Wild relatives genetically close to cultivars are precious genetic resources for plant breeding. ... more Wild relatives genetically close to cultivars are precious genetic resources for plant breeding. Oryza rufipogon, O. barthii, O. glumaepatula, O. meridionalis and O. longistaminata are such wild species, and are also categorized as AA genome species based on their structural similarities. Chromosome segment substitution lines (CSSLs) are a powerful resource in breeding and genetics, and numerous rice CSSLs have been produced. This study aimed to develop DNA markers for evaluation of CSSLs directly by PCR and subsequent gel electrophoresis. We confirmed that up to 155 of 188 markers developed for detection of japonica-indica INDELs could also detect INDELs between rice cultivars and wild AA-species accessions. Percentages of applicable markers were higher in O. rufipogon accessions (61.7 to 85.6%), and lower in accessions of other four AA species (39.8 to 51.4%). These markers were distributed throughout the rice chromosomes, and will be useful for genotyping of CSSLs and other genet...
Since the development of transcriptome analysis systems, many expression evolution studies charac... more Since the development of transcriptome analysis systems, many expression evolution studies characterized evolutionary forces acting on gene expression, without explicit discrimination between global expression differences and tissue specific expression differences. However, different types of gene expression alteration should have different effects on an organism, the evolutionary forces that act on them might be different, and different types of genes might show different types of differential expression between species. To confirm this, we studied differentially expressed (DE) genes among closely related groups that have extensive gene expression atlases, and clarified characteristics of different types of DE genes including the identification of regulating loci for differential expression using expression quantitative loci (eQTL) analysis data. We detected differentially expressed (DE) genes between rice subspecies in five homologous tissues that were verified using japonica and ...
Molecular mechanisms of hybrid breakdown associated with sterility (F2 sterility) are poorly unde... more Molecular mechanisms of hybrid breakdown associated with sterility (F2 sterility) are poorly understood as compared with those of F1 hybrid sterility. Previously, we characterized three unlinked epistatic loci, hybrid sterility-a1 (hsa1), hsa2, and hsa3, responsible for the F2 sterility in a cross between Oryza sativa ssp. indica and japonica. In this study, we identified that the hsa1 locus contains two interacting genes, HSA1a and HSA1b, within a 30-kb region. HSA1a-j (japonica allele) encodes a highly conserved plant-specific domain of unknown function protein (DUF1618), whereas the indica allele (HSA1a-i(s)) has two deletion mutations that cause disruption of domain structure. The second gene, HSA1b-i(s), encodes an uncharacterized protein with some similarity to a nucleotide-binding protein. Homozygous introgression of indica HSA1a-i(s)-HSA1b-i(s) alleles into japonica showed female gamete abortion at an early mitotic stage. The fact that the recombinant haplotype HSA1a-j-HSA1b...
We have constructed a high-density linkage map of rice using an F2 population derived from the cr... more We have constructed a high-density linkage map of rice using an F2 population derived from the cross between a japonica variety, Nipponbare, and an indica variety, Kasalath. A total of 1,383 markers, which consist of cDNA clones from callus and root, genomic clones as well as RAPD markers, have been mapped covering a distance of 1,575 cM. All cDNA clones
Quantitative trait locus (QTL) analysis has been carried out to identify genes that control headi... more Quantitative trait locus (QTL) analysis has been carried out to identify genes that control heading time in rice. One hundred and eighty-six F 2 plants derived from a cross between japonica variety Nipponbare and indica variety Kasalath were used as a primary population for QTL mapping of heading time and more than 850 markers were employed to identify QTLs. QTL
1. In Sprague-Dawley (SD) rats treated for 7 days with malotilate (MAL:250 mg/kg, p.o.), cytochro... more 1. In Sprague-Dawley (SD) rats treated for 7 days with malotilate (MAL:250 mg/kg, p.o.), cytochrome P-450 and b5 contents, aminopyrine N-demethylase and heme oxygenase activities were significantly increased. In Wistar rats, cytochrome b5 content and heme oxygenase and delta-aminolevulinic acid synthetase activities were found to be significantly increased. 2. Among the antipyrine metabolites excreted in urine during the 24 hr after antipyrine (100 mg/kg, i.p.) administration, norantipyrine increased significantly in Sprague-Dawley rats, while a significant increase of 4-hydroxyantipyrine was observed in Wistar rats. 3. The serum dimethadione/trimethadione ratio was only found to be significantly increased in Sprague-Dawley rats. 4. These results indicate that malotilate may have inducible effects on hepatic drug metabolizing enzymes, and that it affects the various cytochrome P-450 isozymes from different strains of rat in different ways.
The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic... more The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of NGS technology, a flood of Oryza species reference genomes and genomic variation information has become available in the last several years. This genomic information combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions deriv...
Short interspersed elements (SINEs) are retroelements found in a wide variety of eukaryote genome... more 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 A-rich or T-rich tail of various size at the 3′ end, flanked by the direct repeat DNA sequences of several nucleotides, indicating that they have proliferated via
Molecular genetics and genomics : MGG, Jan 5, 2015
Defensive and reproductive protein genes undergo rapid evolution. Small, cysteine-rich secreted p... more 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-represented among reproductively expressed proteins. Because of their roles in defense, reproduction and development and their presence in multigene families, CRP variation can have major consequences for plant phenotypic and functional diversification. We surveyed the CRP genes of six closely related Oryza genomes comprising Oryza sativa ssp. japonica and ssp. indica, Oryza glaberrima and three accessions of Oryza rufipogon to observe patterns of evolution in these gene families and the effects of variation on their gene expression. These Oryza genomes, like other plant genomes, have accumulated large reservoirs of CRP sequences, comprising 26 groups totaling between 676 and 843 genes, in contrast to antimicrobial CRPs in animal genomes. Despite the close evolutionary relationships betw...
In flowering plants, knotted1-like homeobox (KNOX) transcription factors play crucial roles in es... more In flowering plants, knotted1-like homeobox (KNOX) transcription factors play crucial roles in establishment and maintenance of the shoot apical meristem (SAM), from which aerial organs such as leaves, stems, and flowers initiate. We report that a rice (Oryza sativa) KNOX gene Oryza sativa homeobox1 (OSH1) represses the brassinosteroid (BR) phytohormone pathway through activation of BR catabolism genes. Inducible overexpression of OSH1 caused BR insensitivity, whereas loss of function showed a BR-overproduction phenotype. Genome-wide identification of loci bound and regulated by OSH1 revealed hormonal and transcriptional regulation as the major function of OSH1. Among these targets, BR catabolism genes CYP734A2, CYP734A4, and CYP734A6 were rapidly upregulated by OSH1 induction. Furthermore, RNA interference knockdown plants of CYP734A genes arrested growth of the SAM and mimicked some osh1 phenotypes. Thus, we suggest that local control of BR levels by KNOX genes is a key regulatory...
The Plant journal : for cell and molecular biology, 2013
A post-zygotic hybridization barrier is often observed in the endosperm of seeds produced by inte... more A post-zygotic hybridization barrier is often observed in the endosperm of seeds produced by interspecific or interploidy crosses. In Arabidopsis thaliana, for example, hybrid endosperm from both types of cross shows altered timing of cellularization and an altered rate of nuclear divisions. Therefore, it has been proposed that interspecific and interploidy crosses share common molecular mechanisms for establishment of an effective species barrier. However, these two types of hybridization barrier may be initiated by different intrinsic cues: the interspecific cross barrier arises after hybridization of genomes with differences in DNA sequences, while the interploidy cross barrier arises after hybridization of genomes with the same DNA sequences but differences in ploidy levels. In this study, we performed interploidy crosses to identify components of the post-hybridization barrier in the endosperm of rice. We performed an intra-cultivar cross of autotetraploid (4n) × diploid (2n) r...
The Plant journal : for cell and molecular biology, 2011
In angiosperms, interspecific crosses often display hybrid incompatibilities that are manifested ... more In angiosperms, interspecific crosses often display hybrid incompatibilities that are manifested as under-proliferation or over-proliferation of endosperm. Recent analyses using crosses between Arabidopsis thaliana and its related species with different ploidy levels have shown that interspecific hybridization causes delayed developmental transition and increased mitotic activity in the endosperm. In this study, we investigated endosperm development in interspecific crosses between diploid Oryza species. In a cross between female O. sativa and male O. punctata, we found that the hybrid endosperm was reduced in size and this cross was associated with precocious developmental transition. By contrast, the cross between O. sativa and O. longistaminata generated enlarged hybrid endosperm at the mid-point of seed development and this cross was associated with delayed developmental transition. Subsequently, the hybrid endosperm displayed a shriveled appearance at the seed maturation stage....
The function of the novel gene MSP1 (MULTIPLE SPOROCYTE), which controls early sporogenic develop... more The function of the novel gene MSP1 (MULTIPLE SPOROCYTE), which controls early sporogenic development, was elucidated by characterizing a retrotransposon-tagged mutation of rice. The MSP1 gene encoded a Leu-rich repeat receptor-like protein kinase. The msp1 mutation gave rise to an excessive number of both male and female sporocytes. In addition, the formation of anther wall layers was disordered and the tapetum layer was lost completely. Although the mutation never affected homologous chromosome pairing and chiasma maintenance, the development of pollen mother cells was arrested at various stages of meiotic prophase I, which resulted in complete male sterility. Meanwhile, plural megaspore mother cells in a mutant ovule generated several megaspores, underwent gametogenesis, and produced germinable seeds when fertilized with wild-type pollen despite disorganized female gametophytes. In situ expression of MSP1 was detected in surrounding cells of male and female sporocytes and some fl...
Wild relatives genetically close to cultivars are precious genetic resources for plant breeding. ... more Wild relatives genetically close to cultivars are precious genetic resources for plant breeding. Oryza rufipogon, O. barthii, O. glumaepatula, O. meridionalis and O. longistaminata are such wild species, and are also categorized as AA genome species based on their structural similarities. Chromosome segment substitution lines (CSSLs) are a powerful resource in breeding and genetics, and numerous rice CSSLs have been produced. This study aimed to develop DNA markers for evaluation of CSSLs directly by PCR and subsequent gel electrophoresis. We confirmed that up to 155 of 188 markers developed for detection of japonica-indica INDELs could also detect INDELs between rice cultivars and wild AA-species accessions. Percentages of applicable markers were higher in O. rufipogon accessions (61.7 to 85.6%), and lower in accessions of other four AA species (39.8 to 51.4%). These markers were distributed throughout the rice chromosomes, and will be useful for genotyping of CSSLs and other genet...
Since the development of transcriptome analysis systems, many expression evolution studies charac... more Since the development of transcriptome analysis systems, many expression evolution studies characterized evolutionary forces acting on gene expression, without explicit discrimination between global expression differences and tissue specific expression differences. However, different types of gene expression alteration should have different effects on an organism, the evolutionary forces that act on them might be different, and different types of genes might show different types of differential expression between species. To confirm this, we studied differentially expressed (DE) genes among closely related groups that have extensive gene expression atlases, and clarified characteristics of different types of DE genes including the identification of regulating loci for differential expression using expression quantitative loci (eQTL) analysis data. We detected differentially expressed (DE) genes between rice subspecies in five homologous tissues that were verified using japonica and ...
Molecular mechanisms of hybrid breakdown associated with sterility (F2 sterility) are poorly unde... more Molecular mechanisms of hybrid breakdown associated with sterility (F2 sterility) are poorly understood as compared with those of F1 hybrid sterility. Previously, we characterized three unlinked epistatic loci, hybrid sterility-a1 (hsa1), hsa2, and hsa3, responsible for the F2 sterility in a cross between Oryza sativa ssp. indica and japonica. In this study, we identified that the hsa1 locus contains two interacting genes, HSA1a and HSA1b, within a 30-kb region. HSA1a-j (japonica allele) encodes a highly conserved plant-specific domain of unknown function protein (DUF1618), whereas the indica allele (HSA1a-i(s)) has two deletion mutations that cause disruption of domain structure. The second gene, HSA1b-i(s), encodes an uncharacterized protein with some similarity to a nucleotide-binding protein. Homozygous introgression of indica HSA1a-i(s)-HSA1b-i(s) alleles into japonica showed female gamete abortion at an early mitotic stage. The fact that the recombinant haplotype HSA1a-j-HSA1b...
We have constructed a high-density linkage map of rice using an F2 population derived from the cr... more We have constructed a high-density linkage map of rice using an F2 population derived from the cross between a japonica variety, Nipponbare, and an indica variety, Kasalath. A total of 1,383 markers, which consist of cDNA clones from callus and root, genomic clones as well as RAPD markers, have been mapped covering a distance of 1,575 cM. All cDNA clones
Quantitative trait locus (QTL) analysis has been carried out to identify genes that control headi... more Quantitative trait locus (QTL) analysis has been carried out to identify genes that control heading time in rice. One hundred and eighty-six F 2 plants derived from a cross between japonica variety Nipponbare and indica variety Kasalath were used as a primary population for QTL mapping of heading time and more than 850 markers were employed to identify QTLs. QTL
1. In Sprague-Dawley (SD) rats treated for 7 days with malotilate (MAL:250 mg/kg, p.o.), cytochro... more 1. In Sprague-Dawley (SD) rats treated for 7 days with malotilate (MAL:250 mg/kg, p.o.), cytochrome P-450 and b5 contents, aminopyrine N-demethylase and heme oxygenase activities were significantly increased. In Wistar rats, cytochrome b5 content and heme oxygenase and delta-aminolevulinic acid synthetase activities were found to be significantly increased. 2. Among the antipyrine metabolites excreted in urine during the 24 hr after antipyrine (100 mg/kg, i.p.) administration, norantipyrine increased significantly in Sprague-Dawley rats, while a significant increase of 4-hydroxyantipyrine was observed in Wistar rats. 3. The serum dimethadione/trimethadione ratio was only found to be significantly increased in Sprague-Dawley rats. 4. These results indicate that malotilate may have inducible effects on hepatic drug metabolizing enzymes, and that it affects the various cytochrome P-450 isozymes from different strains of rat in different ways.
The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic... more The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of NGS technology, a flood of Oryza species reference genomes and genomic variation information has become available in the last several years. This genomic information combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions deriv...
Short interspersed elements (SINEs) are retroelements found in a wide variety of eukaryote genome... more 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 A-rich or T-rich tail of various size at the 3′ end, flanked by the direct repeat DNA sequences of several nucleotides, indicating that they have proliferated via
Molecular genetics and genomics : MGG, Jan 5, 2015
Defensive and reproductive protein genes undergo rapid evolution. Small, cysteine-rich secreted p... more 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-represented among reproductively expressed proteins. Because of their roles in defense, reproduction and development and their presence in multigene families, CRP variation can have major consequences for plant phenotypic and functional diversification. We surveyed the CRP genes of six closely related Oryza genomes comprising Oryza sativa ssp. japonica and ssp. indica, Oryza glaberrima and three accessions of Oryza rufipogon to observe patterns of evolution in these gene families and the effects of variation on their gene expression. These Oryza genomes, like other plant genomes, have accumulated large reservoirs of CRP sequences, comprising 26 groups totaling between 676 and 843 genes, in contrast to antimicrobial CRPs in animal genomes. Despite the close evolutionary relationships betw...
In flowering plants, knotted1-like homeobox (KNOX) transcription factors play crucial roles in es... more In flowering plants, knotted1-like homeobox (KNOX) transcription factors play crucial roles in establishment and maintenance of the shoot apical meristem (SAM), from which aerial organs such as leaves, stems, and flowers initiate. We report that a rice (Oryza sativa) KNOX gene Oryza sativa homeobox1 (OSH1) represses the brassinosteroid (BR) phytohormone pathway through activation of BR catabolism genes. Inducible overexpression of OSH1 caused BR insensitivity, whereas loss of function showed a BR-overproduction phenotype. Genome-wide identification of loci bound and regulated by OSH1 revealed hormonal and transcriptional regulation as the major function of OSH1. Among these targets, BR catabolism genes CYP734A2, CYP734A4, and CYP734A6 were rapidly upregulated by OSH1 induction. Furthermore, RNA interference knockdown plants of CYP734A genes arrested growth of the SAM and mimicked some osh1 phenotypes. Thus, we suggest that local control of BR levels by KNOX genes is a key regulatory...
The Plant journal : for cell and molecular biology, 2013
A post-zygotic hybridization barrier is often observed in the endosperm of seeds produced by inte... more A post-zygotic hybridization barrier is often observed in the endosperm of seeds produced by interspecific or interploidy crosses. In Arabidopsis thaliana, for example, hybrid endosperm from both types of cross shows altered timing of cellularization and an altered rate of nuclear divisions. Therefore, it has been proposed that interspecific and interploidy crosses share common molecular mechanisms for establishment of an effective species barrier. However, these two types of hybridization barrier may be initiated by different intrinsic cues: the interspecific cross barrier arises after hybridization of genomes with differences in DNA sequences, while the interploidy cross barrier arises after hybridization of genomes with the same DNA sequences but differences in ploidy levels. In this study, we performed interploidy crosses to identify components of the post-hybridization barrier in the endosperm of rice. We performed an intra-cultivar cross of autotetraploid (4n) × diploid (2n) r...
The Plant journal : for cell and molecular biology, 2011
In angiosperms, interspecific crosses often display hybrid incompatibilities that are manifested ... more In angiosperms, interspecific crosses often display hybrid incompatibilities that are manifested as under-proliferation or over-proliferation of endosperm. Recent analyses using crosses between Arabidopsis thaliana and its related species with different ploidy levels have shown that interspecific hybridization causes delayed developmental transition and increased mitotic activity in the endosperm. In this study, we investigated endosperm development in interspecific crosses between diploid Oryza species. In a cross between female O. sativa and male O. punctata, we found that the hybrid endosperm was reduced in size and this cross was associated with precocious developmental transition. By contrast, the cross between O. sativa and O. longistaminata generated enlarged hybrid endosperm at the mid-point of seed development and this cross was associated with delayed developmental transition. Subsequently, the hybrid endosperm displayed a shriveled appearance at the seed maturation stage....
The function of the novel gene MSP1 (MULTIPLE SPOROCYTE), which controls early sporogenic develop... more The function of the novel gene MSP1 (MULTIPLE SPOROCYTE), which controls early sporogenic development, was elucidated by characterizing a retrotransposon-tagged mutation of rice. The MSP1 gene encoded a Leu-rich repeat receptor-like protein kinase. The msp1 mutation gave rise to an excessive number of both male and female sporocytes. In addition, the formation of anther wall layers was disordered and the tapetum layer was lost completely. Although the mutation never affected homologous chromosome pairing and chiasma maintenance, the development of pollen mother cells was arrested at various stages of meiotic prophase I, which resulted in complete male sterility. Meanwhile, plural megaspore mother cells in a mutant ovule generated several megaspores, underwent gametogenesis, and produced germinable seeds when fertilized with wild-type pollen despite disorganized female gametophytes. In situ expression of MSP1 was detected in surrounding cells of male and female sporocytes and some fl...
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