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Article
Open AccessOryzaGenome2.1: Database of Diverse Genotypes in Wild Oryza Species
OryzaGenome (http://viewer.shigen.info/oryzagenome21detail/index.xhtml), a feature within Oryzabase (https://shigen.nig.ac.jp/rice/oryzaba...
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Article
Open AccessPotential of Oryza officinalis to augment the cold tolerance genetic mechanisms of Oryza sativa by network complementation
Oryza officinalis is an accessible alien donor for genetic improvement of rice. Comparison across a representative panel of Oryza species showed that the wild O. officinalis and cultivated O. sativa ssp. japonica...
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Article
Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
This article was not made open access when initially published online, which was corrected before print publication. In addition, ORCID links were missing for 12 authors and have been added to the HTML and PDF...
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Article
Open AccessAssembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species
The African wild rice species Oryza longistaminata has several beneficial traits compared to cultivated rice species, such as resistance to biotic stresses, clonal propagation via rhizomes, and increased biomass ...
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Article
Open AccessGenomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that de...
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Article
Open AccessEffect of Wild and Cultivated Rice Genotypes on Rhizosphere Bacterial Community Composition
Deposition and secretion from roots influences the composition of the microbial communities surrounding them in the rhizosphere, and microbial activities influence the growth and health of the plant. Different...
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Article
Open AccessGlobal expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes
Since the development of transcriptome analysis systems, many expression evolution studies characterized evolutionary forces acting on gene expression, without explicit discrimination between global expression...
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Article
Rapid turnover of antimicrobial-type cysteine-rich protein genes in closely related Oryza genomes
Defensive and reproductive protein genes undergo rapid evolution. Small, cysteine-rich secreted peptides (CRPs) act as antimicrobial agents and function in plant intercellular signaling and are over-represente...
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Article
Open AccessRiTE database: a resource database for genus-wide rice genomics and evolutionary biology
Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not...
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Article
Approximate tail probabilities of the maximum of a chi-square field on multi-dimensional lattice points and their applications to detection of loci interactions
In this study, we define a chi-square random field on a multi-dimensional lattice points index set with a direct product covariance structure and consider the distribution of the maximum of this random field. ...
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Article
DDM1 (Decrease in DNA Methylation) genes in rice (Oryza sativa)
Regulation of cytosine methylation in the plant genome is of pivotal in determining the epigenetic states of chromosome regions. Relative tolerance of plant to deficiency in cytosine methylation provides unpar...
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Article
Open AccessA map of rice genome variation reveals the origin of cultivated rice
Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in his...
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Article
Open AccessA simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays
High-density oligonucleotide arrays are effective tools for genoty** numerous loci simultaneously. In small genome species (genome size: < ~300 Mb), whole-genome DNA hybridization to expression arrays has be...
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Article
Open AccessSNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip
High-density short oligonucleotide microarrays are useful tools for studying biodiversity, because they can be used to investigate both nucleotide and expression polymorphisms. However, when different strains ...
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Article
Identification, characterization and interaction of HAP family genes in rice
A HAP complex, which consists of three subunits, namely HAP2 (also called NF-YA or CBF-B), HAP3 (NF-YB/CBF-A) and HAP5 (NF-YC/CBF-C), binds to CCAAT sequences in a promoter to control the expression of target ...
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Article
MNU-induced mutant pools and high performance TILLING enable finding of any gene mutation in rice
Mutant populations are indispensable genetic resources for functional genomics in all organisms. However, suitable rice mutant populations, induced either by chemicals or irradiation still have been rarely dev...
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Chapter
Chromosome and Genome Evolution in Rice
Genomic and species divergences in rice offer a major advantage in genetic and evolutional studies, as well as for practical breeding purposes. The genus Oryza is classified into nine genomes comprising 23 specie...
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Chapter
Rice Retroposon, p-SINE, and Its Use for Classification and Identification of Oryza Species
Short interspersed elements (SINEs) are retroelements found in a wide variety of eukaryote genomes. They are 70- to 500-bp repetitive DNA sequences and each has an internal promoter for RNA polymerase III, an ...
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Article
The centromere composition of multiple repetitive sequences on rice chromosome 5
The large-scale primary structure of the centromeric region of rice chromosome 5 was analyzed, the first example in a cereal species. The yeast artificial chromosome (YAC) and bacterial artificial chromosome ...
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Article
Physical map** of the rice genome with YAC clones
Construction of a rice physical map covered by YAC clones which have been arranged over half of the genome length is presented here. A total of 1285 RFLP and RAPD markers almost evenly distributed on the rice ...
