Maternally expressed FERTILIZATION-INDEPENDENT ENDOSPERM1 regulates seed dormancy and aleurone development in rice.

Seed dormancy, an essential trait for plant adaptation, is determined by the embryo itself and the surrounding tissues. Here, we found that rice (Oryza sativa) FERTILIZATION-INDEPENDENT ENDOSPERM1 (OsFIE1) regulates endosperm-imposed dormancy and the dorsal aleurone thickness in a manner dependent on the parent of origin. Maternally expressed OsFIE1 suppresses gibberellin (GA) biosynthesis in the endosperm by depositing trimethylation of lysine 27 on histone H3 (H3K27me3) marks on GA biosynthesis-related genes, thus inhibiting germination and aleurone differentiation.

OsNF-YB7 inactivates OsGLK1 to inhibit chlorophyll biosynthesis in rice embryo.

As a master regulator of seed development, Leafy Cotyledon 1 (LEC1) promotes chlorophyll (Chl) biosynthesis in , but the mechanism underlying this remains poorly understood. Here, we found that loss of function of , a homolog of rice, leads to chlorophyllous embryo, indicating that plays an opposite role in Chl biosynthesis in rice compared with that in . OsNF-YB7 regulates the expression of a group of genes responsible for Chl biosynthesis and photosynthesis by directly binding to their promoters.

BysR, a LysR-Type Pleiotropic Regulator, Controls Production of Occidiofungin by Activating the LuxR-Type Transcriptional Regulator AmbR1 in sp. Strain JP2-270.

Occidiofungin is a highly effective antifungal glycopeptide produced by certain strains. The gene cluster, responsible for occidiofungin biosynthesis, is regulated by the cluster-specific regulators encoded by an homolog(s) within the same gene cluster, while the extent to which occidiofungin biosynthesis is connected with the core regulation network remains unknown. Here, we report that the LysR-type regulator BysR acts as a pleiotropic regulator and is essential for occidiofungin biosynthesis.

OsYUC11-mediated auxin biosynthesis is essential for endosperm development of rice.

Auxin is a phytohormone essential for plant development. However, our understanding of auxin-regulated endosperm development remains limited. Here, we described rice YUCCA (YUC) flavin-containing monooxygenase encoding gene OsYUC11 as a key contributor to auxin biosynthesis in rice (Oryza sativa) endosperm.

The maternally expressed polycomb group gene is essential for endosperm cellularization and imprinting in rice.

Cellularization is a key event in endosperm development. Polycomb group (PcG) genes, such as (), are vital for the syncytium-to-cellularization transition in plants. In this study, we found that , a rice homolog of the PcG gene (), plays a role similar to that of in regard to seed development, although there is limited sequence similarity between the genes.

Functional divergence of two duplicated Fertilization Independent Endosperm genes in rice with respect to seed development.

Fertilization Independent Endosperm (FIE) is an essential member of Polycomb Repressive Complex 2 (PRC2) that plays important roles in the developmental regulation of plants. OsFIE1 and OsFIE2 are two FIE homologs in the rice genome. Here, we showed that OsFIE1 probably duplicated from OsFIE2 after the origin of the tribe Oryzeae, but has a specific expression pattern and methylation landscape.

OsbZIP76 interacts with OsNF-YBs and regulates endosperm cellularization in rice (Oryza sativa).

Following double fertilization, plant endosperm nuclei undergo syncytial divisions, followed by synchronous cellularization. Cellularization is a key event during endosperm development, but our understanding of its regulation is limited to Arabidopsis. In this study we show that OsbZIP76 regulates cellularization in rice (Oryza sativa).

Genome-wide analysis of fatty acid desaturase genes in rice (Oryza sativa L.).

Fatty acid desaturases can catalyze saturated or unsaturated fatty acids to form a double bond at various locations in the hydrocarbon chain. In the present study, a total of 20 full-length desaturase genes were identified from rice genome. An exhaustive analysis was performed to describe their chromosomal locations, gene structures, phylogeny, cis-regulatory elements, sub-cellular localizations and expression patterns.

Characterization of Imprinted Genes in Rice Reveals Conservation of Regulation and Imprinting with Other Plant Species.

Genomic imprinting is an epigenetic phenomenon by which certain genes display differential expression in a parent-of-origin-dependent manner. Hundreds of imprinted genes have been identified from several plant species. Here, we identified, with a high level of confidence, 208 imprinted gene candidates from rice ().

A group of nuclear factor Y transcription factors are sub-functionalized during endosperm development in monocots.

Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor that consists of three subunits, NF-YA, NF-YB, and NF-YC. Gene functions of NF-Ys during endosperm development are not well understood. In this study, we identified eight rice NF-Y-encoding genes, namely OsNF-YA8, OsNF-YB1,9, and OsNF-YC8,9,10,11,12, that are predominantly expressed in the endosperm.

Identification of virus-derived siRNAs and their targets in RBSDV-infected rice by deep sequencing.

RNA interference (RNAi) is a conserved mechanism against viruses in plants and animals. It is thought to inactivate the viral genome by producing virus-derived small interfering RNAs (vsiRNAs). Rice black-streaked dwarf virus (RBSDV) is transmitted to plants by the small brown planthopper (Laodelphax striatellus), and seriously threatens production of rice in East Asia, particularly Oryza sativa japonica subspecies.

Evolution and Molecular Control of Hybrid Incompatibility in Plants.

Postzygotic reproductive isolation (RI) plays an important role in speciation. According to the stage at which it functions and the symptoms it displays, postzygotic RI can be called hybrid inviability, hybrid weakness or necrosis, hybrid sterility, or hybrid breakdown. In this review, we summarized new findings about hybrid incompatibilities in plants, most of which are from studies on Arabidopsis and rice.

Complete Genome Sequence of Bifidobacterium actinocoloniiforme Type Strain DSM 22766T, Isolated from Bumblebee Digestive Tracts.

Bifidobacteria are one of the most important beneficial bacteria in the gut of mammals and insects. We sequenced the genome of B. actinocoloniiforme DSM 22766, which was isolated from the digestive tracts of bumblebees.

Workable male sterility systems for hybrid rice: Genetics, biochemistry, molecular biology, and utilization.

The exploitation of male sterility systems has enabled the commercialization of heterosis in rice, with greatly increased yield and total production of this major staple food crop. Hybrid rice, which was adopted in the 1970s, now covers nearly 13.6 million hectares each year in China alone.

Characterization of the Ubiquitin-Conjugating Enzyme Gene Family in Rice and Evaluation of Expression Profiles under Abiotic Stresses and Hormone Treatments.

Ubiquitin-conjugating enzyme E2s (UBCs), which catalyze the transfer of ubiquitin to substrate or E3 ligases, are key enzymes in ubiquitination modifications of target proteins. However, little is known about the knowledge of UBC gene family in rice. In this study, a total of 39 UBC encoding genes, which all contained an UBC domain with a cysteine active site, were identified in the rice genome.

Genome-wide transcriptome profiles of rice hybrids and their parents.

Heterosis is a widely studied phenomenon in several plant species. However, its genetic basis still remains to be elucidated. In this study, we used RNA-seq data from two rice genotypes and their reciprocal hybrids, and used a combination of transcriptome profiling and allele-specific expression analysis to identify genes that are differentially expressed in the hybrids and their parents or expressed in an allele-specific manner.

Genome-wide characterisation of gene expression in rice leaf blades at 25 °C and 30 °C.

Rice growth is greatly affected by temperature. To examine how temperature influences gene expression in rice on a genome-wide basis, we utilised recently compiled next-generation sequencing datasets and characterised a number of RNA-sequence transcriptome samples in rice seedling leaf blades at 25 °C and 30 °C. Our analysis indicated that 50.

Splicing and alternative splicing in rice and humans.

Rice is a monocot gramineous crop, and one of the most important staple foods. Rice is considered a model species for most gramineous crops. Extensive research on rice has provided critical guidance for other crops, such as maize and wheat.

[Advance on the cloning and functional analysis of disease resistance genes in rice].

Improving the disease resistance of rice is a major objective in rice breeding programs, which provides a basic guarantee for the good quality and high yield in rice. Recently, substantial progresses on the research of rice disease resistant mechanism had been made. Some important genes had been identified and cloned.

[Discovery and utilization of favorable genes in wild rice].

Wild rice is the closely related wild relatives of cultivated rice. Wild rice provides natural genetic germplasm resources for improving cultivated rice varieties as it possesses many desirable traits and favorable genes, many of which, such as resistance to diseases and insect pests, tolerance to different kinds of stresses and its cytoplasmic male sterility, have been widely used in cultivated rice breeding. In this paper, favorable traits of wild rice germplasm resources and the related genes were summarized, and their utilization potential in rice breeding were also discussed.