Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data

Kawahara, Yoshihiro; Bastide, M. de la; Hamilton, John; Kanamori, Hajime; McCombie, W. Richard; Ouyang, Shuai; Schwartz, David C.; Tanaka, Tsuyoshi; Wu, Jianzhong; Zhou, Shiguo; Childs, Kevin L.; Davidson, Rebecca M.; Lin, Haining; Quesada‐Ocampo, Lina M.; Vaillancourt, Brieanne; Sakai, Hiroaki; Lee, Sung Shin; Kim, Jungsok; Numa, Hisataka; Itoh, Takeshi; Buell, C. Robin; Matsumoto, Takashi

doi:10.1186/1939-8433-6-4

Cited by 1,814 publications

(1,736 citation statements)

References 27 publications

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“…Sequence data from this article can be found in the MSU Rice Genome Annotation Project (http://rice.plantbiology.msu.edu/analyses_search_locus.shtml) databases (Kawahara et al, 2013) under the following accession numbers: OsABF1 (LOC_Os01g64730), Ehd1 (LOC_Os10g32600), Hd1 (LOC_Os06g16370), Hd3a (LOC_Os06g06320), RFT (LOC_Os06g06300), OsPHYB (LOC_Os03g19590), OsCOL4 (LOC_Os02g39710), DTH8 (LOC_Os08g07740), SE5 (LOC_Os06g40080), LFL1 (LOC_Os01g51610), OsMADS56 (LOC_Os10g39130), OsGI (LOC_Os01g08700), Ehd2 (LOC_Os10g28330), Ehd3 (LOC_Os08g01420), Ehd4 (LOC_Os03g02160), OsMADS50 (LOC_Os03g03070), OsMADS51 (LOC_Os01g69850), and OsWRKY104 (LOC_ Os11g02520).…”

Section: Accession Numbersmentioning

confidence: 99%

A Drought-Inducible Transcription Factor Delays Reproductive Timing in Rice

Zhang

Zhao

et al. 2016

Plant Physiol.

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The molecular mechanisms underlying photoperiod or temperature control of flowering time have been recently elucidated, but how plants regulate flowering time in response to other external factors, such as water availability, remains poorly understood. Using a large-scale Hybrid Transcription Factor approach, we identified a bZIP transcriptional factor, O. sativa ABA responsive element binding factor 1 (OsABF1), which acts as a suppressor of floral transition in a photoperiod-independent manner. Simultaneous knockdown of both OsABF1 and its closest homologous gene, OsbZIP40, in rice (Oryza sativa) by RNA interference results in a significantly earlier flowering phenotype. Molecular and genetic analyses demonstrate that a drought regime enhances expression of the OsABF1 gene, which indirectly suppresses expression of the Early heading date 1 (Ehd1) gene that encodes a key activator of rice flowering. Furthermore, we identified a drought-inducible gene named OsWRKY104 that is under the direct regulation of OsABF1. Overexpression of OsWRKY104 can suppress Ehd1 expression and confers a later flowering phenotype in rice. Together, these findings reveal a novel pathway by which rice modulates heading date in response to the change of ambient water availability.Flowering time (or heading date) and drought resistance are two major yield traits in crops, especially rice (Oryza sativa). As global climatic change looms, drought has become the biggest abiotic stress to limit crop yields. Breeders have capitalized on naturally occurring genetic variations to improve or maintain crop yield in times or areas of drought by different strategies (Eisenstein, 2013). Manipulation of floral transition has been a promising way to maximize crop yield during dry periods. This strategy has been successful due to extensive identification of genetic loci and elucidation of molecular mechanisms that control flowering time under diverse or unpredictable environments.Heading date in rice is influenced by many environmental cues such as day length (photoperiod), temperature, nutrition, and water availability. Molecular mechanisms that underlie photoperiod regulation of flowering time have already been characterized, probably because day length is more predictable than other environmental factors during seasonal changes. Rice is a facultative short-day plant that flowers earlier in short days (SDs) than in long days (LDs). Heading date 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1) are two paralogous genes in rice encoding "florigen" molecules expressed in the phloem of leaves and transported to the shoot apical meristem to promote flowering (Tamaki et al., 2007;

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Section: Accession Numbersmentioning

confidence: 99%

A Drought-Inducible Transcription Factor Delays Reproductive Timing in Rice

Zhang

Zhao

et al. 2016

Plant Physiol.

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“…Three putative genes encoding cytochrome P450 monooxygenase (Os01g0602200, Os01g0602400, and Os01g0602500) are annotated at this locus of the japonica model variety Nipponbare in the Rice Annotation Project Database (http://rapdb. dna.affrc.go.jp/; Kawahara et al, 2013;Sakai et al, 2013). On the cytochrome P450 home page (http:// drnelson.uthsc.edu/CytochromeP450.html; Nelson et al, 2004), these genes correspond to CYP72A31, CYP72A32, and CYP72A33, respectively (Supplemental Figs.…”

Section: Positional Cloning Of the Bs-tolerant Genementioning

confidence: 99%

A Novel Rice Cytochrome P450 Gene, CYP72A31, Confers Tolerance to Acetolactate Synthase-Inhibiting Herbicides in Rice and Arabidopsis

et al. 2014

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Target-site and non-target-site herbicide tolerance are caused by the prevention of herbicide binding to the target enzyme and the reduction to a nonlethal dose of herbicide reaching the target enzyme, respectively. There is little information on the molecular mechanisms involved in non-target-site herbicide tolerance, although it poses the greater threat in the evolution of herbicide-resistant weeds and could potentially be useful for the production of herbicide-tolerant crops because it is often involved in tolerance to multiherbicides. Bispyribac sodium (BS) is an herbicide that inhibits the activity of acetolactate synthase. Rice (Oryza sativa) of the indica variety show BS tolerance, while japonica rice varieties are BS sensitive. Map-based cloning and complementation tests revealed that a novel cytochrome P450 monooxygenase, CYP72A31, is involved in BS tolerance. Interestingly, BS tolerance was correlated with CYP72A31 messenger RNA levels in transgenic plants of rice and Arabidopsis (Arabidopsis thaliana). Moreover, Arabidopsis overexpressing CYP72A31 showed tolerance to bensulfuron-methyl (BSM), which belongs to a different class of acetolactate synthase-inhibiting herbicides, suggesting that CYP72A31 can metabolize BS and BSM to a compound with reduced phytotoxicity. On the other hand, we showed that the cytochrome P450 monooxygenase CYP81A6, which has been reported to confer BSM tolerance, is barely involved, if at all, in BS tolerance, suggesting that the CYP72A31 enzyme has different herbicide specificities compared with CYP81A6. Thus, the CYP72A31 gene is a potentially useful genetic resource in the fields of weed control, herbicide development, and molecular breeding in a broad range of crop species.

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“…To annotate the functions of identified gene sets, the gene ontology information from AgriGO (Du et al, 2010; http://bioinfo.cau.edu.cn/agriGO/ analysis.php), Rice Genome Annotation (Kawahara et al, 2013; http://rice. plantbiology.msu.edu/), and Arabidopsis (Arabidopsis thaliana) annotation (ftp://ftp.arabidopsis.org/home/tair/Ontologies/Gene_Ontology/) was used.…”

Section: Go Analysismentioning

confidence: 99%

Dynamic Cytology and Transcriptional Regulation of Rice Lamina Joint Development

2017

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Rice (Oryza sativa) leaf angle is determined by lamina joint and is an important agricultural trait determining leaf erectness and, hence, the photosynthesis efficiency and grain yield. Genetic studies reveal a complex regulatory network of lamina joint development; however, the morphological changes, cytological transitions, and underlying transcriptional programming remain to be elucidated. A systemic morphological and cytological study reveals a dynamic developmental process and suggests a common but distinct regulation of the lamina joint. Successive and sequential cell division and expansion, cell wall thickening, and programmed cell death at the adaxial or abaxial sides form the cytological basis of the lamina joint, and the increased leaf angle results from the asymmetric cell proliferation and elongation. Analysis of the gene expression profiles at four distinct developmental stages ranging from initiation to senescence showed that genes related to cell division and growth, hormone synthesis and signaling, transcription (transcription factors), and protein phosphorylation (protein kinases) exhibit distinct spatiotemporal patterns during lamina joint development. Phytohormones play crucial roles by promoting cell differentiation and growth at early stages or regulating the maturation and senescence at later stages, which is consistent with the quantitative analysis of hormones at different stages. Further comparison with the gene expression profile of leaf inclination1, a mutant with decreased auxin and increased leaf angle, indicates the coordinated effects of hormones in regulating lamina joint. These results reveal a dynamic cytology of rice lamina joint that is fine-regulated by multiple factors, providing informative clues for illustrating the regulatory mechanisms of leaf angle and plant architecture.

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Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data

Cited by 1,814 publications

References 27 publications

A Drought-Inducible Transcription Factor Delays Reproductive Timing in Rice

A Drought-Inducible Transcription Factor Delays Reproductive Timing in Rice

A Novel Rice Cytochrome P450 Gene, CYP72A31, Confers Tolerance to Acetolactate Synthase-Inhibiting Herbicides in Rice and Arabidopsis

Dynamic Cytology and Transcriptional Regulation of Rice Lamina Joint Development

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