Formation of a Stable PSI-PSII Megacomplex in Rice That Conducts Energy Spillover.

In green plants, photosystem I (PSI) and photosystem II (PSII) bind to their respective light-harvesting complexes (LHCI and LHCII) to form the PSI-LHCI supercomplex and the PSII-LHCII supercomplex, respectively. These supercomplexes further form megacomplexes, like PSI-PSII and PSII-PSII in Arabidopsis (Arabidopsis thaliana) and spinach to modulate their light-harvesting properties, but not in the green alga Chlamydomonas reinhardtii. Here, we fractionated and characterized the stable rice PSI-PSII megacomplex.

Establishment of -tagged lines of Koshihikari, an elite variety of rice in Japan.

To utilize a transposon-tagged mutant as a breeding material in rice, an endogenous DNA transposon, , was introduced into Koshihikari by successive backcrossing together with , an active autonomous element. The founder line for -tagged lines of Koshihikari carried on chromosome 9 and transposed on chromosomes 1 and 8 and on chromosome 11. In -tagged lines, there were the most abnormal phenotypic mutants and many aberrant chlorophyll mutants at seedling stage.

Transgenerational activation of an autonomous DNA transposon, Dart1-24, by 5-azaC treatment in rice.

Dart1-24, one of the 37 autonomous DNA transposon Dart1s, was heritably activated by the demethylation of the 5' region following 5-azaC treatment of rice seeds. Transposons are controlled by epigenetic regulations. To obtain newly activated autonomous elements of Dart1, a DNA transposon, in rice, seeds of a stable pale yellow leaf (pyl-stb) mutant caused by the insertion of nDart1-0, a nonautonomous element in OsClpP5, were treated with 5-azaC, a demethylating agent.

LARGE GRAIN Encodes a Putative RNA-Binding Protein that Regulates Spikelet Hull Length in Rice.

Grain size is a key determiner of grain weight, one of the yield components in rice (Oryza sativa). Therefore, to increase grain yield, it is important to elucidate the detailed mechanisms regulating grain size. The Large grain (Lgg) mutant, found in the nonautonomous DNA-based active rice transposon1 (nDart1)-tagged lines of Koshihikari, is caused by a truncated nDart1-3 and 355 bp deletion in the 5' untranslated region of LGG, which encodes a putative RNA-binding protein, through transposon display and cosegregation analysis between grain length and LGG genotype in F2 and F3.

Easy sectioning of whole grain of rice using cryomicrotome.

To obtain a clear intact section of a ripened rice grain, which is suitable for biochemical and histological analysis, the Kawamoto method using a specific adhesive film was applied using a cryomicrotome. The longitudinal and sagittal sections were easily obtained together with the cross-section, and cell characteristics were clearly discerned in the ripened grain. It was demonstrated that the Kawamoto method is readily applicable for intact sectioning of hard tissue, including ripened grain.

Identification of QTLs for yield-related traits in RILs derived from the cross between pLIA-1 carrying chromosome segments and Norin 18 in rice.

To improve rice yield, a wide genetic pool is necessary. It is therefore important to explore wild rice relatives. is a distantly related wild rice relative that carries the AA genome.

A gain-of-function Bushy dwarf tiller 1 mutation in rice microRNA gene miR156d caused by insertion of the DNA transposon nDart1.

A non-autonomous DNA transposon in rice, nDart1, is actively transposed in the presence of an autonomous element, aDart1, under natural conditions. The nDart1-promoted gene tagging line was developed using the endogenous nDart1/aDart1 system to generate various rice mutants effectively. While the dominant mutants were occasionally isolated from the tagging line, it was unclear what causes dominant mutations.

A mutable albino allele in rice reveals that formation of thylakoid membranes requires the SNOW-WHITE LEAF1 gene.

Active DNA transposons are important tools for gene functional analysis. The endogenous non-autonomous transposon, nDart1-0, in rice (Oryza sativa L.) is expected to generate various transposon-insertion mutants because nDart1-0 elements tend to insert into genic regions under natural growth conditions.

Activation and epigenetic regulation of DNA transposon nDart1 in rice.

A large part of the rice genome is composed of transposons. Since active excision/reintegration of these mobile elements may result in harmful genetic changes, many transposons are maintained in a genetically or epigenetically inactivated state. However, some non-autonomous DNA transposons of the nDart1-3 subgroup, including nDart1-0, actively transpose in specific rice lines, such as pyl-v which carries an active autonomous element, aDart1-27, on chromosome 6.

DNA methylation in plants: relationship to small RNAs and histone modifications, and functions in transposon inactivation.

DNA methylation is a type of epigenetic marking that strongly influences chromatin structure and gene expression in plants and mammals. Over the past decade, DNA methylation has been intensively investigated in order to elucidate its control mechanisms. These studies have shown that small RNAs are involved in the induction of DNA methylation, that there is a relationship between DNA methylation and histone methylation, and that the base excision repair pathway has an important role in DNA demethylation.

Examination of transpositional activity of nDart1 at different stages of rice development.

As a useful tool to elucidate gene functions, a rice transposon tagging line has been developed using an active endogenous DNA transposon, nDart1. It was highly desirable to evaluate the transposition timing and frequency of the nDart1 elements during rice development to facilitate the generation of an efficient mutant isolation system. Comparison of the detected new insertions at different stages of rice development by transposon display analysis demonstrated that the last heading tiller carry a higher number of nDart1 elements than the main culm.

A rice mutant displaying a heterochronically elongated internode carries a 100 kb deletion.

We have isolated a recessive rice mutant, designated as indeterminate growth (ing), which displays creeping and apparent heterochronic phenotypes in the vegetative period with lanky and winding culms. Rough mapping and subsequent molecular characterization revealed that the ing mutant carries a large deletion, which corresponds to a 103 kb region in the Nipponbare genome, containing nine annotated genes on chromosome 3. Of these annotated genes, the SLR1 gene encoding a DELLA protein is the only one that is well characterized in its function, and its null mutation, which is caused by a single base deletion in the middle of the intronless SLR1 gene, confers a slender phenotype that bears close resemblance to the ing mutant phenotype.

Transposition and target preferences of an active nonautonomous DNA transposon nDart1 and its relatives belonging to the hAT superfamily in rice.

The nonautonomous nDart1 element in the hAT superfamily is one of a few active DNA transposons in rice. Its transposition can be induced by crossing with a line containing an active autonomous element, aDart1, and stabilized by segregating aDart1. No somaclonal variation should occur in nDart1-promoted gene tagging because no tissue culture is involved in nDart1 activation.

Characterization of autonomous Dart1 transposons belonging to the hAT superfamily in rice.

An endogenous 0.6-kb rice DNA transposon, nDart1-0, was found as an active nonautonomous element in a mutable virescent line, pyl-v, displaying leaf variegations. Here, we demonstrated that the active autonomous element aDart in pyl-v corresponds to Dart1-27 on chromosome 6 in Nipponbare, which carries no active aDart elements, and that aDart and Dart1-27 are identical in their sequences and chromosomal locations, indicating that Dart1-27 is epigenetically silenced in Nipponbare.

Distribution and mapping of an active autonomous aDart element responsible for mobilizing nonautonomous nDart1 transposons in cultivated rice varieties.

An endogenous 0.6-kb rice DNA transposon, nDart1, has been identified as a causative element of a spontaneous mutable virescent allele pyl-v conferring pale-yellow leaves with dark-green sectors in the seedlings, due to somatic excision of nDart1 integrated into the OsClpP5 gene encoding the nuclear-coded chloroplast protease. As the transposition of nDart1 depends on the presence of an active autonomous aDart element in the genome, the plants exhibiting the leaf variegation carry the active aDart element.

Transposon display for active DNA transposons in rice.

Transposon display (TD) is a powerful technique to identify the integration site of transposons in gene tagging as a functional genomic tool for elucidating gene function. Although active endogenous DNA transposons have been used extensively for gene tagging in maize, only two active endogenous DNA transposons in rice have been identified, the 0.43-kb element mPing of the MITE family and the 0.

An active DNA transposon nDart causing leaf variegation and mutable dwarfism and its related elements in rice.

While characterized mutable alleles caused by DNA transposons have been abundant in maize since the discovery of Dissociation conferring variegation by Barbara McClintock, only a few mutable alleles have been described in rice even though the rice genome contains various transposons. Here, we show that a spontaneous mutable virescent allele, pyl-v, is caused by the disruption of the nuclear-coded essential chloroplast protease gene, OsClpP5, due to insertion of a 607-bp non-autonomous DNA transposon, non-autonomous DNA-based active rice transposon one (nDart1), belonging to the hAT superfamily. The transposition of nDart1 can be induced by crossing with a line containing an autonomous element, aDart, and stabilized by segregating out of aDart.

Efficient gene targeting by homologous recombination in rice.

Modification of genes through homologous recombination, termed gene targeting, is the most direct method to characterize gene function. In higher plants, however, the method is far from a common practice. Here we describe an efficient and reproducible procedure with a strong positive/negative selection for gene targeting in rice, which feeds more than half of the world's population and is an important model plant.