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The strength of reproductive isolation often correlates positively with parental divergence in both animals and plants. Here, we assess the relationship between transmission ratio distortion (TRD) of marker loci and parental diver...
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The strength of reproductive isolation often correlates positively with parental divergence in both animals and plants. Here, we assess the relationship between transmission ratio distortion (TRD) of marker loci and parental divergence in intraspecific rice (Oryza sativa L.) crosses. We produced 10 diverse F2 populations by crossing a temperate japonica reference accession with each of 10 donor accessions belonging to subpopulations different from the reference accession, and then genotyped the F2 populations using molecular markers distributed across the entire genome. Significant TRDs ( alpha =0.05) were detected in 9 of the 10 F2 populations. TRD regions on chromosomes 3 and 6 were common to several populations; in contrast, other TRD regions were unique to a single population, indicating the diversification of genomic location of TRDs among the populations. The level of TRD (estimated from the overall number and magnitude of TRDs) was significantly correlated with the genetic distance between the donor accessions and the reference accession. Our results suggest that in intraspecific rice crosses, parental divergence may result in diversification of the TRD pattern, followed by an increase in the level of TRD.
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Increasing leaf photosynthesis offers a possible way to improve yield potential in rice (Oryza sativa L.). Carbon isotope discrimination (Delta(13)C) has potential as an indirect selection criterion. In this study, we searched for...
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Increasing leaf photosynthesis offers a possible way to improve yield potential in rice (Oryza sativa L.). Carbon isotope discrimination (Delta(13)C) has potential as an indirect selection criterion. In this study, we searched for quantitative trait loci (QTLs) controlling Delta(13)C, and assessed their association with leaf photosynthesis. Substitution mapping by using chromosome segment substitution lines (CSSLs), that carry segments from the indica cultivar Kasalath in the genetic background of the japonica cultivar Koshihikari, identified genomic regions affecting Delta(13)C on chromosomes (Chr.) 2, 3, 6, 7, and 12. One of the CSSLs, SL208, in which most regions on Chr. 3 were substituted with Kasalath segments, showed higher leaf stomatal conductance for CO(2) (g (s)) and Delta(13)C than Koshihikari during the vegetative stage although leaf photosynthetic rate did not differ between them. These results suggest an association between Delta(13)C and g (s). To test this association, we performed a QTL analysis for Delta(13)C at vegetative and heading stages in an F(2) population derived from a cross between SL208 and Koshihikari. The results confirmed a QTL controlling Delta(13)C on the long arm of Chr. 3. By using a near-isogenic line specific to Hd6, we ruled out the possibility that variation in Delta(13)C was generated through the pleiotropic effect of heading date.
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The alteration of photoperiod sensitivity has let breeders diversify flowering time in Oryza sativa (rice) and develop cultivars adjusted to a range of growing season periods. Map-based cloning revealed that the rice flowering-tim...
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The alteration of photoperiod sensitivity has let breeders diversify flowering time in Oryza sativa (rice) and develop cultivars adjusted to a range of growing season periods. Map-based cloning revealed that the rice flowering-time quantitative trait locus (QTL) Heading date 16 (Hd16) encodes a casein kinase-I protein. One non-synonymous substitution in Hd16 resulted in decreased photoperiod sensitivity in rice, and this substitution occurred naturally in an old rice cultivar. By using near-isogenic lines with functional or deficient alleles of several rice flowering-time genes, we observed significant digenetic interactions between Hd16 and four other flowering-time genes (Ghd7, Hd1, DTH8 and Hd2). In a near-isogenic line with the weak-photoperiod-sensitivity allele of Hd16, transcription levels of Ehd1, Hd3a, and RFT1 increased under long-day conditions, and transcription levels of Hd3a and RFT1 decreased under short-day conditions. Expression analysis under continuous light and dark conditions showed that Hd16 was not likely to be associated with circadian clock regulation. Biochemical characterization indicated that the functional Hd16 recombinant protein specifically phosphorylated Ghd7. These results demonstrate that Hd16 acts as an inhibitor in the rice flowering pathway by enhancing the photoperiod response as a result of the phosphorylation of Ghd7.
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On-farm conservation of landraces is one strategy to maintain the diversity of crop germplasm in local agro-ecosystems. The genetic structures of landraces are a key biological factor in on-farm conservation strategies. To accumul...
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On-farm conservation of landraces is one strategy to maintain the diversity of crop germplasm in local agro-ecosystems. The genetic structures of landraces are a key biological factor in on-farm conservation strategies. To accumulate a genetic understanding that will help establish a methodology for on-farm conservation, the genetic organization of landraces of aromatic rice in Namdinh province, Vietnam was analysed using RAPD markers. Eighteen RAPD markers detected 38 genotypes among 320 aromatic rice samples growing at 23 sites of farmers' fields and in the experimental field that derived from 13 sites. Geographical variation was observed in the frequency of genotypes, whereas individual landraces could not be distinguished by RAPD markers. Genetic variation within a site was generally smaller than that among sites. The degree of genetic similarity of the plants in a site varied among sites, as did the number of genotypes. Changes in genetic structure over time were investigated using experimental populations each derived from approximately 30 plants from 13 farmers' fields. The differences detected by DNA markers between the genetic structural in the farmers' fields and those in experimental fields suggested that genetic drift is a major cause of these differences. The present study suggests that DNA markers are an essential means to monitor the genetic structures of heterogeneous landraces of rice, and are useful for selecting study sites for the on-farm conservation of genetic diversity as well as for successive monitoring..
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The CC genome of Oryza is found in nine species of Oryza that are distributed on all continents having a tropical climate. Three diploid Oryza species with CC genome are found in Africa and Asia to Papua New Guinea. In southern So...
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The CC genome of Oryza is found in nine species of Oryza that are distributed on all continents having a tropical climate. Three diploid Oryza species with CC genome are found in Africa and Asia to Papua New Guinea. In southern South Asia these three CC genome diploid species can be found, O. eichingeri and O. rhizomatis in Sri Lanka and O. officinalis in India. AA genome wild relatives of rice are also found in the same geographic region. Germplasm of both diploid CC and AA genome Oryza germplasm has recently been collected from Sri Lanka. AFLP analysis was used to compare the genetic diversity of the two Oryza genomes from a similar geographic region in southern South Asia. In addition, the diploid CC Oryza germplasm was also analysed by RAPD and SSR methodologies and the combined results were analysed. The results show that in southern South Asia the diploid CC genome species have a high level of genetic diversity compared to the diploid AA genome species. Molecular marker analysis revealed that populations of O. rhizomatis from northern and southeastern Sri Lanka are genetically differentiated. One accession of O. rhizomatis was aligned with O. eichingeri. This accession was collected from the site of O. rhizomatis that is the closest to a population of O. eichingeri. O. eichingeri showed lower genetic diversity than the other two diploid Oryza CC genome species. O. officinalis accessions from Assam, India, and China were genetically less diverged from O. eichingeri and O. rhizomatis than two accessions of O. officinalis from Kerala state, India..
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Calreticulin is an abundant endo/sarcoplasmic reticulum Ca~(2+)-binding protein. To investigate whether calreticulin (CRO1) is involved in the cold-stress response in rice, a transgenic plant was constructed. The transcriptional l...
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Calreticulin is an abundant endo/sarcoplasmic reticulum Ca~(2+)-binding protein. To investigate whether calreticulin (CRO1) is involved in the cold-stress response in rice, a transgenic plant was constructed. The transcriptional level was decreased within 30 min and recovered within 2 h of a cold treatment. The calreticulin protein was shifted from a soluble fraction to an insoluble fraction by cold stress. Endogenous abscisic acid (ABA) is an important factor in cold response, and the synthesis of ABA was strongly induced in CRO1-sense transgenic rice, the same as in cold-sensitive rice. The phosphorylation of calreticulin increased after cold treatment. Over-expression of calreticulin enhanced the activities of 47 kDa Ca~(2+)-dependent protein kinase (CDPK) that had been induced by cold treatment. The 47-kDa CDPK activity increases more in the cold sensitive variety IR36 and the sense transgenic rice than it does in other varieties. The synthesis of ABA, phosphorylation of calreticulin and 47-kDa CDPK activity induced in sense transgenic rice were the same as in cold-sensitive rice and the phosphorylation of antisense transgenic rice was similar to that of cold-tolerant rice. These results suggest that the calreticulin is involved in the signaling pathway leading to response to cold stress.
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ENOD40 is one of the most intriguing early nodulin genes that is known to be induced very early in response to interaction of legume plants with symbiotic Rhizobium bacteria, but its function in the nodulation process is still not...
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ENOD40 is one of the most intriguing early nodulin genes that is known to be induced very early in response to interaction of legume plants with symbiotic Rhizobium bacteria, but its function in the nodulation process is still not known. Lotus japonicus has two ENOD40 genes: LjENOD40-1 is abundantly induced in very early stages of bacterial infection or Nod factor application, whereas LjENOD40-2 is abundantly expressed only in mature nodules. We generated transgenic lines of L. japonicus with an RNAi (RNA interference) construct that expresses hairpin double-stranded RNA for LjENOD40-1 to induce sequence-specific RNA silencing. In the transgenic plants, expression of both LjENOD40-1 and -2 was significantly reduced, and no accumulation of ENOD40 transcripts was detected upon Mesorhizobium loti inoculation. The transgenic plants exhibited very poor nodulation (only 0-2 nodules per plant) and could not grow well without additional nitrogen supply. Analysis of segregation in the T(2) progeny indicated that the suppression of nodulation is perfectly linked with the presence of the transgene. Microscopic observation of the infection process using lacZ-labeled M. loti, together with expression analysis of infection-related nodulin genes, demonstrated that ENOD40 knock-down did not inhibit the initiation of the bacterial infection process. In contrast, nodule primordium initiation and subsequent nodule development were significantly suppressed in the transgenic plants. These results clearly indicate that ENOD40 is required for nodule initiation and subsequent organogenesis, but is not involved in early infection events.
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Root nodule (RN) symbiosis in legumes shares genes involved in the early signaling pathway with more ancient arbuscular mycorrhiza (AM) symbiosis, which is widespread in higher plants. The non-legume homologs of such genes have be...
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Root nodule (RN) symbiosis in legumes shares genes involved in the early signaling pathway with more ancient arbuscular mycorrhiza (AM) symbiosis, which is widespread in higher plants. The non-legume homologs of such genes have been well documented to be not only essential for the AM symbiosis in non-legume mycorrhizal plants but also functional in the RN symbiosis in legume plants. In contrast, it has not been investigated in detail whether RN symbiosis-specific genes, which are not essential for AM symbiosis, are functionally conserved in non-legumes. Two GRAS-domain transcription factors, NSP1 and NSP2, have been shown to be required for RN symbiosis, but not for AM symbiosis. In this study, we demonstrated that their homologs, OsNSP1 and OsNSP2, from rice are able to fully rescue the RN symbiosis-defective phenotypes of the mutants of corresponding genes in the model legume, Lotus japonicus. Our results indicate that some of the genes essential for RN symbiosis conserve their functions in homologs from non-legumes, which do not nodulate.
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Background: The high-quality sequence information and rich bioinformatics tools available for rice havecontributed to remarkable advances in functional genomics. To facilitate the application of gene functioninformation to the stu...
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Background: The high-quality sequence information and rich bioinformatics tools available for rice havecontributed to remarkable advances in functional genomics. To facilitate the application of gene functioninformation to the study of natural variation in rice, we comprehensively searched for articles related to ricefunctional genomics and extracted information on functionally characterized genes. Results: As of 31 March 2012, 702 functionally characterized genes were annotated. This number represents about1.6% of the predicted loci in the Rice Annotation Project Database. The compiled gene information is organized tofacilitate direct comparisons with quantitative trait locus (QTL) information in the Q-TARO database. Comparison ofgenomic locations between functionally characterized genes and the QTLs revealed that QTL clusters were oftenco-localized with high-density gene regions, and that the genes associated with the QTLs in these clusters weredifferent genes, suggesting that these QTL clusters are likely to be explained by tightly linked but distinct genes. Information on the functionally characterized genes compiled during this study is now available in the Overview ofFunctionally Characterized Genes in Rice Online database (OGRO) on the Q-TARO website (http://qtaro.abr.affrc.go.jp/ogro). The database has two interfaces: a table containing gene information, and a genome viewer that allowsusers to compare the locations of QTLs and functionally characterized genes.Conclusions: OGRO on Q-TARO will facilitate a candidate-gene approach to identifying the genes responsible forQTLs. Because the QTL descriptions in Q-TARO contain information on agronomic traits, such comparisons will alsofacilitate the annotation of functionally characterized genes in terms of their effects on traits important for rice breeding. The increasing amount of information on rice gene function being generated from mutant panels andother types of studies will make the OGRO database even more valuable in the future.
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Using two sets of chromosome segment substitution lines (CSSLs) of crosses between cvs. 'Koshihikari' and 'Kasalath' (Ko/Ka) and between 'Koshihikari' and 'Nona Bokra' (Ko/NB), respectively, we have identified alleles for ten trai...
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Using two sets of chromosome segment substitution lines (CSSLs) of crosses between cvs. 'Koshihikari' and 'Kasalath' (Ko/Ka) and between 'Koshihikari' and 'Nona Bokra' (Ko/NB), respectively, we have identified alleles for ten traits related to productivity (e.g., harvest index and biomass) in rice (Oryza sativa L.). A total of 43 chromosome regions affecting traits (CRATs) in Ko/Ka CSSLs and 40 in Ko/NB CSSLs were detected. Among them, ten and 18 CRATs in Ko/Ka and Ko/NB CSSLs, respectively, had positive effects. A CRAT for harvest index (HI) with a positive allele from 'Kasalath' on chromosome 6 (tentatively named HI6) increased the HI by 25 % relative to 'Koshihikari', raising it to the theoretical upper limit in rice (0.6). Functional analysis using CSSLs with HI6 indicated that HI6 reduced the size of the lower parts of the plant, which is not important for production, while maintaining the size of the other organs related to production (e.g., flag leaf and panicle), resulting in improved nitrogen (N) use efficiency. These results suggest an 'ideal plant type' with improved N use efficiency that can sustain higher yields. A CRAT for the SPAD (soil plant analysis development) value, which is a chlorophyll meter value commonly used as an indicator of leaf N content and strongly associated with the source ability of a leaf, with a 'Nona Bokra' allele on chromosome 4 increased the value by 13 % relative to 'Koshihikari' with no loss of leaf area. These CRATs can be used for the improvement of rice productivity.
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