An integrated map of Oryza sativa L. chromosome 5

The developments of molecular marker-based genetic linkage maps are now routine. Physical maps based on contigs of large insert genomic clones have been established in several plant species. However, integration of genetic, physical, and cytological maps is still a challenge for most plant species. Here we present an integrated map of rice (Oryza sativa L.) chromosome 5, developed by fluorescence in situ hybridization mapping of 18 bacterial artificial chromosome (BAC) clones or PI-derived artificial chromosome (PAC) clones on meiotic pachytene chromosomes. Each BAC/PAC clone was anchored by a restriction fragment length polymorphism marker mapped to the rice genetic linkage map. This molecular cytogenetic map shows the genetic recombination and sequence information of a physical map, correlated to the cytological features of rice chromosome 5. Detailed comparisons of the distances between markers on genetic, cytological, and physical maps, revealed the distributions of recombination events and molecular organization of the chromosomal features of rice chromosome 5 at the pachytene stage. Discordance of distances between the markers was found among the different maps. Our results revealed that neither the recombination events nor the degree of chromatin condensation were evenly distributed along the entire length of chromosome 5. Detailed comparisons of the correlative positions of markers on the genetic, cytological, and physical maps of rice chromosome 5 provide insight into the molecular architecture of rice chromosome 5, in relation to its cytological features and recombination events on the genetic map. The prospective applications of such an integrated cytogenetic map are discussed.     

DIPOS: database of interacting proteins in Oryza sativa

Rice is an important crop throughout the world and is the staple food for about half the world's population. For better breeding and improved production, we need to know the function of rice molecules which facilitate their function through interactions with each other. The database of interacting proteins in Oryza sativa (DIPOS) provides comprehensive information of interacting proteins in rice, where the interactions are predicted using two computational methods, i.e., interologs and domain based methods. DIPOS contains 14?614?067 pairwise interactions among 27?746 proteins, covering about 41% of the whole Oryaza sativa proteome. Furthermore, each interaction is assigned a confidence score which further enables biologists to sort out the important proteins. Biological explanations of pathways and interactions are also provided based on the database. Public access to the DIPOS is available at and .     

Bioactive steroids from Oryza sativa L

Rice is one of the most interesting crops in the world from both the social and the economic point of views. The monoculture practices along with the heavy use of herbicides are characteristic of modern agriculture and are inducing the appearance of tolerant and/or herbicide resistant weed biotypes. This is the case the world's main weed of rice barnyardgrass (Echinochloa crus-galli). Alternative strategies for weed suppression consist of the use of chemicals from rice due to necessity of obtaining new herbicides with new modes of action that could prevent resistance phenomena. In order to carry out a study that guides to the isolation of the most active compounds from rice, different extracts were achieved, and their activities evaluated. So, all the plant material was divided into three parts: fresh plant, dried plant, and fresh plant from Pluviotron. The aerial part was separated from roots in all cases and extracted in water, in organic solvents as well as with the Pluviotron device. The activity of the 12 extracts obtained was evaluated using a generalist bioassay, wheat etiolated coleoptiles bioassay, and a phytotoxic bioassay on barnyardgrass as target species. The bioactive extracts were fractionated and 15 compounds were isolated and identified by spectroscopic methods. Eight of these compounds were isolated for the first time in Oryza sativa. The most phytotoxic compounds on E. crus-galli were ergosterol peroxide and 7-oxo-stigmasterol. In the case of ergosterol peroxide the activity was higher than the commercial herbicide Logran. This is the first report of potential allelopathic activity of steroids on weeds based on their phytotoxicity.     

Phytochrome action in Oryza sativa L.

Summary In-vivo phytochrome determinations in totally etiolated rice seedlings with a dual-wavelength spectrophotometer showed that on a fresh weight basis phytochrome concentration was highest in the coleoptile apex (0.175 of mean) ( O.D.) g^-1 (fresh weight). The age of the seedlings had little effect on the pattern of phytochrome distribution in the coleoptiles.The extent of growth inhibition observed 2 days after the irradiations was proportional to the logarithm of P _fr amount in the coleoptiles at the time of initial exposure to either red or blue light. Ultraviolet irradiation, however, did not induce either reversible growth inhibition or optically detectable phytochrome changes in vivo.After the conversion of P _r to P _fr bya brief red irradiation, non-photochemical transformation of phytochrome was observed in intact coleoptile tissues. Most of the optically measurable P _fr disappeared within 6 hours at 27°, when the total ( O.D.) decreased to about one fifth of the original level. The optical data did not agree with the fact that 50% of the initial physiological reversibility was still observed 9 hours later. No significant difference in dark transformation rate was seen between intact and excised coleoptile tissues.Abbreviations P _r red light absorbing form of phytochrome - P _fr far-red light absorbing form of phytochrome - ( O.D.) the change in the optical density difference reading at two wavelengths, following irradiation of the sample with actinic sources of red and far-red light - UV ultraviolet light     

Phytochrome action in Oryza sativa L.

Summary The mechanical properties of the cell wall were measured in coleoptiles of totally etiolated rice seedlings. Coleoptiles were either decapitated or briefly exposed to red (R) and/or far-red (FR) light. The elastic and plastic extensibilities of the cell wall changed with age (length) of the coleoptiles. Decapitation and exposure to R induced changes in these properties, and the time-courses were similar. Following decapitation or R irradiation, the plastic extensibility of the cell wall decreased more conspicuously than elastic extensibility. Exogenous application of auxin immediately following decapitation alleviated the effect of removal of the tip. FR irradiation reduced both kinds of extensibilities, but its effect was much less than that of R, and it reversed the R-induced effect to the level of tissue treated with FR only. In repeated R-FR treatments, the decrease of elastic extensibility by R and its reversal by FR could be repeated, but the effect of a second irradiation with R after FR on plastic extensibility was not as apparent as that of the first. Reduction of cell-wall extensibility of etiolated rice coleoptiles caused by R light appeared, at least partly, to be due to a reduced auxin supply in the elongating region from the tip, similar to that caused by decapitation.     

Genetic structure and diversity in Oryza sativa L

The population structure of domesticated species is influenced by the natural history of the populations of predomesticated ancestors, as well as by the breeding system and complexity of the breeding practices exercised by humans. Within Oryza sativa, there is an ancient and well-established divergence between the two major subspecies, indica and japonica, but finer levels of genetic structure are suggested by the breeding history. In this study, a sample of 234 accessions of rice was genotyped at 169 nuclear SSRs and two chloroplast loci. The data were analyzed to resolve the genetic structure and to interpret the evolutionary relationships between groups. Five distinct groups were detected, corresponding to indica, aus, aromatic, temperate japonica, and tropical japonica rices. Nuclear and chloroplast data support a closer evolutionary relationship between the indica and the aus and among the tropical japonica, temperate japonica, and aromatic groups. Group differences can be explained through contrasting demographic histories. With the availability of rice genome sequence, coupled with a large collection of publicly available genetic resources, it is of interest to develop a population-based framework for the molecular analysis of diversity in O. sativa.     

MycDB: an integrated mycobacterial database

As part of ongoing efforts to Investigate the molecular biology of the human pathogens in the genus Mycobacterium, a customized database was developed specifically for these organisms and implemented in ACEDB database manager software. The data loaded include the IMMYC Antigen List, details of reagents available from the CDC/WHO Antibody Bank, more than 1 Mb of sequences of mycobacterial genes and proteins from public databases, the physical maps of Mycobacterium leprae and Mycobacterium tuberculosis developed at the institut Pasteur, as well as a subset of the references found in MedLine. The ACEDB software allows both quick and intuitive access to the data and to connections between facts by a simple mouse-driven interface, as well as by more powerful query mechanisms.     

NABIC SNP: an integrated database for SNP markers

AvailabilityThe database is available online for free at http://nabic.rda.go.kr/SNP     

Mapping QTLs for defective female gametophyte development in an inter-subspecific cross in Oryza sativa L.

The embryo-sac is an essential structure for angiosperm reproduction. The cytological and genetic characterization of embryo-sac sterility was examined in a cross between Oryza sativa ssp. indica cv. ZYQ8 and ssp. japonica cultivar, JX17. The arrest of embryo-sac development was manifested following meiosis in the F₁ hybrid. When the megaspore carried the lethal genotype, the nucleus either failed to divide or divided only once, and the immature embryo-sac degenerated. Abortion of the embryo-sac in the indica-japonica hybrid background was not observed in their original parents, and an effect of cytoplasmic gene(s) on embryo-sac sterility in the reciprocal F₁ hybrids was not detected. Using a rice molecular linkage map based on a doubled haploid (DH) population from the cross of ZYQ8 /JX17, we mapped quantitative trait loci (QTLs) for the defective development of the female gametophyte in backcross progenies from the DH lines. The result demonstrated that a polygenic system is involved in both megagametogenesis and postzygotic isolation in inter-subspecific hybrid rice. Received: 4 May 2000 / Accepted: 20 September 2000     

Coleoptile Senescence in Rice (Oryza sativa L.)

We investigated the cellular events associated with cell deathin the coleoptile of rice plants (Oryza sativa L.). Seeds germinatedunder submergence produced coleoptiles that were more elongatedthan those grown under aerobic conditions. Transfer of seedlingsto aerobic conditions was associated with coleoptile opening(i.e. splitting) due to death of specific cells in the sideof the organ. Another type of cell death occurred in the formationof lysigenous aerenchyma. Senescence of the coleoptile was alsonoted, during which discolouration of the chlorophyll and tissuebrowning were apparent. DNA fragmentation was observed by deoxynucleotidyltransferase-mediateddUTP nick end labelling (TUNEL) assay, and further confirmedby the appearance of oligonucleosomal DNA ladders in senescentcoleoptile cells. Two nucleases (Nuc-a and Nuc-b) were detectedby in-gel-assay from proteins isolated from coleoptiles. Nuc-a,commonly observed in three cell death phases required eitherCa²⁺or Mg²⁺, whereas Nuc-b which appeared during senescencerequired both Ca²⁺and Mg²⁺. Both nucleases were strongly inhibitedby Zn²⁺. Copyright 2000 Annals of Botany Company Aerenchyma, rice, cell death, coleoptile, fragmentation, nuclease, Oryza sativa, senescence, split, submergence, TUNEL     

水稻花药特异启动子Osg6B的序列及功能分析

对水稻花药特异表达基因Ｏｓｇ６启动子简称Ｏｓｇ６Ｂ的全序列进行了测定,结果表明,Ｏｓｇ６Ｂ含有１．７３ｋｂ个核苷酸,与文献报道的该启动子相差仅８个核苷酸,两者核苷酸同源性为９９．５％。将Ｏｓｇ６Ｂ同ＧＵＳ基因编码区相连,将构建成的融合基因用基因抢轰击烟草的花药和幼叶,荧光分析结果为含Ｏｓｇ６Ｂ的ＧＵＳ融合基因在大于２ｍｍ烟草花药中的表达量比对照和幼叶均高出８倍,在小于或等于２ｍｍ的花药中,则高达到     

Heterosis breeding in rice (Oryza sativa L.)

Summary Studies conducted at the International Rice Research Institute (IRRI) during 1980 and 1981 have shown up to 73% heterosis, 59% heterobeltiosis and 34% standard heterosis for yield in rice. The latter was estimated in comparison to commercial varieties: IR36 and IR42 (yield 4–5 t/ha in wet season trials and 7–8 t/ha in dry season trials). Generally speaking, absolute yield was lower and extent of standard heterosis was higher in wet season than in dry season with some exception. Yields up to 5.9 t/ha (22% standard heterosis) in the wet season and 10.4 t/ha (34% standard heterosis) in the dry season were obtained. Most of the hybrids performed better in some season while some performed better in both seasons. Hybrids showed better lodging resistance although they were 5–10 cm taller. F₁ hybrids had significant positive correlations with the parental traits viz., yield (r = 0.446), tillering (r = 0.746), height (r = 0.810) and flowering (r = 0.843). Selection of parents among elite breeding lines on the basis of their per se yield performance, diverse origin and resistance to insects and diseases should give heterotic combination. Yield advantage of hybrids was due primarily to increase in number of spikelets per unit area even though tiller number was reduced. Grain weight was either the same or slightly higher. High yielding hybrids also showed significant heterosis and heterobeltiosis for total dry matter and harvest index. For commercial utilization of heterosis in rice, effective male sterility and fertility restoration systems are available and up to 45% natural outcrossing on male sterile lines has been observed. Consequently, F₁ rice hybrid have been successfully developed and used in China. Prospects of developing hybrid rice varieties elsewhere appear bright especially in countries that have organized seed production, certification and distribution programs and where hybrid seed can be produced at a reasonable cost.     

BioSilico: an integrated metabolic database system

BioSilico is a web-based database system that facilitates the search and analysis of metabolic pathways. Heterogeneous metabolic databases including LIGAND, ENZYME, EcoCyc and MetaCyc are integrated in a systematic way, thereby allowing users to efficiently retrieve the relevant information on enzymes, biochemical compounds and reactions. In addition, it provides well-designed view pages for more detailed summary information. BioSilico is developed as an extensible system with a robust systematic architecture.     

水稻体细胞无性系变异

水稻体细胞无性系变异研究取得了很大进展 ,获得了大量抗病、抗逆、优质、矮杆等突变体。对这些突变体遗传分析表明 ,大多数突变性状由 1对或 2对基因控制。水稻体细胞无性系变异的发生与基因型、性状、继代时间、培养方式等有关 ,并具有内在的机制 ,点突变和反转录转座子插入可能是引起水稻无性系变异的两个重要原因。     

HOWDY: an integrated database system for human genome research

HOWDY is an integrated database system for accessing and analyzing human genomic information (http://www-alis.tokyo.jst.go.jp/HOWDY/). HOWDY stores information about relationships between genetic objects and the data extracted from a number of databases. HOWDY consists of an Internet accessible user interface that allows thorough searching of the human genomic databases using the gene symbols and their aliases. It also permits flexible editing of the sequence data. The database can be searched using simple words and the search can be restricted to a specific cytogenetic location. Linear maps displaying markers and genes on contig sequences are available, from which an object can be chosen. Any search starting point identifies all the information matching the query. HOWDY provides a convenient search environment of human genomic data for scientists unsure which database is most appropriate for their search.     

FlyMine: an integrated database for Drosophila and Anopheles genomics

FlyMine is a data warehouse that addresses one of the important challenges of modern biology: how to integrate and make use of the diversity and volume of current biological data. Its main focus is genomic and proteomics data for Drosophila and other insects. It provides web access to integrated data at a number of different levels, from simple browsing to construction of complex queries, which can be executed on either single items or lists.