The Organelle Genomes of Hassawi Rice (Oryza sativa L.) and Its Hybrid in Saudi Arabia: Genome Variation, Rearrangement, and Origins

Hassawi rice (Oryza sativa L.) is a landrace adapted to the climate of Saudi Arabia, characterized by its strong resistance to soil salinity and drought. Using high quality sequencing reads extracted from raw data of a whole genome sequencing project, we assembled both chloroplast (cp) and mitochondrial (mt) genomes of the wild-type Hassawi rice (Hassawi-1) and its dwarf hybrid (Hassawi-2). We discovered 16 InDels (insertions and deletions) but no SNP (single nucleotide polymorphism) is present between the two Hassawi cp genomes. We identified 48 InDels and 26 SNPs in the two Hassawi mt genomes and a new type of sequence variation, termed reverse complementary variation (RCV) in the rice cp genomes. There are two and four RCVs identified in Hassawi-1 when compared to 93-11 (indica) and Nipponbare (japonica), respectively. Microsatellite sequence analysis showed there are more SSRs in the genic regions of both cp and mt genomes in the Hassawi rice than in the other rice varieties. There are also large repeats in the Hassawi mt genomes, with the longest length of 96,168 bp and 96,165 bp in Hassawi-1 and Hassawi-2, respectively. We believe that frequent DNA rearrangement in the Hassawi mt and cp genomes indicate ongoing dynamic processes to reach genetic stability under strong environmental pressures. Based on sequence variation analysis and the breeding history, we suggest that both Hassawi-1 and Hassawi-2 originated from the Indonesian variety Peta since genetic diversity between the two Hassawi cultivars is very low albeit an unknown historic origin of the wild-type Hassawi rice.     

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 .     

Genome Characterization of a Breeding Line Derived from a Cross Between Oryza sativa and Oryza rufipogon

A preliminary screening was conducted on BC3F1 and BC4F1 backcross families developed from crossing Oryza sativa (MR219) and O. rufipogon (IRGC105491). Despite earlier results showing that O. rufipogon alleles (wild introgression) contributed to both number of panicles (qPPL-2) and tillers (qTPL-2) at loci RM250, RM208, and RM48 in line A20 of the BC2F2 population, we observed that wild introgression was lost at loci RM250 and RM208 but retained at locus RM48 in BC3F1 and BC4F1. Progeny tests conducted utilizing genotype and phenotype data on both BC4F1 and a reference population, BC2F7 (A20 line), did not show significant differences between groups having the MR219 allele and wild introgression at locus RM48. This suggests that there is no additive and transgressive effect of wild introgression in the BC3F1 and BC4F1 generated. The presence of wild introgression was largely due to gene contamination by cross-pollination during field breeding practices.     

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.     

水稻snoRNA47基因簇的初步鉴定

通过生物信息学分析 ,在水稻染色体中发现一个新的C/D框snoRNA基因簇。此基因簇含有 3个C/D框snoRNA基因 ,它们都具有典型的C框和D框保守元件 ;末端能形成茎环结构 ;含有一段相同的 1 2nt“引导”序列 ,此序列能与水稻 1 8SrRNA中第 6 2 1位到 6 32位的序列互补配对。通过实验证明 ,这 3种snoRNA的确存在于水稻细胞核内 ,并确定出它们各自 5′端的位置。进一步对此snoRNA基因簇的表达进行研究发现 ,此基因簇中的 3个snoRNA基因共同转录成为一个多顺反子的前体。将这 3种新发现的水稻snoRNA分别命名为OSsnR4 7.1 ,OSsnR4 7.2和OSsnR4 7.3。编码它们的基因已被GenBank收录 ,其登录号分别为 :AF4 5 35 0 4 ,AF4 5 35 0 3和AF4 5 35 0 2     

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。     

Analysis of sialyltransferase-like proteins from Oryza sativa

Sialic acids are widely distributed among living creatures, from bacteria to mammals, but it has been commonly accepted that they do not exist in plants. However, with the progress of genome analyses, putative gene homologs of animal sialyltransferases have been detected in the genome of some plants. In this study, we cloned three genes from Oryza sativa (Japanese rice) that encode sialyltransferase-like proteins, designated OsSTLP1, 2, and 3, and analyzed the enzymatic activity of the proteins. OsSTLP1, 2, and 3 consist of 393, 396, and 384 amino acids, respectively, and each contains sequences similar to the sialyl motifs that are highly conserved among animal sialyltransferases. The recombinant soluble forms of OsSTLPs produced by COS-7 cells were analyzed for sialyltransferase-like activity. OsSTLP1 exhibited such activity toward the oligosaccharide Galbeta1,4GlcNAc and such glycoproteins as asialofetuin, alpha1-acid glycoprotein, and asialo-alpha1-acid glycoprotein; OsSTLP3 exhibited similar activity toward asialofetuin; and OsSTLP2 exhibited no sialyltransferase-like activity. The sialic acid transferred by OsSTLP1 or 3 was linked to galactose of Galbeta1,4GlcNAc through alpha2,6-linkage. This is the first report of plant proteins having sialyltransferase-like activity.     

Long terminal repeat retrotransposons of Oryza sativa

Background  

Long terminal repeat (LTR) retrotransposons constitute a major fraction of the genomes of higher plants. For example, retrotransposons comprise more than 50% of the maize genome and more than 90% of the wheat genome. LTR retrotransposons are believed to have contributed significantly to the evolution of genome structure and function. The genome sequencing of selected experimental and agriculturally important species is providing an unprecedented opportunity to view the patterns of variation existing among the entire complement of retrotransposons in complete genomes.     

The mechanism of phloem loading in rice (Oryza sativa)

Carbohydrates, mainly sucrose, that are synthesized in source organs are transported to sink organs to support growth and development. Phloem loading of sucrose is a crucial step that drives long-distance transport by elevating hydrostatic pressure in the phloem. Three phloem loading strategies have been identified, two active mechanisms, apoplastic loading via sucrose transporters and symplastic polymer trapping, and one passive mechanism. The first two active loading mechanisms require metabolic energy, carbohydrate is loaded into the phloem against a concentration gradient. The passive process, diffusion, involves equilibration of sucrose and other metabolites between cells through plasmodesmata. Many higher plant species including Arabidopsis utilize the active loading mechanisms to increase carbohydrate in the phloem to higher concentrations than that in mesophyll cells. In contrast, recent data revealed that a large number of plants, especially woody species, load sucrose passively by maintaining a high concentration in mesophyll cells. However, it still remains to be determined how the worldwide important cereal crop, rice, loads sucrose into the phloem in source organs. Based on the literature and our results, we propose a potential strategy of phloem loading in rice. Elucidation of the phloem loading mechanism should improve our understanding of rice development and facilitate its manipulation towards the increase of crop productivity.     

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     

Oxygen stress and adaptation of a semi-aquatic plant: rice ( Oryza sativa)

One of the major abiotic stresses that affects plant growth and development is anoxia or hypoxia. Rice is a semi-aquatic plant bestowed with the capability of overcoming oxygen limitation for a considerable period of time. For instance, it can withstand submergence stress either by inherent metabolic adaptations (resistant type), or by keeping its leaves above the water surface by continuously elongating the stem (avoiding type). In the former case, an interplay of several metabolic pathways engaged in anaerobic fermentation keeps the submerged plant alive for a certain period of time. In the latter type, also known as deepwater rice, continuous stem elongation brought about by a series of reactions in planta enables the shoot to remain above the water surface and thus maintain respiration and photosynthesis. However, the earliest event, i.e., sensing the oxygen level that brings about all the changes, has not been clearly understood. This paper intends to evaluate the metabolic adaptations of rice plants to oxygen constraints. Electronic Publication     

Molecular characterization of flavonoid malonyltransferase from Oryza sativa

In this study, a flavonoid malonyltransferase (OsMaT-2) was cloned from Oryza sativa, and the recombinant protein OsMaT-2 was purified via affinity chromatography. OsMaT-2 utilized a variety of flavonoid glucosides, including flavanone glucosides, flavone glucosides, flavonol glucosides, and isoflavone glucosides as substrates, but did not utilize anthocyanin. As an acyl donor, OsMaT-2 utilized only malonyl-CoA. Based on reactions with various quercetin 3-O-sugars, we identified the probable position of malonylation as the 6″-hydroxyl group of the sugar. This is the first report, to the best of our knowledge, of the cloning of a flavonoid malonyltransferase from O. sativa.     

水稻花粉发育的分子机理

水稻的小孢子母细胞在花粉囊中进行减数分裂产生小孢子,小孢子进一步发育成花粉粒。当花粉成熟时,花粉粒从花粉囊中释放出来进行受精。分子生物学的研究已经发现了一些参与这一过程的基因,包括控制花粉囊组织的分化、小孢子母细胞的减数分裂、小孢子的发育和花药的开裂等。本文旨在总结水稻花粉发育过程及其调控分子机制的研究进展。     

Characterization of a set of phytochrome-interacting factor-like bHLH proteins in Oryza sativa

The model dicotyledon Arabidopsis thaliana has a characteristic small sub-family of phytochrome-interacting bHLH (basic Helix-Loop-Helix) factors, which are collectively designated the PIL (or PIF) (PHYTOCHROME INTERACTING FACTOR-LIKE) family proteins. In this study, we identified and characterized a set of highly homologous members (designated OsPIL11 to OsPIL16) in the model monocotyledon rice (Oryza sativa). Some of them (OsPIL11, OsPIL12, and OsPIL13) showed the ability to interact with the putative OsPRR1 (PSEUDO-RESPONSE REGULATOR 1) clock component, as far as the results of yeast two-hybrid assays were concerned. It was found that the expression of OsPIL13 is under the control of circadian rhythms (clock), while the expression of OsPIL15 is negatively regulated by light upon the onset to light exposure of etiolated seedlings. When the rice genes (OsPIL11 to OsPIL15) were over-expressed in A. thaliana, the resulting transgenic seedlings displayed anomalous morphologies with very long hypocotyls during early photomorphogenesis. These results suggest the view that the identified OsPILs are functional counterparts (or orthologs) of AtPILs, which are known to play important roles in red light-mediated (phyA and/or phyB-dependent) signal transduction pathways at immediate positions downstream of the photoreceptor in A. thaliana.     

Genetic engineering of Oryza sativa by particle bombardment

Genetic engineering of rice (Oryza sativa L. cv. Pusa basmati 1) using synthetic Cry1Ac gene has been achieved by “particle bombardment”. Scutellar tissues excised after 5 – 6 d from mature seeds cultured on induction medium were bombarded using gold particles coated with a mixture of Cry1Ac and marker genes on medium with osmoticum. Bombarded tissues were subjected to 30 mg dm⁻³ hygromycin selection for two cycles. The selected calli after GUS assay were transferred to shoot regeneration medium. Regenerated shoots were rooted and plantlets (T₀) were grown to full maturity. Polymerase chain reaction (PCR) analysis of T₀ plants using Cry1Ac specific primers revealed the presence of Cry1Ac gene in 65 % plants. Phenotypic assay, β-glucuronidase assay and PCR during T₁ generation revealed the inheritance of the Cry1Ac and marker genes along with the native plant genes.