Growth responses of NaCl stressed rice (Oryza sativa L.) plants ...

African Journals Online (AJOL)

GREGORY

2010-09-27

Sep 27, 2010 ... 3Department of Statistics, University of Sindh Jamshoro, Pakistan. 4Mityari Sugar Mills ... Key words: Oryza sativa L., seedling biomass, epidermal cells, proline content. ... Attempts to reduce the soil salinity, using mechanical.

Growth responses of NaCl stressed rice (Oryza sativa L.) plants ...

African Journals Online (AJOL)

GREGORY

2010-09-27

Sep 27, 2010 ... Growth responses of NaCl stressed rice (Oryza sativa. L.) plants ... 2008), which is a real threat to human's food security. Existed situation may ..... content and composition of essential oil and minerals in black cumin. (Nigella ...

Could abiotic stress tolerance in wild relatives of rice be used to improve Oryza sativa?

Science.gov (United States)

Atwell, Brian J; Wang, Han; Scafaro, Andrew P

2014-02-01

Oryza sativa and Oryza glaberrima have been selected to acquire and partition resources efficiently as part of the process of domestication. However, genetic diversity in cultivated rice is limited compared to wild Oryza species, in spite of 120,000 genotypes being held in gene banks. By contrast, there is untapped diversity in the more than 20 wild species of Oryza, some having been collected from just a few coastal locations (e.g. Oryza schlechteri), while others are widely distributed (e.g. Oryza nivara and Oryza rufipogon). The extent of DNA sequence diversity and phenotypic variation is still being established in wild Oryza, with genetic barriers suggesting a vast range of morphologies and function even within species, such as has been demonstrated for Oryza meridionalis. With increasing climate variability and attempts to make more marginal land arable, abiotic and biotic stresses will be managed over the coming decades by tapping into the genetic diversity of wild relatives of O. sativa. To help create a more targeted approach to sourcing wild rice germplasm for abiotic stress tolerance, we have created a climate distribution map by plotting the natural occurrence of all Oryza species against corresponding temperature and moisture data. We then discuss interspecific variation in phenotype and its significance for rice, followed by a discussion of ways to integrate germplasm from wild relatives into domesticated rice. Crown Copyright © 2013. Published by Elsevier Ireland Ltd. All rights reserved.

Can rice (Oryza sativa) mitigate pesticides and nutrients in agricultural runoff?

Science.gov (United States)

Phytoremediation of nutrients and pesticides in runoff is a growing conservation effort, particularly in agriculturally intensive areas such as the lower Mississippi River Valley. In the current study, rice (Oryza sativa) was examined for its mitigation capacity of nitrogen, phosphorus, diazinon, a...

Variation of photosynthetic tolerance of rice cultivars (Oryza sativa L ...

African Journals Online (AJOL)

STORAGESEVER

2010-03-01

Mar 1, 2010 ... (Oryza sativa L.) to chilling temperature in the light. Xia Li*, Kun Cao, Chao .... 2 mol) formed red-brown trimethine that can be detected quantitatively with spectrophoto- ..... ses through the generation of appropriate signals (H2O2) and the balance ..... was under weak light intensity (Murata, 1989). Light.

Genome-wide comparative in silico analysis of the RNA helicase gene family in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza sativa.

Science.gov (United States)

Xu, Ruirui; Zhang, Shizhong; Huang, Jinguang; Zheng, Chengchao

2013-01-01

RNA helicases are enzymes that are thought to unwind double-stranded RNA molecules in an energy-dependent fashion through the hydrolysis of NTP. RNA helicases are associated with all processes involving RNA molecules, including nuclear transcription, editing, splicing, ribosome biogenesis, RNA export, and organelle gene expression. The involvement of RNA helicase in response to stress and in plant growth and development has been reported previously. While their importance in Arabidopsis and Oryza sativa has been partially studied, the function of RNA helicase proteins is poorly understood in Zea mays and Glycine max. In this study, we identified a total of RNA helicase genes in Arabidopsis and other crop species genome by genome-wide comparative in silico analysis. We classified the RNA helicase genes into three subfamilies according to the structural features of the motif II region, such as DEAD-box, DEAH-box and DExD/H-box, and different species showed different patterns of alternative splicing. Secondly, chromosome location analysis showed that the RNA helicase protein genes were distributed across all chromosomes with different densities in the four species. Thirdly, phylogenetic tree analyses identified the relevant homologs of DEAD-box, DEAH-box and DExD/H-box RNA helicase proteins in each of the four species. Fourthly, microarray expression data showed that many of these predicted RNA helicase genes were expressed in different developmental stages and different tissues under normal growth conditions. Finally, real-time quantitative PCR analysis showed that the expression levels of 10 genes in Arabidopsis and 13 genes in Zea mays were in close agreement with the microarray expression data. To our knowledge, this is the first report of a comparative genome-wide analysis of the RNA helicase gene family in Arabidopsis, Oryza sativa, Zea mays and Glycine max. This study provides valuable information for understanding the classification and putative functions of

Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication.

Science.gov (United States)

Zhang, Fantao; Xu, Tao; Mao, Linyong; Yan, Shuangyong; Chen, Xiwen; Wu, Zhenfeng; Chen, Rui; Luo, Xiangdong; Xie, Jiankun; Gao, Shan

2016-04-26

It is widely accepted that cultivated rice (Oryza sativa L.) was domesticated from common wild rice (Oryza rufipogon Griff.). Compared to other studies which concentrate on rice origin, this study is to genetically elucidate the substantially phenotypic and physiological changes from wild rice to cultivated rice at the whole genome level. Instead of comparing two assembled genomes, this study directly compared the Dongxiang wild rice (DXWR) Illumina sequencing reads with the Nipponbare (O. sativa) complete genome without assembly of the DXWR genome. Based on the results from the comparative genomics analysis, structural variations (SVs) between DXWR and Nipponbare were determined to locate deleted genes which could have been acquired by Nipponbare during rice domestication. To overcome the limit of the SV detection, the DXWR transcriptome was also sequenced and compared with the Nipponbare transcriptome to discover the genes which could have been lost in DXWR during domestication. Both 1591 Nipponbare-acquired genes and 206 DXWR-lost transcripts were further analyzed using annotations from multiple sources. The NGS data are available in the NCBI SRA database with ID SRP070627. These results help better understanding the domestication from wild rice to cultivated rice at the whole genome level and provide a genomic data resource for rice genetic research or breeding. One finding confirmed transposable elements contribute greatly to the genome evolution from wild rice to cultivated rice. Another finding suggested the photophosphorylation and oxidative phosphorylation system in cultivated rice could have adapted to environmental changes simultaneously during domestication.

Assessment of genomic relationship between Oryza sativa and ...

African Journals Online (AJOL)

The hybrid was produced between these two species at the International Rice Research Institute using embryo rescue technique. The chromosome pairing was examined in pollen mother cells of O. australinesis, O. sativa and the hybrid between O. sativa and O. australinesis. The hybrid was highly sterile with pollen stain ...

An ecogeographic analysis of Oryza series Sativae in Asia and the Pacific

NARCIS (Netherlands)

Banaticla-Hilario, M.C.N.

2012-01-01

The non-cultivated speciesof the genus Oryza can provide a genetic arsenal of useful traits for improving the widely cultivated and consumed Asian rice (O. sativa). The diversity of these valuable plant resources must be well understood to ensure their effective in- and ex-situ

Genetic analysis of yield and yield components in Oryza sativa x ...

African Journals Online (AJOL)

... inheritance of yield and yield components and to estimate the heritabilities of important quantitative traits in rice (Oryza sativa L.). Six generations viz., P1, P2, F1, F2, BCP1 and BCP2 of a cross between IET6279 and IR70445-146-3-3 were used for the study. Generation mean analysis suggested that additive effects had a ...

Robustness and strategies of adaptation among farmer varieties of African Rice (Oryza glaberrima) and Asian Rice (Oryza sativa) across West Africa.

Science.gov (United States)

Mokuwa, Alfred; Nuijten, Edwin; Okry, Florent; Teeken, Béla; Maat, Harro; Richards, Paul; Struik, Paul C

2013-01-01

This study offers evidence of the robustness of farmer rice varieties (Oryza glaberrima and O. sativa) in West Africa. Our experiments in five West African countries showed that farmer varieties were tolerant of sub-optimal conditions, but employed a range of strategies to cope with stress. Varieties belonging to the species Oryza glaberrima - solely the product of farmer agency - were the most successful in adapting to a range of adverse conditions. Some of the farmer selections from within the indica and japonica subspecies of O. sativa also performed well in a range of conditions, but other farmer selections from within these two subspecies were mainly limited to more specific niches. The results contradict the rather common belief that farmer varieties are only of local value. Farmer varieties should be considered by breeding programmes and used (alongside improved varieties) in dissemination projects for rural food security.

Robustness and Strategies of Adaptation among Farmer Varieties of African Rice (Oryza glaberrima) and Asian Rice (Oryza sativa) across West Africa

Science.gov (United States)

Maat, Harro; Richards, Paul; Struik, Paul C.

2013-01-01

This study offers evidence of the robustness of farmer rice varieties (Oryza glaberrima and O. sativa) in West Africa. Our experiments in five West African countries showed that farmer varieties were tolerant of sub-optimal conditions, but employed a range of strategies to cope with stress. Varieties belonging to the species Oryza glaberrima – solely the product of farmer agency – were the most successful in adapting to a range of adverse conditions. Some of the farmer selections from within the indica and japonica subspecies of O. sativa also performed well in a range of conditions, but other farmer selections from within these two subspecies were mainly limited to more specific niches. The results contradict the rather common belief that farmer varieties are only of local value. Farmer varieties should be considered by breeding programmes and used (alongside improved varieties) in dissemination projects for rural food security. PMID:23536754

Rice is the seed of the monocot plants Oryza sativa (Asian rice) or ...

African Journals Online (AJOL)

BIOTECH

2013-10-16

Oct 16, 2013 ... of culture. The regenerated plantlets were transferred to pots for acclimatization. About 80% of plants were survived in the greenhouse condition. Key words: Somatic embryogenesis, immature zygotic embryos, Indica rice, plant regeneration. INTRODUCTION. Rice (Oryza sativa L.) is one of the most ...

Robustness and Strategies of Adaptation among Farmer Varieties of African Rice (Oryza glaberrima) and Asian Rice (Oryza sativa) across West Africa

NARCIS (Netherlands)

Mokuwa, A.; Nuijten, H.A.C.P.; Okry, F.; Teeken, B.W.E.; Maat, H.; Richards, P.; Struik, P.C.

2013-01-01

This study offers evidence of the robustness of farmer rice varieties (Oryza glaberrima and O. sativa) in West Africa. Our experiments in five West African countries showed that farmer varieties were tolerant of sub-optimal conditions, but employed a range of strategies to cope with stress.

Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

DEFF Research Database (Denmark)

Vongsangnak, Wanwipa; Olsen, Peter; Hansen, Kim

2008-01-01

Background: Since ancient times the filamentous fungus Aspergillus oryzae has been used in the fermentation industry for the production of fermented sauces and the production of industrial enzymes. Recently, the genome sequence of A. oryzae with 12,074 annotated genes was released but the number...... to a genome scale metabolic model of A. oryzae. Results: Our assembled EST sequences we identified 1,046 newly predicted genes in the A. oryzae genome. Furthermore, it was possible to assign putative protein functions to 398 of the newly predicted genes. Noteworthy, our annotation strategy resulted...... model was validated and shown to correctly describe the phenotypic behavior of A. oryzae grown on different carbon sources. Conclusion: A much enhanced annotation of the A. oryzae genome was performed and a genomescale metabolic model of A. oryzae was reconstructed. The model accurately predicted...

ALOGAMIA EM ARROZ (Oryza sativa L. E RELAÇÃO COM CARACTERÍSTICAS AGRONÔMICAS RICE (Oryza sativa L. ALLOGAMY AND RELATIONSHIP WITH AGRONOMIC TRAITS

Directory of Open Access Journals (Sweden)

Péricles de Carvalho Ferreira Neves

2007-09-01

Full Text Available

A produção de sementes híbridas de arroz, utilizando a técnica chinesa, requer uma grande quantidade de mão-de-obra e é cara. Alternativas para aumentar a taxa de polinização cruzada podem ajudar a reduzir tal custo. A Embrapa Arroz e Feijão desenvolve um projeto de produção de híbridos através da transferência de caracteres alogâmicos (comprimento de estigma e antera da Oryza longistaminata A. Chev. para a cultivada Oryza sativa L. O objetivo deste estudo foi determinar as correlações genética e fenotípica entre esses caracteres e os agronômicos. O. longistaminata foi cruzada com a O. sativa e retrocruzada duas vezes para a cultivada. Foram obtidas 25 linhagens F3:6 e estudadas as correlações entre os caracteres alogâmicos (comprimento de estigma, antera e espigueta e os agronômicos (comprimento de estigma, antera, espigueta, arista e panícula, esterilidade, degrane, altura de planta, perfilhos por planta, e exserção de panícula. O desenho experimental utilizado foi o de blocos ao acaso com quatro repetições. Os ensaios foram conduzidos em dois locais dentro da área experimental da Embrapa Arroz e Feijão. Em geral, foram observadas pequenas correlações genética e fenotípica entre caracteres alogâmicos e agronômicos. Elevada e significativa associação foi observada entre o comprimento de estigma e o de anteras, o comprimento de estigma e o de arista, o comprimento de antera e o de arista, e o comprimento de panícula e a altura de planta.

PALAVRAS-CHAVE: Oryza longistaminata; taxa de autopolinização; arroz híbrido; produção de sementes.

Sensory acceptability evaluation of irradiated rice, oryza sativa indica

International Nuclear Information System (INIS)

Loaharanu, S.; Sutantawong, M.; Ungsunanatawiwat, A.

1971-01-01

The non-glutinous and glutinous types of polished rice, Oryza sativa indica were subjected to gamma rays at ambient temperature and stored at 27+-1 0 C for one week. The irradiated rice was cooked and tasted by members of trained panel. Using Hedonic scale and Triangle test, the acceptability of irradiated rice was justified. Gamma irradiation up to 100 krads did not significantly cause off-color, off-odor and off flavor in irradiated non-glutino rice. Glutinous rice irradiated at 60 krads could not be significantly differentiated from non-irradiated sample

Construction of six Oryza sativa x O. rufipogon Chromosome Segment Substitution Line (CSSL) Libraries

Science.gov (United States)

Transgressive variation has been observed in rice (Oryza sativa) as an increase in grain yield and attributed to the ancestral parent, O. rufipogon, in mapping populations developed from several adapted rice varieties crossed with a single O. rufipogon accession. To explore this phenomenon of transg...

Origin of Oryza sativa in China inferred by nucleotide polymorphisms of organelle DNA.

Directory of Open Access Journals (Sweden)

Xin Wei

Full Text Available China is rich of germplasm resources of common wild rice (Oryza rufipogon Griff. and Asian cultivated rice (O. sativa L. which consists of two subspecies, indica and japonica. Previous studies have shown that China is one of the domestication centers of O. sativa. However, the geographic origin and the domestication times of O. sativa in China are still under debate. To settle these disputes, six chloroplast loci and four mitochondrial loci were selected to examine the relationships between 50 accessions of Asian cultivated rice and 119 accessions of common wild rice from China based on DNA sequence analysis in the present study. The results indicated that Southern China is the genetic diversity center of O. rufipogon and it might be the primary domestication region of O. sativa. Molecular dating suggested that the two subspecies had diverged 0.1 million years ago, much earlier than the beginning of rice domestication. Genetic differentiations and phylogeography analyses indicated that indica was domesticated from tropical O. rufipogon while japonica was domesticated from O. rufipogon which located in higher latitude. These results provided molecular evidences for the hypotheses of (i Southern China is the origin center of O. sativa in China and (ii the two subspecies of O. sativa were domesticated multiple times.

Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome.

Directory of Open Access Journals (Sweden)

Keyan Zhao

2010-05-01

Full Text Available The domestication of Asian rice (Oryza sativa was a complex process punctuated by episodes of introgressive hybridization among and between subpopulations. Deep genetic divergence between the two main varietal groups (Indica and Japonica suggests domestication from at least two distinct wild populations. However, genetic uniformity surrounding key domestication genes across divergent subpopulations suggests cultural exchange of genetic material among ancient farmers.In this study, we utilize a novel 1,536 SNP panel genotyped across 395 diverse accessions of O. sativa to study genome-wide patterns of polymorphism, to characterize population structure, and to infer the introgression history of domesticated Asian rice. Our population structure analyses support the existence of five major subpopulations (indica, aus, tropical japonica, temperate japonica and GroupV consistent with previous analyses. Our introgression analysis shows that most accessions exhibit some degree of admixture, with many individuals within a population sharing the same introgressed segment due to artificial selection. Admixture mapping and association analysis of amylose content and grain length illustrate the potential for dissecting the genetic basis of complex traits in domesticated plant populations.Genes in these regions control a myriad of traits including plant stature, blast resistance, and amylose content. These analyses highlight the power of population genomics in agricultural systems to identify functionally important regions of the genome and to decipher the role of human-directed breeding in refashioning the genomes of a domesticated species.

EKSPLORASI CENDAWAN ENDOFIT DARI TANAMAN PADI SEBAGAI AGENS PEMACU PERTUMBUHAN TANAMAN (The Exploration of Endophytic Fungi from Oryza sativa as Plant Growth Promoting Agents)

OpenAIRE

Wilia, Weni; Hayati, Islah; Ristyadi, Dwi

2013-01-01

Endophityc fungi have been successfully isolated from Oryza sativa atLaboratory of Plant Disease, Agriculture Faculty University of Jambi. Theaim of this research was to get endophityc fungi from Oryza sativa. Therewere three (3) candidates of endophityc fungi that have been successfullyisolated. Pathogenosity test which was done showed that all of fungi wereendophityc fungi. Those fungi were identified as endophityc fungi due to theseed of paddy could growth normally in pure culture of endop...

A walk on the wild side: Oryza species as source for rice abiotic stress tolerance.

Science.gov (United States)

Menguer, Paloma Koprovski; Sperotto, Raul Antonio; Ricachenevsky, Felipe Klein

2017-01-01

Oryza sativa, the common cultivated rice, is one of the most important crops for human consumption, but production is increasingly threatened by abiotic stresses. Although many efforts have resulted in breeding rice cultivars that are relatively tolerant to their local environments, climate changes and population increase are expected to soon call for new, fast generation of stress tolerant rice germplasm, and current within-species rice diversity might not be enough to overcome such needs. The Oryza genus contains other 23 wild species, with only Oryza glaberrima being also domesticated. Rice domestication was performed with a narrow genetic diversity, and the other Oryza species are a virtually untapped genetic resource for rice stress tolerance improvement. Here we review the origin of domesticated Oryza sativa from wild progenitors, the ecological and genomic diversity of the Oryza genus, and the stress tolerance variation observed for wild Oryza species, including the genetic basis underlying the tolerance mechanisms found. The summary provided here is important to indicate how we should move forward to unlock the full potential of these germplasms for rice improvement.

The complete chloroplast genomes of Cannabis sativa and Humulus lupulus.

Science.gov (United States)

Vergara, Daniela; White, Kristin H; Keepers, Kyle G; Kane, Nolan C

2016-09-01

Cannabis and Humulus are sister genera comprising the entirety of the Cannabaceae sensu stricto, including C. sativa L. (marijuana, hemp), and H. lupulus L. (hops) as two economically important crops. These two plants have been used by humans for many purposes including as a fiber, food, medicine, or inebriant in the case of C. sativa, and as a flavoring component in beer brewing in the case of H. lupulus. In this study, we report the complete chloroplast genomes for two distinct hemp varieties of C. sativa, Italian "Carmagnola" and Russian "Dagestani", and one Czech variety of H. lupulus "Saazer". Both C. sativa genomes are 153 871 bp in length, while the H. lupulus genome is 153 751 bp. The genomes from the two C. sativa varieties differ in 16 single nucleotide polymorphisms (SNPs), while the H. lupulus genome differs in 1722 SNPs from both C. sativa cultivars.

Two complete chloroplast genome sequences of Cannabis sativa varieties.

Science.gov (United States)

Oh, Hyehyun; Seo, Boyoung; Lee, Seunghwan; Ahn, Dong-Ha; Jo, Euna; Park, Jin-Kyoung; Min, Gi-Sik

2016-07-01

In this study, we determined the complete chloroplast (cp) genomes from two varieties of Cannabis sativa. The genome sizes were 153,848 bp (the Korean non-drug variety, Cheungsam) and 153,854 bp (the African variety, Yoruba Nigeria). The genome structures were identical with 131 individual genes [86 protein-coding genes (PCGs), eight rRNA, and 37 tRNA genes]. Further, except for the presence of an intron in the rps3 genes of two C. sativa varieties, the cp genomes of C. sativa had conservative features similar to that of all known species in the order Rosales. To verify the position of C. sativa within the order Rosales, we conducted phylogenetic analysis by using concatenated sequences of all PCGs from 17 complete cp genomes. The resulting tree strongly supported monophyly of Rosales. Further, the family Cannabaceae, represented by C. sativa, showed close relationship with the family Moraceae. The phylogenetic relationship outlined in our study is well congruent with those previously shown for the order Rosales.

A Hypersensitivity-Like Response to Meloidogyne graminicola in Rice (Oryza sativa).

Science.gov (United States)

Phan, Ngan Thi; De Waele, Dirk; Lorieux, Mathias; Xiong, Lizhong; Bellafiore, Stephane

2018-04-01

Meloidogyne graminicola is a major plant-parasitic nematode affecting rice cultivation in Asia. Resistance to this nematode was found in the African rice genotypes Oryza glaberrima and O. longistaminata; however, due to interspecific hybrid sterility, the introgression of resistance genes in the widely consumed O. sativa varieties remains challenging. Recently, resistance was found in O. sativa and, here, we report for the first time the histological and genetic characterization of the resistance to M. graminicola in Zhonghua 11, an O. sativa variety. Bright-light microscopy and fluorescence observations of the root tissue of this variety revealed that the root cells surrounding the nematode displayed a hypersensitivity-like reaction with necrotic cells at early stages of infection when nematodes are migrating in the root's mesoderm. An accumulation of presumably phenolic compounds in the nematodes' neighboring root cells was also observed. In addition, at a later stage of infection, not only were few feeding sites observed but also the giant cells were underdeveloped, underlining an incompatible interaction. Furthermore, we generated a hybrid O. sativa population by crossing Zhonghua 11 with the susceptible O. sativa variety IR64 in order to describe the genetic background of this resistance. Our data suggested that the resistance to M. graminicola infection was qualitative rather than quantitative and, therefore, major resistance genes must be involved in this infection process. The full characterization of the defense mechanism and the preliminary study of the genetic inheritance of novel sources of resistance to Meloidogyne spp. in rice constitute a major step toward their use in crop breeding.

Association analysis of three diverse rice (Oryza sativa L.) germplasm collections for loci regulating grain quality traits

Science.gov (United States)

In rice (Oryza sativa L.), end-use/cooking quality is vital for producers and millions of consumers worldwide. Grain quality is a complex trait with interacting genetic and environmental factors. Deciphering the complex genetic architecture associated with grain quality, will provide vital informati...

Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view.

Science.gov (United States)

Huang, Pu; Molina, Jeanmaire; Flowers, Jonathan M; Rubinstein, Samara; Jackson, Scott A; Purugganan, Michael D; Schaal, Barbara A

2012-09-01

Asian wild rice (Oryza rufipogon) that ranges widely across the eastern and southern part of Asia is recognized as the direct ancestor of cultivated Asian rice (O. sativa). Studies of the geographic structure of O. rufipogon, based on chloroplast and low-copy nuclear markers, reveal a possible phylogeographic signal of subdivision in O. rufipogon. However, this signal of geographic differentiation is not consistently observed among different markers and studies, with often conflicting results. To more precisely characterize the phylogeography of O. rufipogon populations, a genome-wide survey of unlinked markers, intensively sampled from across the entire range of O. rufipogon is critical. In this study, we surveyed sequence variation at 42 genome-wide sequence tagged sites (STS) in 108 O. rufipogon accessions from throughout the native range of the species. Using Bayesian clustering, principal component analysis and amova, we conclude that there are two genetically distinct O. rufipogon groups, Ruf-I and Ruf-II. The two groups exhibit a clinal variation pattern generally from north-east to south-west. Different from many earlier studies, Ruf-I, which is found mainly in China and the Indochinese Peninsula, shows genetic similarity with one major cultivated rice variety, O. satvia indica, whereas Ruf-II, mainly from South Asia and the Indochinese Peninsula, is not found to be closely related to cultivated rice varieties. The other major cultivated rice variety, O. sativa japonica, is not found to be similar to either O. rufipogon groups. Our results support the hypothesis of a single origin of the domesticated O. sativa in China. The possible role of palaeoclimate, introgression and migration-drift balance in creating this clinal variation pattern is also discussed. © 2012 Blackwell Publishing Ltd.

Transfer of bacterial blight resistance from Oryza meyeriana to O.Sativa L.by asymmetric somatic hybridization

Institute of Scientific and Technical Information of China (English)

ZHU Yongsheng; CHEN Baotang; YU Shunwu; ZHANG Duanpin; ZHANG Xueqin; YAN Qiusheng

2004-01-01

Asymmetric somatic hybrid plants were produced between cultivated rice (Oryza sativa L.) and wild species [O. Meyeriana (Zoll. etMor, exSteud.)] with high resistance to rice bacterial blight. X-ray-irradiated protoplasts of the wild species were used as donor and chemically fused with iodoacetamide-inactivated protoplasts of rice cv. 02428to produce hybrids. Seventy-two plants were regenerated from 623 calli based on metabolic complementation. The morphological characters of the plants closely resembled that of the rice. Simple sequence repeats were employed to identify their hybridity. Cytological analysis of root-tips revealed that their chromosome number varied in the range of 27-38. The somatic hybrids were inoculated with strains of Xanthamonas oryzae pv. Oryzae at adult growth stage and demonstrated the resistance to bacterial blight introgression from the O. Meyeriana.

Enhanced production of fructosyltransferase in Aspergillus oryzae by genome shuffling.

Science.gov (United States)

Wang, Shenghai; Duan, Mengjie; Liu, Yalan; Fan, Sen; Lin, Xiaoshan; Zhang, Yi

2017-03-01

To breed Aspergillus oryzae strains with high fructosyltransferase (FTase) activity using intraspecific protoplast fusion via genome-shuffling. A candidate library was developed using UV/LiCl of the conidia of A. oryzae SBB201. By screening for enzyme activity and cell biomass, two mutants (UV-11 and UV-76) were chosen for protoplast fusion and subsequent genome shuffling. After three rounds of genome recombination, a fusion mutant RIII-7 was obtained. Its FTase activity was 180 U g -1 , approximately double that of the original strain, and RIII-7 was genetically stable. In fermentation culture, FTase activity of the genome-shuffled strain reached a maximum of 353 U g -1 using substrate-feeding method, and this value was approximately 3.4-times higher than that of the original strain A. oryzae SBB201. Intraspecific protoplast fusion of A. oryzae significantly enhanced FTase activity and generated a potentially useful strain for industrial production.

Tanggap Pertumbuhan dan Produksi Padi (Oryza sativa L.) Varietas Ciherang Terhadap Pemberian Pupuk Organik

OpenAIRE

Sari, Vira Irma

2011-01-01

VIRA IRMA SARI. Response of Growth and Production of Rice (Oryza sativa L.) Variety Ciherang to The Application of Organic Fertilizer. Scarcity of inorganic fertilizer and the negative effect caused by inorganic fertilizer continuing to make organic fertilizer as a solution to overcome these problems. The availability of organic fertilizers is expected that the farmers can get the optimal production and profit, because the organic fertilizer is cheaper and easy ...

X-ray diffraction analysis and in vitro characterization of the UAM2 protein from Oryza sativa

DEFF Research Database (Denmark)

Welner, Ditte Hededam; Tsai, Alex Yi-Lin; DeGiovanni, Andy M.

2017-01-01

protein from Oryza sativa (OsUAM2) were undertaken. Here, X-ray diffraction data are reported, as well as analysis of the oligomeric state in the crystal and in solution. OsUAM2 crystallizes readily but forms highly radiation-sensitive crystals with limited diffraction power, requiring careful low......, a requirement for a structural metal ion....

A genome-wide association study of a global rice panel reveals resistance in Oryza sativa to root-knot nematodes.

Science.gov (United States)

Dimkpa, Stanley O N; Lahari, Zobaida; Shrestha, Roshi; Douglas, Alex; Gheysen, Godelieve; Price, Adam H

2016-02-01

The root-knot nematode Meloidogyne graminicola is one of the most serious nematode pests worldwide and represents a major constraint on rice production. While variation in the susceptibility of Asian rice (Oryza sativa) exists, so far no strong and reliable resistance has been reported. Quantitative trait loci for partial resistance have been reported but no underlying genes have been tagged or cloned. Here, 332 accessions of the Rice Diversity Panel 1 were assessed for gall formation, revealing large variation across all subpopulations of rice and higher susceptibility in temperate japonica accessions. Accessions Khao Pahk Maw and LD 24 appeared to be resistant, which was confirmed in large pot experiments where no galls were observed. Detailed observations on these two accessions revealed no nematodes inside the roots 2 days after inoculation and very few females after 17 days (5 in Khao Pahk Maw and 100 in the susceptible controls). These two cultivars appear ideal donors for breeding root-knot nematode resistance. A genome-wide association study revealed 11 quantitative trait loci, two of which are close to epistatic loci detected in the Bala x Azucena population. The discussion highlights a small number of candidate genes worth exploring further, in particular many genes with lectin domains and genes on chromosome 11 with homology to the Hordeum Mla locus. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Tracking alien chromosome in sativa background by genomic in situ hybridization

International Nuclear Information System (INIS)

Abbasi, F.M.; Iqbal, M.; Salim, M.

2004-01-01

Genomic in situ hybridization (GISH) was used to look into the genomic constitution of monosomic alien -addition line derived from O. sativa x O. brachyantha. Biotin label genomic DNA from O. brachyantha was used as probe. The probe hybridized to the brachyantha chromosome. No detectable hybridization signal was observed on sativa chromosomes. This differential painting of chromosome enables us to unequivocally discriminate brachyantha chromosome from those of sativa. Results showed the usefulness of GISH in the identification of a single alien chromosome in the sativa background. (author)

Genotype × environment interactions of yield traits in backcross introgression lines derived from Oryza sativa cv. Swarna /Oryza nivara

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Divya Balakrishnan

2016-10-01

Full Text Available Advanced backcross introgression lines (BILs developed from crosses of Oryza sativa var. Swarna/O. nivara accessions were grown and evaluated for yield and related traits. Trials were conducted for consecutive three seasons in field conditions in a randomized complete block design with three replications. Data on yield traits under irrigated conditions were analyzed using the Additive Main Effect and Multiplicative Interaction (AMMI, Genotype and Genotype × Environment Interaction (GGE and modified rank-sum statistic (YSi for yield stability. BILs viz., G3 (14S and G6 (166S showed yield stability across the seasons along with high mean yield performance. G3 is early in flowering with high yield and has good grain quality and medium height, hence could be recommended for most of the irrigated locations. G6 is a late duration genotype, with strong culm strength, high grain number and panicle weight. G6 has higher yield and stability than Swarna but has Swarna grain type. Among the varieties tested DRRDhan 40 and recurrent parent Swarna showed stability for yield traits across the seasons. The component traits thousand grain weight, panicle weight, panicle length, grain number and plant height explained highest genotypic percentage over environment and interaction factors and can be prioritized to dissect stable QTLs/ genes. These lines were genotyped using microsatellite markers covering the entire rice genome and also using a set of markers linked to previously reported yield QTLs. It was observed that wild derived lines with more than 70% of recurrent parent genome were stable and showed enhanced yield levels compared to genotypes with higher donor genome introgressions.

Analysis of the temporal variation of radiation balance components in arid rice (Oryza sativa L.) culture

International Nuclear Information System (INIS)

Prates, J.E.; Coelho, D.T.; Steinmetz, S.

1988-01-01

The time variation of measured radiation balance components in a cultived rice area (Oryza sativa L.) under arid conditions in the Brazil central-west region was analysed. The relation between global solar radiation, radiation balance, reflected radiation and terrestrial effective radiation in three different stages of the culture development: vegetative stage; blooming and maturation, was determined. (M.C.K.) [pt

Fine mapping of S37, a locus responsible for pollen and embryo sac sterility in hybrids between Oryza sativa L. and O. glaberrima Steud.

Science.gov (United States)

Shen, Yumin; Zhao, Zhigang; Ma, Hongyang; Bian, Xiaofeng; Yu, Yang; Yu, Xiaowen; Chen, Haiyuan; Liu, Linglong; Zhang, Wenwei; Jiang, Ling; Zhou, Jiawu; Tao, Dayun; Wan, Jianmin

2015-11-01

Hybrid sterility locus S37 between Oryza glaberrima and Oryza sativa results in both pollen and embryo sac sterility. Interspecific crossing between African cultivated rice Oryza glaberrima and Oryza sativa cultivars is hindered by hybrid sterility. To dissect the mechanism of interspecific hybrid sterility, we developed a near-isogenic line (NIL)-S37 using Dianjingyou1 (DJY1) as the recipient parent and an African cultivated rice variety as the donor parent. Empty pollen and embryo sac sterility were observed in F1 hybrids between DJY1 and NIL-S37. Cytological analyses showed that pollen abortion in the F1 hybrids occurred at the late binucleate stage due to a failure of starch accumulation in pollen grains. In addition, partial abortion of the embryo sac in the F1 hybrid was observed during function megaspore developing into mature embryo sac. Molecular analysis revealed that the semi-sterility was largely caused by the abortion of male and female gametophytes carrying the S37 allele from DJY1. A population of 25,600 plants derived from the hybrid DJY1/NIL-S37 was developed to fine map S37. Based on the physical location of molecular markers, S37 locus was finally delimited to a region of 205 kb on the short arm of chromosome 1 in terms of reference sequences of cv. Nipponbare. Interestingly, an about 97-kb DNA segment was deleted in the NIL-S37 based on BAC clone information of O. glaberrima. Fifty-four open reading frames (ORF) were predicted in this 205-kb region of DJY1, whereas only 31 ORFs were in that of NIL-S37. These results are valuable for cloning of S37 gene and further breaking reproductive isolation between Oryza glaberrima and Oryza sativa cultivars, as well as marker-assisted transferring of the corresponding neutral allele in rice breeding programs.

Oxygen dynamics in submerged rice (Oryza sativa L.)

DEFF Research Database (Denmark)

Colmer, Timothy D.; Pedersen, Ole

2008-01-01

Complete submergence of plants prevents direct O2 and CO2 exchange with air. Underwater photosynthesis can result in marked diurnal changes in O2 supply to submerged plants. Dynamics in pO2 had not been measured directly for submerged rice (Oryza sativa), but in an earlier study, radial O2 loss...... from roots showed an initial peak following shoot illumination.  O2 dynamics in shoots and roots of submerged rice were monitored during light and dark periods, using O2 microelectrodes. Tissue sugar concentrations were also measured.  On illumination of shoots of submerged rice, pO2 increased rapidly...... of magnitude higher than in darkness, enhancing also pO2 in roots.The initial peak in pO2 following illumination of submerged rice was likely to result from high initial rates of net photosynthesis, fuelled by CO2 accumulated during the dark period. Nevertheless, since sugars decline with time in submerged...

Association analysis using USDA diverse rice (Oryza sativa L.) germplasm collections to identify loci influencing grain quality traits

Science.gov (United States)

he USDA rice (Oryza sativa L.) core subset (RCS) was assembled to represent the genetic diversity of the entire USDA-ARS National Small Grains Collection and consists of 1,794 accessions from 114 countries. The USDA rice mini-core (MC) is a subset of 217 accessions from the RCS and was selected to ...

In-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa.

Science.gov (United States)

Kaur, Amritpreet; Pati, Pratap Kumar; Pati, Aparna Maitra; Nagpal, Avinash Kaur

2017-01-01

Pathogenesis related (PR) proteins are low molecular weight family of proteins induced in plants under various biotic and abiotic stresses. They play an important role in plant-defense mechanism. PRs have wide range of functions, acting as hydrolases, peroxidases, chitinases, anti-fungal, protease inhibitors etc. In the present study, an attempt has been made to analyze promoter regions of PR1, PR2, PR5, PR9, PR10 and PR12 of Arabidopsis thaliana and Oryza sativa. Analysis of cis-element distribution revealed the functional multiplicity of PRs and provides insight into the gene regulation. CpG islands are observed only in rice PRs, which indicates that monocot genome contains more GC rich motifs than dicots. Tandem repeats were also observed in 5' UTR of PR genes. Thus, the present study provides an understanding of regulation of PR genes and their versatile roles in plants.

Efecto de la cobertura de rastrojos en la germinación del arroz (Oryza sativa L. y principales malezas asociadas

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Yemel M. Ortega

2005-01-01

Full Text Available Efecto de la cobertura de rastrojos en la germinacióndel arroz (Oryza sativaL. y principales malezas asociadas. Para determinar el grado de interferencia causado por distintas cantidades de rastrojos de arroz (Oryza sativaL. sobrela emergencia de arroz y malezas asociadas al cultivo, en el2003 se realizaron tres experimentos simultáneos en la hacienda el Pelón de la Bajura, Guanacaste, Costa Rica. Se aplicaron nueve tratamientos (0 a 9 t/ha de coberturas con rastrojosde la variedad de arroz CR 1113 para medir los efectos en laemergencia del arroz y malezas. Las malezas asociadas incluyen las más frecuentes en agroecosistemas arroceros inundados: Oryza sativa, Echinochloa colona, Cyperusspp., Fim-bristylisspp., Ludwigiaspp. y Heteranthera limosa. En losprimeros dos experimentos se determinaron relaciones inversas entre el grado de cobertura y la densidad de plántulas demalezas emergidas (R2>0,89, y entre el grado de cobertura yel porcentaje de germinación del arroz (R2=0,86, respectivamente. Usando coberturas con rastrojos de frijol (Phaseolusvulgaris en el tercer experimento, no se observó efecto supresor en la germinación del arroz, probablemente debido a supronta descomposición. Aunque la germinación del arroz nose afectó aún a las intensidades más altas de rastrojos evaluadas, conviene realizar pruebas similares a largo plazo para determinar posibles efectos debidos a la descomposición de residuos, alelopatía y acarreo de herbicidas después de variosciclos consecutivos del cultivo de arroz.

Macromolecular Traits in the African Rice Oryza glaberrima and in Glaberrima/Sativa Crosses, and Their Relevance to Processing.

Science.gov (United States)

Marengo, Mauro; Barbiroli, Alberto; Bonomi, Francesco; Casiraghi, Maria Cristina; Marti, Alessandra; Pagani, Maria Ambrogina; Manful, John; Graham-Acquaah, Seth; Ragg, Enzio; Fessas, Dimitrios; Hogenboom, Johannes A; Iametti, Stefania

2017-10-01

Molecular properties of proteins and starch were investigated in 2 accessions of Oryza glaberrima and Oryza sativa, and in one NERICA cross between the 2 species, to assess traits that could be relevant to transformation into specific foods. Protein nature and organization in O. glaberrima were different from those in O. sativa and in NERICA. Despite the similar cysteine content in all samples, thiol accessibility in O. glaberrima proteins was higher than in NERICA or in O. sativa. Inter-protein disulphide bonds were important for the formation of protein aggregates in O. glaberrima, whereas non-covalent protein-protein interactions were relevant in NERICA and O. sativa. DSC and NMR studies indicated only minor differences in the structure of starch in these species, as also made evident by their microstructural features. Nevertheless, starch gelatinization in O. glaberrima was very different from what was observed in O. sativa and NERICA. The content of soluble species in gelatinized starch from the various species in the presence/absence of treatments with specific enzymes indicated that release of small starch breakdown products was lowest in O. glaberrima, in particular from the amylopectin component. These findings may explain the low glycemic index of O. glaberrima, and provide a rationale for extending the use of O. glaberrima in the production of specific rice-based products, thus improving the economic value and the market appeal of African crops. The structural features of proteins and starch in O. glaberrima are very different from those in O. sativa and in the NERICA cross. These results appear useful as for extending the use of O. glaberrima cultivars in the design and production of specific rice-based products (for example, pasta), that might, in turn, improve the economic value and the market appeal of locally sourced raw materials, by introducing added-value products on the African market. © 2017 Institute of Food Technologists®.

Phytoextraction of cadmium by rice (Oryza sativa L.), soybean (Glycine max (L.) Merr.), and maize (Zea mays L.)

Energy Technology Data Exchange (ETDEWEB)

Murakami, M. [Department of Environmental Chemistry, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-0856 (Japan)]. E-mail: simple@affrc.go.jp; Ae, N. [Department of Environmental Chemistry, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-0856 (Japan)]. E-mail: aenoriha@kobe-u.ac.jp; Ishikawa, S. [Department of Environmental Chemistry, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-0856 (Japan)]. E-mail: isatoru@niaes.affrc.go.jp

2007-01-15

Selecting a phytoextraction plant with high Cd-accumulating ability based on the plant's compatibility with mechanized cultivation techniques may yield more immediately practical results than selection based on high tolerance to Cd. Rice (Oryza sativa L., cv. Nipponbare and Milyang 23), soybean (Glycine max [L.] Merr., cv. Enrei and Suzuyutaka), and maize (Zea mays L., cv. Gold Dent) were grown on one Andosol and two Fluvisols with low concentration of Cd contamination ranging from 0.83 to 4.29 mg Cd kg{sup -1}, during 60 days in pots (550 mL) placed in a greenhouse. Shoot Cd uptake was as follows: Gold Dent < Enrei and Nipponbare < Suzuyutaka and Milyang 23. Several soil Cd fractions after Milyang 23 harvesting decreased most. Milyang 23 accumulated 10-15% of the total soil Cd in its shoot. The Milyang 23 rice is thus promising for phytoextraction of Cd from paddy soils with low contamination level. - Milyang 23 rice (Oryza sativa L.) accumulated 10-15% of the total soil Cd in its shoot.

Phytoextraction of cadmium by rice (Oryza sativa L.), soybean (Glycine max (L.) Merr.), and maize (Zea mays L.)

International Nuclear Information System (INIS)

Murakami, M.; Ae, N.; Ishikawa, S.

2007-01-01

Selecting a phytoextraction plant with high Cd-accumulating ability based on the plant's compatibility with mechanized cultivation techniques may yield more immediately practical results than selection based on high tolerance to Cd. Rice (Oryza sativa L., cv. Nipponbare and Milyang 23), soybean (Glycine max [L.] Merr., cv. Enrei and Suzuyutaka), and maize (Zea mays L., cv. Gold Dent) were grown on one Andosol and two Fluvisols with low concentration of Cd contamination ranging from 0.83 to 4.29 mg Cd kg -1 , during 60 days in pots (550 mL) placed in a greenhouse. Shoot Cd uptake was as follows: Gold Dent < Enrei and Nipponbare < Suzuyutaka and Milyang 23. Several soil Cd fractions after Milyang 23 harvesting decreased most. Milyang 23 accumulated 10-15% of the total soil Cd in its shoot. The Milyang 23 rice is thus promising for phytoextraction of Cd from paddy soils with low contamination level. - Milyang 23 rice (Oryza sativa L.) accumulated 10-15% of the total soil Cd in its shoot

Complete mitochondrial genome of Eruca sativa Mill. (Garden rocket.

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Yankun Wang

Full Text Available Eruca sativa (Cruciferae family is an ancient crop of great economic and agronomic importance. Here, the complete mitochondrial genome of Eruca sativa was sequenced and annotated. The circular molecule is 247,696 bp long, with a G+C content of 45.07%, containing 33 protein-coding genes, three rRNA genes, and 18 tRNA genes. The Eruca sativa mitochondrial genome may be divided into six master circles and four subgenomic molecules via three pairwise large repeats, resulting in a more dynamic structure of the Eruca sativa mtDNA compared with other cruciferous mitotypes. Comparison with the Brassica napus MtDNA revealed that most of the genes with known function are conserved between these two mitotypes except for the ccmFN2 and rrn18 genes, and 27 point mutations were scattered in the 14 protein-coding genes. Evolutionary relationships analysis suggested that Eruca sativa is more closely related to the Brassica species and to Raphanus sativus than to Arabidopsis thaliana.

Differences in the Sensitivity to UVB Radiation of Two Cultivars of Rice (Oryza sativa L.)

OpenAIRE

Jun, Hidema; Hye-Sook, Kang; Tadashi, Kumagai; Institute of Genetic Ecology, Tohoku University; Institute of Genetic Ecology, Tohoku University; Institute of Genetic Ecology, Tohoku University

1996-01-01

The effects of UVB radiation on the growth of two cultivars of Japanese lowland rice (Oryza sativa L.), Sasanishiki and Norin 1, were examined in a phytotron. Supplementation of visible radiation with UVB radiation reduced plant length, tiller number, the fresh and dry weights of the aboveground parts of plants, and the amounts of total leaf nitrogen, chlorophyll, soluble protein and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in the eighth leaf, the youngest fully expanded leaf...

Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica genome: new insights from bioinformatics analysis

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Chepyshko Hanna

2012-07-01

Full Text Available Abstract Background GDSL esterases/lipases are a newly discovered subclass of lipolytic enzymes that are very important and attractive research subjects because of their multifunctional properties, such as broad substrate specificity and regiospecificity. Compared with the current knowledge regarding these enzymes in bacteria, our understanding of the plant GDSL enzymes is very limited, although the GDSL gene family in plant species include numerous members in many fully sequenced plant genomes. Only two genes from a large rice GDSL esterase/lipase gene family were previously characterised, and the majority of the members remain unknown. In the present study, we describe the rice OsGELP (Oryza sativa GDSL esterase/lipase protein gene family at the genomic and proteomic levels, and use this knowledge to provide insights into the multifunctionality of the rice OsGELP enzymes. Results In this study, an extensive bioinformatics analysis identified 114 genes in the rice OsGELP gene family. A complete overview of this family in rice is presented, including the chromosome locations, gene structures, phylogeny, and protein motifs. Among the OsGELPs and the plant GDSL esterase/lipase proteins of known functions, 41 motifs were found that represent the core secondary structure elements or appear specifically in different phylogenetic subclades. The specification and distribution of identified putative conserved clade-common and -specific peptide motifs, and their location on the predicted protein three dimensional structure may possibly signify their functional roles. Potentially important regions for substrate specificity are highlighted, in accordance with protein three-dimensional model and location of the phylogenetic specific conserved motifs. The differential expression of some representative genes were confirmed by quantitative real-time PCR. The phylogenetic analysis, together with protein motif architectures, and the expression profiling were

Fine mapping and introgressing qFIS1-2, a major QTL for kernel fissure resistance in rice (Oryza sativa L.)

Science.gov (United States)

Rice (Oryza sativa L.) kernel fissuring increases breakage during milling and decreases the value of processed rice. This study employed molecular gene tagging methods to fine-map a fissure resistance (FR) locus in ‘Cybonnet’, a semidwarf tropical japonica cultivar, as well as transfer this trait to...

The buffering capacity of stems: genetic architecture of nonstructural carbohydrates in cultivated Asian rice, Oryza sativa.

Science.gov (United States)

Wang, Diane R; Han, Rongkui; Wolfrum, Edward J; McCouch, Susan R

2017-07-01

Harnessing stem carbohydrate dynamics in grasses offers an opportunity to help meet future demands for plant-based food, fiber and fuel production, but requires a greater understanding of the genetic controls that govern the synthesis, interconversion and transport of such energy reserves. We map out a blueprint of the genetic architecture of rice (Oryza sativa) stem nonstructural carbohydrates (NSC) at two critical developmental time-points using a subpopulation-specific genome-wide association approach on two diverse germplasm panels followed by quantitative trait loci (QTL) mapping in a biparental population. Overall, 26 QTL are identified; three are detected in multiple panels and are associated with starch-at-maturity, sucrose-at-maturity and NSC-at-heading. They tag OsHXK6 (rice hexokinase), ISA2 (rice isoamylase) and a tandem array of sugar transporters. This study provides the foundation for more in-depth molecular investigation to validate candidate genes underlying rice stem NSC and informs future comparative studies in other agronomically vital grass species. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Vinegar rice (Oryza sativa L.) produced by a submerged fermentation process from alcoholic fermented rice

OpenAIRE

Spinosa,Wilma Aparecida; Santos Júnior,Vitório dos; Galvan,Diego; Fiorio,Jhonatan Luiz; Gomez,Raul Jorge Hernan Castro

2015-01-01

Considering the limited availability of technology for the production of rice vinegar and also due to the potential consumer product market, this study aimed to use alcoholic fermented rice (rice wine (Oryza sativa L.)) for vinegar production. An alcoholic solution with 6.28% (w/v) ethanol was oxidized by a submerged fermentation process to produce vinegar. The process of acetic acid fermentation occurred at 30 ± 0.3°C in a FRINGS® Acetator (Germany) for the production of vineg...

Genomic affinity between Oryza sativa and Oryza brachyantha as ...

African Journals Online (AJOL)

USER

2010-05-24

May 24, 2010 ... distantly related wild species, usually difficult to produce. These hybrids are ... assessment of genomic relationship between these two species by .... closely related and the sterility of the hybrid may be due to genetics and not ...

Molecular cloning, functional characterization and expression analysis of a novel monosaccharide transporter gene OsMST6 from rice (Oryza sativa L.)

NARCIS (Netherlands)

Wang, Y.; Xiao, Y.; Zhang, Y.; Chai, C.; Wei, G.; Wei, X.; Xu, H.; Wang, M.; Ouwerkerk, P.B.F.; Zhu, Z.

2008-01-01

Monosaccharides transporters play important roles in assimilate supply for sink tissue development. In this study, a new monosaccharide transporter gene OsMST6 was identified from rice (Oryza sativa L.). The predicted OsMST6 protein shows typical features of sugar transporters and shares 79.6%

QTL detection and elite alleles mining for stigma traits in Oryza sativa by association mapping

Directory of Open Access Journals (Sweden)

Xiaojing Dang

2016-08-01

Full Text Available Stigma traits are very important for hybrid seed production in Oryza sativa, which is a self-pollinated crop; however, the genetic mechanism controlling the traits is poorly understood. In this study, we investigated the phenotypic data of 227 accessions across two years and assessed their genotypic variation with 249 simple sequence repeat (SSR markers. By combining phenotypic and genotypic data, a genome-wide association (GWA map was generated. Large phenotypic variations in stigma length (STL, stigma brush-shaped part length (SBPL and stigma non-brush-shaped part length (SNBPL were found. Significant positive correlations were identified among stigma traits. In total, 2,072 alleles were detected among 227 accessions, with an average of 8.3 alleles per SSR locus. GWA mapping detected 6 quantitative trait loci (QTLs for the STL, 2 QTLs for the SBPL and 7 QTLs for the SNBPL. Eleven, 5, and 12 elite alleles were found for the STL, SBPL and SNBPL, respectively. Optimal cross designs were predicted for improving the target traits. The detected genetic variation in stigma traits and QTLs provides helpful information for cloning candidate STL genes and breeding rice cultivars with longer STLs in the future.

Efeito da irradiação gama nas características físico-químicas e sensoriais do arroz (Oryza sativa L. e no desenvolvimento de Sitophilus oryzae L. Effect of gamma irradiation on physico-chemical and sensorial characteristics of rice (Oryza sativa L. and on the development of Sitophilus oryzae L.

Directory of Open Access Journals (Sweden)

Cíntia Fernanda Pedroso Zanão

2009-03-01

Full Text Available A pesquisa teve como objetivo verificar a viabilidade da radiação gama como método de conservação do arroz polido (Oryza sativa L.. As amostras foram irradiadas com doses 0,5; 1,0; 3,0; e 5,0 kGy. Foram realizadas análises da quebra do grão no beneficiamento, da longevidade e reprodução do Sitophilus oryzae L., a composição centesimal, o conteúdo de amilose aparente e propriedades de pasta dos amidos, e análises para cor (instrumental e análise sensorial do arroz cru e cozido. Foi utilizado teste de Tukey (p The objective of this research was to verify the viability of the gamma radiation as polished rice (Oryza sativa L. conservation method. The samples were irradiated with doses of 0.5; 1.0; 3.0; and 5.0 kGy. Analysis of the grain breakage during the enriching process, longevity and reproduction of the Sitophilus oryzae L., centesimal composition, apparent amylose content, starch paste properties, color (instrumental, and the sensorial evaluation of raw and cooked rice were performed. It was verified that the irradiation did not change the percentage of grain breakage during the enrichment process, and it caused a negative effect on the development of insects. The irradiation did not change significantly the centesimal composition and the apparent amylase content. The Tukey test (p < 0.05 was conducted to verify the differences between the treatments. Gamma irradiation affected the pasting properties of the rice flour. Pasting parameters as temperature, peak, final viscosity, and setback values showed decreasing values with irradiation doses. Differences were detected in the sensorial aspect among the samples, and the sample irradiated with the dose of 1.0 kGy presented greater averages. Regarding the instrumental color parameter, it was observed the difference in the values b* indicating that the rice changed the white color for yellowish with the increase in the irradiation dose. The irradiation dose of 1.0 kGy proved the best

Polyploid genome of Camelina sativa revealed by isolation of fatty acid synthesis genes

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Shewmaker Christine K

2010-10-01

Full Text Available Abstract Background Camelina sativa, an oilseed crop in the Brassicaceae family, has inspired renewed interest due to its potential for biofuels applications. Little is understood of the nature of the C. sativa genome, however. A study was undertaken to characterize two genes in the fatty acid biosynthesis pathway, fatty acid desaturase (FAD 2 and fatty acid elongase (FAE 1, which revealed unexpected complexity in the C. sativa genome. Results In C. sativa, Southern analysis indicates the presence of three copies of both FAD2 and FAE1 as well as LFY, a known single copy gene in other species. All three copies of both CsFAD2 and CsFAE1 are expressed in developing seeds, and sequence alignments show that previously described conserved sites are present, suggesting that all three copies of both genes could be functional. The regions downstream of CsFAD2 and upstream of CsFAE1 demonstrate co-linearity with the Arabidopsis genome. In addition, three expressed haplotypes were observed for six predicted single-copy genes in 454 sequencing analysis and results from flow cytometry indicate that the DNA content of C. sativa is approximately three-fold that of diploid Camelina relatives. Phylogenetic analyses further support a history of duplication and indicate that C. sativa and C. microcarpa might share a parental genome. Conclusions There is compelling evidence for triplication of the C. sativa genome, including a larger chromosome number and three-fold larger measured genome size than other Camelina relatives, three isolated copies of FAD2, FAE1, and the KCS17-FAE1 intergenic region, and three expressed haplotypes observed for six predicted single-copy genes. Based on these results, we propose that C. sativa be considered an allohexaploid. The characterization of fatty acid synthesis pathway genes will allow for the future manipulation of oil composition of this emerging biofuel crop; however, targeted manipulations of oil composition and general

An improved Agrobacterium-mediated transformation of recalcitrant indica rice (Oryza sativa L.) cultivars.

Science.gov (United States)

Shri, Manju; Rai, Arti; Verma, Pankaj Kumar; Misra, Prashant; Dubey, Sonali; Kumar, Smita; Verma, Sikha; Gautam, Neelam; Tripathi, Rudra Deo; Trivedi, Prabodh Kumar; Chakrabarty, Debasis

2013-04-01

Agrobacterium-mediated transformation of indica rice varieties has been quite difficult as these are recalcitrant to in vitro responses. In the present study, we established a high-efficiency Agrobacterium tumefaciens-mediated transformation system of rice (Oryza sativa L. ssp. indica) cv. IR-64, Lalat, and IET-4786. Agrobacterium strain EHA-101 harboring binary vector pIG121-Hm, containing a gene encoding for β-glucuronidase (GUS) and hygromycin resistance, was used in the transformation experiments. Manipulation of different concentrations of acetosyringone, days of co-culture period, bacterial suspension of different optical densities (ODs), and the concentrations of L-cysteine in liquid followed by solid co-culture medium was done for establishing the protocol. Among the different co-culture periods, 5 days of co-culture with bacterial cells (OD600 nm = 0.5-0.8) promoted the highest frequency of transformation (83.04 %) in medium containing L-cysteine (400 mg l(-1)). Putative transformed plants were analyzed for the presence of a transgene through genomic PCR and GUS histochemical analyses. Our results also suggest that different cultural conditions and the addition of L-cysteine in the co-culture medium improve the Agrobacterium-mediated transformation frequencies from an average of 12.82 % to 33.33 % in different indica rice cultivars.

Genetic diversity in Oryza glumaepatula wild rice populations in Costa Rica and possible gene flow from O. sativa.

Science.gov (United States)

Fuchs, Eric J; Meneses Martínez, Allan; Calvo, Amanda; Muñoz, Melania; Arrieta-Espinoza, Griselda

2016-01-01

Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation. Specimens from all known O. glumaepatula populations in Costa Rica were analyzed with 444 AFLP markers to characterize genetic diversity and structure. We also compared genetic diversity estimates between O. glumaepatula specimens and O. sativa commercial rice. Our results showed that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. Despite the restricted distribution of this species in Costa Rica, populations are fairly large, reducing the effects of drift on genetic diversity. We found a dismissible but significant structure (θ = 0.02 ± 0.001) among populations. A Bayesian structure analysis suggested that some individuals share a significant proportion of their genomes with O. sativa. These results suggest that gene flow from cultivated O. sativa populations may have occurred in the recent past. These results expose an important biohazard: recurrent hybridization may reduce the genetic diversity of this wild rice species. Introgression may transfer commercial traits into O. glumaepatula, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica.

Formulasi Sediaan Lipstik Menggunakan Ekstrak Beras Ketan Hitam (Oryza sativa L var forma glutinosa) Sebagai Pewarna

OpenAIRE

Utami, Rini

2011-01-01

Black sticky rice (Oryza sativa L.) belongs to Poaceae family which is used by people as food stuffs such as tape and porridge. Black sticky rice is red/purple and its dye stuff is strong enough. In cosmetic, dye stuff is one of the causes of irritation and allergy on skin so that the researcher has made the formulation of lipstick component using natural dye stuff made of black sticky rice. The formulation of lipstick component consisted of some components such as cera alba, lanolin,...

Effects of gamma irradiation on long-storage seeds of Oryza sativa (cv. 2233) and their surface infecting fungal diversity

International Nuclear Information System (INIS)

Maity, J.P.; Kar, S.; Banerjee, S.; Chakraborty, A.; Santra, S.C.

2009-01-01

We have reported an effective 60 Co gamma irradiation method for the removal and long-time prevention of contaminating fungi of Oryza sativa cv-2233, without the losses of seed viabilities. The fungal growth and their population on gamma treated seeds was found to decrease significantly (p 50%) at 2 kGy, whereas total inhibition was noticed at 3 kGy after 1.5 month.

Oryza sativa Chloroplast Signal Recognition Particle 43 (OscpSRP43 Is Required for Chloroplast Development and Photosynthesis.

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Xiang-guang Lv

Full Text Available A rice chlorophyll-deficient mutant w67 was isolated from an ethyl methane sulfonate (EMS-induced IR64 (Oryza sativa L. ssp. indica mutant bank. The mutant exhibited a distinct yellow-green leaf phenotype in the whole plant growth duration with significantly reduced levels of chlorophyll and carotenoid, impaired chloroplast development and lowered capacity of photosynthesis compared with the wild-type IR64. Expression of a number of genes associated with chlorophyll metabolism, chloroplast biogenesis and photosynthesis was significantly altered in the mutant. Genetic analysis indicated that the yellow-green phenotype was controlled by a single recessive nuclear gene located on the short arm of chromosome 3. Using map-based strategy, the mutation was isolated and predicted to encode a chloroplast signal recognition particle 43 KD protein (cpSRP43 with 388 amino acid residuals. A single base substitution from A to T at position 160 resulted in a premature stop codon. OscpSRP43 was constitutively expressed in various organs with the highest level in the leaf. Functional complementation could rescue the mutant phenotype and subcellular localization showed that the cpSRP43:GFP fusion protein was targeted to the chloroplast. The data suggested that Oryza sativa cpSRP43 (OscpSRP43 was required for the normal development of chloroplasts and photosynthesis in rice.

Global Transcriptome Analysis of Combined Abiotic Stress Signaling Genes Unravels Key Players in Oryza sativa L.: An In silico Approach

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Pandiyan Muthuramalingam

2017-05-01

Full Text Available Combined abiotic stress (CAbS affects the field grown plants simultaneously. The multigenic and quantitative nature of uncontrollable abiotic stresses complicates the process of understanding the stress response by plants. Considering this, we analyzed the CAbS response of C3 model plant, Oryza sativa by meta-analysis. The datasets of commonly expressed genes by drought, salinity, submergence, metal, natural expression, biotic, and abiotic stresses were data mined through publically accessible transcriptomic abiotic stress (AbS responsive datasets. Of which 1,175, 12,821, and 42,877 genes were commonly expressed in meta differential, individual differential, and unchanged expressions respectively. Highly regulated 100 differentially expressed AbS genes were derived through integrative meta-analysis of expression data (INMEX. Of this 30 genes were identified from AbS gene families through expression atlas that were computationally analyzed for their physicochemical properties. All AbS genes were physically mapped against O. sativa genome. Comparative mapping of these genes demonstrated the orthologous relationship with related C4 panicoid genome. In silico expression analysis of these genes showed differential expression patterns in different developmental tissues. Protein–protein interaction of these genes, represented the complexity of AbS. Computational expression profiling of candidate genes in response to multiple stresses suggested the putative involvement of OS05G0350900, OS02G0612700, OS05G0104200, OS03G0596200, OS12G0225900, OS07G0152000, OS08G0119500, OS06G0594700, and Os01g0393100 in CAbS. These potential candidate genes need to be studied further to decipher their functional roles in AbS dynamics.

Control of gibberellin A(l) levels by 2, beta-hydroxylation during growth of dwarf Oryza sativa L. var. Tan-ginbozu

International Nuclear Information System (INIS)

Railton, I.D.

1978-01-01

Seedlings of dwarf rice (Oryza sativa L. var. Tan-ginbozu) exhibit a marked growth response to applied gibberellin A(1) and convert this compound into gibberellin A(8). In this study attempts were made to correlate the metabolism of 1,2[ 3 H] gibberellin A(1) and in particular the production of gibberellin A(8) with rice leaf sheath growth

Assessment of genomic relationship between Oryza sativa and ...

African Journals Online (AJOL)

STORAGESEVER

2010-03-01

Mar 1, 2010 ... For genomic in situ hybridization, genomic DNA from O. australiensis was used as probe for the mitotic and meiotic ... Wide hybridization is one of the plant breeding approaches ..... Disease and insect resistance in rice.

A Reference Genome for US Rice

Science.gov (United States)

The development of reference genomes for rice has served as means for understanding the allelic diversity and genetic structure of a cereal grain that feeds half of the world. It has long been understood that Oryza sativa diverged into two major sub-populations Indica and Japonica, over 400 K years ...

The biosynthesis, structure and gelatinization properties of starches from wild and cultivated African rice species (Oryza barthii and Oryza glaberrima).

Science.gov (United States)

Wang, Kai; Wambugu, Peterson W; Zhang, Bin; Wu, Alex Chi; Henry, Robert J; Gilbert, Robert G

2015-09-20

The molecular structure and gelatinization properties of starches from domesticated African rice (Oryza glaberrima) and its wild progenitor (Oryza barthii) are determined and comparison made with Asian domesticated rice (Oryza sativa), the commonest commercial rice. This suggests possible enzymatic processes contributing to the unique traits of the African varieties. These have similar starch structures, including smaller amylose molecules, but larger amounts of amylose chains across the whole amylose chain-length distribution, and higher amylose contents, than O. sativa. They also show a higher proportion of two- and three-lamellae spanning amylopectin branch chains (degree of polymerization 34-100) than O. sativa, which contributes to their higher gelatinization temperatures. Fitting amylopectin chain-length distribution with a biosynthesis-based mathematical model suggests that the reason for this difference might be because O. glaberrima and O. barthii have more active SSIIIa and/or less active SBEIIb enzymes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Genetic analysis of a hybrid sterility gene that causes both pollen and embryo sac sterility in hybrids between Oryza sativa L. and Oryza longistaminata.

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Chen, H; Zhao, Z; Liu, L; Kong, W; Lin, Y; You, S; Bai, W; Xiao, Y; Zheng, H; Jiang, L; Li, J; Zhou, J; Tao, D; Wan, J

2017-09-01

Oryza longistaminata originates from African wild rice and contains valuable traits conferring tolerance to biotic and abiotic stress. However, interspecific crosses between O. longistaminata and Oryza sativa cultivars are hindered by reproductive barriers. To dissect the mechanism of interspecific hybrid sterility, we developed a near-isogenic line (NIL) using indica variety RD23 as the recipient parent and O. longistaminata as the donor parent. Both pollen and embryo sac semi-sterility were observed in F 1 hybrids between RD23 and NIL. Cytological analysis demonstrated that pollen abortion in F 1 hybrids occurred at the early bi-nucleate stage due to a failure of the first mitosis in microspores. Partial embryo sacs in the F 1 hybrids were defective during the functional megaspore formation stage. Most notably, nearly half of the male or female gametes were aborted in heterozygotes S40 i S40 l , regardless of their genotypes. Thus, S40 was indicated as a one-locus sporophytic sterility gene controlling both male and female fertility in hybrids between RD23 and O. longistaminata. A population of 16 802 plants derived from the hybrid RD23/NIL-S40 was developed to fine-map S40. Finally, the S40 locus was delimited to an 80-kb region on the short arm of chromosome 1 in terms with reference sequences of cv. 93-11. Eight open reading frames (ORFs) were localized in this region. On the basis of gene expression and genomic sequence analysis, ORF5 and ORF8 were identified as candidate genes for the S40 locus. These results are helpful in cloning the S40 gene and marker-assisted transferring of the corresponding neutral allele in rice breeding programs.

Genetic variation for traits associated with domestication identified in a cultivated rice, Nipponbare (Oryza sativa ssp. japonica) x ancestral rice, O. nivara, mapping population

Science.gov (United States)

Oryza nivara, the progenitor of cultivated rice, O. sativa, has been the source of novel alleles for resistance to biotic and abiotic stresses, as well as for yield improvement. Many of these alleles were lost during the domestication process. To determine the molecular changes that occurred during ...

Proximate Nutritional Evaluation of Gamma Irradiated Black Rice (Oryza sativa L. cv. Cempo ireng)

Science.gov (United States)

Riyatun; Suharyana; Ramelan, A. H.; Sutarno; Saputra, O. A.; Suryanti, V.

2018-03-01

Black rice is a type of pigmented rice with black bran covering the endosperm of the rice kernel. The main objective of the present study was to provide details information on the proximate composition of third generation of gamma irradiated black rice (Oryza sativa L. cv. Cempo ireng). In respect to the control, generally speaking, there were no significant changes of moisture, lipids, proteins, carbohydrates and fibers contents have been observed for the both gamma irradiated black rice. However, the 200-BR has slightly better nutritional value than that of 300-BR and the control. The mineral contents of 200-BR increased significantly of about 35% than the non-gamma irradiated black rice.

Transposable elements as stress adaptive capacitors induce genomic instability in fungal pathogen Magnaporthe oryzae.

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Sonia Chadha

Full Text Available A fundamental problem in fungal pathogenesis is to elucidate the evolutionary forces responsible for genomic rearrangements leading to races with fitter genotypes. Understanding the adaptive evolutionary mechanisms requires identification of genomic components and environmental factors reshaping the genome of fungal pathogens to adapt. Herein, Magnaporthe oryzae, a model fungal plant pathogen is used to demonstrate the impact of environmental cues on transposable elements (TE based genome dynamics. For heat shock and copper stress exposed samples, eight TEs belonging to class I and II family were employed to obtain DNA profiles. Stress induced mutant bands showed a positive correlation with dose/duration of stress and provided evidences of TEs role in stress adaptiveness. Further, we demonstrate that genome dynamics differ for the type/family of TEs upon stress exposition and previous reports of stress induced MAGGY transposition has underestimated the role of TEs in M. oryzae. Here, we identified Pyret, MAGGY, Pot3, MINE, Mg-SINE, Grasshopper and MGLR3 as contributors of high genomic instability in M. oryzae in respective order. Sequencing of mutated bands led to the identification of LTR-retrotransposon sequences within regulatory regions of psuedogenes. DNA transposon Pot3 was identified in the coding regions of chromatin remodelling protein containing tyrosinase copper-binding and PWWP domains. LTR-retrotransposons Pyret and MAGGY are identified as key components responsible for the high genomic instability and perhaps these TEs are utilized by M. oryzae for its acclimatization to adverse environmental conditions. Our results demonstrate how common field stresses change genome dynamics of pathogen and provide perspective to explore the role of TEs in genome adaptability, signalling network and its impact on the virulence of fungal pathogens.

Identification of a Rice stripe necrosis virus resistance locus and yield component QTLs using Oryza sativa × O. glaberrima introgression lines

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Prado Gustavo

2010-01-01

Full Text Available Abstract Background Developing new population types based on interspecific introgressions has been suggested by several authors to facilitate the discovery of novel allelic sources for traits of agronomic importance. Chromosome segment substitution lines from interspecific crosses represent a powerful and useful genetic resource for QTL detection and breeding programs. Results We built a set of 64 chromosome segment substitution lines carrying contiguous chromosomal segments of African rice Oryza glaberrima MG12 (acc. IRGC103544 in the genetic background of Oryza sativa ssp. tropical japonica (cv. Caiapó. Well-distributed simple-sequence repeats markers were used to characterize the introgression events. Average size of the substituted chromosomal segments in the substitution lines was about 10 cM and covered the whole donor genome, except for small regions on chromosome 2 and 4. Proportions of recurrent and donor genome in the substitution lines were 87.59% and 7.64%, respectively. The remaining 4.78% corresponded to heterozygotes and missing data. Strong segregation distortion was found on chromosomes 3 and 6, indicating the presence of interspecific sterility genes. To illustrate the advantages and the power of quantitative trait loci (QTL detection using substitution lines, a QTL detection was performed for scored traits. Transgressive segregation was observed for several traits measured in the population. Fourteen QTLs for plant height, tiller number per plant, panicle length, sterility percentage, 1000-grain weight and grain yield were located on chromosomes 1, 3, 4, 6 and 9. Furthermore, a highly significant QTL controlling resistance to the Rice stripe necrosis virus was located between SSR markers RM202-RM26406 (44.5-44.8 cM on chromosome 11. Conclusions Development and phenotyping of CSSL libraries with entire genome coverage represents a useful strategy for QTL discovery. Mapping of the RSNV locus represents the first identification

Bekatul (Oryza sativa L. Menghambat Peningkatan Kadar Kolesterol Darah

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Astri Kania

2014-02-01

Full Text Available Abstrak Penyakit kardiovaskuler merupakan penyebab utama kematian dan kecacatan di seluruh dunia, termasuk Indonesia. Penyakit kardiovaskuler disebabkan oleh pembentukan aterosklerosis pada pembuluh darah. Konsumsi larutan tepung bekatul (Oryza sativa L. dapat digunakan sebagai salah satu upaya untuk mencegah terjadinya aterosklerosis dengan cara menghambat peningkatan kadar kolesterol darah. Penelitian ini untuk menilai efek larutan tepung bejatul terhadap penghambatan peningkatan kadar kolesterol darah. Penelitian eksperimental laboratorik dengan rancangan acak lengkap telah dilakukan pada 20 ekor tikus putih jantan galur Wistar yang dibagi menjadi lima kelompok. Kelompok I adalah kontrol negatif yang diberikan diet tinggi lemak dan propiltiurasil (PTU 0,01%, kelompok II merupakan kontrol positif yang hanya diberi pelet. Kelompok III, IV, dan V adalah kelompok perlakuan yang diberikan sediaan uji 0,27 gram/200 gram BB, 0,54 gram/200 gram BB, dan 1,08 gram/200 gram BB, DTL dan PTU 0,01% secara bersamaan. Pengukuran kadar kolesterol darah dilakukan sebelum diberikan perlakuan (hari ke-7 dan setelah diberikan perlakuan (hari ke-21 dengan menggunakan metode kolorimetrik enzimatik. Hasil penelitian ini menunjukkan bahwa larutan tepung bekatul memiliki efek penghambatan terhadap peningkatan kadar kolesterol darah dengan dosis 0,54 gram/200 gram BB. Efek penghambatan tersebut diakibatkan oleh mekanisme interaksi  dari orizanol, fitosterol, dan omega-3 yang terdapat dalam larutan tepung bekatul. Kata kunci: Bekatul, efek penghambatan, kolesterol darah   Rice Bran (Oryza sativa L. Inhibit the Increase of Blood Cholesterol Level Abstract Cardiovascular disease is the major cause of mortality and morbidity in the world, including Indonesia. This disease caused by atherosclerosis formation in blood vessel. Consumption of rice bran is one alternative to prevent atherosclerosis by inhibiting the increase of blood cholesterol level. The Aim of study was to

Extraction of anthocyanins and polyphenols from black rice (Oryza sativa L.) by modeling and assessing their reversibility and stability.

Science.gov (United States)

Pedro, Alessandra Cristina; Granato, Daniel; Rosso, Neiva Deliberali

2016-01-15

This study was aimed the extraction of total flavonoids, anthocyanins and phenolics, as well as the antioxidant activity of black rice (Oryza sativa) and to study the stability in relation to pH, light and copigmentation. Variations in temperature (10-50°C), time (20-80min), and solid-solvent ratio (1:15-1:45) were studied using a Box-Behnken design. The regression models were significant (Pblack rice was cyanidin-3-glucoside. Copyright © 2015 Elsevier Ltd. All rights reserved.

Isolation of stress responsive Psb A gene from rice (Oryza sativa l.) using differential display.

Science.gov (United States)

Tyagi, Aruna; Chandra, Arti

2006-08-01

Differential display (DD) experiments were performed on drought-tolerant rice (Oryza sativa L.) genotype N22 to identify both upregulated and downregulated partial cDNAs with respect to moisture stress. DNA polymorphism was detected between drought-stressed and control leaf tissues on the DD gels. A partial cDNA showing differential expression, with respect to moisture stress was isolated from the gel. Northern blotting analysis was performed using this cDNA as a probe and it was observed that mRNA corresponding to this transcript was accumulated to high level in rice leaves under water deficit stress. At the DNA sequence level, the partial cDNA showed homology with psb A gene encoding for Dl protein.

Genome information of Methylobacterium oryzae, a plant-probiotic methylotroph in the phyllosphere.

Science.gov (United States)

Kwak, Min-Jung; Jeong, Haeyoung; Madhaiyan, Munusamy; Lee, Yi; Sa, Tong-Min; Oh, Tae Kwang; Kim, Jihyun F

2014-01-01

Pink-pigmented facultative methylotrophs in the Rhizobiales are widespread in the environment, and many Methylobacterium species associated with plants produce plant growth-promoting substances. To gain insights into the life style at the phyllosphere and the genetic bases of plant growth promotion, we determined and analyzed the complete genome sequence of Methylobacterium oryzae CBMB20T, a strain isolated from rice stem. The genome consists of a 6.29-Mb chromosome and four plasmids, designated as pMOC1 to pMOC4. Among the 6,274 coding sequences in the chromosome, the bacterium has, besides most of the genes for the central metabolism, all of the essential genes for the assimilation and dissimilation of methanol that are either located in methylotrophy islands or dispersed. M. oryzae is equipped with several kinds of genes for adaptation to plant surfaces such as defense against UV radiation, oxidative stress, desiccation, or nutrient deficiency, as well as high proportion of genes related to motility and signaling. Moreover, it has an array of genes involved in metabolic pathways that may contribute to promotion of plant growth; they include auxin biosynthesis, cytokine biosynthesis, vitamin B12 biosynthesis, urea metabolism, biosorption of heavy metals or decrease of metal toxicity, pyrroloquinoline quinone biosynthesis, 1-aminocyclopropane-1-carboxylate deamination, phosphate solubilization, and thiosulfate oxidation. Through the genome analysis of M. oryzae, we provide information on the full gene complement of M. oryzae that resides in the aerial parts of plants and enhances plant growth. The plant-associated lifestyle of M. oryzae pertaining to methylotrophy and plant growth promotion, and its potential as a candidate for a bioinoculant targeted to the phyllosphere and focused on phytostimulation are illuminated.

Genetic analysis and gene fine mapping of aroma in rice (Oryza sativa L. Cyperales, Poaceae

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Shu Xia Sun

2008-01-01

Full Text Available We investigated inheritance and carried out gene fine mapping of aroma in crosses between the aromatic elite hybrid rice Oryza sativa indica variety Chuanxiang-29B (Ch-29B and the non-aromatic rice O. sativa indica variety R2 and O. sativa japonica Lemont (Le. The F1 grains and leaves were non-aromatic while the F2 non-aroma to aroma segregation pattern was 3:1. The F3 segregation ratio was consistent with the expected 1:2:1 for a single recessive aroma gene in Ch-29B. Linkage analysis between simple sequence repeat (SSR markers and the aroma locus for the aromatic F2 plants mapped the Ch-29B aroma gene to a chromosome 8 region flanked by SSR markers RM23120 at 0.52 cM and RM3459 at 1.23 cM, a replicate F2 population confirming these results. Three bacterial artificial chromosome (BAC clones cover chromosome 8 markers RM23120 and RM3459. Our molecular mapping data from the two populations indicated that the aroma locus occurs in a 142.85 kb interval on BAC clones AP005301 or AP005537, implying that it might be the same gene reported by Bradbury et al (2005a; Plant Biotec J. 3:363-370. The flanking markers Aro7, RM23120 and RM3459 identified by us could greatly accelerate the efficiency and precision of aromatic rice breeding programs.

Comparative physical mapping of rice BAC clones linked to resistance genes Glh,Bph-3 and xa-5 in Oryza sativa L.and O.granulata Nees et Am.ex Watt.

Institute of Scientific and Technical Information of China (English)

XIONG Zhiyong; TAN Guangxuan; YOU Aiqing; HE Guangyuan; SHE Chaowen; LI Lijia; SONG Yunchun

2004-01-01

Oryza granulata Nees et Arn. ex Watt. is one of the three wild relatives of rice, which are the most valuable for study and utilization in China. In this study, the homology and physical locations of three rice resistance genes, Glh,Bph-3 and xa-5 are comparatively analyzed between O. sativa and O. granulata by Southern blotting and fluorescence in situ hybridization (FISH). The results of Southern blotting indicate that there exist homologous sequences of the tested RFLP markers in O. granulata. By using three bacterial artificial chromosome (BAC) clones scanned by the tested RFLP as probes, FISH signals are detected on both mitotic and pachytene chromosomes in O. sativa and O. granulata.Dual-color FISH demonstrates that two of the three BAC clones (14E16 and 38J9) are located on the short arm of the same chromosome pair in O. granulata. Additionally, colinearity is shown for the two clones between O. sativa and O.granulata. Another BAC clone 44B4 is located on the end of the short arm of other chromosome pair in these two species.Although the phylogenetic relationship between O. sativa and O. granulata is the most distinct in Oryza and these two species have evidently different biological features and ecological habits, the relative lengths and arm ratios of the detected chromosomes and the relative positions of the tested clone signals on chromosomes in O. granulata are quite similar to those in O. sativa.

The Perennial Ryegrass GenomeZipper – Targeted Use of Genome Resources for Comparative Grass Genomics

DEFF Research Database (Denmark)

Pfeiffer, Matthias; Martis, Mihaela; Asp, Torben

2013-01-01

(Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold......Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass...... to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous...

Discovery of global genomic re-organization based on comparison of two newly sequenced rice mitochondrial genomes with cytoplasmic male sterility-related genes

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Yamada Mari

2010-03-01

Full Text Available Abstract Background Plant mitochondrial genomes are known for their complexity, and there is abundant evidence demonstrating that this organelle is important for plant sexual reproduction. Cytoplasmic male sterility (CMS is a phenomenon caused by incompatibility between the nucleus and mitochondria that has been discovered in various plant species. As the exact sequence of steps leading to CMS has not yet been revealed, efforts should be made to elucidate the factors underlying the mechanism of this important trait for crop breeding. Results Two CMS mitochondrial genomes, LD-CMS, derived from Oryza sativa L. ssp. indica (434,735 bp, and CW-CMS, derived from Oryza rufipogon Griff. (559,045 bp, were newly sequenced in this study. Compared to the previously sequenced Nipponbare (Oryza sativa L. ssp. japonica mitochondrial genome, the presence of 54 out of 56 protein-encoding genes (including pseudo-genes, 22 tRNA genes (including pseudo-tRNAs, and three rRNA genes was conserved. Two other genes were not present in the CW-CMS mitochondrial genome, and one of them was present as part of the newly identified chimeric ORF, CW-orf307. At least 12 genomic recombination events were predicted between the LD-CMS mitochondrial genome and Nipponbare, and 15 between the CW-CMS genome and Nipponbare, and novel genetic structures were formed by these genomic rearrangements in the two CMS lines. At least one of the genomic rearrangements was completely unique to each CMS line and not present in 69 rice cultivars or 9 accessions of O. rufipogon. Conclusion Our results demonstrate novel mitochondrial genomic rearrangements that are unique in CMS cytoplasm, and one of the genes that is unique in the CW mitochondrial genome, CW-orf307, appeared to be the candidate most likely responsible for the CW-CMS event. Genomic rearrangements were dynamic in the CMS lines in comparison with those of rice cultivars, suggesting that 'death' and possible 'birth' processes of the

All roads lead to weediness: patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian Oryza

Science.gov (United States)

Weedy rice (Oryza spp.), a weedy relative of cultivated rice (O. sativa), invades and persists in cultivated rice fields worldwide. Many weedy rice populations have evolved similar adaptive traits, considered part of the “agricultural weed syndrome,” making this an ideal model to study the genetic b...

Tolerance of different rice genotypes (oryza sativa l.) against the infestation of rice stem borers under natural field conditions

International Nuclear Information System (INIS)

Sarwar, M.; Ahmad, N.; Nasrullah; Tofique, M.

2010-01-01

The present studies report the genotypic responses of 61 rice (Oryza sativa L.) genotypes (35 aromatic and 26 non aromatic) against the infestation of rice stem borers under natural field conditions. The data obtained on these genotypes on larval infestation in combination with yield were the criteria to assess the resistance depicted by them. The studies showed that among aromatic genotypes, 'Khushboo-95' gave the best yield of grain and harboured the least pest infestation (2.81% dead hearts and 1.85% white heads); on the other hand variety 'Sonahri Sugdasi (P)' harboured the highest borers attack (10.37% and 19.30%) and yielded the lowest grain yield. Regarding non-aromatic genotypes, IR8-2.5-11 received least infestation (1.32% and 0.26% dead hearts and white heads, respectively) generating highest yield showing its tolerance to borer's attack, in contrast, genotype IR6-252 harboured the highest infestation (5.65%, 4.28%) and yielded minimum grain indicating its susceptibility. These results demonstrate the expression of resistance gene in the genome of tolerant rice genotypes that can provide season-long protection from the natural infestation of insect pests. (author)

Genome information of Methylobacterium oryzae, a plant-probiotic methylotroph in the phyllosphere.

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Min-Jung Kwak

Full Text Available Pink-pigmented facultative methylotrophs in the Rhizobiales are widespread in the environment, and many Methylobacterium species associated with plants produce plant growth-promoting substances. To gain insights into the life style at the phyllosphere and the genetic bases of plant growth promotion, we determined and analyzed the complete genome sequence of Methylobacterium oryzae CBMB20T, a strain isolated from rice stem. The genome consists of a 6.29-Mb chromosome and four plasmids, designated as pMOC1 to pMOC4. Among the 6,274 coding sequences in the chromosome, the bacterium has, besides most of the genes for the central metabolism, all of the essential genes for the assimilation and dissimilation of methanol that are either located in methylotrophy islands or dispersed. M. oryzae is equipped with several kinds of genes for adaptation to plant surfaces such as defense against UV radiation, oxidative stress, desiccation, or nutrient deficiency, as well as high proportion of genes related to motility and signaling. Moreover, it has an array of genes involved in metabolic pathways that may contribute to promotion of plant growth; they include auxin biosynthesis, cytokine biosynthesis, vitamin B12 biosynthesis, urea metabolism, biosorption of heavy metals or decrease of metal toxicity, pyrroloquinoline quinone biosynthesis, 1-aminocyclopropane-1-carboxylate deamination, phosphate solubilization, and thiosulfate oxidation. Through the genome analysis of M. oryzae, we provide information on the full gene complement of M. oryzae that resides in the aerial parts of plants and enhances plant growth. The plant-associated lifestyle of M. oryzae pertaining to methylotrophy and plant growth promotion, and its potential as a candidate for a bioinoculant targeted to the phyllosphere and focused on phytostimulation are illuminated.

Overcoming the species hybridization barrier by ploidy manipulation in the genus Oryza.

Science.gov (United States)

Tonosaki, Kaoru; Sekine, Daisuke; Ohnishi, Takayuki; Ono, Akemi; Furuumi, Hiroyasu; Kurata, Nori; Kinoshita, Tetsu

2018-02-01

In most eudicot and monocot species, interspecific and interploidy crosses generally display abnormalities in the endosperm that are the major cause of a post-zygotic hybridization barrier. In some eudicot species, however, this type of hybridization barrier can be overcome by the manipulation of ploidy levels of one parental species, suggesting that the molecular mechanisms underlying the species hybridization barrier can be circumvented by genome dosage. We previously demonstrated that endosperm barriers in interspecific and interploidy crosses in the genus Oryza involve overlapping but different mechanisms. This result contrasts with those in the genus Arabidopsis, which shows similar outcomes in both interploidy and interspecific crosses. Therefore, we postulated that an exploration of pathways for overcoming the species hybridization barrier in Oryza endosperm, by manipulating the ploidy levels in one parental species, might provide novel insights into molecular mechanisms. We showed that fertile hybrid seeds could be produced by an interspecific cross of female tetraploid Oryza sativa and male diploid Oryza longistaminata. Although the rate of nuclear divisions did not return to normal levels in the hybrid endosperm, the timing of cellularization, nucellus degeneration and the accumulation of storage products were close to normal levels. In addition, the expression patterns of the imprinted gene MADS87 and YUCCA11 were changed when the species barrier was overcome. These results suggest that the regulatory machinery for developmental transitions and imprinted gene expression are likely to play a central role in overcoming species hybridization barriers by genome dosage in the genus Oryza. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Assessing hybrid sterility in Oryza glaberrima x O. sativa hybrid progenies by PCR marker analysis and crossing with wide compatibility varieties.

Science.gov (United States)

Heuer, Sigrid; Miézan, Kouamé M

2003-09-01

Interspecific crossing of the African indigenous rice Oryza glaberrima with Oryza sativa cultivars is hindered by crossing barriers causing 100% spikelet sterility in F(1) hybrids. Since hybrids are partially female fertile, fertility can be restored by back crossing (BC) to a recurrent male parent. Distinct genetic models on spikelet sterility have been developed predicting, e.g., the existence of a gamete eliminator and/or a pollen killer. Linkage of sterility to the waxy starch synthase gene and the chromogen gene C, both located on chromosome 6, have been demonstrated. We selected a segregating BC(2)F(3) population of semi-sterile O. glaberrima x O. sativa indica hybrid progenies for analyses with PCR markers located at the respective chromosome-6 region. These analyses revealed that semi-sterile plants were heterozygous for a marker (OSR25) located in the waxy promoter, whereas fertile progenies were homozygous for the O. glaberrima allele. Adjacent markers showed no linkage to spikelet sterility. Semi-sterility of hybrid progenies was maintained at least until the F(4) progeny generation, suggesting the existence of a pollen killer in this plant material. Monitoring of reproductive plant development showed that spikelet sterility was at least partially due to an arrest of pollen development at the microspore stage. In order to address the question whether genes responsible for F(1) sterility in intraspecific hybrids ( O. sativa indica x japonica) also cause spikelet sterility in interspecific hybrids, crossings with wide compatibility varieties (WCV) were performed. WCV accessions possess "neutral" S-loci ( S(n)) improving fertility in intraspecific hybrids. This experiment showed that the tested S(n)-loci had no fertility restoring effect in F(1) interspecific hybrids. Pollen development was completely arrested at the microspore stage and grains were never obtained after selfing. This suggests that distinct or additional S-loci are responsible for sterility

The Complete Chloroplast Genome of Wild Rice (Oryza minuta) and Its Comparison to Related Species.

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Asaf, Sajjad; Waqas, Muhammad; Khan, Abdul L; Khan, Muhammad A; Kang, Sang-Mo; Imran, Qari M; Shahzad, Raheem; Bilal, Saqib; Yun, Byung-Wook; Lee, In-Jung

2017-01-01

Oryza minuta , a tetraploid wild relative of cultivated rice (family Poaceae), possesses a BBCC genome and contains genes that confer resistance to bacterial blight (BB) and white-backed (WBPH) and brown (BPH) plant hoppers. Based on the importance of this wild species, this study aimed to understand the phylogenetic relationships of O. minuta with other Oryza species through an in-depth analysis of the composition and diversity of the chloroplast (cp) genome. The analysis revealed a cp genome size of 135,094 bp with a typical quadripartite structure and consisting of a pair of inverted repeats separated by small and large single copies, 139 representative genes, and 419 randomly distributed microsatellites. The genomic organization, gene order, GC content and codon usage are similar to those of typical angiosperm cp genomes. Approximately 30 forward, 28 tandem and 20 palindromic repeats were detected in the O . minuta cp genome. Comparison of the complete O. minuta cp genome with another eleven Oryza species showed a high degree of sequence similarity and relatively high divergence of intergenic spacers. Phylogenetic analyses were conducted based on the complete genome sequence, 65 shared genes and matK gene showed same topologies and O. minuta forms a single clade with parental O. punctata . Thus, the complete O . minuta cp genome provides interesting insights and valuable information that can be used to identify related species and reconstruct its phylogeny.

Using rice genome-wide association studies to identify DNA markers for marker-assisted selection

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Rice association mapping panels are collections of rice (Oryza sativa L.) accessions developed for genome-wide association (GWA) studies. One of these panels, the Rice Diversity Panel 1 (RDP1) was phenotyped by various research groups for several traits of interest, and more recently, genotyped with...

Development of a genome editing technique using the CRISPR/Cas9 system in the industrial filamentous fungus Aspergillus oryzae.

Science.gov (United States)

Katayama, Takuya; Tanaka, Yuki; Okabe, Tomoya; Nakamura, Hidetoshi; Fujii, Wataru; Kitamoto, Katsuhiko; Maruyama, Jun-Ichi

2016-04-01

To develop a genome editing method using the CRISPR/Cas9 system in Aspergillus oryzae, the industrial filamentous fungus used in Japanese traditional fermentation and for the production of enzymes and heterologous proteins. To develop the CRISPR/Cas9 system as a genome editing technique for A. oryzae, we constructed plasmids expressing the gene encoding Cas9 nuclease and single guide RNAs for the mutagenesis of target genes. We introduced these into an A. oryzae strain and obtained transformants containing mutations within each target gene that exhibited expected phenotypes. The mutational rates ranged from 10 to 20 %, and 1 bp deletions or insertions were the most commonly induced mutations. We developed a functional and versatile genome editing method using the CRISPR/Cas9 system in A. oryzae. This technique will contribute to the use of efficient targeted mutagenesis in many A. oryzae industrial strains.

Effect of atmospheric plasma treatment on seed germination of rice (Oryza sativa L.)

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Penado, Keith Nealson M.; Mahinay, Christian Lorenz S.; Culaba, Ivan B.

2018-01-01

Multiple methods of improving plant development have been utilized over the past decades. Despite these improvements, there still exists a need for better planting methods due to the increasing population of a global community. Studies have reported that plasma treatment affects the growth and germination of a variety of plant species, including a multitude of grains which often takes the bulk in the diet of the average human being. This study explores the effect of atmospheric air plasma jet treatment on the seed germination of rice (Oryza sativa L.). The seeds were treated using an atmospheric air plasma jet for 1, 2, and 3 s. The effect of plasma exposure shows a reduction of trichomes on the surface of the seed. This caused a possible increase in wettability which significantly affected the seed germ length but did not affect the seed germination count after the germination period of 72 h.

Variations in characters of diploid-like plants derived from gamma-irradiated tetraploids in rice (Oryza sativa L.)

International Nuclear Information System (INIS)

Yamamoto, K.; Fukuoka, H.; Kageyama, Y.; Takeda, G.

1990-01-01

Full text: Populations of artificial autotetraploids of rice (Oryza sativa L. cvs. 'Nipponbare' and 'Fukunishiki') were repeatedly irradiated with gamma-rays through several generations. Plants which did not differ in appearance from the original diploid plants occurred occasionally in the populations. Nine diploid-like plants were obtained so far, and their generations were advanced without irradiation in order to examine the mode of segregation of characters in their progeny. The results indicate that diploid-like plants with multiple mutant characters could be obtained and that dominant characters, i.e. awned spikelet and coloured apiculus, were included in the mutant characters. The diploid-like plants had 2n=24 chromosomes. (author)

Survey of protein–DNA interactions in Aspergillus oryzae on a genomic scale

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Wang, Chao; Lv, Yangyong; Wang, Bin; Yin, Chao; Lin, Ying; Pan, Li

2015-01-01

The genome-scale delineation of in vivo protein–DNA interactions is key to understanding genome function. Only ∼5% of transcription factors (TFs) in the Aspergillus genus have been identified using traditional methods. Although the Aspergillus oryzae genome contains >600 TFs, knowledge of the in vivo genome-wide TF-binding sites (TFBSs) in aspergilli remains limited because of the lack of high-quality antibodies. We investigated the landscape of in vivo protein–DNA interactions across the A. oryzae genome through coupling the DNase I digestion of intact nuclei with massively parallel sequencing and the analysis of cleavage patterns in protein–DNA interactions at single-nucleotide resolution. The resulting map identified overrepresented de novo TF-binding motifs from genomic footprints, and provided the detailed chromatin remodeling patterns and the distribution of digital footprints near transcription start sites. The TFBSs of 19 known Aspergillus TFs were also identified based on DNase I digestion data surrounding potential binding sites in conjunction with TF binding specificity information. We observed that the cleavage patterns of TFBSs were dependent on the orientation of TF motifs and independent of strand orientation, consistent with the DNA shape features of binding motifs with flanking sequences. PMID:25883143

Comparison of the genomes and transcriptomes associated with the different protease secretions of Aspergillus oryzae 100-8 and 3.042.

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Zhao, Guozhong; Yao, Yunping; Hou, Lihua; Wang, Chunling; Cao, Xiaohong

2014-10-01

Aspergillus oryzae is used to produce traditional fermented foods and beverages. A. oryzae 3.042 produces a neutral protease and an alkaline protease but rarely an acid protease, which is unfavourable to soy-sauce fermentation. A. oryzae 100-8 was obtained by N(+) ion implantation mutagenesis of A. oryzae 3.042, and the protease secretions of these two strains are different. Sequencing the genome of A. oryzae 100-8 and comparing it to the genomes of A. oryzae 100-8 and 3.042 revealed some differences, such as single nucleotide polymorphisms, nucleotide deletion or insertion. Some of these differences may reflect the ability of A. oryzae to secrete proteases. Transcriptional sequencing and analysis of the two strains during the same growth processes provided further insights into the genes and pathways involved in protease secretion.

Cyanobacteria-mediated phenylpropanoids and phytohormones in rice (Oryza sativa) enhance plant growth and stress tolerance.

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Singh, Dhananjaya P; Prabha, Ratna; Yandigeri, Mahesh S; Arora, Dilip K

2011-11-01

Phenylpropanoids, flavonoids and plant growth regulators in rice (Oryza sativa) variety (UPR 1823) inoculated with different cyanobacterial strains namely Anabaena oryzae, Anabaena doliolum, Phormidium fragile, Calothrix geitonos, Hapalosiphon intricatus, Aulosira fertilissima, Tolypothrix tenuis, Oscillatoria acuta and Plectonema boryanum were quantified using HPLC in pot conditions after 15 and 30 days. Qualitative analysis of the induced compounds using reverse phase HPLC and further confirmation with LC-MS/MS showed consistent accumulation of phenolic acids (gallic, gentisic, caffeic, chlorogenic and ferulic acids), flavonoids (rutin and quercetin) and phytohormones (indole acetic acid and indole butyric acid) in rice leaves. Plant growth promotion (shoot, root length and biomass) was positively correlated with total protein and chlorophyll content of leaves. Enzyme activity of peroxidase and phenylalanine ammonia lyase and total phenolic content was fairly high in rice leaves inoculated with O. acuta and P. boryanum after 30 days. Differential systemic accumulation of phenylpropanoids in plant leaves led us to conclude that cyanobacterial inoculation correlates positively with plant growth promotion and stress tolerance in rice. Furthermore, the study helped in deciphering possible mechanisms underlying plant growth promotion and stress tolerance in rice following cyanobacterial inoculation and indicated the less explored avenue of cyanobacterial colonization in stress tolerance against abiotic stress.

A comparison of rice chloroplast genomes

DEFF Research Database (Denmark)

Tang, Jiabin; Xia, Hong'ai; Cao, Mengliang

2004-01-01

Using high quality sequence reads extracted from our whole genome shotgun repository, we assembled two chloroplast genome sequences from two rice (Oryza sativa) varieties, one from 93-11 (a typical indica variety) and the other from PA64S (an indica-like variety with maternal origin of japonica......), which are both parental varieties of the super-hybrid rice, LYP9. Based on the patterns of high sequence coverage, we partitioned chloroplast sequence variations into two classes, intravarietal and intersubspecific polymorphisms. Intravarietal polymorphisms refer to variations within 93-11 or PA64S...

Ortholog Alleles at Xa3/Xa26 Locus Confer Conserved Race-Specific Resistance against Xanthomonas oryzae in Rice

Institute of Scientific and Technical Information of China (English)

Hong-Jing Li; Xiang-Hua Li; Jing-Hua Xiao; Rod A. Wing; Shi-Ping Wang

2012-01-01

The rice disease resistance (R) gene Xa3/Xa26 (having also been named Xa3 and Xa26) against Xanthomonas oryzae pv.oryzae (Xoo),which causes bacterial blight disease,belongs to a multiple gene family clustered in chromosome 11 and is from an AA genome rice cultivar (Oryza sativa L.).This family encodes leucine-rich repeat (LRR) receptor kinasetype proteins.Here,we show that the orthologs (alleles) of Xa3/Xa26,Xa3/Xa26-2,and Xa3/Xa26-3,from wild Oryza species O.officinalis (CC genome) and O.minuta (BBCC genome),respectively,were also R genes against Xoo.Xa3/Xa26-2 and Xa3/Xa26-3 conferred resistance to 16 of the 18 Xoo strains examined.Comparative sequence analysis of the Xa3/Xa26 families in the two wild Oryza species showed that Xa3/Xa26-3 appeared to have originated from the CC genome of O.minuta.The predicted proteins encoded by Xa3/Xa26,Xa3/Xa26-2,and Xa3/Xa26-3 share 91-99％ sequence identity and 94-99％ sequence similarity.Transgenic plants carrying a single copy of Xa3/Xa26,Xa3/Xa26-2,or Xa3/Xa26-3,in the same genetic background,showed a similar resistance spectrum to a set of Xoo strains,although plants carrying Xa3/Xa26-2 or Xa3/Xa26-3 showed lower resistance levels than the plants carrying Xa3/Xa26.These results suggest that the Xa3/Xa26 locus predates the speciation of A and C genome,which is approximately 7.5 million years ago.Thus,the resistance specificity of this locus has been conserved for a long time.

Systematic analysis of rice (Oryza sativa) metabolic responses to herbivory.

Science.gov (United States)

Alamgir, Kabir Md; Hojo, Yuko; Christeller, John T; Fukumoto, Kaori; Isshiki, Ryutaro; Shinya, Tomonori; Baldwin, Ian T; Galis, Ivan

2016-02-01

Plants defend against attack from herbivores by direct and indirect defence mechanisms mediated by the accumulation of phytoalexins and release of volatile signals, respectively. While the defensive arsenals of some plants, such as tobacco and Arabidopsis are well known, most of rice's (Oryza sativa) defence metabolites and their effectiveness against herbivores remain uncharacterized. Here, we used a non-biassed metabolomics approach to identify many novel herbivory-regulated metabolic signatures in rice. Most were up-regulated by herbivore attack while only a few were suppressed. Two of the most prominent up-regulated signatures were characterized as phenolamides (PAs), p-coumaroylputrescine and feruloylputrescine. PAs accumulated in response to attack by both chewing insects, i.e. feeding of the lawn armyworm (Spodoptera mauritia) and the rice skipper (Parnara guttata) larvae, and the attack of the sucking insect, the brown planthopper (Nilaparvata lugens, BPH). In bioassays, BPH insects feeding on 15% sugar solution containing p-coumaroylputrescine or feruloylputrescine, at concentrations similar to those elicited by heavy BPH attack in rice, had a higher mortality compared to those feeding on sugar diet alone. Our results highlight PAs as a rapidly expanding new group of plant defence metabolites that are elicited by herbivore attack, and deter herbivores in rice and other plants. © 2015 John Wiley & Sons Ltd.

Fe deficiency induced changes in rice (Oryza sativa L.) thylakoids.

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Wang, Yuwen; Xu, Chao; Li, Kang; Cai, Xiaojie; Wu, Min; Chen, Guoxiang

2017-01-01

Iron deficiency is an important abiotic stress that limits productivity of crops all over the world. We selected a hybrid rice (Oryza sativa L.), LYPJ, which is super high-yield and widely cultured in China, to investigate changes in the components and structure of thylakoid membranes and photosynthetic performance in response to iron deficiency. Our results demonstrated that photosystem I (PSI) is the primary target for iron deficiency, while the changes in photosystem II (PSII) are important for rebuilding a balance in disrupted energy utilization and dissipation caused by differential degradation of photosynthetic components. The result of immunoblot analysis suggested that the core subunit PsaA declined drastically, while PsbA remained relatively stable. Furthermore, several organizational changes of the photosynthetic apparatus were found by BN-PAGE, including a marked decrease in the PSI core complexes, the Cytb 6 /f complex, and the trimeric form of the LHCII antenna, consistent with the observed unstacking grana. The fluorescence induction analysis indicated a descending PSII activity with energy dissipation enhanced markedly. In addition, we proposed that the crippled CO 2 assimilation could be compensated by the enhanced of phosphoenolpyruvate carboxylase (PEPC), which is suggested by the decreased ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and photosynthetic efficiency.

Molecular cloning and characterization of RGA1 encoding a G protein alpha subunit from rice (Oryza sativa L. IR-36).

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Seo, H S; Kim, H Y; Jeong, J Y; Lee, S Y; Cho, M J; Bahk, J D

1995-03-01

A cDNA clone, RGA1, was isolated by using a GPA1 cDNA clone of Arabidopsis thaliana G protein alpha subunit as a probe from a rice (Oryza sativa L. IR-36) seedling cDNA library from roots and leaves. Sequence analysis of genomic clone reveals that the RGA1 gene has 14 exons and 13 introns, and encodes a polypeptide of 380 amino acid residues with a calculated molecular weight of 44.5 kDa. The encoded protein exhibits a considerable degree of amino acid sequence similarity to all the other known G protein alpha subunits. A putative TATA sequence (ATATGA), a potential CAAT box sequence (AGCAATAC), and a cis-acting element, CCACGTGG (ABRE), known to be involved in ABA induction are found in the promoter region. The RGA1 protein contains all the consensus regions of G protein alpha subunits except the cysteine residue near the C-terminus for ADP-ribosylation by pertussis toxin. The RGA1 polypeptide expressed in Escherichia coli was, however, ADP-ribosylated by 10 microM [adenylate-32P] NAD and activated cholera toxin. Southern analysis indicates that there are no other genes similar to the RGA1 gene in the rice genome. Northern analysis reveals that the RGA1 mRNA is 1.85 kb long and expressed in vegetative tissues, including leaves and roots, and that its expression is regulated by light.

Genomics of Aspergillus oryzae: Learning from the History of Koji Mold and Exploration of Its Future

Science.gov (United States)

Machida, Masayuki; Yamada, Osamu; Gomi, Katsuya

2008-01-01

At a time when the notion of microorganisms did not exist, our ancestors empirically established methods for the production of various fermentation foods: miso (bean curd seasoning) and shoyu (soy sauce), both of which have been widely used and are essential for Japanese cooking, and sake, a magical alcoholic drink consumed at a variety of ritual occasions, are typical examples. A filamentous fungus, Aspergillus oryzae, is the key organism in the production of all these traditional foods, and its solid-state cultivation (SSC) has been confirmed to be the secret for the high productivity of secretory hydrolases vital for the fermentation process. Indeed, our genome comparison and transcriptome analysis uncovered mechanisms for effective degradation of raw materials in SSC: the extracellular hydrolase genes that have been found only in the A. oryzae genome but not in A. fumigatus are highly induced during SSC but not in liquid cultivation. Also, the temperature reduction process empirically adopted in the traditional soy-sauce fermentation processes has been found to be important to keep strong expression of the A. oryzae-specific extracellular hydrolases. One of the prominent potentials of A. oryzae is that it has been successfully applied to effective degradation of biodegradable plastic. Both cutinase, responsible for the degradation of plastic, and hydrophobin, which recruits cutinase on the hydrophobic surface to enhance degradation, have been discovered in A. oryzae. Genomic analysis in concert with traditional knowledge and technology will continue to be powerful tools in the future exploration of A. oryzae. PMID:18820080

Random Mutagenesis of the Aspergillus oryzae Genome Results in Fungal Antibacterial Activity

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Cory A. Leonard

2013-01-01

Full Text Available Multidrug-resistant bacteria cause severe infections in hospitals and communities. Development of new drugs to combat resistant microorganisms is needed. Natural products of microbial origin are the source of most currently available antibiotics. We hypothesized that random mutagenesis of Aspergillus oryzae would result in secretion of antibacterial compounds. To address this hypothesis, we developed a screen to identify individual A. oryzae mutants that inhibit the growth of Methicillin-resistant Staphylococcus aureus (MRSA in vitro. To randomly generate A. oryzae mutant strains, spores were treated with ethyl methanesulfonate (EMS. Over 3000 EMS-treated A. oryzae cultures were tested in the screen, and one isolate, CAL220, exhibited altered morphology and antibacterial activity. Culture supernatant from this isolate showed antibacterial activity against Methicillin-sensitive Staphylococcus aureus, MRSA, and Pseudomonas aeruginosa, but not Klebsiella pneumonia or Proteus vulgaris. The results of this study support our hypothesis and suggest that the screen used is sufficient and appropriate to detect secreted antibacterial fungal compounds resulting from mutagenesis of A. oryzae. Because the genome of A. oryzae has been sequenced and systems are available for genetic transformation of this organism, targeted as well as random mutations may be introduced to facilitate the discovery of novel antibacterial compounds using this system.

Random Mutagenesis of the Aspergillus oryzae Genome Results in Fungal Antibacterial Activity

Science.gov (United States)

Leonard, Cory A.; Brown, Stacy D.; Hayman, J. Russell

2013-01-01

Multidrug-resistant bacteria cause severe infections in hospitals and communities. Development of new drugs to combat resistant microorganisms is needed. Natural products of microbial origin are the source of most currently available antibiotics. We hypothesized that random mutagenesis of Aspergillus oryzae would result in secretion of antibacterial compounds. To address this hypothesis, we developed a screen to identify individual A. oryzae mutants that inhibit the growth of Methicillin-resistant Staphylococcus aureus (MRSA) in vitro. To randomly generate A. oryzae mutant strains, spores were treated with ethyl methanesulfonate (EMS). Over 3000 EMS-treated A. oryzae cultures were tested in the screen, and one isolate, CAL220, exhibited altered morphology and antibacterial activity. Culture supernatant from this isolate showed antibacterial activity against Methicillin-sensitive Staphylococcus aureus, MRSA, and Pseudomonas aeruginosa, but not Klebsiella pneumonia or Proteus vulgaris. The results of this study support our hypothesis and suggest that the screen used is sufficient and appropriate to detect secreted antibacterial fungal compounds resulting from mutagenesis of A. oryzae. Because the genome of A. oryzae has been sequenced and systems are available for genetic transformation of this organism, targeted as well as random mutations may be introduced to facilitate the discovery of novel antibacterial compounds using this system. PMID:23983696

Random Mutagenesis of the Aspergillus oryzae Genome Results in Fungal Antibacterial Activity.

Science.gov (United States)

Leonard, Cory A; Brown, Stacy D; Hayman, J Russell

2013-01-01

Multidrug-resistant bacteria cause severe infections in hospitals and communities. Development of new drugs to combat resistant microorganisms is needed. Natural products of microbial origin are the source of most currently available antibiotics. We hypothesized that random mutagenesis of Aspergillus oryzae would result in secretion of antibacterial compounds. To address this hypothesis, we developed a screen to identify individual A. oryzae mutants that inhibit the growth of Methicillin-resistant Staphylococcus aureus (MRSA) in vitro. To randomly generate A. oryzae mutant strains, spores were treated with ethyl methanesulfonate (EMS). Over 3000 EMS-treated A. oryzae cultures were tested in the screen, and one isolate, CAL220, exhibited altered morphology and antibacterial activity. Culture supernatant from this isolate showed antibacterial activity against Methicillin-sensitive Staphylococcus aureus, MRSA, and Pseudomonas aeruginosa, but not Klebsiella pneumonia or Proteus vulgaris. The results of this study support our hypothesis and suggest that the screen used is sufficient and appropriate to detect secreted antibacterial fungal compounds resulting from mutagenesis of A. oryzae. Because the genome of A. oryzae has been sequenced and systems are available for genetic transformation of this organism, targeted as well as random mutations may be introduced to facilitate the discovery of novel antibacterial compounds using this system.

Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species

Science.gov (United States)

Singh, Sangeeta; Chand, Suresh; Singh, N. K.; Sharma, Tilak Raj

2015-01-01

The resistance (R) genes and defense response (DR) genes have become very important resources for the development of disease resistant cultivars. In the present investigation, genome-wide identification, expression, phylogenetic and synteny analysis was done for R and DR-genes across three species of rice viz: Oryza sativa ssp indica cv 93-11, Oryza sativa ssp japonica and wild rice species, Oryza brachyantha. We used the in silico approach to identify and map 786 R -genes and 167 DR-genes, 672 R-genes and 142 DR-genes, 251 R-genes and 86 DR-genes in the japonica, indica and O. brachyanth a genomes, respectively. Our analysis showed that 60.5% and 55.6% of the R-genes are tandemly repeated within clusters and distributed over all the rice chromosomes in indica and japonica genomes, respectively. The phylogenetic analysis along with motif distribution shows high degree of conservation of R- and DR-genes in clusters. In silico expression analysis of R-genes and DR-genes showed more than 85% were expressed genes showing corresponding EST matches in the databases. This study gave special emphasis on mechanisms of gene evolution and duplication for R and DR genes across species. Analysis of paralogs across rice species indicated 17% and 4.38% R-genes, 29% and 11.63% DR-genes duplication in indica and Oryza brachyantha, as compared to 20% and 26% duplication of R-genes and DR-genes in japonica respectively. We found that during the course of duplication only 9.5% of R- and DR-genes changed their function and rest of the genes have maintained their identity. Syntenic relationship across three genomes inferred that more orthology is shared between indica and japonica genomes as compared to brachyantha genome. Genome wide identification of R-genes and DR-genes in the rice genome will help in allele mining and functional validation of these genes, and to understand molecular mechanism of disease resistance and their evolution in rice and related species. PMID:25902056

Hybridization study of wild rice Oryza glumaepatula with varieties of cultivated rice (O. sativa) and wild (O. grandiglumis)

International Nuclear Information System (INIS)

Villalobos Cascante, Eddier

2015-01-01

The process of interspecific hybridization of the wild species O. glumaepatula is studied with commercial varieties of the species O. sativa and O. grandiglumis, by morphological evaluation and hybrid flow cytometry. Hybrid plants were evaluated of cross between O. glumaepatula, located in the wetlands of Rio Medio Queso and two varieties of O. sativa, Puita Inta and CFX 18 resistant to a herbicide. The technique of Polymerase Chain Reaction Allele Specifies Oligonucleotide (PCR-ASO) was used to detect allelic mutations in the ALS gene conferring herbicide resistance, and it is confirmed the hybrid nature of the plants obtained at crossings. 68 hybrids were obtained: O. glumaepatula x P. Inta, 21 hybrids P. Inta x O. glumaepatula, 4 hybrids O. glumaepatula x CFX-18 and 15 hybrids CFX-18 x O. glumaepatula. 10 morphological descriptors of the genus Oryza were evaluated and determined that are indifferent to the direction and type of crossing, the hybrids resemble to the wild species O. glumaepatula for characters: height, panicle length and ligule length. All hybrids have showed similarity to commercial varieties in flag leaf length. Other characters evaluated in the hybrids have presented maternal effect, heterosis and intermediate values. The protocol of flow cytometry (FCM) is standardized species for Oryza genus analyzing nuclear DNA content of 106 samples of leaf tissue of wild species O. glumaepatula, O. grandiglumis; whose average has been of 0.73 picograms, and natural hybrids product of the cross of these species. The result has been intermediate compared with O. grandiglumis and O. glumaepatula that have made available to 1.0 picograms and 0.50 of DNA respectively. The molecular nature of the hybrids was confirmed in this way. (author) [es

The whole chloroplast genome of wild rice (Oryza australiensis).

Science.gov (United States)

Wu, Zhiqiang; Ge, Song

2016-01-01

The whole chloroplast genome of wild rice (Oryza australiensis) is characterized in this study. The genome size is 135,224  bp, exhibiting a typical circular structure including a pair of 25,776  bp inverted repeats (IRa,b) separated by a large single-copy region (LSC) of 82,212  bp and a small single-copy region (SSC) of 12,470  bp. The overall GC content of the genome is 38.95%. 110 unique genes were annotated, including 76 protein-coding genes, 4 ribosomal RNA genes, and 30t RNA genes. Among these, 18 are duplicated in the inverted repeat regions, 13 genes contain one intron, and 2 genes (rps12 and ycf3) have two introns.

Screening of Oryza sativa L. for HptGene and Evaluation of Hpt Positive Samples Using Houba Retransposon-Based IRAP Markers

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Gözde YÜZBAŞIOĞLU

2017-02-01

Full Text Available Increasing world population needs to enhance agricultural production because of food starvation. Genetically modified organism(GMOis a way to solve this problem. During gene transfers, DNA is inserted into a plant’s genome in a random way. Thisproducesspontaneous genetic changeswith movement of transposable elements, and even increasesvariations. Houbawas described as one of the active retrotransposonsin rice. The aim of this study was to screen rice samples collected from Turkey, and analyse Houba retrotransposon movements with IRAP technique intransgenic ones and their controls. For this purpose, 71 different rice seeds obtained from different regions of Turkey were used for GMO analysis.All samples were screened by real time PCR to test cauliflower mosaic virus (CaMV 35S promoter (P-35S regions, T-NOS (nopaline synthase terminator regions, figwort mosaic virus (FMV regions, bar, patand Cry1ab/ac,and hpt(hygromycin resistance genes. Hptgene was identified in 6samples as a result of real time PCR analysis. These 6transgenic samples with their controls were used for IRAP-PCRanalysisand 0-56% polymorphism ratios were observed in analysed samples. This study is one of the first detailed experimental data of transgenic Oryza sativaL. samples in terms of retrotransposon-based variation.

Isolation and Expression analysis of OsPME1, encoding for a putative Pectin Methyl Esterase from Oryza sativa (subsp. indica).

Science.gov (United States)

Kanneganti, Vydehi; Gupta, Aditya Kumar

2009-04-01

Pectin Methyl Esterases (PMEs) play an essential role during plant development by affecting the mechanical properties of the plant cell walls. Recent studies indicated that PMEs play important role in pollen tube development. In this study, we isolated a 1.3 kb cDNA clone from rice panicle cDNA library. It contained a 1038 bp of open reading frame (ORF) encoding for a putative pectin methyl esterase of 345 aminoacids with a 20 aminoacid signal peptide and was hence designated as OsPME1 (Oryza sativaPectin Methyl Esterase 1). It contained the structural arrangement GXYXE and GXXDFIF, found in the active groups of all PMEs. OsPME1 gene product shared varying identities, ranging from 52 % to 33 % with PMEs from other plant species belonging to Brassicaceae, Fabaceae, Amaranthaceae and Funariaceae. Southern blot analysis indicated that PME1 exists as a single copy in the rice genome. Expression pattern analysis revealed that OsPME1 is expressed only in pollen grains, during the later stages of their development and was also regulated by various abiotic stress treatments and phytohormones. Functional characterization of this pollen specific PME from rice would enable us to understand its role in pollen development.

Common and distinct organ and stress responsive transcriptomic patterns in Oryza sativa and Arabidopsis thaliana

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Castleden Ian

2010-11-01

Full Text Available Abstract Background Arabidopsis thaliana is clearly established as the model plant species. Given the ever-growing demand for food, there is a need to translate the knowledge learned in Arabidopsis to agronomically important species, such as rice (Oryza sativa. To gain a comparative insight into the similarities and differences into how organs are built and how plants respond to stress, the transcriptomes of Arabidopsis and rice were compared at the level of gene orthology and functional categorisation. Results Organ specific transcripts in rice and Arabidopsis display less overlap in terms of gene orthology compared to the orthology observed between both genomes. Although greater overlap in terms of functional classification was observed between root specific transcripts in rice and Arabidopsis, this did not extend to flower, leaf or seed specific transcripts. In contrast, the overall abiotic stress response transcriptome displayed a significantly greater overlap in terms of gene orthology compared to the orthology observed between both genomes. However, ~50% or less of these orthologues responded in a similar manner in both species. In fact, under cold and heat treatments as many or more orthologous genes responded in an opposite manner or were unchanged in one species compared to the other. Examples of transcripts that responded oppositely include several genes encoding proteins involved in stress and redox responses and non-symbiotic hemoglobins that play central roles in stress signalling pathways. The differences observed in the abiotic transcriptomes were mirrored in the presence of cis-acting regulatory elements in the promoter regions of stress responsive genes and the transcription factors that potentially bind these regulatory elements. Thus, both the abiotic transcriptome and its regulation differ between rice and Arabidopsis. Conclusions These results reveal significant divergence between Arabidopsis and rice, in terms of the

Influence of cooking on anthocyanins in black rice (Oryza sativa L. japonica var. SBR).

Science.gov (United States)

Hiemori, Miki; Koh, Eunmi; Mitchell, Alyson E

2009-03-11

The composition and thermal stability of anthocyanins in black rice (Oryza sativa L. japonica var. SBR) produced in California were investigated. Six anthocyanin pigments were identified and quantified by high performance liquid chromatography using photo diode-array detection (HPLC-PDA) and electrospray ionization mass spectrometry [LC-(ESI)MS/MS]. The predominant anthocyanins are cyanidin-3-glucoside (572.47 microg/g; 91.13% of total) and peonidin-3-glucoside (29.78 microg/g; 4.74% of total). Minor constituents included three cyanidin-dihexoside isomers and one cyanidin hexoside. Thermal stability of anthocyanins was assessed in rice cooked using a rice cooker, pressure cooker, or on a gas range. All cooking methods caused significant (P rice cooker (74.2%) and gas range (65.4%). Conversely, levels of protocatechuic acid increased 2.7 to 3.4 times in response to all cooking methods. These findings indicate that cooking black rice results in the thermal degradation of cyanidin-3-glucoside and concomitant production of protocatechuic acid.

Comparative Genome Analysis Between Aspergillus oryzae Strains Reveals Close Relationship Between Sites of Mutation Localization and Regions of Highly Divergent Genes among Aspergillus Species

Science.gov (United States)

Umemura, Myco; Koike, Hideaki; Yamane, Noriko; Koyama, Yoshinori; Satou, Yuki; Kikuzato, Ikuya; Teruya, Morimi; Tsukahara, Masatoshi; Imada, Yumi; Wachi, Youji; Miwa, Yukino; Yano, Shuichi; Tamano, Koichi; Kawarabayasi, Yutaka; Fujimori, Kazuhiro E.; Machida, Masayuki; Hirano, Takashi

2012-01-01

Aspergillus oryzae has been utilized for over 1000 years in Japan for the production of various traditional foods, and a large number of A. oryzae strains have been isolated and/or selected for the effective fermentation of food ingredients. Characteristics of genetic alterations among the strains used are of particular interest in studies of A. oryzae. Here, we have sequenced the whole genome of an industrial fungal isolate, A. oryzae RIB326, by using a next-generation sequencing system and compared the data with those of A. oryzae RIB40, a wild-type strain sequenced in 2005. The aim of this study was to evaluate the mutation pressure on the non-syntenic blocks (NSBs) of the genome, which were previously identified through comparative genomic analysis of A. oryzae, Aspergillus fumigatus, and Aspergillus nidulans. We found that genes within the NSBs of RIB326 accumulate mutations more frequently than those within the SBs, regardless of their distance from the telomeres or of their expression level. Our findings suggest that the high mutation frequency of NSBs might contribute to maintaining the diversity of the A. oryzae genome. PMID:22912434

Comparative genome analysis between Aspergillus oryzae strains reveals close relationship between sites of mutation localization and regions of highly divergent genes among Aspergillus species.

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Umemura, Myco; Koike, Hideaki; Yamane, Noriko; Koyama, Yoshinori; Satou, Yuki; Kikuzato, Ikuya; Teruya, Morimi; Tsukahara, Masatoshi; Imada, Yumi; Wachi, Youji; Miwa, Yukino; Yano, Shuichi; Tamano, Koichi; Kawarabayasi, Yutaka; Fujimori, Kazuhiro E; Machida, Masayuki; Hirano, Takashi

2012-10-01

Aspergillus oryzae has been utilized for over 1000 years in Japan for the production of various traditional foods, and a large number of A. oryzae strains have been isolated and/or selected for the effective fermentation of food ingredients. Characteristics of genetic alterations among the strains used are of particular interest in studies of A. oryzae. Here, we have sequenced the whole genome of an industrial fungal isolate, A. oryzae RIB326, by using a next-generation sequencing system and compared the data with those of A. oryzae RIB40, a wild-type strain sequenced in 2005. The aim of this study was to evaluate the mutation pressure on the non-syntenic blocks (NSBs) of the genome, which were previously identified through comparative genomic analysis of A. oryzae, Aspergillus fumigatus, and Aspergillus nidulans. We found that genes within the NSBs of RIB326 accumulate mutations more frequently than those within the SBs, regardless of their distance from the telomeres or of their expression level. Our findings suggest that the high mutation frequency of NSBs might contribute to maintaining the diversity of the A. oryzae genome.

Why develop O. sativa x O. rufipogon chromosome segment substitution line libraries?

Science.gov (United States)

Transgressive variation has been observed in rice (Oryza sativa) as an increase in grain yield in advanced backcross mapping populations derived from crosses between several adapted O. sativa varieties and a single accession (IRGC105491) of the ancestral parent, O. rufipogon. The phenomena of hybrid...

Rubisco activity is associated with photosynthetic thermotolerance in a wild rice (Oryza meridionalis).

Science.gov (United States)

Scafaro, Andrew P; Yamori, Wataru; Carmo-Silva, A Elizabete; Salvucci, Michael E; von Caemmerer, Susanne; Atwell, Brian J

2012-09-01

Oryza meridionalis is a wild species of rice, endemic to tropical Australia. It shares a significant genome homology with the common domesticated rice Oryza sativa. Exploiting the fact that the two species are highly related but O. meridionalis has superior heat tolerance, experiments were undertaken to identify the impact of temperature on key events in photosynthesis. At an ambient CO(2) partial pressure of 38 Pa and irradiance of 1500 µmol quanta m(-2) s(-1), the temperature optimum of photosynthesis was 33.7 ± 0.8°C for O. meridionalis, significantly higher than the 30.6 ± 0.7°C temperature optimum of O. sativa. To understand the basis for this difference, we measured gas exchange and rubisco activation state between 20 and 42°C and modeled the response to determine the rate-limiting steps of photosynthesis. The temperature response of light respiration (R(light)) and the CO(2) compensation point in the absence of respiration (Γ(*)) were determined and found to be similar for the two species. C3 photosynthesis modeling showed that despite the difference in susceptibility to high temperature, both species had a similar temperature-dependent limitation to photosynthesis. Both rice species were limited by ribulose-1,5-bisphosphate (RuBP) regeneration at temperatures of 25 and 30°C but became RuBP carboxylation limited at 35 and 40°C. The activation state of rubisco in O. meridionalis was more stable at higher temperatures, explaining its greater heat tolerance compared with O. sativa. Copyright © Physiologia Plantarum 2012.

Can Rice (Oryza sativa) Mitigate Pesticides and Nutrients in Agricultural Runoff?

Science.gov (United States)

Moore, M T; Locke, M A

2018-01-01

Phytoremediation of nutrients and pesticides in runoff is a growing conservation effort, particularly in agriculturally intensive areas such as the lower Mississippi River Valley. In the current study, rice (Oryza sativa) was examined for its mitigation capacity of nitrogen, phosphorus, diazinon, and permethrin. Twenty-two high density polyethylene circular containers (56 cm x 45 cm) were used as mesocosms, with 12 mesocosms planted with rice and 10 mesocosms remaining unvegetated. Mesocosms were hydraulically connected and arranged in a series of two, with each system providing a 4 h hydraulic retention time (HRT) for a total system retention time of 8 h. Two treatments (RICE/RICE and RICE/BARE) of four replicates each were utilized, with three replicates of controls (BARE/BARE). Systems with RICE/RICE (8 h HRT) significantly reduced diazinon (p = 0.0126), cis-permethrin (p = 0.0442), filtered orthophosphate (p = 0.0058), and total orthophosphate (p = 0.0123) compared to control systems. No significant differences were noted for trans-permethrin, nitrate, or ammonium. Results indicate promise in phytoremediation of agricultural runoff by rice. If further studies reveal contaminants are not transferred into seeds, then rice could potentially serve as both a remediation tool and food source in countries facing agricultural pollution challenges.

Toxic action of zinc on growth and enzyme activities of rice Oryza sativa L. seedlings

Energy Technology Data Exchange (ETDEWEB)

Nag, P.; Nag, P.; Paul, A.K.; Mukherji, S.

1984-01-01

This paper provides information on the effects of toxic concentrations of zinc sulfate (ZnSO/sub 4/.7H/sub 2/O) on the growth and metabolism of rice Oryza sativa L. seedlings. Root growth inhibition was always more pronounced than was shoot growth inhibition. Root growth was completely inhibited at 40 m M concentration, whereas the magnitude of reduction of shoot length was only 56% at this concentration. Gibberellic acid (GA/sub 3/) was partially capable of relieving zinc inhibition. The activities of peroxidase, IAA oxidase and ascorbic acid oxidase of seedlings increased in response to zinc addition, whereas catalase and IAA synthetase decreased. All the hydrolyzing enzymes, viz., ..cap alpha..-amylase and phytase of endosperm together with RNase and ATPase of the embryo, showed distinct inhibition from the control, the exception being endosperm RNase which was stimulated under zinc treatment. 50 references, 6 figures.

Characterization and evolutionary analysis of ent-kaurene synthase like genes from the wild rice species Oryza rufipogon.

Science.gov (United States)

Toyomasu, Tomonobu; Miyamoto, Koji; Shenton, Matthew R; Sakai, Arisa; Sugawara, Chizu; Horie, Kiyotaka; Kawaide, Hiroshi; Hasegawa, Morifumi; Chuba, Masaru; Mitsuhashi, Wataru; Yamane, Hisakazu; Kurata, Nori; Okada, Kazunori

2016-11-18

Cultivated rice (Oryza sativa) possesses various labdane-related diterpene synthase genes, homologs of ent-copalyl diphosphate synthase (CPS) and ent-kaurene synthase (KS) that are responsible for the biosynthesis of phytohormone gibberellins. The CPS homologs and KS like (KSL) homologs successively converted geranylgeranyl diphosphate to cyclic diterpene hydrocarbons via ent-copalyl diphosphate or syn-copalyl diphosphate in O. sativa. Consequently, a variety of labdane-related diterpenoids, including phytoalexin phytocassanes, momilactones and oryzalexins, have been identified from cultivated rice. Our previous report indicated that the biosynthesis of phytocassanes and momilactones is conserved in Oryza rufipogon, the progenitor of Asian cultivated rice. Moreover, their biosynthetic gene clusters, containing OsCPS2 and OsKSL7 for phytocassane biosynthesis and OsCPS4 and OsKSL4 for momilactone biosynthesis, are also present in the O. rufipogon genome. We herein characterized O. rufipogon homologs of OsKSL5, OsKSL6, OsKSL8 responsible for oryzalexin S biosynthesis, and OsKSL10 responsible for oryzalexins A-F biosynthesis, to obtain more evolutionary insight into diterpenoid biosynthesis in O. sativa. Our phytoalexin analyses showed that no accumulation of oryzalexins was detected in extracts from O. rufipogon leaf blades. In vitro functional analyses indicated that unlike OsKSL10, O. rufipogon KSL10 functions as an ent-miltiradiene synthase, which explains the lack of accumulation of oryzalexins A-F in O. rufipogon. The different functions of KSL5 and KSL8 in O. sativa japonica to those in indica are conserved in each type of O. rufipogon, while KSL6 functions (ent-isokaurene synthases) are well conserved. Our study suggests that O. sativa japonica has evolved distinct specialized diterpenoid metabolism, including the biosynthesis of oryzalexins. Copyright © 2016 Elsevier Inc. All rights reserved.

The draft genome and transcriptome of Cannabis sativa.

Science.gov (United States)

van Bakel, Harm; Stout, Jake M; Cote, Atina G; Tallon, Carling M; Sharpe, Andrew G; Hughes, Timothy R; Page, Jonathan E

2011-10-20

Cannabis sativa has been cultivated throughout human history as a source of fiber, oil and food, and for its medicinal and intoxicating properties. Selective breeding has produced cannabis plants for specific uses, including high-potency marijuana strains and hemp cultivars for fiber and seed production. The molecular biology underlying cannabinoid biosynthesis and other traits of interest is largely unexplored. We sequenced genomic DNA and RNA from the marijuana strain Purple Kush using shortread approaches. We report a draft haploid genome sequence of 534 Mb and a transcriptome of 30,000 genes. Comparison of the transcriptome of Purple Kush with that of the hemp cultivar 'Finola' revealed that many genes encoding proteins involved in cannabinoid and precursor pathways are more highly expressed in Purple Kush than in 'Finola'. The exclusive occurrence of Δ9-tetrahydrocannabinolic acid synthase in the Purple Kush transcriptome, and its replacement by cannabidiolic acid synthase in 'Finola', may explain why the psychoactive cannabinoid Δ9-tetrahydrocannabinol (THC) is produced in marijuana but not in hemp. Resequencing the hemp cultivars 'Finola' and 'USO-31' showed little difference in gene copy numbers of cannabinoid pathway enzymes. However, single nucleotide variant analysis uncovered a relatively high level of variation among four cannabis types, and supported a separation of marijuana and hemp. The availability of the Cannabis sativa genome enables the study of a multifunctional plant that occupies a unique role in human culture. Its availability will aid the development of therapeutic marijuana strains with tailored cannabinoid profiles and provide a basis for the breeding of hemp with improved agronomic characteristics.

Genomic research in Eucalyptus.

Science.gov (United States)

Poke, Fiona S; Vaillancourt, René E; Potts, Brad M; Reid, James B

2005-09-01

Eucalyptus L'Hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to Australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. With the sequencing of the genomes of Arabidopsis thaliana and Oryza sativa and the recent completion of the first tree genome sequence, Populus trichocarpa, attention has turned to the current status of genomic research in Eucalyptus. For several eucalypt species, large segregating families have been established, high-resolution genetic maps constructed and large EST databases generated. Collaborative efforts have been initiated for the integration of diverse genomic projects and will provide the framework for future research including exploiting the sequence of the entire eucalypt genome which is currently being sequenced. This review summarises the current position of genomic research in Eucalyptus and discusses the direction of future research.

Comprehensive phenotypic analysis of rice (Oryza sativa) response to salinity stress

KAUST Repository

Pires, Inês S.

2015-07-22

Increase in soil salinity levels is becoming a major cause of crop yield losses worldwide. Rice (Oryza sativa) is the most salt-sensitive cereal crop, and many studies have focused on rice salinity tolerance, but a global understanding of this crop\\'s response to salinity is still lacking. We systematically analyzed phenotypic data previously collected for 56 rice genotypes to assess the extent to which rice uses three known salinity tolerance mechanisms: shoot-ion independent tolerance (or osmotic tolerance), ion exclusion, and tissue tolerance. In general, our analyses of different phenotypic traits agree with results of previous rice salinity tolerance studies. However, we also established that the three salinity tolerance mechanisms mentioned earlier appear among rice genotypes and that none of them is predominant. Against the pervasive view in the literature that the K+/Na+ ratio is the most important trait in salinity tolerance, we found that the K+ concentration was not significantly affected by salt stress in rice, which puts in question the importance of K+/Na+ when analyzing rice salt stress response. Not only do our results contribute to improve our global understanding of salt stress response in an important crop, but we also use our results together with an extensive literature research to highlight some issues commonly observed in salinity stress tolerance studies and to propose solutions for future experiments.

Quantitative phosphoproteomic analysis of early seed development in rice (Oryza sativa L.).

Science.gov (United States)

Qiu, Jiehua; Hou, Yuxuan; Tong, Xiaohong; Wang, Yifeng; Lin, Haiyan; Liu, Qing; Zhang, Wen; Li, Zhiyong; Nallamilli, Babi R; Zhang, Jian

2016-02-01

Rice (Oryza sativa L.) seed serves as a major food source for over half of the global population. Though it has been long recognized that phosphorylation plays an essential role in rice seed development, the phosphorylation events and dynamics in this process remain largely unknown so far. Here, we report the first large scale identification of rice seed phosphoproteins and phosphosites by using a quantitative phosphoproteomic approach. Thorough proteomic studies in pistils and seeds at 3, 7 days after pollination resulted in the successful identification of 3885, 4313 and 4135 phosphopeptides respectively. A total of 2487 proteins were differentially phosphorylated among the three stages, including Kip related protein 1, Rice basic leucine zipper factor 1, Rice prolamin box binding factor and numerous other master regulators of rice seed development. Moreover, differentially phosphorylated proteins may be extensively involved in the biosynthesis and signaling pathways of phytohormones such as auxin, gibberellin, abscisic acid and brassinosteroid. Our results strongly indicated that protein phosphorylation is a key mechanism regulating cell proliferation and enlargement, phytohormone biosynthesis and signaling, grain filling and grain quality during rice seed development. Overall, the current study enhanced our understanding of the rice phosphoproteome and shed novel insight into the regulatory mechanism of rice seed development.

Role of hydroperoxide lyase in white-backed planthopper (Sogatella furcifera Horváth)-induced resistance to bacterial blight in rice, Oryza sativa L.

Science.gov (United States)

Gomi, Kenji; Satoh, Masaru; Ozawa, Rika; Shinonaga, Yumi; Sanada, Sachiyo; Sasaki, Katsutomo; Matsumura, Masaya; Ohashi, Yuko; Kanno, Hiroo; Akimitsu, Kazuya; Takabayashi, Junji

2010-01-01

A pre-infestation of the white-backed planthopper (WBPH), Sogatella furcifera Horváth, conferred resistance to bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) in rice (Oryza sativa L.) under both laboratory and field conditions. The infestation of another planthopper species, the brown planthopper (BPH) Nilaparvata lugens Stål, did not significantly reduce the incidence of bacterial blight symptoms. A large-scale screening using a rice DNA microarray and quantitative RT-PCR revealed that WBPH infestation caused the upregulation of more defence-related genes than did BPH infestation. Hydroperoxide lyase 2 (OsHPL2), an enzyme for producing C(6) volatiles, was upregulated by WBPH infestation, but not by BPH infestation. One C(6) volatile, (E)-2-hexenal, accumulated in rice after WBPH infestation, but not after BPH infestation. A direct application of (E)-2-hexenal to a liquid culture of Xoo inhibited the growth of the bacterium. Furthermore, a vapour treatment of rice plants with (E)-2-hexenal induced resistance to bacterial blight. OsHPL2-overexpressing transgenic rice plants exhibited increased resistance to bacterial blight. Based on these data, we conclude that OsHPL2 and its derived (E)-2-hexenal play some role in WBPH-induced resistance in rice.

Genetic Diversity and Phenotypic Variation in an Introgression Line Population Derived from an Interspecific Cross between Oryza glaberrima and Oryza sativa.

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Caijin Chen

Full Text Available The introduction of closely related species genomic fragments is an effective way to enrich genetic diversity and creates new germplasms in crops. Here, we studied the genetic diversity of an introgression line (IL population composed of 106 ILs derived from an interspecific tetra cross between O. glaberrima and O. sativa (RAM3/Jin23B//Jin23B///YuetaiB. The proportion of O. glaberrima genome (PGG in the ILs ranged from 0.3% to 36.7%, with an average value of 12.32% which is close to the theoretically expected proportion. A total of 250 polymorphic alleles were amplified by 21 AFLP primer combinations with an average of 12 alleles per primer. Population structure analysis revealed that the IL population can be divided into four genetically distinct subpopulations. Both principal component analysis and neighbor-joining tree analysis showed that ILs with a higher PGG displayed greater genetic diversity. Canonical discriminant analysis identified six phenotypic traits (plant height, yield per plant, filled grain percentage, panicle length, panicle number and days to flowering as the main discriminatory traits among the ILs and between the subpopulations and showed significant phenotypic distances between subpopulations. The effects of PGG on phenotypic traits in the ILs were estimated using a linear admixed model, which showed a significant positive effect on grain yield per plant (0.286±0.117, plant height (0.418 ± 0.132, panicle length (0.663 ± 0.107, and spikelet number per panicle (0.339 ± 0.128, and a significant negative effect on filled grain percentage (-0.267 ± 0.123 and days to flowering (-0.324 ± 0.075. We found that an intermediate range (10% - 20% of PGG was more effective for producing ILs with favorable integrated agronomic traits. Our results confirm that construction of IL population carrying O. glaberrima genomic fragments could be an effective approach to increase the genetic diversity of O. sativa genome and an appropriate

Screening of gamma radiation-induced pathogen resistance rice lines against Xanthomonas oryzae pv. oryzae

Energy Technology Data Exchange (ETDEWEB)

Lim, Chan Ju; Lee, Ha Yeon; Kim, Woong Bom; Ahmad, Raza; Moon, Jae Sun; Kwon, Suk Yoon [Korea Research Institute of Beoscience and Biotechnology, Daejeon (Korea, Republic of); Kim, Dong Sub [Korea Atomic Energy Research Institute, Jeongeup (Korea, Republic of)

2010-09-15

Bacterial blight is one of the most serious diseases of rice (Oryza sativa L.), and it has been known that Xanthomonas oryzae pv. oryzae (Xoo) causes this disease symptom. To develop resistance rice cultivars against Xoo, 3,000 lines of M{sub 3}, which were irradiated with gamma ray, were tested by 'scissor-dip method' primarily, and 191 putative resistant lines were selected. In M{sub 4} generation, these lines were screened again with various ways such as measuring of symptom of bacterial blight in leaf, number of tiller, fresh weight, and phenotypic segregation ratio in next generation. Finally, six resistance lines were selected. RT-PCR analysis revealed that these lines displayed high level of R-genes such as Xa21, Pi36, and Pi-ta. These results indicate that mutations by gamma ray cause disruptions of regulatory signal transduction systems of these R-genes. Furthermore, these selected mutants could be useful for the development of rice cultivar resistant to Xoo.

Molecular evolution of the endosperm starch synthesis pathway genes in rice (Oryza sativa L.) and its wild ancestor, O. rufipogon L.

Science.gov (United States)

Yu, Guoqin; Olsen, Kenneth M; Schaal, Barbara A

2011-01-01

The evolution of metabolic pathways is a fundamental but poorly understood aspect of evolutionary change. One approach for understanding the complexity of pathway evolution is to examine the molecular evolution of genes that together comprise an integrated metabolic pathway. The rice endosperm starch biosynthetic pathway is one of the most thoroughly characterized metabolic pathways in plants, and starch is a trait that has evolved in response to strong selection during rice domestication. In this study, we have examined six key genes (AGPL2, AGPS2b, SSIIa, SBEIIb, GBSSI, ISA1) in the rice endosperm starch biosynthesis pathway to investigate the evolution of these genes before and after rice domestication. Genome-wide sequence tagged sites data were used as a neutral reference to overcome the problems of detecting selection in species with complex demographic histories such as rice. Five variety groups of Oryza sativa (aus, indica, tropical japonica, temperate japonica, aromatic) and its wild ancestor (O. rufipogon) were sampled. Our results showed evidence of purifying selection at AGPL2 in O. rufipogon and strong evidence of positive selection at GBSSI in temperate japonica and tropical japonica varieties and at GBSSI and SBEIIb in aromatic varieties. All the other genes showed a pattern consistent with neutral evolution in both cultivated rice and its wild ancestor. These results indicate the important role of positive selection in the evolution of starch genes during rice domestication. We discuss the role of SBEIIb and GBSSI in the evolution of starch quality during rice domestication and the power and limitation of detecting selection using genome-wide data as a neutral reference.

Chloroplast DNA polymorphism and evolutional relationships between Asian cultivated rice (Oryza sativa) and its wild relatives (O. rufipogon).

Science.gov (United States)

Li, W J; Zhang, B; Huang, G W; Kang, G P; Liang, M Z; Chen, L B

2012-12-17

We analyzed chloroplast DNA (cpDNA) polymorphism and phylogenic relationships between 6 typical indica rice, 4 japonica rice, 8 javanica rice, and 12 Asian common wild rice (Oryza rufipogon) strains collected from different latitudes in China by comparing polymorphism at 9 highly variable regions. One hundred and forty-four polymorphic bases were detected. The O. rufipogon samples had 117 polymorphic bases, showing rich genetic diversity. One hundred and thirty-one bases at 13 sites were identified with indica/japonica characteristics; they showed differences between the indica and japonica subspecies at these sites. The javanica strains and japonica shared similar bases at these 131 polymorphic sites, suggesting that javanica is closely related to japonica. On the basis of length analyses of the open reading frame (ORF)100 and (ORF)29-tRNA-Cys(GCA) (TrnC(GCA)) fragments, the O. rufipogon strains were classified into indica/japonica subgroups, which was consistent with the results of the phylogenic tree assay based on concatenated datasets. These results indicated that differences in indica and japonica also exist in the cpDNA genome of the O. rufipogon strains. However, these differences demonstrated a certain degree of primitiveness and incompleteness, as an O. rufipogon line may show different indica/ japonica attributes at different sites. Consequently, O. rufipogon cannot be simply classified into the indica/japonica types as O. sativa. Our data support the hypothesis that Asian cultivated rice, O. indica and O. japonica, separately evolved from Asian common wild rice (O. rufipogon) strains, which have different indica-japonica differentiation trends.

Vinegar rice (Oryza sativa L. produced by a submerged fermentation process from alcoholic fermented rice

Directory of Open Access Journals (Sweden)

Wilma Aparecida Spinosa

2015-03-01

Full Text Available Considering the limited availability of technology for the production of rice vinegar and also due to the potential consumer product market, this study aimed to use alcoholic fermented rice (rice wine (Oryza sativa L. for vinegar production. An alcoholic solution with 6.28% (w/v ethanol was oxidized by a submerged fermentation process to produce vinegar. The process of acetic acid fermentation occurred at 30 ± 0.3°C in a FRINGS® Acetator (Germany for the production of vinegar and was followed through 10 cycles. The vinegar had a total acidity of 6.85% (w/v, 0.17% alcohol (w/v, 1.26% (w/v minerals and 1.78% (w/v dry extract. The composition of organic acids present in rice vinegar was: cis-aconitic acid (6 mg/L, maleic acid (3 mg/L, trans-aconitic acid (3 mg/L, shikimic + succinic acid (4 mg/L, lactic acid (300 mg/L, formic acid (180 mg/L, oxalic acid (3 mg/L, fumaric acid (3 mg/L and itaconic acid (1 mg/L.

Pengaruh Pemberian Kompos Jerami Dan Pupuk Sp-36 Pada Tanah Sulfat Masam Potensial Terhadap Perubahan Sifat Kimia Serta Pertumbuhan Dan Produksi Padi (Oryza Sativa L.)

OpenAIRE

Bhakari, Herlina Eka

2013-01-01

The objective of this research is to study the effect of rice straw compost and the application of phosphorus fertilizer of SP-36 on chemical characteristic of acid sulphate soils, rice growth and production (Oryza sativa L). This study used a randomized block design factorial, with 2 factors : factor 1 : rice straw compost treatment (J) wich consist of : J0 = 0 ton ha-1 (0 g straw/pot) ; J1 = 10 ton ha-1 (40 g straw/pot); J2 = 20 ton ha-1 (80 g straw /pot); J3 = 30 ton ha-1 ...

Effect of gamma-irradiated sludge on the growth and yield of rice (Oryza sativa L. var. GR-3)

International Nuclear Information System (INIS)

Pandya, G.A.; Prakash, L.; Devasia, Preston; Modi, V.V.

1988-01-01

The effects of gamma-irradiated sludge on the growth and yield of rice (Oryza sativa L. var. GR-3) in pot cultures have been studied. Compared to plants grown only in soil, shoot length, root length, fresh weight, dry weight, total proteins, total soluble sugars, starch and chlorophyll content of plants grown in soil supplemented with unirradiated or gamma-irradiated sludge were found to be significantly increased. Irradiation of sludge significantly stimulated the linear growth of shoot and root systems as well as fresh and dry weights of plants, compared to those grown in soil containing unirradiated sludge. There was also an improvement in the grain yield (weight of seed) when plants were grown in soil supplemented with irradiated sludge. The results obtained suggest that the gamma-irradiated sewage sludge can be beneficially recycled for agricultural uses. (author)

High Levels of Phytophenolics and Antioxidant Activities in Oryza ...

African Journals Online (AJOL)

Purpose: To investigate phenolic levels, phytophenolic profiles and total antioxidant activities of Oryza sativa, unpolished Thai rice. Methods: Unpolished Thai rice strains of Leum Phua, Klam, Hawm Nil and Black Rose were measured for antioxidant activity using 1,1-diphenyl-2-picrylhydrazyl (DPPH), ...

Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes.

Science.gov (United States)

Rauscher, Gilda; Simko, Ivan

2013-01-22

Lettuce (Lactuca sativa L.) is the major crop from the group of leafy vegetables. Several types of molecular markers were developed that are effectively used in lettuce breeding and genetic studies. However only a very limited number of microsattelite-based markers are publicly available. We have employed the method of enriched microsatellite libraries to develop 97 genomic SSR markers. Testing of newly developed markers on a set of 36 Lactuca accession (33 L. sativa, and one of each L. serriola L., L. saligna L., and L. virosa L.) revealed that both the genetic heterozygosity (UHe = 0.56) and the number of loci per SSR (Na = 5.50) are significantly higher for genomic SSR markers than for previously developed EST-based SSR markers (UHe = 0.32, Na = 3.56). Fifty-four genomic SSR markers were placed on the molecular linkage map of lettuce. Distribution of markers in the genome appeared to be random, with the exception of possible cluster on linkage group 6. Any combination of 32 genomic SSRs was able to distinguish genotypes of all 36 accessions. Fourteen of newly developed SSR markers originate from fragments with high sequence similarity to resistance gene candidates (RGCs) and RGC pseudogenes. Analysis of molecular variance (AMOVA) of L. sativa accessions showed that approximately 3% of genetic diversity was within accessions, 79% among accessions, and 18% among horticultural types. The newly developed genomic SSR markers were added to the pool of previously developed EST-SSRs markers. These two types of SSR-based markers provide useful tools for lettuce cultivar fingerprinting, development of integrated molecular linkage maps, and mapping of genes.

Gamma ray, EMS and sodium azide induced effectiveness and efficiency of chlorophyll mutations in basmati rice (Oryza sativa L.)

International Nuclear Information System (INIS)

Singh, Sanjeev; Singh, J.; Singh, R.K.

2001-01-01

The effectiveness and efficiency of gamma ray, EMS, sodium azide alone or in combination in relation to chlorophyll mutations in two varieties of Basmati rice (Oryza sativa L.) in M 2 generation were studied. The chlorophyll mutations were induced by all the doses of mutagens alone or in combination relatively at a fair frequency in both the varieties in M 2 generation. In general, it was found that combination treatments of gamma rays and EMS were observed to be more efficient in Taraori Basmati, while EMS alone and combination treatment of gamma rays and EMS were more efficient in Pusa Basmati 1 on sterility and growth injury basis both. Sodium azide at 0.5 mM was found as the most effective dose in both Taraori Basmati and Pusa Basmati 1 cultivars. (author)

Biochemical and structural properties of cyanases from Arabidopsis thaliana and Oryza sativa.

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Dan Qian

Full Text Available Cyanate is toxic to all organisms. Cyanase converts cyanate to CO₂ and NH₃ in a bicarbonate-dependent reaction. The biophysical functions and biochemical characteristics of plant cyanases are poorly studied, although it has been investigated in a variety of proteobacteria, cyanobacteria and fungi. In this study, we characterised plant cyanases from Arabidopsis thaliana and Oryza sativa (AtCYN and OsCYN. Prokaryotic-expressed AtCYN and OsCYN both showed cyanase activity in vitro. Temperature had a similar influence on the activity of both cyanases, but pH had a differential impact on AtCYN and OsCYN activity. Homology modelling provided models of monomers of AtCYN and OsCYN, and a coimmunoprecipitation assay and gel filtration indicated that AtCYN and OsCYN formed homodecamers. The analysis of single-residue mutants of AtCYN indicated that the conserved catalytic residues also contributed to the stability of the homodecamer. KCNO treatment inhibited Arabidopsis germination and early seedling growth. Plants containing AtCYN or OsCYN exhibited resistance to KCNO stress, which demonstrated that one role of cyanases in plants is detoxification. Transcription level of AtCYN was higher in the flower than in other organs of Arabidopsis. AtCYN transcription was not significantly affected by KCNO treatment in Arabidopsis, but was induced by salt stress. This research broadens our knowledge on plant detoxification of cyanate via cyanase.

A study of technetium 99 uptake by irrigated rice (Oryza sativa L.)

International Nuclear Information System (INIS)

Vandecasteele, C.M.; De Becker, R.; Tang Van Hai; Myttenaere, C.

1983-01-01

The absorption of technetium 99 (an important fission product which can be released in the environment at different steps of the nuclear fuel cycle) by rice (Oryza sativa L.) was studied in nutrient solutions and in flooded soils with contaminated water. The absorption kinetics established in water culture (continuous flowing system) for 99 Tc concentrations ranging from 0.017 to 17 μCi.I - 1 revealed two phases: the former corresponds to the diffusion in the apparent free spaces and the second, which is linear, represents the transfer of 99 Tc from the external medium into the root cells as well as its translocation to the leaves. The study of the desorption mechanism confirmed the existence of these compartments, the second one containing more than 95% of the total activity of the plant. The biological half-life of 99 Tc of the second compartment is so high that decontamination of the plant may not be expected. In soils, toxicity symptoms were observed for a 99 Tc water concentration of 17 μCi.I - 1 . The transfer factors calculated in irrigated soils are very high (>10 3 for the leafy shoots) and the distribution of 99 Tc between the different organs waries with the concentration used. More than 90% of 99 Tc is found in the leafy shoots meanwhile 1% of the plant total activity is only found in the caryopses [fr

Molecular cloning, functional expression and subcellular localization of two putative vacuolar voltage-gated chloride channels in rice (Oryza sativa L.).

Science.gov (United States)

Nakamura, Atsuko; Fukuda, Atsunori; Sakai, Shingo; Tanaka, Yoshiyuki

2006-01-01

We isolated two cDNA clones (OsCLC-1 and OsCLC-2) homologous to tobacco CLC-Nt1, which encodes a voltage-gated chloride channel, from rice (Oryza sativa L. ssp. japonica, cv. Nipponbare). The deduced amino acid sequences were highly conserved (87.9% identity with each other). Southern blot analysis of the rice genomic DNA revealed that OsCLC-1 and OsCLC-2 were single-copy genes on chromosomes 4 and 2, respectively. OsCLC-1 was expressed in most tissues, whereas OsCLC-2 was expressed only in the roots, nodes, internodes and leaf sheaths. The level of expression of OsCLC-1, but not of OsCLC-2, was increased by treatment with NaCl. Both genes could partly substitute for GEF1, which encodes the sole chloride channel in yeast, by restoring growth under ionic stress. These results indicate that both genes are chloride channel genes. The proteins from both genes were immunochemically detected in the tonoplast fraction. Tagged synthetic green fluorescent protein which was fused to OsCLC-1 or OsCLC-2 localized in the vacuolar membranes. These results indicate that the proteins may play a role in the transport of chloride ions across the vacuolar membrane. We isolated loss-of-function mutants of both genes from a panel of rice mutants produced by the insertion of a retrotransposon, Tos17, in the exon region, and found inhibition of growth at all life stages.

Complete Genome Sequence of Bacillus velezensis CBMB205, a Phosphate-Solubilizing Bacterium Isolated from the Rhizoplane of Rice in the Republic of Korea

OpenAIRE

Hwangbo, Kyeong; Um, Yurry; Kim, Ki Yoon; Madhaiyan, Munusamy; Sa, Tong Min; Lee, Yi

2016-01-01

Bacillus velezensis CBMB205 (= KACC 13105T = NCCB 100236T) was isolated from the rhizoplane of rice (Oryza sativa L. cv. O-dae). According to previous studies, this bacterium has several genes that can promote plant growth, such as the phosphorus-solubilizing protein-coding gene. Here, we present the first complete genome of B.?velezensis CBMB205.

Ectopic expression of a vesicle trafficking gene, OsRab7, from Oryza ...

African Journals Online (AJOL)

Jane

2011-07-18

Jul 18, 2011 ... OsRab7, from Oryza sativa, confers tolerance to several ... Key Laboratory of Molecular Biology and Gene Engineering, College of Life Science, Nanchang University, ... The reverse transcription was performed using MMLV.

Whole Mitochondrial Genome Sequencing and Re-Examination of a Cytoplasmic Male Sterility-Associated Gene in Boro-Taichung-Type Cytoplasmic Male Sterile Rice.

Science.gov (United States)

Kazama, Tomohiko; Toriyama, Kinya

2016-01-01

Nuclear genome substitutions between subspecies can lead to cytoplasmic male sterility (CMS) through incompatibility between nuclear and mitochondrial genomes. Boro-Taichung (BT)-type CMS rice was obtained by substituting the nuclear genome of Oryza sativa subsp. indica cultivar Chinsurah Boro II with that of Oryza sativa subsp. japonica cultivar Taichung 65. In BT-type CMS rice, the mitochondrial gene orf79 is associated with male sterility. A complete sequence of the Boro-type mitochondrial genome responsible for BT-type CMS has not been determined to date. Here, we used pyrosequencing to construct the Boro-type mitochondrial genome. The contiguous sequences were assembled into five circular DNA molecules, four of which could be connected into a single circle. The two resulting subgenomic circles were unable to form a reliable master circle, as recombination between them was scarcely detected. We also found an unequal abundance of DNA molecules for the two loci of atp6. These results indicate the presence of multi-partite DNA molecules in the Boro-type mitochondrial genome. Expression patterns were investigated for Boro-type mitochondria-specific orfs, which were not found in the mitochondria from the standard japonica cultivar Nipponbare. Restorer of fertility 1 (RF1)-dependent RNA processing has been observed in orf79-containing RNA but was not detected in other Boro-type mitochondria-specific orfs, supporting the conclusion that orf79 is a unique CMS-associated gene in Boro-type mitochondria.

Carbohydrate-active enzymes from the zygomycete fungus Rhizopus oryzae: a highly specialized approach to carbohydrate degradation depicted at genome level

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Henrissat Bernard

2011-01-01

Full Text Available Abstract Background Rhizopus oryzae is a zygomycete filamentous fungus, well-known as a saprobe ubiquitous in soil and as a pathogenic/spoilage fungus, causing Rhizopus rot and mucomycoses. Results Carbohydrate Active enzyme (CAZy annotation of the R. oryzae identified, in contrast to other filamentous fungi, a low number of glycoside hydrolases (GHs and a high number of glycosyl transferases (GTs and carbohydrate esterases (CEs. A detailed analysis of CAZy families, supported by growth data, demonstrates highly specialized plant and fungal cell wall degrading abilities distinct from ascomycetes and basidiomycetes. The specific genomic and growth features for degradation of easily digestible plant cell wall mono- and polysaccharides (starch, galactomannan, unbranched pectin, hexose sugars, chitin, chitosan, β-1,3-glucan and fungal cell wall fractions suggest specific adaptations of R. oryzae to its environment. Conclusions CAZy analyses of the genome of the zygomycete fungus R. oryzae and comparison to ascomycetes and basidiomycete species revealed how evolution has shaped its genetic content with respect to carbohydrate degradation, after divergence from the Ascomycota and Basidiomycota.

Transcriptomic Analysis and the Expression of Disease-Resistant Genes in Oryza meyeriana under Native Condition.

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Bin He

Full Text Available Oryza meyeriana (O. meyeriana, with a GG genome type (2n = 24, accumulated plentiful excellent characteristics with respect to resistance to many diseases such as rice shade and blast, even immunity to bacterial blight. It is very important to know if the diseases-resistant genes exist and express in this wild rice under native conditions. However, limited genomic or transcriptomic data of O. meyeriana are currently available. In this study, we present the first comprehensive characterization of the O. meyeriana transcriptome using RNA-seq and obtained 185,323 contigs with an average length of 1,692 bp and an N50 of 2,391 bp. Through differential expression analysis, it was found that there were most tissue-specifically expressed genes in roots, and next to stems and leaves. By similarity search against protein databases, 146,450 had at least a significant alignment to existed gene models. Comparison with the Oryza sativa (japonica-type Nipponbare and indica-type 93-11 genomes revealed that 13% of the O. meyeriana contigs had not been detected in O. sativa. Many diseases-resistant genes, such as bacterial blight resistant, blast resistant, rust resistant, fusarium resistant, cyst nematode resistant and downy mildew gene, were mined from the transcriptomic database. There are two kinds of rice bacterial blight-resistant genes (Xa1 and Xa26 differentially or specifically expressed in O. meyeriana. The 4 Xa1 contigs were all only expressed in root, while three of Xa26 contigs have the highest expression level in leaves, two of Xa26 contigs have the highest expression profile in stems and one of Xa26 contigs was expressed dominantly in roots. The transcriptomic database of O. meyeriana has been constructed and many diseases-resistant genes were found to express under native condition, which provides a foundation for future discovery of a number of novel genes and provides a basis for studying the molecular mechanisms associated with disease

Population genomics identifies the origin and signatures of selection of Korean weedy rice

OpenAIRE

He, Qiang; Kim, Kyu?Won; Park, Yong?Jin

2016-01-01

Summary Weedy rice is the same biological species as cultivated rice (Oryza sativa); it is also a noxious weed infesting rice fields worldwide. Its formation and population?selective or ?adaptive signatures are poorly understood. In this study, we investigated the phylogenetics, population structure and signatures of selection of Korean weedy rice by determining the whole genomes of 30 weedy rice, 30 landrace rice and ten wild rice samples. The phylogenetic tree and results of ancestry infere...

Australian wild rice reveals pre-domestication origin of polymorphism deserts in rice genome.

Science.gov (United States)

Krishnan S, Gopala; Waters, Daniel L E; Henry, Robert J

2014-01-01

Rice is a major source of human food with a predominantly Asian production base. Domestication involved selection of traits that are desirable for agriculture and to human consumers. Wild relatives of crop plants are a source of useful variation which is of immense value for crop improvement. Australian wild rices have been isolated from the impacts of domestication in Asia and represents a source of novel diversity for global rice improvement. Oryza rufipogon is a perennial wild progenitor of cultivated rice. Oryza meridionalis is a related annual species in Australia. We have examined the sequence of the genomes of AA genome wild rices from Australia that are close relatives of cultivated rice through whole genome re-sequencing. Assembly of the resequencing data to the O. sativa ssp. japonica cv. Nipponbare shows that Australian wild rices possess 2.5 times more single nucleotide polymorphisms than in the Asian wild rice and cultivated O. sativa ssp. indica. Analysis of the genome of domesticated rice reveals regions of low diversity that show very little variation (polymorphism deserts). Both the perennial and annual wild rice from Australia show a high degree of conservation of sequence with that found in cultivated rice in the same 4.58 Mbp region on chromosome 5, which suggests that some of the 'polymorphism deserts' in this and other parts of the rice genome may have originated prior to domestication due to natural selection. Analysis of genes in the 'polymorphism deserts' indicates that this selection may have been due to biotic or abiotic stress in the environment of early rice relatives. Despite having closely related sequences in these genome regions, the Australian wild populations represent an invaluable source of diversity supporting rice food security.

Australian wild rice reveals pre-domestication origin of polymorphism deserts in rice genome.

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Gopala Krishnan S

Full Text Available BACKGROUND: Rice is a major source of human food with a predominantly Asian production base. Domestication involved selection of traits that are desirable for agriculture and to human consumers. Wild relatives of crop plants are a source of useful variation which is of immense value for crop improvement. Australian wild rices have been isolated from the impacts of domestication in Asia and represents a source of novel diversity for global rice improvement. Oryza rufipogon is a perennial wild progenitor of cultivated rice. Oryza meridionalis is a related annual species in Australia. RESULTS: We have examined the sequence of the genomes of AA genome wild rices from Australia that are close relatives of cultivated rice through whole genome re-sequencing. Assembly of the resequencing data to the O. sativa ssp. japonica cv. Nipponbare shows that Australian wild rices possess 2.5 times more single nucleotide polymorphisms than in the Asian wild rice and cultivated O. sativa ssp. indica. Analysis of the genome of domesticated rice reveals regions of low diversity that show very little variation (polymorphism deserts. Both the perennial and annual wild rice from Australia show a high degree of conservation of sequence with that found in cultivated rice in the same 4.58 Mbp region on chromosome 5, which suggests that some of the 'polymorphism deserts' in this and other parts of the rice genome may have originated prior to domestication due to natural selection. CONCLUSIONS: Analysis of genes in the 'polymorphism deserts' indicates that this selection may have been due to biotic or abiotic stress in the environment of early rice relatives. Despite having closely related sequences in these genome regions, the Australian wild populations represent an invaluable source of diversity supporting rice food security.

Minerales, Ácido Fítico y γ-Oryzanol en harinas integrales y salvados de tres variedades de arroz (Oryza Sativa L) cultivadas en Venezuela

OpenAIRE

Aguilar-García, Carlos; Hevia, Patricio; Núnez, Máryuri

2014-01-01

El propósito de esta investigación fue determinar el contenido de algunos minerales, de ácido fítico y de γ-oryzanol en harinas integrales y salvados de tres cultivares (Cimarrón, Fonaiap 1 y Zeta 15) de arroz (Oryza sativa L) cosechados en Venezuela. Los minerales (Ca, Mg, Fe y Zn) fueron cuantificados por espectrofotometría de absorción atómica, mientras que el fósforo (P) y el ácido fítico fueron estimados a través de un método colorimétrico. El γ-oryzanol se cuantificó por HPLC. En genera...

Genetic diversity analysis of Cuban traditional rice (Oryza sativa L. varieties based on microsatellite markers

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Alba Alvarez

2007-01-01

Full Text Available Microsatellite polymorphism was studied in a sample of 39 traditional rice (Oryza sativa L. varieties and 11 improved varieties widely planted in Cuba. The study was aimed at assessing the extent of genetic variation in traditional and improved varieties and to establish their genetic relationship for breeding purposes. Heterozygosity was analyzed at each microsatellite loci and for each genotype using 10 microsatellite primer pairs. Between varieties genetic relationship was estimated. The number of alleles per microsatellite loci was 4 to 8, averaging 6.6 alleles per locus. Higher heterozygosity (H was found in traditional varieties (H TV = 0.72 than in improved varieties (H IV = 0.42, and 68% of the total microsatellite alleles were found exclusively in the traditional varieties. Genetic diversity, represented by cluster analysis, indicated three different genetic groups based on their origin. Genetic relationship estimates based on the proportion of microsatellite loci with shared alleles indicated that the majority of traditional varieties were poorly related to the improved varieties. We also discuss the more efficient use of the available genetic diversity in future programs involving genetic crosses.

Arsenic uptake and accumulation in rice (Oryza sativa L.) with selenite fertilization and water management.

Science.gov (United States)

Wan, Yanan; Camara, Aboubacar Younoussa; Huang, Qingqing; Yu, Yao; Wang, Qi; Li, Huafen

2018-07-30

The accumulation of arsenic (As) in rice grain is a potential threat to human health. Our study investigated the possible mediatory role of selenite fertilization on As uptake and accumulation by rice (Oryza sativa L.) under different water management regimes (aerobic or flooded) in a pot experiment. Soil solutions were also extracted during the growing season to monitor As dynamics. Results showed that As contents in the soil solutions, seedlings, and mature rice were higher under flooded than under aerobic water management. Under aerobic conditions, selenite additions slightly increased As concentrations in soil solutions (in the last two samplings), but decreased As levels in rice plants. Relative to the control, 0.5 mg kg -1 selenite decreased rice grain As by 27.5%. Under flooded conditions, however, selenite additions decreased As in soil solutions, while increased As in rice grain. Tendencies also showed that selenite additions decreased the proportion of As in rice shoots both at the seedling stage and maturity, and were more effective in aerobic soil. Our results demonstrate that the effect of selenite fertilizer on As accumulation by rice is related to water management. Copyright © 2018 Elsevier Inc. All rights reserved.

The relationship between vacuolation and initiation of PCD in rice (Oryza sativa) aleurone cells

Science.gov (United States)

Zheng, Yan; Zhang, Heting; Deng, Xiaojiang; Liu, Jing; Chen, Huiping

2017-01-01

Vacuole fusion is a necessary process for the establishment of a large central vacuole, which is the central location of various hydrolytic enzymes and other factors involved in death at the beginning of plant programmed cell death (PCD). In our report, the fusion of vacuoles has been presented in two ways: i) small vacuoles coalesce to form larger vacuoles through membrane fusion, and ii) larger vacuoles combine with small vacuoles when small vacuoles embed into larger vacuoles. Regardless of how fusion occurs, a large central vacuole is formed in rice (Oryza sativa) aleurone cells. Along with the development of vacuolation, the rupture of the large central vacuole leads to the loss of the intact plasma membrane and the degradation of the nucleus, resulting in cell death. Stabilizing or disrupting the structure of actin filaments (AFs) inhibits or promotes the fusion of vacuoles, which delays or induces PCD. In addition, the inhibitors of the vacuolar processing enzyme (VPE) and cathepsin B (CathB) block the occurrence of the large central vacuole and delay the progression of PCD in rice aleurone layers. Overall, our findings provide further evidence for the rupture of the large central vacuole triggering the PCD in aleruone layers.

Arsenic accumulation and phosphorus status in two rice (Oryza sativa L.) cultivars surveyed from fields in South China

International Nuclear Information System (INIS)

Lu Ying; Dong, Fei; Deacon, Claire; Chen Huojun; Raab, Andrea; Meharg, Andrew A.

2010-01-01

The consumption of paddy rice (Oryza sativa L.) is a major inorganic arsenic exposure pathway in S.E. Asia. A multi-location survey was undertaken in Guangdong Province, South China to assess arsenic accumulation and speciation in 2 rice cultivars, one an Indica and the other a hybrid Indica. The results showed that arsenic concentrations in rice tissue increased in the order grain < husk < straw < root. Rice grain arsenic content of 2 rice cultivars was significant different and correlated with phosphorus concentration and molar ratio of P/As in shoot, being higher for the Indica cultivar than for the hybrid Indica, which suggests altering shoot phosphorus status as a promising route for breeding rice cultivars with reduced grain arsenic. Speciation of grain arsenic, performed using HPLC-ICP-MS, identified inorganic arsenic as the dominant arsenic species present in the rice grain. - Altering rice shoot phosphorus status is a promising route for breeding rice cultivars with reduced grain arsenic.

Comparative Genome Analysis Between Aspergillus oryzae Strains Reveals Close Relationship Between Sites of Mutation Localization and Regions of Highly Divergent Genes among Aspergillus Species

OpenAIRE

Umemura, Myco; Koike, Hideaki; Yamane, Noriko; Koyama, Yoshinori; Satou, Yuki; Kikuzato, Ikuya; Teruya, Morimi; Tsukahara, Masatoshi; Imada, Yumi; Wachi, Youji; Miwa, Yukino; Yano, Shuichi; Tamano, Koichi; Kawarabayasi, Yutaka; Fujimori, Kazuhiro E.

2012-01-01

Aspergillus oryzae has been utilized for over 1000 years in Japan for the production of various traditional foods, and a large number of A. oryzae strains have been isolated and/or selected for the effective fermentation of food ingredients. Characteristics of genetic alterations among the strains used are of particular interest in studies of A. oryzae. Here, we have sequenced the whole genome of an industrial fungal isolate, A. oryzae RIB326, by using a next-generation sequencing system and ...

OPTIMASI SUHU REAKSI TRANSESTERIFIKASI PADA MINYAK JERAMI PADI (ORYZA SATIVA L. MENJADI BIODIESEL DENGAN MENGGUNAKAN KATALIS CAO DARI KULIT TELUR AYAM

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Tasik Sinta

2016-11-01

Full Text Available The research on optimization of transesterification temperature for production of biodiesel from rice straw oil (Oryza sativa L. using CaO catalyst derived from the chicken egg skin has been conducted. Production of biodiesel was conducted at varied temperatures, namely 30oC, 40oC, 50oC, 60oC and 70oC. The fatty acid compositions of the transesterification products were determined by using GC-MS and the physical and chemical characteristics were determined using SNI Methods 04-7182-2006. The AAS result suggested that the chicken egg skin contained 91.41% CaO. The optimum transesterification temperature was 60oC producing 90,8405% methyl ester. The results of GC-MS showed that the highest percentage of fatty acid was methyl oleic (44.56%.

Elusive Origins of the Extra Genes in Aspergillus oryzae

Science.gov (United States)

Khaldi, Nora; Wolfe, Kenneth H.

2008-01-01

The genome sequence of Aspergillus oryzae revealed unexpectedly that this species has approximately 20% more genes than its congeneric species A. nidulans and A. fumigatus. Where did these extra genes come from? Here, we evaluate several possible causes of the elevated gene number. Many gene families are expanded in A. oryzae relative to A. nidulans and A. fumigatus, but we find no evidence of ancient whole-genome duplication or other segmental duplications, either in A. oryzae or in the common ancestor of the genus Aspergillus. We show that the presence of divergent pairs of paralogs is a feature peculiar to A. oryzae and is not shared with A. nidulans or A. fumigatus. In phylogenetic trees that include paralog pairs from A. oryzae, we frequently find that one of the genes in a pair from A. oryzae has the expected orthologous relationship with A. nidulans, A. fumigatus and other species in the subphylum Eurotiomycetes, whereas the other A. oryzae gene falls outside this clade but still within the Ascomycota. We identified 456 such gene pairs in A. oryzae. Further phylogenetic analysis did not however indicate a single consistent evolutionary origin for the divergent members of these pairs. Approximately one-third of them showed phylogenies that are suggestive of horizontal gene transfer (HGT) from Sordariomycete species, and these genes are closer together in the A. oryzae genome than expected by chance, but no unique Sordariomycete donor species was identifiable. The postulated HGTs from Sordariomycetes still leave the majority of extra A. oryzae genes unaccounted for. One possible explanation for our observations is that A. oryzae might have been the recipient of many separate HGT events from diverse donors. PMID:18725939

Elusive origins of the extra genes in Aspergillus oryzae.

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Nora Khaldi

Full Text Available The genome sequence of Aspergillus oryzae revealed unexpectedly that this species has approximately 20% more genes than its congeneric species A. nidulans and A. fumigatus. Where did these extra genes come from? Here, we evaluate several possible causes of the elevated gene number. Many gene families are expanded in A. oryzae relative to A. nidulans and A. fumigatus, but we find no evidence of ancient whole-genome duplication or other segmental duplications, either in A. oryzae or in the common ancestor of the genus Aspergillus. We show that the presence of divergent pairs of paralogs is a feature peculiar to A. oryzae and is not shared with A. nidulans or A. fumigatus. In phylogenetic trees that include paralog pairs from A. oryzae, we frequently find that one of the genes in a pair from A. oryzae has the expected orthologous relationship with A. nidulans, A. fumigatus and other species in the subphylum Eurotiomycetes, whereas the other A. oryzae gene falls outside this clade but still within the Ascomycota. We identified 456 such gene pairs in A. oryzae. Further phylogenetic analysis did not however indicate a single consistent evolutionary origin for the divergent members of these pairs. Approximately one-third of them showed phylogenies that are suggestive of horizontal gene transfer (HGT from Sordariomycete species, and these genes are closer together in the A. oryzae genome than expected by chance, but no unique Sordariomycete donor species was identifiable. The postulated HGTs from Sordariomycetes still leave the majority of extra A. oryzae genes unaccounted for. One possible explanation for our observations is that A. oryzae might have been the recipient of many separate HGT events from diverse donors.

Xanthomonas oryzae pv oryzae the Causal Agent of Bacterial Leaf Blight of rice: Isolation, Characterization, and Study of Transposon Mutagenesis

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Abdjad Asih Nawangsih

2011-04-01

Full Text Available Xanthomonas oryzae pv oryzae the Causal Agent of Bacterial Leaf Blight of rice: Isolation, Characterization, and Study of Transposon Mutagenesis. X. oryzae pv. oryzae (Xoo causes bacterial leaf blight (BLB of rice (Oryza sativa L., a major disease that constrains production of the staple crop in many countries of the world. Identification of X. oryzae pv. oryzae (Xoo was conducted based on the disease symptoms, pathogenicity, morphological, physiological, and genetic characteristics of bacterial cultures isolated from the infected plants. Fifty bacterial isolates predicted as Xoo have been successfully isolated. They are aerobic, rod shaped, and Gram negative bacteria. The isolates were evaluated for their hypersensitivity in tobacco and pathogenicity in rice plant. Fifty isolates induced hypersensitive reaction in tobacco and showed pathogenicity symptom in rice in different length. Based on physiological test, hypersensitivity and pathogenicity reactions, three bacterial isolates strongly predicted as Xoo, i.e. STG21, STG42, and STG46, were non indole formation, non pigment fluorescent, hydrolyzed casein, catalase activity positive, but negative oxidase. Partial sequencing of 16S rRNA genes of STG21 and STG42 showed 80% and 82% homology with X. oryzae, respectively, while STG46 showed 84% homology with X. campestris. Mini-Tn5 transposon mutagenesis of STG21 generated one of the mutants (M5 lossed it’s ability to induce hypersensitive reaction in tobacco plant and deficient in pathogenicity on rice. The lesion length of rice leaf caused by the mutant M5 decreased up to 80%.

The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics.

Science.gov (United States)

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F X; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-02-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

Complete Genome Sequence of Bacillus velezensis CBMB205, a Phosphate-Solubilizing Bacterium Isolated from the Rhizoplane of Rice in the Republic of Korea.

Science.gov (United States)

Hwangbo, Kyeong; Um, Yurry; Kim, Ki Yoon; Madhaiyan, Munusamy; Sa, Tong Min; Lee, Yi

2016-07-14

Bacillus velezensis CBMB205 (= KACC 13105(T) = NCCB 100236(T)) was isolated from the rhizoplane of rice (Oryza sativa L. cv. O-dae). According to previous studies, this bacterium has several genes that can promote plant growth, such as the phosphorus-solubilizing protein-coding gene. Here, we present the first complete genome of B. velezensis CBMB205. Copyright © 2016 Hwangbo et al.

Genome-wide patterns of nucleotide polymorphism in domesticated rice

DEFF Research Database (Denmark)

Caicedo, Ana L; Williamson, Scott H; Hernandez, Ryan D

2007-01-01

Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments......, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models...... to explain contemporary patterns of polymorphisms in rice, including a (i) selectively neutral population bottleneck model, (ii) bottleneck plus migration model, (iii) multiple selective sweeps model, and (iv) bottleneck plus selective sweeps model. We find that a simple bottleneck model, which has been...

In-silico identification and phylogenetic analysis of auxin efflux ...

African Journals Online (AJOL)

The phytohormone auxin is crucial for plant growth and development. ... genome, which are similar in number with that of monocotyledonous plant Oryza sativa. ... are much closer to Sorghum bicolor and O. sativa PIN genes of the grass family.

Two solanesyl diphosphate synthases with different subcellular localizations and their respective physiological roles in Oryza sativa.

Science.gov (United States)

Ohara, Kazuaki; Sasaki, Kanako; Yazaki, Kazufumi

2010-06-01

Long chain prenyl diphosphates are crucial biosynthetic precursors of ubiquinone (UQ) in many organisms, ranging from bacteria to humans, as well as precursors of plastoquinone in photosynthetic organisms. The cloning and characterization of two solanesyl diphosphate synthase genes, OsSPS1 and OsSPS2, in Oryza sativa is reported here. OsSPS1 was highly expressed in root tissue whereas OsSPS2 was found to be high in both leaves and roots. Enzymatic characterization using recombinant proteins showed that both OsSPS1 and OsSPS2 could produce solanesyl diphosphates as their final product, while OsSPS1 showed stronger activity than OsSPS2. However, an important biological difference was observed between the two genes: OsSPS1 complemented the yeast coq1 disruptant, which does not form UQ, whereas OsSPS2 only very weakly complemented the growth defect of the coq1 mutant. HPLC analyses showed that both OsSPS1 and OsSPS2 yeast transformants produced UQ9 instead of UQ6, which is the native yeast UQ. According to the complementation study, the UQ9 levels in OsSPS2 transformants were much lower than that of OsSPS1. Green fluorescent protein fusion analyses showed that OsSPS1 localized to mitochondria, while OsSPS2 localized to plastids. This suggests that OsSPS1 is involved in the supply of solanesyl diphosphate for ubiquinone-9 biosynthesis in mitochondria, whereas OsSPS2 is involved in providing solanesyl diphosphate for plastoquinone-9 formation. These findings indicate that O. sativa has a different mechanism for the supply of isoprenoid precursors in UQ biosynthesis from Arabidopsis thaliana, in which SPS1 provides a prenyl moiety for UQ9 at the endoplasmic reticulum.

Mapping of Novel QTL Regulating Grain Shattering Using Doubled Haploid Population in Rice (Oryza sativa L.

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Gyu-Ho Lee

2016-01-01

Full Text Available The critical evolutionary step during domestication of major cereals was elimination of seed shattering because the easy-to-shatter trait in wild relatives results in a severe reduction in yield. In this study, we analyzed the QTLs associated with shattering employing a high-density genetic map in doubled haploid (DH population of rice (Oryza sativa L.. A genetic linkage map was generated with 217 microsatellite markers spanning 2082.4 cM and covering 12 rice chromosomes with an average interval of 9.6 cM between markers based on 120 DHLs derived from a cross between Cheongcheong indica type cultivar and Nagdong japonica type cultivar. In the QTL analysis, five QTLs pertaining to the breaking tensile strength (BTS were detected in 2013 and 2015. Two regions of the QTLs related to BTS on chromosome 1 and chromosome 6 were detected. Several important genes are distributed in 1 Mbp region of the QTL on chromosome 6 and they are related to the formation of abscission layer. We decide to name this QTL qSh6 and the candidate genes in the qSh6 region can be employed usefully in further research for cloning.

Genome-wide transcription analyses in rice using tiling microarrays

DEFF Research Database (Denmark)

Li, Lei; Wang, Xiangfeng; Stolc, Viktor

2006-01-01

. We report here a full-genome transcription analysis of the indica rice subspecies using high-density oligonucleotide tiling microarrays. Our results provided expression data support for the existence of 35,970 (81.9%) annotated gene models and identified 5,464 unique transcribed intergenic regions...... that share similar compositional properties with the annotated exons and have significant homology to other plant proteins. Elucidating and mapping of all transcribed regions revealed an association between global transcription and cytological chromosome features, and an overall similarity of transcriptional......Sequencing and computational annotation revealed several features, including high gene numbers, unusual composition of the predicted genes and a large number of genes lacking homology to known genes, that distinguish the rice (Oryza sativa) genome from that of other fully sequenced model species...

Geographic authentication of Asian rice (Oryza sativa L.) using multi-elemental and stable isotopic data combined with multivariate analysis.

Science.gov (United States)

Chung, Ill-Min; Kim, Jae-Kwang; Lee, Kyoung-Jin; Park, Sung-Kyu; Lee, Ji-Hee; Son, Na-Young; Jin, Yong-Ik; Kim, Seung-Hyun

2018-02-01

Rice (Oryza sativa L.) is the world's third largest food crop after wheat and corn. Geographic authentication of rice has recently emerged asan important issue for enhancing human health via food safety and quality assurance. Here, we aimed to discriminate rice of six Asian countries through geographic authentication using combinations of elemental/isotopic composition analysis and chemometric techniques. Principal components analysis could distinguish samples cultivated from most countries, except for those cultivated in the Philippines and Japan. Furthermore, orthogonal projection to latent structure-discriminant analysis provided clear discrimination between rice cultivated in Korea and other countries. The major common variables responsible for differentiation in these models were δ 34 S, Mn, and Mg. Our findings contribute to understanding the variations of elemental and isotopic compositions in rice depending on geographic origins, and offer valuable insight into the control of fraudulent labeling regarding the geographic origins of rice traded among Asian countries. Copyright © 2017 Elsevier Ltd. All rights reserved.

Refino de óleo de farelo de arroz (Oryza sativa L. em condições brandas para preservação do γ-orizanol Refining of rice bran oil (Oryza sativa L. to preserve γ-orizanol

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Luz Maria Paucar-Menacho

2007-08-01

Full Text Available O γ-orizanol é um antioxidante presente no óleo de farelo de arroz, mas ausente em outros óleos vegetais, ao qual têm sido atribuídos efeitos antioxidante e hipocolesterolêmico. O conteúdo de γ-orizanol no óleo de farelo de arroz bruto varia entre 1-2%, mas durante a etapa de neutralização do refino químico, este composto fica retido na borra. O presente trabalho teve por objetivo propor uma técnica alternativa de refino físico em condições brandas para o óleo de farelo de arroz com a finalidade de preservar o γ-orizanol. Utilizou-se farelo de arroz inativado e extrusado obtido a partir do processo de produção do arroz parboilizado, sendo o óleo bruto (Oryza sativa extraído pelo método de expeller. O processo de refino do óleo bruto consistiu nas etapas de degomagem ácida (com H3PO4 85%, centrifugação, clarificação, desodorização a 180 ºC e winterização. Foram realizadas análises para caracterização e comparação do óleo bruto e refinado, seguindo metodologias oficiais da AOCS. Concluiu-se que o processo de refino físico preservou 97% do γ-orizanol, o qual potencializou a estabilidade oxidativa do óleo refinado pelo método alternativo, que apresentou uma melhoria de 33% (13,3 horas a 110 ºC do período de indução da oxidação em relação ao óleo comercial.γ-orizanol is an antioxidant present in rice bran oil, but absent in other vegetable oils, which were attributed to antioxidant and hypocholesterolemic effects. The content of γ-orizanol in crude rice bran oil varies between 1-2%, but during neutralization in chemical refining this substance is transferred to soapstock. The aim of this research is to study an alternative technique of physical refining in light conditions with the purpose of preserving γ-orizanol. Inativacted and extrused rice bran obtained by the production of parboilizated rice was used to extract crude rice bran oil (Oryza sativa by the expeller method. The process of

The Role of Node Restriction on Cadmium Accumulation in the Brown Rice of 12 Chinese Rice (Oryza sativa L.) Cultivars.

Science.gov (United States)

Huang, Gaoxiang; Ding, Changfeng; Guo, Fuyu; Li, Xiaogang; Zhou, Zhigao; Zhang, Taolin; Wang, Xingxiang

2017-11-29

For selection or breeding of rice (Oryza sativa L.) cultivars with low Cd affinity, the role of node Cd restriction on Cd accumulation in brown rice was studied. A pot experiment was conducted to investigate the concentration of Cd in different sections of 12 Chinese rice cultivars. The results indicated that the Cd accumulation in the brown rice was mainly dependent on the root or shoot Cd concentration. Among the cultivars with nearly equal shoot Cd concentrations, Cd accumulation in brown rice was mainly dependent on the transport of Cd in the shoot. However, the Cd transport in the shoot was significantly restricted by the nodes, especially by the first node. Furthermore, the area of the diffuse vascular bundle in the junctional region of the flag leaf and the first node was a key contributor to the variations in Cd restriction by the nodes.

Influence of Rapeseed Cake on Iron Plaque Formation and Cd Uptake by Rice (Oryza sativa L.) Seedlings Exposed to Excess Cd.

Science.gov (United States)

Yang, Wen-Tao; Zhou, Hang; Gu, Jiao-Feng; Zeng, Qing-Ru; Liao, Bo-Han

2017-11-01

A soil spiking experiment at two Cd levels (0.72 and 5.20 mg kg -1 ) was conducted to investigate the effects of rapeseed cake (RSC) at application rates of 0%, 0.75%, 1.5%, and 3.0% (w/w) on iron plaque formation and Cd uptake by rice (Oryza sativa L.) seedlings. The use of RSC did result in a sharp decrease in soil bioavailability of Cd and a significant increase in rice growth, soil pH and organic matter. Application of RSC increased the amount of iron plaque formation and this effectively inhibited the uptake and translocation of Cd into the rice seedlings. RSC was an effective organic additive for increasing rice growth and reducing Cd uptake by rice plant, simultaneously. These results could be used as a reference for the safety use of Cd polluted paddy soil.

Immediate Genetic and Epigenetic Changes in F1 Hybrids Parented by Species with Divergent Genomes in the Rice Genus (Oryza.

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Ying Wu

Full Text Available Inter-specific hybridization occurs frequently in higher plants, and represents a driving force of evolution and speciation. Inter-specific hybridization often induces genetic and epigenetic instabilities in the resultant homoploid hybrids or allopolyploids, a phenomenon known as genome shock. Although genetic and epigenetic consequences of hybridizations between rice subspecies (e.g., japonica and indica and closely related species sharing the same AA genome have been extensively investigated, those of inter-specific hybridizations between more remote species with different genomes in the rice genus, Oryza, remain largely unknown.We investigated the immediate chromosomal and molecular genetic/epigenetic instability of three triploid F1 hybrids produced by inter-specific crossing between species with divergent genomes of Oryza by genomic in situ hybridization (GISH and molecular marker analysis. Transcriptional and transpositional activity of several transposable elements (TEs and methylation stability of their flanking regions were also assessed. We made the following principle findings: (i all three triploid hybrids are stable in both chromosome number and gross structure; (ii stochastic changes in both DNA sequence and methylation occurred in individual plants of all three triploid hybrids, but in general methylation changes occurred at lower frequencies than genetic changes; (iii alteration in DNA methylation occurred to a greater extent in genomic loci flanking potentially active TEs than in randomly sampled loci; (iv transcriptional activation of several TEs commonly occurred in all three hybrids but transpositional events were detected in a genetic context-dependent manner.Artificially constructed inter-specific hybrids of remotely related species with divergent genomes in genus Oryza are chromosomally stable but show immediate and highly stochastic genetic and epigenetic instabilities at the molecular level. These novel hybrids might

HrcQ is necessary for Xanthomonas oryzae pv. oryzae HR-induction in non-host tobacco and pathogenicity in host rice

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Xiaoping Zhang

2013-12-01

Full Text Available Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo, is one of the most destructive diseases of rice (Oryza sativa L. worldwide. The type III secretion system (T3SS of Xoo, encoded by the hrp (hypersensitive response and pathogenicity genes, plays critical roles in conferring pathogenicity in host rice and triggering a hypersensitive response (HR in non-host plants. To investigate the major genes conferring the pathogenicity and avirulence of Xoo, we previously constructed a random Tn5-insertion mutant library of Xoo strain PXO99A. We report here the isolation and characterization of a Tn5-insertion mutant PXM69. Tn5-insertion mutants were screened on indica rice JG30, which is highly susceptible to PXO99A, by leaf-cutting inoculation. Four mutants with reduced virulence were obtained after two rounds of screening. Among them, the mutant PXM69 had completely lost virulence to the rice host and ability to elicit HR in non-host tobacco. Southern blotting analysis showed a single copy of a Tn5-insertion in the genome of PXM69. PCR walking and sequencing analysis revealed that the Tn5 transposon was inserted at nucleotide position 70,192–70,201 in the genome of PXO99A, disrupting the type III hrc (hrp-conserved gene hrcQ, the first gene in the D operon of the hrp cluster in Xoo. To confirm the relationship between the Tn5-insertion and the avirulence phenotype of PXM69, we used the marker exchange mutagenesis to create a PXO99A mutant, ΔhrcQ::KAN, in which the hrcQ was disrupted by a kanamycin-encoding gene cassette at the same site as that of the Tn5-insertion. ΔhrcQ::KAN showed the same phenotype as mutant PXM69. Reintroduction of the wild-type hrcQ gene partially complemented the pathogenic function of PXM69. RT-PCR and cellulase secretion assays showed that the Tn5-disruption of hrcQ did not affect transcription of downstream genes in the D operon and function of the type II secretion system. Our results provide new insights into

HrcQ is necessary for Xanthomonas oryzae pv. oryzae HR-induction in non-host tobacco and pathogenicity in host rice

Institute of Scientific and Technical Information of China (English)

Xiaoping; Zhang; Chunlian; Wang; Chongke; Zheng; Jinying; Che; Yanqiang; Li; Kaijun; Zhao

2013-01-01

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae(Xoo), is one of the most destructive diseases of rice(Oryza sativa L.) worldwide. The type III secretion system(T3SS) of Xoo, encoded by the hrp(hypersensitive response and pathogenicity) genes, plays critical roles in conferring pathogenicity in host rice and triggering a hypersensitive response(HR) in non-host plants. To investigate the major genes conferring the pathogenicity and avirulence of Xoo, we previously constructed a random Tn5-insertion mutant library of Xoo strain PXO99A. We report here the isolation and characterization of a Tn5-insertion mutant PXM69. Tn5-insertion mutants were screened on indica rice JG30, which is highly susceptible to PXO99A, by leaf-cutting inoculation.Four mutants with reduced virulence were obtained after two rounds of screening. Among them, the mutant PXM69 had completely lost virulence to the rice host and ability to elicit HR in non-host tobacco. Southern blotting analysis showed a single copy of a Tn5-insertion in the genome of PXM69. PCR walking and sequencing analysis revealed that the Tn5 transposon was inserted at nucleotide position 70,192–70,201 in the genome of PXO99A, disrupting the type III hrc(hrp-conserved) gene hrcQ, the first gene in the D operon of the hrp cluster in Xoo. To confirm the relationship between the Tn5-insertion and the avirulence phenotype of PXM69, we used the marker exchange mutagenesis to create a PXO99Amutant, ΔhrcQ::KAN, in which the hrcQ was disrupted by a kanamycin-encoding gene cassette at the same site as that of the Tn5-insertion. ΔhrcQ::KAN showed the same phenotype as mutant PXM69. Reintroduction of the wild-type hrcQ gene partially complemented the pathogenic function of PXM69. RT-PCR and cellulase secretion assays showed that the Tn5-disruption of hrcQ did not affect transcription of downstream genes in the D operon and function of the type II secretion system. Our results provide new insights into the pathogenic

Potential of Anti Breast Cancer Black Ethanol Rice Extract (Oryza sativa L. indica In Decreasing Levels of CA 15-3 Serum in the White Mice Sprague dawley in Induction 7.12-Dimethylbenz (α Antracene (DMBA and Estrogen

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Zanuar Abidin

2017-01-01

Full Text Available Breast cancer is cancer that has the high incidence in Indonesia. Black rice (Oryza sativa L. indica is a plant that has an anticancer potency. This research aim is to prove black rice as a potential anticancer by using experimental animals, 20 Sprague Dawley female rats aged 7-8 weeks induced breast cancer by using the combination of 7,12-dimethylbenz (α anthracene (DMBA and estrogen. Rats were divided into two groups, namely the K-induced breast cancer and a group of P-induced cancer and treated with black rice. Black rice is given in the form of ethanol extract at a dose of 75 mg / kg / day for six weeks. Levels of CA 15-3 serum are used as a parameter. The result showed that the differences in levels of serum CA 15-3 are significant (p <0.05. Serum CA 15-3 level in P group is lower than in K group. This study proved that the ethanol extract of black rice (Oryza sativa L. indica has potential as an anticancer breast as indicated by decreased level of serum CA 15-3

RPAN: rice pan-genome browser for ∼3000 rice genomes.

Science.gov (United States)

Sun, Chen; Hu, Zhiqiang; Zheng, Tianqing; Lu, Kuangchen; Zhao, Yue; Wang, Wensheng; Shi, Jianxin; Wang, Chunchao; Lu, Jinyuan; Zhang, Dabing; Li, Zhikang; Wei, Chaochun

2017-01-25

A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Comparative analysis of the genomes of two field isolates of the rice blast fungus Magnaporthe oryzae.

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Minfeng Xue

Full Text Available Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice worldwide. The fungal pathogen is notorious for its ability to overcome host resistance. To better understand its genetic variation in nature, we sequenced the genomes of two field isolates, Y34 and P131. In comparison with the previously sequenced laboratory strain 70-15, both field isolates had a similar genome size but slightly more genes. Sequences from the field isolates were used to improve genome assembly and gene prediction of 70-15. Although the overall genome structure is similar, a number of gene families that are likely involved in plant-fungal interactions are expanded in the field isolates. Genome-wide analysis on asynonymous to synonymous nucleotide substitution rates revealed that many infection-related genes underwent diversifying selection. The field isolates also have hundreds of isolate-specific genes and a number of isolate-specific gene duplication events. Functional characterization of randomly selected isolate-specific genes revealed that they play diverse roles, some of which affect virulence. Furthermore, each genome contains thousands of loci of transposon-like elements, but less than 30% of them are conserved among different isolates, suggesting active transposition events in M. oryzae. A total of approximately 200 genes were disrupted in these three strains by transposable elements. Interestingly, transposon-like elements tend to be associated with isolate-specific or duplicated sequences. Overall, our results indicate that gain or loss of unique genes, DNA duplication, gene family expansion, and frequent translocation of transposon-like elements are important factors in genome variation of the rice blast fungus.

The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics1[C][W

Science.gov (United States)

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F.X.; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-01-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species. PMID:23184232

Hybrid Weakness Found in the Backcross Progeny of an Inter-Specific Cross of Oryza Sativa / O. Glumaepatula

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Sobrizal

2009-01-01

Full Text Available Hybrid breakdown expressed as sterility or weakness or both in F2 or later generations is considered to be a reproductive barrier between two distantly related taxa. Hybrid breakdown that showed poor growth habit with fertile seeds was found in the backcross progenies (BC4F2 which were derived from a cross between a cultivated rice Oryza sativa L. cv. Taichung 65 and a wild rice Oryza glumaepatula Steud (Acc. IRGC 105668 where Taichung 65 was used as a recurrent parent. Through segregation analysis of BC4F2 population, a novel gene for weakness was identified, and this gene was designated as hwf1 (hybrid weakness f-1. RFLP (Restriction Fragment Length Polymorphism analysis was employed to determine the chromosomal location of hwf1 gene. The result revealed that hwf1 was located between G3006 and C933 RFLP markers, with map distances of 0.5 cM and 1.9 cM, respectively, and co-segregated with C708, C820, and R288 on the short arm of chromosome 4. Since both O. glumaepatula (Acc. IRGC 105668 and Taichung 65 that was used as parents showed normal growth habit, the weakness in this study was assumed to be controlled by a set of complementary recessive genes. One of the complementary genes is hwf1 from O. glumaepatula, and another gene should be from Taichung 65, because the genetic background of the BC4F2 populations that were used for analysis is Taichung 65. The gene from Taichung 65 has not been identified yet, therefore, it is necessary to conduct the experiment for finding out the complement of hwf1 gene in near future.

Hybrid Weakness Found In the Backcross Progeny of an Inter-Specific Cross of Oryza Sativa / O. Glumaepatula

International Nuclear Information System (INIS)

Sobrizal; Yoshimura, A

2009-01-01

Hybrid breakdown expressed as sterility or weakness or both in F 2 or later generations is considered to be a reproductive barrier between two distantly related taxa. Hybrid breakdown that showed poor growth habit with fertile seeds was found in the backcross progenies (BC 4 F 2 ) which were derived from a cross between a cultivated rice Oryza sativa L. cv. Taichung 65 and a wild rice Oryza glumaepatula Steud (Acc. IRGC 105668) where Taichung 65 was used as a recurrent parent. Through segregation analysis of BC 4 F 2 population, a novel gene for weakness was identified, and this gene was designated as hwf1 (hybrid weakness f-1). RFLP (Restriction Fragment Length Polymorphism) analysis was employed to determine the chromosomal location of hwf1 gene. The result revealed that hwf1 was located between G3006 and C933 RFLP markers, with map distances of 0.5 cM and 1.9 cM, respectively, and co-segregated with C708, C820, and R288 on the short arm of chromosome 4. Since both O. glumaepatula (Acc. IRGC 105668) and Taichung 65 that was used as parents showed normal growth habit, the weakness in this study was assumed to be controlled by a set of complementary recessive genes. One of the complementary genes is hwf1 from O. glumaepatula, and another gene should be from Taichung 65, because the genetic background of the BC 4 F 2 populations that were used for analysis is Taichung 65. The gene from Taichung 65 has not been identified yet, therefore, it is necessary to conduct the experiment for finding out the complement of hwf1 gene in near future. (author)

Genetic diversity associated with conservation of endangered Dongxiang wild rice (Oryza rufipogon)

Science.gov (United States)

The wild progenitor species (Oryza rufipogon) of Asian cultivated rice (O. sativa) is located in Dongxiang county, China where it is considered the northernmost range worldwide. Nine ex situ and three in situ populations of the Dongxiang wild rice (DXWR) and four groups of modern cultivars were geno...

Physiological and molecular characterization of Si uptake in wild rice species.

Science.gov (United States)

Mitani-Ueno, Namiki; Ogai, Hisao; Yamaji, Naoki; Ma, Jian Feng

2014-07-01

Cultivated rice (Oryza sativa) accumulates high concentration of silicon (Si), which is required for its high and sustainable production. High Si accumulation in cultivated rice is achieved by a high expression of both influx (Lsi1) and efflux (Lsi2) Si transporters in roots. Herein, we physiologically investigated Si uptake, isolated and functionally characterized Si transporters in six wild rice species with different genome types. Si uptake by the roots was lower in Oryza rufipogon, Oryza barthii (AA genome), Oryza australiensis (EE genome) and Oryza punctata (BB genome), but similar in Oryza glumaepatula and Oryza meridionalis (AA genome) compared with the cultivated rice (cv. Nipponbare). However, all wild rice species and the cultivated rice showed similar concentration of Si in the shoots when grown in a field. All species with AA genome showed the same amino acid sequence of both Lsi1 and Lsi2 as O. sativa, whereas species with EE and BB genome showed several nucleotide differences in both Lsi1 and Lsi2. However, proteins encoded by these genes also showed transport activity for Si in Xenopus oocyte. The mRNA expression of Lsi1 in all wild rice species was lower than that in the cultivated rice, whereas the expression of Lsi2 was lower in O. rufipogon and O. barthii but similar in other species. Similar cellular localization of Lsi1 and Lsi2 was observed in all wild rice as the cultivated rice. These results indicate that superior Si uptake, the important trait for rice growth, is basically conserved in wild and cultivated rice species. © 2013 Scandinavian Plant Physiology Society.

Silicon alleviates simulated acid rain stress of Oryza sativa L. seedlings by adjusting physiology activity and mineral nutrients.

Science.gov (United States)

Ju, Shuming; Wang, Liping; Yin, Ningning; Li, Dan; Wang, Yukun; Zhang, Cuiying

2017-11-01

Silicon (Si) has been a modulator in plants under abiotic stresses, such as acid rain. To understand how silicon made an effect on rice (Oryza sativa L.) exposed to simulated acid rain (SAR) stress, the growth, physiologic activity, and mineral nutrient content in leaves of rice were investigated. The results showed that combined treatments with Si (1.0, 2.0, or 4.0 mM) and SAR (pH 4.0, 3.0, or 2.0) obviously improved the rice growth compared with the single treatment with SAR. Incorporation of Si into SAR treatment decreased malondialdehyde (MDA) content; increased soluble protein and proline contents; promoted CAT, POD, SOD, and APX activity; and maintained the K, Ca, Mg, Fe, Zn, Cu content balance in leaves of rice seedlings under SAR stress. The moderate concentration of Si (2.0 mM) was better than the low and high concentration of Si (1.0 and 4.0 mM). Therefore, application of Si could be a better strategy for maintaining the crop productivity in acid rain regions.

Mapping and marker-assisted selection of a brown planthopper resistance gene bph2 in rice (Oryza sativa L.).

Science.gov (United States)

Sun, Li-Hong; Wang, Chun-Ming; Su, Chang-Chao; Liu, Yu-Qiang; Zhai, Hu-Qu; Wan, Jian-Min

2006-08-01

Nilaparvata lugens Stål (brown planthopper, BPH), is one of the major insect pests of rice (Oryza sativa L.) in the temperate rice-growing region. In this study, ASD7 harboring a BPH resistance gene bph2 was crossed to a susceptible cultivar C418, a japonica restorer line. BPH resistance was evaluated using 134 F2:3 lines derived from the cross between "ASD7" and "C418". SSR assay and linkage analysis were carried out to detect bph2. As a result, the resistant gene bph2 in ASD7 was successfully mapped between RM7102 and RM463 on the long arm of chromosome 12, with distances of 7.6 cM and 7.2 cM, respectively. Meanwhile, both phenotypic selection and marker-assisted selection (MAS) were conducted in the BC1F1 and BC2F1 populations. Selection efficiencies of RM7102 and RM463 were determined to be 89.9% and 91.2%, respectively. It would be very beneficial for BPH resistance improvement by using MAS of this gene.

Physico-chemical and sensorial characteristics of rice (Oryza sativa L.) irradiated and the effect in Sitophilus oryzae L. development

International Nuclear Information System (INIS)

Zanao, Cintia Fernanda Pedroso

2007-01-01

Rice is exposed to injuries especially due to the attack of insects, which represent great qualitative and quantitative losses. The aim of the present research was to verify the viability of the gamma irradiation as rice (Oryza sativa L.) conservation method; its efficiency in the control of an important pest for stored grains Sitophilus oryzae L. and the effects that irradiation may present in irradiated grains in relation to the sensory aspect and starch alterations. Samples were composed of polished rice and the gamma irradiation dosages used were 0.5; 1.0; 3.0; and 5.0 kGy, and kept at room temperature. Analyses of the grain breakage percentages during processing and the longevity and reproduction of the rice weevil were performed. Analyses of the centesimal composition, phytic acid, apparent amylose content and starch paste properties were also conducted, as well as analyses of the rice color (instrumental) and acceptability (hedonic test), aimed at the determination of the raw and cooked rice sensory quality. It was verified that the gamma irradiation did not change the grain breakage percentage significantly and caused a negative effect on the insect development. Irradiation did not change the centesimal composition significantly. No significant values of phytic acid were found because during rice processing, the outer part (bran) containing 85-92% of total phytates was removed. Values from 17.33 to 18.44% for the apparent amylose content were found, and irradiation did not affect the rice starch amylose content significantly. The paste properties results were significantly changed, where reduction on the paste temperature, decrease on the time for the occurrence of the peak viscosity, reduction on the final viscosity values were observed. The retrogradation tendency became less intense in starches with increasing irradiation dosages. Statistical differences (p<0.05) were detected in the sensory aspect between irradiated and non-irradiated samples, and the

Effect of selenium application on arsenic uptake in rice (Oryza sativa L.).

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Kaur, Sumandeep; Singh, Dhanwinder; Singh, Kuldip

2017-09-01

Alluvial aquifers of the agrarian state of Punjab of southwestern arid zone used for irrigation of rice crops are rich in arsenic concentration. In the present study, rice (Oryza sativa L.) crops were raised in pots in a greenhouse with a purpose to study whether selenium (Se) application was effective in ameliorating As uptake. The rice crop was irrigated with arsenic laced water (0, 2.5, 5.0, 10.0 μM As L -1 ) throughout the growing period, without and with selenium (0.05 and 0.10 mg kg -1 ) added through mustard biomass, grown ex situ in seleniferous soil. Arsenic uptake and dry matter yield in different parts of the rice crop were assayed after application of As alone and simultaneous supplementations (As + Se). An antagonistic interaction between Se and As was observed. Addition of As through irrigation water significantly reduced yield of rice grain, straw and root. However, subsequent addition of Se helped in mitigating the harmful effect of As and countered the yield reduction caused due to As toxicity. The effect of Se on dry matter yield was more pronounced at its higher dose (0.10 mg kg -1 ) as compared to its lower dose (0.05 mg kg -1 ). The presence of Se either alone or added along with As significantly reduced the As concentration and its uptake by different parts of rice and higher reduction in As concentration was observed with addition of the highest level of applied Se (0.10 mg kg -1 ). Our observations indicated that Se supplementation might be favourable to reduce As accumulation and toxicity in rice crops.

Alternate wetting and drying decreases methylmercury in flooded rice (Oryza sativa) systems

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Tanner, K. Christy; Windham-Myers, Lisamarie; Marvin-DiPasquale, Mark C.; Fleck, Jacob; Linquist, Bruce A.

2018-01-01

In flooded soils, including those found in rice (Oryza sativa L.) fields, microbes convert inorganic Hg to more toxic methylmercury (MeHg). Methylmercury is accumulated in rice grain, potentially affecting health. Methylmercury in rice field surface water can bioaccumulate in wildlife. We evaluated how introducing aerobic periods into an otherwise continuously flooded rice growing season affects MeHg dynamics. Conventional continuously flooded (CF) rice field water management was compared with alternate wetting and drying, where irrigation was stopped twice during the growing season, allowing soil to dry to 35% volumetric moisture content, at which point plots were reflooded (AWD-35). Methylmercury studies began at harvest in Year 3 and throughout Year 4 of a 4-yr replicated field experiment. Bulk soil, water, and plant samples were analyzed for MeHg and total Hg (THg), and iron (Fe) speciation was measured in soil samples. Rice grain yield over 4 yr did not differ between treatments. Soil chemistry responded quickly to AWD-35 dry-downs, showing significant oxidation of Fe(II) accompanied by a significant reduction of MeHg concentration (76% reduction at harvest) compared with CF. Surface water MeHg decreased by 68 and 39% in the growing and fallow seasons, respectively, suggesting that the effects of AWD-35 management can last through to the fallow season. The AWD-35 treatment reduced rice grain MeHg and THg by 60 and 32%, respectively. These results suggest that the more aerobic conditions caused by AWD-35 limited the activity of Hg(II)-methylating microbes and may be an effective way to reduce MeHg concentrations in rice ecosystems.

Black rice (Oryza sativa L.) extracts induce osteoblast differentiation and protect against bone loss in ovariectomized rats.

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Jang, Woo-Seok; Seo, Cho-Rong; Jang, Hwan Hee; Song, No-Joon; Kim, Jong-Keun; Ahn, Jee-Yin; Han, Jaejoon; Seo, Woo Duck; Lee, Young Min; Park, Kye Won

2015-01-01

Osteoporosis, an age associated skeletal disease, exhibits increased adipogenesis at the expense of osteogenesis from common osteoporotic bone marrow cells. In this study, black rice (Oryza sativa L.) extracts (BRE) were identified as osteogenic inducers. BRE stimulated the alkaline phosphatase (ALP) activity in both C3H10T1/2 and primary bone marrow cells. Similarly, BRE increased mRNA expression of ALP and osterix. Oral administration of BRE in OVX rats prevented decreases in bone density and strength. By contrast, BRE inhibited adipocyte differentiation of mesenchymal C3H10T1/2 cells and prevented increases in body weight and fat mass in high fat diet fed obese mice, further suggesting the dual effects of BRE on anti-adipogenesis and pro-osteogenesis. UPLC analysis identified cyanidin-3-O-glucoside and peonidin-3-O-glucoside as main anti-adipogenic effectors but not for pro-osteogenic induction. In mechanism studies, BRE selectively stimulated Wnt-driven luciferase activities. BRE treatment also induced Wnt-specific target genes such as Axin2, WISP2, and Cyclin D1. Taken together, these data suggest that BRE is a potentially useful ingredient to protect against age related osteoporosis and diet induced obesity.

Role of salicylic acid in alleviating oxidative damage in rice roots (Oryza sativa) subjected to cadmium stress

International Nuclear Information System (INIS)

Guo, B.; Liang, Y.C.; Zhu, Y.G.; Zhao, F.J.

2007-01-01

Time-dependent changes in enzymatic and non-enzymatic antioxidants, and lipid peroxidation were investigated in roots of rice (Oryza sativa) grown hydroponically with Cd, with or without pretreatment of salicylic acid (SA). Exposure to 50 μM Cd significantly decreased root growth, and activities of superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD), but increased the concentrations of H 2 O 2 , malondialdehyde (MDA), ascorbic acid (AsA), glutathione (GSH) and non-protein thiols (NPT). However, pretreatment with 10 μM SA enhanced the activities of antioxidant enzymes and the concentrations of non-enzymatic antioxidants, but lowered the concentrations of H 2 O 2 and MDA in the Cd-stressed rice compared with the Cd treatment alone. Pretreatment with SA alleviated the Cd-induced inhibition of root growth. The results showed that pretreatment with SA enhanced the antioxidant defense activities in Cd-stressed rice, thus alleviating Cd-induced oxidative damage and enhancing Cd tolerance. The possible mechanism of SA-induced H 2 O 2 signaling in mediating Cd tolerance was discussed. - Pretreatment with SA enhanced the antioxidant defense activities in Cd-stressed rice, thus alleviating Cd-induced oxidative damage and enhancing Cd tolerance

Zinco, chumbo e cádmio em plantas de arroz (Oryza Sativa L. cultivadas em solo após adição de resíduo siderúrgico Zinc, lead and cadmium influence in rice plants (Oryza Sativa L. cultivated in soil with addition of siderurgical residue

Directory of Open Access Journals (Sweden)

André Fernão Martins de Andrade

2008-10-01

Full Text Available Os efeitos da aplicação de resíduo siderúrgico, proveniente da concentração de zinco em lama de altos-fornos siderúrgicos, como fonte de zinco para plantas de arroz (Oryza Sativa L. BRS Curinga e a toxicidade devida ao cádmio e ao chumbo no resíduo, foram estudados em experimento de casa de vegetação. O material de solo usado foi proveniente do horizonte A e B de um Latossolo Vermelho-Amarelo e do horizonte A de um Neossolo Flúvico, coletados no município de Pinheiral, Estado do Rio de Janeiro. Foram aplicadas quatro doses de resíduo (94; 281; 844 e 2531kg ha-1. Foi determinado o teor de zinco, cádmio e chumbo na raiz e na parte aérea das plantas de arroz. As plantas crescidas no horizonte A do Neossolo Flúvico apresentaram a maior produção de matéria seca e a maior acumulação de zinco e a menor de cádmio. As plantas de arroz desenvolvidas no horizonte B do Latossolo apresentaram a menor produção de matéria seca, menor acumulação de zinco e a maior de chumbo, enquanto que as cultivadas no horizonte A do Latossolo apresentaram a mais elevada produção de matéria seca dos três substratos utilizados. O zinco e o chumbo concentraram-se, principalmente, nas raízes das plantas, e o cádmio se concentrou na parte aérea. Pelas características apresentadas nos solos estudados e pelas concentrações fitotóxicas do chumbo e do cádmio encontradas nas plantas desenvolvidas sobre o horizonte B do Latossolo, não é recomendável a utilização desse resíduo como fonte de zinco para a cultura do arroz.The effects of application of siderurgical residue, originated from the zinc concentration in siderurgical high-ovens mud, as supply of zinc for rice plants (Oryza Sativa L. and the toxicity due to cadmium and lead from the residue, were studied in a greenhouse experiment.The period of the experiment was from April of 2005 to March of 2006. The soil materials were from the A and B horizons of a Yellow - Red Oxisol, and the A

Genetic relationships between interspecific lines derived from Oryza glaberrima and Oryza sativa crosses using microsatellites and agro-morphological markers

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Moukoumbi, Y.D.; Kolade, O.; Drame, K.N.; Sie, M.; Ndjiondjo, M.N.

2015-07-01

New Rice(s) for Africa (NERICA) are high yielding rice varieties mostly cultivated in Sub-Saharan Africa and developed by the Africa Rice Center. This study is aimed at investigating the proportion of introgression of parental genomic contribution of 60 lowland NERICA varieties and establishment of molecular profiling. Agro-morphological data from 17 characteristics was recorded and significant (p<0.05) to high significant (p<0.0001) differences were obtained with leaf length and width, plant height at maturity, days to heading, maturity, primary and secondary branching of panicles, and grain width and grain thickness. A total of 114 microsatellite polymorphic markers covering 2183.13 cM of the rice genome showed the proportions of alleles introgressed from the donor parent (Oryza glaberrima) into 52 lowland NERICA lines (TOG5681 and IR64) as follows: 11% for BC2, 6.07% for BC3, and 7.55% for BC4. The introgression proportions for the eight remaining lowland NERICA lines derived from other crosses ranged from 5.5 to 11.3%. The proportion recorded with the recurrent parent was 83.99%. The highest introgression proportions of the O. glaberrima allele for all 60 lowland NERICA lines were found on chromosomes 2, 6 and 12 (TOG5681/IR64) and on chromosome 3 with NERIC-L-29 (TOG5681/IR1529-680-3-2). Multivariate analyses performed using an association of agro-morphological and molecular data revealed two major groups according to the distribution of the lowland NERICAs including the lowland NERICAs released were found in cluster 1 of the dendrogram. Genetic and genomic studies, QTL identification and analysis using agro-morphologically significant traits revealed should be used to develop mega-varieties adapted in rice growth conditions in Sub-Saharan Africa. (Author)

Development of a quantitative pachytene chromosome map and its unification with somatic chromosome and linkage maps of rice (Oryza sativa L.).

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Ohmido, Nobuko; Iwata, Aiko; Kato, Seiji; Wako, Toshiyuki; Fukui, Kiichi

2018-01-01

A quantitative pachytene chromosome map of rice (Oryza sativa L.) was developed using imaging methods. The map depicts not only distribution patterns of chromomeres specific to pachytene chromosomes, but also the higher order information of chromosomal structures, such as heterochromatin (condensed regions), euchromatin (decondensed regions), the primary constrictions (centromeres), and the secondary constriction (nucleolar organizing regions, NOR). These features were image analyzed and quantitatively mapped onto the map by Chromosome Image Analyzing System ver. 4.0 (CHIAS IV). Correlation between H3K9me2, an epigenetic marker and formation and/or maintenance of heterochromatin, thus was, clearly visualized. Then the pachytene chromosome map was unified with the existing somatic chromosome and linkage maps by physically mapping common DNA markers among them, such as a rice A genome specific tandem repeat sequence (TrsA), 5S and 45S ribosomal RNA genes, five bacterial artificial chromosome (BAC) clones, four P1 bacteriophage artificial chromosome (PAC) clones using multicolor fluorescence in situ hybridization (FISH). Detailed comparison between the locations of the DNA probes on the pachytene chromosomes using multicolor FISH, and the linkage map enabled determination of the chromosome number and short/long arms of individual pachytene chromosomes using the chromosome number and arm assignment designated for the linkage map. As a result, the quantitative pachytene chromosome map was unified with two other major rice chromosome maps representing somatic prometaphase chromosomes and genetic linkages. In conclusion, the unification of the three rice maps serves as an indispensable basic information, not only for an in-depth comparison between genetic and chromosomal data, but also for practical breeding programs.

Germination and plantlet regeneration of encapsulated microshoots of aromatic rice (Oryza sativa L. Cv. MRQ 74).

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Taha, Rosna Mat; Saleh, Azani; Mahmad, Noraini; Hasbullah, Nor Azlina; Mohajer, Sadegh

2012-01-01

Plant tissues such as somatic embryos, apical shoot tips, axillary shoot buds, embryogenic calli, and protocom-like bodies are potential micropropagules that have been considered for creating synthetic seeds. In the present study, 3-5 mm microshoots of Oryza sativa L. Cv. MRQ 74 were used as explant sources for obtaining synthetic seeds. Microshoots were induced from stem explants on Murashige and Skoog (MS) medium supplemented with 1.5 mg/L benzylaminopurine (BAP). They were encapsulated in 3% (w/v) sodium alginate, 3% sucrose, 0.1 mg/L BAP, and 0.1 mg/L α-Naphthalene acetic acid (NAA). Germination and plantlet regeneration of the encapsulated seeds were tested by culturing them on various germination media. The effect of storage period (15-30 days) was also investigated. The maximum germination and plantlet regeneration (100.0%) were recorded on MS media containing 3% sucrose and 0.8% agar with and without 0.1 mg/L BAP. However, a low germination rate (6.67%) was obtained using top soil as a sowing substrate. The germination rate of the encapsulated microshoots decreased from 93.33% to 3.33% after 30 days of storage at 4°C in the dark. Therefore, further research is being done to improve the germination rate of the synthetic seeds.

Characterization and genetic mapping of a Photoperiod-sensitive dwarf 1 locus in rice (Oryza sativa L.).

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Li, Riqing; Xia, Jixing; Xu, Yiwei; Zhao, Xiucai; Liu, Yao-Guang; Chen, Yuanling

2014-01-01

Plant height is an important agronomic trait for crop architecture and yield. Most known factors determining plant height function in gibberellin or brassinosteroid biosynthesis or signal transduction. Here, we report a japonica rice (Oryza sativa ssp. japonica) dominant dwarf mutant, Photoperiod-sensitive dwarf 1 (Psd1). The Psd1 mutant showed impaired cell division and elongation, and a severe dwarf phenotype under long-day conditions, but nearly normal growth in short-day. The plant height of Psd1 mutant could not be rescued by gibberellin or brassinosteroid treatment. Genetic analysis with R1 and F2 populations determined that Psd1 phenotype was controlled by a single dominant locus. Linkage analysis with 101 tall F2 plants grown in a long-day season, which were derived from a cross between Psd1 and an indica cultivar, located Psd1 locus on chromosome 1. Further fine-mapping with 1017 tall F2 plants determined this locus on an 11.5-kb region. Sequencing analysis of this region detected a mutation site in a gene encoding a putative lipid transfer protein; the mutation produces a truncated C-terminus of the protein. This study establishes the genetic foundation for understanding the molecular mechanisms regulating plant cell division and elongation mediated by interaction between genetic and environmental factors.

The humic acids from vermicompost protect rice (Oryza sativa L.) plants against a posterior hidric stress

International Nuclear Information System (INIS)

Guridi-Izquierdo, Fernando; Martínez-Balmori, Dariellys; Rosquete-Bassó, Mayelín; Calderín-García, Andrés; Louro-Berbara, Ricardo L.

2017-01-01

The humic acids (HA) from two different vermicompost were extracted, isolated, purified and partially characterized, to evaluate their possible protection in rice (Oryza sativa L.) plants against an hydric stress. Differences in elemental composition, as the coagulation threshold value and E4/E6 relation in their UV-Vis spectra were found. Two concentrations (40 and 60 mg L-1) of both HA were included in the nutritive solutions for rice plants in controlled conditions. It was verified that the previous treatment with the HA during six days stimulated the root biomass production. Later the HA were excluded and was an hydric deficit induced by adding polietilenglicol (PEG-6000) in the initially treated plants and in a group of those used as control. After 96 hours of this final condition the net radical biomass, the photosynthetic pigments content and the root membrane permeability were evaluated. In the plants previously treated with HA (at the concentration 60 mg HA L-1), the root membrane permeability, the net radical biomass production and the “a” chlorophyll content had no differences when compared with those without stress. It was concluded that the previous treatment with the HA protected the rice plants against a posterior hydric stress that was induced. (author)

Molecular characterization and genetic diversity of different genotypes of Oryza sativa and Oryza glaberrima

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Caijin Chen

2017-11-01

Conclusions: Genetic diversity studies revealed that 50 rice types were clustered into different subpopulations whereas three genotypes were admixtures. Molecular fingerprinting and 10 specific markers were obtained to identify the 53 rice genotypes. These results can facilitate the potential utilization of sibling species in rice breeding and molecular classification of O. sativa and O. glaberrima germplasms.

Quantitative Classification of Rice (Oryza sativa L.) Root Length and Diameter Using Image Analysis.

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Gu, Dongxiang; Zhen, Fengxian; Hannaway, David B; Zhu, Yan; Liu, Leilei; Cao, Weixing; Tang, Liang

2017-01-01

Quantitative study of root morphological characteristics of plants is helpful for understanding the relationships between their morphology and function. However, few studies and little detailed and accurate information of root characteristics were reported in fine-rooted plants like rice (Oryza sativa L.). The aims of this study were to quantitatively classify fine lateral roots (FLRs), thick lateral roots (TLRs), and nodal roots (NRs) and analyze their dynamics of mean diameter (MD), lengths and surface area percentage with growth stages in rice plant. Pot experiments were carried out during three years with three rice cultivars, three nitrogen (N) rates and three water regimes. In cultivar experiment, among the three cultivars, root length of 'Yangdao 6' was longest, while the MD of its FLR was the smallest, and the mean diameters for TLR and NR were the largest, the surface area percentage (SAP) of TLRs (SAPT) was the highest, indicating that Yangdao 6 has better nitrogen and water uptake ability. High N rate increased the length of different types of roots and increased the MD of lateral roots, decreased the SAP of FLRs (SAPF) and TLRs, but increased the SAP of NRs (SAPN). Moderate decrease of water supply increased root length and diameter, water stress increased the SAPF and SAPT, but decreased SAPN. The quantitative results indicate that rice plant tends to increase lateral roots to get more surface area for nitrogen and water uptake when available assimilates are limiting under nitrogen and water stress environments.

Effector-mediated suppression of chitin-triggered immunity by Magnaporthe oryzae is necessary for rice blast disease

NARCIS (Netherlands)

Mentlak, T.A.; Kombrink, A.; Shinya, T.; Ryder, L.S.; Otomo, I.; Saitoh, H.; Terauchi, R.; Nishizawa, Y.; Shibuya, N.; Thomma, B.P.H.J.; Talbot, N.J.

2012-01-01

Plants use pattern recognition receptors to defend themselves from microbial pathogens. These receptors recognize pathogen-associated molecular patterns (PAMPs) and activate signaling pathways that lead to immunity. In rice (Oryza sativa), the chitin elicitor binding protein (CEBiP) recognizes

Effect of coated urea on cadmium accumulation in Oryza sativa L. grown in contaminated soil.

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Xu, Chao; Wu, Zisong; Zhu, Qihong; Zhu, Hanhua; Zhang, Yangzhu; Huang, Daoyou

2015-11-01

Experiments were conducted to determine the effects of three types of coated urea on the accumulation of cadmium (Cd) in rice (Oryza sativa L.) grown in contaminated soil. Pot-culture experiments were conducted in a greenhouse from July to November 2012 on the rice cultivar "Hua Hang Si Miao" in Guangzhou (China). The experimental design was completely randomized with four treatments and three replications. The treatments were control (CK) (N 0 mg/kg), prilled urea (PU) (N 200 mg/kg), polymer-coated urea (PCU) (N 200 mg/kg), and sulfur-coated urea (SCU) (N 200 mg/kg). Our results indicated that applications of PCU and SCU slightly increased the dry weight of rice grains. The application of SCU significantly decreased the CaCl2 and toxicity characteristic leaching procedure (TCLP)-extractable Cd concentrations by 15.4 and 56.1%, respectively. Sequential extractions showed that PCU and SCU applications led to a significant decrease in Cd in the exchangeable fraction and an increase in the bound iron (Fe) and manganese (Mn) oxides fractions. Cd concentrations in grains treated with PCU were reduced by 11.7%, whereas SCU significantly reduced Cd concentrations by 29.1%. SCU reduced Cd transfer from the straws to the grain. Our results demonstrated that PCU and SCU may be effective in mitigating Cd accumulation in rice grown in acidic Cd-contaminated soil, especially in plants receiving SCU.

Cadmium and lead content in several brands of rice grains (Oryza sativa) in central Iran.

Science.gov (United States)

Shakerian, A; Rahimi, E; Ahmadi, M

2012-11-01

The aim of this study was to investigate the cadmium (Cd) and lead (Pb) content of several commercially available brands of rice grains (Oryza sativa) in central Iran. A total of 67 samples of the most widely consumed brands of rice grains were purchased from local bazaar markets in Shahrekord, Iran. The first step, grains of raw rice were digested by acid digestion method and then were analyzed by atomic absorption spectrometer. The results showed that Cd concentration in rice grains ranged from 0.0378 to 0.1225 ppm dry weight and its average concentration was 0.062 ± 0.019 ppm and Pb content ranged from 0.0405 to 0.1281 ppm dry weight and its average concentration was 0.068 ± 0.0185 ppm. Cd and Pb concentrations in the sampled rice grains were lower in comparison with their upper limits (0.2 and 0.2 ppm for Cd and Pb, respectively) approved by food sanitary standard. Therefore, it can be concluded that there is no health problems due to the consumption of brands of rice grains, for these two elements. The results indicated that weekly intake of Cd and Pb from rice grains was below the provisional tolerable weekly intakes recommended by WHO/FAO.

Influence of lead on atrazine uptake by rice (Oryza sativa L.) seedlings from nutrient solution.

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Su, Yu-Hong; Zhu, Yong-Guan

2005-01-01

Atrazine is a widely used herbicide, and its persistence in soil and water causes environmental concerns. In the past, plant uptake processes are mainly investigated for single contaminants. However, in many cases, contaminants co-exist in environmental matrix, such as soil, and plant uptake of one contaminant may be influenced by its co-existing ones. The uptake of atrazine by rice seedlings (Oryza sativa L.) from nutrient solution through the roots was investigated in a solution culture, over an exposure period of 4 weeks. Atrazine accumulation in plant tissues was determined by gas chromatography, and lead was determined using atomic absorption spectrometry. With different ratios of atrazine and Pb2+ concentrations in solution, the observed atrazine concentrations in shoots and roots varied significantly. In atrazine-Pb2+ mixture systems, the added Pb2+ either increased or decreased the concentrations or BCFs of atrazine in seedlings (relative to those without Pb2+), depending on the atrazine-Pb2+ ratio in nutrient solution. The enhanced atrazine uptake results presumably from atrazine-Pb2+ complex formation. The reduced atrazine uptake, which occurred mainly at high atrazine concentrations, is attributed to atrazine toxicity that inhibited seedling growth and transpiration. The formation of atrazine-Pb2+ complex both in the solution and within plant tissues may affect the accumulation of both contaminants by rice plants.

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice.

Science.gov (United States)

Brozynska, Marta; Copetti, Dario; Furtado, Agnelo; Wing, Rod A; Crayn, Darren; Fox, Glen; Ishikawa, Ryuji; Henry, Robert J

2017-06-01

The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Ultrastructure of Oryza glumaepatula , a wild rice species endemic of tropical America

Directory of Open Access Journals (Sweden)

Ethel Sánchez

2005-06-01

Full Text Available Oryza glumaepatula is a perennial wild rice species,endemic to tropical America, previously known as the Latin American race of Oryza rufipogon .In Costa Rica, it is found in the northern region of the country, mainly in the wetland of the Medio Queso River, Los Chiles, Alajuela. It is diploid, of AA type genome and because of its genetic relatedness to cultivated rice it is included in the O.sativa complex. We describe the ultrastructure of leaf blade, spikelet, ligule and auricles. Special emphasis is given to those traits of major taxonomic value for O.glumaepatula and to those characters that distinguish this species from O. rufipogon and O. sativa . O. glumaepatula has a leaf blade covered with tombstone-shaped, oblong and spheroid epicuticular wax papillae. It has diamond-shaped stomata surrounded by spherical papillae, rows of zipper-like silica cells, bulky prickle trichomes of ca .40 mu m in length and small hirsute trichomes of ca. 32 mu m in length.The central vein is covered with large,globular papillae of ca. 146 mu m in length,a characteristic that distinguishes this species from O.rufipogon and O.sativa. The border of the leaf blade exhibits a row of even-sized bulky prickle trichomes of ca .42.5 mu m in length.Auricles have attenuated trichomes of ca .5.5 mm in length on the edges and small bicellular trichomes of 120 mu m in length on the surface.The ligule has a large number of short attenuated trichomes on its surface of 100 mu m in length.These latter two traits have important taxonomic value since they were found in O.glumaepatula but not found in O.sativa or in O.rufipogon . The spikelet has the typical morphology of the Oryza genus. Fertile lemmas have abundant spines, a trait shared with O.rufipogon but not with O.sativa. The sterile lemmas are wing-shaped with serrated borders,a characteristic that distinguishes this species from O. rufipogon and O.sativa. All the ultrastructure characters observed in O.glumaepatula from

Comparison of physiological and anatomical changes of C3 (Oryza sativa [L.]) and C4 (Echinochloa crusgalli [L.]) leaves in response to drought stress

Science.gov (United States)

Hamim, Hamim; Banon, Sri; Dorly, Dorly

2016-01-01

The experiment aimed to analyse the different response of C3 (Oryza sativa L.) and C4 (Echinochloa crusgalli L.) species to drought stress based on physiological and anatomical properties. Seeds of rice (Oryza sativa) and Echinochloa (Echinochloa crusgalli) were grown in 15 cm (D) pot for 6 weeks under well-watered conditions. After 6 weeks the plants were divided into two groups, (1) well-watered which were watered daily, and (2) drought stress which were withheld from watering for 6 days. After 6 days of drought, the plants were then re-watered to analyse plant recovery. During drought period, the plants were analysed for growth, leaf relative water content (RWC), photosynthesis, and leaf anatomy. Drought stress significantly reduced leaf RWC of both species, but the reduction was bigger in rice than in Echinochloa. The maximum efficiency of photosynthesis (Fv/Fm) was decrease significantly in response to drought stress by about 48.04% in rice, while it was only 34.40% in Echinochloa. Anatomical analysis showed drought treatment tended to reduce leaf thickness in the area of bulliform cell, major- as well as intervein and xylem diameter, more in Echinochloa than in rice, suggesting that the decrease of vein and xylem diameter is among the anatomical parameters that is important to overcome from drought stress in Echinochloa. The number of chloroplast in the mesophyll cell and bundle sheath cell (BSC) was different between these two species, where in Echinochloa chloroplast was found in both mesophyll as well as BSC, while in rice it was only found in mesophyll cell, confirmed that Echinochloa is a C4 and rice is a C3 species. Interestingly, in Echinochloa, the number of chloroplast was significantly increased due to drought stress in BSC, but not in mesophyll cell. The number of starch granules also dramatically increased in response to drought in the mesophyll cells of rice and Echinochloa, and in the bundle sheath cell of Echinochloa which indicate that C3

OsPIN5b modulates rice (Oryza sativa) plant architecture and yield by changing auxin homeostasis, transport and distribution.

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Lu, Guangwen; Coneva, Viktoriya; Casaretto, José A; Ying, Shan; Mahmood, Kashif; Liu, Fang; Nambara, Eiji; Bi, Yong-Mei; Rothstein, Steven J

2015-09-01

Plant architecture attributes such as tillering, plant height and panicle size are important agronomic traits that determine rice (Oryza sativa) productivity. Here, we report that altered auxin content, transport and distribution affect these traits, and hence rice yield. Overexpression of the auxin efflux carrier-like gene OsPIN5b causes pleiotropic effects, mainly reducing plant height, leaf and tiller number, shoot and root biomass, seed-setting rate, panicle length and yield parameters. Conversely, reduced expression of OsPIN5b results in higher tiller number, more vigorous root system, longer panicles and increased yield. We show that OsPIN5b is an endoplasmic reticulum (ER) -localized protein that participates in auxin homeostasis, transport and distribution in vivo. This work describes an example of an auxin-related gene where modulating its expression can simultaneously improve plant architecture and yield potential in rice, and reveals an important effect of hormonal signaling on these traits. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Transgenerational inheritance of modified DNA methylation patterns and enhanced tolerance induced by heavy metal stress in rice (Oryza sativa L.).

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Ou, Xiufang; Zhang, Yunhong; Xu, Chunming; Lin, Xiuyun; Zang, Qi; Zhuang, Tingting; Jiang, Lili; von Wettstein, Diter; Liu, Bao

2012-01-01

DNA methylation is sensitive and responsive to stressful environmental conditions. Nonetheless, the extent to which condition-induced somatic methylation modifications can impose transgenerational effects remains to be fully understood. Even less is known about the biological relevance of the induced epigenetic changes for potentially altered well-being of the organismal progenies regarding adaptation to the specific condition their progenitors experienced. We analyzed DNA methylation pattern by gel-blotting at genomic loci representing transposable elements and protein-coding genes in leaf-tissue of heavy metal-treated rice (Oryza sativa) plants (S0), and its three successive organismal generations. We assessed expression of putative genes involved in establishing and/or maintaining DNA methylation patterns by reverse transcription (RT)-PCR. We measured growth of the stressed plants and their unstressed progenies vs. the control plants. We found (1) relative to control, DNA methylation patterns were modified in leaf-tissue of the immediately treated plants, and the modifications were exclusively confined to CHG hypomethylation; (2) the CHG-demethylated states were heritable via both maternal and paternal germline, albeit often accompanying further hypomethylation; (3) altered expression of genes encoding for DNA methyltransferases, DNA glycosylase and SWI/SNF chromatin remodeling factor (DDM1) were induced by the stress; (4) progenies of the stressed plants exhibited enhanced tolerance to the same stress their progenitor experienced, and this transgenerational inheritance of the effect of condition accompanying heritability of modified methylation patterns. Our findings suggest that stressful environmental condition can produce transgenerational epigenetic modifications. Progenies of stressed plants may develop enhanced adaptability to the condition, and this acquired trait is inheritable and accord with transmission of the epigenetic modifications. We suggest

Exploring the power of rice (O. sativa x O. rufipogon) chromosome segment substitution line libraries

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Transgressive variation was reported as an increase in grain yield for several rice (Oryza sativa x O. rufipogon) advanced backcross mapping populations. The objective of this study was to develop chromosome segment substitution line (CSSL) libraries to further dissect the reported transgressive var...

Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing

OpenAIRE

Wang, Bin; Guo, Guangwu; Wang, Chao; Lin, Ying; Wang, Xiaoning; Zhao, Mouming; Guo, Yong; He, Minghui; Zhang, Yong; Pan, Li

2010-01-01

Aspergillus oryzae, an important filamentous fungus used in food fermentation and the enzyme industry, has been shown through genome sequencing and various other tools to have prominent features in its genomic composition. However, the functional complexity of the A. oryzae transcriptome has not yet been fully elucidated. Here, we applied direct high-throughput paired-end RNA-sequencing (RNA-Seq) to the transcriptome of A. oryzae under four different culture conditions. With the high resoluti...

Comparative genomic analysis identified a mutation related to enhanced heterologous protein production in the filamentous fungus Aspergillus oryzae.

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Jin, Feng-Jie; Katayama, Takuya; Maruyama, Jun-Ichi; Kitamoto, Katsuhiko

2016-11-01

Genomic mapping of mutations using next-generation sequencing technologies has facilitated the identification of genes contributing to fundamental biological processes, including human diseases. However, few studies have used this approach to identify mutations contributing to heterologous protein production in industrial strains of filamentous fungi, such as Aspergillus oryzae. In a screening of A. oryzae strains that hyper-produce human lysozyme (HLY), we previously isolated an AUT1 mutant that showed higher production of various heterologous proteins; however, the underlying factors contributing to the increased heterologous protein production remained unclear. Here, using a comparative genomic approach performed with whole-genome sequences, we attempted to identify the genes responsible for the high-level production of heterologous proteins in the AUT1 mutant. The comparative sequence analysis led to the detection of a gene (AO090120000003), designated autA, which was predicted to encode an unknown cytoplasmic protein containing an alpha/beta-hydrolase fold domain. Mutation or deletion of autA was associated with higher production levels of HLY. Specifically, the HLY yields of the autA mutant and deletion strains were twofold higher than that of the control strain during the early stages of cultivation. Taken together, these results indicate that combining classical mutagenesis approaches with comparative genomic analysis facilitates the identification of novel genes involved in heterologous protein production in filamentous fungi.

Chemical Modification of Oryza sativa Linnaeus Husk with Urea for Removal of Brilliant Vital Red and Murexide Dyes from Water by Adsorption in Environmentally Benign Way

International Nuclear Information System (INIS)

Rehman, R.; Mahmud, T.; Kanwal, F.; Aslam, M.N.; Nisar, H.

2013-01-01

Oryza sativa Linnaeus is an important food item all around the world. Due to its huge consumption, a large amount of rice husk is generated as agrowaste which can be used for water treatment by adsorption. Its adsorption capacity further can be enhanced by chemical medication. In the present study, urea modified rice husk has been used for removing Brilliant Vital Red and Murexide form water in an efficient way. After optimizing operating conditions, isothermal and thermodynamical studies were carried out, which showed that maximum adsorption capacity of urea modified rice husk for removing Brilliant Vital Red and Murexide dyes were 28.93 and 30.74 mg.g/sup -1/. Adsorbent characterization was carried out by recording its FT-IR spectra. (author)

The Role of Drosophila Merlin in the Control of Mitosis Exit and Development

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2008-07-01

chrysosporium --- http://genome.jgi-p Aspergillus flavus --- http://www.tigr.or Arabidopsis thaliana --- http://www.tigr.or Oryza sativa --- http...distinguish colon and ovarian adenocarcinomas: identi- fication, genomic, proteomic , and tissue array profiling. Cancer Res 2003;63:5243–50. 108

Rim 2/Hipa CACTA transposon display ; A new genetic marker technique in Oryza species

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Lee Ju

2005-03-01

Full Text Available Abstract Background Transposons constitute the major fractions of repetitive sequences in eukaryotes, and have been crucial in the shaping of current genomes. Transposons are generally divided into two classes according to the mechanism underlying their transposition: RNA intermediate class 1 and DNA intermediate class 2. CACTA is a class 2 transposon superfamily, which is found exclusively in plants. As some transposons, including the CACTA superfamily, are highly abundant in plant species, and their nucleotide sequences are highly conserved within a family, they can be utilized as genetic markers, using a slightly modified version of the conventional AFLP protocol. Rim2 /Hipa is a CACTA transposon family having 16 bp consensus TIR sequences to be present in high copy numbers in rice genome. This research was carried out in order to develop a Rim2/Hipa CACTA-AFLP or Rim2/Hipa CACTA-TD (transposon display, hereafter Rim2/Hipa-TD protocol for the study of genetic markers in map construction and the study of genetic diversity in rice. Results Rim2/Hipa-TD generated ample polymorphic profiles among the different rice accessions, and the amplification profiles were highly reproducible between different thermocyclers and Taq polymerases. These amplification profiles allowed for clear distinction between two different ecotypes, Japonica and Indica, of Oryza sativa. In the analysis of RIL populations, the Rim2/Hipa-TD markers were found to be segregated largely in a dominant manner, although in a few cases, non-parental bands were observed in the segregating populations. Upon linkage analysis, the Rim2/Hipa-TD markers were found to be distributed in the regions proximal to the centromeres of the chromosomes. The distribution of the Rim2/Hipa CACTA elements was surveyed in 15 different Oryza species via Rim2/Hipa-TD. While Rim2/Hipa-TD yielded ample amplification profiles between 100 to 700 bp in the AA diploid Oryza species, other species having BB, CC

Genomics of interaction between the brown planthopper and rice.

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Jing, Shengli; Zhao, Yan; Du, Bo; Chen, Rongzhi; Zhu, Lili; He, Guangcun

2017-02-01

Rice (Oryza sativa L.) and the brown planthopper (Nilaparvata lugens (Stål)) form a model system for dissection of the mechanism of interaction between insect pest and crop. In this review, we focus on the genomics of BPH-rice interaction. On the side of rice, a number of BPH-resistance genes have been identified genetically. Thirteen of these genes have been cloned which shed a light on the molecular basis of the interaction. On the aspect of BPH, a lot of salivary proteins have been identified using transcriptome and proteome techniques. The genetic loci of virulence were mapped in BPH genome based on the linkage map. The understanding of interaction between BPH and rice will provide novel insights into efficient control of this pest. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Quantitative Classification of Rice (Oryza sativa L.) Root Length and Diameter Using Image Analysis

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Gu, Dongxiang; Zhen, Fengxian; Hannaway, David B.; Zhu, Yan; Liu, Leilei; Cao, Weixing; Tang, Liang

2017-01-01

Quantitative study of root morphological characteristics of plants is helpful for understanding the relationships between their morphology and function. However, few studies and little detailed and accurate information of root characteristics were reported in fine-rooted plants like rice (Oryza sativa L.). The aims of this study were to quantitatively classify fine lateral roots (FLRs), thick lateral roots (TLRs), and nodal roots (NRs) and analyze their dynamics of mean diameter (MD), lengths and surface area percentage with growth stages in rice plant. Pot experiments were carried out during three years with three rice cultivars, three nitrogen (N) rates and three water regimes. In cultivar experiment, among the three cultivars, root length of ‘Yangdao 6’ was longest, while the MD of its FLR was the smallest, and the mean diameters for TLR and NR were the largest, the surface area percentage (SAP) of TLRs (SAPT) was the highest, indicating that Yangdao 6 has better nitrogen and water uptake ability. High N rate increased the length of different types of roots and increased the MD of lateral roots, decreased the SAP of FLRs (SAPF) and TLRs, but increased the SAP of NRs (SAPN). Moderate decrease of water supply increased root length and diameter, water stress increased the SAPF and SAPT, but decreased SAPN. The quantitative results indicate that rice plant tends to increase lateral roots to get more surface area for nitrogen and water uptake when available assimilates are limiting under nitrogen and water stress environments. PMID:28103264

Hybrid Sterility in Rice (Oryza sativa L.) Involves the Tetratricopeptide Repeat Domain Containing Protein.

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Yu, Yang; Zhao, Zhigang; Shi, Yanrong; Tian, Hua; Liu, Linglong; Bian, Xiaofeng; Xu, Yang; Zheng, Xiaoming; Gan, Lu; Shen, Yumin; Wang, Chaolong; Yu, Xiaowen; Wang, Chunming; Zhang, Xin; Guo, Xiuping; Wang, Jiulin; Ikehashi, Hiroshi; Jiang, Ling; Wan, Jianmin

2016-07-01

Intersubspecific hybrid sterility is a common form of reproductive isolation in rice (Oryza sativa L.), which significantly hampers the utilization of heterosis between indica and japonica varieties. Here, we elucidated the mechanism of S7, which specially causes Aus-japonica/indica hybrid female sterility, through cytological and genetic analysis, map-based cloning, and transformation experiments. Abnormal positioning of polar nuclei and smaller embryo sac were observed in F1 compared with male and female parents. Female gametes carrying S7(cp) and S7(i) were aborted in S7(ai)/S7(cp) and S7(ai)/S7(i), respectively, whereas they were normal in both N22 and Dular possessing a neutral allele, S7(n) S7 was fine mapped to a 139-kb region in the centromere region on chromosome 7, where the recombination was remarkably suppressed due to aggregation of retrotransposons. Among 16 putative open reading frames (ORFs) localized in the mapping region, ORF3 encoding a tetratricopeptide repeat domain containing protein was highly expressed in the pistil. Transformation experiments demonstrated that ORF3 is the candidate gene: downregulated expression of ORF3 restored spikelet fertility and eliminated absolutely preferential transmission of S7(ai) in heterozygote S7(ai)/S7(cp); sterility occurred in the transformants Cpslo17-S7(ai) Our results may provide implications for overcoming hybrid embryo sac sterility in intersubspecific hybrid rice and utilization of hybrid heterosis for cultivated rice improvement. Copyright © 2016 by the Genetics Society of America.

Effects of ozone on growth, yield and leaf gas exchange rates of four Bangladeshi cultivars of rice (Oryza sativa L.)

International Nuclear Information System (INIS)

Akhtar, Nahid; Yamaguchi, Masahiro; Inada, Hidetoshi; Hoshino, Daiki; Kondo, Taisuke; Fukami, Motohiro; Funada, Ryo; Izuta, Takeshi

2010-01-01

To assess the effects of tropospheric O 3 on rice cultivated in Bangladesh, four Bangladeshi cultivars (BR11, BR14, BR28 and BR29) of rice (Oryza sativa L.) were exposed daily to charcoal-filtered air or O 3 at 60 and 100 nl l -1 (10:00-17:00) from 1 July to 28 November 2008. The whole-plant dry mass and grain yield per plant of the four cultivars were significantly reduced by the exposure to O 3 . The exposure to O 3 significantly reduced net photosynthetic rate of the 12th and flag leaves of the four cultivars. The sensitivity to O 3 of growth, yield and leaf gas exchange rates was not significantly different among the four cultivars. The present study suggests that the sensitivity to O 3 of yield of the four Bangladeshi rice cultivars is greater than that of American rice cultivars and is similar to that of Japanese rice cultivars and that O 3 may detrimentally affect rice production in Bangladesh. - Bangladeshi cultivars of rice are sensitive to O 3 below 100 ppb.

Germination and Plantlet Regeneration of Encapsulated Microshoots of Aromatic Rice (Oryza sativa L. Cv. MRQ 74

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Rosna Mat Taha

2012-01-01

Full Text Available Plant tissues such as somatic embryos, apical shoot tips, axillary shoot buds, embryogenic calli, and protocom-like bodies are potential micropropagules that have been considered for creating synthetic seeds. In the present study, 3–5 mm microshoots of Oryza sativa L. Cv. MRQ 74 were used as explant sources for obtaining synthetic seeds. Microshoots were induced from stem explants on Murashige and Skoog (MS medium supplemented with 1.5 mg/L benzylaminopurine (BAP. They were encapsulated in 3% (w/v sodium alginate, 3% sucrose, 0.1 mg/L BAP, and 0.1 mg/L α-Naphthalene acetic acid (NAA. Germination and plantlet regeneration of the encapsulated seeds were tested by culturing them on various germination media. The effect of storage period (15–30 days was also investigated. The maximum germination and plantlet regeneration (100.0% were recorded on MS media containing 3% sucrose and 0.8% agar with and without 0.1 mg/L BAP. However, a low germination rate (6.67% was obtained using top soil as a sowing substrate. The germination rate of the encapsulated microshoots decreased from 93.33% to 3.33% after 30 days of storage at 4°C in the dark. Therefore, further research is being done to improve the germination rate of the synthetic seeds.

Biochemical and anatomical changes and yield reduction in rice (Oryza sativa L.) under varied salinity regimes.

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Hakim, M A; Juraimi, Abdul Shukor; Hanafi, M M; Ismail, Mohd Razi; Selamat, Ahmad; Rafii, M Y; Latif, M A

2014-01-01

Five Malaysian rice (Oryza sativa L.) varieties, MR33, MR52, MR211, MR219, and MR232, were tested in pot culture under different salinity regimes for biochemical response, physiological activity, and grain yield. Three different levels of salt stresses, namely, 4, 8, and 12 dS m(-1), were used in a randomized complete block design with four replications under glass house conditions. The results revealed that the chlorophyll content, proline, sugar content, soluble protein, free amino acid, and yield per plant of all the genotypes were influenced by different salinity levels. The chlorophyll content was observed to decrease with salinity level but the proline increased with salinity levels in all varieties. Reducing sugar and total sugar increased up to 8 dS m(-1) and decreased up to 12 dS m(-1). Nonreducing sugar decreased with increasing the salinity levels in all varieties. Soluble protein and free amino acid also decreased with increasing salinity levels. Cortical cells of MR211 and MR232 did not show cell collapse up to 8 dS m(-1) salinity levels compared to susceptible checks (IR20 and BRRI dhan29). Therefore, considering all parameters, MR211 and MR232 showed better salinity tolerance among the tested varieties. Both cluster and principal component analyses depict the similar results.

Biochemical and Anatomical Changes and Yield Reduction in Rice (Oryza sativa L. under Varied Salinity Regimes

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M. A. Hakim

2014-01-01

Full Text Available Five Malaysian rice (Oryza sativa L. varieties, MR33, MR52, MR211, MR219, and MR232, were tested in pot culture under different salinity regimes for biochemical response, physiological activity, and grain yield. Three different levels of salt stresses, namely, 4, 8, and 12 dS m−1, were used in a randomized complete block design with four replications under glass house conditions. The results revealed that the chlorophyll content, proline, sugar content, soluble protein, free amino acid, and yield per plant of all the genotypes were influenced by different salinity levels. The chlorophyll content was observed to decrease with salinity level but the proline increased with salinity levels in all varieties. Reducing sugar and total sugar increased up to 8 dS m−1 and decreased up to 12 dS m−1. Nonreducing sugar decreased with increasing the salinity levels in all varieties. Soluble protein and free amino acid also decreased with increasing salinity levels. Cortical cells of MR211 and MR232 did not show cell collapse up to 8 dS m−1 salinity levels compared to susceptible checks (IR20 and BRRI dhan29. Therefore, considering all parameters, MR211 and MR232 showed better salinity tolerance among the tested varieties. Both cluster and principal component analyses depict the similar results.

Differences in the sensitivity to UVB radiation of two cultivars of rice (Oryza sativa L.)

International Nuclear Information System (INIS)

Hidema, J.; Kang, H.S.; Kumagai, T.

1996-01-01

The effects of UVB radiation on the growth of two cultivars of Japanese lowland rice (Oryza sativa L.), Sasanishiki and Norin 1, were examined in a phytotron. Supplementation of visible radiation with UVB radiation reduced plant length, tiller number, the fresh and dry weights of the aboveground parts of plants, an the amounts of total leaf nitrogen, chlorophyll, soluble protein and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in the eight leaf, the youngest fully expanded leaf. By contrast, UVB radiation significantly increased the accumulation of UV-absorbing compounds. There was a difference between the two cultivars in the resistance to the effects of UVB radiation. The reduction in the amounts of Rubisco was smaller in Sasanishiki, while the increase in the accumulation of UV-absorbing compounds was greater in Sasanishiki. Parameters of plant growth, with the exception of the amount of Rubisco, decreased in direct proportion to decreases in total leaf nitrogen in plants grown under lower or the Rubisco content of Norin 1 grown under a high dose of UVB radiation was exceptionally marked, and was not observed similarly in Sasanishiki. The results suggest that the remarkable reduction in rubisco content in NOrin 1 might have been due to the specific effects of UVB radiation. It is also suggested that the difference between cultivars in the resistance to UVB radiation might be due to the differences in the levels of Rubisco and in UV-absorbing compounds that are induced by UVB radiation

Metabolomics analysis of TiO2 nanoparticles induced toxicological effects on rice (Oryza sativa L.).

Science.gov (United States)

Wu, Biying; Zhu, Lizhong; Le, X Chris

2017-11-01

The wide occurrence and high environmental concentration of titanium dioxide nanoparticles (nano-TiO 2 ) have raised concerns about their potential toxic effects on crops. In this study, we employed a GC-MS-based metabolomic approach to investigate the potential toxicity of nano-TiO 2 on hydroponically-cultured rice (Oryza sativa L.) after exposed to 0, 100, 250 or 500 mg/L of nano-TiO 2 for fourteen days. Results showed that the biomass of rice was significantly decreased and the antioxidant defense system was significantly disturbed after exposure to nano-TiO 2 . One hundred and five identified metabolites showed significant difference compared to the control, among which the concentrations of glucose-6-phosphate, glucose-1-phosphate, succinic and isocitric acid were increased most, while the concentrations of sucrose, isomaltulose, and glyoxylic acid were decreased most. Basic energy-generating ways including tricarboxylic acid cycle and the pentose phosphate pathway, were elevated significantly while the carbohydrate synthesis metabolism including starch and sucrose metabolism, and glyoxylate and dicarboxylate metabolism were inhibited. However, the biosynthetic formation of most of the identified fatty acids, amino acids and secondary metabolites which correlated to crop quality, were increased. The results suggest that the metabolism of rice plants is distinctly disturbed after exposure to nano-TiO 2 , and nano-TiO 2 would have a mixed effect on the yield and quality of rice. Copyright © 2017 Elsevier Ltd. All rights reserved.

Identification of molecular markers linked to rice bacterial blight resistance genes from Oryza meyeriana

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Jing WANG,Chen CHENG,Yanru ZHOU,Yong YANG,Qiong MEI,Junmin LI,Ye CHENG,Chengqi YAN,Jianping CHEN

2015-09-01

Full Text Available Y73 is a progeny of asymmetric somatic hybridization between Oryza sativa cv. Dalixiang and the wild rice species Oryza meyeriana. Inoculation with a range of strains of Xanthomonas oryzae pv. oryzae showed that Y73 had inherited a high level of resistance to rice bacterial blight (BB from its wild parent. An F2 population of 7125 individuals was constructed from the cross between Y73 and a BB-susceptible cultivar IR24. After testing 615 SSR and STS markers covering the 12 rice chromosomes, 186 markers were selected that showed polymorphism between Y73 and IR24. Molecular markers linked to the BB resistance genes in Y73 were scanned using the F2 population and the polymorphic markers. The SSR marker RM128 on chromosome 1, the STS marker R03D159 on chromosome 3 and the STS marker R05D104 on chromosome 5 were found to be linked to the rice BB resistance genes in Y73.

Uptake of Total Petroleum Hydrocarbon (TPH) and Polycyclic Aromatic Hydrocarbons (PAHs) by Oryza sativa L. Grown in Soil Contaminated with Crude Oil.

Science.gov (United States)

Patowary, Rupshikha; Patowary, Kaustuvmani; Devi, Arundhuti; Kalita, Mohan Chandra; Deka, Suresh

2017-01-01

The purpose of this study was to determine whether total petroleum hydrocarbon (TPH) and polycyclic aromatic hydrocarbons (PAHs) present in crude oil contaminated sites are transferred to roots, shoots and finally the grains of rice crops (Oryza sativa L.) grown in those sites. Soil was artificially contaminated with crude oil at concentrations of 0, 1000, 5000, 10,000, and 15,000 mg/kg, followed by planting of rice seedlings. After harvest, TPH in plant samples were measured, and it was determined that the uptake of TPH by the plants gradually increased as the concentration of oil in soil increased. Further, from GC-MS analysis, it was observed that PAHs including naphthalene and phenanthrene bioaccumulated in rice plant parts. Vital physico-chemical properties of soil were also altered due to crude oil contamination. Our study revealed that rice plants grown in crude oil polluted sites can uptake TPH including PAHs, thus emphasising the importance of prior investigation of soil condition before cultivation of crops.

Water and radiation use efficiencies of transplanted rice (Oryza sativa L.) at different plant densities and irrigation regimes under semi-arid environment

International Nuclear Information System (INIS)

Ahmad, S.; Ali, H.; Shad, S.A.; Zia-ul-Haq, M.; Ahmad, A.; Maqsood, M.; Khan, M.B.; Mehmood, S.; Hussain, A.

2008-01-01

Growth and yield of rice (Oryza sativa L.), in response to plant densities and irrigation (optimum to stress) were analyzed in terms of interception and utilization of photo-synthetically active radiation (PAR) and water use efficiency (WUE). The amount of PAR intercepted and cumulative evapotranspiration (ET) by each treatment was estimated from the measured leaf area index. The relationships between total dry matter grain yield and accumulated intercepted PAR and cumulative ET were linear. Yield differences among the treatments were attributed to the amount of PAR intercepted and water transpired their efficiencies of utilization or both. The fraction of intercepted radiation and WUE was significantly affected by the plant densities and various irrigation regimes, while, radiation utilization efficiency (RUE) and water use efficiency (WUE) for TDM varied from 1.15 g MJ-1 to 1.36 g MJ-1 and 22.6 kg per ha mm-1 to 24.3 kg per ha mm-1 during both the seasons

Effect of fluoride on photosynthesis, growth and accumulation of four widely cultivated rice (Oryza sativa L.) varieties in India.

Science.gov (United States)

Mondal, Naba Kumar

2017-10-01

Long-term use of fluoride contaminated groundwater to irrigate crops; especially paddy rice (Oryza sativa L.) has resulted in elevated soil fluoride levels in Eastern India. There is, therefore, growing concern regarding accumulation of fluoride in rice grown on these soils. A laboratory experiment was conducted to investigate the effect of F on germination and phytotoxicity of four varieties of rice (Orzya sativa L.) (MTU-1010; IET-4094; IET-4786 and GB-1) grown in petri dish in a green house with inorganic sodium fluoride (NaF). Three different levels (0, 5, 10 and 20mg/L) of NaF solution were applied. At the end of the experiment (28 days), biochemical analysis (pigment, sugar, protein, amino acid and phenol), lipid peroxidation, root ion leakage and catalase activity along with fluoride accumulation and fresh and dry weight of roots and shoots of four cultivars were measured. The results revealed that all the four studied varieties exhibited gradual decrease of germination pattern with increasing concentration of F. Pigment and growth morphological study clearly demonstrated that the variety IET-4094 was the least influenced by F compare to the other three varieties of rice. The translocation factor (TF) was recorded to be the highest for variety IET-4786 (0.215 ± 0.03) at 5mg/L F concentration. All the four varieties showed higher level of fluoride accumulation in root than in shoot. Variable results were recorded for biochemical parameters and lipid peroxidation. Catalase activity and relative conductivity (root ion leakage) gradually increased with increasing F concentration for all the four varieties. It is speculated that fluoride accumulation in rice straw at very high levels will affect the feeding cattle and such contaminated straw could be a direct threat to their health and also, indirectly, to human health via presumably contaminated meat and milk. Copyright © 2017. Published by Elsevier Inc.

WRKY transcription factor genes in wild rice Oryza nivara.

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Xu, Hengjian; Watanabe, Kenneth A; Zhang, Liyuan; Shen, Qingxi J

2016-08-01

The WRKY transcription factor family is one of the largest gene families involved in plant development and stress response. Although many WRKY genes have been studied in cultivated rice (Oryza sativa), the WRKY genes in the wild rice species Oryza nivara, the direct progenitor of O. sativa, have not been studied. O. nivara shows abundant genetic diversity and elite drought and disease resistance features. Herein, a total of 97 O. nivara WRKY (OnWRKY) genes were identified. RNA-sequencing demonstrates that OnWRKY genes were generally expressed at higher levels in the roots of 30-day-old plants. Bioinformatic analyses suggest that most of OnWRKY genes could be induced by salicylic acid, abscisic acid, and drought. Abundant potential MAPK phosphorylation sites in OnWRKYs suggest that activities of most OnWRKYs can be regulated by phosphorylation. Phylogenetic analyses of OnWRKYs support a novel hypothesis that ancient group IIc OnWRKYs were the original ancestors of only some group IIc and group III WRKYs. The analyses also offer strong support that group IIc OnWRKYs containing the HVE sequence in their zinc finger motifs were derived from group Ia WRKYs. This study provides a solid foundation for the study of the evolution and functions of WRKY genes in O. nivara. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Comparative analysis and relationships of six important crop ...

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tools using complete chloroplast genomes. Results obtained depict cases of major genome rearrangements, translocation, duplication, inversion and deletion of genes. Members of the poaceae family indicate a close relationship in the nature of conserved sequences while Oryza sativa and. Chlorella vulgaris, which are not ...

Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice

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Olsen Kenneth M

2010-06-01

Full Text Available Abstract Background Weedy rice (red rice, a conspecific weed of cultivated rice (Oryza sativa L., is a significant problem throughout the world and an emerging threat in regions where it was previously absent. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We use genome-wide patterns of single nucleotide polymorphism (SNP variation in a broad geographic sample of weedy, domesticated, and wild Oryza samples to infer the origin and demographic processes influencing U.S. weedy rice evolution. Results We find greater population structure than has been previously reported for U.S. weedy rice, and that the multiple, genetically divergent populations have separate origins. The two main U.S. weedy rice populations share genetic backgrounds with cultivated O. sativa varietal groups not grown commercially in the U.S., suggesting weed origins from domesticated ancestors. Hybridization between weedy groups and between weedy rice and local crops has also led to the evolution of distinct U.S. weedy rice populations. Demographic simulations indicate differences among the main weedy groups in the impact of bottlenecks on their establishment in the U.S., and in the timing of divergence from their cultivated relatives. Conclusions Unlike prior research, we did not find unambiguous evidence for U.S. weedy rice originating via hybridization between cultivated and wild Oryza species. Our results demonstrate the potential for weedy life-histories to evolve directly from within domesticated lineages. The diverse origins of U.S. weedy rice populations demonstrate the multiplicity of evolutionary forces that can influence the emergence of weeds from a single species complex.

Genomics reveals traces of fungal phenylpropanoid-flavonoid metabolic pathway in the f ilamentous fungus Aspergillus oryzae.

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Juvvadi, Praveen Rao; Seshime, Yasuyo; Kitamoto, Katsuhiko

2005-12-01

Fungal secondary metabolites constitute a wide variety of compounds which either play a vital role in agricultural, pharmaceutical and industrial contexts, or have devastating effects on agriculture, animal and human affairs by virtue of their toxigenicity. Owing to their beneficial and deleterious characteristics, these complex compounds and the genes responsible for their synthesis have been the subjects of extensive investigation by microbiologists and pharmacologists. A majority of the fungal secondary metabolic genes are classified as type I polyketide synthases (PKS) which are often clustered with other secondary metabolism related genes. In this review we discuss on the significance of our recent discovery of chalcone synthase (CHS) genes belonging to the type III PKS superfamily in an industrially important fungus, Aspergillus oryzae. CHS genes are known to play a vital role in the biosynthesis of flavonoids in plants. A comparative genome analyses revealed the unique character of A. oryzae with four CHS-like genes (csyA, csyB, csyC and csyD) amongst other Aspergilli (Aspergillus nidulans and Aspergillus fumigatus) which contained none of the CHS-like genes. Some other fungi such as Neurospora crassa, Fusarium graminearum, Magnaporthe grisea, Podospora anserina and Phanerochaete chrysosporium also contained putative type III PKSs, with a phylogenic distinction from bacteria and plants. The enzymatically active nature of these newly discovered homologues is expected owing to the conservation in the catalytic residues across the different species of plants and fungi, and also by the fact that a majority of these genes (csyA, csyB and csyD) were expressed in A. oryzae. While this finding brings filamentous fungi closer to plants and bacteria which until recently were the only ones considered to possess the type III PKSs, the presence of putative genes encoding other principal enzymes involved in the phenylpropanoid and flavonoid biosynthesis (viz

Can Cd translocation in Oryza sativa L. be attenuated by arbuscular mycorrhizal fungi in the presence of EDTA?

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Huang, Xiaochen; An, Guangnan; Zhu, Shishu; Wang, Li; Ma, Fang

2018-04-01

Arbuscular mycorrhizal (AM) fungi play an important role in plant tolerance of heavy metal contamination. In this study, a pot experiment was conducted to illustrate the effects of the two AM fungi species Funneliformis mosseae (Fm) and Rhizophagus irregularis (Ri) on plant growth of Oryza sativa L. either with or without ethylenediamine tetraacetate (EDTA) addition and during exposure to five Cd concentrations (in the range of 0-5 mg kg -1 ). The results showed that Fm inoculation achieved greater mycorrhizal colonization and mycorrhizal dependency indexes than Ri inoculation. In addition, the effects of AM fungi on Cd biosorption and translocation in rice were also investigated in the presence of EDTA. Despite cooperative adsorption, the Freundlich isotherm could describe the biosorption effects of Cd on rice roots regardless of AM fungi inoculation or EDTA addition. Cd concentrations in mycorrhizal roots increased but decreased in mycorrhizal shoots in contrast to the control treatment. Although EDTA addition negatively inhibited the uptake of Cd to mycorrhizal shoots, lower translocation factor (TF) and bioconcentration factor (BCF) were still observed in treatments with EDTA compared to control treatment. Our findings suggest that Ri and Fm inoculation enhanced Cd immobilization in the roots, thus preventing Cd entry into the food chain during exposure to low and high Cd stress, respectively.

Changes in gene expression and catalase activity in Oryza sativa L. under abiotic stress.

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Vighi, I L; Benitez, L C; do Amaral, M N; Auler, P A; Moraes, G P; Rodrigues, G S; da Maia, L C; Pinto, L S; Braga, E J B

2016-11-03

Different rice (Oryza sativa L.) genotypes were subjected to high salinity and low temperature (150 mM NaCl and 13°C, respectively) for 0, 6, 24, 48, or 72 h. We evaluated the simultaneous expression of the genes OsCATA, OsCATB, and OsCATC, correlated gene expression with enzyme activity, and verified the regulation of these genes through identification of cis-elements in the promoter region. The hydrogen peroxide content increased in a tolerant genotype and decreased in a sensitive genotype under both stress conditions. Lipid peroxidation increased in the tolerant genotype when exposed to cold, and in the sensitive genotype when exposed to high salinity. Catalase activity significantly increased in both genotypes when subjected to 13°C. In the tolerant genotype, OsCATA and OsCATB were the most responsive to high salinity and cold, while in the sensitive genotype, OsCATA and OsCATC responded positively to saline stress, as did OsCATA and OsCATB to low temperature. Cis-element analysis identified different regulatory sequences in the catalase promoter region of each genotype. The sensitive genotype maintained a better balance between hydrogen oxyacid levels, catalase activity, and lipid peroxidation under low temperature than the resistant genotype. OsCATA and OsCATB were the most responsive in the salt-tolerant genotype to cold, OsCATA and OsCATC were the most responsive to saline stress, and OsCATA and OsCATB were the most responsive to chilling stress in the sensitive genotype. There were positive correlations between catalase activity and OsCATB expression in the tolerant genotype under saline stress and in the sensitive genotype under cold stress.

In silico Analysis of 3′-End-Processing Signals in Aspergillus oryzae Using Expressed Sequence Tags and Genomic Sequencing Data

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Tanaka, Mizuki; Sakai, Yoshifumi; Yamada, Osamu; Shintani, Takahiro; Gomi, Katsuya

2011-01-01

To investigate 3′-end-processing signals in Aspergillus oryzae, we created a nucleotide sequence data set of the 3′-untranslated region (3′ UTR) plus 100 nucleotides (nt) sequence downstream of the poly(A) site using A. oryzae expressed sequence tags and genomic sequencing data. This data set comprised 1065 sequences derived from 1042 unique genes. The average 3′ UTR length in A. oryzae was 241 nt, which is greater than that in yeast but similar to that in plants. The 3′ UTR and 100 nt sequence downstream of the poly(A) site is notably U-rich, while the region located 15–30 nt upstream of the poly(A) site is markedly A-rich. The most frequently found hexanucleotide in this A-rich region is AAUGAA, although this sequence accounts for only 6% of all transcripts. These data suggested that A. oryzae has no highly conserved sequence element equivalent to AAUAAA, a mammalian polyadenylation signal. We identified that putative 3′-end-processing signals in A. oryzae, while less well conserved than those in mammals, comprised four sequence elements: the furthest upstream U-rich element, A-rich sequence, cleavage site, and downstream U-rich element flanking the cleavage site. Although these putative 3′-end-processing signals are similar to those in yeast and plants, some notable differences exist between them. PMID:21586533

Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes

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Saski, Christopher; Lee, Seung-Bum; Fjellheim, Siri; Guda, Chittibabu; Jansen, Robert K.; Luo, Hong; Tomkins, Jeffrey; Rognli, Odd Arne; Clarke, Jihong Liu

2009-01-01

Comparisons of complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera to six published grass chloroplast genomes reveal that gene content and order are similar but two microstructural changes have occurred. First, the expansion of the IR at the SSC/IRa boundary that duplicates a portion of the 5′ end of ndhH is restricted to the three genera of the subfamily Pooideae (Agrostis, Hordeum and Triticum). Second, a 6 bp deletion in ndhK is shared by Agrostis, Hordeum, Oryza and Triticum, and this event supports the sister relationship between the subfamilies Erhartoideae and Pooideae. Repeat analysis identified 19–37 direct and inverted repeats 30 bp or longer with a sequence identity of at least 90%. Seventeen of the 26 shared repeats are found in all the grass chloroplast genomes examined and are located in the same genes or intergenic spacer (IGS) regions. Examination of simple sequence repeats (SSRs) identified 16–21 potential polymorphic SSRs. Five IGS regions have 100% sequence identity among Zea mays, Saccharum officinarum and Sorghum bicolor, whereas no spacer regions were identical among Oryza sativa, Triticum aestivum, H. vulgare and A. stolonifera despite their close phylogenetic relationship. Alignment of EST sequences and DNA coding sequences identified six C–U conversions in both Sorghum bicolor and H. vulgare but only one in A. stolonifera. Phylogenetic trees based on DNA sequences of 61 protein-coding genes of 38 taxa using both maximum parsimony and likelihood methods provide moderate support for a sister relationship between the subfamilies Erhartoideae and Pooideae. PMID:17534593

Duplication and diversification of the LEAFY HULL STERILE1 and Oryza sativa MADS5 SEPALLATA lineages in graminoid Poales

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Christensen Ashley R

2012-02-01

Full Text Available Abstract Background Gene duplication and the subsequent divergence in function of the resulting paralogs via subfunctionalization and/or neofunctionalization is hypothesized to have played a major role in the evolution of plant form. The LEAFY HULL STERILE1 (LHS1 SEPALLATA (SEP genes have been linked with the origin and diversification of the grass spikelet, but it is uncertain 1 when the duplication event that produced the LHS1 clade and its paralogous lineage Oryza sativa MADS5 (OSM5 occurred, and 2 how changes in gene structure and/or expression might have contributed to subfunctionalization and/or neofunctionalization in the two lineages. Methods Phylogenetic relationships among 84 SEP genes were estimated using Bayesian methods. RNA expression patterns were inferred using in situ hybridization. The patterns of protein sequence and RNA expression evolution were reconstructed using maximum parsimony (MP and maximum likelihood (ML methods, respectively. Results Phylogenetic analyses mapped the LHS1/OSM5 duplication event to the base of the grass family. MP character reconstructions estimated a change from cytosine to thymine in the first codon position of the first amino acid after the Zea mays MADS3 (ZMM3 domain converted a glutamine to a stop codon in the OSM5 ancestor following the LHS1/OSM5 duplication event. RNA expression analyses of OSM5 co-orthologs in Avena sativa, Chasmanthium latifolium, Hordeum vulgare, Pennisetum glaucum, and Sorghum bicolor followed by ML reconstructions of these data and previously published analyses estimated a complex pattern of gain and loss of LHS1 and OSM5 expression in different floral organs and different flowers within the spikelet or inflorescence. Conclusions Previous authors have reported that rice OSM5 and LHS1 proteins have different interaction partners indicating that the truncation of OSM5 following the LHS1/OSM5 duplication event has resulted in both partitioned and potentially novel gene

The response of rice (Oryza sativa L. to elevated night temperature with application of Pyraclostobin

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T.Y. Wahjanto

2016-07-01

Full Text Available Rice productivity is having a problem related with climate change phenomenon, mainly the global warming. The rising of temperature in some country threat the rice production. The increasing of temperature is a major limiting factor that affects yield through the growth and development of rice plant. This study was aimed to examine the response of rice (Oryza sativa L. to elevated night temperature with the application of Pyraclostobin. A glasshouse experiment that was conducted from March to August 2015 at Brawijaya University Research Station of Jatikerto – Malang, used nested plot design with three replications and two treatments. The first treatments were the night temperature level (normal temperature, increased 2oC, and increased 4oC. The second treatments were the concentration of Pyraclostrobin (0 ppm, 400 ppm and 800 ppm. Results of the study showed that the increase of temperature at night for about 2oC and 4oC, as well as application of Pyraclostrobin, affected growth and yield of rice. Application of Pyraclostrobin by concentrations of 400 ppm and 800 ppm effectively reduced yield loss by increasing night temperature of 2oC, which resulted in 20.20% and 24.93%, respectively, in comparison with the control; while the increase of night temperature by 4oC have resulted 26.86% and 33.33% in comparison with the control. Pyraclostrobin was effective in maintaining percentage of the filled spikelets by the increase of temperature at night for about 2oC and 4oC.

PENETAPAN KADAR FENOLIK TOTAL DAN FLAVONOID TOTAL EKSTRAK BERAS HITAM (Oryza sativa L DARI KALIMANTAN SELATAN

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Anna Khumaira Sari

2017-10-01

Full Text Available The black rice contains anthocyanin compounds which are included in the flavonoids and phenolic compounds. Flavonoids contained in black rice are phenolic components that act as a preventive of hydroxyl and superoxide radicals by protecting membrane lipids against damaging oxidation reactions and phenol compounds also have bacteriocid, antimetic, antihelmintic, antiinflammatory, antimicrobial, anticancer and other degenerative diseases. The aim of this research were to measure total phenolic content and total flavonoid in ethanol extract of black rice (Oryza sativa L. Total phenol content were measured by Folin-Ciocalteu method with gallic acid mean while total flavonoid content were measured by colorimetry method using reagent AlCl3 10% and 5% acetic acid. There are seven variation samples of black rice obtained from seven different places in South Kalimantan. The result of this study, qualitative analysis showed that all samples positive contained flavonoids, alkaloids and tannins. The total phenol content of the seven samples was 100,58 ± 1,344; 91.14 ± 1.699; 96.50 ± 1.529; 77.64 ± 0.462; 81,16 ± 0,614; 112.47 ± 1.040; 81,50 ± 2,928 mgGAE/mg extract and the percent of total flavonoid content from seven samples was 8,53 ± 0,208%; 8.11 ± 0.343%; 7.69 ± 0.446%; 6.03 ± 0.227%; 4.97 ± 0.169%; 3.74 ± 0.210%; 5.02 ± 0.403%.

Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis

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Itoh Takeshi

2010-02-01

Full Text Available Abstract Background Rice is one of the most important food crops in the world. With increasing world demand for food crops, there is an urgent need to develop new cultivars that have enhanced performance with regard to yield, disease resistance, and so on. Wild rice is expected to provide useful genetic resources that could improve the present cultivated species. However, the quantity and quality of these unexplored resources remain unclear. Recent accumulation of the genomic information of both cultivated and wild rice species allows for their comparison at the molecular level. Here, we compared the genome sequence of Oryza sativa ssp. japonica with sets of bacterial artificial chromosome end sequences (BESs from two wild rice species, O. rufipogon and O. nivara, and an African rice species, O. glaberrima. Results We found that about four to five percent of the BESs of the two wild rice species and about seven percent of the African rice could not be mapped to the japonica genome, suggesting that a substantial number of genes have been lost in the japonica rice lineage; however, their close relatives still possess their counterpart genes. We estimated that during evolution, O. sativa has lost at least one thousand genes that are still preserved in the genomes of the other species. In addition, our BLASTX searches against the non-redundant protein sequence database showed that disease resistance-related proteins were significantly overrepresented in the close relative-specific genomic portions. In total, 235 unmapped BESs of the three relatives matched 83 non-redundant proteins that contained a disease resistance protein domain, most of which corresponded to an NBS-LRR domain. Conclusion We found that the O. sativa lineage appears to have recently experienced massive gene losses following divergence from its wild ancestor. Our results imply that the domestication process accelerated large-scale genomic deletions in the lineage of Asian

Black Rice (Oryza sativa L., Poaceae) Extract Reduces Hippocampal Neuronal Cell Death Induced by Transient Global Cerebral Ischemia in Mice.

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Hwang, Sun-Nyoung; Kim, Jae-Cheon; Bhuiyan, Mohammad Iqbal Hossain; Kim, Joo Youn; Yang, Ji Seon; Yoon, Shin Hee; Yoon, Kee Dong; Kim, Seong Yun

2018-04-01

Rice is the most commonly consumed grain in the world. Black rice has been suggested to contain various bioactive compounds including anthocyanin antioxidants. There is currently little information about the nutritional benefits of black rice on brain pathology. Here, we investigated the effects of black rice ( Oryza sativa L ., Poaceae) extract (BRE) on the hippocampal neuronal damage induced by ischemic insult. BRE (300 mg/kg) was orally administered to adult male C57BL/6 mice once a day for 21 days. Bilateral common carotid artery occlusion (BCCAO) was performed for 23 min on the 8th day of BRE or vehicle administration. Histological analyses conducted on the 22nd day of BRE or vehicle administration revealed that administering BRE profoundly attenuated neuronal cell death, inhibited reactive astrogliosis, and prevented loss of glutathione peroxidase expression in the hippocampus when compared to vehicle treatment. In addition, BRE considerably ameliorated BCCAO-induced memory impairment on the Morris water maze test from the 15th day to the 22nd day of BRE or vehicle administration. These results indicate that chronic administration of BRE is potentially beneficial in cerebral ischemia.

Mitochondrial Genome Analysis of Wild Rice (Oryza minuta) and Its Comparison with Other Related Species.

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Asaf, Sajjad; Khan, Abdul Latif; Khan, Abdur Rahim; Waqas, Muhammad; Kang, Sang-Mo; Khan, Muhammad Aaqil; Shahzad, Raheem; Seo, Chang-Woo; Shin, Jae-Ho; Lee, In-Jung

2016-01-01

Oryza minuta (Poaceae family) is a tetraploid wild relative of cultivated rice with a BBCC genome. O. minuta has the potential to resist against various pathogenic diseases such as bacterial blight (BB), white backed planthopper (WBPH) and brown plant hopper (BPH). Here, we sequenced and annotated the complete mitochondrial genome of O. minuta. The mtDNA genome is 515,022 bp, containing 60 protein coding genes, 31 tRNA genes and two rRNA genes. The mitochondrial genome organization and the gene content at the nucleotide level are highly similar (89%) to that of O. rufipogon. Comparison with other related species revealed that most of the genes with known function are conserved among the Poaceae members. Similarly, O. minuta mt genome shared 24 protein-coding genes, 15 tRNA genes and 1 ribosomal RNA gene with other rice species (indica and japonica). The evolutionary relationship and phylogenetic analysis revealed that O. minuta is more closely related to O. rufipogon than to any other related species. Such studies are essential to understand the evolutionary divergence among species and analyze common gene pools to combat risks in the current scenario of a changing environment.

Monitoring expression profiles of rice (Oryza sativa L.) genes under abiotic stresses using cDNA Microarray Analysis (abstract)

International Nuclear Information System (INIS)

Rabbani, M.A.

2005-01-01

Transcript regulation in response to cold, drought, high salinity and ABA application was investigated in rice (Oryza sativa L., Nipponbare) with microarray analysis including approx. 1700 independent DNA elements derived from three cDNA libraries constructed from 15-day old rice seedlings stressed with drought, cold and high salinity. A total of 141 non-redundant genes were identified, whose expression ratios were more than three-fold compared with the control genes for at least one of stress treatments in microarray analysis. However, after RNA gel blot analysis, a total of 73 genes were identified, among them the transcripts of 36, 62, 57 and 43 genes were found increased after cold, drought, high salinity and ABA application, respectively. Sixteen of these identified genes have been reported previously to be stress inducible in rice, while 57 of which are novel that have not been reported earlier as stress responsive in rice. We observed a strong association in the expression patterns of stress responsive genes and found 15 stress inducible genes that responded to all four treatments. Based on Venn diagram analysis, 56 genes were induced by both drought and high salinity, whereas 22 genes were upregulated by both cold and high salinity stress. Similarly 43 genes were induced by both drought stress and ABA application, while only 17 genes were identified as cold and ABA inducible genes. These results indicated the existence of greater cross talk between drought, ABA and high salinity stress signaling processes than those between cold and ABA, and cold and high salinity stress signaling pathways. The cold, drought, high salinity and ABA inducible genes were classified into four gene groups from their expression profiles. Analysis of data enabled us to identify a number of promoters and possible cis-acting DNA elements of several genes induced by a variety of abiotic stresses by combining expression data with genomic sequence data of rice. Comparative analysis of

Genome-Wide Association Mapping and Genomic Selection for Alfalfa (Medicago sativa) Forage Quality Traits.

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Biazzi, Elisa; Nazzicari, Nelson; Pecetti, Luciano; Brummer, E Charles; Palmonari, Alberto; Tava, Aldo; Annicchiarico, Paolo

2017-01-01

Genetic progress for forage quality has been poor in alfalfa (Medicago sativa L.), the most-grown forage legume worldwide. This study aimed at exploring opportunities for marker-assisted selection (MAS) and genomic selection of forage quality traits based on breeding values of parent plants. Some 154 genotypes from a broadly-based reference population were genotyped by genotyping-by-sequencing (GBS), and phenotyped for leaf-to-stem ratio, leaf and stem contents of protein, neutral detergent fiber (NDF) and acid detergent lignin (ADL), and leaf and stem NDF digestibility after 24 hours (NDFD), of their dense-planted half-sib progenies in three growing conditions (summer harvest, full irrigation; summer harvest, suspended irrigation; autumn harvest). Trait-marker analyses were performed on progeny values averaged over conditions, owing to modest germplasm × condition interaction. Genomic selection exploited 11,450 polymorphic SNP markers, whereas a subset of 8,494 M. truncatula-aligned markers were used for a genome-wide association study (GWAS). GWAS confirmed the polygenic control of quality traits and, in agreement with phenotypic correlations, indicated substantially different genetic control of a given trait in stems and leaves. It detected several SNPs in different annotated genes that were highly linked to stem protein content. Also, it identified a small genomic region on chromosome 8 with high concentration of annotated genes associated with leaf ADL, including one gene probably involved in the lignin pathway. Three genomic selection models, i.e., Ridge-regression BLUP, Bayes B and Bayesian Lasso, displayed similar prediction accuracy, whereas SVR-lin was less accurate. Accuracy values were moderate (0.3-0.4) for stem NDFD and leaf protein content, modest for leaf ADL and NDFD, and low to very low for the other traits. Along with previous results for the same germplasm set, this study indicates that GBS data can be exploited to improve both quality traits

Risk assessment of potentially toxic element pollution in soils and rice (Oryza sativa) in a typical area of the Yangtze River Delta

International Nuclear Information System (INIS)

Hang Xiaoshuai; Wang Huoyan; Zhou Jianmin; Ma Chengling; Du Changwen; Chen Xiaoqin

2009-01-01

Soil pollution with potentially toxic elements (PTEs) resulting from rapid industrial development has caused major concerns. Selected PTEs and their accumulation and distribution in soils and rice (Oryza sativa) collected from Changshu, east China, were analyzed to evaluate the potential health risk to the local population. The soils were primarily contaminated with Hg, followed by Cu, Cd, Pb, and Zn. The concentrations of Pb, Hg, and Cd of 46, 32, and 1 rice samples exceeded their national maximum allowable levels in foods, respectively. Spatial distributions of total Cr, Cu, Pb, Zn, and Cd in soils shared similar geographical trends. The risk assessment of PTEs through rice consumption suggests that the concentrations of Cu, Pb, and Cd in some rice samples exceed their reference oral dose for adults and children. In general, there was no target hazard quotient value of any individual element that was greater than 1, but hazard index values for adults and children were 1.726 and 1.523, respectively. - Industrial development has led to increased risk from potentially toxic elements in soils and rice.

Coordination of Leaf Photosynthesis, Transpiration, and Structural Traits in Rice and Wild Relatives (Genus Oryza).

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Giuliani, Rita; Koteyeva, Nuria; Voznesenskaya, Elena; Evans, Marc A; Cousins, Asaph B; Edwards, Gerald E

2013-07-01

The genus Oryza, which includes rice (Oryza sativa and Oryza glaberrima) and wild relatives, is a useful genus to study leaf properties in order to identify structural features that control CO(2) access to chloroplasts, photosynthesis, water use efficiency, and drought tolerance. Traits, 26 structural and 17 functional, associated with photosynthesis and transpiration were quantified on 24 accessions (representatives of 17 species and eight genomes). Hypotheses of associations within, and between, structure, photosynthesis, and transpiration were tested. Two main clusters of positively interrelated leaf traits were identified: in the first cluster were structural features, leaf thickness (Thick(leaf)), mesophyll (M) cell surface area exposed to intercellular air space per unit of leaf surface area (S(mes)), and M cell size; a second group included functional traits, net photosynthetic rate, transpiration rate, M conductance to CO(2) diffusion (g(m)), stomatal conductance to gas diffusion (g(s)), and the g(m)/g(s) ratio.While net photosynthetic rate was positively correlated with gm, neither was significantly linked with any individual structural traits. The results suggest that changes in gm depend on covariations of multiple leaf (S(mes)) and M cell (including cell wall thickness) structural traits. There was an inverse relationship between Thick(leaf) and transpiration rate and a significant positive association between Thick(leaf) and leaf transpiration efficiency. Interestingly, high g(m) together with high g(m)/g(s) and a low S(mes)/g(m) ratio (M resistance to CO(2) diffusion per unit of cell surface area exposed to intercellular air space) appear to be ideal for supporting leaf photosynthesis while preserving water; in addition, thick M cell walls may be beneficial for plant drought tolerance.

Expression, purification, crystallization and preliminary X-ray analysis of rice (Oryza sativa L.) Os4BGlu12 β-glucosidase

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Sansenya, Sompong; Ketudat Cairns, James R.; Opassiri, Rodjana

2010-01-01

Recombinant rice Os4BGlu12 β-glucosidase purified from E. coli was crystallized with and without 2,4-dinitrophenyl-2-deoxy-2-fluoro-β-d-glucopyranoside. Rice (Oryza sativa L.) Os4BGlu12, a glycoside hydrolase family 1 β-glucosidase (EC 3.2.1.21), was expressed as a fusion protein with an N-terminal thioredoxin/His 6 tag in Escherichia coli strain Origami B (DE3) and purified with subsequent removal of the N-terminal tag. Native Os4BGlu12 and its complex with 2,4-dinitrophenyl-2-deoxy-2-fluoro-β-d-glucopyranoside (DNP2FG) were crystallized using 19% polyethylene glycol (3350 or 2000, respectively) in 0.1 M Tris–HCl pH 8.5, 0.16 M NaCl at 288 K. Diffraction data sets for the apo and inhibitor-bound forms were collected to 2.50 and 2.45 Å resolution, respectively. The space group and the unit-cell parameters of the crystal indicated the presence of two molecules per asymmetric unit, with a solvent content of 50%. The structure of Os4BGlu12 was successfully solved in space group P4 3 2 1 2 by molecular replacement using the white clover cyanogenic β-glucosidase structure as a search model

Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae

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Deng Jixin

2009-02-01

Full Text Available Abstract Background Magnaporthe oryzae, the causal agent of blast disease of rice, is the most destructive disease of rice worldwide. The genome of this fungal pathogen has been sequenced and an automated annotation has recently been updated to Version 6 http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/MultiDownloads.html. However, a comprehensive manual curation remains to be performed. Gene Ontology (GO annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly. Methods A similarity-based (i.e., computational GO annotation with manual review was conducted, which was then integrated with a literature-based GO annotation with computational assistance. For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M. oryzae and GO proteins from multiple organisms with published associations to GO terms. Significant alignment pairs were manually reviewed. Functional assignments were further cross-validated with manually reviewed data, conserved domains, or data determined by wet lab experiments. Additionally, biological appropriateness of the functional assignments was manually checked. Results In total, 6,286 proteins received GO term assignment via the homology-based annotation, including 2,870 hypothetical proteins. Literature-based experimental evidence, such as microarray, MPSS, T-DNA insertion mutation, or gene knockout mutation, resulted in 2,810 proteins being annotated with GO terms. Of these, 1,673 proteins were annotated with new terms developed for Plant-Associated Microbe Gene Ontology (PAMGO. In addition, 67 experiment-determined secreted proteins were annotated with PAMGO terms. Integration of the two data sets resulted in 7,412 proteins (57% being annotated with 1,957 distinct and specific GO terms. Unannotated proteins

Genetic study of resistance to inhibitory effects of UV radiation in rice (Oryza sativa)

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Sato, T.; Kang, H.S.; Kumagai, T.

1994-01-01

Genetic analysis of resistance to the inhibitory effects of UV radiation on growth of rice (Oryza sativa L.) cultivars was carried out. Some experimental plants were grown in visible radiation supplemented with UV radiation containing a large amount of UV-B and a small amount of UV-C in a phytotron, while others were grown without UV radiation. The degree of resistance to UV radiation was estimated in terms of the degree of reduction caused by supplemental UV radiation in the fresh weight of the aboveground plant parts and the chlorophyll content per unit fresh weight. Fresh weight and chlorophyll content in F 2 plants generated by reciprocally crossing cv. Sasanishiki, a cultivar more resistant to UV radiation, and Norin 1, a cultivar less resistant to such radiation exhibited a normal frequency distribution. The heritabilities of these two properties in F 2 plants were low under conditions of non-supplemental UV radiation. Under elevated UV radiation, the F 2 population shifted to the lower range of fresh weight and chlorophyll content, and the means were close to those of Norin 1. The heritabilities of these two properties were the same in the reciprocal crosses, indicating that maternal inheritance was not involved. Inheritance of chlorophyll content per unit fresh weight was further determined in F 3 lines generated by self-fertilizing F 2 plants of Sasanishiki and Norin 1. The results showed that the F 3 population was segregated into three genotypes, namely, resistant homozygotes, segregated heterozygotes and sensitive homozygotes, with a ratio of 1:65:16. It was thus evident that the resistance to the inhibitory effect of elevated UV radiation in these rice plants was controlled by recessive polygenes. (author)

Isolation and characterization of a Ds-tagged rice (Oryza sativa L.) GA-responsive dwarf mutant defective in an early step of the gibberellin biosynthesis pathway.

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Margis-Pinheiro, Marcia; Zhou, Xue-Rong; Zhu, Qian-Hao; Dennis, Elizabeth S; Upadhyaya, Narayana M

2005-03-01

We have isolated a severe dwarf transposon (Ds) insertion mutant in rice (Oryza sativa L.), which could be differentiated early in the seedling stage by reduced shoot growth and dark green leaves, and later by severe dwarfism and failure to initiate flowering. These mutants, however, showed normal seed germination and root growth. One of the sequences flanking Ds, rescued from the mutant, was of a chromosome 4-located putative ent-kaurene synthase (KS) gene, encoding the enzyme catalyzing the second step of the gibberellin (GA) biosynthesis pathway. Dwarf mutants were always homozygous for this Ds insertion and no normal plants homozygous for this mutation were recovered in the segregating progeny, indicating that the Ds insertion mutation is recessive. As mutations in three recently reported rice GA-responsive dwarf mutant alleles and the dwarf mutation identified in this study mapped to the same locus, we designate the corresponding gene OsKS1. The osks1 mutant seedlings were responsive to exogenous gibberellin (GA3). OsKS1 transcripts of about 2.3 kb were detected in leaves and stem of wild-type plants, but not in germinating seeds or roots, suggesting that OsKS1 is not involved in germination or root growth. There are at least five OsKS1-like genes in the rice genome, four of which are also represented in rice expressed sequence tag (EST) databases. All OsKS1-like genes are transcribed with different expression patterns. ESTs corresponding to all six OsKS genes are represented in other cereal databases including barley, wheat and maize, suggesting that they are biologically active.

Methodical characterization of rice ( Oryza sativa bran oil from Pakistan

Directory of Open Access Journals (Sweden)

Mahmood, Zahid

2005-06-01

Full Text Available The hexane-extracted oil content of four varieties of rice (Oryza sativa viz. Super Kernel, 386, 385 and Basmati, bran was ranged 14.70-19.10 %. Other physical and chemical parameters of the extracted oils were as follow: Iodine value 112.40, 109.80, 105.1 and 103.70; refractive index ( 40 °C 1.4650, 1.4680, 1.4657 and 1.4660; density ( 40 °C 0.919, 0.913, 0.909 and 0.911; saponification value 183, 177, 186 and 190; unsaponifiable matter 6.15, 5.60, 4.98 and 5.40 % respectively. Tocopherols ( α, γ and δ in the oils were: 284.00, 175.12, 180.42, 300.06; 83.40, 98.70, 120.70, 90.60; 75.16, 57.20, 39.32, 83.00 mg/kg respectively. The contents of tocotrienols ( α, γ and δ in the oils were: 120.30, 106.00, 95.20, 135.74; 196.00, 125.00, 210.0, 276.41; 72.50, 20.00, 39.30, 64.00 mg/kg respectively. The amount of γ - Oryzanol in the investigated oils was ranged 415.12-802.05 The induction periods (Rancimat, 20 L/h, 120 °C of the crude oils were 6.81, 5.99, 6.39 and 7.40 h respectively. The major sterol fractions of the oils consisted of campesterol ranged (10.10-19.20%, stigmasterol (14.00-19.28 %, b -sitosterol (49.30-58.20 %, and D5 ,avenasterol (8.14-13.05 %. The investigated varieties ( Super Kernel, 386, 385 and Basmati of rice bran oil were found to contain high levels of oleic acid 42.67, 38.59, 40.68 and 36.78 % followed by linoleic and palmitic acids 31.58, 33.80, 28.70, 30.51 and 17.00, 14.88, 19.63, 20.00 % respectively. The contents of myristic, stearic and arachidic acids was 1.50, 2.02, 4.28, 1.00; 2.64, 2.87, 4.02, 7.48; and 1.28, 3.00, 1.00, 1.00 % respectively. A number of parameters of the investigated rice bran oils indigenous to Pakistan were comparable to those of typical rice bran and some other vegetable oils, reported in the literature. The results of the present analysis as compared with those of different vegetable oils demonstrated rice bran to be a potential oil source and thus could be useful

The rice XA21 ectodomain fused to the Arabidopsis EFR cytoplasmic domain confers resistance to Xanthomonas oryzae pv. oryzae.

Science.gov (United States)

Thomas, Nicholas C; Oksenberg, Nir; Liu, Furong; Caddell, Daniel; Nalyvayko, Alina; Nguyen, Yen; Schwessinger, Benjamin; Ronald, Pamela C

2018-01-01

Rice ( Oryza sativa ) plants expressing the XA21 cell-surface receptor kinase are resistant to Xanthomonas oryzae pv. oryzae (Xoo) infection. We previously demonstrated that expressing a chimeric protein containing the ELONGATION FACTOR Tu RECEPTOR (EFR) ectodomain and the XA21 endodomain (EFR:XA21) in rice does not confer robust resistance to Xoo . To test if the XA21 ectodomain is required for Xoo resistance, we produced transgenic rice lines expressing a chimeric protein consisting of the XA21 ectodomain and EFR endodomain (XA21:EFR) and inoculated these lines with Xoo . We also tested if the XA21:EFR rice plants respond to a synthetic sulfated 21 amino acid derivative (RaxX21-sY) of the activator of XA21-mediated immunity, RaxX. We found that five independently transformed XA21:EFR rice lines displayed resistance to Xoo as measured by lesion length analysis, and showed that five lines share characteristic markers of the XA21 defense response (generation of reactive oxygen species and defense response gene expression) after treatment with RaxX21-sY. Our results indicate that expression of the XA21:EFR chimeric receptor in rice confers resistance to Xoo . These results suggest that the endodomain of the EFR and XA21 immune receptors are interchangeable and the XA21 ectodomain is the key determinant conferring robust resistance to Xoo .

Comparative Chemistry of Aspergillus oryzae (RIB40) and A. flavus (NRRL 3357)

Science.gov (United States)

Rank, Christian; Klejnstrup, Marie Louise; Petersen, Lene Maj; Kildgaard, Sara; Frisvad, Jens Christian; Gotfredsen, Charlotte Held; Larsen, Thomas Ostenfeld

2012-01-01

Aspergillus oryzae and A. flavus are important species in industrial biotechnology and food safety and have been some of the first aspergilli to be fully genome sequenced. Bioinformatic analysis has revealed 99.5% gene homology between the two species pointing towards a large coherence in the secondary metabolite production. In this study we report on the first comparison of secondary metabolite production between the full genome sequenced strains of A. oryzae (RIB40) and A. flavus (NRRL 3357). Surprisingly, the overall chemical profiles of the two strains were mostly very different across 15 growth conditions. Contrary to previous studies we found the aflatrem precursor 13-desoxypaxilline to be a major metabolite from A. oryzae under certain growth conditions. For the first time, we additionally report A. oryzae to produce parasiticolide A and two new analogues hereof, along with four new alkaloids related to the A. flavus metabolites ditryptophenalines and miyakamides. Generally the secondary metabolite capability of A. oryzae presents several novel end products likely to result from the domestication process from A. flavus. PMID:24957367

Cell biology of the Koji mold Aspergillus oryzae.

Science.gov (United States)

Kitamoto, Katsuhiko

2015-01-01

Koji mold, Aspergillus oryzae, has been used for the production of sake, miso, and soy sauce for more than one thousand years in Japan. Due to the importance, A. oryzae has been designated as the national micro-organism of Japan (Koku-kin). A. oryzae has been intensively studied in the past century, with most investigations focusing on breeding techniques and developing methods for Koji making for sake brewing. However, the understanding of fundamental biology of A. oryzae remains relatively limited compared with the yeast Saccharomyces cerevisiae. Therefore, we have focused on studying the cell biology including live cell imaging of organelles, protein vesicular trafficking, autophagy, and Woronin body functions using the available genomic information. In this review, I describe essential findings of cell biology of A. oryzae obtained in our study for a quarter of century. Understanding of the basic biology will be critical for not its biotechnological application, but also for an understanding of the fundamental biology of other filamentous fungi.

Exogenous application of rutin and gallic acid regulate antioxidants and alleviate reactive oxygen generation in Oryza sativa L.

Science.gov (United States)

Singh, Akanksha; Gupta, Rupali; Pandey, Rakesh

2017-04-01

The effect of rutin and gallic acid on growth, phytochemical and defense gene activation of rice ( Oryza sativa L.) was investigated. The seeds of rice were primed with different concentrations of rutin and gallic acid (10-60 µg mL -1 ) to explicate the effect on germination on water agar plates. Further, to study the effect of most effective concentrations of gallic acid (60 µg mL -1 ) and rutin (50 µg mL -1 ), greenhouse pot experiment was set up to determine the changes in growth, antioxidant and defense parameters. The results revealed more pronounced effect of gallic acid on total chlorophyll and carotenoids as well as on total flavonoid content and free radical scavenging activities. Gene expression analysis of OsWRKY71, PAL, CHS and LOX genes involved in strengthening the plant defense further validated the results obtained from the biochemical analysis. Microscopic analysis also confirmed reduction in total reactive oxygen species, free radicals like H 2 O 2 and O 2 - by exogenous application of gallic acid and rutin. The data obtained thus suggest that both gallic acid and rutin can affect the growth and physiology of rice plants and therefore can be used to develop effective plant growth promoters and as substitute of biofertilizers for maximizing their use in field conditions.

Engineering the Oryza sativa cell wall with rice NAC transcription factors regulating secondary wall formation

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Kouki eYoshida

2013-10-01

Full Text Available Plant tissues that require structural rigidity synthesize a thick, strong secondary cell wall of lignin, cellulose and hemicelluloses in a complicated bridged structure. Master regulators of secondary wall synthesis were identified in dicots, and orthologs of these regulators have been identified in monocots, but regulation of secondary cell wall formation in monocots has not been extensively studied. Here we demonstrate that the rice transcription factors SECONDARY WALL NAC DOMAIN PROTEINs (SWNs can regulate secondary wall formation in rice (Oryza sativa and are potentially useful for engineering the monocot cell wall. The OsSWN1 promoter is highly active in sclerenchymatous cells of the leaf blade and less active in xylem cells. By contrast, the OsSWN2 promoter is highly active in xylem cells and less active in sclerenchymatous cells. OsSWN2 splicing variants encode two proteins; the shorter protein (OsSWN2S has very low transcriptional activation ability, but the longer protein (OsSWN2L and OsSWN1 have strong transcriptional activation ability. In rice, expression of an OsSWN2S chimeric repressor, driven by the OsSWN2 promoter, resulted in stunted growth and para-wilting (leaf rolling and browning under normal water conditions due to impaired vascular vessels. The same OsSWN2S chimeric repressor, driven by the OsSWN1 promoter, caused a reduction of cell wall thickening in sclerenchymatous cells, a drooping leaf phenotype, reduced lignin and xylose contents and increased digestibility as forage. These data suggest that OsSWNs regulate secondary wall formation in rice and manipulation of OsSWNs may enable improvements in monocotyledonous crops for forage or biofuel applications.

Growth promotion and inhibition of the Amazonian wild rice species Oryza grandiglumis to survive flooding.

Science.gov (United States)

Okishio, Takuma; Sasayama, Daisuke; Hirano, Tatsuya; Akimoto, Masahiro; Itoh, Kazuyuki; Azuma, Tetsushi

2014-09-01

In Asian cultivated rice (Oryza sativa), distinct mechanisms to survive flooding are activated in two groups of varieties. Submergence-tolerant rice varieties possessing the SUBMERGENCE1A (SUB1A) gene display reduced growth during flash floods at the seedling stage and resume growth after the flood recedes, whereas deepwater rice varieties possessing the SNORKEL1 (SK1) and SNORKEL2 (SK2) genes display enhanced growth based on internodal elongation during prolonged submergence at the mature stage. In this study, we investigated the occurrence of these growth responses to submergence in the wild rice species Oryza grandiglumis, which is native to the Amazon floodplains. When subjected to gradual submergence, adult plants of O. grandiglumis accessions showed enhanced internodal elongation with rising water level and their growth response closely resembled that of deepwater varieties of O. sativa with high floating capacity. On the other hand, when subjected to complete submergence, seedlings of O. grandiglumis accessions displayed reduced shoot growth and resumed normal growth after desubmergence, similar to the response of submergence-tolerant varieties of O. sativa. Neither SUB1A nor the SK genes were detected in the O. grandiglumis accessions. These results indicate that the O. grandiglumis accessions are capable of adapting successfully to flooding by activating two contrasting mechanisms as the situation demands and that each mechanism of adaptation to flooding is not mediated by SUB1A or the SK genes.

Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing.

Science.gov (United States)

Wang, Bin; Guo, Guangwu; Wang, Chao; Lin, Ying; Wang, Xiaoning; Zhao, Mouming; Guo, Yong; He, Minghui; Zhang, Yong; Pan, Li

2010-08-01

Aspergillus oryzae, an important filamentous fungus used in food fermentation and the enzyme industry, has been shown through genome sequencing and various other tools to have prominent features in its genomic composition. However, the functional complexity of the A. oryzae transcriptome has not yet been fully elucidated. Here, we applied direct high-throughput paired-end RNA-sequencing (RNA-Seq) to the transcriptome of A. oryzae under four different culture conditions. With the high resolution and sensitivity afforded by RNA-Seq, we were able to identify a substantial number of novel transcripts, new exons, untranslated regions, alternative upstream initiation codons and upstream open reading frames, which provide remarkable insight into the A. oryzae transcriptome. We were also able to assess the alternative mRNA isoforms in A. oryzae and found a large number of genes undergoing alternative splicing. Many genes and pathways that might be involved in higher levels of protein production in solid-state culture than in liquid culture were identified by comparing gene expression levels between different cultures. Our analysis indicated that the transcriptome of A. oryzae is much more complex than previously anticipated, and these results may provide a blueprint for further study of the A. oryzae transcriptome.

Comparative Chemistry of Aspergillus oryzae (RIB40) and A. flavus (NRRL 3357)

OpenAIRE

Rank, Christian; Klejnstrup, Marie Louise; Petersen, Lene Maj; Kildgaard, Sara; Frisvad, Jens Christian; Gotfredsen, Charlotte Held; Larsen, Thomas Ostenfeld

2012-01-01

Aspergillus oryzae and A. flavus are important species in industrial biotechnology and food safety and have been some of the first aspergilli to be fully genome sequenced. Bioinformatic analysis has revealed 99.5% gene homology between the two species pointing towards a large coherence in the secondary metabolite production. In this study we report on the first comparison of secondary metabolite production between the full genome sequenced strains of A. oryzae (RIB40) and A. flavus (NRRL 3357...

Arsenate exposure affects amino acids, mineral nutrient status and antioxidants in rice (Oryza sativa L.) genotypes.

Science.gov (United States)

Dwivedi, S; Tripathi, R D; Tripathi, P; Kumar, A; Dave, R; Mishra, S; Singh, R; Sharma, D; Rai, U N; Chakrabarty, D; Trivedi, P K; Adhikari, B; Bag, M K; Dhankher, O P; Tuli, R

2010-12-15

Simulated pot experiments were conducted on four rice (Oryza sativa L.) genotypes (Triguna, IR-36, PNR-519, and IET-4786) to examine the effects of As(V) on amino acids and mineral nutrient status in grain along with antioxidant response to arsenic exposure. Rice genotypes responded differentially to As(V) exposure in terms of amino acids and antioxidant profiles. Total amino acid content in grains of all rice genotypes was positively correlated with arsenic accumulation. While, most of the essential amino acids increased in all cultivars except IR-36, glutamic acid and glycine increased in IET-4786 and PNR-519. The level of nonprotein thiols (NPTs) and the activities of superoxide dismutase (SOD; EC 1.15.1.1), glutathione reductase (GR; EC 1.6.4.2) and ascorbate peroxidase (APX; EC 1.11.1.11) increased in all rice cultivars except IET-4786. A significant genotypic variation was also observed in specific arsenic uptake (SAU; mg kg(-1)dw), which was in the order of Triguna (134) > IR-36 (71) > PNR-519 (53) > IET-4786 (29). Further, application of As(V) at lower doses (4 and 8 mg L(-1) As) enhanced the accumulation of selenium (Se) and other nutrients (Fe, P, Zn, and S), however, higher dose (12 mg L(-1) As) limits the nutrient uptake in rice. In conclusion, low As accumulating genotype, IET-4786, which also had significantly induced level of essential amino acids, seems suitable for cultivation in moderately As contaminated soil and would be safe for human consumption.

Genomewide analysis of the lateral organ boundaries domain gene ...

Indian Academy of Sciences (India)

of plants such as Arabidopsis, Oryza sativa, Zea mays, poplar, apple and tomato. However ... found to share a similar intron/exon structure and gene length within the same class. .... ches against the proteome and genome files downloaded.

Risk Assessment of Heavy Metals Contamination in Paddy Soil, Plants, and Grains (Oryza sativa L.) at the East Coast of India

Science.gov (United States)

Satpathy, Deepmala; Reddy, M. Vikram; Dhal, Soumya Prakash

2014-01-01

Heavy metals known to be accumulated in plants adversely affect human health. This study aims to assess the effects of agrochemicals especially chemical fertilizers applied in paddy fields, which release potential toxic heavy metals into soil. Those heavy metals get accumulated in different parts of paddy plant (Oryza sativa L.) including the grains. Concentrations of nonessential toxic heavy metals (Cd, Cr, and Pb) and the micronutrients (Cu, Mn, and Zn) were measured in the paddy field soil and plant parts. Mn and Cd are found to be accumulated more in shoot than in root. The metal transfer factors from soil to rice plant were significant for Pb, Cd, Cu, Cr, Mn, and Zn. The ranking order of bioaccumulation factor (BAF) for heavy metals was Zn > Mn > Cd > Cu > Cr > Pb indicating that the accumulation of micronutrients was more than that of nonessential toxic heavy metals. The concentrations of heavy metals were found to be higher in paddy field soils than that of the nearby control soil but below permissible limits. The higher Health Index (HI) values of rice consuming adults (1.561) and children (1.360) suggest their adverse health effects in the near future. PMID:24995308

Determination of residues of imazapic and imazaphic in rice (Oryza sativa) by HPLC

International Nuclear Information System (INIS)

Silva Trejos, Paulina

2005-01-01

A requirement to introduce a pesticide in the harvest of any product for the human consume is imperative to determine that it will not leave residues that can injure the human healthy. In this research the residues of imazapic and imazapyr, both systemic herbicides of the imidazolinone family, were determined in rice (Oryza sativa) by extraction of the samples with the extraction solvent prepared by mixing 40 mL of HC1 1 N, 2400 mL of methanol pesticide grade and 1560 mL of bidistilled water. An aliquot of the extract was concentrated approximately to 10 mL in a rotary evaporator; water was added to the concentrated extract and dissolution to 10 % m/v of lead acetate and it was regulated the pH to 6,2 with dissolution of NaOH 1 N. This dissolution was centrifuged and from the floating liquid and aliquot was measured to regulate the pH to 2,1 with dissolution of HC1 1 N. After it was extracted with dichlormethan and the join extracts were carried to dryness in the rotary evaporator. The residues were dissolved in ultrapure water of pH 2,5 and they were injected in HPLC chromatograph with a C 8 column. The validation of the analytical method obtained were: 5,1 x 10 -2 to 5,1 x 10 -3 μg/mL for linearity; (1,5 x 10 -3 , 5,0 x 10 -3 , 7,8 x 10 -3 , 2,6 x 10 -2 ) μg/mL for imazapyr and imazapic for the detection and quantification limits equivalent to 5,0 x 10 -2 mg/kg in rice; the percent of recovery were 80 % and 125 %, for imazapyr and imazapic and finally, the precision for the retention time, the area and for concentration were: 0,003 % standard deviations, 18 500 and 0,008, respectively. (author) [es

Dicty_cDB: Contig-U14908-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available id:none) Oryza sativa (japonica cultivar... 86 2e-15 FJ787361_1( FJ787361 |pid:none) Nicotiana repanda prote...|pid:none) Oryza sativa (japonica cultivar-gr... 84 8e-15 FJ787374_1( FJ787374 |pid:none) Nicotiana repanda ...15 FJ787369_1( FJ787369 |pid:none) Nicotiana repanda protein kinase-c... 84 8e-15 EU722820_1( EU722820 |pid:... 1e-14 AB016885_14( AB016885 |pid:none) Arabidopsis thaliana genomic DNA,... 83 1e-14 FJ787371_1( FJ787371 |pid:none) Nicotiana repan...da protein kinase-c... 83 1e-14 A84518( A84518 ) probable receptor-like protein kin

Selección preliminar de plantas de arroz con resistencia vertical A pyricularia oryzae Cav por inducción de mutaciones (ING

Directory of Open Access Journals (Sweden)

A Cruz

2016-03-01

Full Text Available Seeds of rice Oryza sativa L. cv. CR-1113 susceptible to blast disease Pyricularia oryzae Cav. Were subjected to gamma radiation with 60Co using doses of 15 and 20 krads to obtain and select mutant plants with vertical resistance to blast. A total of 80.000 rice plants per treatment were individually evaluated in the second mutant generation (M2 at tillering and panicle emergence. Vertical resistance was observed in 47 and 8 plants from the 15 and 20 krads treatments respectively.

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

... Oryza sativa; indica rice; cDNA libraries; rice genome; drought tolerance. ... Putative functions were assigned at a stringency E value of 10-6 in BLASTN and ... School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India ...

Dicty_cDB: Contig-U04816-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available one) Oryza sativa genomic DNA, chromos... 89 9e-17 FM877967_1( FM877967 |pid:none) Asclepias curassavic.... 86 1e-15 FM877966_1( FM877966 |pid:none) Asclepias curassavica partial mRNA...

Analysis of transactivation potential of rice (Oryza sativa L.) heat shock factors.

Science.gov (United States)

Lavania, Dhruv; Dhingra, Anuradha; Grover, Anil

2018-06-01

Based on yeast one-hybrid assays, we show that the presence of C-terminal AHA motifs is not a prerequisite for transactivation potential in rice heat shock factors. Transcriptional activation or transactivation (TA) of heat stress responsive genes takes place by binding of heat shock factors (Hsfs) to heat shock elements. Analysis of TA potential of thirteen rice (Oryza sativa L.) Hsfs (OsHsfs) carried out in this study by yeast one-hybrid assay showed that OsHsfsA3 possesses strong TA potential while OsHsfs A1a, A2a, A2b, A4a, A4d, A5, A7b, B1, B2a, B2b, B2c and B4d lack TA potential. From a near complete picture of TA potential of the OsHsf family (comprising of 25 members) emerging from this study and an earlier report from our group (Mittal et al. in FEBS J 278(17):3076-3085, 2011), it is concluded that (1) overall, six OsHsfs, namely A3, A6a, A6b, A8, C1a and C1b possess TA potential; (2) four class A OsHsfs, namely A3, A6a, A6b and A8 have TA potential out of which A6a and A6b contain AHA motifs while A3 and A8 lack AHA motifs; (3) nine class A OsHsfs, namely A1a, A2a, A2b, A2e, A4a, A4d, A5, A7a and A7b containing AHA motif(s) lack TA function in the yeast assay system; (4) all class B OsHsfs lack AHA motifs and TA potential (B4a not analyzed) and (5) though all class C OsHsf members lack AHA motifs, two members C1a and C1b possess TA function, while one member C2a lacks TA potential (C2b not analyzed). Thus, the presence or absence of AHA motif is possibly not the only factor determining TA potential of OsHsfs. Our findings will help to identify the transcriptional activators of rice heat shock response.

qEMF3, a novel QTL for the early-morning flowering trait from wild rice, Oryza officinalis, to mitigate heat stress damage at flowering in rice, O. sativa.

Science.gov (United States)

Hirabayashi, Hideyuki; Sasaki, Kazuhiro; Kambe, Takashi; Gannaban, Ritchel B; Miras, Monaliza A; Mendioro, Merlyn S; Simon, Eliza V; Lumanglas, Patrick D; Fujita, Daisuke; Takemoto-Kuno, Yoko; Takeuchi, Yoshinobu; Kaji, Ryota; Kondo, Motohiko; Kobayashi, Nobuya; Ogawa, Tsugufumi; Ando, Ikuo; Jagadish, Krishna S V; Ishimaru, Tsutomu

2015-03-01

A decline in rice (Oryza sativa L.) production caused by heat stress is one of the biggest concerns resulting from future climate change. Rice spikelets are most susceptible to heat stress at flowering. The early-morning flowering (EMF) trait mitigates heat-induced spikelet sterility at the flowering stage by escaping heat stress during the daytime. We attempted to develop near-isogenic lines (NILs) for EMF in the indica-type genetic background by exploiting the EMF locus from wild rice, O. officinalis (CC genome). A stable quantitative trait locus (QTL) for flower opening time (FOT) was detected on chromosome 3. A QTL was designated as qEMF3 and it shifted FOT by 1.5-2.0 h earlier for cv. Nanjing 11 in temperate Japan and cv. IR64 in the Philippine tropics. NILs for EMF mitigated heat-induced spikelet sterility under elevated temperature conditions completing flower opening before reaching 35°C, a general threshold value leading to spikelet sterility. Quantification of FOT of cultivars popular in the tropics and subtropics did not reveal the EMF trait in any of the cultivars tested, suggesting that qEMF3 has the potential to advance FOT of currently popular cultivars to escape heat stress at flowering under future hotter climates. This is the first report to examine rice with the EMF trait through marker-assisted breeding using wild rice as a genetic resource. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

NCBI nr-aa BLAST: CBRC-OSAT-07-0071 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-OSAT-07-0071 ref|NP_001060484.1| Os07g0650600 [Oryza sativa (japonica cultivar...-group)] dbj|BAC20065.2| BLE2 protein [Oryza sativa (japonica cultivar-group)] dbj|BAD32037.1| BLE2 protein [Oryza sativa (jap...onica cultivar-group)] dbj|BAF22398.1| Os07g0650600 [Oryza sativa (japonica cultivar-group)] NP_001060484.1 0.0 59% ...

Comparative chemistry of Aspergillus oryzae (RIB40) and A. flavus (NRRL 3357)

DEFF Research Database (Denmark)

Rank, Christian; Klejnstrup, Marie Louise; Petersen, Lene Maj

2012-01-01

Aspergillus oryzae and A. flavus are important species in industrial biotechnology and food safety and have been some of the first aspergilli to be fully genome sequenced. Bioinformatic analysis has revealed 99.5% gene homology between the two species pointing towards a large coherence in the sec...... alkaloids related to the A. flavus metabolites ditryptophenalines and miyakamides. Generally the secondary metabolite capability of A. oryzae presents several novel end products likely to result from the domestication process from A. flavus.......Aspergillus oryzae and A. flavus are important species in industrial biotechnology and food safety and have been some of the first aspergilli to be fully genome sequenced. Bioinformatic analysis has revealed 99.5% gene homology between the two species pointing towards a large coherence...

Complexity of rice Hsp100 gene family: lessons from rice genome ...

Indian Academy of Sciences (India)

Madhu Sudhan

2007-03-29

Mar 29, 2007 ... Chaperonins are a class of molecular chaperones found in prokaryotes and in the ... Keywords. Chaperone, gene family, Hsp100, Oryza sativa ..... Sculpting the proteome with AAA+ proteases and disassembly machines; Cell ...

Competition between rice (Oryza sativa L.) and (barnyardgrass (Echinochloa crus-galli (L.) P. Beauv.) as affected by methanol foliar application.

Science.gov (United States)

Rezaeieh, Alireza D; Aminpanah, Hashem; Sadeghi, Seyed M

2015-01-01

Pot experiment was conducted in Iran, to evaluate the effect of methanol on competition between rice (Oryza sativa) and barnyardgrass (Echinochloa crus-galli). The experiment was conducted as a randomized complete block design with a factorial treatment arrangement and three replicates. Factors were two aqueous methanol foliar applications (0, and 14% v/v) and five rice: barnyardgrass ratios (100:0, 75:25, 50:50, 25:6, and 0:100). Replacement series diagrams for aboveground dry weight illustrated that 'Shiroudi' was more competitive than barnyardgrass as averaged across methanol foliar applications. When methanol was not sprayed, the lines for 'Shiroudi' and barnyardgrass intersected at 75:25 rice: barnyardgrass ratio, but when methanol was sprayed at 14% v/v, the lines for 'Shiroudi' and barnyardgrass intersect at the left of the 75:25 rice: barnyardgrass mixture proportion. These indicate that methanol application reduced competitive ability of 'Shiroudi' against barnyardgrass for aboveground biomass accumulation. At the same time, Methanol foliar application significantly reduced the relative crowding coefficient of 'Shiroudi' while simultaneously it significantly increased the relative crowding coefficient of barnyard grass. This indicates that methanol foliar application reduced the competitive ability of 'Shiroudi' against barnyardgrass for shoot biomass accumulation. This experiment illustrated that foliar spray of aqueous methanol can not be recommended for rice under weedy conditions.

A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China.

Science.gov (United States)

Yu, Jun; Wong, Gane Ka-Shu; Liu, Siqi; Wang, Jian; Yang, Huanming

2007-06-29

In May 2000, the Beijing Institute of Genomics formally announced the launch of a comprehensive crop genome research project on rice genomics, the Chinese Superhybrid Rice Genome Project. SRGP is not simply a sequencing project targeted to a single rice (Oryza sativa L.) genome, but a full-swing research effort with an ultimate goal of providing inclusive basic genomic information and molecular tools not only to understand biology of the rice, both as an important crop species and a model organism of cereals, but also to focus on a popular superhybrid rice landrace, LYP9. We have completed the first phase of SRGP and provide the rice research community with a finished genome sequence of an indica variety, 93-11 (the paternal cultivar of LYP9), together with ample data on subspecific (between subspecies) polymorphisms, transcriptomes and proteomes, useful for within-species comparative studies. In the second phase, we have acquired the genome sequence of the maternal cultivar, PA64S, together with the detailed catalogues of genes uniquely expressed in the parental cultivars and the hybrid as well as allele-specific markers that distinguish parental alleles. Although SRGP in China is not an open-ended research programme, it has been designed to pave a way for future plant genomics research and application, such as to interrogate fundamentals of plant biology, including genome duplication, polyploidy and hybrid vigour, as well as to provide genetic tools for crop breeding and to carry along a social burden-leading a fight against the world's hunger. It began with genomics, the newly developed and industry-scale research field, and from the world's most populous country. In this review, we summarize our scientific goals and noteworthy discoveries that exploit new territories of systematic investigations on basic and applied biology of rice and other major cereal crops.

Characterization of High-Value Bioactives in Some Selected Varieties of Pakistani Rice (Oryza sativa L.)

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Zubair, Muhammad; Anwar, Farooq; Ashraf, Muhammad; Uddin, Md. Kamal

2012-01-01

The present study reports the composition and variation of fatty acids, sterols, tocopherols and γ-oryzanol among selected varieties namely Basmati Super, Basmati 515, Basmati 198, Basmati 385, Basmati 2000, Basmati 370, Basmati Pak, KSK-139, KS-282 and Irri-6 of Pakistani rice (Oryza sativa L). Oil content extracted with n-hexane from different varieties of brown rice seed (unpolished rice) ranged from 1.92% to 2.72%. Total fatty acid contents among rice varieties tested varied between 18240 and 25840 mg/kg brown rice seed. The rice tested mainly contained oleic (6841–10952 mg/kg) linoleic (5453–7874 mg/kg) and palmitic acid (3613–5489 mg/kg). The amounts of total phytosterols (GC and GC-MS analysis), with main contribution from β-sitosterol (445–656 mg/kg), campesterol (116–242 mg/kg), Δ5-avenasterol (89–178 mg/kg) and stigmasterol (75–180 mg/kg) were established to be 739.4 to 1330.4 mg/kg rice seed. The content of α-, γ- and δ-tocopherols as analyzed by HPLC varied from 39.0–76.1, 21.6–28.1 and 6.5–16.5 mg/kg rice seed, respectively. The amounts of different γ-oryzanol components (HPLC data), identified as cycloartenyl ferulate, 24-methylene cycloartanyl ferulate, campesteryl ferulate and β-sitosteryl ferulate, were in the range of 65.5–103.6, 140.2–183.1, 29.8–45.5 and 8.6–10.4 mg/kg rice seed, respectively. Overall, the concentration of these bioactives was higher in the Basmati rice cultivars showing their functional food superiority. In conclusion, the tested varieties of Pakistani rice, especially the Basmati cultivars, can provide best ingredients for functional foods. PMID:22605998

Characterization of High-Value Bioactives in Some Selected Varieties of Pakistani Rice (Oryza sativa L.

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Md. Kamal Uddin

2012-04-01

Full Text Available The present study reports the composition and variation of fatty acids, sterols, tocopherols and γ-oryzanol among selected varieties namely Basmati Super, Basmati 515, Basmati 198, Basmati 385, Basmati 2000, Basmati 370, Basmati Pak, KSK-139, KS-282 and Irri-6 of Pakistani rice (Oryza sativa L. Oil content extracted with n-hexane from different varieties of brown rice seed (unpolished rice ranged from 1.92% to 2.72%. Total fatty acid contents among rice varieties tested varied between 18240 and 25840 mg/kg brown rice seed. The rice tested mainly contained oleic (6841–10952 mg/kg linoleic (5453–7874 mg/kg and palmitic acid (3613–5489 mg/kg. The amounts of total phytosterols (GC and GC-MS analysis, with main contribution from β-sitosterol (445–656 mg/kg, campesterol (116–242 mg/kg, ∆5-avenasterol (89–178 mg/kg and stigmasterol (75–180 mg/kg were established to be 739.4 to 1330.4 mg/kg rice seed. The content of α-, γ- and δ-tocopherols as analyzed by HPLC varied from 39.0–76.1, 21.6–28.1 and 6.5–16.5 mg/kg rice seed, respectively. The amounts of different γ-oryzanol components (HPLC data, identified as cycloartenyl ferulate, 24-methylene cycloartanyl ferulate, campesteryl ferulate and β-sitosteryl ferulate, were in the range of 65.5–103.6, 140.2–183.1, 29.8–45.5 and 8.6–10.4 mg/kg rice seed, respectively. Overall, the concentration of these bioactives was higher in the Basmati rice cultivars showing their functional food superiority. In conclusion, the tested varieties of Pakistani rice, especially the Basmati cultivars, can provide best ingredients for functional foods.

Determination of contents and antioxidant activity of free and bound phenolics compounds and in vitro digestibility of commercial black and red rice (Oryza sativa L.) varieties.

Science.gov (United States)

Sumczynski, Daniela; Kotásková, Eva; Družbíková, Helena; Mlček, Jiří

2016-11-15

Black and red rices (Oryza sativa L.) were analysed for total flavonoids and phenolics and the HPLC profile including both free and bound phenolic fractions. Moreover, antioxidant activity and in vitro digestibility was determined. Content of flavonoids and polyphenols as well as antioxidant activity was higher in free phenolic fractions. Bound flavonoids in black rices were not significant contributors to antioxidant activity. The main free phenolics in black rices were ferulic, protocatechuic and trans-p-coumaric acids, while the major free phenolics in red rices were catechin, protocatechuic and caffeic acids. The main bound phenolics in black rices were ferulic and vanillic acids and quercetin, in red rice types, they were ferulic, syringic, trans-p-coumaric acids and quercetin. Newly, the presence of m-coumaric acid in red rices was detected. Steam cooked rices showed very high levels of organic matter digestibility, whereas red rices were significantly more digestible than black rices (p<0.05). Copyright © 2016 Elsevier Ltd. All rights reserved.

Biogenic synthesis, characterization of silver nanoparticles using multani mitti (fullers earth), tomato (solanum lycopersicum) seeds, rice husk (oryza sativa) and evaluation of their potential antimicrobial activity

International Nuclear Information System (INIS)

Dar, P.; Hina, A.; Anwar, J.

2016-01-01

The synthesis of silver nanoparticles of three different biogenic materials Multani mitti (Fullers earth), Tomato (Solanum lycopersicum) seeds, Rice Husk (Oryza sativa) was carried out. The possible presence and variability of comprehensive biomolecules in these materials turned as capping and reducing agents which optimize the reduction rate and stabilization of silver nanoparticles. Characterizations were determined by using ultraviolet-visible (UV-Vis) spectroscopy, Scanning electron microscope (SEM), Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD). Stable silver nanoparticles of average size 4.6, 41.1 and 10.6 nm were obtained for Multani mitti, tomato seeds and rice husk respectively. Phenolic and carboxylic biomolecules were identified as active reducing agents of Ag+2 to Ag0. The antimicrobial activity was carried out against Klebsiella pneumonia, Salmonella enterica, Escherichia coli and Staphylococcus aureus strains by using well diffusion method. Maximum zone of inhibition (ZOI) was found against Staphylococcus aureus by all of the three biogenic materials. (author)

Exploration of plant genomes in the FLAGdb++ environment

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Leplé Jean-Charles

2011-03-01

Full Text Available Abstract Background In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published results, and facilitate the exploration and development of both existing hypotheses and new ideas. Results The FLAGdb++ information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Available through a JAVA application, original interfaces and tools assist the functional study of plant genes by considering them in their specific context: chromosome, gene family, orthology group, co-expression cluster and functional network. FLAGdb++ is mainly dedicated to the exploration of large gene groups in order to decipher functional connections, to highlight shared or specific structural or functional features, and to facilitate translational tasks between plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera. Conclusion Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb++ presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge. First launched in 2002, a 15th version of FLAGdb++ is now available and comprises four model plant genomes and over eight million genomic features.

iTRAQ-based proteomic analysis reveals the mechanisms of silicon-mediated cadmium tolerance in rice (Oryza sativa) cells.

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Ma, Jie; Sheng, Huachun; Li, Xiuli; Wang, Lijun

2016-07-01

Silicon (Si) can alleviate cadmium (Cd) stress in rice (Oryza sativa) plants, however, the understanding of the molecular mechanisms at the single-cell level remains limited. To address these questions, we investigated suspension cells of rice cultured in the dark environment in the absence and presence of Si with either short- (12 h) or long-term (5 d) Cd treatments using a combination of isobaric tags for relative and absolute quantitation (iTRAQ), fluorescent staining, and inductively coupled plasma mass spectroscopy (ICP-MS). We identified 100 proteins differentially regulated by Si under the short- or long-term Cd stress. 70% of these proteins were down-regulated, suggesting that Si may improve protein use efficiency by maintaining cells in the normal physiological status. Furthermore, we showed two different mechanisms for Si-mediated Cd tolerance. Under the short-term Cd stress, the Si-modified cell walls inhibited the uptake of Cd ions into cells and consequently reduced the expressions of glycosidase, cell surface non-specific lipid-transfer proteins (nsLTPs), and several stress-related proteins. Under the long-term Cd stress, the amount of Cd in the cytoplasm in Si-accumulating (+Si) cells was decreased by compartmentation of Cd into vacuoles, thus leading to a lower expression of glutathione S-transferases (GST). These results provide protein-level insights into the Si-mediated Cd detoxification in rice single cells. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Influence of chelating ligands on arsenic uptake by hydroponically grown rice seedlings (Oryza sativa L.): a preliminary study

Energy Technology Data Exchange (ETDEWEB)

Rahman, Mohammad A.; Hasegawa, Hiroshi; Ueda, Kazumasa; Maki, Teruya [Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa (Japan); Rahman, M.M. [Department of Botany, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka (Bangladesh)

2008-06-15

Ferric (oxyhydro-)oxides (FeO{sub x}) precipitate in the rhizosphere at neutral or alkaline pH and are adsorbed on the plant root surfaces. Consequently, the higher binding affinity of arsenate to FeO{sub x} and the low iron phytoavailability of the precipitated FeO{sub x} make the phytoremediation of arsenic difficult. In the present study, the influence of chelating ligands on arsenic and iron uptake by hydroponically grown rice seedlings (Oryza sativa L.) was investigated. When chelating ligands were not treated to the growth medium, about 63 and 71% of the total arsenic and iron were distributed in the root extract (outer root surfaces) of rice, respectively. On the other hand, ethylenediaminetetraacetic acid (EDTA), ethylenediaminedisuccinic acid (EDDS) and hydroxyiminodisuccinic acid (HIDS) desorbed a significant amount of arsenic from FeO{sub x} of the outer root surfaces. Therefore, the uptake of arsenic and iron into the roots and their subsequent translocation to the shoots of the rice seedlings increased significantly. The order of increasing arsenic uptake by chelating ligands was HIDS > EDTA > EDDS. Methylglycinediacetic acid (MGDA) and iminodisuccinic acid (IDS) might not be effective in arsenic solubilization from FeO{sub x}. The results suggest that EDDS and HIDS would be a good and environmentally safe choice to accelerate arsenic phytoavailability in the phytoremediation process because of their biodegradability and would be a competent alternative to the widely used non-biodegradable and environmentally persistent EDTA. (Abstract Copyright [2008], Wiley Periodicals, Inc.)

Improvement of nitrogen accumulation and metabolism in rice (Oryza sativa L.) by the endophyte Phomopsis liquidambari.

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Yang, Bo; Ma, Hai-Yan; Wang, Xiao-Mi; Jia, Yong; Hu, Jing; Li, Xia; Dai, Chuan-Chao

2014-09-01

The fungal endophyte Phomopsis liquidambari can enhance nitrogen (N) uptake and metabolism of rice plants under hydroponic conditions. To investigate the effects of P. liquidambari on N accumulation and metabolism in rice (Oryza sativa L.) under field conditions during the entire growing season (S1, the seedling stage; S2, the tillering stage; S3, the heading stage; S4, the ripening stage), we utilized pot experiments to examine metabolic and physiological levels in both shoot and root tissues of rice, with endophyte (E+) and without endophyte (E-), in response to three different N levels. We found that under low-N treatment, P. liquidambari symbiosis increased the rice yield and N use efficiency by 12% and by 11.59%, respectively; that the total N contents in E+ rice plants at the four growth stages were separately increased by 29.05%, 14.65%, 21.06% and 18.38%, respectively; and that the activities of nitrate reductase and glutamine synthetase in E+ rice roots and shoots were significantly increased by fungal infection during the S1 to S3 stages. Moreover, P. liquidambari significantly increased the free NH4(+), NO3(-), amino acid and soluble protein contents in infected rice tissues under low-N treatment during the S1 to S3 stages. The obtained results offer novel data concerning the systemic changes induced by P. liquidambari in rice during the entire growth period and confirm the hypothesis that the rice-P. liquidambari interaction improved the N accumulation and metabolism of rice plants, consequently increasing rice N utilization in nutrient-limited soil. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Genomic dissection of small RNAs in wild rice (Oryza rufipogon): lessons for rice domestication.

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Wang, Yu; Bai, Xuefei; Yan, Chenghai; Gui, Yiejie; Wei, Xinghua; Zhu, Qian-Hao; Guo, Longbiao; Fan, Longjiang

2012-11-01

The lack of a MIRNA set and genome sequence of wild rice (Oryza rufipogon) has prevented us from determining the role of MIRNA genes in rice domestication. In this study, a genome, three small RNA populations and a degradome of O. rufipogon were sequenced by Illumina platform and the expression levels of microRNAs (miRNAs) were investigated by miRNA chips. A de novo O. rufipogon genome was assembled using c. 55× coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on c. 5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these, O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting a loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression differences between wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated that MIRNA genes, like protein-coding genes, might have been significantly shaped during rice domestication and could be one of the driving forces that contributed to rice domestication. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

Comparative Mapping of Seed Dormancy Loci Between Tropical and Temperate Ecotypes of Weedy Rice (Oryza sativa L.

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Lihua Zhang

2017-08-01

Full Text Available Genotypic variation at multiple loci for seed dormancy (SD contributes to plant adaptation to diverse ecosystems. Weedy rice (Oryza sativa was used as a model to address the similarity of SD genes between distinct ecotypes. A total of 12 quantitative trait loci (QTL for SD were identified in one primary and two advanced backcross (BC populations derived from a temperate ecotype of weedy rice (34.3°N Lat.. Nine (75% of the 12 loci were mapped to the same positions as those identified from a tropical ecotype of weedy rice (7.1°N Lat.. The high similarity suggested that the majority of SD genes were conserved during the ecotype differentiation. These common loci are largely those collocated/linked with the awn, hull color, pericarp color, or plant height loci. Phenotypic correlations observed in the populations support the notion that indirect selections for the wild-type morphological characteristics, together with direct selections for germination time, were major factors influencing allelic distributions of SD genes across ecotypes. Indirect selections for crop-mimic traits (e.g., plant height and flowering time could also alter allelic frequencies for some SD genes in agroecosystems. In addition, 3 of the 12 loci were collocated with segregation distortion loci, indicating that some gametophyte development genes could also influence the genetic equilibria of SD loci in hybrid populations. The SD genes with a major effect on germination across ecotypes could be used as silencing targets to develop transgene mitigation (TM strategies to reduce the risk of gene flow from genetically modified crops into weed/wild relatives.

Inhibition of cadmium ion uptake in rice (Oryza sativa) cells by a wall-bound form of silicon.

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Liu, Jian; Ma, Jie; He, Congwu; Li, Xiuli; Zhang, Wenjun; Xu, Fangsen; Lin, Yongjun; Wang, Lijun

2013-11-01

The stresses acting on plants that are alleviated by silicon (Si) range from biotic to abiotic stresses, such as heavy metal toxicity. However, the mechanism of stress alleviation by Si at the single-cell level is poorly understood. We cultivated suspended rice (Oryza sativa) cells and protoplasts and investigated them using a combination of plant nutritional and physical techniques including inductively coupled plasma mass spectrometry (ICP-MS), the scanning ion-selective electrode technique (SIET) and X-ray photoelectron spectroscopy (XPS). We found that most Si accumulated in the cell walls in a wall-bound organosilicon compound. Total cadmium (Cd) concentrations in protoplasts from Si-accumulating (+Si) cells were significantly reduced at moderate concentrations of Cd in the culture medium compared with those from Si-limiting (-Si) cells. In situ measurement of cellular fluxes of the cadmium ion (Cd(2+) ) in suspension cells and root cells of rice exposed to Cd(2+) and/or Si treatments showed that +Si cells significantly inhibited the net Cd(2+) influx, compared with that in -Si cells. Furthermore, a net negative charge (charge density) within the +Si cell walls could be neutralized by an increase in the Cd(2+) concentration in the measuring solution. A mechanism of co-deposition of Si and Cd in the cell walls via a [Si-wall matrix]Cd co-complexation may explain the inhibition of Cd ion uptake, and may offer a plausible explanation for the in vivo detoxification of Cd in rice. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression

DEFF Research Database (Denmark)

Li, Xin; Zhu, Jingde; Hu, Fengyi

2012-01-01

DNA methylation plays important biological roles in plants and animals. To examine the rice genomic methylation landscape and assess its functional significance, we generated single-base resolution DNA methylome maps for Asian cultivated rice Oryza sativa ssp. japonica, indica and their wild rela...

Complete genome sequence of the biofilm-forming Curtobacterium sp. strain BH-2-1-1, isolated from lettuce (Lactuca sativa) originating from a conventional field in Norway.

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Dees, Merete Wiken; Brurberg, May Bente; Lysøe, Erik

2016-12-01

Here, we present the 3,795,952 bp complete genome sequence of the biofilm-forming Curtobacterium sp. strain BH-2-1-1, isolated from conventionally grown lettuce ( Lactuca sativa ) from a field in Vestfold, Norway. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession CP017580.

Quantitative Genetic Analysis for Yield and Yield Components in Boro Rice (Oryza sativa L.

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Supriyo CHAKRABORTY

2010-03-01

Full Text Available Twenty-nine genotypes of boro rice (Oryza sativa L. were grown in a randomized block design with three replications in plots of 4m x 1m with a crop geometry of 20 cm x 20 cm between November-April, in Regional Agricultural Research Station, Nagaon, India. Quantitative data were collected on five randomly selected plants of each genotype per replication for yield/plant, and six other yield components, namely plant height, panicles/plant, panicle length, effective grains/panicle, 100 grain weight and harvest index. Mean values of the characters for each genotype were used for analysis of variance and covariance to obtain information on genotypic and phenotypic correlation along with coheritability between two characters. Path analyses were carried out to estimate the direct and indirect effects of boro rice�s yield components. The objective of the study was to identify the characters that mostly influence the yield for increasing boro rice productivity through breeding program. Correlation analysis revealed significant positive genotypic correlation of yield/plant with plant height (0.21, panicles/plant (0.53, panicle length (0.53, effective grains/panicle (0.57 and harvest index (0.86. Path analysis based on genotypic correlation coefficients elucidated high positive direct effect of harvest index (0.8631, panicle length (0.2560 and 100 grain weight (0.1632 on yield/plant with a residual effect of 0.33. Plant height and panicles/plant recorded high positive indirect effect on yield/plant via harvest index whereas effective grains/panicle on yield/plant via harvest index and panicle length. Results of the present study suggested that five component characters, namely harvest index, effective grains/plant, panicle length, panicles/plant and plant height influenced the yield of boro rice. A genotype with higher magnitude of these component characters could be either selected from the existing genotypes or evolved by breeding program for genetic

Effects of silicon on Oryza sativa L. seedling roots under simulated acid rain stress.

Science.gov (United States)

Ju, Shuming; Yin, Ningning; Wang, Liping; Zhang, Cuiying; Wang, Yukun

2017-01-01

Silicon (Si) has an important function in reducing the damage of environmental stress on plants. Acid rain is a serious abiotic stress factor, and Si can alleviate the stress induced by acid rain on plants. Based on these assumptions, we investigated the effects of silicon on the growth, root phenotype, mineral element contents, hydrogen peroxide (H2O2) and antioxidative enzymes of rice (Oryza sativa L.) seedling roots under simulated acid rain (SAR) stress. The results showed that the combined or single effects of Si and/or SAR on rice roots depend on the concentration of Si and the pH of the SAR. The combined or single effects of a low or moderate concentration of Si (1.0 or 2.0 mM) and light SAR (pH 4.0) enhanced the growth of rice roots, and the combined effects were stronger than those of the single treatment. A high concentration of Si (4.0 mM) or severe SAR (pH 2.0) exerted deleterious effects. The incorporation of Si (1.0, 2.0 or 4.0 mM) into SAR with pH 3.0 or 2.0 promoted the rice root growth, decreased the H2O2 content, increased the Si concentration and the superoxide dismutase (SOD), catalase (CAT), peroxidase (POD) and ascorbate peroxidase (APX) activities, maintained the balance of mineral element (K, Ca, Mg, Fe, Zn, and Cu) concentrations in the roots of rice seedlings compared with SAR alone. The alleviatory effects observed with a moderate concentration of Si (2.0 mM) were better than the effects obtained with a low or high concentration of Si (1.0 or 4.0 mM). The observed effects were due to disruptions in the absorption and utilization of mineral nutrients and impacts on the activity of antioxidant enzymes in roots, and this conclusion suggests that the degree of rice root damage caused by acid rain might be attributed to not only acid rain but also the level of Si in the soil.

Effects of silicon on Oryza sativa L. seedling roots under simulated acid rain stress

Science.gov (United States)

Wang, Liping; Zhang, Cuiying; Wang, Yukun

2017-01-01

Silicon (Si) has an important function in reducing the damage of environmental stress on plants. Acid rain is a serious abiotic stress factor, and Si can alleviate the stress induced by acid rain on plants. Based on these assumptions, we investigated the effects of silicon on the growth, root phenotype, mineral element contents, hydrogen peroxide (H2O2) and antioxidative enzymes of rice (Oryza sativa L.) seedling roots under simulated acid rain (SAR) stress. The results showed that the combined or single effects of Si and/or SAR on rice roots depend on the concentration of Si and the pH of the SAR. The combined or single effects of a low or moderate concentration of Si (1.0 or 2.0 mM) and light SAR (pH 4.0) enhanced the growth of rice roots, and the combined effects were stronger than those of the single treatment. A high concentration of Si (4.0 mM) or severe SAR (pH 2.0) exerted deleterious effects. The incorporation of Si (1.0, 2.0 or 4.0 mM) into SAR with pH 3.0 or 2.0 promoted the rice root growth, decreased the H2O2 content, increased the Si concentration and the superoxide dismutase (SOD), catalase (CAT), peroxidase (POD) and ascorbate peroxidase (APX) activities, maintained the balance of mineral element (K, Ca, Mg, Fe, Zn, and Cu) concentrations in the roots of rice seedlings compared with SAR alone. The alleviatory effects observed with a moderate concentration of Si (2.0 mM) were better than the effects obtained with a low or high concentration of Si (1.0 or 4.0 mM). The observed effects were due to disruptions in the absorption and utilization of mineral nutrients and impacts on the activity of antioxidant enzymes in roots, and this conclusion suggests that the degree of rice root damage caused by acid rain might be attributed to not only acid rain but also the level of Si in the soil. PMID:28291806

Identifikasi Transgene pada Tanaman Padi (oryza sativa var. koshihikari yang Ditransformasi dengan Bantuan Agrobacterium tumefaciens, Menggunakan Metode Tanpa Teknik Kultur Jaringan.

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I Putu Suparthana

2015-04-01

Full Text Available Metode transformasi tanaman dengan bantuan Agrobacterium tumefaciens biasa dilakukan dengan melibatkan teknik kultur jaringan, akan tetapi teknik kultur jaringan memiliki beberapa kelemahan yaitu memerlukan suatu kondisi steril, memakan banyak waktu, sering terjadi mutasi dalam proses kultur in vitro dan sejumlah tanaman bersifat rekalsitran pada tahap regenerasi. Disisi lain metode baru (in planta transformation system yang dikembangkan dalam penelitian ini mampu mengatasi kelemahan-kelemahan tersebut. Penelitian dilakukan pada tanaman padi dengan bantuan A. tumefaciens sebagai inokulum namun tidak melibatkan teknik kultur jaringan pada masa regenerasinya. Biji padi (Oryza sativa L. var. Koshihikari direndam dalam air selama 2 hari, dengan demikian embrionya yang mengandung sel apikal meristem dapat diinokulasi dengan cara menusukkan jarum yang telah dicelupkan dalam inokulum. Biji padi yang telah diinokulasi selanjutnya ditumbuhkan dilapangan selayaknya pembenihan biasa tanpa perlakuan steril. Untuk menentukan keberhasilan teknik ini, dua jenis strain mutan A. tumefaciens (M-21 dan LBA4404 digunakan dalam transformasi. Mutan M-21 mengandung Tn5 tersisip dalam gen iaaM dan mutan LBA4404 membawa binari plasmid vektor. Transgen dari mutan M-21 dapat diidentifikasi dari perubahan fenotipe pada tanaman padi transgenik sedangkan dari mutan LBA4404 dapat diidentifikasi dengan uji histokimia dan ketahanan terhadap antibitik (hygromycin B.Kata kunci: in planta transformation, A. tumefaciens, transformation method

Small kernel 1 encodes a pentatricopeptide repeat protein required for mitochondrial nad7 transcript editing and seed development in maize (Zea mays) and rice (Oryza sativa).

Science.gov (United States)

Li, Xiao-Jie; Zhang, Ya-Feng; Hou, Mingming; Sun, Feng; Shen, Yun; Xiu, Zhi-Hui; Wang, Xiaomin; Chen, Zong-Liang; Sun, Samuel S M; Small, Ian; Tan, Bao-Cai

2014-09-01

RNA editing modifies cytidines (C) to uridines (U) at specific sites in the transcripts of mitochondria and plastids, altering the amino acid specified by the DNA sequence. Here we report the identification of a critical editing factor of mitochondrial nad7 transcript via molecular characterization of a small kernel 1 (smk1) mutant in Zea mays (maize). Mutations in Smk1 arrest both the embryo and endosperm development. Cloning of Smk1 indicates that it encodes an E-subclass pentatricopeptide repeat (PPR) protein that is targeted to mitochondria. Loss of SMK1 function abolishes the C → U editing at the nad7-836 site, leading to the retention of a proline codon that is edited to encode leucine in the wild type. The smk1 mutant showed dramatically reduced complex-I assembly and NADH dehydrogenase activity, and abnormal biogenesis of the mitochondria. Analysis of the ortholog in Oryza sativa (rice) reveals that rice SMK1 has a conserved function in C → U editing of the mitochondrial nad7-836 site. T-DNA knock-out mutants showed abnormal embryo and endosperm development, resulting in embryo or seedling lethality. The leucine at NAD7-279 is highly conserved from bacteria to flowering plants, and analysis of genome sequences from many plants revealed a molecular coevolution between the requirement for C → U editing at this site and the existence of an SMK1 homolog. These results demonstrate that Smk1 encodes a PPR-E protein that is required for nad7-836 editing, and this editing is critical to NAD7 function in complex-I assembly in mitochondria, and hence to embryo and endosperm development in maize and rice. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

OryzaGenome: Genome Diversity Database of Wild Oryza Species

KAUST Repository

Ohyanagi, Hajime; Ebata, Toshinobu; Huang, Xuehui; Gong, Hao; Fujita, Masahiro; Mochizuki, Takako; Toyoda, Atsushi; Fujiyama, Asao; Kaminuma, Eli; Nakamura, Yasukazu; Feng, Qi; Wang, Zi Xuan; Han, Bin; Kurata, Nori

2015-01-01

. Portable VCF (variant call format) file or tabdelimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/ scaffolds/contigs and genome-wide variation information for almost all

Allelic variants of OsHKT1;1 underlie the divergence between indica and japonica subspecies of rice (Oryza sativa for root sodium content.

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Malachy T Campbell

2017-06-01

Full Text Available Salinity is a major factor limiting crop productivity. Rice (Oryza sativa, a staple crop for the majority of the world, is highly sensitive to salinity stress. To discover novel sources of genetic variation for salt tolerance-related traits in rice, we screened 390 diverse accessions under 14 days of moderate (9 dS·m-1 salinity. In this study, shoot growth responses to moderate levels of salinity were independent of tissue Na+ content. A significant difference in root Na+ content was observed between the major subpopulations of rice, with indica accessions displaying higher root Na+ and japonica accessions exhibiting lower root Na+ content. The genetic basis of the observed variation in phenotypes was elucidated through genome-wide association (GWA. The strongest associations were identified for root Na+:K+ ratio and root Na+ content in a region spanning ~575 Kb on chromosome 4, named Root Na+ Content 4 (RNC4. Two Na+ transporters, HKT1;1 and HKT1;4 were identified as candidates for RNC4. Reduced expression of both HKT1;1 and HKT1;4 through RNA interference indicated that HKT1;1 regulates shoot and root Na+ content, and is likely the causal gene underlying RNC4. Three non-synonymous mutations within HKT1;1 were present at higher frequency in the indica subpopulation. When expressed in Xenopus oocytes the indica-predominant isoform exhibited higher inward (negative currents and a less negative voltage threshold of inward rectifying current activation compared to the japonica-predominant isoform. The introduction of a 4.5kb fragment containing the HKT1;1 promoter and CDS from an indica variety into a japonica background, resulted in a phenotype similar to the indica subpopulation, with higher root Na+ and Na+:K+. This study provides evidence that HKT1;1 regulates root Na+ content, and underlies the divergence in root Na+ content between the two major subspecies in rice.

microRNAs targeting DEAD-box helicases are involved in salinity stress response in rice (Oryza sativa L.

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Macovei Anca

2012-10-01

Full Text Available Abstract Background Rice (Oryza sativa L., one of the most important food crop in the world, is considered to be a salt-sensitive crop. Excess levels of salt adversely affect all the major metabolic activities, including cell wall damage, cytoplasmic lysis and genomic stability. In order to cope with salt stress, plants have evolved high degrees of developmental plasticity, including adaptation via cascades of molecular networks and changes in gene expression profiles. Posttranscriptional regulation, through the activity of microRNAs, also plays an important role in the plant response to salinity conditions. MicroRNAs are small endogenous RNAs that modulate gene expression and are involved in the most essential physiological processes, including plant development and adaptation to environmental changes. Results In the present study, we investigated the expression profiles of osa-MIR414, osa-MIR408 and osa-MIR164e along with their targeted genes, under salinity stress conditions in wild type and transgenic rice plants ectopically expressing the PDH45 (Pea DNA Helicase gene. The present miRNAs were predicted to target the OsABP (ATP-Binding Protein, OsDSHCT (DOB1/SK12/helY-like DEAD-box Helicase and OsDBH (DEAD-Box Helicase genes, included in the DEAD-box helicase family. An in silico characterization of the proteins was performed and the miRNAs predicted targets were validated by RLM-5′RACE. The qRT-PCR analysis showed that the OsABP, OsDBH and OsDSHCT genes were up-regulated in response to 100 and 200 mM NaCl treatments. The present study also highlighted an increased accumulation of the gene transcripts in wild type plants, with the exception of the OsABP mRNA which showed the highest level (15.1-fold change compared to control in the transgenic plants treated with 200 mM NaCl. Salinity treatments also affected the expression of osa-MIR414, osa-MIR164e and osa-MIR408, found to be significantly down-regulated, although the changes in mi

Possible cleavage sites of glutelin partial degradation confirmed by immunological analysis in globulin-less mutants of rice (Oryza sativa L.).

Science.gov (United States)

Khan, Nadar; Yamaguchi, Satoru; Katsube-Tanaka, Tomoyuki

2017-10-01

Proteolytic cleavage or partial degradation of proteins is one of the important post-translational modifications for various biological processes, but it is difficult to analyze. Previously, we demonstrated that some subunits of the major rice (Oryza sativa L.) seed storage protein glutelin are partially degraded to produce newly identified polypeptides X1-X5 in mutants in which another major seed storage protein globulin is absent. In this study, the new polypeptides X3 and X4/X5 were immunologically confirmed to be derived from GluA3 and GluA1/GluA2 subunits, respectively. Additionally, the new polypeptides X1 and X2 were at least in part the α polypeptides of the GluB4 subunit partially degraded at the C-terminus. Simulated 2D-PAGE migration patterns of intact and partially degraded α polypeptides based on the calculation of their MWs and pIs enabled us to narrow or predict the possible locations of cleavage sites. The predicted cleavage sites were also verified by the comparison of 2D-PAGE patterns between seed-extracted and E. coli-expressed proteins of the intact and truncated α polypeptides. The results and methodologies demonstrated here would be useful for analyses of partial degradation of proteins and the structure-function relationships of rice seed protein bodies. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture

DEFF Research Database (Denmark)

Li, Lei; Wang, Xiangfeng; Xia, Mian

2005-01-01

BACKGROUND: Sequencing and annotation of the genome of rice (Oryza sativa) have generated gene models in numbers that top all other fully sequenced species, with many lacking recognizable sequence homology to known genes. Experimental evaluation of these gene models and identification of new mode...

Heterologous Production of a Novel Cyclic Peptide Compound, KK-1, in Aspergillus oryzae

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Akira Yoshimi

2018-04-01

Full Text Available A novel cyclic peptide compound, KK-1, was originally isolated from the plant-pathogenic fungus Curvularia clavata. It consists of 10 amino acid residues, including five N-methylated amino acid residues, and has potent antifungal activity. Recently, the genome-sequencing analysis of C. clavata was completed, and the biosynthetic genes involved in KK-1 production were predicted by using a novel gene cluster mining tool, MIDDAS-M. These genes form an approximately 75-kb cluster, which includes nine open reading frames, containing a non-ribosomal peptide synthetase (NRPS gene. To determine whether the predicted genes were responsible for the biosynthesis of KK-1, we performed heterologous production of KK-1 in Aspergillus oryzae by introduction of the cluster genes into the genome of A. oryzae. The NRPS gene was split in two fragments and then reconstructed in the A. oryzae genome, because the gene was quite large (approximately 40 kb. The remaining seven genes in the cluster, excluding the regulatory gene kkR, were simultaneously introduced into the strain of A. oryzae in which NRPS had already been incorporated. To evaluate the heterologous production of KK-1 in A. oryzae, gene expression was analyzed by RT-PCR and KK-1 productivity was quantified by HPLC. KK-1 was produced in variable quantities by a number of transformed strains, along with expression of the cluster genes. The amount of KK-1 produced by the strain with the greatest expression of all genes was lower than that produced by the original producer, C. clavata. Therefore, expression of the cluster genes is necessary and sufficient for the heterologous production of KK-1 in A. oryzae, although there may be unknown factors limiting productivity in this species.

Heterologous Production of a Novel Cyclic Peptide Compound, KK-1, in Aspergillus oryzae.

Science.gov (United States)

Yoshimi, Akira; Yamaguchi, Sigenari; Fujioka, Tomonori; Kawai, Kiyoshi; Gomi, Katsuya; Machida, Masayuki; Abe, Keietsu

2018-01-01

A novel cyclic peptide compound, KK-1, was originally isolated from the plant-pathogenic fungus Curvularia clavata . It consists of 10 amino acid residues, including five N -methylated amino acid residues, and has potent antifungal activity. Recently, the genome-sequencing analysis of C. clavata was completed, and the biosynthetic genes involved in KK-1 production were predicted by using a novel gene cluster mining tool, MIDDAS-M. These genes form an approximately 75-kb cluster, which includes nine open reading frames, containing a non-ribosomal peptide synthetase (NRPS) gene. To determine whether the predicted genes were responsible for the biosynthesis of KK-1, we performed heterologous production of KK-1 in Aspergillus oryzae by introduction of the cluster genes into the genome of A. oryzae . The NRPS gene was split in two fragments and then reconstructed in the A. oryzae genome, because the gene was quite large (approximately 40 kb). The remaining seven genes in the cluster, excluding the regulatory gene kkR , were simultaneously introduced into the strain of A. oryzae in which NRPS had already been incorporated. To evaluate the heterologous production of KK-1 in A. oryzae , gene expression was analyzed by RT-PCR and KK-1 productivity was quantified by HPLC. KK-1 was produced in variable quantities by a number of transformed strains, along with expression of the cluster genes. The amount of KK-1 produced by the strain with the greatest expression of all genes was lower than that produced by the original producer, C. clavata . Therefore, expression of the cluster genes is necessary and sufficient for the heterologous production of KK-1 in A. oryzae , although there may be unknown factors limiting productivity in this species.

Response of oxidative stress defense systems in rice (Oryza sativa) leaves with supplemental UV-B radiation

International Nuclear Information System (INIS)

Dai, Q.; Yan, B.; Huang, S.; Liu, X.; Peng, S.; Miranda, M.L.L.; Chavez, A.Q.; Vergara, B.S.; Olszyk, D.M.

1997-01-01

The impact of elevated ultraviolet-B radiation (UV-B, 280–320 nm) on membrane systems and lipid peroxidation, and possible involvement of active oxygen radicals was investigated in leaves of two UV-B susceptible rice cultivars (Oryza sativa L. cvs IR74 and Dular). Rice seedlings were grown in a greenhouse for 10 days and then treated with biologically effective UV-B (UV-B BE ) radiation for 28 days. Oxidative stress effects were evaluated by measuring superoxide anion (O 2 ) generation rate, hydrogen peroxide (H 2 O 2 ) content, malondialdehyde (MDA) concentration and relative electrolyte conductivity (EC) for IR74 and Dular at 0 (control), 6 or 13 kJ m −2 day −1 UV-B BE . Significant increases in these parameters were found in rice plants grown at 13 vs 0 kJ m −2 day −1 UV-B BE after 28 days; indicating that disruption of membrane systems may be an eventual reason for UV-B-induced injury in rice plants. There was a positive correlation between O 2 − generation and increases in EC or MDA in leaves. Activities of enzymatic and nonenzymatic free radical scavengers were measured for IR74 after 7, 14, 21 and 28 days of exposure to 13 or 0 UV-B BE to evaluate dynamics of these responses over time. Activities of catalase and superoxide dismutase (but not ascorbate peroxidase) and concentrations of ascorbic acid and glutathione were enhanced by 13 vs 0 UV-B BE after 14 days of UV-B exposure. Further exposure to 28 days of UV-B was associated with a decline in enzyme activities and ascorbic acid, but not glutathione. It is suggested that UV-B-induced injury may be associated with disturbance of active oxygen metabolism through the destruction and alteration of both enzymatic and nonenzymatic defense systems in rice. (author)

The influence of soil water status on Oryza Sativa Var. MR220 in KADA rice agroecosystem

International Nuclear Information System (INIS)

Nashriyah Mat; Ismail Che Haron; Mazleha Maskin; Mohd Razi Ismail

2006-01-01

A study to determine the influence of soil water status on rice plant Oryza sativa var. MR220 after panicle initiation stage was carried out at Ladang Merdeka Mulong Lating in the Kemubu Agricultural Development Authority (KADA) area, Kelantan. Five water management treatments imposed on direct seeded rice were; T1. Continuous flooding, T2. Early flooding up to panicle initiation stage followed by saturated (F55-saturated), T3. Early flooding for the first month followed by saturated (F-30 saturated), T4. Continuous saturated, and T5. Continuous field capacity condition throughout the growth stage. The treatments were arranged in Randomized Complete Block Design (RCBD) with four replicates. Results showed significant differences in soil moisture content in the order of T1>T2>T3>T4>T5. Significant differences were also observed in rice plant water content at 68 DAS (days after seeding) in the order of T2>T3>T4>T1>T5. Moisture content also showed significant differences between replicates in the order of R1>R2>R3>R4 and R2>R1>R3>R4; in rice plant and ricefield soil, respectively. Results however showed no significant difference in leaf stomatal conductance due to water stress. Rice plant moisture, soil moisture and leaf stomatal conductance showed no interaction. Published results show that even though overall crop yield was reduced by sheath blight and panicle blast incidence that occur at later stage in 2004-2005 field trials, highest grain yields were obtained from T2 (off season) and T4 (main season). Saturated condition seems to be the most suitable method of growing rice under minimal water input in KADA rice agroecosystem. (Author)

Combined Mass Spectrometry-Based Metabolite Profiling of Different Pigmented Rice (Oryza sativa L. Seeds and Correlation with Antioxidant Activities

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Ga Ryun Kim

2014-09-01

Full Text Available Nine varieties of pigmented rice (Oryza sativa L. seeds that were black, red, or white were used to perform metabolite profiling by using ultra-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF-MS and gas chromatography (GC TOF-MS, to measure antioxidant activities. Clear grouping patterns determined by the color of the rice seeds were identified in principle component analysis (PCA derived from UPLC-Q-TOF-MS. Cyanidin-3-glucoside, peonidin-3-glucoside, proanthocyanidin dimer, proanthocyanidin trimer, apigenin-6-C-glugosyl-8-C-arabiboside, tricin-O-rhamnoside-O-hexoside, and lipids were identified as significantly different secondary metabolites. In PCA score plots derived from GC-TOF-MS, Jakwangdo (JKD and Ilpoom (IP species were discriminated from the other rice seeds by PC1 and PC2. Valine, phenylalanine, adenosine, pyruvate, nicotinic acid, succinic acid, maleic acid, malonic acid, gluconic acid, xylose, fructose, glucose, maltose, and myo-inositol were significantly different primary metabolites in JKD species, while GABA, asparagine, xylitol, and sucrose were significantly distributed in IP species. Analysis of antioxidant activities revealed that black and red rice seeds had higher activity than white rice seeds. Cyanidin-3-glucoside, peonidin-3-glucoside, proanthocyanidin dimers, proanthocyanidin trimers, and catechin were highly correlated with antioxidant activities, and were more plentiful in black and red rice seeds. These results are expected to provide valuable information that could help improve and develop rice-breeding techniques.

Glomus mosseae enhances root growth and Cu and Pb acquisition of upland rice (Oryza sativa L.) in contaminated soils.

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Lin, Aijun; Zhang, Xuhong; Yang, Xiaojin

2014-12-01

A pot culture experiment was carried out to investigate the roles of Glomus mosseae in Cu and Pb acquisition by upland rice (Oryza sativa L.) and the interactions between Cu and Pb. The soil was treated with three Cu levels (0, 100 and 200 mg kg(-1)) and three Pb levels (0, 300, and 600 mg kg(-1)). All treatments were designed with (+M) or without (-M) G. mosseae inoculation in a randomized block design. The addition of Cu and Pb significantly decreased root mycorrhizal colonization. Compared with -M, +M significantly increased root biomass in almost all treatments, and also significantly increased shoot biomass in the Pb(0)Cu(200), Pb(300)Cu(0), and all Pb(600) treatments. AM fungi enhanced plant Cu acquisition, but decreased plant Cu concentrations with all Cu plus Pb treatments, except for shoot in the Cu(200)Pb(600) treatment. Irrespective of Cu and Pb levels, +M plants had higher Pb uptakes than -M plants, but had lower root Pb and higher shoot Pb concentrations than those of -M plants. Another interpretation for the higher shoot Pb concentration in +M plants relied on Cu-Pb interactions. The study provided further evidences for the protective effects of AM fungi on upland rice against Cu and Pb contamination, and uncovered the phenomenon that Cu addition could promote Pb uptake and Pb partitioning to shoot. The possible mechanisms by which AM fungi can alleviate the toxicity induced by Cu and Pb are also discussed.

Distribution of Silicified Microstructures, Regulation of Cinnamyl Alcohol Dehydrogenase and Lodging Resistance in Silicon and Paclobutrazol Mediated Oryza sativa

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Deivaseeno Dorairaj

2017-07-01

Full Text Available Lodging is a phenomenon that affects most of the cereal crops including rice, Oryza sativa. This is due to the fragile nature of herbaceous plants whose stems are non-woody, thus affecting its ability to grow upright. Silicon (Si, a beneficial nutrient is often used to toughen and protect plants from biotic and abiotic stresses. Deposition of Si in plant tissues enhances the rigidity and stiffness of the plant as a whole. Silicified cells provide the much needed strength to the culm to resist breaking. Lignin plays important roles in cell wall structural integrity, stem strength, transport, mechanical support, and plant pathogen defense. The aim of this study is to resolve effects of Si on formation of microstructure and regulation of cinnamyl alcohol dehydrogenase (CAD, a key gene responsible for lignin biosynthesis. Besides evaluating silicon, paclobutrazol (PBZ a plant growth retartdant that reduces internode elongation is also incorporated in this study. Hardness, brittleness and stiffness were improved in presence of silicon thus reducing lodging. Scanning electron micrographs with the aid of energy dispersive x-ray (EDX was used to map silicon distribution. Presence of trichomes, silica cells, and silica bodies were detected in silicon treated plants. Transcripts of CAD gene was also upregulated in these plants. Besides, phloroglucinol staining showed presence of lignified vascular bundles and sclerenchyma band. In conclusion, silicon treated rice plants showed an increase in lignin content, silicon content, and formation of silicified microstructures.

Highly efficient gene targeting in Aspergillus oryzae industrial strains under ligD mutation introduced by genome editing: Strain-specific differences in the effects of deleting EcdR, the negative regulator of sclerotia formation.

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Nakamura, Hidetoshi; Katayama, Takuya; Okabe, Tomoya; Iwashita, Kazuhiro; Fujii, Wataru; Kitamoto, Katsuhiko; Maruyama, Jun-Ichi

2017-07-11

Numerous strains of Aspergillus oryzae are industrially used for Japanese traditional fermentation and for the production of enzymes and heterologous proteins. In A. oryzae, deletion of the ku70 or ligD genes involved in non-homologous end joining (NHEJ) has allowed high gene targeting efficiency. However, this strategy has been mainly applied under the genetic background of the A. oryzae wild strain RIB40, and it would be laborious to delete the NHEJ genes in many A. oryzae industrial strains, probably due to their low gene targeting efficiency. In the present study, we generated ligD mutants from the A. oryzae industrial strains by employing the CRISPR/Cas9 system, which we previously developed as a genome editing method. Uridine/uracil auxotrophic strains were generated by deletion of the pyrG gene, which was subsequently used as a selective marker. We examined the gene targeting efficiency with the ecdR gene, of which deletion was reported to induce sclerotia formation under the genetic background of the strain RIB40. As expected, the deletion efficiencies were high, around 60~80%, in the ligD mutants of industrial strains. Intriguingly, the effects of the ecdR deletion on sclerotia formation varied depending on the strains, and we found sclerotia-like structures under the background of the industrial strains, which have never been reported to form sclerotia. The present study demonstrates that introducing ligD mutation by genome editing is an effective method allowing high gene targeting efficiency in A. oryzae industrial strains.

Enhanced resistance to blast fungus in rice (Oryza sativa L.) by expressing the ribosome-inactivating protein α-momorcharin.

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Qian, Qian; Huang, Lin; Yi, Rong; Wang, Shuzhen; Ding, Yi

2014-03-01

Rice blast caused by Magnaporthe grisea is one of the three major diseases that seriously affect the rice production. Alpha-momorcharin (α-MC), a ribosome-inactivating protein (RIP) isolated from Momordica charantia seeds, has antifungal effects in vitro. In this study, the α-MC gene was constitutively expressed under the control of the 2×35S promoter in transgenic rice (Oryza sativa L.) using an Agrobacterium tumefaciens-mediated method. The nine transgenic plants were obtained and confirmed by PCR and RT-PCR, and the four (B2, B4, B7 and B9) of them whose copy numbers were 1, 2, 3 and 3, respectively, were shown to express the α-MC protein by Western blot. The molecular weight of α-MC in transgenic plants was approximately 38 kDa larger than the purified α-MC protein (28 kDa) in vitro. When the confirmed T1 generations were inoculated with a suspension of M. grisea spores for ten days, the lesions on leaves of transgenic plants were much lesser than those found on wild type (WT). According to the criteria of International Rice Research Institute standard, the mean values for morbidity and disease index numbers were 29.8% and 14.9%, respectively, which were lower than for WT. It is unclear whether RIPs could impact plant fitness and however our results suggest that the α-MC protein is an effective antifungal protein preventing rice blast in transgenic rice. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Recurrent parent genome recovery analysis in a marker-assisted backcrossing program of rice (Oryza sativa L.).

Science.gov (United States)

Miah, Gous; Rafii, Mohd Y; Ismail, Mohd R; Puteh, Adam B; Rahim, Harun A; Latif, Mohammad A

2015-02-01

Backcross breeding is the most commonly used method for incorporating a blast resistance gene into a rice cultivar. Linkage between the resistance gene and undesirable units can persist for many generations of backcrossing. Marker-assisted backcrossing (MABC) along with marker-assisted selection (MAS) contributes immensely to overcome the main limitation of the conventional breeding and accelerates recurrent parent genome (RPG) recovery. The MABC approach was employed to incorporate (a) blast resistance gene(s) from the donor parent Pongsu Seribu 1, the blast-resistant local variety in Malaysia, into the genetic background of MR219, a popular high-yielding rice variety that is blast susceptible, to develop a blast-resistant MR219 improved variety. In this perspective, the recurrent parent genome recovery was analyzed in early generations of backcrossing using simple sequence repeat (SSR) markers. Out of 375 SSR markers, 70 markers were found polymorphic between the parents, and these markers were used to evaluate the plants in subsequent generations. Background analysis revealed that the extent of RPG recovery ranged from 75.40% to 91.3% and from 80.40% to 96.70% in BC1F1 and BC2F1 generations, respectively. In this study, the recurrent parent genome content in the selected BC2F2 lines ranged from 92.7% to 97.7%. The average proportion of the recurrent parent in the selected improved line was 95.98%. MAS allowed identification of the plants that are more similar to the recurrent parent for the loci evaluated in backcross generations. The application of MAS with the MABC breeding program accelerated the recovery of the RP genome, reducing the number of generations and the time for incorporating resistance against rice blast. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Assessment and genetic analysis of heavy metal content in rice grain using an Oryza sativa × O. rufipogon backcross inbred line population.

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Huang, De-Run; Fan, Ye-Yang; Hu, Biao-Lin; Xiao, Ye-Qing; Chen, Da-Zhou; Zhuang, Jie-Yun

2018-03-01

Heavy metal accumulation in rice is a growing concern for public health. Backcross inbred lines derived from an interspecific cross of Oryza sativa × O. rufipogon were grown in two distinct ecological locations (Hangzhou and Lingshui, China). The objective of this study was to characterise the contents of heavy metal in rice grains, and to identify quantitative trait loci (QTLs) for heavy metal contents. The contents of Ni, As, Pb, Cr and Hg in milled rice showed a significant decline as compared with those in brown rice, whereas the content of Cd showed little change. The concentration of heavy metal in rice grain varied greatly between the two environments. A total of 24 QTLs responsible for heavy metal contents were detected, including two for both the brown and milled rice, 13 for brown rice only, and nine for milled rice only. All the QTLs except two had the enhancing alleles derived from O. rufipogon. Sixteen QTLs were clustered in six chromosomal regions. Environmental variation plays an important role in the heavy metal contents in rice grain. QTLs detected in this study might be useful for breeding rice varieties with low heavy metal content. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Modulation in the activity of purified tonoplast H+-ATPase by tonoplast glycolipids prepared from cultured rice (Oryza sativa L. var. Boro) cells.

Science.gov (United States)

Yamaguchi, M; Kasamo, K

2001-05-01

Glycolipids, phospholipids, and neutral lipids were extracted from the tonoplast fraction of cultured rice cells (Oryza sativa L. var. Boro). Acyl steryl glucoside (ASG) and glucocerebroside (GlcCer) were also prepared from this fraction. We determined the effects of these tonoplast lipids on the activity of H+-ATPase which was delipidated and purified from the tonoplast fraction. Exogenously added tonoplast phospholipids stimulated the activity of purified tonoplast H+-ATPase, but tonoplast glycolipids did not. When tonoplast glycolipids or tonoplast ASG was added in the presence of tonoplast phospholipids, they decreased the phospholipid-induced activation of the tonoplast H+-ATPase; tonoplast GlcCer only caused a small decrease. Steryl glucoside (SG) did not cause any decrease in this activation. Phospholipids, ASG, and GlcCer made up 35 mol%, 20 mol% and 7 mol% of the total lipids of the tonoplast fraction of cultured rice cells, respectively, and these glycolipid levels were enough to depress the phospholipid-induced activation of the tonoplast H+-ATPASE: These results revealed that H+-ATPase activity in the tonoplast may be modulated toward activation and depression by tonoplast phospholipids and glycolipids, respectively. The acylation of SG would be responsible for the depression in the phospholipid-induced H+-ATPase activity.

Allelic Variation in the Perennial Ryegrass FLOWERING LOCUS T Gene is Associated with Changes in Flowering Time across a Range of Populations

DEFF Research Database (Denmark)

Skøt, Leif; Sanderson, Ruth; Thomas, Ann

2011-01-01

The Arabidopsis (Arabidopsis thaliana) FLOWERING LOCUS T (FT) gene and its orthologs in other plant species (e.g. rice [Oryza sativa] OsFTL2/Hd3a) have an established role in the photoperiodic induction of flowering response. The genomic and phenotypic variations associated with the perennial...

Mapping QTLs for submergence tolerance during germination in rice

African Journals Online (AJOL)

STORAGESEVER

2008-08-04

Aug 4, 2008 ... Key words: Oryza sativa L, anaerobic germination, QTL analysis. INTRODUCTION. Two main ... The study was conducted at NG-01 greenhouse, Genome and. Mapping (GML), the .... ABC transporter family protein ..... differences of germination habits in rice seeds with special reference to plant breeding (in ...

Transcriptome Analysis of Early Responsive Genes in Rice during Magnaporthe oryzae Infection

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Yiming Wang

2014-12-01

Full Text Available Rice blast disease caused by Magnaporthe oryzae is one of the most serious diseases of cultivated rice (Oryza sativa L. in most rice-growing regions of the world. In order to investigate early response genes in rice, we utilized the transcriptome analysis approach using a 300 K tilling microarray to rice leaves infected with compatible and incompatible M. oryzae strains. Prior to the microarray experiment, total RNA was validated by measuring the differential expression of rice defense-related marker genes (chitinase 2, barwin, PBZ1, and PR-10 by RT-PCR, and phytoalexins (sakuranetin and momilactone A with HPLC. Microarray analysis revealed that 231 genes were up-regulated (>2 fold change, p < 0.05 in the incompatible interaction compared to the compatible one. Highly expressed genes were functionally characterized into metabolic processes and oxidation-reduction categories. The oxidative stress response was induced in both early and later infection stages. Biotic stress overview from MapMan analysis revealed that the phytohormone ethylene as well as signaling molecules jasmonic acid and salicylic acid is important for defense gene regulation. WRKY and Myb transcription factors were also involved in signal transduction processes. Additionally, receptor-like kinases were more likely associated with the defense response, and their expression patterns were validated by RT-PCR. Our results suggest that candidate genes, including receptor-like protein kinases, may play a key role in disease resistance against M. oryzae attack.

Deciphering the signaling mechanisms of the plant cell wall degradation machinery in Aspergillus oryzae

DEFF Research Database (Denmark)

Udatha, D. B. R. K. Gupta; Topakas, Evangelos; Salazar, Margarita Pena

2015-01-01

is required to rationally engineer filamentous fungi for more efficient bioconversion of different types of biomass. Results: In this study we focused on ten chemically defined inducers to drive expression of cellulases, hemicellulases and accessory enzymes in the model filamentous fungus Aspergillus oryzae....... oryzae genome were only partially explained by the chemical similarity of the enzyme inducers. Genes encoding enzymes that have attracted considerable interest such as cellobiose dehydrogenases and copper-dependent polysaccharide mono-oxygenases presented a substrate-specific induction. Several homology...... in 2360 reactions in the genome scale metabolic network of A. oryzae, was performed through a two-step molecular docking against the binding pockets of the transcription factors AoXlnR and AoAmyR. A total of six metabolites viz., sulfite (H2SO3), sulfate (SLF), uroporphyrinogen III (UPGIII), ethanolamine...

Ethylene is not involved in adaptive responses to flooding in the Amazonian wild rice species Oryza grandiglumis.

Science.gov (United States)

Okishio, Takuma; Sasayama, Daisuke; Hirano, Tatsuya; Akimoto, Masahiro; Itoh, Kazuyuki; Azuma, Tetsushi

2015-02-01

The Amazonian wild rice Oryza grandiglumis has two contrasting adaptation mechanisms to flooding submergence: a quiescence response to complete submergence at the seedling stage and an escape response based on internodal elongation to partial submergence at the mature stage. We investigated possible factors that trigger these responses. In stem segments excised from mature O. grandiglumis plants, complete submergence only slightly promoted internodal elongation with increased ethylene levels in the internodes, while partial submergence substantially promoted internodal elongation without increased ethylene levels in the internodes. Incubation of non-submerged stem segments under a continuous flow of humidified ethylene-free air promoted internodal elongation to the same extent as that observed for partially submerged segments. Applied ethylene had little effect on the internodal elongation of non-submerged segments irrespective of humidity conditions. These results indicate that the enhanced internodal elongation of submerged O. grandiglumis plants is not triggered by ethylene accumulated during submergence but by the moist surroundings provided by submergence. The growth of shoots in O. grandiglumis seedlings was not promoted by ethylene or complete submergence, as is the case in O. sativa cultivars possessing the submergence-tolerant gene SUB1A. However, because the genome of O. grandiglumis lacks the SUB1A gene, the quiescence response of O. grandiglumis seedlings to complete submergence may be regulated by a mechanism distinct from that involved in the response of submergence-tolerant O. sativa cultivars. Copyright © 2014 Elsevier GmbH. All rights reserved.

Genetic analysis and fine mapping of LH1 and LH2, a set of complementary genes controlling late heading in rice (Oryza sativa L.).

Science.gov (United States)

Liu, Shuang; Wang, Feng; Gao, Li Jun; Li, Jin Hua; Li, Rong Bai; Gao, Han Liang; Deng, Guo Fu; Yang, Jin Shui; Luo, Xiao Jin

2012-12-01

Heading date in rice (Oryza sativa L.) is a critical agronomic trait with a complex inheritance. To investigate the genetic basis and mechanism of gene interaction in heading date, we conducted genetic analysis on segregation populations derived from crosses among the indica cultivars Bo B, Yuefeng B and Baoxuan 2. A set of dominant complementary genes controlling late heading, designated LH1 and LH2, were detected by molecular marker mapping. Genetic analysis revealed that Baoxuan 2 contains both dominant genes, while Bo B and Yuefeng B each possess either LH1 or LH2. Using larger populations with segregant ratios of 3 : 1, we fine-mapped LH1 to a 63-kb region near the centromere of chromosome 7 flanked by markers RM5436 and RM8034, and LH2 to a 177-kb region on the short arm of chromosome 8 between flanking markers Indel22468-3 and RM25. Some candidate genes were identified through sequencing of Bo B and Yuefeng B in these target regions. Our work provides a solid foundation for further study on gene interaction in heading date and has application in marker-assisted breeding of photosensitive hybrid rice in China.

Random Mutagenesis of the Aspergillus oryzae Genome Results in Fungal Antibacterial Activity

OpenAIRE

Leonard, Cory A.; Brown, Stacy D.; Hayman, J. Russell

2013-01-01

Multidrug-resistant bacteria cause severe infections in hospitals and communities. Development of new drugs to combat resistant microorganisms is needed. Natural products of microbial origin are the source of most currently available antibiotics. We hypothesized that random mutagenesis of Aspergillus oryzae would result in secretion of antibacterial compounds. To address this hypothesis, we developed a screen to identify individual A. oryzae mutants that inhibit the growth of Methicillin-res...

Identification of heterotic loci associated with yield-related traits in Chinese common wild rice (Oryza rufipogon Griff.).

Science.gov (United States)

Luo, Xiaojin; Wu, Shuang; Tian, Feng; Xin, Xiaoyun; Zha, Xiaojun; Dong, Xianxin; Fu, Yongcai; Wang, Xiangkun; Yang, Jinshui; Sun, Chuanqing

2011-07-01

Many rice breeding programs have currently reached yield plateaus as a result of limited genetic variability in parental strains. Dongxiang common wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and serves as an important gene pool for the genetic improvement of rice cultivars. In this study, heterotic loci (HLs) associated with six yield-related traits were identified in wild and cultivated rice and investigated using a set of 265 introgression lines (ILs) of O. rufipogon Griff. in the background of the Indica high-yielding cultivar Guichao 2 (O. sativa L.). Forty-two HLs were detected by a single point analysis of mid-parent heterosis values from test cross F(1) offspring, and 30 (71.5%) of these HLs showed significantly positive effects, consistent with the superiority shown by the F(1) test cross population in the six yield-related traits under study. Genetic mapping of hsp11, a locus responsible for the number of spikelets per panicle, confirmed the utility of these HLs. The results indicate that favorable HLs capable of improving agronomic traits are available. The identification of HLs between wild rice and cultivated rice could lead to a new strategy for the application of heterosis in rice breeding. Copyright © 2011. Published by Elsevier Ireland Ltd.

Sexual Polyploidization in Medicago sativa L.: Impact on the Phenotype, Gene Transcription, and Genome Methylation.

Science.gov (United States)

Rosellini, Daniele; Ferradini, Nicoletta; Allegrucci, Stefano; Capomaccio, Stefano; Zago, Elisa Debora; Leonetti, Paola; Balech, Bachir; Aversano, Riccardo; Carputo, Domenico; Reale, Lara; Veronesi, Fabio

2016-04-07

Polyploidization as the consequence of 2n gamete formation is a prominent mechanism in plant evolution. Studying its effects on the genome, and on genome expression, has both basic and applied interest. We crossed two diploid (2n = 2x = 16) Medicago sativa plants, a subsp. falcata seed parent, and a coerulea × falcata pollen parent that form a mixture of n and 2n eggs and pollen, respectively. Such a cross produced full-sib diploid and tetraploid (2n = 4x = 32) hybrids, the latter being the result of bilateral sexual polyploidization (BSP). These unique materials allowed us to investigate the effects of BSP, and to separate the effect of intraspecific hybridization from those of polyploidization by comparing 2x with 4x full sib progeny plants. Simple sequence repeat marker segregation demonstrated tetrasomic inheritance for all chromosomes but one, demonstrating that these neotetraploids are true autotetraploids. BSP brought about increased biomass, earlier flowering, higher seed set and weight, and larger leaves with larger cells. Microarray analyses with M. truncatula gene chips showed that several hundred genes, related to diverse metabolic functions, changed their expression level as a consequence of polyploidization. In addition, cytosine methylation increased in 2x, but not in 4x, hybrids. Our results indicate that sexual polyploidization induces significant transcriptional novelty, possibly mediated in part by DNA methylation, and phenotypic novelty that could underpin improved adaptation and reproductive success of tetraploid M. sativa with respect to its diploid progenitor. These polyploidy-induced changes may have promoted the adoption of tetraploid alfalfa in agriculture. Copyright © 2016 Rosellini et al.

Sexual Polyploidization in Medicago sativa L.: Impact on the Phenotype, Gene Transcription, and Genome Methylation

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Daniele Rosellini

2016-04-01

Full Text Available Polyploidization as the consequence of 2n gamete formation is a prominent mechanism in plant evolution. Studying its effects on the genome, and on genome expression, has both basic and applied interest. We crossed two diploid (2n = 2x = 16 Medicago sativa plants, a subsp. falcata seed parent, and a coerulea × falcata pollen parent that form a mixture of n and 2n eggs and pollen, respectively. Such a cross produced full-sib diploid and tetraploid (2n = 4x = 32 hybrids, the latter being the result of bilateral sexual polyploidization (BSP. These unique materials allowed us to investigate the effects of BSP, and to separate the effect of intraspecific hybridization from those of polyploidization by comparing 2x with 4x full sib progeny plants. Simple sequence repeat marker segregation demonstrated tetrasomic inheritance for all chromosomes but one, demonstrating that these neotetraploids are true autotetraploids. BSP brought about increased biomass, earlier flowering, higher seed set and weight, and larger leaves with larger cells. Microarray analyses with M. truncatula gene chips showed that several hundred genes, related to diverse metabolic functions, changed their expression level as a consequence of polyploidization. In addition, cytosine methylation increased in 2x, but not in 4x, hybrids. Our results indicate that sexual polyploidization induces significant transcriptional novelty, possibly mediated in part by DNA methylation, and phenotypic novelty that could underpin improved adaptation and reproductive success of tetraploid M. sativa with respect to its diploid progenitor. These polyploidy-induced changes may have promoted the adoption of tetraploid alfalfa in agriculture.

Detailed analysis of targeted gene mutations caused by the Platinum-Fungal TALENs in Aspergillus oryzae RIB40 strain and a ligD disruptant.

Science.gov (United States)

Mizutani, Osamu; Arazoe, Takayuki; Toshida, Kenji; Hayashi, Risa; Ohsato, Shuichi; Sakuma, Tetsushi; Yamamoto, Takashi; Kuwata, Shigeru; Yamada, Osamu

2017-03-01

Transcription activator-like effector nucleases (TALENs), which can generate DNA double-strand breaks at specific sites in the desired genome locus, have been used in many organisms as a tool for genome editing. In Aspergilli, including Aspergillus oryzae, however, the use of TALENs has not been validated. In this study, we performed genome editing of A. oryzae wild-type strain via error of nonhomologous end-joining (NHEJ) repair by transient expression of high-efficiency Platinum-Fungal TALENs (PtFg TALENs). Targeted mutations were observed as various mutation patterns. In particular, approximately half of the PtFg TALEN-mediated deletion mutants had deletions larger than 1 kb in the TALEN-targeting region. We also conducted PtFg TALEN-based genome editing in A. oryzae ligD disruptant (ΔligD) lacking the ligD gene involved in the final step of the NHEJ repair and found that mutations were still obtained as well as wild-type. In this case, the ratio of the large deletions reduced compared to PtFg TALEN-based genome editing in the wild-type. In conclusion, we demonstrate that PtFg TALENs are sufficiently functional to cause genome editing via error of NHEJ in A. oryzae. In addition, we reveal that genome editing using TALENs in A. oryzae tends to cause large deletions at the target region, which were partly suppressed by deletion of ligD. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Reduction of aflatoxin-beta/sub 1/ and ochratoxin-A levels in polished basmati rice (oryza sativa linn.) by different cooking methods

International Nuclear Information System (INIS)

Hussain, A.; Luttfullah, G.

2009-01-01

Rice (Oryza sativa Linn) is one of the basic diets of Pakistan. The aim of present study was to evaluate the effect of different cooking methods on the levels of aflatoxin-B/sub 1/ (AFB.) and ochratoxin-A (OTA). For this purpose the rice samples were artificially contaminated with AFB1 and ochratoxin-A (OTA) individually and simultaneously. The samples were then submitted to three different cooking methods i.e. normal cooking, cooking in an excess of water and in a microwave oven. After treatment, the both toxins were determined by thin layer chromatography (TLC) technique. The highest myco toxin reductions were observed when rice samples cooked in excess water (87.5 % for AFB1 and 86.6 % for OTA), followed by normal cooking (84.0 % for AFB, and 83.0 % for OTA) and microwave oven cooking (72.5 % for AFB1 and 82.4 % for OTA). The samples artificially contaminated with both AFB1 and OTA, the highest reductions were also observed for rice cooked in excess water (87.5 and 83.0 %) than cooked by normal cooking (82.5 and 766 %), and by microwave oven cooking (77.6 and 75.9 %). The rates of toxin reduction were relatively lower in samples artificially simultaneously contaminated with AFB1 and OTA, than the rice samples contaminated with AFB. and OTA individually. (author)

Efficient CRISPR/Cas9-Mediated Genome Editing Using a Chimeric Single-Guide RNA Molecule

KAUST Repository

Butt, Haroon; Eid, Ayman; Ali, Zahir; Atia, Mohamed A. M.; Mokhtar, Morad M.; Hassan, Norhan; Lee, Ciaran M.; Bao, Gang; Mahfouz, Magdy M.

2017-01-01

used CRISPR/Cas9 to generate targeted double-strand breaks and to deliver an RNA repair template for HDR in rice (Oryza sativa). We used chimeric single-guide RNA (cgRNA) molecules carrying both sequences for target site specificity (to generate

Silicon mitigates heavy metal stress by regulating P-type heavy metal ATPases, Oryza sativa low silicon genes, and endogenous phytohormones

Science.gov (United States)

2014-01-01

Background Silicon (Si) application has been known to enhance the tolerance of plants against abiotic stresses. However, the protective mechanism of Si under heavy metals contamination is poorly understood. The aim of this study was to assess the role of Si in counteracting toxicity due to cadmium (Cd) and copper (Cu) in rice plants (Oryza sativa). Results Si significantly improved the growth and biomass of rice plants and reduced the toxic effects of Cd/Cu after different stress periods. Si treatment ameliorated root function and structure compared with non-treated rice plants, which suffered severe root damage. In the presence of Si, the Cd/Cu concentration was significantly lower in rice plants, and there was also a reduction in lipid peroxidation and fatty acid desaturation in plant tissues. The reduced uptake of metals in the roots modulated the signaling of phytohormones involved in responses to stress and host defense, such as abscisic acid, jasmonic acid, and salicylic acid. Furthermore, the low concentration of metals significantly down regulated the mRNA expression of enzymes encoding heavy metal transporters (OsHMA2 and OsHMA3) in Si-metal-treated rice plants. Genes responsible for Si transport (OsLSi1 and OsLSi2), showed a significant up-regulation of mRNA expression with Si treatment in rice plants. Conclusion The present study supports the active role of Si in the regulation of stresses from heavy metal exposure through changes in root morphology. PMID:24405887

Enhancement of gama-aminobutyric acid (GABA) and other health-related metabolites in germinated red rice (Oryza sativa L.) by ultrasonication.

Science.gov (United States)

Ding, Junzhou; Ulanov, Alexander V; Dong, Mengyi; Yang, Tewu; Nemzer, Boris V; Xiong, Shanbai; Zhao, Siming; Feng, Hao

2018-01-01

Red rice (Oryza sativa L.) that has a red (reddish brown) bran layer in de-hulled rice is known to contain rich biofunctional components. Germination is an effective technique to improve the nutritional quality, digestibility, and flavor of de-hulled rice. Ultrasonication, a form of physical stimulation, has been documented as a novel approach to improve the nutritional quality of plant-based food. This study was undertaken to test the use of ultrasound to enhance the nutritional value of red rice. Ultrasonication (5min, 16W/L) was applied to rice during soaking or after 66h germination. Changes of metabolites (amino acids, sugars, and organic acids) in red rice treated by ultrasonication were determined using a GC/MS plant primary metabolomics analysis platform. Differential expressed metabolites were identified through multivariate statistical analysis. Results showed that γ-aminobutyric acid (GABA) and riboflavin (vitamin B 2 ) in red rice significantly increased after germination for 72h, and then experienced a further increase after treatment by ultrasound at different stages during germination. The metabolomics analysis showed that some plant metabolites, i.e. GABA, O-phosphoethanolamine, and glucose-6-phosphate were significantly increased after the ultrasonic treatment (VIP>1.5) in comparison with the untreated germinated rice. The findings of this study showed that controlled germination with ultrasonic stress is an effective method to enhance GABA and other health-promoted components in de-hulled rice. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis of genetic and genotype X environment interaction effects for agronomic traits of rice (oryza sativa l.) in salt tolerance

International Nuclear Information System (INIS)

Zhou, H.K.; Hayat, Y.; Fang, L.J.; Guo, R.F.; He, J.M.; Xu, H.M.

2010-01-01

A diallel cross experiment of 4 rice (Oryza sativa L.) female and 6 male varieties was conducted to study the genetic effects and their interaction with salt-stress condition of 7 agronomic traits in normal and salt-stressed planting conditions. The panicle length (PL), effective number of panicles per plant (ENP), plumped number of grains per panicles (PNG), total number of grains per panicles (TNG), 1000-grain weight (W), seed setting ratio (SSR) and grain weight per plant (PGW), were investigated. A genetic model including additive effect, dominance effect and their interaction effects with environment (ADE) was employed for analysis of data. It was observed that significant (p<0.05) additive effects, dominance effects, additive X environment interaction effects and dominance X environment interaction effects exist for most of the agronomic traits of rice. In addition, significant (p<0.05) narrow sense heritabilities of ENP, PNG, TNG, W and PGW were found, indicating that the genetic performance of these traits are greatly affected by salt stress condition. A significant (p<0.05) negative correlations in the additive effects and additive X environment interaction effects detected between ENP and PNG suggesting that selection on increasing of ENP can reduce PNG. In addition, there exist a highly significant (p<0.01) positive dominance correlation among the dominance effects of the ENP, PNG and TNG, which shows that it is possible to breed salt-tolerant rice variety by coordinating large panicle and multi-panicle in utilization of heterosis. (author)

Complete genome sequence of the biofilm-forming Microbacterium sp. strain BH-3-3-3, isolated from conventional field-grown lettuce (Lactuca sativa) in Norway.

Science.gov (United States)

Dees, Merete Wiken; Brurberg, May Bente; Lysøe, Erik

2017-03-01

The genus Microbacterium contains bacteria that are ubiquitously distributed in various environments and includes plant-associated bacteria that are able to colonize tissue of agricultural crop plants. Here, we report the 3,508,491 bp complete genome sequence of Microbacterium sp. strain BH-3-3-3, isolated from conventionally grown lettuce ( Lactuca sativa ) from a field in Vestfold, Norway. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession CP017674.

PENGARUH RHIZOPUS ORYZAE DAN ASPERGILLUS ORYZAE TERHADAP KUALITAS KECAP

Directory of Open Access Journals (Sweden)

Dewi Sabita Slamet

2012-11-01

Full Text Available Telah diteliti pengganti fermentasi mikroorganisme Aspergillus oryzae Rhyzopus oryzae dan campuran Aspergillus dan Rhyzopus oryzae, dengan perendaman dalam larutan garam 20% dalam waktu yang berbeda terhadap kualitas kecap.Lamanya perendaman dalam larutan garam 20% yang berbeda menghasilkan kadar protein kecap yang berbeda. Aspergillus oryzae lebih baik dalam menghasilkan enzima protease dari pada Rhyzopus oryzae.Uji organoleptik menunjukkan perbedaan tidak bermakna dalam hal rasa maupun aroma antar kecap yang dibuat dengan strain jamur yang berlainan serta waktu perendaman yang berbeda. Untuk membuat kecap, sebaiknya dilakukan perendaman dalam larutan garam 20% selama 14 hari.

The chemical heritage of Aspergillus flavus in A. oryzae RIB 40

OpenAIRE

Rank, Christian; Klejnstrup, Marie Louise; Petersen, Lene Maj; Frisvad, Jens Christian; Larsen, Thomas Ostenfeld

2011-01-01

Aspergillus oryzae is a very important species in biotechnology and has been used for centuries in traditional Asian fermentation. The RIB40 strain is particularly interesting as it was one of the first genome sequenced Aspergilli together with A. flavus, a prominent food and feed contaminant capable of producing aflatoxin. These species can be perceived as ecotypes. We have analyzed A. oryzae RIB40 and found that the chemical potential could be enhanced significantly under certain conditions...

Genome-scale analysis of the high-efficient protein secretion system of Aspergillus oryzae.

Science.gov (United States)

Liu, Lifang; Feizi, Amir; Österlund, Tobias; Hjort, Carsten; Nielsen, Jens

2014-06-24

The koji mold, Aspergillus oryzae is widely used for the production of industrial enzymes due to its particularly high protein secretion capacity and ability to perform post-translational modifications. However, systemic analysis of its secretion system is lacking, generally due to the poorly annotated proteome. Here we defined a functional protein secretory component list of A. oryzae using a previously reported secretory model of S. cerevisiae as scaffold. Additional secretory components were obtained by blast search with the functional components reported in other closely related fungal species such as Aspergillus nidulans and Aspergillus niger. To evaluate the defined component list, we performed transcriptome analysis on three α-amylase over-producing strains with varying levels of secretion capacities. Specifically, secretory components involved in the ER-associated processes (including components involved in the regulation of transport between ER and Golgi) were significantly up-regulated, with many of them never been identified for A. oryzae before. Furthermore, we defined a complete list of the putative A. oryzae secretome and monitored how it was affected by overproducing amylase. In combination with the transcriptome data, the most complete secretory component list and the putative secretome, we improved the systemic understanding of the secretory machinery of A. oryzae in response to high levels of protein secretion. The roles of many newly predicted secretory components were experimentally validated and the enriched component list provides a better platform for driving more mechanistic studies of the protein secretory pathway in this industrially important fungus.

Polyhydroxyalcanoates of strains of Azospirillum spp. isolated of roots of Lycopersicon esculentum Mill. “tomato” and Oryza sativa L. “rice” in Lambayeque

Directory of Open Access Journals (Sweden)

Katty Baca

2010-12-01

Full Text Available In this work was determined the concentration of polyhydroxyalkanoates (PHAs of Azospirillum strains isolated from roots of Lycopersicon esculentum Mill "tomato" and Oryza sativa L. "rice" as an alternative to accumulation of petroleum-based plastics. Previously disinfected root were plated in Nfb semisolid medium where nitrogen-fixing bacteria were recognized by a whitish film on the surface and turn from green to blue. The genus Azospirillum was identified in Congo red agar medium, obtained 96 isolates of A. lipoferum and A. brasilense on tomato and rice. Batch fermentation was performed with broth Azotobacter modified feeding a saturated solution of malic acid every 12 hours and were stained with Sudan Black B. Strains were selected with the greatest number of PHAs granules (in tomato, 18 of A. lipoferum and 2 of A. brasilense; in rice, 10 of A. lipoferum and 10 of A. brasilense and quantified the biomass and PHAs. PHAs concentration reached 0.661 gL-1 in A. lipoferum KM(T-73 and 0.738 gL-1 in A. brasilense KM(T-19, both isolated from tomato. Strains of A. lipoferum and A. brasilense isolated from tomato reached a higher concentration of biomass and PHAs against the strains of rice.

Plant growth enhancing effects by a siderophore-producing endophytic streptomycete isolated from a Thai jasmine rice plant (Oryza sativa L. cv. KDML105).

Science.gov (United States)

Rungin, Siriwan; Indananda, Chantra; Suttiviriya, Pavinee; Kruasuwan, Worarat; Jaemsaeng, Ratchaniwan; Thamchaipenet, Arinthip

2012-10-01

An endophytic Streptomyces sp. GMKU 3100 isolated from roots of a Thai jasmine rice plant (Oryza sativa L. cv. KDML105) showed the highest siderophore production on CAS agar while phosphate solubilization and IAA production were not detected. A mutant of Streptomyces sp. GMKU 3100 deficient in just one of the plant growth promoting traits, siderophore production, was generated by inactivation of a desD-like gene encoding a key enzyme controlling the final step of siderophore biosynthesis. Pot culture experiments revealed that rice and mungbean plants inoculated with the wild type gave the best enhancement of plant growth and significantly increased root and shoot biomass and lengths compared with untreated controls and siderophore-deficient mutant treatments. Application of the wild type in the presence or absence of ferric citrate significantly promoted plant growth of both plants. The siderophore-deficient mutant clearly showed the effect of this important trait involved in plant-microbe interaction in enhancement of growth in rice and mungbean plants supplied with sequestered iron. Our results highlight the value of a substantial understanding of the relationship of the plant growth promoting properties of endophytic actinomycetes to the plants. Endophytic actinomycetes, therefore, can be applied as potentially safe and environmentally friendly biofertilizers in agriculture.

Breeding for blast-disease-resistant and high-yield Thai jasmine rice (Oryza sativa L. cv. KDML 105) mutants using low-energy ion beams

Science.gov (United States)

Mahadtanapuk, S.; Teraarusiri, W.; Phanchaisri, B.; Yu, L. D.; Anuntalabhochai, S.

2013-07-01

Low-energy ion beam was applied on mutation induction for plant breeding of blast-disease-resistant Thai jasmine rice (Oryza sativa L. cv. KDML 105). Seeds of the wild-type rice were bombarded in vacuum by nitrogen ion beam at energy of 60-80 keV to a beam fluence range of 2 × 1016-2 × 1017 ions/cm2. The ion-bombarded rice seeds were grown in soil for 2 weeks as transplanted rice in plastic pots at 1 seedling/pot. The seedlings were then screened for blast resistance by Pyricularia grisea inoculation with 106 spores/ml concentrations. The blast-resistant rice mutant was planted up to F6 generation with the consistent phenotypic variation. The high percentage of the blast-disease-resistant rice was analyzed with DNA fingerprint. The HAT-RAPD (high annealing temperature-random amplified polymorphic DNA) marker revealed the modified polymorphism fragment presenting in the mutant compared with wild type (KDML 105). The cDNA fingerprints were investigated and the polymorphism fragment was subcloned into pGEM-T easy vector and then sequenced. The sequence of this fragment was compared with those already contained in the database, and the fragment was found to be related to the Spotted leaf protein 11 (Spl11).

Soil-to-plant transfer factors of trace and major elements in rice plant (Oryza Sativa) at Kalpakkam

International Nuclear Information System (INIS)

Sreedevi, K.R.; Rajaram, S.; Thulasi Brindha, J.; Venkataraman, S.; Hegde, A.G.

2011-01-01

The objective of this study was to evaluate the distribution of trace and major elements in rice plant (Oryza Sativa) which is the staple diet of the public at Kalpakkam. The transfer factor from soil to various parts of plant was also studied. Trace and major elements such as Fe, Mn, Zn, Co, Cu, Ni, Cr, Cd, Pb , Sr, K, Ca and Mg were selected based on their role in nutrition and also to study the behaviour of their radioactive counterparts. Among the trace elements Fe concentration was observed to be maximum in soil, the mean value of which was 18394 mg/kg dry wt. Cadmium concentration was observed to be minimum with the mean value of 2 mg/kg dry wt. The maximum and minimum concentration observed in the rice grain were due to Zn and Cd and the values were found to be 9 and 0.044 mg/kg dry wt, respectively. In the stem and leaves part the maximum and minimum concentration was due to Fe and Cd and the values were found to be 26.8 and 0.12 mg/kg dry wt. Similarly in the root part Fe and Cd concentrations were found to be maximum and minimum, respectively. Among the different parts of the rice plant, trace elements concentration in root was maximum and in stem and leaves major elements concentration was maximum. Transfer factor from soil to plant parts was computed. In general, the transfer factor was maximum in root, followed by stem and leaves and grain for trace elements. The transfer factor computed for whole rice plant was maximum for Zn and minimum for Sr which is a significant observation from radiological point of view. (author)

Growth and Cd uptake by rice (Oryza sativa) in acidic and Cd-contaminated paddy soils amended with steel slag.

Science.gov (United States)

He, Huaidong; Tam, Nora F Y; Yao, Aijun; Qiu, Rongliang; Li, Wai Chin; Ye, Zhihong

2017-12-01

Contamination of rice (Oryza sativa) by Cd is of great concern. Steel slag could be used to amend Cd-contaminated soils and make them safe for cereal production. This work was conducted to study the effects of steel slag on Cd uptake and growth of rice plants in acidic and Cd-contaminated paddy soils and to determine the possible mechanisms behind these effects. Pot (rhizobag) experiments were conducted using rice plants grown on two acidic and Cd-contaminated paddy soils with or without steel slag amendment. Steel slag amendment significantly increased grain yield by 36-45% and root catalase activity, and decreased Cd concentrations in brown rice by 66-77% compared with the control, in both soils. Steel slag amendment also markedly decreased extractable soil Cd, Cd concentrations in pore-water and Cd translocation from roots to above-ground parts. It also significantly increased soil pH, extractable Si and Ca in soils and Ca concentrations in roots. Significant positive correlations were found between extractable soil Cd and Cd concentrations in rice tissues, but it was negatively correlated with soil pH and extractable Si. Calcium in root tissues significantly and negatively correlated with Cd translocation factors from roots to straw. Overall, steel slag amendment not only significantly promoted rice growth but decreased Cd accumulation in brown rice. These benefits appear to be related to improvements in soil conditions (e.g. increasing pH, extractable Si and Ca), a reduction in extractable soil Cd, and suppression of Cd translocation from roots to above-ground parts. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparative genomic analysis of the WRKY III gene family in populus, grape, arabidopsis and rice.

Science.gov (United States)

Wang, Yiyi; Feng, Lin; Zhu, Yuxin; Li, Yuan; Yan, Hanwei; Xiang, Yan

2015-09-08

WRKY III genes have significant functions in regulating plant development and resistance. In plant, WRKY gene family has been studied in many species, however, there still lack a comprehensive analysis of WRKY III genes in the woody plant species poplar, three representative lineages of flowering plant species are incorporated in most analyses: Arabidopsis (a model plant for annual herbaceous dicots), grape (one model plant for perennial dicots) and Oryza sativa (a model plant for monocots). In this study, we identified 10, 6, 13 and 28 WRKY III genes in the genomes of Populus trichocarpa, grape (Vitis vinifera), Arabidopsis thaliana and rice (Oryza sativa), respectively. Phylogenetic analysis revealed that the WRKY III proteins could be divided into four clades. By microsynteny analysis, we found that the duplicated regions were more conserved between poplar and grape than Arabidopsis or rice. We dated their duplications by Ks analysis of Populus WRKY III genes and demonstrated that all the blocks were formed after the divergence of monocots and dicots. Strong purifying selection has played a key role in the maintenance of WRKY III genes in Populus. Tissue expression analysis of the WRKY III genes in Populus revealed that five were most highly expressed in the xylem. We also performed quantitative real-time reverse transcription PCR analysis of WRKY III genes in Populus treated with salicylic acid, abscisic acid and polyethylene glycol to explore their stress-related expression patterns. This study highlighted the duplication and diversification of the WRKY III gene family in Populus and provided a comprehensive analysis of this gene family in the Populus genome. Our results indicated that the majority of WRKY III genes of Populus was expanded by large-scale gene duplication. The expression pattern of PtrWRKYIII gene identified that these genes play important roles in the xylem during poplar growth and development, and may play crucial role in defense to drought

Dicty_cDB: Contig-U12372-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available 2e-11 AP005795_18( AP005795 |pid:none) Oryza sativa Japonica Group genom... 74 2e-11 AY155346_1( AY155346 |pid:none) Bactrocera cucu...rbitae white eye pr... 73 2e-11 (Q9M9E1) RecName: Full=Pleiotropic drug resistance

An assessment of Wx microsatellite allele, alkali degradation and differentiation of chloroplast DNA in traditional black rice (Oryza sativa L.) from Thailand and Lao PDR.

Science.gov (United States)

Prathepha, Preecha

2007-01-15

Thailand and Lao PDR are the country's rich rice diversity. To contribute a significant knowledge for development new rice varieties, a collection of 142 black rice (Oryza sativa) accessions were determined for variation of physico-chemical properties, Wx microsatellite allele, Wx allele and chloroplast DNA type. The results showed that amylose content of black rice accessions were ranged from 1.9 to 6.8%. All of the alkali disintegration types (high, intermediate and low) was observed in these rice with average of 1.75 on the 1-3 digestibility scale. The unique Wx microsatellite allele (CT)17 was found in these samples and all black rice strains carried Wx(b) allele. In addition, all black rice accessions were found the duplication of the 23 bp sequence motif in the exon 2 of the wx gene. This evidence is a common phenomenon in glutinous rice. Based on two growing condition for black rice, rainfed lowland and rainfed upland, chloroplast DNA type was distinct from each other. All rice strains from rainfed lowland was deletion plastotype, but all other rainfed upland strains were non-deletion types.

Secretome of Aspergillus oryzae in Shaoxing rice wine koji.

Science.gov (United States)

Zhang, Bo; Guan, Zheng-Bing; Cao, Yu; Xie, Guang-Fa; Lu, Jian

2012-04-16

Shaoxing rice wine is the most famous and representative Chinese rice wine. Aspergillus oryzae SU16 is used in the manufacture of koji, the Shaoxing rice wine starter culture. In the current study, a comprehensive analysis of the secretome profile of A. oryzae SU16 in Shaoxing rice wine koji was performed for the first time. The proteomic analysis for the identification of the secretory proteins was done using two-dimensional electrophoresis combined with matrix-assisted laser desorption/ionization-tandem time of flight mass spectrometry based on the annotated A. oryzae genome sequence. A total of 41 unique proteins were identified from the secretome. These proteins included 17 extracellular proteins following the classical secretory pathway, and 10 extracellular proteins putatively secreted by the non-classical secretory pathway. The present secretome profile greatly differed from previous reports on A. oryzae growing in other solid-state nutrient sources. Several new secretory or putative secretory proteins were also found. These proteomic data will significantly aid the advancement of research on the secretome of A. oryzae, especially in solid-state cultures, and in elucidating the production process mechanism of Shaoxing rice wine koji. The findings may promote the technological development and innovation of the Shaoxing rice wine industry. Copyright © 2012 Elsevier B.V. All rights reserved.

Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis.

Science.gov (United States)

Narsai, Reena; Devenish, James; Castleden, Ian; Narsai, Kabir; Xu, Lin; Shou, Huixia; Whelan, James

2013-12-01

Omics research in Oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. Rice DB has been designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or 'expressology', thus using and combining available information from two pre-eminent plant models. To establish Rice DB, gene identifiers (more than 40 types) and annotations from a variety of sources were compiled, functional information based on large-scale and individual studies was manually collated, hundreds of microarrays were analysed to generate expression annotations, and the occurrences of potential functional regulatory motifs in promoter regions were calculated. A range of computational subcellular localization predictions were also run for all putative proteins encoded in the rice genome, and experimentally confirmed protein localizations have been collated, curated and linked to functional studies in rice. A single search box allows anything from gene identifiers (for rice and/or Arabidopsis), motif sequences, subcellular location, to keyword searches to be entered, with the capability of Boolean searches (such as AND/OR). To demonstrate the utility of Rice DB, several examples are presented including a rice mitochondrial proteome, which draws on a variety of sources for subcellular location data within Rice DB. Comparisons of subcellular location, functional annotations, as well as transcript expression in parallel with Arabidopsis reveals examples of conservation between rice and Arabidopsis, using Rice DB (http://ricedb.plantenergy.uwa.edu.au). © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome.

Science.gov (United States)

Verwaaijen, Bart; Wibberg, Daniel; Nelkner, Johanna; Gordin, Miriam; Rupp, Oliver; Winkler, Anika; Bremges, Andreas; Blom, Jochen; Grosch, Rita; Pühler, Alfred; Schlüter, Andreas

2018-02-10

Lettuce (Lactuca sativa, L.) is an important annual plant of the family Asteraceae (Compositae). The commercial lettuce cultivar Tizian has been used in various scientific studies investigating the interaction of the plant with phytopathogens or biological control agents. Here, we present the de novo draft genome sequencing and gene prediction for this specific cultivar derived from transcriptome sequence data. The assembled scaffolds amount to a size of 2.22 Gb. Based on RNAseq data, 31,112 transcript isoforms were identified. Functional predictions for these transcripts were determined within the GenDBE annotation platform. Comparison with the cv. Salinas reference genome revealed a high degree of sequence similarity on genome and transcriptome levels, with an average amino acid identity of 99%. Furthermore, it was observed that two large regions are either missing or are highly divergent within the cv. Tizian genome compared to cv. Salinas. One of these regions covers the major resistance complex 1 region of cv. Salinas. The cv. Tizian draft genome sequence provides a valuable resource for future functional and transcriptome analyses focused on this lettuce cultivar. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular Mapping of QTLs for Yield and Yield-Related Traits in Oryza sativa cv Swarna × O. nivara (IRGC81848 Backcross Population

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B.P. MALLIKARJUNA SWAMY

2011-09-01

Full Text Available Advanced backcross QTL analysis was used to identify QTLs for seven yield and yield-related traits in a BC2F2 population from the cross between a popular Oryza sativa cv Swarna and O. nivara IRGC81848. Transgressive segregants with more than 15% increased effect over Swarna were observed for all the traits except days to heading and days to 50% flowering. Thirty QTLs were detected for seven yield and yield-related traits using interval and composite interval mapping. Enhancing alleles at 13 (45% of these QTLs were derived from O. nivara, and enhancing alleles at all the QTLs for stem diameter and rachis diameter were derived from O. nivara. Three stem diameter QTLs, two rachis diameter QTLs and one number of secondary branches QTL identified by both Interval and composite interval mapping contributed more than 15% of the total phenotypic variance. The QTL epistasis was significant for stem diameter and plot yield. The most significant QTLs qSD7.2, qSD8.1 and qSD9.1 for stem diameter, qRD9.1 for rachis diameter and qNSB1.1 for number of secondary branches are good targets to evaluate their use in marker-assisted selection. O. nivara is a good source of novel alleles for yield related traits and reveals major effect QTLs suitable for marker-assisted selection.

Purification, crystallization and preliminary X-ray analysis of recombinant betaine aldehyde dehydrogenase 2 (OsBADH2), a protein involved in jasmine aroma, from Thai fragrant rice (Oryza sativa L.)

International Nuclear Information System (INIS)

Kuaprasert, Buabarn; Silprasit, Kun; Horata, Natharinee; Khunrae, Pongsak; Wongpanya, Ratree; Boonyalai, Nonlawat; Vanavichit, Apichart; Choowongkomon, Kiattawee

2011-01-01

Crystals of betaine aldehyde dehydrogenase 2 from rice (O. sativa L.) belonged to a C-centred orthorhombic space group and diffraceted X-rays to 2.6 Å resolution. Fragrant rice (Oryza sativa L.) betaine aldehyde dehydrogenase 2 (OsBADH2) is a key enzyme in the synthesis of fragrance aroma compounds. The extremely low activity of OsBADH2 in catalyzing the oxidation of acetaldehyde is believed to be crucial for the accumulation of the volatile compound 2-acetyl-1-pyrroline (2AP) in many scented plants, including fragrant rice. Recombinant fragrant rice OsBADH2 was expressed in Escherichia coli as an N-terminal hexahistidine fusion protein, purified using Ni Sepharose affinity chromatography and crystallized using the microbatch method. Initial crystals were obtained within 24 h using 0.1 M Tris pH 8.5 with 30%(w/v) PEG 4000 and 0.2 M magnesium chloride as the precipitating agent at 291 K. Crystal quality was improved when the enzyme was cocrystallized with NAD + . Improved crystals were grown in 0.1 M HEPES pH 7.4, 24%(w/v) PEG 4000 and 0.2 M ammonium chloride and diffracted to beyond 2.95 Å resolution after being cooled in a stream of N 2 immediately prior to X-ray diffraction experiments. The crystals belonged to space group C222 1 , with unit-cell parameters a = 66.03, b = 183.94, c = 172.28 Å. An initial molecular-replacement solution has been obtained and refinement is in progress

A novel non-thermostable deuterolysin from Aspergillus oryzae.

Science.gov (United States)

Maeda, Hiroshi; Katase, Toru; Sakai, Daisuke; Takeuchi, Michio; Kusumoto, Ken-Ichi; Amano, Hitoshi; Ishida, Hiroki; Abe, Keietsu; Yamagata, Youhei

2016-09-01

Three putative deuterolysin (EC 3.4.24.29) genes (deuA, deuB, and deuC) were found in the Aspergillus oryzae genome database ( http://www.bio.nite.go.jp/dogan/project/view/AO ). One of these genes, deuA, was corresponding to NpII gene, previously reported. DeuA and DeuB were overexpressed by recombinant A. oryzae and were purified. The degradation profiles against protein substrates of both enzymes were similar, but DeuB showed wider substrate specificity against peptidyl MCA-substrates compared with DeuA. Enzymatic profiles of DeuB except for thermostability also resembled those of DeuA. DeuB was inactivated by heat treatment above 80° C, different from thermostable DeuA. Transcription analysis in wild type A. oryzae showed only deuB was expressed in liquid culture, and the addition of the proteinous substrate upregulated the transcription. Furthermore, the NaNO3 addition seems to eliminate the effect of proteinous substrate for the transcription of deuB.

Journal of Biosciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Volume 40 Issue 4 October 2015 pp 819-828 Articles. Flux balance analysis of genome-scale metabolic model of rice (Oryza sativa): Aiming to increase biomass · Rahul Shaw Sudip Kundu · More Details Abstract Fulltext PDF. Due to socio-economic reasons, it is essential to design efficient stress-tolerant, more nutritious, ...

Caracterização agromorfológica interpopulacional em Oryza glumaepatula Interpopulational agro-morphological haracterization of Oryza glumaepatula

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Mariana Silva Rosa

2006-01-01

Full Text Available O gênero Oryza apresenta duas espécies cultivadas e 21 espécies silvestres, sendo quatro originárias da América do Sul e Central. Dentre essas, a única espécie diplóide é Oryza glumaepatula Steud., compatível em cruzamentos com a espécie cultivada O. sativa L. O objetivo deste trabalho foi caracterizar, por meio de caracteres agromorfológicos, oito populações de O. glumaepatula, coletadas em diferentes bacias hidrográficas brasileiras. O experimento foi realizado em casa de vegetação utilizando-se o delineamento em blocos ao acaso com oito tratamentos e seis repetições. Cada parcela foi constituída de quatro plantas, obtendo-se o total de 24 plantas por população. Foram avaliadas três características agronômicas e 18 características morfológicas. Os dados foram analisados utilizando-se estatísticas univariadas e multivariadas. Os resultados mostraram diferenças significativas entre populações para todos os caracteres avaliados, o que indica a grande variabilidade genética observada para todas as populações. Os resultados da análise de componentes principais foram similares aos da análise de agrupamento que classificou as populações em quatro grupos, sendo um grupo para cinco populações da Amazônia, um grupo para uma população do Rio Negro, e dois grupos, um para cada população originária do Rio Xingu e do Rio Paraguai, no Pantanal. A população com características agronômicas mais desejáveis, maior produção de sementes e maior número de perfilhos foi a PG-4, originária do Pantanal Matogrossense, seguida da população JA-4, do Rio Japurá.The genus Oryza contains two cultivated and 21 wild species, and four of these wild species originated from South and Central America. Among these, the only diploid species, compatible in crossing experiments with the cultivated O. sativa L. is O. glumaepatula Steud. The objective of this research was to characterize with morpho-agronomic traits eight

Production of oleic acid ethyl ester catalyzed by crude rice bran (Oryza sativa lipase in a modified fed-batch system: problem and its solution

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Indro Prastowo

2015-01-01

Full Text Available A fed-batch system was modified for the enzymatic production of Oleic Acid Ethyl Ester (OAEE using rice bran (Oryza sativa lipase by retaining the substrate molar ratio (ethanol/oleic acid at 2.05: 1 during the reaction. It resulted in an increase in the ester conversion up to 76.8% in the first 6 h of the reaction, and then followed by a decrease from 76.8% to 22.9% in 6 h later. Meanwhile, the production of water in the reaction system also showed a similar trend to the trend of ester production. The water was hypothesized to lead lipase to reverse the reaction which resulted in a decrease in both (water and esters in the last 6 h of the reaction. In order to overcome the problem, zeolite powders (25 and 50 mg/ml were added into the reaction system at 5 h of the reaction. As the result, final ester conversions increased drastically up to 90 - 95.7% (1.17 – 1.24 times. The addition also proved a hypothesis that the water was involved in reducing the ester conversion in the last 6 h of the reaction. Thus, the combination was effective to produce the high final ester conversion.

Flavonoid glycosides from leaves and straw of Oryza sativa and their effects of cytotoxicity on a macrophage cell line and allelopathic on weed germination

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Ill-Min Chung

2018-03-01

Full Text Available Five new flavonoids namely, 5-hydroxy-6-isoprenyl-7,4′-dimethoxyflavonol-3-O-β-d-arabinofuranoside (1, 5,7-dihydroxy-4′-methoxyflavone-7-O-β-d-arabinopyranosyl-2′′-n-decan-1′′′-oate (2, 3-butanoyl-5,6,8-trihydroxy-7,4′-dimethoxyflavonol--5-O-β-d-glucopyranoside (3, 7, 4′-dimethoxy-5-hydroxyflavone-5-O-α-d-arabinopyranosyl-(2′′ → 1′′′-O-α-d-arabinopyranoside (4, and 5,6-dihydroxy-7, 4′-dimethoxyflavone-5-O-α-d-glucopyranoside (5, together with two known compounds, were isolated from the methanol extract of Oryza sativa leaves and straw. Their structures of new compounds were elucidated by 1D and 2D NMR spectral methods, viz: COSY, HMBC and HSQC aided by mass techniques and IR spectroscopy. The cytotoxicity of these compounds (1–7 were assessed by using (RAW 264.7 mouse macrophages cell line, and allelopathic effects of compounds (1–7 on the germination characteristics of barnyardgrass (Echinochloa oryzicola and pigweed (Chenopodium album L. were also evaluated. The compounds 1, 6 and 7 showed cytotoxicity and compounds 1–7 exhibited significant inhibitory activity on the seed germination of two weed species.

Determination of Optimal Harvest Time of Chuchung Variety Green Rice(®) (Oryza sativa L.) with High Contents of GABA, γ-Oryzanol, and α-Tocopherol.

Science.gov (United States)

Kim, Hoon; Kim, Oui-Woung; Ha, Ae Wha; Park, Soojin

2016-06-01

In our previous study, an early-maturing variety of rice (Oryza sativa L.), Jinbu can have feature with unique green color, various phytochemicals as well as nutritive components by the optimal early harvesting, called Green Rice(®) (GR). The aims of the present field experiments were to evaluate the changes in the weight of 1,000 kernels, yield, and contents of proximate and bioactive compounds in Chuchung, a mid-late maturing variety, during the pre-harvest maturation of rough rice and to research the appropriate harvest time and potent bioactivity of Chuchung GR. The weights of 1,000 kernels of Chuchung GR dramatically increased until 27 days after heading (DAH). The yields of Chuchung GR declined after 27 DAH and significantly declined to 0.0% after 45 DAH. The caloric value and total mineral contents were higher in the GR than in the full ripe stage, the brown rice (BR). In the GR, the contents of bioactive compounds, such as γ-aminobutyric acid, γ-oryzanol, and α-tocopherol, were much higher (P<0.05) than those in the BR, specifically during 24~27 DAH. Therefore, bioactive Chuchung GR can be produced with a reasonable yield at 24~27 DAH and it could be useful for applications in various nutritive and functional food products.

Determination of Optimal Harvest Time of Chuchung Variety Green Rice® (Oryza sativa L.) with High Contents of GABA, γ-Oryzanol, and α-Tocopherol

Science.gov (United States)

Kim, Hoon; Kim, Oui-Woung; Ha, Ae Wha; Park, Soojin

2016-01-01

In our previous study, an early-maturing variety of rice (Oryza sativa L.), Jinbu can have feature with unique green color, various phytochemicals as well as nutritive components by the optimal early harvesting, called Green Rice® (GR). The aims of the present field experiments were to evaluate the changes in the weight of 1,000 kernels, yield, and contents of proximate and bioactive compounds in Chuchung, a mid-late maturing variety, during the pre-harvest maturation of rough rice and to research the appropriate harvest time and potent bioactivity of Chuchung GR. The weights of 1,000 kernels of Chuchung GR dramatically increased until 27 days after heading (DAH). The yields of Chuchung GR declined after 27 DAH and significantly declined to 0.0% after 45 DAH. The caloric value and total mineral contents were higher in the GR than in the full ripe stage, the brown rice (BR). In the GR, the contents of bioactive compounds, such as γ-aminobutyric acid, γ-oryzanol, and α-tocopherol, were much higher (P<0.05) than those in the BR, specifically during 24~27 DAH. Therefore, bioactive Chuchung GR can be produced with a reasonable yield at 24~27 DAH and it could be useful for applications in various nutritive and functional food products. PMID:27390725

Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters in Aspergillus oryzae: A Representative Case Study

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Nachon Raethong

2016-01-01

Full Text Available Aspergillus oryzae is widely used for the industrial production of enzymes. In A. oryzae metabolism, transporters appear to play crucial roles in controlling the flux of molecules for energy generation, nutrients delivery, and waste elimination in the cell. While the A. oryzae genome sequence is available, transporter annotation remains limited and thus the connectivity of metabolic networks is incomplete. In this study, we developed a metabolic annotation strategy to understand the relationship between the sequence, structure, and function for annotation of A. oryzae metabolic transporters. Sequence-based analysis with manual curation showed that 58 genes of 12,096 total genes in the A. oryzae genome encoded metabolic transporters. Under consensus integrative databases, 55 unambiguous metabolic transporter genes were distributed into channels and pores (7 genes, electrochemical potential-driven transporters (33 genes, and primary active transporters (15 genes. To reveal the transporter functional role, a combination of homology modeling and molecular dynamics simulation was implemented to assess the relationship between sequence to structure and structure to function. As in the energy metabolism of A. oryzae, the H+-ATPase encoded by the AO090005000842 gene was selected as a representative case study of multilevel linkage annotation. Our developed strategy can be used for enhancing metabolic network reconstruction.

Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters in Aspergillus oryzae: A Representative Case Study.

Science.gov (United States)

Raethong, Nachon; Wong-Ekkabut, Jirasak; Laoteng, Kobkul; Vongsangnak, Wanwipa

2016-01-01

Aspergillus oryzae is widely used for the industrial production of enzymes. In A. oryzae metabolism, transporters appear to play crucial roles in controlling the flux of molecules for energy generation, nutrients delivery, and waste elimination in the cell. While the A. oryzae genome sequence is available, transporter annotation remains limited and thus the connectivity of metabolic networks is incomplete. In this study, we developed a metabolic annotation strategy to understand the relationship between the sequence, structure, and function for annotation of A. oryzae metabolic transporters. Sequence-based analysis with manual curation showed that 58 genes of 12,096 total genes in the A. oryzae genome encoded metabolic transporters. Under consensus integrative databases, 55 unambiguous metabolic transporter genes were distributed into channels and pores (7 genes), electrochemical potential-driven transporters (33 genes), and primary active transporters (15 genes). To reveal the transporter functional role, a combination of homology modeling and molecular dynamics simulation was implemented to assess the relationship between sequence to structure and structure to function. As in the energy metabolism of A. oryzae, the H(+)-ATPase encoded by the AO090005000842 gene was selected as a representative case study of multilevel linkage annotation. Our developed strategy can be used for enhancing metabolic network reconstruction.

Emerging importance of helicases in plant stress tolerance: characterization of Oryza sativa repair helicase XPB2 promoter and its functional validation in tobacco under multiple stresses

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Shailendra eRaikwar

2015-12-01

Full Text Available Genetic material always remains at the risk of spontaneous or induced damage which challenges the normal functioning of DNA molecule, thus, DNA repair is vital to protect the organisms against genetic damage. DNA hHelicases, the unique molecular motors, are emerged as potentialprospective molecules to engineer stress tolerance in plants and are involved in a variety of DNA nucleic acid metabolismc processes including DNA repair. The DNA repair helicase, OsXPB2 is an evolutionary conserved protein present in different organisms, including plants. Availability of few efficient promoters for gene expression in plants provoked us to study the promoter of XPB for better understanding of gene regulation under stress The analysis of promoter sequence from plant genome is important in understanding the gene regulation. Hereconditions. Here, we report the in silico analysis of novel stress inducible promoter of rice Oryza sativa OsXPB2 (OsXPB2. gene is reported. The in vivo validation of functionality/activity of novel stress inducible promoter of rice OsXPB2 gene promoter under abiotic and hormonal stress conditions was performed by Agrobacterium-mediated transient assay in tobacco leaves using OsXPB2::GUS chimeric construct. Our resultsThe present research revealed that OsXPB2 promoter contains cis-elements accounting for various abiotic stresses (salt, dehydration or cold and hormone (Auxin, ABA or MeJA induced GUS expression/activity in the promoter-reporter assay. The promoter region of OsXPB2 contains CACG, GTAACG, CACGTG, CGTCA CCGCCGCGCT cis acting-elements which are reported to be salt, dehydration, cold, MeJA or ABA responsive, respectively. Functional analysis was done by Agrobacterium-transient assays using agroinfiltration in tobacco leaves, followed by GUS staining and fluorescence quantitative analyses. The results revealed high induction of GUS activity under multiple abiotic stresses as compared to mock treated control. The present

The Population Structure of African Cultivated Rice Oryza glaberrima (Steud.)

DEFF Research Database (Denmark)

Semon, Mande; Nielsen, Rasmus; Jones, Monty P.

2005-01-01

Genome-wide linkage disequilibrium (LD) was investigated for 198 accessions of Oryza glaberrima using 93 nuclear microsatellite markers. Significantly elevated levels of LD were detected, even among distantly located markers. Free recombination among loci at the population genetic level was shown...

Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae

DEFF Research Database (Denmark)

Coutinho, Pedro M.; Andersen, Mikael Rørdam; Kolenova, Katarina

2009-01-01

The plant polysaccharide degradative potential of Aspergillus nidulans was analysed in detail and compared to that of Aspergillus niger and Aspergillus oryzae using a combination of bioinformatics, physiology and transcriptomics. Manual verification indicated that 28.4% of the A. nidulans ORFs...... between the Aspergilli in the presence Of putative regulatory sequences in the promoters of the ORFs Of this Study and correlation of the presence Of putative XlnR binding sites to induction by xylose was detected for A. niger. These data demonstrate differences at genome content, Substrate specificity...

The genomic view of genes responsive to the antagonistic phytohormones, abscisic acid, and gibberellin.

Science.gov (United States)

Yazaki, Junshi; Kikuchi, Shoshi

2005-01-01

We now have the various genomics tools for monocot (Oryza sativa) and a dicot (Arabidopsis thaliana) plant. Plant is not only a very important agricultural resource but also a model organism for biological research. It is important that the interaction between ABA and GA is investigated for controlling the transition from embryogenesis to germination in seeds using genomics tools. These studies have investigated the relationship between dormancy and germination using genomics tools. Genomics tools identified genes that had never before been annotated as ABA- or GA-responsive genes in plant, detected new interactions between genes responsive to the two hormones, comprehensively characterized cis-elements of hormone-responsive genes, and characterized cis-elements of rice and Arabidopsis. In these research, ABA- and GA-regulated genes have been classified as functional proteins (proteins that probably function in stress or PR tolerance) and regulatory proteins (protein factors involved in further regulation of signal transduction). Comparison between ABA and/or GA-responsive genes in rice and those in Arabidopsis has shown that the cis-element has specificity in each species. cis-Elements for the dehydration-stress response have been specified in Arabidopsis but not in rice. cis-Elements for protein storage are remarkably richer in the upstream regions of the rice gene than in those of Arabidopsis.

Biallelic and Genome Wide Association Mapping of Germanium Tolerant Loci in Rice (Oryza sativa L..

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Partha Talukdar

Full Text Available Rice plants accumulate high concentrations of silicon. Silicon has been shown to be involved in plant growth, high yield, and mitigating biotic and abiotic stresses. However, it has been demonstrated that inorganic arsenic is taken up by rice through silicon transporters under anaerobic conditions, thus the ability to efficiently take up silicon may be considered either a positive or a negative trait in rice. Germanium is an analogue of silicon that produces brown lesions in shoots and leaves, and germanium toxicity has been used to identify mutants in silicon and arsenic transport. In this study, two different genetic mapping methods were performed to determine the loci involved in germanium sensitivity in rice. Genetic mapping in the biparental cross of Bala × Azucena (an F6 population and a genome wide association (GWA study with 350 accessions from the Rice Diversity Panel 1 were conducted using 15 μM of germanic acid. This identified a number of germanium sensitive loci: some co-localised with previously identified quantitative trait loci (QTL for tissue silicon or arsenic concentration, none co-localised with Lsi1 or Lsi6, while one single nucleotide polymorphism (SNP was detected within 200 kb of Lsi2 (these are genes known to transport silicon, whose identity was discovered using germanium toxicity. However, examining candidate genes that are within the genomic region of the loci detected above reveals genes homologous to both Lsi1 and Lsi2, as well as a number of other candidate genes, which are discussed.

Black rice (Oryza sativa L.) extract modulates ultraviolet-induced expression of matrix metalloproteinases and procollagen in a skin cell model.

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Han, Mira; Bae, Jung-Soo; Ban, Jae-Jun; Shin, Hee Soon; Lee, Dong Hun; Chung, Jin Ho

2018-05-01

Exposure of the skin to ultraviolet (UV) radiation causes extracellular matrix (ECM) collapse in the dermis, owing to an increase in matrix metalloproteinase (MMP) production in both the epidermis and dermis, and a decrease in type I collagen expression in the dermis. Recently, black rice (Oryza sativa L.) was reported to have a wide range of pharmacological effects in various settings. However, the effects of black rice extract (BRE) on UV‑irradiated skin cells have not yet been characterized. BRE treatment did not affect cell morphology and viability of HaCaT and human dermal fibroblasts (HDF). We demonstrated that BRE downregulated basal and UV‑induced MMP‑1 expression in HaCaT cells. Furthermore, BRE significantly increased type I procollagen expression, and decreased MMP‑1 and MMP‑3 expression in UV‑irradiated HDF. The underlying mechanisms of these results involve a decrease in p38 and c‑Jun N‑terminal kinase activity, and suppression of UV‑induced activation of activator protein‑1 (AP‑1). BRE reduced UV‑induced reactive oxygen species production in HaCaT cells in a dose‑dependent manner. Indeed, mass spectrometry revealed that BRE contained antioxidative flavonoid components such as cyanidin‑3‑O‑β‑D‑glycoside and taxifolin‑7‑O‑glucoside. These findings suggest that BRE attenuates UV‑induced ECM damage by modulating mitogen‑activated protein kinase and AP‑1 signaling, and could be used as an active ingredient for preventing photoaging of the skin.

Improvement of efficient in vitro regeneration potential of mature callus induced from Malaysian upland rice seed (Oryza sativa cv. Panderas).

Science.gov (United States)

Mohd Din, Abd Rahman Jabir; Iliyas Ahmad, Fauziah; Wagiran, Alina; Abd Samad, Azman; Rahmat, Zaidah; Sarmidi, Mohamad Roji

2016-01-01

A new and rapid protocol for optimum callus production and complete plant regeneration has been assessed in Malaysian upland rice (Oryza sativa) cv. Panderas. The effect of plant growth regulator (PGR) on the regeneration frequency of Malaysian upland rice (cv. Panderas) was investigated. Mature seeds were used as a starting material for callus induction experiment using various concentrations of 2,4-D and NAA. Optimal callus induction frequency at 90% was obtained on MS media containing 2,4-D (3 mg L(-1)) and NAA (2 mg L(-1)) after 6 weeks while no significant difference was seen on tryptophan and glutamine parameters. Embryogenic callus was recorded as compact, globular and light yellowish in color. The embryogenic callus morphology was further confirmed with scanning electron microscopy (SEM) analysis. For regeneration, induced calli were treated with various concentrations of Kin (0.5-1.5 mg L(-1)), BAP, NAA and 0.5 mg L(-1) of TDZ. The result showed that the maximum regeneration frequency (100%) was achieved on MS medium containing BAP (0.5 mg L(-1)), Kin (1.5 mg L(-1)), NAA (0.5 mg L(-1)) and TDZ (0.5 mg L(-1)) within four weeks. Developed shoots were successfully rooted on half strength MS free hormone medium and later transferred into a pot containing soil for acclimatization. This cutting-edge finding is unique over the other existing publishable data due to the good regeneration response by producing a large number of shoots.

Do Si/As ratios in growth medium affect arsenic uptake, arsenite efflux and translocation of arsenite in rice (Oryza sativa)?

Science.gov (United States)

Zhang, Min; Zhao, Quanli; Xue, Peiying; Zhang, Shijie; Li, Bowen; Liu, Wenju

2017-10-01

Silicon (Si) may decrease the uptake and accumulation of arsenic (As) in rice. However, the effects of Si/As ratios in growth medium on arsenic uptake, arsenite efflux to the external medium and translocation of arsenite in rice are currently unclear. Rice seedlings (Oryza sativa L.) were exposed to nutrient solutions with 10 μM arsenite [As(III)] or 10 μM arsenate [As(V)] to explore the influence of different silicic acid concentrations (0, 10, 100, 1000 μM) on arsenic uptake and translocation of arsenite with or without 91 μM phosphate for 24 h. Arsenic speciation was determined in nutrient solutions, roots, and shoots. In the arsenite treatments, different Si/As ratios (1:1, 10:1, 100:1) did not affect As(III) uptake by rice roots, however they did inhibit translocation of As(III) from roots to shoots significantly (P rice roots and shoots. A Si/As ratio of 100:1 reduced As(III) translocation from roots to shoots markedly without phosphate. When phosphate was supplied, As(III) translocation from roots to shoots was significantly inhibited by Si/As ratios of 10:1 and 100:1. The results indicated that in the presence of P, different silicic acid concentrations did not impact arsenite uptake and transport in rice when arsenite was supplied. However, a Si/As ratio of 100:1 inhibited As(V) uptake, as well as As(III) efflux and translocation from roots to shoots when arsenate was supplied. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genetic dissection of black grain rice by the development of a near isogenic line.

Science.gov (United States)

Maeda, Hiroaki; Yamaguchi, Takuya; Omoteno, Motoyasu; Takarada, Takeshi; Fujita, Kenji; Murata, Kazumasa; Iyama, Yukihide; Kojima, Yoichiro; Morikawa, Makiko; Ozaki, Hidenobu; Mukaino, Naoyuki; Kidani, Yoshinori; Ebitani, Takeshi

2014-06-01

Rice (Oryza sativa L.) can produce black grains as well as white. In black rice, the pericarp of the grain accumulates anthocyanin, which has antioxidant activity and is beneficial to human health. We developed a black rice introgression line in the genetic background of Oryza sativa L. 'Koshihikari', which is a leading variety in Japan. We used Oryza sativa L. 'Hong Xie Nuo' as the donor parent and backcrossed with 'Koshihikari' four times, resulting in a near isogenic line (NIL) for black grains. A whole genome survey of the introgression line using DNA markers suggested that three regions, on chromosomes 1, 3 and 4 are associated with black pigmentation. The locus on chromosome 3 has not been identified previously. A mapping analysis with 546 F2 plants derived from a cross between the black rice NIL and 'Koshihikari' was evaluated. The results indicated that all three loci are essential for black pigmentation. We named these loci Kala1, Kala3 and Kala4. The black rice NIL was evaluated for eating quality and general agronomic traits. The eating quality was greatly superior to that of 'Okunomurasaki', an existing black rice variety. The isogenicity of the black rice NIL to 'Koshihikari' was very high.

[Effect of selenium on the uptake and translocation of manganese, iron, phosphorus and selenium in rice (Oryza sativa L.)].

Science.gov (United States)

Hu, Ying; Huang, Yi-Zong; Huang, Yan-Chao; Liu, Yun-Xia; Liang, Jian-Hong

2013-10-01

A pot experiment was conducted to clarify the effect of selenium on the uptake and translocation of manganese (Mn), iron (Fe) , phosphorus (P) and selenium (Se) in rice ( Oryza sativa L.). The results showed that addition of Se led to the significant increase of Se concentration in iron plaque on the root surface, root, shoot, husk and brown rice, and significant decrease of Mn concentration in shoot, husk and brown rice. At the Se concentrations of 0.5 and 1.0 mg.kg-1 in soil, Mn concentrations in rice shoot decreased by 32. 2% and 35.0% respectively, in husk 22.0% and 42.6% , in brown rice 27.5% and 28.5% , compared with the Se-free treatment. There was no significant effect of Se on the P and Fe concentrations in every parts of rice, except for Fe concentrations in husk. The translocation of P and Fe from iron plaque, root, shoot and husk to brown rice was not significantly affected by Se addition, but Mn translocation from iron plaque and root to brown rice was significantly inhibited by Se addition. Addition of 1.0 mg.kg-1. Se resulted in the decrease of translocation factor from iron plaque and root to brown rice by 38.9% and 37.9%, respectively, compared with the control treatment. The distribution ratios of Mn, Fe, P and Se in iron plaque, root, shoot, husk and brown rice were also affected by Se addition. The results indicated that Mn uptake, accumulation and translocation in rice could be decreased by the addition of Se in soil, therefore, Se addition could reduce the Mn harm to human health through food chain.

Comparison of phenotyping methods for resistance to stem rot and aggregated sheath spot in rice

Science.gov (United States)

Stem and sheath diseases caused by Sclerotium oryzae Cattaneo (SCL) and Rhizoctonia oryzae-sativae Sawada Mordue (ROS) can severely reduce rice (Oryza sativa L.) yield and grain quality. Genetic resistance is the best strategy to control them. Phenotypic selection for resistance is hampered due to a...

The chemical heritage of Aspergillus flavus in A. oryzae RIB 40

DEFF Research Database (Denmark)

Rank, Christian; Klejnstrup, Marie Louise; Petersen, Lene Maj

Aspergillus oryzae is a very important species in biotechnology and has been used for centuries in traditional Asian fermentation. The RIB40 strain is particularly interesting as it was one of the first genome sequenced Aspergilli together with A. flavus, a prominent food and feed contaminant...... capable of producing aflatoxin. These species can be perceived as ecotypes. We have analyzed A. oryzae RIB40 and found that the chemical potential could be enhanced significantly under certain conditions. Delicate analysis of their metabolic profiles allow for chemical insight on the transcription level...

Comparison of gene co-networks reveals the molecular mechanisms of the rice (Oryza sativa L.) response to Rhizoctonia solani AG1 IA infection.

Science.gov (United States)

Zhang, Jinfeng; Zhao, Wenjuan; Fu, Rong; Fu, Chenglin; Wang, Lingxia; Liu, Huainian; Li, Shuangcheng; Deng, Qiming; Wang, Shiquan; Zhu, Jun; Liang, Yueyang; Li, Ping; Zheng, Aiping

2018-05-05

Rhizoctonia solani causes rice sheath blight, an important disease affecting the growth of rice (Oryza sativa L.). Attempts to control the disease have met with little success. Based on transcriptional profiling, we previously identified more than 11,947 common differentially expressed genes (TPM > 10) between the rice genotypes TeQing and Lemont. In the current study, we extended these findings by focusing on an analysis of gene co-expression in response to R. solani AG1 IA and identified gene modules within the networks through weighted gene co-expression network analysis (WGCNA). We compared the different genes assigned to each module and the biological interpretations of gene co-expression networks at early and later modules in the two rice genotypes to reveal differential responses to AG1 IA. Our results show that different changes occurred in the two rice genotypes and that the modules in the two groups contain a number of candidate genes possibly involved in pathogenesis, such as the VQ protein. Furthermore, these gene co-expression networks provide comprehensive transcriptional information regarding gene expression in rice in response to AG1 IA. The co-expression networks derived from our data offer ideas for follow-up experimentation that will help advance our understanding of the translational regulation of rice gene expression changes in response to AG1 IA.

Effect of peanut shell and wheat straw biochar on the availability of Cd and Pb in a soil-rice (Oryza sativa L.) system.

Science.gov (United States)

Xu, Chao; Chen, Hao-Xiang; Xiang, Qian; Zhu, Han-Hua; Wang, Shuai; Zhu, Qi-Hong; Huang, Dao-You; Zhang, Yang-Zhu

2018-01-01

Soil amendments, such as biochar, have been used to enhance the immobilization of heavy metals in contaminated soil. A pot experiment was conducted to immobilize the available cadmium (Cd) and lead (Pb) in soil using peanut shell biochar (PBC) and wheat straw biochar (WBC), and to observe the accumulation of these heavy metals in rice (Oryza sativa L.). The application of PBC and WBC led to significantly higher pH, soil organic carbon (SOC), and cation exchange capacity (CEC) in paddy soil, while the content of MgCl 2 -extractable Cd and Pb was lower than that of untreated soil. MgCl 2 -extractable Cd and Pb showed significant negative correlations with pH, SOC, and CEC (p rice plants. Specially, when compared to the corresponding concentrations in rice grown in control soils, 5% PBC addition lowered Cd and Pb concentrations in grains by 22.9 and 12.2%, respectively, while WBC addition lowered them by 29.1 and 15.0%, respectively. Compared to Pb content, Cd content was reduced to a greater extent in grain by PBC and WBC. These results suggest that biochar application is effective for immobilizing Cd and Pb in contaminated paddy soil, and reduces their bioavailability in rice. Biochar could be used as a soil amendment for the remediation of soils contaminated with heavy metals.

Genome cluster database. A sequence family analysis platform for Arabidopsis and rice.

Science.gov (United States)

Horan, Kevin; Lauricha, Josh; Bailey-Serres, Julia; Raikhel, Natasha; Girke, Thomas

2005-05-01

The genome-wide protein sequences from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) spp. japonica were clustered into families using sequence similarity and domain-based clustering. The two fundamentally different methods resulted in separate cluster sets with complementary properties to compensate the limitations for accurate family analysis. Functional names for the identified families were assigned with an efficient computational approach that uses the description of the most common molecular function gene ontology node within each cluster. Subsequently, multiple alignments and phylogenetic trees were calculated for the assembled families. All clustering results and their underlying sequences were organized in the Web-accessible Genome Cluster Database (http://bioinfo.ucr.edu/projects/GCD) with rich interactive and user-friendly sequence family mining tools to facilitate the analysis of any given family of interest for the plant science community. An automated clustering pipeline ensures current information for future updates in the annotations of the two genomes and clustering improvements. The analysis allowed the first systematic identification of family and singlet proteins present in both organisms as well as those restricted to one of them. In addition, the established Web resources for mining these data provide a road map for future studies of the composition and structure of protein families between the two species.

Extração, análise e distribuição dos ácidos fenólicos em genótipos pigmentados e não pigmentados de arroz (Oryza sativa L. Extraction, analysis and distribution of phenolic acids in pigmented and non-pigmented genotypes of rice (Oryza sativa L.

Directory of Open Access Journals (Sweden)

Nádia Valéria Mussi de Mira

2008-12-01

Full Text Available Neste estudo, avaliaram-se a distribuição dos Compostos Fenólicos Totais (CFT e o perfil de ácidos fenólicos, presentes nas frações, solúvel e insolúvel de dez genótipos de arroz (Oryza sativa L. de pericarpo pigmentado e não pigmentado. Devido à sua elevada capacidade antioxidante, os compostos fenólicos vem sendo apontados como possíveis promotores da saúde. Grande parte corresponde aos ácidos fenólicos presentes no grão sob a forma solúvel (livre e conjugada e insolúvel (ligada. Na literatura há poucas informações sobre a contribuição dos compostos fenólicos ligados, cujos teores são costumeiramente subestimados. Os CFT foram quantificados pelo método de Folin-Ciocalteau, enquanto os ácidos fenólicos por RP-HPLC. Na fração solúvel dos genótipos pigmentados, os teores de CFT foram variáveis, mas, em média, 5,7 vezes maiores do que nos não pigmentados (média de 3468 e 602 µg eq. Ácido Ferúlico (AF/g arroz, respectivamente, principalmente devido à presença de antocianinas e proantocianidinas. Na fração insolúvel, os pigmentados apresentaram duas vezes mais CFT do que os não pigmentados (825 e 378 µg eq. AF/g arroz, respectivamente, provavelmente devido à retenção de antocianinas e proantocianidinas, mesmo após cinco extrações consecutivas. Dentre os ácidos fenólicos, o ácido ferúlico foi o principal componente em todos os genótipos estudados, exceto no arroz preto, no qual predominou o ácido protocatecóico.This study was conducted to evaluate the distribution of total phenolic compounds and phenolic acids in the soluble and insoluble fractions of 10 rice (Oryza sativa L. genotypes with pigmented or non-pigmented pericarp. These compounds were reported to exert beneficial effects on human health due to their high antioxidant activities. The total phenolic compounds (CFT in both fractions was determined by the Folin-Ciocalteau method and phenolic acids RP-HPLC with Diode-Array Detection

Development of microsatellite markers specific for the short arm of rye (Secale cereale L.) chromosome 1

Czech Academy of Sciences Publication Activity Database

Kofler, R.; Bartoš, Jan; Gong, L.; Stift, G.; Suchánková, Pavla; Šimková, Hana; Berenyi, M.; Burg, K.; Doležel, Jaroslav; Lelley, T.

2008-01-01

Roč. 117, č. 6 (2008), s. 915-926 ISSN 0040-5752 R&D Projects: GA ČR GA521/04/0607; GA ČR GP521/06/P412 Institutional research plan: CEZ:AV0Z50380511 Keywords : NON-LTR RETROTRANSPOSONS * ORYZA-SATIVA L. * PLANT GENOMES Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.490, year: 2008

Evaluation and characterization of advanced rice mutant line of rice (Oryza sativa), MR219-4 and MR219-9 under drought condition

International Nuclear Information System (INIS)

Abdul Rahim Harun; Zarith Shafika Kamarudin; Abdullah, M.Z.; Anna, L.P.K.; Sobri Hussain; Rusli Ibrahim; Khairuddin abdul Rahim

2012-01-01

Two advance rice mutant lines, MR219-4 and MR219-9 derived from mutagenesis of Oryza sativa cv. MR219 with gamma radiation at 300 Gy were evaluated in simulated drought condition in the greenhouse at Malaysian Nuclear Agency. The mutants were evaluated simultaneously with ARN1, a drought resistant variety and MR211 a susceptible cultivar as a check. Randomized complete block design with three replicates was used in the experiment. The evaluation and selection were done based on leaf rolling and leaf drying as well as other agronomic traits, such as, number of tillers per plant, plant height, flag leaf area, grain weight per plant, grain yield per plant, 100-grain weight, harvest index, panicle length and plant biomass. The mutants MR219-4 showed moderate tolerance and MR219-9 showed tolerance to drought respectively as compare to the check variety (ARN1, MR211) and control MR219. Leaf rolling, leaf drying, days to flowering and days to maturity are valuable secondary traits that may provide additional information for selection because of associating with the plant survival under water stress. Further research on expression of drought-tolerant lines under different drought conditions is essential in order to identify particular traits that are associated with drought tolerance and high yield potential. Similarly the importance of secondary traits, relative to other putative traits for drought tolerance, needs to be tested in various environments. (author)

Rice diversity panels available through the genetic stocks oryza collection

Science.gov (United States)

The Genetic Stocks Oryza (GSOR) Collection was established in 2004 at the USDA-ARS, Dale Bumpers National Rice Research Center (DBNRRC) located in Stuttgart, AR. The mission of GSOR is to provide unique genetic resources to the rice research community for genetic and genomics related research. GSOR ...

In silico Allergenicity Study of Insect resistant genetically Modified Rice (Oryza sativa L. for assessment of biosafety

Directory of Open Access Journals (Sweden)

S.K. Das

2017-12-01

Full Text Available India is one of the world's largest producers of rice (Oryza sativa, accounting for 20% of all world rice production. However, lepidopteran pests severely impact the harvest of rice, which leads to environmental pollution and increase production cost. Alternatively, genetic engineering methods may be used to prevent rice pests and increase production of rice in a safe and environmentally friendly manner. Bacillus thuringiensis (Bt genes have been widely used to generate genetically modified (GM crops because the expressed cry1Ab protein confers resistance to lepidopteron pests. The proteins expressed by these genes may lead to food safety problems. Thus, safety evaluations are necessary prior to commercialization. Bioinformatics analysis for allergenicity assessment of cry1Ab protein is performed using different allergen databases viz. FARRP SDAP, Allergome, and Algpred to identify any potential sequence matches to allergen proteins that might indicate allergenic cross-reactivity with the query sequence. A full FASTA search was performed to identify highly similar proteins. However; the full length search cannot identify discontinuous or conformational epitopes that depend upon the tertiary structure of the protein.So every possible contiguous 80-amino acid sequence of each query protein was searched for determining the similarity. The proteins sequence can be searched using FASTA/BLAST for broad homology to known allergens to identify any short sequence that might represent an allergenic epitope. The domains in the Cry protein sequences were searched using Interproscan for potential similarity at the domain level. The results showed neither significant alignment nor similarity of cry1Ab protein at full sequence, domain, and epitope level with any of the known allergen proteins in the full sequence matching. Matching the 80 amino acid and matching of 8 amino acids showed no similarity to determine the epitope potential. From literature survey

The Effect of Silicon on Photosynthesis and Expression of Its Relevant Genes in Rice (Oryza sativa L.) under High-Zinc Stress

Science.gov (United States)

Song, Alin; Li, Ping; Fan, Fenliang; Li, Zhaojun; Liang, Yongchao

2014-01-01

The main objectives of this study were to elucidate the roles of silicon (Si) in alleviating the effects of 2 mM zinc (high Zn) stress on photosynthesis and its related gene expression levels in leaves of rice (Oryza sativa L.) grown hydroponically with high-Zn stress. The results showed that photosynthetic parameters, including net photosynthetic rate, transpiration rate, stomatal conductance, intercellular CO2 concentration, chlorophyll concentration and the chlorophyll fluorescence, were decreased in rice exposed to high-Zn treatment. The leaf chloroplast structure was disordered under high-Zn stress, including uneven swelling, disintegrated and missing thylakoid membranes, and decreased starch granule size and number, which, however, were all counteracted by the addition of 1.5 mM Si. Furthermore, the expression levels of Os08g02630 (PsbY), Os05g48630 (PsaH), Os07g37030 (PetC), Os03g57120 (PetH), Os09g26810 and Os04g38410 decreased in Si-deprived plants under high-Zn stress. Nevertheless, the addition of 1.5 mM Si increased the expression levels of these genes in plants under high-Zn stress at 72 h, and the expression levels were higher in Si-treated plants than in Si-deprived plants. Therefore, we conclude that Si alleviates the Zn-induced damage to photosynthesis in rice. The decline of photosynthesis in Zn-stressed rice was attributed to stomatal limitation, and Si activated and regulated some photosynthesis-related genes in response to high-Zn stress, consequently increasing photosynthesis. PMID:25426937

Low pH-induced changes of antioxidant enzyme and ATPase activities in the roots of rice (Oryza sativa L. seedlings.

Directory of Open Access Journals (Sweden)

Yi-Kai Zhang

Full Text Available Soil acidification is the main problem in the current rice production. Here, the effects of low pH on the root growth, reactive oxygen species metabolism, plasma membrane functions, and the transcript levels of the related genes were investigated in rice seedlings (Oryza sativa L. in a hydroponic system at pH 3.5, 4.5, and 5.5. There were two hybrid rice cultivars in this trial, including Yongyou 12 (YY12, a japonica hybrid and Zhongzheyou 1 (ZZY1, an indica hybrid. Higher H+ activity markedly decreased root length, the proportion of fine roots, and dry matter production, but induced a significant accumulation of hydrogen peroxide (H2O2, and led to serious lipid peroxidation in the roots of the two varieties. The transcript levels of copper/zinc superoxide dismutase 1 (Cu/Zn SOD1, copper/zinc superoxide dismutase 2 (Cu/Zn SOD2, catalase A (CATA and catalase B (CATB genes in YY12 and ZZY1 roots were significantly down-regulated after low pH exposure for two weeks. Meanwhile, a significant decrease was observed in the expression of the P-type Ca2+-ATPases in roots at pH 3.5. The activities of antioxidant enzymes (SOD, CAT and plasma membrane (PM Ca2+-ATPase in the two varieties were dramatically inhibited by strong rhizosphere acidification. However, the expression levels of ascorbate peroxidase 1 (APX1 and PM H+-ATPase isoform 7 were up-regulated under H+ stress compared with the control. Significantly higher activities of APX and PM H+-ATPase could contribute to the adaptation of rice roots to low pH.

Impact of postharvest drying conditions on in vitro starch digestibility and estimated glycemic index of cooked non-waxy long-grain rice (Oryza sativa L.).

Science.gov (United States)

Donlao, Natthawuddhi; Ogawa, Yukiharu

2017-02-01

Wet paddy needs to be dried to reduce its moisture content after harvesting. In this study, effects of postharvest drying condition on in vitro starch digestibility and estimated glycemic index of cooked rice (Oryza sativa L.) were investigated. Varying drying conditions, i.e. hot-air drying at 40, 65, 90 and 115 °C, and sun drying were applied to raw paddy. After husking and polishing, polished grains were cooked using an electric rice cooker. Cooked samples were analyzed for their moisture content and amount of resistant and total starch. Five samples in both intact grain and slurry were digested under simulated in vitro gastrointestinal digestion process. The in vitro starch digestion rate was measured and the hydrolysis index (HI) and estimated glycemic index (eGI) were calculated. Cooked rice obtained from hot-air drying showed relatively lower HI and eGI than that obtained from sun-drying. Among samples from hot-air drying treatment, eGI of cooked rice decreased with increasing drying temperature, except for the drying temperature of 115 °C. As a result, cooked rice from the hot-air drying at 90 °C showed lowest eGI. The results indicated that cooked rice digestibility was affected by postharvest drying conditions. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Species identification of Cannabis sativa using real-time quantitative PCR (qPCR).

Science.gov (United States)

Johnson, Christopher E; Premasuthan, Amritha; Satkoski Trask, Jessica; Kanthaswamy, Sree

2013-03-01

Most narcotics-related cases in the United States involve Cannabis sativa. Material is typically identified based on the cystolithic hairs on the leaves and with chemical tests to identify of the presence of cannabinoids. Suspect seeds are germinated into a viable plant so that morphological and chemical tests can be conducted. Seed germination, however, causes undue analytical delays. DNA analyses that involve the chloroplast and nuclear genomes have been developed for identification of C. sativa materials, but they require several nanograms of template DNA. Using the trnL 3' exon-trnF intragenic spacer regions within the C. sativa chloroplast, we have developed a real-time quantitative PCR assay that is capable of identifying picogram amounts of chloroplast DNA for species determination of suspected C. sativa material. This assay provides forensic science laboratories with a quick and reliable method to identify an unknown sample as C. sativa. © 2013 American Academy of Forensic Sciences.

[Quantifying rice (Oryza sativa L.) photo-assimilated carbon input into soil organic carbon pools following continuous 14C labeling].

Science.gov (United States)

Nie, San-An; Zhou, Ping; Ge, Ti-Da; Tong, Cheng-Li; Xiao, He-Ai; Wu, Jin-Shui; Zhang, Yang-Zhu

2012-04-01

The microcosm experiment was carried out to quantify the input and distribution of photo-assimilated C into soil C pools by using a 14C continuous labeling technique. Destructive samplings of rice (Oryza sativa) were conducted after labeling for 80 days. The allocation of 14C-labeled photosynthates in plants and soil C pools such as dissolved organic C (DOC) and microbial biomass C (MBC) in rice-planted soil were examined over the 14C labeling span. The amounts of rice shoot and root biomass C was ranged from 1.86 to 5.60 g x pot(-1), 0.46 to 0.78 g x pot(-1) in different tested paddy soils after labeling for 80 days, respectively. The amount of 14C in the soil organic C (14C-SOC) was also dependent on the soils, ranged from 114.3 to 348.2 mg x kg(-1), accounting for 5.09% to 6.62% of the rice biomass 14C, respectively. The amounts of 14C in the dissolved organic C (14C-DOC) and in the microbial biomass C(14C-MBC), as proportions of 14C-SOC, were 2.21%-3.54% and 9.72% -17.2%, respectively. The 14C-DOC, 14C-MBC, and 14C-SOC as proportions of total DOC, MBC, and SOC, respectively, were 6.72% -14.64%, 1.70% -7.67%, and 0.73% -1.99%, respectively. Moreover, the distribution and transformation of root-derived C had a greater influence on the dynamics of DOC and MBC than on the dynamics of SOC. Further studies are required to ascertain the functional significance of soil microorganisms (such as C-sequestering bacteria and photosynthetic bacteria) in the paddy system.

Seed Germination Behaviors Of Some Aerobic Rice Cultivars Oryza Sativa L After Priming With Polyethylene Glycol-8000 Peg-8000

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Elkheir H.A

2015-08-01

Full Text Available Seed Priming Is Famous Technique To Accelerate Seed Germination Behaviors. This Experiment Was Conducted To Study The Effect Of Polyethylene Glycol-8000 Peg-8000 As Priming Agent On Seed Germination Behavior Of Some Aerobic Rice Cultivars Oryza Sativa L. Experiment Was Carried Out By Using Two-Factor Three Aerobic Rice Cultivars And Peg With Four Replications Which Arranged In Factorial System Design And Conducted With Completely Randomized Design. The Factor Was Varieties Which Were Inpago 8 V1 Ir64 V2 And Situbagendit V3 Combine With 4 Levels Of Peg Concentrations 0100 And 200 Gl-1 And Control With No Treatment. Experiment Was Repeated 4 Times So Total Number Of Experimental Units Were 48. Germination Parameters Measured Were Germination Percentage Germination Index Days Of 50 Germination Seedling Fresh Weight Mg Seedling Shoot Fresh Weight And Root Fresh Weight Mg Seedling Dry Weigh Mg Seedling Shoot Dry Weight And Root Dry Weight Mg ShootRoot Ratio Seedling Length Cm Seedling Root Length Cm And Shoot Length Cm And Seed Vigor Index. The Results Indicated That Seed Priming Significantly Affected Germination Behaviors Compared With Control Depending Upon Varieties. The Highest Germination Was Obtained Under Laboratory And Greenhouse Condition By The Treatment Of Peg 200 G L-1 On The Situbagendit And Ir-64 Variety 90.25 And 93.33 Respectively Compared To Control In Inpago-8 In Both Laboratory 75.75 And Greenhouse 80 . As Implementation To Increase Seed And Seedling Vigor Of Rice It Is A Best Practice To Use Peg Priming With 200 Gl-1 Solutions Depend Upon Varietal Response And We Suggest That More Research About The Effect Of Peg As Seed Priming Techniques On Seed Germination Behavior Of Many Grain Crops Is Needed To Confirm The Methodology.

Copper and ectopic expression of the Arabidopsis transport protein COPT1 alter iron homeostasis in rice (Oryza sativa L.).

Science.gov (United States)

Andrés-Bordería, Amparo; Andrés, Fernando; Garcia-Molina, Antoni; Perea-García, Ana; Domingo, Concha; Puig, Sergi; Peñarrubia, Lola

2017-09-01

Copper deficiency and excess differentially affect iron homeostasis in rice and overexpression of the Arabidopsis high-affinity copper transporter COPT1 slightly increases endogenous iron concentration in rice grains. Higher plants have developed sophisticated mechanisms to efficiently acquire and use micronutrients such as copper and iron. However, the molecular mechanisms underlying the interaction between both metals remain poorly understood. In the present work, we study the effects produced on iron homeostasis by a wide range of copper concentrations in the growth media and by altered copper transport in Oryza sativa plants. Gene expression profiles in rice seedlings grown under copper excess show an altered expression of genes involved in iron homeostasis compared to standard control conditions. Thus, ferritin OsFER2 and ferredoxin OsFd1 mRNAs are down-regulated whereas the transcriptional iron regulator OsIRO2 and the nicotianamine synthase OsNAS2 mRNAs rise under copper excess. As expected, the expression of OsCOPT1, which encodes a high-affinity copper transport protein, as well as other copper-deficiency markers are down-regulated by copper. Furthermore, we show that Arabidopsis COPT1 overexpression (C1 OE ) in rice causes root shortening in high copper conditions and under iron deficiency. C1 OE rice plants modify the expression of the putative iron-sensing factors OsHRZ1 and OsHRZ2 and enhance the expression of OsIRO2 under copper excess, which suggests a role of copper transport in iron signaling. Importantly, the C1 OE rice plants grown on soil contain higher endogenous iron concentration than wild-type plants in both brown and white grains. Collectively, these results highlight the effects of rice copper status on iron homeostasis, which should be considered to obtain crops with optimized nutrient concentrations in edible parts.

Modulation of proton pumping across proteoliposome membranes reconstituted with tonoplast H(+)-ATPase from cultured rice (Oryza sativa L. var. Boro) cells by acyl steryl glucoside and steryl glucoside.

Science.gov (United States)

Yamaguchi, Mineo; Kasamo, Kunihiro

2002-07-01

Tonoplast H(+)-ATPase purified from cultured rice cells (Oryza sativa L. var. Boro) was reconstituted into asolectin liposomes containing steryl glucoside (SG) or acyl steryl glucoside (ASG), and the effects of SG and ASG on proton pumping, ATP-hydrolysis activity and proton permeability of the proteoliposome membranes were investigated. In the proteoliposomes containing 10 mol% SG, proton pumping and ATP-hydrolysis activity were increased to around 140% of those in SG-free proteoliposomes. In the proteoliposomes containing ASG, proton pumping and ATP-hydrolysis activity were decreased to one-tenth of those in ASG-free proteoliposomes at 15 mol% ASG; however, activity increased again slightly in the range between 20 and 40 mol% ASG. The change in proton pumping across the proteoliposome membrane is not due to a change of proteoliposome size nor to the location of the catalytic site of the tonoplast H(+)-ATPase in the proteoliposomes. SG and ASG also reduced the passive proton permeability of the proteoliposomes. These results show that SG and ASG modulate proton pumping across the tonoplast toward stimulation and depression, respectively, and they reduce the passive proton permeability of the tonoplast.

Genetic dissection of black grain rice by the development of a near isogenic line

OpenAIRE

Maeda, Hiroaki; Yamaguchi, Takuya; Omoteno, Motoyasu; Takarada, Takeshi; Fujita, Kenji; Murata, Kazumasa; Iyama, Yukihide; Kojima, Yoichiro; Morikawa, Makiko; Ozaki, Hidenobu; Mukaino, Naoyuki; Kidani, Yoshinori; Ebitani, Takeshi

2014-01-01

Rice (Oryza sativa L.) can produce black grains as well as white. In black rice, the pericarp of the grain accumulates anthocyanin, which has antioxidant activity and is beneficial to human health. We developed a black rice introgression line in the genetic background of Oryza sativa L. ‘Koshihikari’, which is a leading variety in Japan. We used Oryza sativa L. ‘Hong Xie Nuo’ as the donor parent and backcrossed with ‘Koshihikari’ four times, resulting in a near isogenic line (NIL) for black g...

A hairy-leaf gene, BLANKET LEAF, of wild Oryza nivara increases photosynthetic water use efficiency in rice.

Science.gov (United States)

Hamaoka, Norimitsu; Yasui, Hideshi; Yamagata, Yoshiyuki; Inoue, Yoko; Furuya, Naruto; Araki, Takuya; Ueno, Osamu; Yoshimura, Atsushi

2017-12-01

High water use efficiency is essential to water-saving cropping. Morphological traits that affect photosynthetic water use efficiency are not well known. We examined whether leaf hairiness improves photosynthetic water use efficiency in rice. A chromosome segment introgression line (IL-hairy) of wild Oryza nivara (Acc. IRGC105715) with the genetic background of Oryza sativa cultivar 'IR24' had high leaf pubescence (hair). The leaf hairs developed along small vascular bundles. Linkage analysis in BC 5 F 2 and F 3 populations showed that the trait was governed by a single gene, designated BLANKET LEAF (BKL), on chromosome 6. IL-hairy plants had a warmer leaf surface in sunlight, probably due to increased boundary layer resistance. They had a lower transpiration rate under moderate and high light intensities, resulting in higher photosynthetic water use efficiency. Introgression of BKL on chromosome 6 from O. nivara improved photosynthetic water use efficiency in the genetic background of IR24.

Bacterial mediated amelioration of drought stress in drought tolerant ...

African Journals Online (AJOL)

Bacterial mediated amelioration of drought stress in drought tolerant and susceptible cultivars of rice ( Oryza sativa L.) ... and IR-64 (drought sensitive) cultivars of rice (Oryza sativa L.) under different level of drought stress. ... from 32 Countries:.

Revisiting the chlorophyll biosynthesis pathway using genome scale metabolic model of Oryza sativa japonica

Science.gov (United States)

Chatterjee, Ankita; Kundu, Sudip

2015-01-01

Chlorophyll is one of the most important pigments present in green plants and rice is one of the major food crops consumed worldwide. We curated the existing genome scale metabolic model (GSM) of rice leaf by incorporating new compartment, reactions and transporters. We used this modified GSM to elucidate how the chlorophyll is synthesized in a leaf through a series of bio-chemical reactions spanned over different organelles using inorganic macronutrients and light energy. We predicted the essential reactions and the associated genes of chlorophyll synthesis and validated against the existing experimental evidences. Further, ammonia is known to be the preferred source of nitrogen in rice paddy fields. The ammonia entering into the plant is assimilated in the root and leaf. The focus of the present work is centered on rice leaf metabolism. We studied the relative importance of ammonia transporters through the chloroplast and the cytosol and their interlink with other intracellular transporters. Ammonia assimilation in the leaves takes place by the enzyme glutamine synthetase (GS) which is present in the cytosol (GS1) and chloroplast (GS2). Our results provided possible explanation why GS2 mutants show normal growth under minimum photorespiration and appear chlorotic when exposed to air. PMID:26443104

Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina).

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Schwartze, Volker U; Winter, Sascha; Shelest, Ekaterina; Marcet-Houben, Marina; Horn, Fabian; Wehner, Stefanie; Linde, Jörg; Valiante, Vito; Sammeth, Michael; Riege, Konstantin; Nowrousian, Minou; Kaerger, Kerstin; Jacobsen, Ilse D; Marz, Manja; Brakhage, Axel A; Gabaldón, Toni; Böcker, Sebastian; Voigt, Kerstin

2014-08-01

Lichtheimia species are the second most important cause of mucormycosis in Europe. To provide broader insights into the molecular basis of the pathogenicity-associated traits of the basal Mucorales, we report the full genome sequence of L. corymbifera and compared it to the genome of Rhizopus oryzae, the most common cause of mucormycosis worldwide. The genome assembly encompasses 33.6 MB and 12,379 protein-coding genes. This study reveals four major differences of the L. corymbifera genome to R. oryzae: (i) the presence of an highly elevated number of gene duplications which are unlike R. oryzae not due to whole genome duplication (WGD), (ii) despite the relatively high incidence of introns, alternative splicing (AS) is not frequently observed for the generation of paralogs and in response to stress, (iii) the content of repetitive elements is strikingly low (<5%), (iv) L. corymbifera is typically haploid. Novel virulence factors were identified which may be involved in the regulation of the adaptation to iron-limitation, e.g. LCor01340.1 encoding a putative siderophore transporter and LCor00410.1 involved in the siderophore metabolism. Genes encoding the transcription factors LCor08192.1 and LCor01236.1, which are similar to GATA type regulators and to calcineurin regulated CRZ1, respectively, indicating an involvement of the calcineurin pathway in the adaption to iron limitation. Genes encoding MADS-box transcription factors are elevated up to 11 copies compared to the 1-4 copies usually found in other fungi. More findings are: (i) lower content of tRNAs, but unique codons in L. corymbifera, (ii) Over 25% of the proteins are apparently specific for L. corymbifera. (iii) L. corymbifera contains only 2/3 of the proteases (known to be essential virulence factors) in comparison to R. oryzae. On the other hand, the number of secreted proteases, however, is roughly twice as high as in R. oryzae.

Database Description - RMOS | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available base Description General information of database Database name RMOS Alternative nam...arch Unit Shoshi Kikuchi E-mail : Database classification Plant databases - Rice Microarray Data and other Gene Expression Database...s Organism Taxonomy Name: Oryza sativa Taxonomy ID: 4530 Database description The Ric...19&lang=en Whole data download - Referenced database Rice Expression Database (RED) Rice full-length cDNA Database... (KOME) Rice Genome Integrated Map Database (INE) Rice Mutant Panel Database (Tos17) Rice Genome Annotation Database

Genome-wide DNA polymorphism in the indica rice varieties RGD-7S and Taifeng B as revealed by whole genome re-sequencing.

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Fu, Chong-Yun; Liu, Wu-Ge; Liu, Di-Lin; Li, Ji-Hua; Zhu, Man-Shan; Liao, Yi-Long; Liu, Zhen-Rong; Zeng, Xue-Qin; Wang, Feng

2016-03-01

Next-generation sequencing technologies provide opportunities to further understand genetic variation, even within closely related cultivars. We performed whole genome resequencing of two elite indica rice varieties, RGD-7S and Taifeng B, whose F1 progeny showed hybrid weakness and hybrid vigor when grown in the early- and late-cropping seasons, respectively. Approximately 150 million 100-bp pair-end reads were generated, which covered ∼86% of the rice (Oryza sativa L. japonica 'Nipponbare') reference genome. A total of 2,758,740 polymorphic sites including 2,408,845 SNPs and 349,895 InDels were detected in RGD-7S and Taifeng B, respectively. Applying stringent parameters, we identified 961,791 SNPs and 46,640 InDels between RGD-7S and Taifeng B (RGD-7S/Taifeng B). The density of DNA polymorphisms was 256.8 SNPs and 12.5 InDels per 100 kb for RGD-7S/Taifeng B. Copy number variations (CNVs) were also investigated. In RGD-7S, 1989 of 2727 CNVs were overlapped in 218 genes, and 1231 of 2010 CNVs were annotated in 175 genes in Taifeng B. In addition, we verified a subset of InDels in the interval of hybrid weakness genes, Hw3 and Hw4, and obtained some polymorphic InDel markers, which will provide a sound foundation for cloning hybrid weakness genes. Analysis of genomic variations will also contribute to understanding the genetic basis of hybrid weakness and heterosis.

Molecular detection of Xanthomonas oryzae pv. oryzae, Xanthomonas oryzae pv. oryzicola, and Burkholderia glumae in infected rice seeds and leaves

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Polymerase chain reaction (PCR) is particularly useful for plant pathogen detection. In the present study, multiplex PCR and SYBR green real-time PCR were developed to facilitate simultaneous detection of three important rice pathogens, Xanthomonas oryzae pv. oryzae, X. oryzae pv. oryzicola, and Bur...

Response of yield and yield components of rice (Oryza sativa L. cv. Tarom Hashemi in rice, duck and Azolla (Azolla sp. farming

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M Gharavi Baigi

2016-05-01

Full Text Available In order to evaluate the yield and yield components of rice (Oryza sativa L. cv. Tarom Hashemi in integrated rice, duck and Azolla, an experiment was conducted at the Research Farm of Sari University of Agricultural Sciences and Natural Resources during 2012. Experiment was arranged in split plot based on a randomized complete block design with three replications. The number of ducks as main plots at four levels (0, 400, 800 and 1200 ducks.ha-1 and Nitrogen source as sub plots at four levels (without Azolla and nitrogen, Azolla, Azolla+nitrogen and nitrogen were the treatments. Analysis of variance showed highly significant differences for the number of ducks, Azolla+nitrogen and their interaction effects of plant height, number of tillers.plant-1, number of panicle.plant-1, number of grains.panicle-1, panicle weight, panicle dry weight and grain yield. The results revealed that the highest values of plant height (133 cm, number of tillers (38 tillers.plant-1, number of panicle (24 numbers.plant-1, number of grains (171 numbers.panicle-1, panicle weight (23 g, panicle dry weight (13 g and grain yield (4 t.ha-1 were recorded in 1200 duck pieces per hectare while treated with Azolla (500 g.m-2 and nitrogen (50 kg.ha-1. In conclusion, results of the current experiment showed that increasing of duck number from 400 to 1200 pieces.ha-1 along with Azolla and nitrogen could enhance the yield and yield components of rice (Tarom Hashemi cultivar.

Potential Application of the Oryza sativa Monodehydroascorbate Reductase Gene (OsMDHAR to Improve the Stress Tolerance and Fermentative Capacity of Saccharomyces cerevisiae.

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Il-Sup Kim

Full Text Available Monodehydroascorbate reductase (MDHAR; EC 1.6.5.4 is an important enzyme for ascorbate recycling. To examine whether heterologous expression of MDHAR from Oryza sativa (OsMDHAR can prevent the deleterious effects of unfavorable growth conditions, we constructed a transgenic yeast strain harboring a recombinant plasmid carrying OsMDHAR (p426GPD::OsMDHAR. OsMDHAR-expressing yeast cells displayed enhanced tolerance to hydrogen peroxide by maintaining redox homoeostasis, proteostasis, and the ascorbate (AsA-like pool following the accumulation of antioxidant enzymes and molecules, metabolic enzymes, and molecular chaperones and their cofactors, compared to wild-type (WT cells carrying vector alone. The addition of exogenous AsA or its analogue isoascorbic acid increased the viability of WT and ara2Δ cells under oxidative stress. Furthermore, the survival of OsMDHAR-expressing cells was greater than that of WT cells when cells at mid-log growth phase were exposed to high concentrations of ethanol. High OsMDHAR expression also improved the fermentative capacity of the yeast during glucose-based batch fermentation at a standard cultivation temperature (30°C. The alcohol yield of OsMDHAR-expressing transgenic yeast during fermentation was approximately 25% (0.18 g·g-1 higher than that of WT yeast. Accordingly, OsMDHAR-expressing transgenic yeast showed prolonged survival during the environmental stresses produced during fermentation. These results suggest that heterologous OsMDHAR expression increases tolerance to reactive oxygen species-induced oxidative stress by improving cellular redox homeostasis and improves survival during fermentation, which enhances fermentative capacity.

Rice black streaked dwarf virus P7-2 forms a SCF complex through binding to Oryza sativa SKP1-like proteins, and interacts with GID2 involved in the gibberellin pathway.

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Tao, Tao; Zhou, Cui-Ji; Wang, Qian; Chen, Xiang-Ru; Sun, Qian; Zhao, Tian-Yu; Ye, Jian-Chun; Wang, Ying; Zhang, Zong-Ying; Zhang, Yong-Liang; Guo, Ze-Jian; Wang, Xian-Bing; Li, Da-Wei; Yu, Jia-Lin; Han, Cheng-Gui

2017-01-01

As a core subunit of the SCF complex that promotes protein degradation through the 26S proteasome, S-phase kinase-associated protein 1 (SKP1) plays important roles in multiple cellular processes in eukaryotes, including gibberellin (GA), jasmonate, ethylene, auxin and light responses. P7-2 encoded by Rice black streaked dwarf virus (RBSDV), a devastating viral pathogen that causes severe symptoms in infected plants, interacts with SKP1 from different plants. However, whether RBSDV P7-2 forms a SCF complex and targets host proteins is poorly understood. In this study, we conducted yeast two-hybrid assays to further explore the interactions between P7-2 and 25 type I Oryza sativa SKP1-like (OSK) proteins, and found that P7-2 interacted with eight OSK members with different binding affinity. Co-immunoprecipitation assay further confirmed the interaction of P7-2 with OSK1, OSK5 and OSK20. It was also shown that P7-2, together with OSK1 and O. sativa Cullin-1, was able to form the SCF complex. Moreover, yeast two-hybrid assays revealed that P7-2 interacted with gibberellin insensitive dwarf2 (GID2) from rice and maize plants, which is essential for regulating the GA signaling pathway. It was further demonstrated that the N-terminal region of P7-2 was necessary for the interaction with GID2. Overall, these results indicated that P7-2 functioned as a component of the SCF complex in rice, and interaction of P7-2 with GID2 implied possible roles of the GA signaling pathway during RBSDV infection.

Rice black streaked dwarf virus P7-2 forms a SCF complex through binding to Oryza sativa SKP1-like proteins, and interacts with GID2 involved in the gibberellin pathway.

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Tao Tao

Full Text Available As a core subunit of the SCF complex that promotes protein degradation through the 26S proteasome, S-phase kinase-associated protein 1 (SKP1 plays important roles in multiple cellular processes in eukaryotes, including gibberellin (GA, jasmonate, ethylene, auxin and light responses. P7-2 encoded by Rice black streaked dwarf virus (RBSDV, a devastating viral pathogen that causes severe symptoms in infected plants, interacts with SKP1 from different plants. However, whether RBSDV P7-2 forms a SCF complex and targets host proteins is poorly understood. In this study, we conducted yeast two-hybrid assays to further explore the interactions between P7-2 and 25 type I Oryza sativa SKP1-like (OSK proteins, and found that P7-2 interacted with eight OSK members with different binding affinity. Co-immunoprecipitation assay further confirmed the interaction of P7-2 with OSK1, OSK5 and OSK20. It was also shown that P7-2, together with OSK1 and O. sativa Cullin-1, was able to form the SCF complex. Moreover, yeast two-hybrid assays revealed that P7-2 interacted with gibberellin insensitive dwarf2 (GID2 from rice and maize plants, which is essential for regulating the GA signaling pathway. It was further demonstrated that the N-terminal region of P7-2 was necessary for the interaction with GID2. Overall, these results indicated that P7-2 functioned as a component of the SCF complex in rice, and interaction of P7-2 with GID2 implied possible roles of the GA signaling pathway during RBSDV infection.

In planta gene expression analysis of Xanthomonas oryzae pathovar oryzae, African strain MAI1

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Verdier Valérie

2010-06-01

Full Text Available Abstract Background Bacterial leaf blight causes significant yield losses in rice crops throughout Asia and Africa. Although both the Asian and African strains of the pathogen, Xanthomonas oryzae pv. oryzae (Xoo, induce similar symptoms, they are nevertheless genetically different, with the African strains being more closely related to the Asian X. oryzae pv. oryzicola (Xoc. Results Changes in gene expression of the African Xoo strain MAI1 in the susceptible rice cultivar Nipponbare were profiled, using an SSH Xoo DNA microarray. Microarray hybridization was performed comparing bacteria recovered from plant tissues at 1, 3, and 6 days after inoculation (dai with bacteria grown in vitro. A total of 710 bacterial genes were found to be differentially expressed, with 407 up-regulated and 303 down-regulated. Expression profiling indicated that less than 20% of the 710 bacterial transcripts were induced in the first 24 h after inoculation, whereas 63% were differentially expressed at 6 dai. The 710 differentially expressed genes were one-end sequenced. 535 sequences were obtained from which 147 non-redundant sequences were identified. Differentially expressed genes were related to metabolism, secretion and transport, pathogen adherence to plant tissues, plant cell-wall degradation, IS elements, and virulence. In addition, various other genes encoding proteins with unknown function or showing no similarity to other proteins were also induced. The Xoo MAI1 non-redundant set of sequences was compared against several X. oryzae genomes, revealing a specific group of genes that was present only in MAI1. Numerous IS elements were also found to be differentially expressed. Quantitative real-time PCR confirmed 86% of the identified profile on a set of 14 genes selected according to the microarray analysis. Conclusions This is the first report to compare the expression of Xoo genes in planta across different time points during infection. This work shows that

Physiological basis of genetic variation in leaf photosynthesis among rice (Oryza sativa L.) introgression lines under drought and well-watered conditions

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Yin, Xinyou

2012-01-01

To understand the physiological basis of genetic variation and resulting quantitative trait loci (QTLs) for photosynthesis in a rice (Oryza sativa L.) introgression line population, 13 lines were studied under drought and well-watered conditions, at flowering and grain filling. Simultaneous gas exchange and chlorophyll fluorescence measurements were conducted at various levels of incident irradiance and ambient CO2 to estimate parameters of a model that dissects photosynthesis into stomatal conductance (g s), mesophyll conductance (g m), electron transport capacity (J max), and Rubisco carboxylation capacity (V cmax). Significant genetic variation in these parameters was found, although drought and leaf age accounted for larger proportions of the total variation. Genetic variation in light-saturated photosynthesis and transpiration efficiency (TE) were mainly associated with variation in g s and g m. One previously mapped major QTL of photosynthesis was associated with variation in g s and g m, but also in J max and V cmax at flowering. Thus, g s and g m, which were demonstrated in the literature to be responsible for environmental variation in photosynthesis, were found also to be associated with genetic variation in photosynthesis. Furthermore, relationships between these parameters and leaf nitrogen or dry matter per unit area, which were previously found across environmental treatments, were shown to be valid for variation across genotypes. Finally, the extent to which photosynthesis rate and TE can be improved was evaluated. Virtual ideotypes were estimated to have 17.0% higher photosynthesis and 25.1% higher TE compared with the best genotype investigated. This analysis using introgression lines highlights possibilities of improving both photosynthesis and TE within the same genetic background. PMID:22888131

Genome assembly of the fungus Cochliobolus miyabeanus, and transcriptome analysis during early stages of infection on American wild rice (Zizania palustris L.)

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Cochliobolus miyabeanus causes a severe, yield-reducing leaf spot disease on rice (Oryza sativa) and two North American specialty crops, American wildrice (Zizania palustris) and switchgrass (Panicum virgatum). Despite the importance of the pathogen in wildrice, little is known about mechanisms of p...

Application of glycine reduces arsenic accumulation and toxicity in Oryza sativa L. by reducing the expression of silicon transporter genes.

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Kumar Dubey, Arvind; Kumar, Navin; Ranjan, Ruma; Gautam, Ambedkar; Pande, Veena; Sanyal, Indraneel; Mallick, Shekhar

2018-02-01

The present study was intended to investigate the role of amino acid glycine in detoxification of As in Oryza sativa L. The growth parameters such as, shoot length and fresh weight were decreased during As(III) and As(V) toxicity. However, the application of glycine recovered the growth parameters against As stress. The application of glycine reduced the As accumulation in all the treatments, and it was more effective against As(III) treatment and reduced the accumulation by 68% in root and 71% in shoot. Similarly, the translocation of As from root to shoot, was higher against As(III) and As(V) treatments, whereas, reduced upon glycine application. The translocation of Fe and Na was also affected by As, which was lower under As(III) and As(V) treatments. However, the application of glycine significantly enhanced the translocation of Fe and Na in the shoot. Besides, the expression of lower silicon transporters i.e. Lsi-1 and Lsi-2 was observed to be significantly suppressed in the root with the application of glycine against As treatment. Similarly, the expression of three GRX and two GST gene isoforms were found to be significantly increased with glycine application. Simultaneously, the activities of antioxidant enzymes i.e. l-arginine dependent NOS, SOD, NTR and GRX were found to be significantly enhanced in the presence of glycine. Increased activities of antioxidant enzymes coincided with the decreased level of TBARS and H 2 O 2 in rice seedlings. Overall, the results suggested that the application of glycine reduces As accumulation through suppressing the gene expression of lower silicon transporters and ameliorates As toxicity by enhancing antioxidants defense mechanism in rice seedlings. Copyright © 2017 Elsevier Inc. All rights reserved.

RICD: A rice indica cDNA database resource for rice functional genomics

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Zhang Qifa

2008-11-01

Full Text Available Abstract Background The Oryza sativa L. indica subspecies is the most widely cultivated rice. During the last few years, we have collected over 20,000 putative full-length cDNAs and over 40,000 ESTs isolated from various cDNA libraries of two indica varieties Guangluai 4 and Minghui 63. A database of the rice indica cDNAs was therefore built to provide a comprehensive web data source for searching and retrieving the indica cDNA clones. Results Rice Indica cDNA Database (RICD is an online MySQL-PHP driven database with a user-friendly web interface. It allows investigators to query the cDNA clones by keyword, genome position, nucleotide or protein sequence, and putative function. It also provides a series of information, including sequences, protein domain annotations, similarity search results, SNPs and InDels information, and hyperlinks to gene annotation in both The Rice Annotation Project Database (RAP-DB and The TIGR Rice Genome Annotation Resource, expression atlas in RiceGE and variation report in Gramene of each cDNA. Conclusion The online rice indica cDNA database provides cDNA resource with comprehensive information to researchers for functional analysis of indica subspecies and for comparative genomics. The RICD database is available through our website http://www.ncgr.ac.cn/ricd.

A database of PCR primers for the chloroplast genomes of higher plants

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Heinze, Berthold

2007-01-01

Background Chloroplast genomes evolve slowly and many primers for PCR amplification and analysis of chloroplast sequences can be used across a wide array of genera. In some cases 'universal' primers have been designed for the purpose of working across species boundaries. However, the essential information on these primer sequences is scattered throughout the literature. Results A database is presented here which assembles published primer information for chloroplast DNA. Additional primers were designed to fill gaps where little or no primer information could be found. Amplicons are either the genes themselves (typically useful in studies of sequence variation in higher-order phylogeny) or they are spacers, introns, and intergenic regions (for studies of phylogeographic patterns within and among species). The current list of 'generic' primers consists of more than 700 sequences. Wherever possible, we give the locations of the primers in the thirteen fully sequenced chloroplast genomes (Nicotiana tabacum, Atropa belladonna, Spinacia oleracea, Arabidopsis thaliana, Populus trichocarpa, Oryza sativa, Pinus thunbergii, Marchantia polymorpha, Zea mays, Oenothera elata, Acorus calamus, Eucalyptus globulus, Medicago trunculata). Conclusion The database described here is designed to serve as a resource for researchers who are venturing into the study of poorly described chloroplast genomes, whether for large- or small-scale DNA sequencing projects, to study molecular variation or to investigate chloroplast evolution. PMID:17326828

A database of PCR primers for the chloroplast genomes of higher plants

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Heinze Berthold

2007-02-01

Full Text Available Abstract Background Chloroplast genomes evolve slowly and many primers for PCR amplification and analysis of chloroplast sequences can be used across a wide array of genera. In some cases 'universal' primers have been designed for the purpose of working across species boundaries. However, the essential information on these primer sequences is scattered throughout the literature. Results A database is presented here which assembles published primer information for chloroplast DNA. Additional primers were designed to fill gaps where little or no primer information could be found. Amplicons are either the genes themselves (typically useful in studies of sequence variation in higher-order phylogeny or they are spacers, introns, and intergenic regions (for studies of phylogeographic patterns within and among species. The current list of 'generic' primers consists of more than 700 sequences. Wherever possible, we give the locations of the primers in the thirteen fully sequenced chloroplast genomes (Nicotiana tabacum, Atropa belladonna, Spinacia oleracea, Arabidopsis thaliana, Populus trichocarpa, Oryza sativa, Pinus thunbergii, Marchantia polymorpha, Zea mays, Oenothera elata, Acorus calamus, Eucalyptus globulus, Medicago trunculata. Conclusion The database described here is designed to serve as a resource for researchers who are venturing into the study of poorly described chloroplast genomes, whether for large- or small-scale DNA sequencing projects, to study molecular variation or to investigate chloroplast evolution.

Purification and enzymatic characterization of secretory glycoside hydrolase family 3 (GH3) aryl β-glucosidases screened from Aspergillus oryzae genome.

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Kudo, Kanako; Watanabe, Akira; Ujiie, Seiryu; Shintani, Takahiro; Gomi, Katsuya

2015-12-01

By a global search of the genome database of Aspergillus oryzae, we found 23 genes encoding putative β-glucosidases, among which 10 genes with a signal peptide belonging to glycoside hydrolase family 3 (GH3) were overexpressed in A. oryzae using the improved glaA gene promoter. Consequently, crude enzyme preparations from three strains, each harboring the genes AO090038000223 (bglA), AO090103000127 (bglF), and AO090003001511 (bglJ), showed a substrate preference toward p-nitrophenyl-β-d-glucopyranoside (pNPGlc) and thus were purified to homogeneity and enzymatically characterized. All the purified enzymes (BglA, BglF, and BglJ) preferentially hydrolyzed aryl β-glycosides, including pNPGlc, rather than cellobiose, and these enzymes were proven to be aryl β-glucosidases. Although the specific activity of BglF toward all the substrates tested was significantly low, BglA and BglJ showed appreciably high activities toward pNPGlc and arbutin. The kinetic parameters of BglA and BglJ for pNPGlc suggested that both the enzymes had relatively higher hydrolytic activity toward pNPGlc among the fungal β-glucosidases reported. The thermal and pH stabilities of BglA were higher than those of BglJ, and BglA was particularly stable in a wide pH range (pH 4.5-10). In contrast, BglJ was the most heat- and alkaline-labile among the three β-glucosidases. Furthermore, BglA was more tolerant to ethanol than BglJ; as a result, it showed much higher hydrolytic activity toward isoflavone glycosides in the presence of ethanol than BglJ. This study suggested that the mining of novel β-glucosidases exhibiting higher activity from microbial genome sequences is of great use for the production of beneficial compounds such as isoflavone aglycones. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Efficient CRISPR/Cas9-Mediated Genome Editing Using a Chimeric Single-Guide RNA Molecule

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Butt, Haroon

2017-08-24

The CRISPR/Cas9 system has been applied in diverse eukaryotic organisms for targeted mutagenesis. However, targeted gene editing is inefficient and requires the simultaneous delivery of a DNA template for homology-directed repair (HDR). Here, we used CRISPR/Cas9 to generate targeted double-strand breaks and to deliver an RNA repair template for HDR in rice (Oryza sativa). We used chimeric single-guide RNA (cgRNA) molecules carrying both sequences for target site specificity (to generate the double-strand breaks) and repair template sequences (to direct HDR), flanked by regions of homology to the target. Gene editing was more efficient in rice protoplasts using repair templates complementary to the non-target DNA strand, rather than the target strand. We applied this cgRNA repair method to generate herbicide resistance in rice, which showed that this cgRNA repair method can be used for targeted gene editing in plants. Our findings will facilitate applications in functional genomics and targeted improvement of crop traits.

Magnesium-induced alterations in the photosynthetic performance and resistance of rice plants infected with Bipolaris oryzae

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Wiler Ribas Moreira

2015-08-01

Full Text Available Brown spot (BS, caused by the fungus Bipolaris oryzae, is one of the most important diseases contracted by rice. We investigated the effect of magnesium (Mg on the development of BS, caused by Bipolaris oryzae, and the effects of disease development on the photosynthetic performance of rice (Oryza sativa L. plants (cv. Metica-1 grown in nutrient solutions containing 0.25 or 4.0 mM of Mg. Assessments of BS severity, leaf Mg and pigment concentrations (total chlorophylls and carotenoids, were carried out at 120 h after inoculation, in addition to gas exchange parameters,. Higher leaf concentration of Mg was observed in plants supplied with 4.0 mM Mg than in those supplied with 0.25 mM. The increase in leaf Mg was accompanied by a decrease in BS severity, higher concentration of total chlorophyll and better photosynthetic performance. Plants supplied with 4.0 mM Mg had higher average values for carbon assimilation, stomatal conductance and internal leaf CO2 concentration when compared with plants supplied with 0.25 mM Mg. Conversely, the concentration of carotenoids was lower in plants supplied with the higher Mg rate. These results suggest that Mg suppresses disease severity and preserves photosynthetic performance by allowing for better stomatal conductance and, consequently, greater availability of CO2 at the carboxylation sites.

Genome Wide Identification, Evolutionary, and Expression Analysis of VQ Genes from Two Pyrus Species.

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Cao, Yunpeng; Meng, Dandan; Abdullah, Muhammad; Jin, Qing; Lin, Yi; Cai, Yongping

2018-04-23

The VQ motif-containing gene, a member of the plant-specific genes, is involved in the plant developmental process and various stress responses. The VQ motif-containing gene family has been studied in several plants, such as rice ( Oryza sativa ), maize ( Zea mays ), and Arabidopsis ( Arabidopsis thaliana ). However, no systematic study has been performed in Pyrus species, which have important economic value. In our study, we identified 41 and 28 VQ motif-containing genes in Pyrus bretschneideri and Pyrus communis , respectively. Phylogenetic trees were calculated using A. thaliana and O. sativa VQ motif-containing genes as a template, allowing us to categorize these genes into nine subfamilies. Thirty-two and eight paralogous of VQ motif-containing genes were found in P. bretschneideri and P. communis , respectively, showing that the VQ motif-containing genes had a more remarkable expansion in P. bretschneideri than in P. communis . A total of 31 orthologous pairs were identified from the P. bretschneideri and P. communis VQ motif-containing genes. Additionally, among the paralogs, we found that these duplication gene pairs probably derived from segmental duplication/whole-genome duplication (WGD) events in the genomes of P. bretschneideri and P. communis , respectively. The gene expression profiles in both P. bretschneideri and P. communis fruits suggested functional redundancy for some orthologous gene pairs derived from a common ancestry, and sub-functionalization or neo-functionalization for some of them. Our study provided the first systematic evolutionary analysis of the VQ motif-containing genes in Pyrus , and highlighted the diversification and duplication of VQ motif-containing genes in both P. bretschneideri and P. communis .

CatB is Critical for Total Catalase Activity and Reduces Bactericidal Effects of Phenazine-1-Carboxylic Acid on Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola.

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Pan, Xiayan; Wu, Jian; Xu, Shu; Duan, Yabing; Zhou, Mingguo

2017-02-01

Rice bacterial leaf blight, caused by Xanthomonas oryzae pv. oryzae, and rice bacterial leaf streak, caused by X. oryzae pv. oryzicola, are major diseases of rice. Phenazine-1-carboxylic acid (PCA) is a natural product that is isolated from Pseudomonas spp. and is used to control many important rice diseases in China. We previously reported that PCA disturbs the redox balance, which results in the accumulation of reactive oxygen species in X. oryzae pv. oryzae. In this study, we found that PCA significantly upregulated the transcript levels of catB and katE, which encode catalases, and that PCA sensitivity was reduced when X. oryzae pvs. oryzae and oryzicola were cultured with exogenous catalase. Furthermore, catB deletion mutants of X. oryzae pvs. oryzae and oryzicola showed dramatically decreased total catalase activity, increased sensitivity to PCA, and reduced virulence in rice. In contrast, deletion mutants of srpA and katG, which also encode catalases, exhibited little change in PCA sensitivity. The results indicate that catB in both X. oryzae pvs. oryzae and oryzicola encodes a catalase that helps protect the bacteria against PCA-induced stress.

Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement

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Tae-Sung Kim

2015-11-01

Full Text Available The vetch (Vicia sativa is one of the most important annual forage legumes globally due to its multiple uses and high nutritional content. Despite these agronomical benefits, many drawbacks, including cyano-alanine toxin, has reduced the agronomic value of vetch varieties. Here, we used 454 technology to sequence the two V. sativa subspecies (ssp. sativa and ssp. nigra to enrich functional information and genetic marker resources for the vetch research community. A total of 86,532 and 47,103 reads produced 35,202 and 18,808 unigenes with average lengths of 735 and 601 bp for V. sativa sativa and V. sativa nigra, respectively. Gene Ontology annotations and the cluster of orthologous gene classes were used to annotate the function of the Vicia transcriptomes. The Vicia transcriptome sequences were then mined for simple sequence repeat (SSR and single nucleotide polymorphism (SNP markers. About 13% and 3% of the Vicia unigenes contained the putative SSR and SNP sequences, respectively. Among those SSRs, 100 were chosen for the validation and the polymorphism test using the Vicia germplasm set. Thus, our approach takes advantage of the utility of transcriptomic data to expedite a vetch breeding program.

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Genetics; Volume 93; Issue 1. Genomewide survey and characterization of metacaspase gene family in rice (Oryza sativa). Likai Wang Hua Zhang. Research Article Volume 93 Issue 1 April ... Keywords. metacaspases; OsMC gene family; expression profiles; domestication; rice; Oryza sativa.

Interactions of rice (Oryza sativa L.) and PAH-degrading bacteria (Acinetobacter sp.) on enhanced dissipation of spiked phenanthrene and pyrene in waterlogged soil.

Science.gov (United States)

Gao, Y; Yu, X Z; Wu, S C; Cheung, K C; Tam, N F Y; Qian, P Y; Wong, M H

2006-12-15

The effects of cultivation of rice (Oryza sativa L.) and PAH-degrading bacteria (Acinetobacter sp.) separately, and in combination, on the dissipation of spiked phenanthrene and pyrene (0, 50+50, 100+100, 200+200 mg kg(-1)) in waterlogged soil were studied using pot trials. The population of introduced PAH-degrading bacteria remained at 10(5) CFU g(-1) dry soil after 20 days of treatment with Acinetobacter sp. only, but increased to 10(6) when planted with rice simultaneously. Shoot and root biomass of rice when grown alone was adversely affected by spiked PAHs, but significantly increased by 2-55% and 8-409%, respectively, when inoculated with Acinetobacter sp.. Phenanthrene and pyrene concentrations in roots ranged from 1-27 and 20-98 mg kg(-1), respectively, while their concentrations in shoots were generally lower than 0.2 mg kg(-1). The dissipation of phenanthrene was mainly due to abiotic loss as 70-78% phenanthrene was lost from the control soil at the end of 80 days, while removal of 86-87% phenanthrene had been achieved after 40 days in the treatment co-cultivated with Acinetobacter sp. and rice. Compared with the control where only 6-15% of pyrene was removed from soil, a much higher dissipation of pyrene (43-62%) was attained for the treatments co-cultivated with Acinetobacter sp. and rice at the end of 80 days. The results demonstrated that co-cultivation of rice and PAH-degrading bacteria may have a great potential to accelerate the bioremediation process of PAH-contaminated soil under waterlogged conditions.

Breeding for blast-disease-resistant and high-yield Thai jasmine rice (Oryza sativa L. cv. KDML 105) mutants using low-energy ion beams

International Nuclear Information System (INIS)

Mahadtanapuk, S.; Teraarusiri, W.; Phanchaisri, B.; Yu, L.D.; Anuntalabhochai, S.

2013-01-01

Highlights: •N-ion beam bombarded Thai jasmine rice seeds to induce mutation. •Mutants with blast-disease resistance and high yield were screened. •Gene involved in the blast-disease resistance was analyzed. •The gene responsible for the resistance was linked to Spotted leaf protein 11. -- Abstract: Low-energy ion beam was applied on mutation induction for plant breeding of blast-disease-resistant Thai jasmine rice (Oryza sativa L. cv. KDML 105). Seeds of the wild-type rice were bombarded in vacuum by nitrogen ion beam at energy of 60–80 keV to a beam fluence range of 2 × 10 16 –2 × 10 17 ions/cm 2 . The ion-bombarded rice seeds were grown in soil for 2 weeks as transplanted rice in plastic pots at 1 seedling/pot. The seedlings were then screened for blast resistance by Pyricularia grisea inoculation with 10 6 spores/ml concentrations. The blast-resistant rice mutant was planted up to F6 generation with the consistent phenotypic variation. The high percentage of the blast-disease-resistant rice was analyzed with DNA fingerprint. The HAT-RAPD (high annealing temperature-random amplified polymorphic DNA) marker revealed the modified polymorphism fragment presenting in the mutant compared with wild type (KDML 105). The cDNA fingerprints were investigated and the polymorphism fragment was subcloned into pGEM-T easy vector and then sequenced. The sequence of this fragment was compared with those already contained in the database, and the fragment was found to be related to the Spotted leaf protein 11 (Spl11)

Grain Yield, Dry Weight and Phosphorus Accumulation and Translocation in Two Rice (Oryza sativa L. Varieties as Affected by Salt-Alkali and Phosphorus

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Zhijie Tian

2017-08-01

Full Text Available Salt-alkali is the main threat to global crop production. The functioning of phosphorus (P in alleviating damage to crops from saline-alkaline stress may be dependent on the variety of crop but there is little published research on the topic. This pot experiment was conducted to study if P has any effect on rice (Oryza sativa L. yield, dry matter and P accumulation and translocation in salt-alkaline soils. Plant dry weight and P content at heading and harvest stages of two contrasting saline-alkaline tolerant (Dongdao-4 and sensitive (Tongyu-315 rice varieties were examined under two saline-alkaline (light versus severe soils and five P supplements (P0, P50, P100, P150 and P200 kg ha−1. The results were: in light saline-alkaline soil, the optimal P levels were found for P150 for Dongdao-4 and for P100 for Tongyu-315 with the greatest grain dry weight and P content. Two rice varieties obtained relatively higher dry weight and P accumulation and translocation in P0. In severe saline-alkaline soil, however, dry weight and P accumulation and translocation, 1000-grain weight, seed-setting rate and grain yield significantly decreased, but effectively increased with P application for Dongdao-4. Tongyu-315 showed lower sensitivity to P nutrition. Thus, a more tolerant variety could have a stronger capacity to absorb and translocate P for grain filling, especially in severe salt-alkaline soils. This should be helpful for consideration in rice breeding and deciding a reasonable P application in saline-alkaline soil.

Ability of Rf5 and Rf6 to Restore Fertility of Chinsurah Boro II-type Cytoplasmic Male Sterile Oryza Sativa (ssp. Japonica) Lines.

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Zhang, Honggen; Che, Jianlan; Ge, Yongshen; Pei, Yan; Zhang, Lijia; Liu, Qiaoquan; Gu, Minghong; Tang, Shuzhu

2017-12-01

Three-line Oryza sativa (ssp. japonica) hybrids have been developed mainly using Chinsurah Boro II (BT)-type cytoplasmic male sterility (CMS). The Rf1 gene restores the fertility of BT-type CMS lines, and is the only fertility restorer gene (Rf) that has been used to produce three-line japonica hybrids. Using more Rf genes to breed BT-type restorer lines may broaden the genetic diversity of the restorer lines, and represents a viable approach to improve the heterosis level of BT-type japonica hybrids. We identified two major Rf genes from '93-11' that are involved in restoring the fertility of BT-type CMS plants. These genes were identified from resequenced chromosome segment substitution lines derived from a cross between the japonica variety 'Nipponbare' and the indica variety '93-11'. Molecular mapping results revealed that these genes were Rf5 and Rf6, which are the Rf genes that restore fertility to Honglian-type CMS lines. The BT-type F 1 hybrids with either Rf5 or Rf6 exhibited normal seed setting rates, but F 1 plants carrying Rf6 showed more stable seed setting rates than those of plants carrying Rf5 under heat-stress conditions. Furthermore, the seed setting rates of F 1 hybrids carrying both Rf5 and Rf6 were more stable than that of F 1 plants carrying only one Rf gene. Rf6 is an important genetic resource for the breeding of BT-type japonica restorer lines. Our findings may be useful for breeders interested in developing BT-type japonica hybrids.

Genomic diversity among Basmati rice ( Oryza sativa L) mutants ...

African Journals Online (AJOL)

Mutation breeding can be considered successful in obtaining new cultivars and broadening the genetic base of rice crop. In order to obtain new varieties of rice with improved agronomic and grain characteristics, gamma radiation (60Co) has been used to generate novel mutants of the Basmati rice. In this study rice cultivars ...

Carbon-14 dynamics in rice: an extension of the ORYZA2000 model

Energy Technology Data Exchange (ETDEWEB)

Galeriu, D.; Melintescu, A. [' ' Horia Hulubei' ' National Institute for Physics and Nuclear Engineering, Life and Environmental Physics Department, 30 Reactorului St., POB MG-6, Bucharest-Magurele (Romania)

2014-03-15

Carbon-14 ({sup 14}C) is a radionuclide of major interest in nuclear power production. The Fukushima accident changed the public attitude on the use of nuclear energy all over the world. In terms of nuclear safety, the need of quality-assured radiological models was emphasized by many international organizations, and for models used by decision-makers (i.e. regulatory environmental models and radiological models), a moderate conservatism, transparency, relative simplicity and user friendliness are required. Because the interaction between crops and the environment is complex and regulated by many feedback mechanisms, however, these requirements are difficult to accomplish. The present study makes a step forward regarding the development of a robust model dealing with food contamination after a short-term accidental emission and considers a single crop species, rice (Oryza sativa), one of the most widely used rice species. Old and more recent experimental data regarding the carbon dynamics in rice plants are reviewed, and a well-established crop growth model, ORYZA2000, is used and adapted in order to assess the dynamics of {sup 14}C in rice after a short-term exposure to {sup 14}CO{sub 2}. Here, the model is used to investigate the role of the genotype, management and weather on the concentration of radiocarbon at harvest. (orig.)

Genome-scale analysis of the high-efficient protein secretion system of Aspergillus oryzae

DEFF Research Database (Denmark)

Liu, Lifang; Feizi, Amir; Osterlund, Tobias

2014-01-01

related fungal species such as Aspergillus nidulans and Aspergillus niger. To evaluate the defined component list, we performed transcriptome analysis on three a-amylase over-producing strains with varying levels of secretion capacities. Specifically, secretory components involved in the ER......Background: The koji mold, Aspergillus oryzae is widely used for the production of industrial enzymes due to its particularly high protein secretion capacity and ability to perform post-translational modifications. However, systemic analysis of its secretion system is lacking, generally due...... to the poorly annotated proteome. Results: Here we defined a functional protein secretory component list of A. oryzae using a previously reported secretory model of S. cerevisiae as scaffold. Additional secretory components were obtained by blast search with the functional components reported in other closely...

Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa).

Science.gov (United States)

Begum, Hasina; Spindel, Jennifer E; Lalusin, Antonio; Borromeo, Teresita; Gregorio, Glenn; Hernandez, Jose; Virk, Parminder; Collard, Bertrand; McCouch, Susan R

2015-01-01

Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.

The Application of Restriction Landmark Genome Scanning Method for Surveillance of Non-Mendelian Inheritance in F1 Hybrids

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Tomoko Takamiya

2009-01-01

Full Text Available We analyzed inheritance of DNA methylation in reciprocal F1 hybrids (subsp. japonica cv. Nipponbare × subsp. indica cv. Kasalath of rice (Oryza sativa L. using restriction landmark genome scanning (RLGS, and detected differing RLGS spots between the parents and reciprocal F1 hybrids. MspI/HpaII restriction sites in the DNA from these different spots were suspected to be heterozygously methylated in the Nipponbare parent. These spots segregated in F1 plants, but did not segregate in selfed progeny of Nipponbare, showing non-Mendelian inheritance of the methylation status. As a result of RT-PCR and sequencing, a specific allele of the gene nearest to the methylated sites was expressed in reciprocal F1 plants, showing evidence of biased allelic expression. These results show the applicability of RLGS for scanning of non-Mendelian inheritance of DNA methylation and biased allelic expression.

Transcriptome analysis of WRKY gene family in Oryza officinalis Wall ex Watt and WRKY genes involved in responses to Xanthomonas oryzae pv. oryzae stress.

Science.gov (United States)

Jiang, Chunmiao; Shen, Qingxi J; Wang, Bo; He, Bin; Xiao, Suqin; Chen, Ling; Yu, Tengqiong; Ke, Xue; Zhong, Qiaofang; Fu, Jian; Chen, Yue; Wang, Lingxian; Yin, Fuyou; Zhang, Dunyu; Ghidan, Walid; Huang, Xingqi; Cheng, Zaiquan

2017-01-01

Oryza officinalis Wall ex Watt, a very important and special wild rice species, shows abundant genetic diversity and disease resistance features, especially high resistance to bacterial blight. The molecular mechanisms of bacterial blight resistance in O. officinalis have not yet been elucidated. The WRKY transcription factor family is one of the largest gene families involved in plant growth, development and stress response. However, little is known about the numbers, structure, molecular phylogenetics, and expression of the WRKY genes under Xanthomonas oryzae pv. oryzae (Xoo) stress in O. officinalis due to lacking of O. officinalis genome. Therefore, based on the RNA-sequencing data of O. officinalis, we performed a comprehensive study of WRKY genes in O. officinalis and identified 89 OoWRKY genes. Then 89 OoWRKY genes were classified into three groups based on the WRKY domains and zinc finger motifs. Phylogenetic analysis strongly supported that the evolution of OoWRKY genes were consistent with previous studies of WRKYs, and subgroup IIc OoWRKY genes were the original ancestors of some group II and group III OoWRKYs. Among the 89 OoWRKY genes, eight OoWRKYs displayed significantly different expression (>2-fold, pWRKY family of transcription factors in O.officinalis. Insight was gained into the classification, evolution, and function of the OoWRKY genes, revealing the putative roles of eight significantly different expression OoWRKYs in Xoo strains PXO99 and C5 stress responses in O.officinalis. This study provided a better understanding of the evolution and functions of O. officinalis WRKY genes, and suggested that manipulating eight significantly different expression OoWRKYs would enhance resistance to bacterial blight.

Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina.

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Volker U Schwartze

2014-08-01

Full Text Available Lichtheimia species are the second most important cause of mucormycosis in Europe. To provide broader insights into the molecular basis of the pathogenicity-associated traits of the basal Mucorales, we report the full genome sequence of L. corymbifera and compared it to the genome of Rhizopus oryzae, the most common cause of mucormycosis worldwide. The genome assembly encompasses 33.6 MB and 12,379 protein-coding genes. This study reveals four major differences of the L. corymbifera genome to R. oryzae: (i the presence of an highly elevated number of gene duplications which are unlike R. oryzae not due to whole genome duplication (WGD, (ii despite the relatively high incidence of introns, alternative splicing (AS is not frequently observed for the generation of paralogs and in response to stress, (iii the content of repetitive elements is strikingly low (<5%, (iv L. corymbifera is typically haploid. Novel virulence factors were identified which may be involved in the regulation of the adaptation to iron-limitation, e.g. LCor01340.1 encoding a putative siderophore transporter and LCor00410.1 involved in the siderophore metabolism. Genes encoding the transcription factors LCor08192.1 and LCor01236.1, which are similar to GATA type regulators and to calcineurin regulated CRZ1, respectively, indicating an involvement of the calcineurin pathway in the adaption to iron limitation. Genes encoding MADS-box transcription factors are elevated up to 11 copies compared to the 1-4 copies usually found in other fungi. More findings are: (i lower content of tRNAs, but unique codons in L. corymbifera, (ii Over 25% of the proteins are apparently specific for L. corymbifera. (iii L. corymbifera contains only 2/3 of the proteases (known to be essential virulence factors in comparison to R. oryzae. On the other hand, the number of secreted proteases, however, is roughly twice as high as in R. oryzae.

An overproduction of astellolides induced by genetic disruption of chromatin-remodeling factors in Aspergillus oryzae.

Science.gov (United States)

Shinohara, Yasutomo; Kawatani, Makoto; Futamura, Yushi; Osada, Hiroyuki; Koyama, Yasuji

2016-01-01

The filamentous fungus Aspergillus oryzae is an important industrial mold. Recent genomic analysis indicated that A. oryzae has a large number of biosynthetic genes for secondary metabolites (SMs), but many of the SMs they produce have not been identified. For better understanding of SMs production by A. oryzae, we screened a gene-disruption library of transcription factors including chromatin-remodeling factors and found two gene disruptions that show similarly altered SM production profiles. One is a homolog of Aspergillus nidulans cclA, a component of the histone 3 lysine 4 (H3K4) methyltransferase complex of proteins associated with Set1 complex, and the other, sppA, is an ortholog of Saccharomyces cerevisiae SPP1, another component of a complex of proteins associated with Set1 complex. The cclA and sppA disruptions in A. oryzae are deficient in trimethylation of H3K4. Furthermore, one of the SMs that increased in the cclA disruptant was identified as astellolide F (14-deacetyl astellolide B). These data indicate that both cclA and sppA affect production of SMs including astellolides by affecting the methylation status of H3K4 in A. oryzae.

The imprints of the high light and UV-B stresses in Oryza sativa L. 'Kanchana' seedlings are differentially modulated.

Science.gov (United States)

Faseela, Parammal; Puthur, Jos T

2018-01-01

High light and ultraviolet-B radiation (UV-B) are generally considered to have negative impact on photosynthesis and plant growth. The present study evaluates the tolerance potential of three cultivars of Oryza sativa L. (Kanchana, Mattatriveni and Harsha) seedlings towards high light and UV-B stress on the basis of photosynthetic pigment degradation, chlorophyll a fluorescence parameters and rate of lipid peroxidation, expressed by malondialdehyde content. Surprisingly, it was revealed that Kanchana was the most sensitive cultivar towards high light and at the same time it was the most tolerant cultivar towards UV-B stress. This contrasting feature of Kanchana towards high light and UV-B tolerance was further studied by analyzing photosystem (PS) I and II activity, mitochondrial activity, chlorophyll a fluorescence transient, enzymatic and non-enzymatic antioxidant defense system. Due to the occurrence of more PS I and PSII damages, the inhibition of photochemical efficiency and emission of dissipated energy as heat or fluorescence per PSII reaction center was higher upon high light exposure than UV-B treatments in rice seedlings of Kanchana. The mitochondrial activity was also found to be drastically altered upon high light as compared to UV-B treatments. The UV-B induced accumulation of non-enzymatic antioxidants (proline, total phenolics, sugar and ascorbate) and enzymatic antioxidants (ascorbate peroxidase, guaiacol peroxidase, superoxide dismutase and glutathione reductase) in rice seedlings than those subjected to high light exposure afforded more efficient protection against UV-B radiation in rice seedlings. Our results proved that high tolerance of Kanchana towards UV-B than high light treatments, correlated linearly with the protected photosynthetic and mitochondrial machinery which was provided by upregulation of antioxidants particularly by total phenolics, ascorbate and ascorbate peroxidase in rice seedlings. Data presented in this study conclusively

Regulation of glutamine synthetase isoforms in two differentially drought-tolerant rice (Oryza sativa L.) cultivars under water deficit conditions.

Science.gov (United States)

Singh, Kamal Krishna; Ghosh, Shilpi

2013-02-01

KEY MESSAGE : The regulation of GS isoforms by WD was organ specific. Two GS isoforms i.e. OsGS1;1 and OsGS2 were differentially regulated in IR-64 (drought-sensitive) and Khitish (drought-tolerant) cultivars of rice. Water deficit (WD) has adverse effect on rice (Oryza sativa L.) and acclimation requires essential reactions of primary metabolism to continue. Rice plants utilize ammonium as major nitrogen source, which is assimilated into glutamine by the reaction of Glutamine synthetase (GS, EC 6.3.1.2). Rice plants possess one gene (OsGS2) for chloroplastic GS2 and three genes (OsGS1;1, OsGS1;2 and OsGS1;3) for cytosolic GS1. Here, we report the effect of WD on regulation of GS isoforms in drought-sensitive (cv. IR-64) and drought-tolerant (cv. Khitish) rice cultivars. Under WD, total GS activity in root and leaf decreased significantly in IR-64 seedlings in comparison to Khitish seedlings. The reduced GS activity in IR-64 leaf was mainly due to decrease in GS2 activity, which correlated with decrease in corresponding transcript and polypeptide contents. GS1 transcript and polypeptide accumulated in leaf during WD, however, GS1 activity was maintained at a constant level. Total GS activity in stem of both the varieties was insensitive to WD. Among GS1 genes, OsGS1;1 expression was differently regulated by WD in the two rice varieties. Its transcript accumulated more abundantly in IR-64 leaf than in Khitish leaf. Following WD, OsGS1;1 mRNA level in stem and root tissues declined in IR-64 and enhanced in Khitish. A steady OsGS1;2 expression patterns were noted in leaf, stem and root of both the cultivars. Results suggest that OsGS2 and OsGS1;1 expression may contribute to drought tolerance of Khitish cultivar under WD conditions.

Concentrations of arsenic and lead in rice (Oryza sativa L.) in Iran: A systematic review and carcinogenic risk assessment.

Science.gov (United States)

Fakhri, Yadolah; Bjørklund, Geir; Bandpei, Anoushiravan Mohseni; Chirumbolo, Salvatore; Keramati, Hassan; Hosseini Pouya, Rokhsane; Asadi, Anvar; Amanidaz, Nazak; Sarafraz, Mansour; Sheikhmohammad, Amir; Alipour, Mohamadreza; Baninameh, Zahra; Mohseni, Seyed Mohsen; Sarkhosh, Maryam; Ghasemi, Seyed Mehdi

2018-03-01

Exposure to heavy metals such as arsenic (As), lead (Pb), and cadmium (Cd) in either the short or the long term can cause cancers in humans. Dietary intake and consumption of rice (Oryza sativa L.) is increasing in Iran, and several studies on the concentration of heavy metals in rice have been carried out in this country in recent years. In this perspective, the main objective of the present study was to investigate, even via a meta-analysis of the existing literature, the presence of As and Pb in rice from many geographical areas in Iran, as well as to estimate the carcinogenic risk of these heavy metals in rice consumers. The results of the present ten years-spanning systematic review indicate that 21 reports, collecting a total of 2088 samples, were performed between 2008 and October 2017. The minimum and maximum concentration of As was observed in the Golestan area (0.01 ± 0.01 mg/kg d.w) and the Gillan region (3 mg/kg d.w); and Pb in the Shahrekord (0.07 ± 0.02 mg/kg d.w) and Mazandaran (35 mg/kg d.w). The meta-analysis of data showed that pooled concentration of As in the rice was 0.04 (95%CI: 0.02-0.06 mg/kg d.w), which resulted lower than the National Standard (NS) limits. However, the pooled concentration of Pb in the rice was 0.38 (95%CI: 0.25-0.5 mg/kg d.w), i.e., higher than NS limits. The heterogeneity was significant between As (I 2  = 63%, P value = .003) and Pb (I 2  = 96%, P value rice content of As and Pb are at considerable carcinogenesis risk (ILCR > 10 -3 ). Therefore a decreased level of heavy metals in rice cultivation should be encouraged and performed in next planning. Copyright © 2018 Elsevier Ltd. All rights reserved.

Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data.

Science.gov (United States)

Edwards, J D; Baldo, A M; Mueller, L A

2016-01-01

Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. Rice research has benefited from early adoption and extensive use of simple sequence repeat (SSR) markers; however, the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new pipeline, using a stepwise relaxation of stringency, was used to map SSR primers onto the latest rice pseudomolecule assembly. The SSR markers and experimentally assayed amplicon sizes are presented in a relational database with a web-based front end, and are available as a track loaded in a genome browser with links connecting the browser and database. The combined capabilities of Ricebase link genetic markers, genome context, allele states across rice germplasm and potentially user curated phenotypic interpretations as a community resource for genetic discovery and breeding in rice. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the United States.

Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection.

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Xianfa Xie

Full Text Available Oryza sativa or Asian cultivated rice is one of the major cereal grass species domesticated for human food use during the Neolithic. Domestication of this species from the wild grass Oryza rufipogon was accompanied by changes in several traits, including seed shattering, percent seed set, tillering, grain weight, and flowering time. Quantitative trait locus (QTL mapping has identified three genomic regions in chromosome 3 that appear to be associated with these traits. We would like to study whether these regions show signatures of selection and whether the same genetic basis underlies the domestication of different rice varieties. Fragments of 88 genes spanning these three genomic regions were sequenced from multiple accessions of two major varietal groups in O. sativa--indica and tropical japonica--as well as the ancestral wild rice species O. rufipogon. In tropical japonica, the levels of nucleotide variation in these three QTL regions are significantly lower compared to genome-wide levels, and coalescent simulations based on a complex demographic model of rice domestication indicate that these patterns are consistent with selection. In contrast, there is no significant reduction in nucleotide diversity in the homologous regions in indica rice. These results suggest that there are differences in the genetic and selective basis for domestication between these two Asian rice varietal groups.

A novel epistatic interaction at two loci causing hybrid male sterility in an inter-subspecific cross of rice (Oryza sativa L.).

Science.gov (United States)

Kubo, Takahiko; Yamagata, Yoshiyuki; Eguchi, Maki; Yoshimura, Atsushi

2008-12-01

Postzygotic reproductive isolation (RI) often arises in inter-subspecific crosses as well as inter-specific crosses of rice (Oryza sativa L.). To further understand the genetic architecture of the postzygotic RI, we analyzed genes causing hybrid sterility and hybrid breakdown in a rice inter-subspecific cross. Here we report hybrid male sterility caused by epistatic interaction between two novel genes, S24 and S35, which were identified on rice chromosomes 5 and 1, respectively. Genetic analysis using near-isogenic lines (NILs) carrying IR24 (ssp. indica) segments with Asominori (ssp. japonica) genetic background revealed a complicated aspect of the epistasis. Allelic interaction at the S24 locus in the heterozygous plants caused abortion of male gametes carrying the Asominori allele (S24-as) independent of the S35 genotype. On the other hand, male gametes carrying the Asominori allele at the S35 locus (S35-as) showed abortion only when the IR24 allele at the S24 locus (S24-ir) was concurrently introgressed into the S35 heterozygous plants, indicating that the sterility phenotype due to S35 was dependent on the S24 genotype through negative epistasis between S24-ir and S35-as alleles. Due to the interaction between S24 and S35, self-pollination of the double heterozygous plants produced pollen-sterile progeny carrying the S24-ir/S24-ir S35-as/S35-ir genotype in addition to the S24 heterozygous plants. This result suggests that the S35 gene might function as a modifier of S24. This study presents strong evidence for the importance of epistatic interaction as a part of the genetic architecture of hybrid sterility in rice. In addition, it suggests that diverse systems have been developed as postzygotic RI mechanisms within the rice.

In silico analysis of cis-acting regulatory elements in 5' regulatory regions of sucrose transporter gene families in rice (Oryza sativa Japonica) and Arabidopsis thaliana.

Science.gov (United States)

Ibraheem, Omodele; Botha, Christiaan E J; Bradley, Graeme

2010-12-01

The regulation of gene expression involves a multifarious regulatory system. Each gene contains a unique combination of cis-acting regulatory sequence elements in the 5' regulatory region that determines its temporal and spatial expression. Cis-acting regulatory elements are essential transcriptional gene regulatory units; they control many biological processes and stress responses. Thus a full understanding of the transcriptional gene regulation system will depend on successful functional analyses of cis-acting elements. Cis-acting regulatory elements present within the 5' regulatory region of the sucrose transporter gene families in rice (Oryza sativa Japonica cultivar-group) and Arabidopsis thaliana, were identified using a bioinformatics approach. The possible cis-acting regulatory elements were predicted by scanning 1.5kbp of 5' regulatory regions of the sucrose transporter genes translational start sites, using Plant CARE, PLACE and Genomatix Matinspector professional databases. Several cis-acting regulatory elements that are associated with plant development, plant hormonal regulation and stress response were identified, and were present in varying frequencies within the 1.5kbp of 5' regulatory region, among which are; A-box, RY, CAT, Pyrimidine-box, Sucrose-box, ABRE, ARF, ERE, GARE, Me-JA, ARE, DRE, GA-motif, GATA, GT-1, MYC, MYB, W-box, and I-box. This result reveals the probable cis-acting regulatory elements that possibly are involved in the expression and regulation of sucrose transporter gene families in rice and Arabidopsis thaliana during cellular development or environmental stress conditions. Copyright © 2010 Elsevier Ltd. All rights reserved.

Ehd4 encodes a novel and Oryza-genus-specific regulator of photoperiodic flowering in rice.

Directory of Open Access Journals (Sweden)

He Gao

Full Text Available Land plants have evolved increasingly complex regulatory modes of their flowering time (or heading date in crops. Rice (Oryza sativa L. is a short-day plant that flowers more rapidly in short-day but delays under long-day conditions. Previous studies have shown that the CO-FT module initially identified in long-day plants (Arabidopsis is evolutionary conserved in short-day plants (Hd1-Hd3a in rice. However, in rice, there is a unique Ehd1-dependent flowering pathway that is Hd1-independent. Here, we report isolation and characterization of a positive regulator of Ehd1, Early heading date 4 (Ehd4. ehd4 mutants showed a never flowering phenotype under natural long-day conditions. Map-based cloning revealed that Ehd4 encodes a novel CCCH-type zinc finger protein, which is localized to the nucleus and is able to bind to nucleic acids in vitro and transactivate transcription in yeast, suggesting that it likely functions as a transcriptional regulator. Ehd4 expression is most active in young leaves with a diurnal expression pattern similar to that of Ehd1 under both short-day and long-day conditions. We show that Ehd4 up-regulates the expression of the "florigen" genes Hd3a and RFT1 through Ehd1, but it acts independently of other known Ehd1 regulators. Strikingly, Ehd4 is highly conserved in the Oryza genus including wild and cultivated rice, but has no homologs in other species, suggesting that Ehd4 is originated along with the diversification of the Oryza genus from the grass family during evolution. We conclude that Ehd4 is a novel Oryza-genus-specific regulator of Ehd1, and it plays an essential role in photoperiodic control of flowering time in rice.

AcEST: DK958823 [AcEST

Lifescience Database Archive (English)

Full Text Available MPPLEG 2401 >sp|Q8AZM0|POLS_BSNV Structural polyprotein OS=Blotched snakehead virus PE=1 SV=1 Length = 1069 ...p|Q68749|POLG_HCVBB Genome polyprotein OS=Hepatitis C virus gen... 33 0.98 sp|Q8AZM0|POLS_BSNV Structural polyprotein OS=Blotched sna...kehead... 31 4.8 sp|Q7XWS7|FH12_ORYSJ Formin-like protein 12 OS=Oryza sativa subs..

Dicty_cDB: Contig-U14112-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available Oryza sativa Japonica Group genom... 77 8e-14 FJ787374_1( FJ787374 |pid:none) Nicotiana repanda protein kin..._1( FJ787369 |pid:none) Nicotiana repanda protein kinase-c... 79 1e-13 AC004260_13( AC004260 |pid:none) Arab...8... 72 2e-12 FJ787371_1( FJ787371 |pid:none) Nicotiana repanda protein kinase-c... 75 2e-12 FB875947_1( FB8

Metagenome analysis of the root endophytic microbial community of Indian rice (O. sativa L.

Directory of Open Access Journals (Sweden)

Subhadipa Sengupta

2017-06-01

Full Text Available This study reports the root endophytic microbial community profile in rice (Oryza sativa L., the largest food crop of Asia, using 16S rRNA gene amplicon sequencing. Metagenome of OS01 and OS04 consisted of 11,17,900 sequences with 300 Mbp size and average 55.6% G + C content. Data of this study are available at NCBI Bioproject (PRJNA360379. The taxonomic analysis of 843 OTU's showed that the sequences belonged to four major phyla revealing dominance of Proteobacteria, Firmicutes, Cyanobacteria and Actinobacteria. Results reveal the dominance of Bacillus as major endophytic genera in rice roots, probably playing a key role in Nitrogen fixation.

A cell wall-degrading esterase of Xanthomonas oryzae requires a unique substrate recognition module for pathogenesis on rice.

Science.gov (United States)

Aparna, Gudlur; Chatterjee, Avradip; Sonti, Ramesh V; Sankaranarayanan, Rajan

2009-06-01

Xanthomonas oryzae pv oryzae (Xoo) causes bacterial blight, a serious disease of rice (Oryza sativa). LipA is a secretory virulence factor of Xoo, implicated in degradation of rice cell walls and the concomitant elicitation of innate immune responses, such as callose deposition and programmed cell death. Here, we present the high-resolution structural characterization of LipA that reveals an all-helical ligand binding module as a distinct functional attachment to the canonical hydrolase catalytic domain. We demonstrate that the enzyme binds to a glycoside ligand through a rigid pocket comprising distinct carbohydrate-specific and acyl chain recognition sites where the catalytic triad is situated 15 A from the anchored carbohydrate. Point mutations disrupting the carbohydrate anchor site or blocking the pocket, even at a considerable distance from the enzyme active site, can abrogate in planta LipA function, exemplified by loss of both virulence and the ability to elicit host defense responses. A high conservation of the module across genus Xanthomonas emphasizes the significance of this unique plant cell wall-degrading function for this important group of plant pathogenic bacteria. A comparison with the related structural families illustrates how a typical lipase is recruited to act on plant cell walls to promote virulence, thus providing a remarkable example of the emergence of novel functions around existing scaffolds for increased proficiency of pathogenesis during pathogen-plant coevolution.

Population Dynamics Among six Major Groups of the Oryza rufipogon Species Complex, Wild Relative of Cultivated Asian Rice.

Science.gov (United States)

Kim, HyunJung; Jung, Janelle; Singh, Namrata; Greenberg, Anthony; Doyle, Jeff J; Tyagi, Wricha; Chung, Jong-Wook; Kimball, Jennifer; Hamilton, Ruaraidh Sackville; McCouch, Susan R

2016-12-01

Understanding population structure of the wild progenitor of Asian cultivated rice (O. sativa), the Oryza rufipogon species complex (ORSC), is of interest to plant breeders and contributes to our understanding of rice domestication. A collection of 286 diverse ORSC accessions was evaluated for nuclear variation using genotyping-by-sequencing (113,739 SNPs) and for chloroplast variation using Sanger sequencing (25 polymorphic sites). Six wild subpopulations were identified, with 25 % of accessions classified as admixed. Three of the wild groups were genetically and geographically closely related to the O. sativa subpopulations, indica, aus and japonica, and carried O. sativa introgressions; the other three wild groups were genetically divergent, had unique chloroplast haplotypes, and were located at the geographical extremes of the species range. The genetic subpopulations were significantly correlated (r 2  = 0.562) with traditional species designations, O. rufipogon (perennial) and O. nivara (annual), differentiated based on morphology and life history. A wild diversity panel of 95 purified (inbred) accessions was developed for future genetic studies. Our results suggest that the cultivated aus subpopulation is most closely related to an annual wild relative, japonica to a perennial wild relative, and indica to an admixed population of diverse annual and perennial wild ancestors. Gene flow between ORSC and O. sativa is common in regions where rice is cultivated, threatening the identity and diversity of wild ORSC populations. The three geographically isolated ORSC populations harbor variation rarely seen in cultivated rice and provide a unique window into the genetic composition of ancient rice subpopulations.

Breeding for blast-disease-resistant and high-yield Thai jasmine rice (Oryza sativa L. cv. KDML 105) mutants using low-energy ion beams

Energy Technology Data Exchange (ETDEWEB)

Mahadtanapuk, S. [School of Agriculture and Natural Resources, University of Phayao, Phayao 56000 (Thailand); Teraarusiri, W. [Central Laboratory, University of Phayao, Phayao 56000 (Thailand); Phanchaisri, B. [Science and Technology Research Institute, Chiang Mai University, Chiang Mai 50200 (Thailand); Yu, L.D., E-mail: yuld@frnf.science.cmu.ac.th [Plasma and Beam Physics Research Facility, Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok 10400 (Thailand); Anuntalabhochai, S., E-mail: burinka@hotmail.com [Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand)

2013-07-15

Highlights: •N-ion beam bombarded Thai jasmine rice seeds to induce mutation. •Mutants with blast-disease resistance and high yield were screened. •Gene involved in the blast-disease resistance was analyzed. •The gene responsible for the resistance was linked to Spotted leaf protein 11. -- Abstract: Low-energy ion beam was applied on mutation induction for plant breeding of blast-disease-resistant Thai jasmine rice (Oryza sativa L. cv. KDML 105). Seeds of the wild-type rice were bombarded in vacuum by nitrogen ion beam at energy of 60–80 keV to a beam fluence range of 2 × 10{sup 16}–2 × 10{sup 17} ions/cm{sup 2}. The ion-bombarded rice seeds were grown in soil for 2 weeks as transplanted rice in plastic pots at 1 seedling/pot. The seedlings were then screened for blast resistance by Pyricularia grisea inoculation with 10{sup 6} spores/ml concentrations. The blast-resistant rice mutant was planted up to F6 generation with the consistent phenotypic variation. The high percentage of the blast-disease-resistant rice was analyzed with DNA fingerprint. The HAT-RAPD (high annealing temperature-random amplified polymorphic DNA) marker revealed the modified polymorphism fragment presenting in the mutant compared with wild type (KDML 105). The cDNA fingerprints were investigated and the polymorphism fragment was subcloned into pGEM-T easy vector and then sequenced. The sequence of this fragment was compared with those already contained in the database, and the fragment was found to be related to the Spotted leaf protein 11 (Spl11)

Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

Directory of Open Access Journals (Sweden)

Sofie Van Holle

2017-05-01

Full Text Available Lectins are present throughout the plant kingdom and are reported to be involved in diverse biological processes. In this study, we provide a comparative analysis of the lectin families from model species in a phylogenetic framework. The analysis focuses on the different plant lectin domains identified in five representative core angiosperm genomes (Arabidopsis thaliana, Glycine max, Cucumis sativus, Oryza sativa ssp. japonica and Oryza sativa ssp. indica. The genomes were screened for genes encoding lectin domains using a combination of Basic Local Alignment Search Tool (BLAST, hidden Markov models, and InterProScan analysis. Additionally, phylogenetic relationships were investigated by constructing maximum likelihood phylogenetic trees. The results demonstrate that the majority of the lectin families are present in each of the species under study. Domain organization analysis showed that most identified proteins are multi-domain proteins, owing to the modular rearrangement of protein domains during evolution. Most of these multi-domain proteins are widespread, while others display a lineage-specific distribution. Furthermore, the phylogenetic analyses reveal that some lectin families evolved to be similar to the phylogeny of the plant species, while others share a closer evolutionary history based on the corresponding protein domain architecture. Our results yield insights into the evolutionary relationships and functional divergence of plant lectins.

Cross genome comparisons of serine proteases in Arabidopsis and rice

Directory of Open Access Journals (Sweden)

Sowdhamini R

2006-08-01

Full Text Available Abstract Background Serine proteases are one of the largest groups of proteolytic enzymes found across all kingdoms of life and are associated with several essential physiological pathways. The availability of Arabidopsis thaliana and rice (Oryza sativa genome sequences has permitted the identification and comparison of the repertoire of serine protease-like proteins in the two plant species. Results Despite the differences in genome sizes between Arabidopsis and rice, we identified a very similar number of serine protease-like proteins in the two plant species (206 and 222, respectively. Nearly 40% of the above sequences were identified as potential orthologues. Atypical members could be identified in the plant genomes for Deg, Clp, Lon, rhomboid proteases and species-specific members were observed for the highly populated subtilisin and serine carboxypeptidase families suggesting multiple lateral gene transfers. DegP proteases, prolyl oligopeptidases, Clp proteases and rhomboids share a significantly higher percentage orthology between the two genomes indicating substantial evolutionary divergence was set prior to speciation. Single domain architectures and paralogues for several putative subtilisins, serine carboxypeptidases and rhomboids suggest they may have been recruited for additional roles in secondary metabolism with spatial and temporal regulation. The analysis reveals some domain architectures unique to either or both of the plant species and some inactive proteases, like in rhomboids and Clp proteases, which could be involved in chaperone function. Conclusion The systematic analysis of the serine protease-like proteins in the two plant species has provided some insight into the possible functional associations of previously uncharacterised serine protease-like proteins. Further investigation of these aspects may prove beneficial in our understanding of similar processes in commercially significant crop plant species.

Silicon treatment to rice (oryza sativa l. cv 'gopumbyeo') plants during different growth periods and its effects on growth and grain yield

International Nuclear Information System (INIS)

Kim, Y.H.; Waqas, M.; Kamran, M.

2012-01-01

Silicon (Si) has been considered a beneficial element for plant growth. We have assessed the effects of Si application on rice (Oryza sativa L.) growth and its grain yield at field level. For this, we performed two experiments. In experiment 1, we applied Si of three different concentrations (liquid Si-10, 25 and 36%) to the seedbed of rice before transplantation into paddy field. The results of this experiment showed that Si application to rice seedbeds did not affected the rice plant height and shoot fresh weight but its application significantly increased the pushing resistance of rice plants from 12.2-16.7% as compared with water applied control plants. The lodging index of Si treated rice plants significantly decreased (13.7% on LS-25) as compared with control. Similarly, Si treated plants had significantly higher yield. Upon Si treatment (LS-36), the grain yield per 10 acre and panicles per plant were 15.1% and 6. 3% higher than the water treated control plants respectively. The best concentration (LS-36%) revealed in the first experiment was foliar applied at 10 days before heading stage, initial tilling stage and panicle initiation stage to the rice leaves and we observed that shoot biomass was not significantly different between control and Si treated plants. However, significantly higher pushing resistance (10.5%-13.8%) and plant height (12.2%-16.7%) were observed while lower lodging index (7.6-7.8%) was recorded for Si treated plants as compared to control plants. Similarly, Si application increased the number of panicles per plant as well as the grain yield per 10 acre as compared to control. In conclusion, the Si application can significantly regulate plant growth and yield if applied at proper time with feasible concentration. (author)

Reactive oxygen species induced by heat stress during grain filling of rice (Oryza sativa L.) are involved in occurrence of grain chalkiness.

Science.gov (United States)

Suriyasak, Chetphilin; Harano, Keisuke; Tanamachi, Koichiro; Matsuo, Kazuhiro; Tamada, Aina; Iwaya-Inoue, Mari; Ishibashi, Yushi

2017-09-01

Heat stress during grain filling increases rice grain chalkiness due to increased activity of α-amylase, which hydrolyzes starch. In rice and barley seeds, reactive oxygen species (ROS) produced after imbibition induce α-amylase activity via regulation of gibberellin (GA) and abscisic acid (ABA) levels during seed germination. Here, we examined whether ROS is involved in induction of grain chalkiness by α-amylase in developing rice grains under heat stress. To elucidate the role of ROS in grain chalkiness, we grew post-anthesis rice plants (Oryza sativa L. cv. Koshihikari) under control (25°C) or heat stress (30°C) conditions with or without antioxidant (dithiothreitol) treatment. The developing grains were analyzed for expression of NADPH oxidases, GA biosynthesis genes (OsGA3ox1, OsGA20ox1), ABA catabolism genes (OsABA8'OH1, OsABA8'OH2) and an α-amylase gene (OsAmy3E), endogenous H 2 O 2 content and the grain quality. In grains exposed to heat stress, the expression of NADPH oxidase genes (especially, OsRbohB, OsRbohD, OsRbohF and OsRbohI) and the ROS content increased. Heat stress also increased the expression of OsGA3ox1, OsGA20ox1, OsABA8'OH1, OsABA8'OH2 and OsAmy3E. On the other hand, dithiothreitol treatment reduced the effects of heat stress on the expression of these genes and significantly reduced grain chalkiness induced by heat stress. These results suggest that, similar to cereal seed germination mechanism, ROS produced under heat stress is involved in α-amylase induction in maturating rice grains through GA/ABA metabolism, and consequently caused grain chalkiness. Copyright © 2017 Elsevier GmbH. All rights reserved.

Cadmium accumulation characteristics of low-cadmium rice (Oryza sativa L.) line and F1 hybrids grown in cadmium-contaminated soils.

Science.gov (United States)

Li, Kun; Yu, Haiying; Li, Tingxuan; Chen, Guangdeng; Huang, Fu

2017-07-01

Cadmium (Cd) pollution has threatened severely to food safety and human health. A pot experiment and a field experiment were conducted to investigate the difference of Cd accumulation between rice (Oryza sativa L.) lines and F 1 hybrids in Cd-contaminated soils. The adverse effect on biomass of rice lines was greater than that of F 1 hybrids under Cd treatments in the pot experiment. The variations of Cd concentration among rice cultivars in different organs were smaller in stem and leaf, but larger in root and ear. Average proportion of Cd in root of F 1 hybrids was 1.39, 1.39, and 1.16 times higher than those of rice lines at the treatment of 1, 2, and 4 mg Cd kg -1 soil, respectively. Cd concentrations in ear of F 1 hybrids were significantly lower than rice lines with the reduction from 29.24 to 50.59%. Cd concentrations in brown rice of all F 1 hybrids were less than 0.2 mg kg -1 at 1 mg Cd kg -1 soil, in which Lu98A/YaHui2816, 5406A/YaHui2816, and C268A/YaHui2816 could be screened out as cadmium-safe cultivars (CSCs) for being safe even at 2 mg Cd kg -1 soil. C268A/YaHui2816 showed the lowest Cd concentration in root among F 1 hybrids, while Lu98A/YaHui2816 and 5406A/YaHui2816 showed lower capability of Cd translocation from root to shoot under Cd exposure, which eventually caused the lower Cd accumulation in brown rice. The lower level of Cd translocation contributed to reducing the accumulation of Cd in brown rice had been validated by the field experiment. Thus, Lu98A/YaHui2816, 5406A/YaHui2816, and C268A/YaHui2816 could be considered as potential CSCs to cultivate in Cd-contaminated soils (<2 mg Cd kg -1 soil).

Analysis of nucleotide diversity among alleles of the major bacterial blight resistance gene Xa27 in cultivars of rice (Oryza sativa) and its wild relatives.

Science.gov (United States)

Bimolata, Waikhom; Kumar, Anirudh; Sundaram, Raman Meenakshi; Laha, Gouri Shankar; Qureshi, Insaf Ahmed; Reddy, Gajjala Ashok; Ghazi, Irfan Ahmad

2013-08-01

Xa27 is one of the important R-genes, effective against bacterial blight disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo). Using natural population of Oryza, we analyzed the sequence variation in the functionally important domains of Xa27 across the Oryza species. DNA sequences of Xa27 alleles from 27 rice accessions revealed higher nucleotide diversity among the reported R-genes of rice. Sequence polymorphism analysis revealed synonymous and non-synonymous mutations in addition to a number of InDels in non-coding regions of the gene. High sequence variation was observed in the promoter region including the 5'UTR with 'π' value 0.00916 and 'θ w ' = 0.01785. Comparative analysis of the identified Xa27 alleles with that of IRBB27 and IR24 indicated the operation of both positive selection (Ka/Ks > 1) and neutral selection (Ka/Ks ≈ 0). The genetic distances of alleles of the gene from Oryza nivara were nearer to IRBB27 as compared to IR24. We also found the presence of conserved and null UPT (upregulated by transcriptional activator) box in the isolated alleles. Considerable amino acid polymorphism was localized in the trans-membrane domain for which the functional significance is yet to be elucidated. However, the absence of functional UPT box in all the alleles except IRBB27 suggests the maintenance of single resistant allele throughout the natural population.

Genetic, physiological and modelling approaches towards tolerance to salinity and low nitrogen supply in rice (Oryza sativa L.)

NARCIS (Netherlands)

Manneh, B.

2004-01-01

Keywords:   Rice, O ryza sativa , yield potential, yield gap, salinity, nitrogen supply, agro-ecosystems, Recombinant Inbred Line, genotype × environment interaction, yield components, adaptability, molecular markers, QTL, biomass, leaf area, leaf N, dry matter

All roads lead to weediness: Patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian Oryza.

Science.gov (United States)

Huang, Zhongyun; Young, Nelson D; Reagon, Michael; Hyma, Katie E; Olsen, Kenneth M; Jia, Yulin; Caicedo, Ana L

2017-06-01

Weedy rice (Oryza spp.), a weedy relative of cultivated rice (O. sativa), infests and persists in cultivated rice fields worldwide. Many weedy rice populations have evolved similar adaptive traits, considered part of the 'agricultural weed syndrome', making this an ideal model to study the genetic basis of parallel evolution. Understanding parallel evolution hinges on accurate knowledge of the genetic background and origins of existing weedy rice groups. Using population structure analyses of South Asian and US weedy rice, we show that weeds in South Asia have highly heterogeneous genetic backgrounds, with ancestry contributions both from cultivated varieties (aus and indica) and wild rice. Moreover, the two main groups of weedy rice in the USA, which are also related to aus and indica cultivars, constitute a separate origin from that of Asian weeds. Weedy rice populations in South Asia largely converge on presence of red pericarps and awns and on ease of shattering. Genomewide divergence scans between weed groups from the USA and South Asia, and their crop relatives are enriched for loci involved in metabolic processes. Some candidate genes related to iconic weedy traits and competitiveness are highly divergent between some weed-crop pairs, but are not shared among all weed-crop comparisons. Our results show that weedy rice is an extreme example of recurrent evolution, and suggest that most populations are evolving their weedy traits through different genetic mechanisms. © 2017 John Wiley & Sons Ltd.

Database Description - RMG | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available ase Description General information of database Database name RMG Alternative name ...raki 305-8602, Japan National Institute of Agrobiological Sciences E-mail : Database... classification Nucleotide Sequence Databases Organism Taxonomy Name: Oryza sativa Japonica Group Taxonomy ID: 39947 Database...rnal: Mol Genet Genomics (2002) 268: 434–445 External Links: Original website information Database...available URL of Web services - Need for user registration Not available About This Database Database Descri

Database Description - RED | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available ase Description General information of database Database name RED Alternative name Rice Expression Database...enome Research Unit Shoshi Kikuchi E-mail : Database classification Plant databases - Rice Database classifi...cation Microarray, Gene Expression Organism Taxonomy Name: Oryza sativa Taxonomy ID: 4530 Database descripti... Article title: Rice Expression Database: the gateway to rice functional genomics...nt Science (2002) Dec 7 (12):563-564 External Links: Original website information Database maintenance site

Assessment of genetic diversity of Xanthomonas oryzae pv. oryzae

Institute of Scientific and Technical Information of China (English)

无

2000-01-01

@@Bacterial blight of rice, caused by Xanthomonas oryzae pv. Oryzae(Xoo. ), is one of the major rice diseases in China. Making clear the shift of genetic diversity of the pathogen will provide important information for rice breeding. Strains collected from 11 provinces located in Southern region of the Changjiang River in China were assessed by using inoculation method and IS-PCR(Insertion Sequence-Based Polymerase Chain Reaction) analysis.

Pengaruh Pemberian Kompos Jerami Dan Pupuk Sp-36 Pada Tanah Sulfat Masam Potensial Terhadap Perubahan Sifat Kimia Serta Pertumbuhan Dan Produksi Padi (Oriza Sativa L.)

OpenAIRE

Bhakari, Herlina Eka; Fauzi, Fauzi; Hanum, Hamidah

2013-01-01

The objective of this research was to study the effect of rice straw compost and the application ofphosphorus fertilizer of SP-36 on chemical characteristic of acid sulphate soils, rice growth andproduction (Oryza sativa L). This research was conducted in greenhouse agricultural departments,Universities Northen Sumatera, Medan. This study used a randomized block design factorial, with2 factors : factor 1 : rice straw compost treatment (J) wich consist of : J0 = 0 ton ha-1(0 g straw/pot); J1 =...

Oryza sativa

Indian Academy of Sciences (India)

2014-04-25

Apr 25, 2014 ... Gaps (marked with dashes) have been introduced to ..... Genomi-wide association study of flowering time and grain yield traits in a worldwide ... stages of programmed cell death in maize root cells by using comet assay and ...

Plant STAND P-loop NTPases: a current perspective of genome distribution, evolution, and function : Plant STAND P-loop NTPases: genomic organization, evolution, and molecular mechanism models contribute broadly to plant pathogen defense.

Science.gov (United States)

Arya, Preeti; Acharya, Vishal

2018-02-01

STAND P-loop NTPase is the common weapon used by plant and other organisms from all three kingdoms of life to defend themselves against pathogen invasion. The purpose of this study is to review comprehensively the latest finding of plant STAND P-loop NTPase related to their genomic distribution, evolution, and their mechanism of action. Earlier, the plant STAND P-loop NTPase known to be comprised of only NBS-LRRs/AP-ATPase/NB-ARC ATPase. However, recent finding suggests that genome of early green plants comprised of two types of STAND P-loop NTPases: (1) mammalian NACHT NTPases and (2) NBS-LRRs. Moreover, YchF (unconventional G protein and members of P-loop NTPase) subfamily has been reported to be exceptionally involved in biotic stress (in case of Oryza sativa), thereby a novel member of STAND P-loop NTPase in green plants. The lineage-specific expansion and genome duplication events are responsible for abundance of plant STAND P-loop NTPases; where "moderate tandem and low segmental duplication" trajectory followed in majority of plant species with few exception (equal contribution of tandem and segmental duplication). Since the past decades, systematic research is being investigated into NBS-LRR function supported the direct recognition of pathogen or pathogen effectors by the latest models proposed via 'integrated decoy' or 'sensor domains' model. Here, we integrate the recently published findings together with the previous literature on the genomic distribution, evolution, and distinct models proposed for functional molecular mechanism of plant STAND P-loop NTPases.

AcEST: DK957741 [AcEST

Lifescience Database Archive (English)

Full Text Available yza sativa subs... 148 3e-34 tr|A2Y2K9|A2Y2K9_ORYSI Putative uncharacterized protein OS=Oryza... 148 3e-34 t...70 SALLKIDVPLMFIGDDASPGL 190 >tr|A2Y2K9|A2Y2K9_ORYSI Putative uncharacterized protein OS=Oryza sativa subsp.

Main: 1EQK [RPSD[Archive

Lifescience Database Archive (English)

Full Text Available 1EQK イネ Rice Oryza sativa L. Cysteine Proteinase Inhibitor-I Oryza Sativa Molecule: Oryzacystatin-I; Chai...n: A; Engineered: Yes Hydrolase Inhibitor K.Nagata, N.Kudo, K.Abe, S.Arai, M.Tanokura ...K.Nagata, N.Kudo, K.Abe, S.Arai, M.Tanokura Three-Dimensional Solution Structure Of Oryzacystatin-I, A Cyste

Influences of nitrogen and potassium top dressing on yield and yield ...

African Journals Online (AJOL)

STORAGESEVER

2010-05-03

May 3, 2010 ... (K) top dressing on grain yield and yield components of rice (Oryza sativa cv. Tarrom) and to ... positive reciprocal effect on crops, and was an important approach in ..... dressing fertilization (Figures 2a, b and c), but nitrogen levels of upper fully .... (Brassica napus L.)–rice (Oryza sativa L.) rotation. Plant Soil ...

A rare sugar, d-allose, confers resistance to rice bacterial blight with upregulation of defense-related genes in Oryza sativa.

Science.gov (United States)

Kano, Akihito; Gomi, Kenji; Yamasaki-Kokudo, Yumiko; Satoh, Masaru; Fukumoto, Takeshi; Ohtani, Kouhei; Tajima, Shigeyuki; Izumori, Ken; Tanaka, Keiji; Ishida, Yutaka; Tada, Yasuomi; Nishizawa, Yoko; Akimitsu, Kazuya

2010-01-01

We investigated responses of rice plant to three rare sugars, d-altrose, d-sorbose, and d-allose, due to establishment of mass production methods for these rare sugars. Root growth and shoot growth were significantly inhibited by d-allose but not by the other rare sugars. A large-scale gene expression analysis using a rice microarray revealed that d-allose treatment causes a high upregulation of many defense-related, pathogenesis-related (PR) protein genes in rice. The PR protein genes were not upregulated by other rare sugars. Furthermore, d-allose treatment of rice plants conferred limited resistance of the rice against the pathogen Xanthomonas oryzae pv. oryzae but the other tested sugars did not. These results indicate that d-allose has a growth inhibitory effect but might prove to be a candidate elicitor for reducing disease development in rice.

Root uptake of 14C leached from the low-level radioactive waste for sub-surface disposal with engineered barriers by Oryza sativa L. (2). Distribution of 14C in rice plant on the case using acetic acid as 14C-source

International Nuclear Information System (INIS)

Suzuki, Hiroyuki; Ishii, Nobuyoshi; Tagami, Keiko; Uchida, Shigeo

2012-01-01

The behavior of 14 C from radioactive waste in paddy rice (Oryza sativa L.) at different stages of plant development was studied using the hydroponic and acetic acid as 14 C-source. For 14 C-application, plant root was soaked for 2 hours in a nutrient solution containing 14 C-acetic acid at the vegetative growth stage (Aug. 2, 2007), heading (flowering) stage (Aug. 30, 2007) and milk-ripe stage (Sep. 13, 2007). In final sampling day (Mar. 5, 2008), 0.88 - 1.96% of the applied radioactivity was recovered from whole plant, however, the ratio of recovered radioactivity was not different at the growth stage. The distribution of 14 C absorbed at each stage to each organ was noted to be highest in the submersed root through all the stages. Therefore the mixing of the root residue at the time of plowing would result in enhancement of the soil persistence of 14 C. (author)

Effects of timing and severity of salinity stress on rice (Oryza sativa L.) yield, grain composition, and starch functionality.

Science.gov (United States)

Thitisaksakul, Maysaya; Tananuwong, Kanitha; Shoemaker, Charles F; Chun, Areum; Tanadul, Orn-u-ma; Labavitch, John M; Beckles, Diane M

2015-03-04

The aim of this work was to examine agronomic, compositional, and functional changes in rice (Oryza sativa L. cv. Nipponbare) grains from plants grown under low-to-moderate salinity stress in the greenhouse. Plants were grown in sodium chloride-containing soil (2 or 4 dS/m(2) electrical conductivity), which was imposed 4-weeks after transplant (called Seedling EC2 and EC4) or after the appearance of the anthers (called Anthesis EC2 and EC4). The former simulates field conditions while the latter permits observation of the isolated effect of salt on grain filling processes. Key findings of this study are the following: (i) Plants showed adaptive responses to prolonged salt treatment with no negative effects on grain weight or fertility. Seedling EC2 plants had more panicles and enhanced caryopsis dimensions, while surprisingly, Seedling EC4 plants did not differ from the control group in the agronomic parameters measured. (ii) Grain starch increased in Seedling EC4 (32.6%) and Anthesis EC2 (39%), respectively, suggesting a stimulatory effect of salt on starch accumulation. (iii) The salinity treatment of 2 dS/m(2) was better tolerated at anthesis than the 4 dS/m(2) treatment as the latter led to reduced grain weight (28.8%) and seed fertility (19.4%) and compensatory increases in protein (20.1%) and nitrogen (19.8%) contents. (iv) Although some salinity treatments led to changes in starch content, these did not alter starch fine structure, morphology, or composition. We observed no differences in reducing sugar and amylose content or starch granule size distribution among any of the treatments. The only alterations in starch were limited to small changes in thermal properties and glucan chain distribution, which were only seen in the Anthesis EC4 treatment. This similarity of compositional and functional features was supported by multivariate analysis of all variables measured, which suggested that differences due to treatments were minimal. Overall, this study

Authenticity of rice (Oryza sativa L.) geographical origin based on analysis of C, N, O and S stable isotope ratios: a preliminary case report in Korea, China and Philippine.

Science.gov (United States)

Chung, Ill-Min; Kim, Jae-Kwang; Prabakaran, Mayakrishnan; Yang, Jin-Hee; Kim, Seung-Hyun

2016-05-01

Although rice (Oryza sativa L.) is the third largest food crop, relatively fewer studies have been reported on rice geographical origin based on light element isotope ratios in comparison with other foods such as wine, beef, juice, oil and milk. Therefore this study tries to discriminate the geographical origin of the same rice cultivars grown in different Asian countries using the analysis of C, N, O and S stable isotope ratios and chemometrics. The δ(15) NAIR , δ(18) OVSMOW and δ(34) SVCDT values of brown rice were more markedly influenced by geographical origin than was the δ(13) CVPDB value. In particular, the combination of δ(18) OVSMOW and δ(34) SVCDT more efficiently discriminated rice geographical origin than did the remaining combinations. Principal component analysis (PCA) revealed a clear discrimination between different rice geographical origins but not between rice genotypes. In particular, the first components of PCA discriminated rice cultivated in the Philippines from rice cultivated in China and Korea. The present findings suggest that analysis of the light element isotope composition combined with chemometrics can be potentially applicable to discriminate rice geographical origin and also may provide a valuable insight into the control of improper or fraudulent labeling regarding the geographical origin of rice worldwide. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

Fine de novo sequencing of a fungal genome using only SOLiD short read data: verification on Aspergillus oryzae RIB40.

Directory of Open Access Journals (Sweden)

Myco Umemura

Full Text Available The development of next-generation sequencing (NGS technologies has dramatically increased the throughput, speed, and efficiency of genome sequencing. The short read data generated from NGS platforms, such as SOLiD and Illumina, are quite useful for mapping analysis. However, the SOLiD read data with lengths of <60 bp have been considered to be too short for de novo genome sequencing. Here, to investigate whether de novo sequencing of fungal genomes is possible using only SOLiD short read sequence data, we performed de novo assembly of the Aspergillus oryzae RIB40 genome using only SOLiD read data of 50 bp generated from mate-paired libraries with 2.8- or 1.9-kb insert sizes. The assembled scaffolds showed an N50 value of 1.6 Mb, a 22-fold increase than those obtained using only SOLiD short read in other published reports. In addition, almost 99% of the reference genome was accurately aligned by the assembled scaffold fragments in long lengths. The sequences of secondary metabolite biosynthetic genes and clusters, whose products are of considerable interest in fungal studies due to their potential medicinal, agricultural, and cosmetic properties, were also highly reconstructed in the assembled scaffolds. Based on these findings, we concluded that de novo genome sequencing using only SOLiD short reads is feasible and practical for molecular biological study of fungi. We also investigated the effect of filtering low quality data, library insert size, and k-mer size on the assembly performance, and recommend for the assembly use of mild filtered read data where the N50 was not so degraded and the library has an insert size of ∼2.0 kb, and k-mer size 33.

Dicty_cDB: SHH233 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available SH (Link to library) SHH233 (Link to dictyBase) - - - Contig-U11264-1 - (Link to Or...c08.g1 Strongyloides ratti whole genome shotgun library (SRAAGSS 004) Strongyloides ratti genomic...iginal site) - - SHH233Z 563 - - - - Show SHH233 Library SH (Link to library) Clone ID SHH233 (Link to dicty...631_5( AY458631 |pid:none) Uncultured marine bacterium 159 cl... 84 3e-15 CU92816...86F1 NIH_MGC_58 Homo sapiens cDNA clone IMAGE:4069772 5', mRNA sequence. 46 0.86 1 AP008210 |AP008210.1 Oryza sativa (japonica culti

Bio-protective microbial agents from rhizosphere eco-systems trigger plant defense responses provide protection against sheath blight disease in rice (Oryza sativa L.).

Science.gov (United States)

Singh, Udai B; Malviya, Deepti; Wasiullah; Singh, Shailendra; Pradhan, Jatindra K; Singh, Bhanu P; Roy, Manish; Imram, Mohd; Pathak, Neelam; Baisyal, B M; Rai, Jai P; Sarma, B K; Singh, Rajiv K; Sharma, P K; Kaur, Saman Deep; Manna, M C; Sharma, Sushil K; Sharma, Arun K

2016-11-01

Sheath blight of rice (Oryza sativa L.) caused by Rhizoctonia solani is a major disease and attempts are being made to develop microbe based technologies for biocontrol of this pathogen. However, the mechanisms of biocontrol are not fully understood and still require indepth study in the backdrop of emerging concepts in biological systems. The present investigation was aimed at deciphering the mechanisms of biocontrol of sheath blight of rice employing Pseudomonas fluorescens and Trichoderma harzianum as model agents for biocontrol. Initially 25, 5 and 5 strains of P. fluorescens, T. viride and T. harzianum, respectively, were screened for their biocontrol potential. Out of which, six strains with higher value of percent inhibition of fungal mycelium in dual plate assay were selected. The role of P. fluorescens, T. viride and T. harzianum were investigated in induction and bioaccumulation of natural antioxidants, defence-related biomolecules and other changes in plant which lead not only to growth promotion but also protection from pathogenic stress conditions in rice. The two most promising strains, P. fluorescens PF-08 and T. harzianum UBSTH-501 selected on the basis of in planta evaluation, when applied individually or in combination, significantly enhanced the accumulation of defence-related biomolecules, enzymes and exhibited biocontrol potential against R. solani. A modified/newly developed delivery system was applied for the first time in the experiments involving inoculation of plants with both bioagents, viz. P. fluorescens PF-08 and T. harzianum UBSTH-501. Results suggested that application of P. fluorescens PF-08 and T. harzianum UBSTH-501 alone or in combination, not only helps in control of the disease but also increases plant growth along with reduction in application of toxic chemical pesticides. Copyright © 2016 Elsevier GmbH. All rights reserved.

A model explaining genotypic and ontogenetic variation of leaf photosynthetic rate in rice (Oryza sativa) based on leaf nitrogen content and stomatal conductance.

Science.gov (United States)

Ohsumi, Akihiro; Hamasaki, Akihiro; Nakagawa, Hiroshi; Yoshida, Hiroe; Shiraiwa, Tatsuhiko; Horie, Takeshi

2007-02-01

Identification of physiological traits associated with leaf photosynthetic rate (Pn) is important for improving potential productivity of rice (Oryza sativa). The objectives of this study were to develop a model which can explain genotypic variation and ontogenetic change of Pn in rice under optimal conditions as a function of leaf nitrogen content per unit area (N) and stomatal conductance (g(s)), and to quantify the effects of interaction between N and g(s) on the variation of Pn. Pn, N and g(s) were measured at different developmental stages for the topmost fully expanded leaves in ten rice genotypes with diverse backgrounds grown in pots (2002) and in the field (2001 and 2002). A model of Pn that accounts for carboxylation and CO diffusion processes, and assumes that the ratio of internal conductance to g(s) is constant, was constructed, and its goodness of fit was examined. Considerable genotypic differences in Pn were evident for rice throughout development in both the pot and field experiments. The genotypic variation of Pn was correlated with that of g(s) at a given stage, and the change of Pn with plant development was closely related to the change of N. The variation of g(s) among genotypes was independent of that of N. The model explained well the variation in Pn of the ten genotypes grown under different conditions at different developmental stages. Conclusions The response of Pn to increased N differs with g(s), and the increase in Pn of genotypes with low g(s) is smaller than that of genotypes with high g(s). Therefore, simultaneous improvements of these two traits are essential for an effective breeding of rice genotypes with increased Pn.

Genomic organization of plant aminopropyl transferases.

Science.gov (United States)

Rodríguez-Kessler, Margarita; Delgado-Sánchez, Pablo; Rodríguez-Kessler, Gabriela Theresia; Moriguchi, Takaya; Jiménez-Bremont, Juan Francisco

2010-07-01

Aminopropyl transferases like spermidine synthase (SPDS; EC 2.5.1.16), spermine synthase and thermospermine synthase (SPMS, tSPMS; EC 2.5.1.22) belong to a class of widely distributed enzymes that use decarboxylated S-adenosylmethionine as an aminopropyl donor and putrescine or spermidine as an amino acceptor to form in that order spermidine, spermine or thermospermine. We describe the analysis of plant genomic sequences encoding SPDS, SPMS, tSPMS and PMT (putrescine N-methyltransferase; EC 2.1.1.53). Genome organization (including exon size, gain and loss, as well as intron number, size, loss, retention, placement and phase, and the presence of transposons) of plant aminopropyl transferase genes were compared between the genomic sequences of SPDS, SPMS and tSPMS from Zea mays, Oryza sativa, Malus x domestica, Populus trichocarpa, Arabidopsis thaliana and Physcomitrella patens. In addition, the genomic organization of plant PMT genes, proposed to be derived from SPDS during the evolution of alkaloid metabolism, is illustrated. Herein, a particular conservation and arrangement of exon and intron sequences between plant SPDS, SPMS and PMT genes that clearly differs with that of ACL5 genes, is shown. The possible acquisition of the plant SPMS exon II and, in particular exon XI in the monocot SPMS genes, is a remarkable feature that allows their differentiation from SPDS genes. In accordance with our in silico analysis, functional complementation experiments of the maize ZmSPMS1 enzyme (previously considered to be SPDS) in yeast demonstrated its spermine synthase activity. Another significant aspect is the conservation of intron sequences among SPDS and PMT paralogs. In addition the existence of microsynteny among some SPDS paralogs, especially in P. trichocarpa and A. thaliana, supports duplication events of plant SPDS genes. Based in our analysis, we hypothesize that SPMS genes appeared with the divergence of vascular plants by a processes of gene duplication and the

Determination of supplier-to-supplier and lot-to-lot variability in glycation of recombinant human serum albumin expressed in Oryza sativa.

Directory of Open Access Journals (Sweden)

Grant E Frahm

Full Text Available The use of different expression systems to produce the same recombinant human protein can result in expression-dependent chemical modifications (CMs leading to variability of structure, stability and immunogenicity. Of particular interest are recombinant human proteins expressed in plant-based systems, which have shown particularly high CM variability. In studies presented here, recombinant human serum albumins (rHSA produced in Oryza sativa (Asian rice (OsrHSA from a number of suppliers have been extensively characterized and compared to plasma-derived HSA (pHSA and rHSA expressed in yeast (Pichia pastoris and Saccharomyces cerevisiae. The heterogeneity of each sample was evaluated using size exclusion chromatography (SEC, reversed-phase high-performance liquid chromatography (RP-HPLC and capillary electrophoresis (CE. Modifications of the samples were identified by liquid chromatography-mass spectrometry (LC-MS. The secondary and tertiary structure of the albumin samples were assessed with far U/V circular dichroism spectropolarimetry (far U/V CD and fluorescence spectroscopy, respectively. Far U/V CD and fluorescence analyses were also used to assess thermal stability and drug binding. High molecular weight aggregates in OsrHSA samples were detected with SEC and supplier-to-supplier variability and, more critically, lot-to-lot variability in one manufactures supplied products were identified. LC-MS analysis identified a greater number of hexose-glycated arginine and lysine residues on OsrHSA compared to pHSA or rHSA expressed in yeast. This analysis also showed supplier-to-supplier and lot-to-lot variability in the degree of glycation at specific lysine and arginine residues for OsrHSA. Both the number of glycated residues and the degree of glycation correlated positively with the quantity of non-monomeric species and the chromatographic profiles of the samples. Tertiary structural changes were observed for most OsrHSA samples which

Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study.

Science.gov (United States)

Wang, Quanxiu; Xie, Weibo; Xing, Hongkun; Yan, Ju; Meng, Xiangzhou; Li, Xinglei; Fu, Xiangkui; Xu, Jiuyue; Lian, Xingming; Yu, Sibin; Xing, Yongzhong; Wang, Gongwei

2015-06-01

Chlorophyll content is one of the most important physiological traits as it is closely related to leaf photosynthesis and crop yield potential. So far, few genes have been reported to be involved in natural variation of chlorophyll content in rice (Oryza sativa) and the extent of variations explored is very limited. We conducted a genome-wide association study (GWAS) using a diverse worldwide collection of 529 O. sativa accessions. A total of 46 significant association loci were identified. Three F2 mapping populations with parents selected from the association panel were tested for validation of GWAS signals. We clearly demonstrated that Grain number, plant height, and heading date7 (Ghd7) was a major locus for natural variation of chlorophyll content at the heading stage by combining evidence from near-isogenic lines and transgenic plants. The enhanced expression of Ghd7 decreased the chlorophyll content, mainly through down-regulating the expression of genes involved in the biosynthesis of chlorophyll and chloroplast. In addition, Narrow leaf1 (NAL1) corresponded to one significant association region repeatedly detected over two years. We revealed a high degree of polymorphism in the 5' UTR and four non-synonymous SNPs in the coding region of NAL1, and observed diverse effects of the major haplotypes. The loci or candidate genes identified would help to fine-tune and optimize the antenna size of canopies in rice breeding. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.

Database Description - KOME | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available base Description General information of database Database name KOME Alternative nam... Sciences Plant Genome Research Unit Shoshi Kikuchi E-mail : Database classification Plant databases - Rice ...Organism Taxonomy Name: Oryza sativa Taxonomy ID: 4530 Database description Information about approximately ...Hayashizaki Y, Kikuchi S. Journal: PLoS One. 2007 Nov 28; 2(11):e1235. External Links: Original website information Database...OS) Rice mutant panel database (Tos17) A Database of Plant Cis-acting Regulatory

Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants

OpenAIRE

Pires, Nuno; Dolan, Liam

2009-01-01

Basic helix-loop-helix (bHLH) proteins are a class of transcription factors found throughout eukaryotic organisms. Classification of the complete sets of bHLH proteins in the sequenced genomes of Arabidopsis thaliana and Oryza sativa (rice) has defined the diversity of these proteins among flowering plants. However, the evolutionary relationships of different plant bHLH groups and the diversity of bHLH proteins in more ancestral groups of plants are currently unknown. In this study, we use wh...

Toward integration of genomic selection with crop modelling: the development of an integrated approach to predicting rice heading dates.

Science.gov (United States)

Onogi, Akio; Watanabe, Maya; Mochizuki, Toshihiro; Hayashi, Takeshi; Nakagawa, Hiroshi; Hasegawa, Toshihiro; Iwata, Hiroyoshi

2016-04-01

It is suggested that accuracy in predicting plant phenotypes can be improved by integrating genomic prediction with crop modelling in a single hierarchical model. Accurate prediction of phenotypes is important for plant breeding and management. Although genomic prediction/selection aims to predict phenotypes on the basis of whole-genome marker information, it is often difficult to predict phenotypes of complex traits in diverse environments, because plant phenotypes are often influenced by genotype-environment interaction. A possible remedy is to integrate genomic prediction with crop/ecophysiological modelling, which enables us to predict plant phenotypes using environmental and management information. To this end, in the present study, we developed a novel method for integrating genomic prediction with phenological modelling of Asian rice (Oryza sativa, L.), allowing the heading date of untested genotypes in untested environments to be predicted. The method simultaneously infers the phenological model parameters and whole-genome marker effects on the parameters in a Bayesian framework. By cultivating backcross inbred lines of Koshihikari × Kasalath in nine environments, we evaluated the potential of the proposed method in comparison with conventional genomic prediction, phenological modelling, and two-step methods that applied genomic prediction to phenological model parameters inferred from Nelder-Mead or Markov chain Monte Carlo algorithms. In predicting heading dates of untested lines in untested environments, the proposed and two-step methods tended to provide more accurate predictions than the conventional genomic prediction methods, particularly in environments where phenotypes from environments similar to the target environment were unavailable for training genomic prediction. The proposed method showed greater accuracy in prediction than the two-step methods in all cross-validation schemes tested, suggesting the potential of the integrated approach in

Genomic profiling of rice sperm cell transcripts reveals conserved and distinct elements in the flowering plant male germ lineage.

Science.gov (United States)

Russell, Scott D; Gou, Xiaoping; Wong, Chui E; Wang, Xinkun; Yuan, Tong; Wei, Xiaoping; Bhalla, Prem L; Singh, Mohan B

2012-08-01

Genomic assay of sperm cell RNA provides insight into functional control, modes of regulation, and contributions of male gametes to double fertilization. Sperm cells of rice (Oryza sativa) were isolated from field-grown, disease-free plants and RNA was processed for use with the full-genome Affymetrix microarray. Comparison with Gene Expression Omnibus (GEO) reference arrays confirmed expressionally distinct gene profiles. A total of 10,732 distinct gene sequences were detected in sperm cells, of which 1668 were not expressed in pollen or seedlings. Pathways enriched in male germ cells included ubiquitin-mediated pathways, pathways involved in chromatin modeling including histones, histone modification and nonhistone epigenetic modification, and pathways related to RNAi and gene silencing. Genome-wide expression patterns in angiosperm sperm cells indicate common and divergent themes in the male germline that appear to be largely self-regulating through highly up-regulated chromatin modification pathways. A core of highly conserved genes appear common to all sperm cells, but evidence is still emerging that another class of genes have diverged in expression between monocots and dicots since their divergence. Sperm cell transcripts present at fusion may be transmitted through plasmogamy during double fertilization to effect immediate post-fertilization expression of early embryo and (or) endosperm development. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

sativa L.) Cultivars

African Journals Online (AJOL)

Abstract. Ten rice cultivars from the International Rice Germplasm Centre originating from Bangladesh were analysedfor the~r genetics of resistance to bacterial blight. The test cultivars were selected on the basis of their high level ofresistance to races IV & VI ofXanthomonas oryzae pv. oryzae. The mode ofinheri- tance was ...