RFLP analysis of the progeny from Oryza alta Swallen x Oryza sativa L.

RFLP analyses were carried out in the progeny from a cross of two phylogenetically distant rice species, wild rice Oryza alta Swallen (CCDD, 2n = 48) and cultivated rice O. sativa L. (AA, 2n = 24). The sterile plants gave heterozygous RFLP patterns at most of the loci detected. They looked more like their wild rice parent, with 36 chromosomes in their root-tip cells and pollen mother cells. In two partially fertile plants, however, most of the markers that were used showed RFLP patterns similar to the cultivated parent, O. sativa. By cytological study, it was found that nearly one-third of the chromosomes had been eliminated in the partially fertile plants. Their seeds have short awns, which is a characteristic of their wild parent, O. alta. An introgression occurred in one of the partially fertile plants, which led to the discussion about a nonconventional mechanism in wide hybridization for transference of wild rice chromosome segments to cultivated rice chromosomes.     

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.     

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     

Development and mapping of Oryza glumaepatula-derived microsatellite markers in the interspecific cross Oryza glumaepatula x O. sativa

Wild germplasm of domesticated crops is a source of genetic variation little utilized in breeding programs. Interspecific crosses can potentially uncover novel gene combinations that can be important for quantitative trait analysis. The combined use of wide crosses and genetic maps of chromosomal regions associated with quantitative traits can be used to broaden the genetic basis of rice breeding programs. Oryza glumaepatula is a diploid (AA genome) wild rice species native from South and Central America. A genetic map was constructed with 162 PCR-based markers (155 microsatellite and 7 STS markers) using a backcross population derived from the cross O. glumaepatula, accession RS-16 from the Brazilian Amazon Region x O. sativa BG-90-2, an elite rice inbred line. The map included 47 new SSR markers developed from an O. glumaepatula genomic library enriched for AG/TC sequences. All SSR markers were able to amplify the O. sativa genome, indicating a high degree of SSR flanking region conservation between O. glumaepatula and O. sativa species. The map covered 1500.4 cM, with an average of one marker every 10 cM. Despite some chromosomes being more densely mapped, the overall coverage was similar to other maps developed for rice. The advantage to construct a SSR-based map is to permit the combination of the speed of the PCR reaction, and the codominant nature of the SSR marker, facilitating the QTL analysis and marker assisted selection for rice breeding programs.     

Alien genes introgression and development of monosomic alien addition lines from Oryza latifolia Desv. to rice,Oryza sativa L.

Oryza latifolia, a tetraploid wild relative of cultivated rice is an important source of resistance to bacterial blight (BB), the brown planthopper (BPH) and the whitebacked planthopper (WBPH). Interspecific hybrids were obtained between an elite breeding line (IR31917-45-3-2) of Oryza sativa (2n=24 AA) and O. latifolia Acc. No. 100914 (2n=48 CCDD). The crossability in F1 was 7.58% and it ranged from 0.11 to 0.62 in backcross generations. The F1 hybrid showed 2-6 II, 0-2 III, 0-1 IV and 22-32 I; the mean being 3.92 II + 0.11 III + 0.02 IV + 27.30 I per cell at diakinesis. Monosomic alien addition lines (MAALs) having a 2n chromosome complement of O. sativa and one chromosome of O. latifolia were characterized based on morphology and isozyme banding pattern. The MAALs were designated as MAAL-1, MAAL-2, MAAL-4, MAAL-5, MAAL-6, MAAL-7, MAAL-8, MAAL-9, MAAL-10, MAAL-11 and MAAL-12. The female transmission rates of the alien chromosome varied from 4.4 to 35.5%, whereas 8 of the 11 MAALs transmitted the alien chromosome through the male gamete, the range being 1.7% (MAAL 10) to 11.9% (MAAL 12). Disomic progenies in BC3 and BC4 generations had complete resemblance to the O. sativa parent. Of the 2,295 disomic BC3F3 progenies, 309 showed introgression for resistance to BPH and 188 each for WBPH and BB resistance. Four plant progenies which were resistant to both BPH and WBPH were also resistant to BB race 2 of the Philippines. Nine of the 34 BC3F1 plants showed introgression for ten allozymes of O. latifolia, such as Est5, Amp1, Pgi1, Mdh3, Pgi2, Amp3, Pgd2, Est9, Amp2 and Sdh1, located on 8 of the 12 chromosomes. Alien introgression was also detected for morphological traits such as long awns, earliness, black hull, purple stigma and apiculus. Abnormal plants with many wild-species traits suddenly appeared in normal disomic progenies. These plants showing instability and abnormal segregation behaviour are being investigated for the activation of transposons.     

Genetic structure of Oryza rufipogon Griff. in China

Oryza rufipogon Griff. (common wild rice; CWR) is the ancestor of Asian cultivated rice (Oryza sativa L.). Investigation of the genetic structure and diversity of CWR in China will provide information about the origin of cultivated rice and the grain quality and yield. In this study, we used 36 simple sequence repeat (SSR) markers to assay 889 accessions, which were highly representative of whole germplasm in China. The analysis revealed a hierarchical genetic structure within CWR. First, CWR has diverged into two ecotypic populations, a south subtropical population (SSP) and a middle subtropical population (MSP), probably owing to natural selection by the different climates. The distribution of specific alleles and haplotypes indicated that Chinese CWR had both indica-like and japonica-like variations; the SSP was an indica-like type, whereas the MSP was more japonica-like. The SSP and MSP further diverged into five (HN, GD-GX1, GX2, FJ and YN) and two (JX-HuN1 and HuN2) geographical populations, respectively. The genetic data suggest the isolation by distance, although water systems also appear to play an important role in the formation of homogenous populations, and occasionally landscape was also involved. The population GD-GX1, which grew widely in Guangdong and Guangxi provinces, was the largest geographical population in China. It had a high level of genetic diversity (GD) and the closest genetic relationship with other inferred populations. The population HN, with the smallest SSR molecular weights and the highest level of GD, may be the most ancestral population.     

稻属单拷贝核基因TPI序列分析及其在疣粒野生稻鉴定中的应用

通过对稻属(Oryza L.)及其近缘属等18个禾本科植物单拷贝核基因TPI序列进行扩增和测序,分析其系统进化关系及序列差异,并设计鉴定疣粒野生稻(O.granulata)特异的分子标记.序列分析表明,栽培稻间TPI基因序列碱基变异少,野生稻相对变异丰富,其中疣粒野生稻变异尤为明显,根据疣粒野生稻的TPI基因序列特异位点设计引物,利用这一分子标记对疣粒野生稻进行准确鉴定.     

The transfer RNA genes in Oryza sativa L. ssp. indica

The availability of the draft genome sequence of Oryza sativa L ssp. indica has made it possible to study the rice tRNA genes. A total of 596 tRNA genes, including 3 selenocysteine tRNA genes and one suppressor tRNA gene are identified in 127551 rice contigs. There are 45 species of tRNA genes and the revised wobble hypothesis proposed by Guthrie and Abelson is perfectly obeyed. The relationship between codon usage and the number of corresponding tRNA genes is discussed. Redundancy may exist in the present list of tRNA genes and novel ones may be found in the future. A set of 33 tRNA genes is discovered in the complete chloroplast genome of Oryza sativa L. ssp. indica. These tRNA genes are identical to those in ssp. japonica identified by us independently from the origional annotation.     

High amylose mutants of rice,Oryza sativa L.

Summary Five mutant lines of rice with increased amylose content in starch granules were identified among floury endosperm mutants. The amylose contents of the mutants ranged from 29.4% to 35.4% and were about twice as high as that of the normal counterpart. Starch properties of the high amylose mutants were analyzed by column chromatography, X-ray diffractometry, photopastegraphy and scanning electron microscopy. The high amylose mutants produced longer unit chains of amylopectin than those of the normal counterpart as well as an increased amount of amylose. A X-ray diffractogram of starch in the mutant was characterized by a type B pattern, while that in the normal counterpart showed a type A pattern which is typical for starches of common cereals. The temperatures at the initiation of gelatinization of the mutants were much higher than that for the normal counterpart. The endosperm cells of the mutant were loosely packed with irregular round-shaped starch granules, whereas those of the normal counterpart were densely packed with polyhedral starch granules. Judging from the results obtained, it was concluded that starch properties of the high amylose mutants of rice were similar to those of the amylose-extender (ae) mutant of maize.     

应用RFLP研究水稻基因突变的特性

选用覆盖整个水稻遗传图谱的１２９和１０６个ＤＮＡ探针,分别分析了灿稻品系ＩＲ５４、５４６０、５４６０Ｓ之间和粳稻品系农垦５８、农垦５８Ｓ及其育性回复突变系之间的ＲＥＬＰ。在ＩＲ５４／５４６０、５４６０／５４６０Ｓ和ＩＲ５４／５４６０Ｓ检测到ＲＦＬＰ的探数分别为４３、１４和３２。而且,５４６０／５４６０Ｓ的多态性探针均能在ＩＲ５４和５４６０之间检测到差异性,其中１１个（７８．６％）在５４６０Ｓ与ＩＲ     

Population genetic structure of Oryza rufipogon and Oryza nivara: implications for the origin of O. nivara

Ecological speciation plays a primary role in driving species divergence and adaptation. Oryza rufipogon and Oryza nivara are two incipient species at the early stage of speciation with distinct differences in morphology, life history traits and habitat preference, and therefore provide a unique model for the study of ecological speciation. However, the population genetic structure of the ancestral O. rufipogon has been controversial despite substantial study, and the origin of the derivative O. nivara remains unclear. Here, based on sequences of 10 nuclear and two chloroplast loci from 26 wild populations across the entire geographic ranges of the two species, we conducted comprehensive analyses using population genetics, phylogeography and species distribution modelling (SDM) approaches. In addition to supporting the two previously reported major subdivisions, we detected four genetically distinct groups within O. rufipogon and found no correlation between the genetic groups and either species identity or geographical regions. The SDM clearly showed substantial change in the distribution range of O. rufipogon in history, demonstrating that the repeated extinction and colonization of local populations due to multiple glacial–interglacial cycles during the Quaternary was most likely the main factor shaping the confounding population genetic structure of O. rufipogon. Moreover, we found significant differences between the two species in climate preferences, suggestive of an important role for climatic factors in the adaptation, persistence and expansion of O. nivara. Finally, based on the genetic pattern and dynamics of the O. nivara populations, we hypothesize that O. nivara might have independently originated multiple times from different O. rufipogon populations.     

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.     

药用野生稻和栽培稻挥发油的化学成分比较研究

本文采用水蒸气蒸馏法提取抗褐飞虱品种药用野生稻(Oryza officinalis)和感褐飞虱品种栽培稻(O.sativa)的挥发油,并运用气相色谱-质谱法(GC/MS)对二者的化学成分进行种类和含量的比较分析。结果表明,两种植物材料的挥发油在种类和含量上存在明显差异,如,糠醛(药用野生稻7.60%栽培稻0%;2,3-苯并二氢呋喃(药用野生稻10.80%,栽培稻3.32%);4-乙烯基-2-甲氧苯酚(药用野生稻22.99%,栽培稻7.32%)。推测含量较高的糠醛、2,3-苯并二氢呋喃和4-乙烯基-2-甲氧苯酚可能是药用野生稻对褐飞虱的活性成份。     

Basis of selectivity of cyhalofop-butyl in Oryza sativa L.

Cyhalofop-butyl (CB), 2-[4-(4-cyano-2-fluorophenoxy)phenoxy]propanoic acid, butyl ester (R), is an aryloxyphenoxypropionate (AOPP) herbicide for postemergence use in rice to control grasses, mainly Echinochloa spp. Similar to other AOPP and cyclohexanedione herbicides, the site of action of CB is acetyl-coenzyme A carboxylase (ACCase), an enzyme in fatty acid biosynthesis. The mechanisms involved in the selectivity of CB in rice (Oryza sativa L.)—absorption, translocation, metabolism, and ACCase susceptibility—were studied. Studies of in vitro inhibition of ACCase in E. oryzoides and O. sativa L. species discounted any differential active site sensitivity as the basis of tolerance to CB. The O. sativa L. cuticle was uniformly covered by waxes, with predominantly unshaped large waxes randomly distributed, obtaining absorption values of under 30%, 24 h after application (HAA). The E. oryzoides cuticle formed a non-uniform covered reticule, with less wax density and areas lacking in waxes reaching maximum values of absorption rising to 73%, 24 HAA. Translocation studies revealed no significant differences, either between species, or between times, remaining in the treated leaf. There was a good correlation between the rate of metabolism and plant tolerance. Plant metabolism studies demonstrated that tolerant rice inactivated the esterases producing a lack of functionality thus reducing the conversion of CB to cyhalofop acid, which is the active form of the herbicide. Moreover, it increased the metabolism of the herbicide forming non toxic metabolites much faster than E. oryzoides. It was concluded that the basis of rice tolerance to CB was a lack of esterase functionality, a reduced absorption through the cuticle and an increase in cyhalofop acid metabolism.     

水稻和拟南芥中几丁质酶的分析

几丁质酶（EC3．2．1．14）是一种降解几丁质的糖苷酶,广泛存在于各种生物体中,并在植物中对病原真菌起重要抗性作用。首先通过BLAST在GenBank中对其同源性进行搜索,用SMART分析其结构。基于水稻和拟南芥的基因组注释,借助4个生物学软件（SignalP3．0,TMHMM2．0,TargetP1．1andbig—PiPredictor）,分析了水稻所有37条和拟南芥所有24条几丁质酶序列,发现有些几丁质酶都分泌到细胞外,有些定位于液泡中,水稻中仅25条和拟南芥中仅16条几丁质酶序列有信号肽,这些信号肽的平均长度为24．8aa。利用ClustalX和MEGA3．1两个生物软件分析了59条几丁质酶序列和25条标准几丁质酶的系统发育关系,这些几丁质酶可分为Ⅰ、Ⅱ、Ⅲ、Ⅳ、Ⅴ和Ⅵ等6大类。这种聚类结果与几丁质酶传统分为7类有些差异。通过对6大类中各个氨基酸残基的分析,发现丙氨酸、甘氨酸、丝氨酸和亮氨酸的使用频率在每类中都非常高,而蛋氨酸、组氨酸、色氨酸和半胱氨酸均低于20％。各大类中彼此之间的某些氨基酸使用频率明显不同,Ⅰ-Ⅵ分别富含丙氨酸、缬氨酸、亮氨酸、半胱氨酸、丝氨酸和赖氨酸。     

水稻蔗糖转运基因家族研究进展

蔗糖是韧皮部同化碳运输的主要形式,植物蔗糖转运体(SUT,Sucrose transporters)在参与植物碳素分配中起着重要的作用.编码SUT蛋白的基因在许多双子叶和单子叶植物中都已被分离.目前已经在水稻中鉴定出了5个蔗糖共运体(Sucrose symporter)基因家族成员.对这5个成员在水稻中的鉴定、克隆和表达分析,以及其蛋白结构、分类与进化进行了综述.这些信息可用于探索杂交稻高产的同化物分配和运输的分子原因.     

Identification of novel stress-regulated microRNAs from Oryza sativa L.

MicroRNAs (miRNAs) are a type of small non-coding RNA found in eukaryotes. They play a key role in gene expression by down-regulating gene expression and are involved in the environment stress response in plants. Although a large number of miRNAs have been identified from Arabidopsis, few studies have focused on Oryza sativa miRNAs, especially on stress-related miRNAs. Five cDNA libraries of small RNAs from rice seedlings treated with cold, dehydration, salinity, and abscisic acid (ABA), as well as wild-type seedlings, were constructed. Seven rice novel miRNAs were identified by Northern analysis, and their expression patterns under different stress treatments were determined. Results showed that the expression of several novel miRNAs was regulated by one or more stress treatments. Our identification of novel stress-related miRNAs in rice suggests that these miRNAs might be involved in rice stress response pathways.