of density and abundance of first instars were observed at terraced rice fields (YE) with continuous water in- and outflow through sluices in a hilly area. In contrast, immature populations increased quickly in flat rice fields (AN, SK). High density and abundance of fourth instars were encountered before midseason drying in rice fields (AN) with less flow and little loss of water, because of construction of an independent irrigation and drainage system. The midseason drying and the alternating flooding and draining after the drying effectively suppressed the occurrence of immatures. Early final draining for harvesting eliminated mass production of mosquitoes, even if the density was high in some rice fields. Differences in timing of seasonal rice-culturing procedures and water management were assumed to be effective in controlling the seasonal occurrence of C. tritaeniorhynchus.

Agriculture↗
PubMed2002

Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project.

BLASTX alignment between 189.5 Mb of rice genomic sequence and translated Arabidopsis thaliana annotated coding sequences (CDS) identified 60 syntenic regions involving 4-22 rice orthologs covering < or =3.2 cM (centiMorgan). Most regions are <3 cM in length. A detailed and updated version of a table representing these regions is available on our web site. Thirty-five rice loci match two distinct A.thaliana loci, as expected from the duplicated nature of the A.thaliana genome. One A.thaliana locus matches two distinct rice regions, suggesting that rice chromosomal sequence duplications exist. A high level of rearrangement characterizing the 60 syntenic regions illustrates the ancient nature of the speciation between A.thaliana and rice. The apparent reduced level of microcollinearity implies the dispersion to new genomic locations, via transposon activity, of single or small clusters of genes in the rice genome, which represents a significant additional effector of plant genome evolution.

Arabidopsis↗
PubMed2003

The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists.

Rice is not only a major food staple for the world's population but it also is a model species for a major group of flowering plants, the monocotyledonous plants. Draft genomic sequence of two subspecies of rice, Oryza sativa spp. japonica and indica ssp. are publicly available. To provide the community with a resource to data-mine the rice genome, we have constructed an annotation resource for rice (http://www.tigr.org/tdb/e2k1/osa1/). In this resource, we have annotated the rice genome for gene content, identified motifs/domains within the predicted genes, constructed a rice repeat database, identified related sequences in other plant species, and identified syntenic sequences between rice and maize. All of the data is available through web-based interfaces, FTP downloads, and a Distributed Annotation System.

Chromosomes, Artificial↗
PubMed2005

Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice.

The transcription factors dehydration-responsive element-binding protein 1s (DREB1s)/C-repeat-binding factors (CBFs) specifically interact with the DRE/CRT cis-acting element and control the expression of many stress-inducible genes in Arabidopsis. The genes for DREB1 orthologs, OsDREB1A and OsDREB1B from rice, are induced by cold stress, and overexpression of DREB1 or OsDREB1 induced strong expression of stress-responsive genes in transgenic Arabidopsis plants, resulting in increased tolerance to high-salt and freezing stresses. In this study, we generated transgenic rice plants overexpressing the OsDREB1 or DREB1 genes. These transgenic rice plants showed not only growth retardation under normal growth conditions but also improved tolerance to drought, high-salt and low-temperature stresses like the transgenic Arabidopsis plants overexpressing OsDREB1 or DREB1. We also detected elevated contents of osmoprotectants such as free proline and various soluble sugars in the transgenic rice as in the transgenic Arabidopsis plants. We identified target stress-inducible genes of OsDREB1A in the transgenic rice using microarray and RNA gel blot analyses. These genes encode proteins that are thought to function in stress tolerance in the plants. These results indicate that the DREB1/CBF cold-responsive pathway is conserved in rice and the DREB1-type genes are quite useful for improvement of stress tolerance to environmental stresses in various kinds of transgenic plants including rice.

Arabidopsis↗
PubMed1991

Analysis of rice Act1 5' region activity in transgenic rice plants.

The 5' region of the rice actin 1 gene (Act1) has been developed as an efficient regulator of foreign gene expression in transgenic rice plants. To determine the pattern and level of rice Act1 5' region activity, transgenic rice plants containing the Act1 5' region fused to a bacterial beta-glucuronidase (Gus) coding sequence were generated. Two independent clonal lines of transgenic rice plants were analyzed in detail. Quantitative analysis showed that tissue from these transgenic rice plants have a level of GUS protein that represents as much as 3% of total soluble protein. We were able to demonstrate that Act1-Gus gene expression is constitutive throughout the sporophytic and gametophytic tissues of these transgenic rice plants. Plants from one transgenic line were analyzed for the segregation of GUS activity in pollen by in situ histochemical staining, and the inheritance and stability of Act1-Gus expression were assayed in subsequently derived progeny plants.

Actins↗
PubMed2005

Rice NRR, a negative regulator of disease resistance, interacts with Arabidopsis NPR1 and rice NH1.

Arabidopsis NPR1/NIM1 is a key regulator of systemic acquired resistance (SAR), which confers lasting broad-spectrum resistance. Over-expression of Arabidopsis NPR1 or the NPR1 homolog 1 (NH1) in rice results in enhanced resistance to the pathogen Xanthomonasoryzae pv. oryzae (Xoo), suggesting the presence of a related defense pathway in rice. We investigated this pathway in rice by identifying proteins that interact with NH1. Here we report the isolation and characterization of a rice cDNA encoding a novel protein, named NRR (for negative regulator of resistance). NRR interacts with NPR1 in the NPR1-interacting domain (NI25) consisting of 25 amino acids. NRR also interacts with NH1; however, NI25 was not sufficient for a strong interaction, indicating a difference between the rice and the Arabidopsis proteins. Silencing of NRR in rice had little effect on resistance to Xoo. When constitutively over-expressed in rice, NRR affected basal resistance, age-related resistance and Xa21-mediated resistance, causing enhanced susceptibility to Xoo. This phenotype was correlated with elevated NRR mRNA and protein levels and increased Xoo growth. Over-expression of NRR suppressed the induction of defense-related genes. NRR:GFP (green fluorescent protein) protein was localized to the nucleus, indicating that NRR may act directly to suppress the activation of defense genes. The fact that NRR compromises Xa21-mediated resistance indicates cross-talk or overlap between NH1- and Xa21-mediated pathways.

Amino Acid Sequence↗
PubMed2002

AOX1c, a novel rice gene for alternative oxidase; comparison with rice AOX1a and AOX1b.

A novel gene for alternative oxidase (AOX) was isolated from rice (Oryza sativa L.) and characterized. The deduced amino acid sequence of the novel AOX gene contains features that are conserved among other AOXs. This AOX gene was designated AOX1c based on a phylogenetic analysis of the AOX genes. Northern hybridization analyses revealed that AOX1c and AOX1a/AOX1b transcripts accumulated differently in various rice organs and rice seedlings under low temperature conditions. AOX1c mRNA was mainly present in young leaves under constant light, mature leaves and panicles after heading, but it was not detected in young etiolated leaves and young roots of seedlings or young panicles. On the other hand, the mRNAs of the rice AOX1a and AOX1b genes were mainly present in young roots and mature leaves. Under low temperature conditions, the steady-state mRNA levels of the rice AOX1a and AOX1b genes clearly increased with time but the rice AOX1c gene was apparently not responsive to low temperature. The rice AOX gene family and differences in their regulation are discussed.

Amino Acid Sequence↗
PubMed2004

Effect of rice bug Leptocorisa oratorius (Hemiptera: Alydidae) on rice yield, grain quality, and seed viability.

The effect of Leptocorisa oratorius (F.) on the yield, grain quality, and seed viability of four rice, Oryza sativa L., lines was studied. Three of the lines, C2, IR64, and PSBRc20, are grown in the Philippines. The fourth, IR72164-201-1 is an unreleased experimental line of an O. sativa japonica x O. sativa indica cross. Each line was exposed to four infestation densities for 21 d. L. oratorius feeding produced unfilled and partially filled grains, resulting in a negative correlation of yield to rice bug density. When filled grains were sown, germination rates were negatively correlated with rice bug densities. The percentage of discolored grains was positively correlated with L. oratorius density on all rice lines. At the same infestation rates, PSBRc20 and IR64 had higher yields, less damaged grain, and higher germination rates than IR72164-201-1 and C2, suggesting host plant tolerance to rice bug feeding. The economic injury levels (EILs) currently used for rice bug management are based solely on yield loss estimates. The results of this study suggest that EIL for rice bugs should be revised to take into account reductions in grain quality and seed germination rates in addition to yield loss.

Agriculture↗
PubMed2001

[QTL analysis of anther length and ratio of stigma exsertion, two key traits of classification for cultivated rice (Oryza sativa L.) and common wild rice (O. rufipogon Griff.)].

A genetic map including 120 RFLP markers covering 1418.2 cM has been constructed using a BC1 population derived from a cross between common wild rice (Oryza rufipogon Griff.) from Dongxiang, Jiangxi Province, China, and an elite Indica variety Guichao 2. The linkage orders and genetic distances of markers in this map are consistent with the map constructed by Rice Genome Program of Japan except the markers of short arm of Chromosome 1. The QTLs analysis of anther length and ratio of stigma exsertion, two key traits of classification for cultivated rice and common wild rice indicated that there are two QTLs controlling anther length located at the region of C424-G39 of Chromosome 2, and C2807-C1263 of Chromosome 9 respectively. It was also found that there are two QTLs controlling ratio of stigma exsertion, and located at the region of C2289-R1553 of Chromosome 5 and G1149-R1963 of Chromosome 8 respectively. The detected QTLs affecting the key traits of classification for wild rice and cultivated rice will be useful for study of molecular evolution mechanism of cultivated rice.

Chromosome Mapping↗
PubMed2002

The potential of intermittent irrigation for increasing rice yields, lowering water consumption, reducing methane emissions, and controlling malaria in African rice fields.

Rice production in sub-Saharan Africa has more than doubled in the last 3 decades and the potential to further develop rice-harvested areas is considerable. Several studies have demonstrated that the transformation of arable land into rice irrigation might create suitable habitats for large populations of disease vectors. Prominent among those are anopheline mosquitoes responsible for transmission of malaria. The method of irrigation on an intermittent basis during the rice-cropping calendar has gained renewed interest as a potentially effective malaria control strategy since the early 1980s. We review the experiences of the past 80 years with intermittent irrigation in the cultivation of rice. This method has been shown to reduce significantly the density of malaria vectors by curtailing their larval development. Furthermore, reduced methane emissions and water savings with at least equal yields were achieved in intermittently irrigated rice fields. We explore and discuss under what conditions intermittent irrigation might be beneficial in new rice-growing areas and identify steps that have to be taken to expand such programs in the future.

Africa South of the Sahara↗
PubMed1991

Rice protein 16KD--a major allergen in rice grain extract.

The allergenic activity of Rice protein 16 KD (RP16KD) isolated from water soluble rice proteins was examined by radioallergosorbent test (RAST), RAST inhibition and histamine release assay. All of the 31 sera which showed positive RAST values for rice grain extract were positive for RP16KD RAST. Furthermore, there was a significant correlation (r = 0.56, p less than 0.01) between these RAST values. PR16KD effectively inhibited IgE binding to the rice grain extract disc in RAST inhibition assays using 4 sera with positive RAST values for both antigens. In 17 subjects with positive RAST values for rice grain extract, a significant positive correlation (r = 0.53, p less than 0.05) was found between the maximum percent histamine releases from their leukocytes by rice grain extract and RP16KD. These data strongly suggest that RP16KD is one of the major allergens of rice grain.

Allergens↗
PubMedDate not supplied

[Comparison of the nutritional value between brown rice and white rice].

Cereals are considered an important source of nutrients both in human and animal nourishment. In this paper nutritional value of brown rice is compared to that of white rice in relation to nutrients. Results show that despite higher nutrients contents of brown rice compared to white rice, experimental datas does not provide evidence that the brown rice diet is better than the diet based on white rice. Possible antinutricional factors present in brown rice have adverse effects on bioavailability of this cereal nutrients.

Dietary Fiber↗
PubMed2002

The influence of plant age on tolerance of rice to injury by the rice water weevil, Lissorhoptrus oryzophilus (Coleoptera: Curculionidae).

For most plant species, tolerance to many types of herbivory increases as plants age, but the applicability of this pattern to root herbivory has not been tested. Injury to roots of rice plants by larvae of the rice water weevil, Lissorhoptrus oryzophilus Kuschel, causes severe reductions in yields in the United States. It is generally thought that young rice plants, because their root systems are smaller, are less tolerant than older plants of root feeding by L. oryzophilus. Field experiments were conducted to test this hypothesis. Plots of rice (4.7 to 6.5 m2) were established and subjected to natural infestations of L. oryzophilus larvae. A soil insecticide was applied to plots at different times during the tillering phase of rice in order to manipulate the timing of weevil infestation. The impact of these treatments (timings of insecticide applications) was assessed by comparing relationships between yield loss and larval pressure for each treatment using analysis of covariance. Yield losses ranged from 13% to over 40% in plots not treated with insecticide. Patterns of yield losses from plots treated with insecticide at different times were best explained by the hypothesis that yield loss is determined both by the age of plants infested and by the size of larvae infesting plants. Young plants appear to be less tolerant than older plants, and feeding by large larvae appears to be more deleterious than feeding by smaller larvae. Management practices that delay infestation of rice by L. oryzophilus until plants are older may be an important component of management programmes for this pest.

Animals↗
PubMed2003

Proteomic analysis of differentially expressed proteins induced by rice blast fungus and elicitor in suspension-cultured rice cells.

We used two-dimensional electrophoresis (2-DE) and other proteomic approaches to identify proteins expressed in suspension-cultured rice cells in response to the rice blast fungus, Magnaporthe grisea. Proteins were extracted from suspension-cultured cells at 24 and 48 h after rice blast fungus inoculation or treatment with elicitor or other signal molecules such as jasmonic acid (JA), salicylic acid, and H(2)O(2). The proteins were then polyethylene glycol fractionated before separation by 2-DE. Fourteen protein spots were induced or increased by the treatments, which we analyzed by N-terminal or internal amino acid sequencing. Twelve proteins from six different genes were identified. Rice pathogen-related protein class 10 (OsPR-10), isoflavone reductase like protein, beta-glucosidase, and putative receptor-like protein kinase were among those induced by rice blast fungus; these have not previously been reported in suspension-cultured rice cells. Six isoforms of probenazole-inducible protein (PBZ1) and two isoforms of salt-induced protein (SalT) that responded to blast fungus, elicitor, and JA were also resolved on a 2-DE gel and identified by proteome analysis. The expression level of these induced proteins both in suspension-cultured cells and in leaves of whole plants was analyzed by Western blot. PBZ1, OsPR-10, and SalT proteins from incompatible reactions were induced earlier and to a greater extent than those in compatible reactions. Proteome analysis can thus distinguish differences in the timing and amount of protein expression induced by pathogens and other signal molecules in incompatible and compatible interactions.

Antibodies↗