Rice Expression Database(RED):An integrated RNA-Seq-derived gene expression database for rice

Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community.Here,we present RED(Rice Expression Database;http://expression.ic4r.org),an integrated database of rice gene expression profiles derived entirely from RNA-Seq data.RED features a comprehensive collection of 284 high-quality RNA-Seq experiments,integrates a large number of gene expression profiles and covers a wide range of rice growth stages as well as various treatments.Based on massive expression profiles,RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene(s) of interest.Besides,it provides user-friendly web interfaces for querying,browsing and visualizing expression profiles of concerned genes.Together,as a core resource in BIG Data Center,RED bears great utility for characterizing the function of rice genes and better understanding important biological processes and mechanisms underlying complex agronomic traits in rice.     

转基因水稻的研究和应用

植物基因工程的兴起,使特定的外源基因引入植物细胞成为可能。水稻转基因研究是国内外植物分子遗传学研究的热点之一。近十几年来,水稻转基因研究已取得显著进展。综述了水稻基因转化的方法、转基因技术在水稻上的应用及外源基因在转基因后代中的遗传表达的研究进展。     

水稻花发育的分子生物学研究进展

水稻是世界上最重要的粮食作为之一,也是单子叶植物发育生物学研究较理想的模式植物。水稻花器官还是粮食赖以形成的基础。对水稻花发育的研究已开始成为植物分子遗传学的一个新的焦点。近年来有关水稻花发育基因调控的研究已取得了长足的进展,本文从水稻花的诱导、花分生组织的形成和花器官的发育三个方面综述近年来国内外的研究进展。 Abstract:Rice (Oryza sativa L.) is not only one of the most important food crops in the world,but also a model plant for study of molecular developmental biology in monocots.In addition,the rice floral organs provide the basis for grain formation.Study of rice floral development has become a new focus of plant molecular genetics.Recently,notable progress has been made in study of gene regulation in rice floral development.In the review,genetic and molecular mechanisms of floral induction,floral meristem formation,and floral organ development in rice are summarized.     

Gene targeting by homologous recombination as a biotechnological tool for rice functional genomics

The modification of an endogenous gene into a designed sequence by homologous recombination, termed gene targeting (GT), has broad implications for basic and applied research. Rice (Oryza sativa), with a sequenced genome of 389 Mb, is one of the most important crops and a model plant for cereals, and the single-copy gene Waxy on chromosome 6 has been modified with a frequency of 1% per surviving callus by GT using a strong positive-negative selection. Because the strategy is independent of gene-specific selection or screening, it is in principle applicable to any gene. However, a gene in the multigene family or a gene carrying repetitive sequences may preclude efficient homologous recombination-promoted GT due to the occurrence of ectopic recombination. Here, we describe an improved GT procedure whereby we obtained nine independent transformed calli having the alcohol dehydrogenase2 (Adh2) gene modified with a frequency of approximately 2% per surviving callus and subsequently isolated eight fertile transgenic plants without the concomitant occurrence of undesirable ectopic events, even though the rice genome carries four Adh genes, including a newly characterized Adh3 gene, and a copy of highly repetitive retroelements is present adjacent to the Adh2 gene. The results indicate that GT using a strong positive-negative selection can be widely applicable to functional genomics in rice and presumably in other higher plants.     

Rice Cluster I methanogens, an important group of Archaea producing greenhouse gas in soil

Methane, which is an important greenhouse gas, is to a large part produced by methanogenic archaea in anoxic soils and sediments. Rice Cluster I methanogens have been characterized on the basis of their 16S rRNA and mcrA gene sequences, and were found to form a separate lineage within the phylogenetic radiation of Methanosarcinales and Methanomicrobiales. As isolation has not been achieved until recently, our knowledge of distribution, physiology and environmental significance of Rice Cluster I is solely based on molecular biology techniques. Rice Cluster I seems to be widely distributed, particularly in rice fields, possibly occupying different niches among the methane producers. One niche seems to be methane production on roots driven by plant photosynthesis, contributing substantially to the release of methane from rice fields into the atmosphere.     

Interindividual variation in epigenomic phenomena in humans

Our knowledge of regulatory mechanisms of gene expression and other chromosomal processes related to DNA methylation and chromatin state is continuing to grow at a rapid pace. Understanding how these epigenomic phenomena vary between individuals will have an impact on understanding their broader role in determining variation in gene expression and biochemical, physiological, and behavioural phenotypes. In this review we survey recent progress in this area, focusing on data available from humans. We highlight the role of obligatory (sequence-dependent) epigenomic variation as an important mechanism for generating interindividual variation that could impact our understanding of the mechanistic basis of complex trait architecture.     

Update and challenges on proteomics in rice

Rice is not only an important agricultural resource but also a model plant for biological research. Our previous review highlighted different aspects of the construction of rice proteome database, cataloguing rice proteins of different tissues and organelle, differential proteomics using 2-DE and functional characterization of some of the proteins identified (Komatsu, S., Tanaka, N., Proteomics 2005, 5, 938-949). In this review, the powerfulness and weaknesses of proteomic technologies as a whole and limitations of the currently used techniques in rice proteomics are discussed. The information obtained from these techniques regarding proteins modification, protein-protein interaction and the development of new methods for differential proteomics will aid in deciphering more precisely the functions of known and/or unknown proteins in rice.     

Expression and inheritance of hypersensitive resistance to rice hoja blanca virus mediated by the viral nucleocapsid protein gene in transgenic rice

Rice hoja blanca virus (RHBV) is a major virus disease of economic importance affecting rice in northern South America, Central America and the Caribbean. This is the first report of transgenic resistance to RHBV and the transformation of an indica rice variety from Latin America. Rice transformed with the RHBV nucleocapsid protein ( N) gene had a significant reduction in disease development. Several reactions were observed that ranged from susceptible to completely resistant plants (immunity). The resistant reactions were characterized by the production of local lesions like a hypersensitive reaction or a recovery phenotype with the emergence of symptom-less new leaves. These transgenic RHBV-resistant rice lines expressed the N gene RNA at low levels that were below the detection limit by Northern blots and only resolved by RT-PCR. The nucleocapsid protein could not be detected in any of the transgenic plants either by Western or ELISA tests. These results suggest that the resistance encoded by the N gene in these plants appears to be mediated by RNA. When challenged with RHBV, the resistant transgenic lines showed a significant increased performance for important agronomic traits including the number of tillers, the number of grains per plant and the yield as compared to the susceptible control. Furthermore, upon inoculation some of the most-resistant transgenic lines showed agronomic traits similar to the uninoculated non-transgenic Cica 8 control. Using both agronomic traits and disease severity as criteria, several of the most-resistant lines were followed through the R(4) generation and demonstrated that the N gene and RHBV resistance was inherited in a stable manner. These transgenic rice lines could become a new genetic resource in developing RHBV-resistant cultivars.     

Systematic approaches to using the FOX hunting system to identify useful rice genes

Ectopic gene expression, or the gain-of-function approach, has the advantage that once the function of a gene is known the gene can be transferred to many different plants by transformation. We previously reported a method, called FOX hunting, that involves ectopic expression of Arabidopsis full-length cDNAs in Arabidopsis to systematically generate gain-of-function mutants. This technology is most beneficial for generating a heterologous gene resource for analysis of useful plant gene functions. As an initial model we generated more than 23 000 independent Arabidopsis transgenic lines that expressed rice fl-cDNAs (Rice FOX Arabidopsis lines). The short generation time and rapid and efficient transformation frequency of Arabidopsis enabled the functions of the rice genes to be analyzed rapidly. We screened rice FOX Arabidopsis lines for alterations in morphology, photosynthesis, element accumulation, pigment accumulation, hormone profiles, secondary metabolites, pathogen resistance, salt tolerance, UV signaling, high light tolerance, and heat stress tolerance. Some of the mutant phenotypes displayed by rice FOX Arabidopsis lines resulted from the expression of rice genes that had no homologs in Arabidopsis . This result demonstrated that rice fl-cDNAs could be used to introduce new gene functions in Arabidopsis. Furthermore, these findings showed that rice gene function could be analyzed by employing Arabidopsis as a heterologous host. This technology provides a framework for the analysis of plant gene function in a heterologous host and of plant improvement by using heterologous gene resources.