Gene_locus Report for: orysa-q33aq0

Drought and salt stresses, as major environmental abiotic stresses in agriculture worldwide, affect plant growth and crop productivity and quality. The development of crops with higher drought and salt tolerance is therefore highly desirable. Here, we reported the isolation and biological function and molecular characterization of a novel maspardin gene OsMas1 from rice. The OsMas1 protein was localized to the cytoplasm. The expression levels of OsMas1 were up-regulated under mannitol, PEG6000, NaCl and ABA treatments in rice. The OsMas1 gene was introduced into rice cultivar Zhonghua 11 (wild-type, WT) and OsMas1-overexpression (OsMas1-OE) plants exhibited significantly enhanced salt and drought tolerance, while OsMas1-interference (OsMas1-RNAi) plants exhibited decreased tolerance to salt and drought stresses, compared with WT. OsMas1-OE plants exhibited enhanced hypersensitive, while OsMas1-RNAi plants showed less sensitive to exogenous ABA treatment at both germination and post-germination stages. ABA, proline and K+ content and superoxide dismutase (SOD), catalase (CAT), peroxidase (POD) and photosynthesis activities were significantly increased, while malonaldehyde (MDA), hydrogen peroxide (H2O2), superoxide anion radical (O2-) and Na+ content were significantly decreased in OsMas1-OE plants compared with OsMas1-RNAi and WT plants. Overexpression of OsMas1 up-regulated the genes involved in ABA signaling, proline biosynthesis, ROS-scavenging system, photosynthesis and ion transport under salt and drought stresses. Collectively, our results indicate that OsMas1 gene functions in improving salt and drought tolerance in rice, which may serve as a candidate gene for enhancing the resistance to abiotic stresses in crops.

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

Rice is the world's most important food crop and a model for cereal research. At 430 megabases in size, its genome is the most compact of the cereals. We report the sequence of chromosome 10, the smallest of the 12 rice chromosomes (22.4 megabases), which contains 3471 genes. Chromosome 10 contains considerable heterochromatin with an enrichment of repetitive elements on 10S and an enrichment of expressed genes on 10L. Multiple insertions from organellar genomes were detected. Collinearity was apparent between rice chromosome 10 and sorghum and maize. Comparison between the draft and finished sequence demonstrates the importance of finished sequence.

Drought and salt stresses, as major environmental abiotic stresses in agriculture worldwide, affect plant growth and crop productivity and quality. The development of crops with higher drought and salt tolerance is therefore highly desirable. Here, we reported the isolation and biological function and molecular characterization of a novel maspardin gene OsMas1 from rice. The OsMas1 protein was localized to the cytoplasm. The expression levels of OsMas1 were up-regulated under mannitol, PEG6000, NaCl and ABA treatments in rice. The OsMas1 gene was introduced into rice cultivar Zhonghua 11 (wild-type, WT) and OsMas1-overexpression (OsMas1-OE) plants exhibited significantly enhanced salt and drought tolerance, while OsMas1-interference (OsMas1-RNAi) plants exhibited decreased tolerance to salt and drought stresses, compared with WT. OsMas1-OE plants exhibited enhanced hypersensitive, while OsMas1-RNAi plants showed less sensitive to exogenous ABA treatment at both germination and post-germination stages. ABA, proline and K+ content and superoxide dismutase (SOD), catalase (CAT), peroxidase (POD) and photosynthesis activities were significantly increased, while malonaldehyde (MDA), hydrogen peroxide (H2O2), superoxide anion radical (O2-) and Na+ content were significantly decreased in OsMas1-OE plants compared with OsMas1-RNAi and WT plants. Overexpression of OsMas1 up-regulated the genes involved in ABA signaling, proline biosynthesis, ROS-scavenging system, photosynthesis and ion transport under salt and drought stresses. Collectively, our results indicate that OsMas1 gene functions in improving salt and drought tolerance in rice, which may serve as a candidate gene for enhancing the resistance to abiotic stresses in crops.

The wild species of the genus Oryza contain a largely untapped reservoir of agronomically important genes for rice improvement. Here we report the 261-Mb de novo assembled genome sequence of Oryza brachyantha. Low activity of long-terminal repeat retrotransposons and massive internal deletions of ancient long-terminal repeat elements lead to the compact genome of Oryza brachyantha. We model 32,038 protein-coding genes in the Oryza brachyantha genome, of which only 70% are located in collinear positions in comparison with the rice genome. Analysing breakpoints of non-collinear genes suggests that double-strand break repair through non-homologous end joining has an important role in gene movement and erosion of collinearity in the Oryza genomes. Transition of euchromatin to heterochromatin in the rice genome is accompanied by segmental and tandem duplications, further expanded by transposable element insertions. The high-quality reference genome sequence of Oryza brachyantha provides an important resource for functional and evolutionary studies in the genus Oryza.

The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

Rice is the world's most important food crop and a model for cereal research. At 430 megabases in size, its genome is the most compact of the cereals. We report the sequence of chromosome 10, the smallest of the 12 rice chromosomes (22.4 megabases), which contains 3471 genes. Chromosome 10 contains considerable heterochromatin with an enrichment of repetitive elements on 10S and an enrichment of expressed genes on 10L. Multiple insertions from organellar genomes were detected. Collinearity was apparent between rice chromosome 10 and sorghum and maize. Comparison between the draft and finished sequence demonstrates the importance of finished sequence.