Survey of rice blast race identity for blast resistance gene identification in the USA and Puerto Rico

USDA-ARS?s Scientific Manuscript database

Rice blast disease is a significant threat to stable rice production in the USA and worldwide. The major resistance gene (Pi-ta) located within a cluster of resistance genes on rice chromosome 12 has been demonstrated to confer resistance to the rice blast disease. Katy, a rice cultivar released in ...

Identification and DUS Testing of Rice Varieties through Microsatellite Markers

PubMed Central

Pourabed, Ehsan; Jazayeri Noushabadi, Mohammad Reza; Jamali, Seyed Hossein; Moheb Alipour, Naser; Zareyan, Abbas; Sadeghi, Leila

2015-01-01

Identification and registration of new rice varieties are very important to be free from environmental effects and using molecular markers that are more reliable. The objectives of this study were, first, the identification and distinction of 40 rice varieties consisting of local varieties of Iran, improved varieties, and IRRI varieties using PIC, and discriminating power, second, cluster analysis based on Dice similarity coefficient and UPGMA algorithm, and, third, determining the ability of microsatellite markers to separate varieties utilizing the best combination of markers. For this research, 12 microsatellite markers were used. In total, 83 polymorphic alleles (6.91 alleles per locus) were found. In addition, the variation of PIC was calculated from 0.52 to 0.9. The results of cluster analysis showed the complete discrimination of varieties from each other except for IR58025A and IR58025B. Moreover, cluster analysis could detect the most of the improved varieties from local varieties. Based on the best combination of markers analysis, five pair primers together have shown the same results of all markers for detection among all varieties. Considering the results of this research, we can propose that microsatellite markers can be used as a complementary tool for morphological characteristics in DUS tests. PMID:25755666

Single-wavelength based Thai jasmine rice identification with polynomial fitting function and neural network analysis

NASA Astrophysics Data System (ADS)

Suwansukho, Kajpanya; Sumriddetchkajorn, Sarun; Buranasiri, Prathan

2013-06-01

We previously showed that a combination of image thresholding, chain coding, elliptic Fourier descriptors, and artificial neural network analysis provided a low false acceptance rate (FAR) and a false rejection rate (FRR) of 11.0% and 19.0%, respectively, in identify Thai jasmine rice from three unwanted rice varieties. In this work, we highlight that only a polynomial function fitting on the determined chain code and the neural network analysis are highly sufficient in obtaining a very low FAR of < 3.0% and a very low 0.3% FRR for the separation of Thai jasmine rice from Chainat 1 (CNT1), Prathumtani 1 (PTT1), and Hom-Pitsanulok (HPSL) rice varieties. With this proposed approach, the analytical time is tremendously suppressed from 4,250 seconds down to 2 seconds, implying extremely high potential in practical deployment.

Identification of gibberellin acid-responsive proteins in rice leaf sheath using proteomics.

PubMed

Gu, Jia-Yu; Wang, Ye; Zhang, Xu; Zhang, Shi-Hua; Gao, Yin; An, Cheng-Cai

2010-06-01

The phytohormone gibberellin acid (GA) controls many aspects of plant development. In this study, we identified proteins that are differentially expressed between the rice (Oryza sativa L.) GA-deficient cultivar, Aijiaonante, and its parental line, Nante. Proteins were extracted from rice leaf sheath and examined by 2DGE. Among more than 1200 protein spots reproducibly detected on each gel, 29 were found to be highly up-regulated by GAs in Nante, and 6 were down-regulated by GAs in Aijiaonante. These 35 proteins were identified by MALDI-TOF MS and were classified into three groups based on their putative function in metabolism, stress/defense processes and signal transduction. These data suggest that metabolic pathways are the main target of regulation by GAs during rice development. Our results provide new information about the involvement of GAs in rice development.

Chemometrical characterization of four italian rice varieties based on genetic and chemical analyses.

PubMed

Brandolini, Vincenzo; Coïsson, Jean Daniel; Tedeschi, Paola; Barile, Daniela; Cereti, Elisabetta; Maietti, Annalisa; Vecchiati, Giorgio; Martelli, Aldo; Arlorio, Marco

2006-12-27

This paper describes a method for achieving qualitative identification of four rice varieties from two different Italian regions. To estimate the presence of genetic diversity among the four rice varieties, we used polymerase chain reaction-randomly amplified polymorphic DNA (PCR-RAPD) markers, and to elucidate whether a relationship exists between the ground and the specific characteristics of the product, we studied proximate composition, fatty acid composition, mineral content, and total antioxidant capacity. Using principal component analysis on genomic and compositional data, we were able to classify rice samples according to their variety and their district of production. This work also examined the discrimination ability of different parameters. It was found that genomic data give the best discrimination based on varieties, indicating that RAPD assays could be useful in discriminating among closely related species, while compositional analyses do not depend on the genetic characters only but are related to the production area.

Identification of genetic loci underlying the kernel fissure-resistance exhibited by 'cypress' and 'saber'

USDA-ARS?s Scientific Manuscript database

The economic value of broken rice is about half that of whole milled rice, so one goal of producers, millers, and rice breeders is to reduce broken grains that result from the dehusking and milling processes One of the primary causes of rice breakage is fissuring, or cracking, of the rice before it ...

Evapotranspiration measurement and modeling in Mid-South irrigated rice

USDA-ARS?s Scientific Manuscript database

Nearly 75% of US rice is grown in the humid mid-South. Rice requires more water to produce than other crops (corn, soybean, and cotton). The identification of rice evapotranspiration and irrigation demand is paramount to understand regional water use and water allocation. Drill-seeded, commercial si...

Identification of broad spectrum rice blast resistance genes with IRRI Rice monogenic lines

USDA-ARS?s Scientific Manuscript database

Rice blast disease, caused by the fungus Magnaporthe oryzae, is the most destructive rice disease worldwide. This disease is managed with a combination of the use of resistant cultivars, application of fungicides, and improved cultural practices. Among them, the use of resistant cultivars is the mos...

Characterization and quantification of γ-oryzanol in grains of 16 Korean rice varieties.

PubMed

Kim, Heon Woong; Kim, Jung Bong; Cho, Soo-Muk; Cho, Il Kyu; Li, Qing X; Jang, Hwan-Hee; Lee, Sung-Hyeon; Lee, Young-Min; Hwang, Kyung-A

2015-03-01

γ-Oryzanol, a mixture of ferulic acid esters of triterpene alcohols and sterols, is a nutritionally important group of rice secondary metabolites. A library of 27 γ-oryzanol was assembled from existing data and used to assist identification and quantification of γ-oryzanol isolated from 16 Korean rice varieties (11 white and 5 pigmented). γ-Oryzanol was analyzed with liquid chromatography with diode array detection and electrospray ionization mass spectrometry. Nineteen different γ-oryzanol were observed and identified as stigmasterol, campesterol and sitosterol or common and hydroxylated triterpene alcohols. In the 16 varieties, the total γ-oryzanol content averaged 43.8 mg/100 g (range, 26.7-61.6 mg/100 g), which Josaengheugchal exhibited the highest level (61.6 mg/100 g). The Korean rice varieties were classified based on qualitative and quantitative γ-oryzanol data by multivariate statistical analysis. Clusters of specialty rice varieties exhibited higher γ-oryzanol levels than those of common rice varieties.

IDENTIFICATION OF DIMETHYLTHIOARSINIC ACID BY ICP-MS AND IC-ESI-MS/MS IN RICE SAMPLES

EPA Science Inventory

Recently, sulfur analogs of well known arsenicals have been identified in biological and dietary matrices. In this presentation, the detection and identification of dimethylthioarsinic acid (DMTA) will be reported in rice samples after an enzymatic extraction. The enzymatic ext...

Proteomics characterization of different bran proteins between aromatic and nonaromatic rice (Oryza sativa L. ssp. indica).

PubMed

Trisiriroj, Arunee; Jeyachok, Narumon; Chen, Shui-Tein

2004-07-01

Proteomic approach is applied for the analysis of seed brans of 14 rice varieties (Oryza sativa L. ssp. indica) which can classify to five aromatic rice and nine nonaromatic rice. The two-dimensional electrophoresis (2-DE) protein patterns for 14 rice varieties were similar within pH ranges of 3-10 and 4-7. To characterize aromatic group-specific proteins, we compared 2-D gels of aromatic rice to nonaromatic rice using PDQUEST image analysis. Four out of six differential spots were identified as hypothetical proteins, but one (SSP 7003) was identified by matrix assisted laser desoption/ionization-quardrupole-time of fight (MALDI-Q-TOF) as prolamin with three matching peptides based on NCBI database. Prolamin is a class of storage proteins with three different polypeptides of 10, 13, and 16 kDa. Spot SSP7003 was identified as a 13 kDa polypeptide of prolamin by combination of mass spectroscopy and N-terminal sequence analyses. In contrast, one sulfur-rich 16 kDa polypeptide of prolamin was found in extremely high intensity in brans of deep-water rice compared to nondeep-water rice. Our results suggest that proteomics is a powerful step to open the way for the identification of rice varieties.

Characterization of rice blast resistance gene Pi61(t) in rice germplasm

USDA-ARS?s Scientific Manuscript database

Identification of resistance (R) genes to races of Magnaporthe oryzae in rice germplasm is essential for the development of rice cultivars with long lasting blast resistance. In the present study, one major quantitative trait locus, qPi93-3, was fine mapped using a recombinant inbred line (RIL), F8 ...

The distribution of the invasive pest, rice water weevil Lissorhoptrus oryzophilus (Coleoptera: Curculionidae), is expanding in Europe: First record in the Balkans, confirmed by CO1 DNA barcoding

USDA-ARS?s Scientific Manuscript database

This is the first report of the invasive rice pest, rice water weevil (Lissorhoptrus oryzophilus Kuschel) in the Balkans. Adult specimens were collected in flooded rice fields in the principal rice-growing region of Central Macedonia, Greece during July-August, 2016. Morphological identification was...

Identification of quantitative trait loci (QTLs) responsible for sheath blight resistance in rice using recombinant inbred line population of Lemont X Jasmine 85

USDA-ARS?s Scientific Manuscript database

Rice sheath blight (RSB) caused by the soil borne pathogen Rhizoctonia solani, is one of the most destructive diseases of rice, causing severe losses in rice yield and quality annually. The major gene (s) governing the resistance to RSB have not been found in cultivated rice worldwide. However, ri...

Impact of SNPs on Protein Phosphorylation Status in Rice (Oryza sativa L.).

PubMed

Lin, Shoukai; Chen, Lijuan; Tao, Huan; Huang, Jian; Xu, Chaoqun; Li, Lin; Ma, Shiwei; Tian, Tian; Liu, Wei; Xue, Lichun; Ai, Yufang; He, Huaqin

2016-11-11

Single nucleotide polymorphisms (SNPs) are widely used in functional genomics and genetics research work. The high-quality sequence of rice genome has provided a genome-wide SNP and proteome resource. However, the impact of SNPs on protein phosphorylation status in rice is not fully understood. In this paper, we firstly updated rice SNP resource based on the new rice genome Ver. 7.0, then systematically analyzed the potential impact of Non-synonymous SNPs (nsSNPs) on the protein phosphorylation status. There were 3,897,312 SNPs in Ver. 7.0 rice genome, among which 9.9% was nsSNPs. Whilst, a total 2,508,261 phosphorylated sites were predicted in rice proteome. Interestingly, we observed that 150,197 (39.1%) nsSNPs could influence protein phosphorylation status, among which 52.2% might induce changes of protein kinase (PK) types for adjacent phosphorylation sites. We constructed a database, SNP_rice, to deposit the updated rice SNP resource and phosSNPs information. It was freely available to academic researchers at http://bioinformatics.fafu.edu.cn. As a case study, we detected five nsSNPs that potentially influenced heterotrimeric G proteins phosphorylation status in rice, indicating that genetic polymorphisms showed impact on the signal transduction by influencing the phosphorylation status of heterotrimeric G proteins. The results in this work could be a useful resource for future experimental identification and provide interesting information for better rice breeding.

Quantification of vitamin E and gamma-oryzanol components in rice germ and bran.

PubMed

Yu, Shanggong; Nehus, Zachary T; Badger, Thomas M; Fang, Nianbai

2007-09-05

Rice bran is a rich natural source of vitamin E and gamma-oryzanol, which have been extensively studied and reported to possess important health-promoting properties. However, commercial rice bran is a mixture of rice bran and germ, and profiles of vitamin E and gamma-oryzanol components in these two different materials are less well-studied. In the current study, vitamin E and gamma-oryzanol components in rice bran and germ were analyzed by liquid chromatography/mass spectrometry/mass spectrometry. The components were identified by electrospray ionization mass spectrometry (ESI-MS) with both positive- and negative-ion modes. Both deprotonated molecular ion [M - H](-) and protonated molecular ion [M + H](+) found as the base peaks in spectra of vitamin E components made ESI-MS a valuable analytic method in detecting vitamin E compounds, especially when they were at very low levels in samples. Ultraviolet absorption was used for quantification of vitamin E and gamma-oryzanol components. While the level of vitamin E in rice germ was 5 times greater than in rice bran, the level of gamma-oryzanol in rice germ was 5 times lower than in rice bran. Also, the major vitamin E component was alpha-tocopherol in rice germ and gamma-tocotrienol in rice bran. These data suggest that rice bran and germ have significantly different profiles of vitamin E and gamma-oryzanol components. The method enables rapid and direct on-line identification and quantification of the vitamin E and gamma-oryzanol components in rice bran and germ.

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

PubMed

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.

Classification of rice grain varieties arranged in scattered and heap fashion using image processing

NASA Astrophysics Data System (ADS)

Bhat, Sudhanva; Panat, Sreedath; N, Arunachalam

2017-03-01

Inspection and classification of food grains is a manual process in many of the food grain processing industries. Automation of such a process is going to be beneficial for industries facing shortage of skilled workforce. Machine Vision techniques are some of the popular approaches for developing such automations. Most of the existing works on the topic deal with identification of the rice variety by analyzing images of well separated and isolated rice grains from which a lot of geometrical features can be extracted. This paper proposes techniques to estimate geometrical parameters from the images of scattered as well as heaped rice grains where the grain boundaries are not clearly identifiable. A methodology based on convexity is proposed to separate touching rice grains in the scattered rice grain images and get their geometrical parameters. And in case of heaped arrangement a Pixel-Distance Contribution Function is defined and is used to get points inside rice grains and then to find the boundary points of rice grains. These points are fit with the equation of an ellipse to estimate their lengths and breadths. The proposed techniques are applied on images of scattered and heaped rice grains of different varieties. It is shown that each variety gives a unique set of results.

Identification and expression analysis of CYS-A1, CYS-C1, NIT4 genes in rice seedlings exposed to cyanide.

PubMed

Yu, Xiao-Zhang; Lin, Yu-Juan; Lu, Chun-Jiao; Zhang, Xue-Hong

2017-09-01

Involvement of genes (CYS-A1, CYS-C1 and NIT4) encoded with cysteine synthase, β-cyanoalanine synthase, nitrilase and cyanide metabolisms are evident in Arabidopsis. In the present study, identifications of CYS-A1, CYS-C1 and NIT4, predictions of conserved motifs, and constructions of phylogenetic relationships, based on their amino acid sequences in rice, were conducted. In order to elucidate the transcriptional responses of these cyanide-degrading genes, two candidate homologues were selected for each gene to test their expression changes upon exposure to exogenous KCN in rice seedlings using RT-PCR. Results showed that all selected candidate homologous genes were differentially expressed at different exposure points in roots and shoots of rice seedlings, suggesting their distinct roles during cyanide assimilation. Both candidate homologues for CYS-A1 constantly exhibited more abundant transcripts in comparison to control. However, only one candidate homologue for CYS-C1 and NIT4 showed a remarkable up-regulation during KCN exposure. Analysis of both tissue and solution cyanide indicated that rice seedlings were quickly able to metabolize exogenous KCN with minor accumulation in plant tissues. In conclusion, significant up-regulation of CYS-A1 suggested that the endogenous pool of cysteine catalyzed by cysteine synthase does not restrict the conversion of exogenous KCN into cyanoalanine through the β-cyanoalanine pathway. However, insufficient responses of the transcription level of NIT4 suggested that NIT enzyme may be a limiting factor for cyanoalanine assimilation by rice seedlings.

Identification of large masses of citrus fruit and rice fields in eastern Spain

NASA Technical Reports Server (NTRS)

Desagredo, F. L.; Salinas, F. G.

1973-01-01

ERTS-1 imagery has been successfully used for the identification of large areas of citrus groves and rice fields in the Valencia region of Eastern Spain. Results are encouraging and will facilitate the elaboration of a land use map with a fair degree of definition once methods prove to be fully operational.

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

PubMed

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.

Current advance methods for the identification of blast resistance genes in rice.

PubMed

Tanweer, Fatah A; Rafii, Mohd Y; Sijam, Kamaruzaman; Rahim, Harun A; Ahmed, Fahim; Latif, Mohammad A

2015-05-01

Rice blast caused by Magnaporthe oryzae is one of the most devastating diseases of rice around the world and crop losses due to blast are considerably high. Many blast resistant rice varieties have been developed by classical plant breeding and adopted by farmers in various rice-growing countries. However, the variability in the pathogenicity of the blast fungus according to environment made blast disease a major concern for farmers, which remains a threat to the rice industry. With the utilization of molecular techniques, plant breeders have improved rice production systems and minimized yield losses. In this article, we have summarized the current advanced molecular techniques used for controlling blast disease. With the advent of new technologies like marker-assisted selection, molecular mapping, map-based cloning, marker-assisted backcrossing and allele mining, breeders have identified more than 100 Pi loci and 350 QTL in rice genome responsible for blast disease. These Pi genes and QTLs can be introgressed into a blast-susceptible cultivar through marker-assisted backcross breeding. These molecular techniques provide timesaving, environment friendly and labour-cost-saving ways to control blast disease. The knowledge of host-plant interactions in the frame of blast disease will lead to develop resistant varieties in the future. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Genetic analysis of genetic basis of a physiological disorder "straighthead’’ in rice (Oryza sativa L.)

USDA-ARS?s Scientific Manuscript database

Straighthead is a physiological disorder in rice that causes yield losses and is a serious threat to rice production worldwide. Identification of QTL conferring resistance will help develop resistant cultivars for straighthead control. We conducted linkage mapping to identify QTL involved with strai...

Genomics-based precision breeding approaches to improve drought tolerance in rice.

PubMed

Swamy, B P Mallikarjuna; Kumar, Arvind

2013-12-01

Rice (Oryza sativa L.), the major staple food crop of the world, faces a severe threat from widespread drought. The development of drought-tolerant rice varieties is considered a feasible option to counteract drought stress. The screening of rice germplasm under drought and its characterization at the morphological, genetic, and molecular levels revealed the existence of genetic variation for drought tolerance within the rice gene pool. The improvements made in managed drought screening and selection for grain yield under drought have significantly contributed to progress in drought breeding programs. The availability of rice genome sequence information, genome-wide molecular markers, and low-cost genotyping platforms now makes it possible to routinely apply marker-assisted breeding approaches to improve grain yield under drought. Grain yield QTLs with a large and consistent effect under drought have been indentified and successfully pyramided in popular rice mega-varieties. Various rice functional genomics resources, databases, tools, and recent advances in "-omics" are facilitating the characterization of genes and pathways involved in drought tolerance, providing the basis for candidate gene identification and allele mining. The transgenic approach is successful in generating drought tolerance in rice under controlled conditions, but field-level testing is necessary. Genomics-assisted drought breeding approaches hold great promise, but a well-planned integration with standardized phenotyping is highly essential to exploit their full potential. Copyright © 2013 Elsevier Inc. All rights reserved.

Identification and characterization of filamentous fungi isolated from fermentation starters for Hong Qu glutinous rice wine brewing.

PubMed

Lv, Xu-Cong; Huang, Zhi-Qing; Zhang, Wen; Rao, Ping-Fan; Ni, Li

2012-01-01

Hong Qu glutinous rice wine is one of the most popular traditional rice wines in China. Traditionally, this wine is brewed from glutinous rice with the addition of wine fermentation starters (Hong Qu (also called red yeast rice) and White Qu). The objective of this study was to investigate the variability of filamentous fungi associated with traditional fermentation starters through a traditional culture-dependent method and a molecular identification approach. In this study, forty-three filamentous fungi were separated by traditional culture-dependent means (macro- and microscopic characteristics) from 10 fermentation starters and classified into 16 different species based on morphological examination and the internal transcribed spacer (ITS) sequences analysis. It was observed that the genus Aspergillus had the highest number (14 isolates) of isolates followed by Rhizopus (11 isolates), Monascus (5 isolates) and Penicillium (4 isolates). The species R. oryzae, A. niger, A. flavus and M. purpureus were frequently found in wine starter samples, among which R. oryzae was the most frequent species. The enzyme-producing properties (glucoamylase, α-amylase and protease) of all fungal isolates from different starters were also evaluated. A. flavus, R. oryzae and M. purpureus were found to be better glucoamylase producers. A. flavus, R. oryzae and A.oryzae exhibited higher activity of α-amylase. A. flavus and A. oryzae had higher protease activity. However, some fungal isolates of the same species exhibited a significant variability in the production levels for all determined enzyme activity. This study is the first to identify filamentous fungi associated with the starter of Hong Qu glutinous rice wine using both traditional and molecular methods. The results enrich our knowledge of liquor-related micro-organisms, and can be used to promote the development of the traditional fermentation technology.

SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure

PubMed Central

2012-01-01

Background Single nucleotide polymorphism (SNP) validation and large-scale genotyping are required to maximize the use of DNA sequence variation and determine the functional relevance of candidate genes for complex stress tolerance traits through genetic association in rice. We used the bead array platform-based Illumina GoldenGate assay to validate and genotype SNPs in a select set of stress-responsive genes to understand their functional relevance and study the population structure in rice. Results Of the 384 putative SNPs assayed, we successfully validated and genotyped 362 (94.3%). Of these 325 (84.6%) showed polymorphism among the 91 rice genotypes examined. Physical distribution, degree of allele sharing, admixtures and introgression, and amino acid replacement of SNPs in 263 abiotic and 62 biotic stress-responsive genes provided clues for identification and targeted mapping of trait-associated genomic regions. We assessed the functional and adaptive significance of validated SNPs in a set of contrasting drought tolerant upland and sensitive lowland rice genotypes by correlating their allelic variation with amino acid sequence alterations in catalytic domains and three-dimensional secondary protein structure encoded by stress-responsive genes. We found a strong genetic association among SNPs in the nine stress-responsive genes with upland and lowland ecological adaptation. Higher nucleotide diversity was observed in indica accessions compared with other rice sub-populations based on different population genetic parameters. The inferred ancestry of 16% among rice genotypes was derived from admixed populations with the maximum between upland aus and wild Oryza species. Conclusions SNPs validated in biotic and abiotic stress-responsive rice genes can be used in association analyses to identify candidate genes and develop functional markers for stress tolerance in rice. PMID:22921105

Marker development for rice blast resistance gene Pi66(t) and application in USDA rice mini-core collection

USDA-ARS?s Scientific Manuscript database

Molecular markers are useful for the identification of critical genes controlling agricultural traits of interest in crop germplasm and for the utilization of these genes in crop improvement using marker assisted selection (MAS). The improvement of blast disease resistance of rice varieties is one o...

Identification of major blast resistance genes in the southern US

USDA-ARS?s Scientific Manuscript database

Resistance (R) genes in rice play important roles in preventing infections of rice blast fungus, Magnaporthe oryzae. In order to identify more R genes for different rice growing areas in the Southern US, an extensive field survey of the blast fungus was performed from 2012 to 2013. A total of 500 is...

Large scale germplasm screening for identification of novel rice blast resistance sources

PubMed Central

Vasudevan, Kumar; Vera Cruz, Casiana M.; Gruissem, Wilhelm; Bhullar, Navreet K.

2014-01-01

Rice is a major cereal crop that contributes significantly to global food security. Biotic stresses, including the rice blast fungus, cause severe yield losses that significantly impair rice production worldwide. The rapid genetic evolution of the fungus often overcomes the resistance conferred by major genes after a few years of intensive agricultural use. Therefore, resistance breeding requires continuous efforts of enriching the reservoir of resistance genes/alleles to effectively tackle the disease. Seed banks represent a rich stock of genetic diversity, however, they are still under-explored for identifying novel genes and/or their functional alleles. We conducted a large-scale screen for new rice blast resistance sources in 4246 geographically diverse rice accessions originating from 13 major rice-growing countries. The accessions were selected from a total collection of over 120,000 accessions based on their annotated rice blast resistance information in the International Rice Genebank. A two-step resistance screening protocol was used involving natural infection in a rice uniform blast nursery and subsequent artificial infections with five single rice blast isolates. The nursery-resistant accessions showed varied disease responses when infected with single isolates, suggesting the presence of diverse resistance genes/alleles in this accession collection. In addition, 289 accessions showed broad-spectrum resistance against all five single rice blast isolates. The selected resistant accessions were genotyped for the presence of the Pi2 resistance gene, thereby identifying potential accessions for isolation of allelic variants of this blast resistance gene. Together, the accession collection with broad spectrum and isolate specific blast resistance represent the core material for isolation of previously unknown blast resistance genes and/or their allelic variants that can be deployed in rice breeding programs. PMID:25324853

Identification of rice supply chain risk to DKI Jakarta through Cipinang primary rice market

NASA Astrophysics Data System (ADS)

Sugiarto, D.; Ariwibowo, A.; Mardianto, I.; Surjasa, D.

2018-01-01

This paper identifies several sources of risks in DKI Jakarta rice supply chain that through Cipinang Primary Rice Market (CPRM). Secondary data from several sources were collected and analysed using pareto chart and time series analysis. Based on the pareto analysis, it was known that there was a change in the order of suppliers whereas in 2011, 80% of the supply came only from Cirebon, Karawang and Bandung (West Java Province). While in 2015 the main source of supply changed to Cirebon, Central Java and Karawang. Linear trend equation using decomposition model for Cirebon and Karawang showed trend of decreasing monthly supply while Central Java had a positive trend. Harvest area of wetland paddy in Cirebon and Karawang showed a negative trend in the last 6 years. The data also showed that West Java Province was the province with the largest rice crop area affected by plant organism attack and drought disaster in 2015. DKI Jakarta had several potential supply chain risks from rice supply, drought risk and pests risk where the province of West Java, which previously could become a major supplier began to require supply assistance from other provinces, especially Central Java.

Secretome of Aspergillus oryzae in Shaoxing rice wine koji.

PubMed

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.

Identification of conserved drought stress responsive gene-network across tissues and developmental stages in rice.

PubMed

Smita, Shuchi; Katiyar, Amit; Pandey, Dev Mani; Chinnusamy, Viswanathan; Archak, Sunil; Bansal, Kailash Chander

2013-01-01

Identification of genes that are coexpressed across various tissues and environmental stresses is biologically interesting, since they may play coordinated role in similar biological processes. Genes with correlated expression patterns can be best identified by using coexpression network analysis of transcriptome data. In the present study, we analyzed the temporal-spatial coordination of gene expression in root, leaf and panicle of rice under drought stress and constructed network using WGCNA and Cytoscape. Total of 2199 differentially expressed genes (DEGs) were identified in at least three or more tissues, wherein 88 genes have coordinated expression profile among all the six tissues under drought stress. These 88 highly coordinated genes were further subjected to module identification in the coexpression network. Based on chief topological properties we identified 18 hub genes such as ABC transporter, ATP-binding protein, dehydrin, protein phosphatase 2C, LTPL153 - Protease inhibitor, phosphatidylethanolaminebinding protein, lactose permease-related, NADP-dependent malic enzyme, etc. Motif enrichment analysis showed the presence of ABRE cis-elements in the promoters of > 62% of the coordinately expressed genes. Our results suggest that drought stress mediated upregulated gene expression was coordinated through an ABA-dependent signaling pathway across tissues, at least for the subset of genes identified in this study, while down regulation appears to be regulated by tissue specific pathways in rice.

[Rice endogenous nitrogen fixing and growth promoting bacterium Herbaspirillum seropedicae DX35].

PubMed

Wang, Xiucheng; Cao, Yanhua; Tang, Xue; Ma, Xiaotong; Gao, Jusheng; Zhang, Xiaoxia

2014-03-04

To screen efficient nitrogen fixation endophytes from rice and to analyze their growth-promoting properties. We isolated strains from the roots of rice in the field where it has a rice-rice-green manure rotation system for 30 years. Efficient strains were screened by acetylene reduction assay. Phylogenetic analysis is based on 16S rRNA gene, nifH gene and the composition of fatty acid. In addition, we also detected the ability of indole acetic acid secretion through the Salkowski colorimetric method, measured the production of siderophore through the blue plate assay and detected phosphate solubilization, to analyze the growth-promoting properties. A total of 48 strains were isolated, in which DX35 has the highest nitrogenase activity. It belongs to Herbaspirillum seropedicae after identification. Its nitrogenase activity (181.21 nmol C2H4/(mg protein x h)) was 10 times as much as the reference strain Azotobacter chroococcum ACCC10006. In addition, it also can secrete siderophore and solubilize phosphorus. Strain DX35, belonging to Herbaspirillum seropedicae, is an efficient nitrogen fixation endophytes.

Identification of genes and physiological factors that reduce accumulation of arsenic in rice grain

USDA-ARS?s Scientific Manuscript database

The arsenic (As) levels in rice grains and food products can reach toxic levels when produced under certain growing conditions. The World Health Organization (WHO) recently set a CODEX limit of 0.2 ppm inorganic As in milled white rice, and lower limits may be set for baby food products. While studi...

A preliminary survey on the occurrence of mycotoxigenic fungi and mycotoxins contaminating red rice at consumer level in Selangor, Malaysia.

PubMed

Samsudin, Nik Iskandar Putra; Abdullah, Noorlidah

2013-05-01

Red rice is a fermented product of Monascus spp. It is widely consumed by Malaysian Chinese who believe in its pharmacological properties. The traditional method of red rice preparation disregards safety regulation and renders red rice susceptible to fungal infestation and mycotoxin contamination. A preliminary study was undertaken aiming to determine the occurrence of mycotoxigenic fungi and mycotoxins contamination on red rice at consumer level in Selangor, Malaysia. Fifty red rice samples were obtained and subjected to fungal isolation, enumeration, and identification. Citrinin, aflatoxin, and ochratoxin-A were quantitated by ELISA based on the presence of predominant causal fungi. Fungal loads of 1.4 × 10(4) to 2.1 × 10(6) CFU/g exceeded Malaysian limits. Monascus spp. as starter fungi were present in 50 samples (100%), followed by Penicillium chrysogenum (62%), Aspergillus niger (54%), and Aspergillus flavus (44%). Citrinin was present in 100% samples (0.23-20.65 mg/kg), aflatoxin in 92% samples (0.61-77.33 μg/kg) and Ochratoxin-A in 100% samples (0.23-2.48 μg/kg); 100% citrinin and 76.09% aflatoxin exceeded Malaysian limits. The presence of mycotoxigenic fungi served as an indicator of mycotoxins contamination and might imply improper production, handling, transportation, and storage of red rice. Further confirmatory analysis (e.g., HPLC) is required to verify the mycotoxins level in red rice samples and to validate the safety status of red rice.

Molecular identification of Aspergillus and Eurotium species isolated from rice and their toxin-producing ability.

PubMed

Yazdani, D; Zainal Abidin, M A; Tan, Y H; Kamaruzaman, S

2011-01-01

Thirty milled rice samples were collected from retailers in 4 provinces of Malaysia. These samples were evaluated for Aspergillus spp. infection by direct plating on malt extract salt agar (MESA). All Aspergillus holomorphs were isolated and identified using nucleotide sequences of ITS 1 and ITS 2 of rDNA. Five anamorphs (Aspergillus flavus, A. oryzae, A. tamarii, A. fumigatus and A. niger) and 5 teleomorphs (Eurotium rubrum, E. amstelodami, E. chevalieri, E. cristatum and E. tonophilum) were identified. The PCR-sequencing based technique for sequences of ITS 1 and ITS 2 is a fast technique for identification of Aspergillus and Eurotium species, although it doesn't work flawlessly for differentiation of Eurotium species. All Aspergillus and Eurotium isolates were screened for their ability to produce aflatoxin and ochratoxin A (OTA) by HPLC and TLC techniques. Only A. flavus isolate UPM 89 was able to produce aflatoxins B1 and B2.

A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate.

PubMed

Takai, Toshiyuki; Adachi, Shunsuke; Taguchi-Shiobara, Fumio; Sanoh-Arai, Yumiko; Iwasawa, Norio; Yoshinaga, Satoshi; Hirose, Sakiko; Taniguchi, Yojiro; Yamanouchi, Utako; Wu, Jianzhong; Matsumoto, Takashi; Sugimoto, Kazuhiko; Kondo, Katsuhiko; Ikka, Takashi; Ando, Tsuyu; Kono, Izumi; Ito, Sachie; Shomura, Ayahiko; Ookawa, Taiichiro; Hirasawa, Tadashi; Yano, Masahiro; Kondo, Motohiko; Yamamoto, Toshio

2013-01-01

Improvement of leaf photosynthesis is an important strategy for greater crop productivity. Here we show that the quantitative trait locus GPS (GREEN FOR PHOTOSYNTHESIS) in rice (Oryza sativa L.) controls photosynthesis rate by regulating carboxylation efficiency. Map-based cloning revealed that GPS is identical to NAL1 (NARROW LEAF1), a gene previously reported to control lateral leaf growth. The high-photosynthesis allele of GPS was found to be a partial loss-of-function allele of NAL1. This allele increased mesophyll cell number between vascular bundles, which led to thickened leaves, and it pleiotropically enhanced photosynthesis rate without the detrimental side effects observed in previously identified nal1 mutants, such as dwarf plant stature. Furthermore, pedigree analysis suggested that rice breeders have repeatedly selected the high-photosynthesis allele in high-yield breeding programs. The identification and utilization of NAL1 (GPS) can enhance future high-yield breeding and provides a new strategy for increasing rice productivity.

A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate

PubMed Central

Takai, Toshiyuki; Adachi, Shunsuke; Taguchi-Shiobara, Fumio; Sanoh-Arai, Yumiko; Iwasawa, Norio; Yoshinaga, Satoshi; Hirose, Sakiko; Taniguchi, Yojiro; Yamanouchi, Utako; Wu, Jianzhong; Matsumoto, Takashi; Sugimoto, Kazuhiko; Kondo, Katsuhiko; Ikka, Takashi; Ando, Tsuyu; Kono, Izumi; Ito, Sachie; Shomura, Ayahiko; Ookawa, Taiichiro; Hirasawa, Tadashi; Yano, Masahiro; Kondo, Motohiko; Yamamoto, Toshio

2013-01-01

Improvement of leaf photosynthesis is an important strategy for greater crop productivity. Here we show that the quantitative trait locus GPS (GREEN FOR PHOTOSYNTHESIS) in rice (Oryza sativa L.) controls photosynthesis rate by regulating carboxylation efficiency. Map-based cloning revealed that GPS is identical to NAL1 (NARROW LEAF1), a gene previously reported to control lateral leaf growth. The high-photosynthesis allele of GPS was found to be a partial loss-of-function allele of NAL1. This allele increased mesophyll cell number between vascular bundles, which led to thickened leaves, and it pleiotropically enhanced photosynthesis rate without the detrimental side effects observed in previously identified nal1 mutants, such as dwarf plant stature. Furthermore, pedigree analysis suggested that rice breeders have repeatedly selected the high-photosynthesis allele in high-yield breeding programs. The identification and utilization of NAL1 (GPS) can enhance future high-yield breeding and provides a new strategy for increasing rice productivity. PMID:23985993

Identification of an abundant 56 kDa protein implicated in food allergy as granule-bound starch synthase

USDA-ARS?s Scientific Manuscript database

Rice, the staple food of South and East Asian counties, is considered to be hypoallergenic. However, several clinical studies have documented rice-induced allergy in sensitive patients. Rice proteins with molecular weights of 14-16 kDa, 26 kDa, 33 kDa and 56 kDa have been identified as allergens. Re...

Identification and comparative expression profiles of chemoreception genes revealed from major chemoreception organs of the rice leaf folder, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae)

USDA-ARS?s Scientific Manuscript database

To better understand the olfactory mechanism in the rice leaf folder, Cnaphalocrocis medinalis (Guenée), one of the most serious insect pests of rice in Asia, we have established six partial transcriptomes from antennae, tarsus, and reproductive organs of male and female adults. A total of 102 genes...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Euan; Kempson, Ivan; Juhasz, Albert L.

The consumption of arsenic (As) contaminated rice is an important exposure route for humans in countries where rice cultivation employs As contaminated irrigation water. Arsenic toxicity and mobility are a function of its chemical-speciation. The distribution and identification of As in the rice plant are hence necessary to determine the uptake, transformation and potential risk posed by As contaminated rice. In this study we report on the distribution and chemical-speciation of As in rice (Oryza sativa Quest) by X-ray fluorescence (XRF) and X-ray absorption near edge structure (XANES) measurements of rice plants grown in As contaminated paddy water. Investigations ofmore » {mu}XRF images from rice tissues found that As was present in all rice tissues, and its presence correlated with the presence of iron at the root surface and copper in the rice leaf. X-ray absorption near edge structure analysis of rice tissues identified that inorganic As was the predominant form of As in all rice tissues studied, and that arsenite became increasingly dominant in the aerial portion of the rice plant.« less

Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

PubMed Central

Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Duan, Lingfeng; Chen, Guoxing; Jiang, Ni; Fang, Wei; Feng, Hui; Xie, Weibo; Lian, Xingming; Wang, Gongwei; Luo, Qingming; Zhang, Qifa; Liu, Qian; Xiong, Lizhong

2014-01-01

Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gene, SD1. Based on a performance evaluation of the HRPF and GWAS results, we demonstrate that high-throughput phenotyping has the potential to replace traditional phenotyping techniques and can provide valuable gene identification information. The combination of the multifunctional phenotyping tools HRPF and GWAS provides deep insights into the genetic architecture of important traits. PMID:25295980

The mature anther-preferentially expressed genes are associated with pollen fertility, pollen germination and anther dehiscence in rice.

PubMed

Ling, Sheng; Chen, Caisheng; Wang, Yang; Sun, Xiaocong; Lu, Zhanhua; Ouyang, Yidan; Yao, Jialing

2015-02-19

The anthers and pollen grains are critical for male fertility and hybrid rice breeding. The development of rice mature anther and pollen consists of multiple continuous stages. However, molecular mechanisms regulating mature anther development were poorly understood. In this study, we have identified 291 mature anther-preferentially expressed genes (OsSTA) in rice based on Affymetrix microarray data. Gene Ontology (GO) analysis indicated that OsSTA genes mainly participated in metabolic and cellular processes that are likely important for rice anther and pollen development. The expression patterns of OsSTA genes were validated using real-time PCR and mRNA in situ hybridizations. Cis-element identification showed that most of the OsSTA genes had the cis-elements responsive to phytohormone regulation. Co-expression analysis of OsSTA genes showed that genes annotated with pectinesterase and calcium ion binding activities were rich in the network, suggesting that OsSTA genes could be involved in pollen germination and anther dehiscence. Furthermore, OsSTA RNAi transgenic lines showed male-sterility and pollen germination defects. The results suggested that OsSTA genes function in rice male fertility, pollen germination and anther dehiscence and established molecular regulating networks that lay the foundation for further functional studies.

Identification and quantification of anthocyanin pigments in colored rice.

PubMed

Kim, Min-Kyoung; Kim, Han-Ah; Koh, Kwangoh; Kim, Hee-Seon; Lee, Young Sang; Kim, Yong Ho

2008-01-01

Anthocyanin pigments from varieties of black, red and wild rice were identified and quantified to evaluate their potential as nutritional function, natural colorants or functional food ingredients. Anthocyanin extraction was conducted with acidified methanol with 0.1M HCl (85:15, v/v) and identification of anthocyanin, aglycone and sugar moieties was conducted by comparison with purified standards by HPLC, Ultraviolet-Visible absorption spectrophotometer and paper chromatography. Black and wild rice showed three different types of pigments by HPLC whereas red rice variety did not show any anthocyanins. Out of three pigments detected, one (peak 2) was characterized as cyanidin-3-glucoside (C3G) by comparison of spectroscopic and chromatographic properties with an authentic standard, and another (peak 3) was tentatively identified as cyanidin-fructoside on the basis of spectroscopic properties with lambda(max) of aglycone in 1% HCl methanol at 537 nm, electrospray ionization mass spectra with major ions at 449 and 287 m/z and chromatographic properties. But another pigment (peak 1) has not been characterized. The most abundant anthocyanin in black and wild rice was C3G.

Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding

PubMed Central

Luo, Zhijing; Chen, Mingjiao; Zhao, Xiangxiang; Zhang, Dabing; Qi, Yiping; Yuan, Zheng

2016-01-01

Rapid and accurate genome-wide marker detection is essential to the marker-assisted breeding and functional genomics studies. In this work, we developed an integrated software, AgroMarker Finder (AMF: http://erp.novelbio.com/AMF), for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. By application of AMF, a total of 90,743 high-quality markers (82,878 SNPs and 7,865 InDels) were detected between rice varieties JP69 and Jiaoyuan5A. The density of the identified markers is 0.2 per Kb for SNP markers, and 0.02 per Kb for InDel markers. Sequencing validation revealed that the accuracy of genome-wide marker detection by AMF is 93%. In addition, a validated subset of 82 SNPs and 31 InDels were found to be closely linked to 117 important agronomic trait genes, providing a basis for subsequent marker-assisted selection (MAS) and variety identification. Furthermore, we selected 12 markers from 31 validated InDel markers to identify seed authenticity of variety Jiaoyuanyou69, and we also identified 10 markers closely linked to the fragrant gene BADH2 to minimize linkage drag for Wuxiang075 (BADH2 donor)/Jiachang1 recombinants selection. Therefore, this software provides an efficient approach for marker identification from RAD-seq data, and it would be a valuable tool for plant MAS and variety protection. PMID:26799713

Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding.

PubMed

Fan, Wei; Zong, Jie; Luo, Zhijing; Chen, Mingjiao; Zhao, Xiangxiang; Zhang, Dabing; Qi, Yiping; Yuan, Zheng

2016-01-01

Rapid and accurate genome-wide marker detection is essential to the marker-assisted breeding and functional genomics studies. In this work, we developed an integrated software, AgroMarker Finder (AMF: http://erp.novelbio.com/AMF), for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. By application of AMF, a total of 90,743 high-quality markers (82,878 SNPs and 7,865 InDels) were detected between rice varieties JP69 and Jiaoyuan5A. The density of the identified markers is 0.2 per Kb for SNP markers, and 0.02 per Kb for InDel markers. Sequencing validation revealed that the accuracy of genome-wide marker detection by AMF is 93%. In addition, a validated subset of 82 SNPs and 31 InDels were found to be closely linked to 117 important agronomic trait genes, providing a basis for subsequent marker-assisted selection (MAS) and variety identification. Furthermore, we selected 12 markers from 31 validated InDel markers to identify seed authenticity of variety Jiaoyuanyou69, and we also identified 10 markers closely linked to the fragrant gene BADH2 to minimize linkage drag for Wuxiang075 (BADH2 donor)/Jiachang1 recombinants selection. Therefore, this software provides an efficient approach for marker identification from RAD-seq data, and it would be a valuable tool for plant MAS and variety protection.

RFID Student Educational Experiences at the UNT College of Engineering: A Sequential Approach to Creating a Project-Based RFID Course

ERIC Educational Resources Information Center

Vaidyanathan, V. V.; Varanasi, M. R.; Kougianos, E.; Wang, Shuping; Raman, H.

2009-01-01

This paper describes radio frequency identification (RFID) projects, designed and implemented by students in the College of Engineering at the University of North Texas, as part of their senior-design project requirement. The paper also describes an RFID-based project implemented at Rice Middle School in Plano, TX, which went on to win multiple…

Direct and reverse pollen-mediated gene flow between GM rice and red rice weed

PubMed Central

Serrat, X.; Esteban, R.; Peñas, G.; Català, M. M.; Melé, E.; Messeguer, J.

2013-01-01

Potential risks of genetically modified (GM) crops must be identified before their commercialization, as happens with all new technologies. One of the major concerns is the proper risk assessment of adventitious presence of transgenic material in rice fields due to cross-pollination. Several studies have been conducted in order to quantify pollen-mediated gene flow from transgenic rice (Oryza sativa) to both conventional rice and red rice weed (O. sativa f. spontanea) under field conditions. Some of these studies reported GM pollen-donor rice transferring GM traits to red rice. However, gene flow also occurs in the opposite direction, in a phenomenon that we have called reverse gene flow, resulting in transgenic seeds that have incorporated the traits of wild red rice. We quantified reverse gene flow using material from two field trials. A molecular analysis based on amplified fragment length polymorphisms was carried out, being complemented with a phenotypic identification of red rice traits. In both field trials, the reverse gene flow detected was greater than the direct gene flow. The rate of direct gene flow varied according to the relative proportions of the donor (GM rice) and receptor (red rice) plants and was influenced by wind direction. The ecological impact of reverse gene flow is limited in comparison with that of direct gene flow because non-shattered and non-dormant seeds would be obtained in the first generation. Hybrid seed would remain in the spike and therefore most of it would be removed during harvesting. Nevertheless, this phenomenon must be considered in fields used for elite seed production and in developing countries where farmers often keep some seed for planting the following year. In these cases, there is a higher risk of GM red rice weed infestation increasing from year to year and therefore a proper monitoring plan needs to be established.

Landuse change identification using SPOT 6 for food security analysis of Denpasar City, Bali Province, Indonesia

NASA Astrophysics Data System (ADS)

Supardan, N.; Panularsih, M.; Darmawan, M.

2018-05-01

Land use change was common in Indonesia, including Bali, especially land conversion from paddy field to other uses. Based on statistics data of Bali 2015, the area of rice fields continues to decline every year, both irrigated and rain-fed rice fields. This study was conducted to analyze land use change and its impact on food security in Denpasar. Land use change dynamics can be observed by multi-temporal land use changes. GIS analysis was performed to obtain spatial land use changes in the study area by using topographic map 1: 25,000 with data sources 2002 and land cover classification of SPOT 6 image acquisition 2015. The results of GIS analysis indicate that settlement and built-up area increased by 1,736 hectares and the area of rice field decreased by 1,695 hectares during 13 years. The increasing of settlement rate was 133,5 ha / year and the decreasing of rice field was 130 ha / year. Meanwhile, the result of food availability analysis shows that the Denpasar City still deficit of rice amount 48,997 tons in 2014, and 69,175 tons in 2015 or only fulfill about 45% of food requirement.

Characterization, identification and application of lactic Acid bacteria isolated from forage paddy rice silage.

PubMed

Ni, Kuikui; Wang, Yanping; Li, Dongxia; Cai, Yimin; Pang, Huili

2015-01-01

There has been growing interest to develop forage rice as a new feed resource for livestock. This study was to characterize the natural population of lactic acid bacteria (LAB) and select potentially excellent strains for paddy rice silage preparation in China. One hundred and twenty-six strains were isolated and screened from paddy rice silage prepared using a small-scale fermentation system, and ninety-nine of these isolates were considered to be LAB based on their Gram-positive and catalase-negative morphology and the production of most of their metabolic products as lactic acid. These isolates were divided into eight groups (A-H) on the basis of their morphological and biochemical characteristics. The Group A to H strains were identified as Lactobacillus (L.) plantarum subsp. plantarum (species ratio: 8.1%), L. casei (5.1%), Leuconostoc (Ln.) pseudomesenteroides (11.1%), Pediococcus (P.) pentosaceus (24.2%), Enterococcus (E.) mundtii (12.1%), Lactococcus (Lc.) garvieae (15.2%), E. faecium (9.1%) and Lc. lactis subsp. lactis (15.2%) based on sequence analyses of their 16S rRNA and recA genes. P. pentosaceus was the most abundant member of the LAB population in the paddy rice silage. A selected strain, namely L. casei R 465, was found to be able to grow under low pH conditions and to improve the silage quality with low pH and a relatively high content of lactic acid. This study demonstrated that forage paddy rice silage contains abundant LAB species and its silage can be well preserved by inoculation with LAB, and that strain R 465 can be a potentially excellent inoculant for paddy rice silage.

Characterization, Identification and Application of Lactic Acid Bacteria Isolated from Forage Paddy Rice Silage

PubMed Central

Ni, Kuikui; Wang, Yanping; Li, Dongxia; Cai, Yimin; Pang, Huili

2015-01-01

There has been growing interest to develop forage rice as a new feed resource for livestock. This study was to characterize the natural population of lactic acid bacteria (LAB) and select potentially excellent strains for paddy rice silage preparation in China. One hundred and twenty-six strains were isolated and screened from paddy rice silage prepared using a small-scale fermentation system, and ninety-nine of these isolates were considered to be LAB based on their Gram-positive and catalase-negative morphology and the production of most of their metabolic products as lactic acid. These isolates were divided into eight groups (A-H) on the basis of their morphological and biochemical characteristics. The Group A to H strains were identified as Lactobacillus (L.) plantarum subsp. plantarum (species ratio: 8.1%), L. casei (5.1%), Leuconostoc (Ln.) pseudomesenteroides (11.1%), Pediococcus (P.) pentosaceus (24.2%), Enterococcus (E.) mundtii (12.1%), Lactococcus (Lc.) garvieae (15.2%), E. faecium (9.1%) and Lc. lactis subsp. lactis (15.2%) based on sequence analyses of their 16S rRNA and recA genes. P. pentosaceus was the most abundant member of the LAB population in the paddy rice silage. A selected strain, namely L. casei R 465, was found to be able to grow under low pH conditions and to improve the silage quality with low pH and a relatively high content of lactic acid. This study demonstrated that forage paddy rice silage contains abundant LAB species and its silage can be well preserved by inoculation with LAB, and that strain R 465 can be a potentially excellent inoculant for paddy rice silage. PMID:25803578

Innate immunity in rice

PubMed Central

Chen, Xuewei; Ronald, Pamela C.

2011-01-01

Advances in studies of rice innate immunity have led to the identification and characterization of host sensors encoding receptor kinases that perceive conserved microbial signatures. The non-RD domain, a newly recognized hallmark of these receptor kinases is highly expanded in rice (Oryza sativa) compared with Arabidopsis (Arabidopsis thaliana). Researchers have also identified a diverse array of microbial effectors from bacterial and fungal pathogens that triggers immune responses upon perception. These include both, effectors that indirectly target host Nucleotide binding site/Leucine rice repeat (NBS-LRR) proteins and transcription activator-like (TAL) effectors that directly bind promoters of host genes. Here we review the recognition and signaling events that govern rice innate immunity. PMID:21602092

Identification of the Rice Wines with Different Marked Ages by Electronic Nose Coupled with Smartphone and Cloud Storage Platform

PubMed Central

Wei, Zhebo; Xiao, Xize

2017-01-01

In this study, a portable electronic nose (E-nose) was self-developed to identify rice wines with different marked ages—all the operations of the E-nose were controlled by a special Smartphone Application. The sensor array of the E-nose was comprised of 12 MOS sensors and the obtained response values were transmitted to the Smartphone thorough a wireless communication module. Then, Aliyun worked as a cloud storage platform for the storage of responses and identification models. The measurement of the E-nose was composed of the taste information obtained phase (TIOP) and the aftertaste information obtained phase (AIOP). The area feature data obtained from the TIOP and the feature data obtained from the TIOP-AIOP were applied to identify rice wines by using pattern recognition methods. Principal component analysis (PCA), locally linear embedding (LLE) and linear discriminant analysis (LDA) were applied for the classification of those wine samples. LDA based on the area feature data obtained from the TIOP-AIOP proved a powerful tool and showed the best classification results. Partial least-squares regression (PLSR) and support vector machine (SVM) were applied for the predictions of marked ages and SVM (R2 = 0.9942) worked much better than PLSR. PMID:29088076

Identification of the Rice Wines with Different Marked Ages by Electronic Nose Coupled with Smartphone and Cloud Storage Platform.

PubMed

Wei, Zhebo; Xiao, Xize; Wang, Jun; Wang, Hui

2017-10-31

In this study, a portable electronic nose (E-nose) was self-developed to identify rice wines with different marked ages-all the operations of the E-nose were controlled by a special Smartphone Application. The sensor array of the E-nose was comprised of 12 MOS sensors and the obtained response values were transmitted to the Smartphone thorough a wireless communication module. Then, Aliyun worked as a cloud storage platform for the storage of responses and identification models. The measurement of the E-nose was composed of the taste information obtained phase (TIOP) and the aftertaste information obtained phase (AIOP). The area feature data obtained from the TIOP and the feature data obtained from the TIOP-AIOP were applied to identify rice wines by using pattern recognition methods. Principal component analysis (PCA), locally linear embedding (LLE) and linear discriminant analysis (LDA) were applied for the classification of those wine samples. LDA based on the area feature data obtained from the TIOP-AIOP proved a powerful tool and showed the best classification results. Partial least-squares regression (PLSR) and support vector machine (SVM) were applied for the predictions of marked ages and SVM (R² = 0.9942) worked much better than PLSR.

Rice Molecular Breeding Laboratories in the Genomics Era: Current Status and Future Considerations

PubMed Central

Collard, Bert C. Y.; Vera Cruz, Casiana M.; McNally, Kenneth L.; Virk, Parminder S.; Mackill, David J.

2008-01-01

Using DNA markers in plant breeding with marker-assisted selection (MAS) could greatly improve the precision and efficiency of selection, leading to the accelerated development of new crop varieties. The numerous examples of MAS in rice have prompted many breeding institutes to establish molecular breeding labs. The last decade has produced an enormous amount of genomics research in rice, including the identification of thousands of QTLs for agronomically important traits, the generation of large amounts of gene expression data, and cloning and characterization of new genes, including the detection of single nucleotide polymorphisms. The pinnacle of genomics research has been the completion and annotation of genome sequences for indica and japonica rice. This information—coupled with the development of new genotyping methodologies and platforms, and the development of bioinformatics databases and software tools—provides even more exciting opportunities for rice molecular breeding in the 21st century. However, the great challenge for molecular breeders is to apply genomics data in actual breeding programs. Here, we review the current status of MAS in rice, current genomics projects and promising new genotyping methodologies, and evaluate the probable impact of genomics research. We also identify critical research areas to “bridge the application gap” between QTL identification and applied breeding that need to be addressed to realize the full potential of MAS, and propose ideas and guidelines for establishing rice molecular breeding labs in the postgenome sequence era to integrate molecular breeding within the context of overall rice breeding and research programs. PMID:18528527

Identification of the main retrogradation-related properties of rice starch.

PubMed

Lian, Xijun; Kang, Haiqi; Sun, Haibo; Liu, Lizeng; Li, Lin

2015-02-11

The retrogradation of rice in shelf life is the biggest barrier to the industrial production of traditional foods using rice as material. Many rice breeders have tried their best to screen low-retrogradation rice cultivars without a specific indicator. To identify the main retrogradation-related properties of rice, the starch, amylose, and amylopectin from 16 rice cultivars were extracted from rice powder and their physicochemical properties, such as visible absorbance, infrared, average molecule weight (amylopectin), chain-length distribution (amylopectin), X-ray diffraction, and differential scanning calorimetry, were determined. The correlation between starch retrogradation rates and those physicochemical properties was investigated. The results show that a significant positive correlation (R(2) = 0.85; r = 0.926; p < 0.01) exists only between proportions of the chains [degree of polymerization (DP) > 10] in amylopectin and the retrogradation rates of different rice starches. The findings in the paper offer a shortcut for rice breeders to screen cultivars with a low retrogradation rate. Because the genes related to the branching enzyme control the DP of amylopectin, they can be exploited as molecular markers to screen low-retrogradation rice cultivars.

Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research

PubMed Central

Sharma, Rita; Cao, Peijian; Jung, Ki-Hong; Sharma, Manoj K.; Ronald, Pamela C.

2013-01-01

Glycoside hydrolases (GH) catalyze the hydrolysis of glycosidic bonds in cell wall polymers and can have major effects on cell wall architecture. Taking advantage of the massive datasets available in public databases, we have constructed a rice phylogenomic database of GHs (http://ricephylogenomics.ucdavis.edu/cellwalls/gh/). This database integrates multiple data types including the structural features, orthologous relationships, mutant availability, and gene expression patterns for each GH family in a phylogenomic context. The rice genome encodes 437 GH genes classified into 34 families. Based on pairwise comparison with eight dicot and four monocot genomes, we identified 138 GH genes that are highly diverged between monocots and dicots, 57 of which have diverged further in rice as compared with four monocot genomes scanned in this study. Chromosomal localization and expression analysis suggest a role for both whole-genome and localized gene duplications in expansion and diversification of GH families in rice. We examined the meta-profiles of expression patterns of GH genes in twenty different anatomical tissues of rice. Transcripts of 51 genes exhibit tissue or developmental stage-preferential expression, whereas, seventeen other genes preferentially accumulate in actively growing tissues. When queried in RiceNet, a probabilistic functional gene network that facilitates functional gene predictions, nine out of seventeen genes form a regulatory network with the well-characterized genes involved in biosynthesis of cell wall polymers including cellulose synthase and cellulose synthase-like genes of rice. Two-thirds of the GH genes in rice are up regulated in response to biotic and abiotic stress treatments indicating a role in stress adaptation. Our analyses identify potential GH targets for cell wall modification. PMID:23986771

[Effect of climatic mean value change on the evaluation result of rice delayed cold damage in Liaoning Province, Northeast China].

PubMed

Ji, Rui-peng; Yu, Wen-ying; Wu, Jin-wen; Feng, Rui; Zhang, Yu-shu

2015-06-01

The anomaly of mean temperature summation from May to September (ΔT5-9) was commonly used to assess delayed cold damage of rice in Northeast China, but whether the change of statistics years for climatic mean value (ΣT5-9) would affect the, evaluation results of Liaoning rice under cold damage needed to be further studied. By using the meteorological industry standard of the People's Republic of China "technical standard on rice cold damage evaluation" (QX/T 182- 2013) and the supplemental indices (ΔT5-9), the index (ΣT5-9) was calculated in four periods 1961-1990 (S1), 1971-2000 (S2), 1981-2010 (S3) and 1961-2010 (S4), and the spatial and temporal changes of cold damage in Liaoning Province were analyzed based on the ratio between cold damage stations and total stations (IOC) and the occurrence frequency. The results showed that the heat condition (Σ T5-9) in rice growing season increased obviously and the spatial and temporal changes were significant from 1961 to 2010. The original meteorological index of rice cold damage was improved by using quadratic polynomial model. The identification results were similar between S2 and S4. The variation coefficient of IOC in S3 was lower than that of the other three. Compared with the typical rice yield reduction years, the evaluation results accorded better with the actual situation in evaluating the rice delayed cold damage in Liaoning during study period by using the S3 climate mean value. The results could provide evidence for accurately evaluating the variation of rice cold damage in spatial and temporal distribution in Liaoning Province under the background of global climate change.

A preliminary study on identification of Thai rice samples by INAA and statistical analysis

NASA Astrophysics Data System (ADS)

Kongsri, S.; Kukusamude, C.

2017-09-01

This study aims to investigate the elemental compositions in 93 Thai rice samples using instrumental neutron activation analysis (INAA) and to identify rice according to their types and rice cultivars using statistical analysis. As, Mg, Cl, Al, Br, Mn, K, Rb and Zn in Thai jasmine rice and Sung Yod rice samples were successfully determined by INAA. The accuracy and precision of the INAA method were verified by SRM 1568a Rice Flour. All elements were found to be in a good agreement with the certified values. The precisions in term of %RSD were lower than 7%. The LODs were obtained in range of 0.01 to 29 mg kg-1. The concentration of 9 elements distributed in Thai rice samples was evaluated and used as chemical indicators to identify the type of rice samples. The result found that Mg, Cl, As, Br, Mn, K, Rb, and Zn concentrations in Thai jasmine rice samples are significantly different but there was no evidence that Al is significantly different from concentration in Sung Yod rice samples at 95% confidence interval. Our results may provide preliminary information for discrimination of rice samples and may be useful database of Thai rice.

Global Identification and Characterization of Transcriptionally Active Regions in the Rice Genome

PubMed Central

Stolc, Viktor; Deng, Wei; He, Hang; Korbel, Jan; Chen, Xuewei; Tongprasit, Waraporn; Ronald, Pamela; Chen, Runsheng; Gerstein, Mark; Wang Deng, Xing

2007-01-01

Genome tiling microarray studies have consistently documented rich transcriptional activity beyond the annotated genes. However, systematic characterization and transcriptional profiling of the putative novel transcripts on the genome scale are still lacking. We report here the identification of 25,352 and 27,744 transcriptionally active regions (TARs) not encoded by annotated exons in the rice (Oryza. sativa) subspecies japonica and indica, respectively. The non-exonic TARs account for approximately two thirds of the total TARs detected by tiling arrays and represent transcripts likely conserved between japonica and indica. Transcription of 21,018 (83%) japonica non-exonic TARs was verified through expression profiling in 10 tissue types using a re-array in which annotated genes and TARs were each represented by five independent probes. Subsequent analyses indicate that about 80% of the japonica TARs that were not assigned to annotated exons can be assigned to various putatively functional or structural elements of the rice genome, including splice variants, uncharacterized portions of incompletely annotated genes, antisense transcripts, duplicated gene fragments, and potential non-coding RNAs. These results provide a systematic characterization of non-exonic transcripts in rice and thus expand the current view of the complexity and dynamics of the rice transcriptome. PMID:17372628

Genome-wide identification of DNA methylation provides insights into the association of gene expression in rice exposed to pesticide atrazine

PubMed Central

Lu, Yi Chen; Feng, Sheng Jun; Zhang, Jing Jing; Luo, Fang; Zhang, Shuang; Yang, Hong

2016-01-01

Atrazine (ATR) is a pesticide widely used for controlling weeds for crop production. Crop contamination with ATR negatively affects crop growth and development. This study presents the first genome-wide single-base-resolution maps of DNA methylation in ATR-exposed rice. Widespread differences were identified in CG and non-CG methylation marks between the ATR-exposed and ATR-free (control) rice. Most of DNA methyltransferases, histone methyltransferases and DNA demethylase were differentially regulated by ATR. We found more genes hypermethylated than those hypomethylated in the regions of upstream, genebody and downstream under ATR exposure. A stringent group of 674 genes (p < 0.05, two-fold change) with a strong preference of differential expression in ATR-exposed rice was identified. Some of the genes were identified in a subset of loss of function mutants defective in DNA methylation/demethylation. Provision of 5-azacytidine (AZA, inhibitor of DNA methylation) promoted the rice growth and reduced ATR content. By UPLC/Q-TOF-MS/MS, 8 degraded products and 9 conjugates of ATR in AZA-treated rice were characterized. Two of them has been newly identified in this study. Our data show that ATR-induced changes in DNA methylation marks are possibly involved in an epigenetic mechanism associated with activation of specific genes responsible for ATR degradation and detoxification. PMID:26739616

A 400-year phytolith-based reconstruction of wild rice (Zizania palustris) abundance from Mud Lake core sediments, Fond du Lac Band of Lake Superior Chippewa Reservation, Minnesota, USA.

NASA Astrophysics Data System (ADS)

Munoz, R.; Caylor, E.; Yost, C. L.; Drake, C.; Ladwig, J. L.; Myrbo, A.; Howes, T.

2014-12-01

Wild rice (Zizania palustris L.) is an aquatic grass with spiritual and subsistence significance to Native people of the Great Lakes region of North America. Mud Lake (Mashkiigwaagamaag), located on the Fond du Lac Band of Lake Superior Chippewa Reservation in Carlton County, Minnesota, USA, once supported an extensive population of wild rice (manoomin). However, early 20th century attempts to ditch and drain surrounding wetlands for landuse intensification severely altered the natural hydrological system that supports wild rice. Fond du Lac Resource Management (FDLRM) technicians are currently working to increase the wild rice population in Mud Lake. As part of these efforts, this phytolith study was undertaken to better understand how wild rice abundance has fluctuated over the past 400 years, with particular emphasis on the 19th and 20th centuries. Phytoliths are microscopic opal silica plant remains that are incorporated into soils and lake sediments after the plant-parts that contain them decay. Wild rice produces phytolith morphotypes that are unequivocally diagnostic. Mud Lake core MNMN-MUD11-1C-1P-1 (46°43'38.39"N, 92°42'2.45"W) was piston cored by LacCore (National Lacustrine Core Facility) and FDLRM technicians on 24 May 2011. Initial core descriptions, multi-sensor core logging, phytolith sampling and phytolith extractions were completed during the summer of 2014 at LacCore. Wild rice phytolith identification and quantification was conducted on twelve samples using brightfield microscopy at 400x magnification. Wild rice phytolith concentration values ranged from 68 to 2,300 phytoliths/cm3. Wild rice accumulation rates ranged from 9 to 383 phytoliths/ cm2/yr, peaking in 1952 AD. Wild rice abundance in Mud Lake appears to be influenced by a complex set of variables that include anthropogenic disturbance, climatic events and aquatic plant community succession.

Deployment of the Burkholderia glumae type III secretion system as an efficient tool for translocating pathogen effectors to monocot cells.

PubMed

Sharma, Shailendra; Sharma, Shiveta; Hirabuchi, Akiko; Yoshida, Kentaro; Fujisaki, Koki; Ito, Akiko; Uemura, Aiko; Terauchi, Ryohei; Kamoun, Sophien; Sohn, Kee Hoon; Jones, Jonathan D G; Saitoh, Hiromasa

2013-05-01

Genome sequences of plant fungal pathogens have enabled the identification of effectors that cooperatively modulate the cellular environment for successful fungal growth and suppress host defense. Identification and characterization of novel effector proteins are crucial for understanding pathogen virulence and host-plant defense mechanisms. Previous reports indicate that the Pseudomonas syringae pv. tomato DC3000 type III secretion system (T3SS) can be used to study how non-bacterial effectors manipulate dicot plant cell function using the effector detector vector (pEDV) system. Here we report a pEDV-based effector delivery system in which the T3SS of Burkholderia glumae, an emerging rice pathogen, is used to translocate the AVR-Pik and AVR-Pii effectors of the fungal pathogen Magnaporthe oryzae to rice cytoplasm. The translocated AVR-Pik and AVR-Pii showed avirulence activity when tested in rice cultivars containing the cognate R genes. AVR-Pik reduced and delayed the hypersensitive response triggered by B. glumae in the non-host plant Nicotiana benthamiana, indicative of an immunosuppressive virulence activity. AVR proteins fused with fluorescent protein and nuclear localization signal were delivered by B. glumae T3SS and observed in the nuclei of infected cells in rice, wheat, barley and N. benthamiana. Our bacterial T3SS-enabled eukaryotic effector delivery and subcellular localization assays provide a useful method for identifying and studying effector functions in monocot plants. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

Metabolite Profiling of Diverse Rice Germplasm and Identification of Conserved Metabolic Markers of Rice Roots in Response to Long-Term Mild Salinity Stress

PubMed Central

Nam, Myung Hee; Bang, Eunjung; Kwon, Taek Yun; Kim, Yuran; Kim, Eun Hee; Cho, Kyungwon; Park, Woong June; Kim, Beom-Gi; Yoon, In Sun

2015-01-01

The sensitivity of rice to salt stress greatly depends on growth stages, organ types and cultivars. Especially, the roots of young rice seedlings are highly salt-sensitive organs that limit plant growth, even under mild soil salinity conditions. In an attempt to identify metabolic markers of rice roots responding to salt stress, metabolite profiling was performed by 1H-NMR spectroscopy in 38 rice genotypes that varied in biomass accumulation under long-term mild salinity condition. Multivariate statistical analysis showed separation of the control and salt-treated rice roots and rice genotypes with differential growth potential. By quantitative analyses of 1H-NMR data, five conserved salt-responsive metabolic markers of rice roots were identified. Sucrose, allantoin and glutamate accumulated by salt stress, whereas the levels of glutamine and alanine decreased. A positive correlation of metabolite changes with growth potential and salt tolerance of rice genotypes was observed for allantoin and glutamine. Adjustment of nitrogen metabolism in rice roots is likely to be closely related to maintain the growth potential and increase the stress tolerance of rice. PMID:26378525

Employing machine learning for reliable miRNA target identification in plants

PubMed Central

2011-01-01

Background miRNAs are ~21 nucleotide long small noncoding RNA molecules, formed endogenously in most of the eukaryotes, which mainly control their target genes post transcriptionally by interacting and silencing them. While a lot of tools has been developed for animal miRNA target system, plant miRNA target identification system has witnessed limited development. Most of them have been centered around exact complementarity match. Very few of them considered other factors like multiple target sites and role of flanking regions. Result In the present work, a Support Vector Regression (SVR) approach has been implemented for plant miRNA target identification, utilizing position specific dinucleotide density variation information around the target sites, to yield highly reliable result. It has been named as p-TAREF (plant-Target Refiner). Performance comparison for p-TAREF was done with other prediction tools for plants with utmost rigor and where p-TAREF was found better performing in several aspects. Further, p-TAREF was run over the experimentally validated miRNA targets from species like Arabidopsis, Medicago, Rice and Tomato, and detected them accurately, suggesting gross usability of p-TAREF for plant species. Using p-TAREF, target identification was done for the complete Rice transcriptome, supported by expression and degradome based data. miR156 was found as an important component of the Rice regulatory system, where control of genes associated with growth and transcription looked predominant. The entire methodology has been implemented in a multi-threaded parallel architecture in Java, to enable fast processing for web-server version as well as standalone version. This also makes it to run even on a simple desktop computer in concurrent mode. It also provides a facility to gather experimental support for predictions made, through on the spot expression data analysis, in its web-server version. Conclusion A machine learning multivariate feature tool has been implemented in parallel and locally installable form, for plant miRNA target identification. The performance was assessed and compared through comprehensive testing and benchmarking, suggesting a reliable performance and gross usability for transcriptome wide plant miRNA target identification. PMID:22206472

Employing machine learning for reliable miRNA target identification in plants.

PubMed

Jha, Ashwani; Shankar, Ravi

2011-12-29

miRNAs are ~21 nucleotide long small noncoding RNA molecules, formed endogenously in most of the eukaryotes, which mainly control their target genes post transcriptionally by interacting and silencing them. While a lot of tools has been developed for animal miRNA target system, plant miRNA target identification system has witnessed limited development. Most of them have been centered around exact complementarity match. Very few of them considered other factors like multiple target sites and role of flanking regions. In the present work, a Support Vector Regression (SVR) approach has been implemented for plant miRNA target identification, utilizing position specific dinucleotide density variation information around the target sites, to yield highly reliable result. It has been named as p-TAREF (plant-Target Refiner). Performance comparison for p-TAREF was done with other prediction tools for plants with utmost rigor and where p-TAREF was found better performing in several aspects. Further, p-TAREF was run over the experimentally validated miRNA targets from species like Arabidopsis, Medicago, Rice and Tomato, and detected them accurately, suggesting gross usability of p-TAREF for plant species. Using p-TAREF, target identification was done for the complete Rice transcriptome, supported by expression and degradome based data. miR156 was found as an important component of the Rice regulatory system, where control of genes associated with growth and transcription looked predominant. The entire methodology has been implemented in a multi-threaded parallel architecture in Java, to enable fast processing for web-server version as well as standalone version. This also makes it to run even on a simple desktop computer in concurrent mode. It also provides a facility to gather experimental support for predictions made, through on the spot expression data analysis, in its web-server version. A machine learning multivariate feature tool has been implemented in parallel and locally installable form, for plant miRNA target identification. The performance was assessed and compared through comprehensive testing and benchmarking, suggesting a reliable performance and gross usability for transcriptome wide plant miRNA target identification.

Identification of a Pi9 containing rice germplasm with a newly developed robust marker

USDA-ARS?s Scientific Manuscript database

The Pi9 gene, originating from Oryza minuta, is an effective resistance gene for controlling rice blast disease (Magnaporthe oryzae). However, currently available linked DNA markers do not accurately identify the function of Pi9, thus hindering its efficient incorporation into new cultivars through...

Survey and identification of panicle blanking bacteria in Arkansas

USDA-ARS?s Scientific Manuscript database

Outbreaks of bacterial panicle blight (BPB) of rice in recent past years have resulted in severe yield losses in the Southern United States including Arkansas. Bacterial species, Burkholderia glumae was identified as the main causative agent among others causing BPB in rice. The symptoms of BPB inc...

Comparative transcriptome profiling of resistant and susceptible rice genotypes in response to the seedborne pathogen Fusarium fujikuroi.

PubMed

Matić, Slavica; Bagnaresi, Paolo; Biselli, Chiara; Orru', Luigi; Amaral Carneiro, Greice; Siciliano, Ilenia; Valé, Giampiero; Gullino, Maria Lodovica; Spadaro, Davide

2016-08-11

Fusarium fujikuroi is the causal agent of bakanae, the most significant seed-borne disease of rice. Molecular mechanisms regulating defence responses of rice towards this fungus are not yet fully known. To identify transcriptional mechanisms underpinning rice resistance, a RNA-seq comparative transcriptome profiling was conducted on infected seedlings of selected rice genotypes at one and three weeks post germination (wpg). Twelve rice genotypes were screened against bakanae disease leading to the identification of Selenio and Dorella as the most resistant and susceptible cultivars, respectively. Transcriptional changes were more appreciable at 3 wpg, suggesting that this infection stage is essential to study the resistance mechanisms: 3,119 DEGs were found in Selenio and 5,095 in Dorella. PR1, germin-like proteins, glycoside hydrolases, MAP kinases, and WRKY transcriptional factors were up-regulated in the resistant genotype upon infection with F. fujikuroi. Up-regulation of chitinases and down-regulation of MAP kinases and WRKY transcriptional factors were observed in the susceptible genotype. Gene ontology (GO) enrichment analyses detected in Selenio GO terms specific to response to F. fujikuroi: 'response to chitin', 'jasmonic acid biosynthetic process', and 'plant-type hypersensitive response', while Dorella activated different mechanisms, such as 'response to salicylic acid stimulus' and 'gibberellin metabolic process', which was in agreement with the production of gibberellin A3 in Dorella plants. RNA-seq profiling was performed for the first time to analyse response of rice to F. fujikuroi infection. Our findings allowed the identification of genes activated in one- and three- week-old rice seedlings of two genotypes infected with F. fujikuroi. Furthermore, we found the pathways involved in bakanae resistance, such as response to chitin, JA-dependent signalling and hypersensitive response. Collectively, this provides important information to elucidate the molecular and cellular processes occurring in rice during F. fujikuroi infection and to develop bakanae resistant rice germplasm.

Microbiological hazard identification and exposure assessment of poultry products sold in various localities of Hyderabad, India.

PubMed

Sudershan, Rao V; Naveen Kumar, R; Kashinath, L; Bhaskar, V; Polasa, K

2012-01-01

A study was carried out to identify microbiological hazards and assess their exposure associated with consumption of poultry based street food served in different localities of Hyderabad. The study indicated that chicken 65, chicken fried rice, chicken noodles, chicken Manchuria and chilly chicken are the most common recipes. A process flow diagram was developed to identify critical control points in the food item. After analysis of the samples at each level of preparation, it was observed that rice and noodles were kept at room temperature for about 5-6 hrs which was a critical control point. A total of 376 samples including chicken fried rice, chicken noodles, boiled noodles and boiled rice were collected from circle 1, 2, 3, 4, 5, 6, and 7 of Greater Hyderabad municipal corporation (GHMC) and analyzed for microbiological examination. The most prevalent pathogenic bacteria isolated were S. aureus (3.4 log 10 cfu/g) and B. cereus (3.4 log 10 cfu/g). Salmonella spp. was present in salads (3.2 log 10 cfu/g) and hand washings of the food handler (3.5 log 10 cfu/g). Salmonella contamination was found in salads served along with chicken fried rice and chicken noodles than in the food.

Microbiological Hazard Identification and Exposure Assessment of Poultry Products Sold in Various Localities of Hyderabad, India

PubMed Central

Sudershan, Rao V.; Naveen Kumar, R.; Kashinath, L.; Bhaskar, V.; Polasa, K.

2012-01-01

A study was carried out to identify microbiological hazards and assess their exposure associated with consumption of poultry based street food served in different localities of Hyderabad. The study indicated that chicken 65, chicken fried rice, chicken noodles, chicken Manchuria and chilly chicken are the most common recipes. A process flow diagram was developed to identify critical control points in the food item. After analysis of the samples at each level of preparation, it was observed that rice and noodles were kept at room temperature for about 5-6 hrs which was a critical control point. A total of 376 samples including chicken fried rice, chicken noodles, boiled noodles and boiled rice were collected from circle 1, 2, 3, 4, 5, 6, and 7 of Greater Hyderabad municipal corporation (GHMC) and analyzed for microbiological examination. The most prevalent pathogenic bacteria isolated were S. aureus (3.4 log 10 cfu/g) and B. cereus (3.4 log 10 cfu/g). Salmonella spp. was present in salads (3.2 log 10 cfu/g) and hand washings of the food handler (3.5 log 10 cfu/g). Salmonella contamination was found in salads served along with chicken fried rice and chicken noodles than in the food. PMID:22593705

Isolation and identification of an allelopathic phenylethylamine in rice.

PubMed

Le Thi, Ho; Lin, Chung-Ho; Smeda, Reid J; Leigh, Nathan D; Wycoff, Wei G; Fritschi, Felix B

2014-12-01

Allelopathy is the process whereby an organic chemical (allelochemical) released from one plant influences the growth and development of other plants. Allelochemicals produced by specific rice (Oryza sativa L.) cultivars have potential to manage barnyard grass (Echinochloa crus-galli L.), a major yield-limiting weed species in rice production systems in Asia and North America. In this study, isolation and identification of an allelopathic compound, N-trans-cinnamoyltyramine (NTCT), in a Vietnamese rice cultivar 'OM 5930' was accomplished through bioassay-guided purification using reversed-phase liquid chromatography coupled with spectroscopic techniques, including tandem mass spectrometry, high resolution mass spectrometry, as well as one-dimensional and two-dimensional (1)H NMR and (13)C NMR spectroscopy. The identified compound, NTCT is considered a β-phenylethylamine. NTCT inhibited root and hypocotyl growth of cress (Lepidium sativum L.), barnyard grass and red sprangletop (Leptochloa chinensis L. Nees) at concentrations as low as 0.24 μM. The ED50 (concentration required for 50% inhibition) of NTCT on barnyard grass root and hypocotyl elongation were 1.35 and 1.85 μM, respectively. Results further demonstrated that mortality of barnyard grass and red sprangletop seedlings was >80% at a concentration of 2.4 μM of NTCT. By 20 days after transplanting, 0.425 nmol of NTCT per OM 5930 rice seedling was released into the culture solution. With concentrations of 42 μg g(-1) fresh weight, production of NTCT in intact rice plants can be considered high. These findings suggest that developing plants of Vietnamese rice cultivar OM 5930 release NTCT and may be utilized to suppress barnyard grass in rice fields. The potency of NTCT may encourage development of this compound as a bio-herbicide. Copyright © 2014 Elsevier Ltd. All rights reserved.

Use of molecular markers in identification and characterization of resistance to rice blast in India.

PubMed

Yadav, Manoj Kumar; S, Aravindan; Ngangkham, Umakanta; Shubudhi, H N; Bag, Manas Kumar; Adak, Totan; Munda, Sushmita; Samantaray, Sanghamitra; Jena, Mayabini

2017-01-01

Rice blast disease caused by Magnaporthe oryzae is one of the most destructive disease causing huge losses to rice yield in different parts of the world. Therefore, an attempt has been made to find out the resistance by screening and studying the genetic diversity of eighty released rice varieties by National Rice Research Institute, Cuttack (NRVs) using molecular markers linked to twelve major blast resistance (R) genes viz Pib, Piz, Piz-t, Pik, Pik-p, Pikm Pik-h, Pita/Pita-2, Pi2, Pi9, Pi1 and Pi5. Out of which, nineteen varieties (23.75%) showed resistance, twenty one were moderately resistant (26.25%) while remaining forty varieties (50%) showed susceptible in uniform blast nursery. Rice varieties possessing blast resistance genes varied from four to twelve and the frequencies of the resistance genes ranged from 0 to 100%. The cluster analysis grouped the eighty NRVs into two major clusters at 63% level of genetic similarity coefficient. The PIC value for seventeen markers varied from 0 to 0.37 at an average of 0.20. Out of seventeen markers, only five markers, 195R-1, Pi9-i, Pita3, YL155/YL87 and 40N23r corresponded to three broad spectrum R genes viz. Pi9, Pita/Pita2 and Pi5 were found to be significantly associated with the blast disease with explaining phenotypic variance from 3.5% to 7.7%. The population structure analysis and PCoA divided the entire 80 NRVs into two sub-groups. The outcome of this study would help to formulate strategies for improving rice blast resistance through genetic studies, plant-pathogen interaction, identification of novel R genes, development of new resistant varieties through marker-assisted breeding for improving rice blast resistance in India and worldwide.

Accelerating public sector rice breeding with high-density KASP markers derived from whole genome sequencing of indica rice.

PubMed

Steele, Katherine A; Quinton-Tulloch, Mark J; Amgai, Resham B; Dhakal, Rajeev; Khatiwada, Shambhu P; Vyas, Darshna; Heine, Martin; Witcombe, John R

2018-01-01

Few public sector rice breeders have the capacity to use NGS-derived markers in their breeding programmes despite rapidly expanding repositories of rice genome sequence data. They rely on > 18,000 mapped microsatellites (SSRs) for marker-assisted selection (MAS) using gel analysis. Lack of knowledge about target SNP and InDel variant loci has hampered the uptake by many breeders of Kompetitive allele-specific PCR (KASP), a proprietary technology of LGC genomics that can distinguish alleles at variant loci. KASP is a cost-effective single-step genotyping technology, cheaper than SSRs and more flexible than genotyping by sequencing (GBS) or array-based genotyping when used in selection programmes. Before this study, there were 2015 rice KASP marker loci in the public domain, mainly identified by array-based screening, leaving large proportions of the rice genome with no KASP coverage. Here we have addressed the urgent need for a wide choice of appropriate rice KASP assays and demonstrated that NGS can detect many more KASP to give full genome coverage. Through re-sequencing of nine indica rice breeding lines or released varieties, this study has identified 2.5 million variant sites. Stringent filtering of variants generated 1.3 million potential KASP assay designs, including 92,500 potential functional markers. This strategy delivers a 650-fold increase in potential selectable KASP markers at a density of 3.1 per 1 kb in the indica crosses analysed and 377,178 polymorphic KASP design sites on average per cross. This knowledge is available to breeders and has been utilised to improve the efficiency of public sector breeding in Nepal, enabling identification of polymorphic KASP at any region or quantitative trait loci in relevant crosses. Validation of 39 new KASP was carried out by genotyping progeny from a range of crosses to show that they detected segregating alleles. The new KASP have replaced SSRs to aid trait selection during marker-assisted backcrossing in these crosses, where target traits include rice blast and BLB resistance loci. Furthermore, we provide the software for plant breeders to generate KASP designs from their own datasets.

Phylogenetic Diversity of Lactic Acid Bacteria Associated with Paddy Rice Silage as Determined by 16S Ribosomal DNA Analysis

PubMed Central

Ennahar, Saïd; Cai, Yimin; Fujita, Yasuhito

2003-01-01

A total of 161 low-G+C-content gram-positive bacteria isolated from whole-crop paddy rice silage were classified and subjected to phenotypic and genetic analyses. Based on morphological and biochemical characters, these presumptive lactic acid bacterium (LAB) isolates were divided into 10 groups that included members of the genera Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, and Weissella. Analysis of the 16S ribosomal DNA (rDNA) was used to confirm the presence of the predominant groups indicated by phenotypic analysis and to determine the phylogenetic affiliation of representative strains. The virtually complete 16S rRNA gene was PCR amplified and sequenced. The sequences from the various LAB isolates showed high degrees of similarity to those of the GenBank reference strains (between 98.7 and 99.8%). Phylogenetic trees based on the 16S rDNA sequence displayed high consistency, with nodes supported by high bootstrap values. With the exception of one species, the genetic data was in agreement with the phenotypic identification. The prevalent LAB, predominantly homofermentative (66%), consisted of Lactobacillus plantarum (24%), Lactococcus lactis (22%), Leuconostoc pseudomesenteroides (20%), Pediococcus acidilactici (11%), Lactobacillus brevis (11%), Enterococcus faecalis (7%), Weissella kimchii (3%), and Pediococcus pentosaceus (2%). The present study, the first to fully document rice-associated LAB, showed a very diverse community of LAB with a relatively high number of species involved in the fermentation process of paddy rice silage. The comprehensive 16S rDNA-based approach to describing LAB community structure was valuable in revealing the large diversity of bacteria inhabiting paddy rice silage and enabling the future design of appropriate inoculants aimed at improving its fermentation quality. PMID:12514026

Phylogenetic diversity of lactic acid bacteria associated with paddy rice silage as determined by 16S ribosomal DNA analysis.

PubMed

Ennahar, Saïd; Cai, Yimin; Fujita, Yasuhito

2003-01-01

A total of 161 low-G+C-content gram-positive bacteria isolated from whole-crop paddy rice silage were classified and subjected to phenotypic and genetic analyses. Based on morphological and biochemical characters, these presumptive lactic acid bacterium (LAB) isolates were divided into 10 groups that included members of the genera Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, and WEISSELLA: Analysis of the 16S ribosomal DNA (rDNA) was used to confirm the presence of the predominant groups indicated by phenotypic analysis and to determine the phylogenetic affiliation of representative strains. The virtually complete 16S rRNA gene was PCR amplified and sequenced. The sequences from the various LAB isolates showed high degrees of similarity to those of the GenBank reference strains (between 98.7 and 99.8%). Phylogenetic trees based on the 16S rDNA sequence displayed high consistency, with nodes supported by high bootstrap values. With the exception of one species, the genetic data was in agreement with the phenotypic identification. The prevalent LAB, predominantly homofermentative (66%), consisted of Lactobacillus plantarum (24%), Lactococcus lactis (22%), Leuconostoc pseudomesenteroides (20%), Pediococcus acidilactici (11%), Lactobacillus brevis (11%), Enterococcus faecalis (7%), Weissella kimchii (3%), and Pediococcus pentosaceus (2%). The present study, the first to fully document rice-associated LAB, showed a very diverse community of LAB with a relatively high number of species involved in the fermentation process of paddy rice silage. The comprehensive 16S rDNA-based approach to describing LAB community structure was valuable in revealing the large diversity of bacteria inhabiting paddy rice silage and enabling the future design of appropriate inoculants aimed at improving its fermentation quality.

Genetic analysis and identification of SSR markers associated with rice blast disease in a BC2F1 backcross population.

PubMed

Hasan, N; Rafii, M Y; Abdul Rahim, H; Nusaibah, S A; Mazlan, N; Abdullah, S

2017-01-23

Rice (Oryza sativa L.) blast disease is one of the most destructive rice diseases in the world. The fungal pathogen, Magnaporthe oryzae, is the causal agent of rice blast disease. Development of resistant cultivars is the most preferred method to achieve sustainable rice production. However, the effectiveness of resistant cultivars is hindered by the genetic plasticity of the pathogen genome. Therefore, information on genetic resistance and virulence stability are vital to increase our understanding of the molecular basis of blast disease resistance. The present study set out to elucidate the resistance pattern and identify potential simple sequence repeat markers linked with rice blast disease. A backcross population (BC 2 F 1 ), derived from crossing MR264 and Pongsu Seribu 2 (PS2), was developed using marker-assisted backcross breeding. Twelve microsatellite markers carrying the blast resistance gene clearly demonstrated a polymorphic pattern between both parental lines. Among these, two markers, RM206 and RM5961, located on chromosome 11 exhibited the expected 1:1 testcross ratio in the BC 2 F 1 population. The 195 BC 2 F 1 plants inoculated against M. oryzae pathotype P7.2 showed a significantly different distribution in the backcrossed generation and followed Mendelian segregation based on a single-gene model. This indicates that blast resistance in PS2 is governed by a single dominant gene, which is linked to RM206 and RM5961 on chromosome 11. The findings presented in this study could be useful for future blast resistance studies in rice breeding programs.

Mapping Quantitative Trait Loci Associated with Toot Traits Using Sequencing-Based Genotyping Chromosome Segment Substitution Lines Derived from 9311 and Nipponbare in Rice (Oryza sativa L.).

PubMed

Zhou, Yong; Dong, Guichun; Tao, Yajun; Chen, Chen; Yang, Bin; Wu, Yue; Yang, Zefeng; Liang, Guohua; Wang, Baohe; Wang, Yulong

2016-01-01

Identification of quantitative trait loci (QTLs) associated with rice root morphology provides useful information for avoiding drought stress and maintaining yield production under the irrigation condition. In this study, a set of chromosome segment substitution lines derived from 9311 as the recipient and Nipponbare as donor, were used to analysis root morphology. By combining the resequencing-based bin-map with a multiple linear regression analysis, QTL identification was conducted on root number (RN), total root length (TRL), root dry weight (RDW), maximum root length (MRL), root thickness (RTH), total absorption area (TAA) and root vitality (RV), using the CSSL population grown under hydroponic conditions. A total of thirty-eight QTLs were identified: six for TRL, six for RDW, eight for the MRL, four for RTH, seven for RN, two for TAA, and five for RV. Phenotypic effect variance explained by these QTLs ranged from 2.23% to 37.08%, and four single QTLs had more than 10% phenotypic explanations on three root traits. We also detected the correlations between grain yield (GY) and root traits, and found that TRL, RTH and MRL had significantly positive correlations with GY. However, TRL, RDW and MRL had significantly positive correlations with biomass yield (BY). Several QTLs identified in our population were co-localized with some loci for grain yield or biomass. This information may be immediately exploited for improving rice water and fertilizer use efficiency for molecular breeding of root system architectures.

Identification of seedling vigor-associated quantitative trait loci in temperate japonica rice

USDA-ARS?s Scientific Manuscript database

A quantitative trait loci (QTL) analysis of seedling vigor traits was conducted under dry-seeded conditions using 176 recombinant inbred lines developed from a cross of two California temperate japonica rice varieties M-203 and M-206. Height at early seedling (HES) and late seedling (HLS) stage, gro...

Identification of blast resistance genes for managing rice blast disease

USDA-ARS?s Scientific Manuscript database

Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating diseases worldwide. In the present study, an international set of monogenic differentials carrying 24 major blast resistance (R) genes (Pia, Pib, Pii, Pik, Pik-h, Pik-m, Pik-p, Pik-s, Pish, Pit, Pita, Pita2,...

PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice and chickpea

PubMed Central

Singh, Urminder; Rajkumar, Mohan Singh; Garg, Rohini

2017-01-01

Abstract Long non-coding RNAs (lncRNAs) make up a significant portion of non-coding RNAs and are involved in a variety of biological processes. Accurate identification/annotation of lncRNAs is the primary step for gaining deeper insights into their functions. In this study, we report a novel tool, PLncPRO, for prediction of lncRNAs in plants using transcriptome data. PLncPRO is based on machine learning and uses random forest algorithm to classify coding and long non-coding transcripts. PLncPRO has better prediction accuracy as compared to other existing tools and is particularly well-suited for plants. We developed consensus models for dicots and monocots to facilitate prediction of lncRNAs in non-model/orphan plants. The performance of PLncPRO was quite better with vertebrate transcriptome data as well. Using PLncPRO, we discovered 3714 and 3457 high-confidence lncRNAs in rice and chickpea, respectively, under drought or salinity stress conditions. We investigated different characteristics and differential expression under drought/salinity stress conditions, and validated lncRNAs via RT-qPCR. Overall, we developed a new tool for the prediction of lncRNAs in plants and showed its utility via identification of lncRNAs in rice and chickpea. PMID:29036354

Disruption of a Rice Pentatricopeptide Repeat Protein Causes a Seedling-Specific Albino Phenotype and Its Utilization to Enhance Seed Purity in Hybrid Rice Production1[W][OA

PubMed Central

Su, Ning; Hu, Mao-Long; Wu, Dian-Xing; Wu, Fu-Qing; Fei, Gui-Lin; Lan, Ying; Chen, Xiu-Ling; Shu, Xiao-Li; Zhang, Xin; Guo, Xiu-Ping; Cheng, Zhi-Jun; Lei, Cai-Lin; Qi, Cun-Kou; Jiang, Ling; Wang, Haiyang; Wan, Jian-Min

2012-01-01

The pentatricopeptide repeat (PPR) gene family represents one of the largest gene families in higher plants. Accumulating data suggest that PPR proteins play a central and broad role in modulating the expression of organellar genes in plants. Here we report a rice (Oryza sativa) mutant named young seedling albino (ysa) derived from the rice thermo/photoperiod-sensitive genic male-sterile line Pei'ai64S, which is a leading male-sterile line for commercial two-line hybrid rice production. The ysa mutant develops albino leaves before the three-leaf stage, but the mutant gradually turns green and recovers to normal green at the six-leaf stage. Further investigation showed that the change in leaf color in ysa mutant is associated with changes in chlorophyll content and chloroplast development. Map-based cloning revealed that YSA encodes a PPR protein with 16 tandem PPR motifs. YSA is highly expressed in young leaves and stems, and its expression level is regulated by light. We showed that the ysa mutation has no apparent negative effects on several important agronomic traits, such as fertility, stigma extrusion rate, selfed seed-setting rate, hybrid seed-setting rate, and yield heterosis under normal growth conditions. We further demonstrated that ysa can be used as an early marker for efficient identification and elimination of false hybrids in commercial hybrid rice production, resulting in yield increases by up to approximately 537 kg ha−1. PMID:22430843

Effective screen of CRISPR/Cas9-induced mutants in rice by single-strand conformation polymorphism.

PubMed

Zheng, Xuelian; Yang, Shixin; Zhang, Dengwei; Zhong, Zhaohui; Tang, Xu; Deng, Kejun; Zhou, Jianping; Qi, Yiping; Zhang, Yong

2016-07-01

A method based on DNA single-strand conformation polymorphism is demonstrated for effective genotyping of CRISPR/Cas9-induced mutants in rice. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) has been widely adopted for genome editing in many organisms. A large proportion of mutations generated by CRISPR/Cas9 are very small insertions and deletions (indels), presumably because Cas9 generates blunt-ended double-strand breaks which are subsequently repaired without extensive end-processing. CRISPR/Cas9 is highly effective for targeted mutagenesis in the important crop, rice. For example, homozygous mutant seedlings are commonly recovered from CRISPR/Cas9-treated calli. However, many current mutation detection methods are not very suitable for screening homozygous mutants that typically carry small indels. In this study, we tested a mutation detection method based on single-strand conformational polymorphism (SSCP). We found it can effectively detect small indels in pilot experiments. By applying the SSCP method for CRISRP-Cas9-mediated targeted mutagenesis in rice, we successfully identified multiple mutants of OsROC5 and OsDEP1. In conclusion, the SSCP analysis will be a useful genotyping method for rapid identification of CRISPR/Cas9-induced mutants, including the most desirable homozygous mutants. The method also has high potential for similar applications in other plant species.

Identification of introgressed alien chromosome segments associated with grain quality in Oryza rufipogon x MR219 advanced breeding lines using SSR markers.

PubMed

Fasahat, P; Muhammad, K; Abdullah, A; Wickneswari, R

2012-09-26

A limited backcross procedure was utilized to introgress genes associated with grain quality traits from Oryza rufipogon (Accession No. IRGC 105491), a wild rice from Malaysia, to the cultivated rice O. sativa cv. MR219, a popular high yielding Malaysian rice cultivar. A set of 10 BC(2)F(7) progenies were selected based on the field performance and phenotypic appearance in BC(2)F(5) and BC(2)F(6) generations, which initially started with 266 progenies in the BC(2)F(2) generation. These 10 advanced breeding lines are similar to each other but differ in several important grain quality traits, which can be traced to O. rufipogon introgressions. Phenotyping and genotyping of BC(2)F(7) variants were considered for QTL analysis. The introgressed lines did not show any significant changes compared to the recurrent parent MR219 for the traits grain density and milled rice percentage. All 10 progenies showed significantly higher head rice percentages (70-88%) than the recurrent parent MR219. Variants G13 and G15 had higher amylose contents than MR219. All variants were analyzed using polymorphic SSR markers. Of the 34 SSR markers, only 18 showed introgression from O. rufipogon for chromosomes 1, 2, 3, 5, 6, 8, 10, and 11. Graphical genotypes were prepared for each variant, and association between the introgression regions and the traits that increased grain quality was visualized. Based on marker trait association, some of the QTLs are stable across environments and genetic backgrounds and could be used universally.

West Java Snack Mapping based on Snack Types, Main Ingredients, and Processing Techniques

NASA Astrophysics Data System (ADS)

Nurani, A. S.; Subekti, S.; Ana

2016-04-01

The research was motivated by lack of literature on archipelago snack especially from West Java. It aims to explore the snack types, the processing techniques, and the main ingredients by planning a learning material on archipelago cake especially from West Java. The research methods used are descriptive observations and interviews. The samples were randomly chosen from all regions in West Java. The findings show the identification of traditional snack from West java including: 1. snack types which are similar in all regions as research sample namely: opak, rangginang, nagasari, aliagrem, cuhcur, keripik, semprong, wajit, dodol, kecimpring, combro, tape ketan, and surabi. The typical snack types involve burayot (Garut), simping kaum (Purwakarta), surabi hejo (Karawang), papais cisaat (Subang), Papais moyong, opak bakar (Kuningan), opak oded, ranggesing (Sumedang), gapit, tapel (Cirebon), gulampo, kue aci (Tasikmalaya), wajit cililin, gurilem (West Bandung), and borondong (Bandung District); 2. various processing techniques namely: steaming, boiling, frying, caramelizing, baking, grilling, roaster, sugaring; 3. various main ingredients namely rice, local glutinous rice, rice flour, glutinous rice flour, starch, wheat flour, hunkue flour, cassava, sweet potato, banana, nuts, and corn; 4. snack classification in West Java namely (1) traditional snack, (2) creation-snack, (3) modification-snack, (4) outside influence-snack.

Identification of Potential Anticancer Activities of Novel Ganoderma lucidum Extracts Using Gene Expression and Pathway Network Analysis

PubMed Central

Kao, Chi H.J.; Bishop, Karen S.; Xu, Yuanye; Han, Dug Yeo; Murray, Pamela M.; Marlow, Gareth J.; Ferguson, Lynnette R.

2016-01-01

Ganoderma lucidum (lingzhi) has been used for the general promotion of health in Asia for many centuries. The common method of consumption is to boil lingzhi in water and then drink the liquid. In this study, we examined the potential anticancer activities of G. lucidum submerged in two commonly consumed forms of alcohol in East Asia: malt whiskey and rice wine. The anticancer effect of G. lucidum, using whiskey and rice wine-based extraction methods, has not been previously reported. The growth inhibition of G. lucidum whiskey and rice wine extracts on the prostate cancer cell lines, PC3 and DU145, was determined. Using Affymetrix gene expression assays, several biologically active pathways associated with the anticancer activities of G. lucidum extracts were identified. Using gene expression analysis (real-time polymerase chain reaction [RT-PCR]) and protein analysis (Western blotting), we confirmed the expression of key genes and their associated proteins that were initially identified with Affymetrix gene expression analysis. PMID:27006591

Identification of trans-acting factors regulating SamDC expression in Oryza sativa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Basu, Supratim, E-mail: supratim_genetics@yahoo.co.in; Division of Plant Biology, Bose Institute, Kolkata; Roychoudhury, Aryadeep

2014-03-07

Highlights: • Identification of cis elements responsible for SamDC expression by in silico analysis. • qPCR analysis of SamDC expression to abiotic and biotic stress treatments. • Detection of SamDC regulators using identified cis-elements as probe by EMSA. • Southwestern Blot analysis to predict the size of the trans-acting factors. - Abstract: Abiotic stress affects the growth and productivity of crop plants; to cope with the adverse environmental conditions, plants have developed efficient defense machinery comprising of antioxidants like phenolics and flavonoids, and osmolytes like polyamines. SamDC is a key enzyme in the polyamine biosynthesis pathway in plants. In ourmore » present communication we have done in silico analysis of the promoter region of SamDC to look for the presence of different cis-regulatory elements contributing to its expression. Based on the presence of different cis-regulatory elements we completed comparative analysis of SamDC gene expression in rice lamina of IR-29 and Nonabokra by qPCR in response to the abiotic stress treatments of salinity, drought, cold and the biotic stress treatments of ABA and light. Additionally, to explore the role of the cis-regulatory elements in regulating the expression of SamDC gene in plants we comparatively analyzed the binding of rice nuclear proteins prepared from IR-29 and Nonabokra undergoing various stress treatments. The intensity of the complex formed was low and inducible in IR-29 in contrast to Nonabokra. Southwestern blot analysis helped in predicting the size of the trans-acting factors binding to these cis-elements. To our knowledge this is the first report on the comprehensive analysis of SamDC gene expression in rice and identification of the trans-acting factors regulating its expression.« less

Identification of heavy-ion radiation-induced microRNAs in rice

NASA Astrophysics Data System (ADS)

Zhang, Meng; Liang, Shujian; Hang, Xiaoming; Sun, Yeqing

As an excellent model organism for studying the effects of environmental stress, rice was used to assess biological effect of the space radiation environment. Rice abnormal development or growth was observed frequently after seeds space flight. MicroRNAs (miRNAs) are a family of small non-coding regulatory RNAs, which have significant roles in regulating development and stress responses in plant. To identify whether the miRNAs were involved in biological effects of heavy-ion radiation, the germinated seeds of rice were exposed to 20 Gy dose of 12 C heavy-ion radiation which could induce rice development retarded. The microarray was used to monitor rice (Oryza sativa) miRNAs expression profiles under radiation stress. Members of miR164 family and miR156a-j were found up-regulated significantly, and confirmed by relative quantifi-cation real-time PCR. We found that the expression of the miR156 and miR164 increased and targets genes expression decrease was closely bound up with the irradiation rice phenotypes changes.

Plant genetic transformation efficiency of selected Malaysian rice based on selectable marker gene (hptII).

PubMed

Htwe, Nwe Nwe; Ling, Ho Chai; Zaman, Faridah Qamaruz; Maziah, Mahmood

2014-04-01

Rice is one of the most important cereal crops with great potential for biotechnology progress. In transformation method, antibiotic resistance genes are routinely used as powerful markers for selecting transformed cells from surrounding non-transformed cells. In this study, the toxicity level of hygromycin was optimized for two selected mutant rice lines, MR219 line 4 and line 9. The mature embryos were isolated and cultured on an MS medium with different hygromycin concentrations (0, 20, 40, 60, 80 and 100 mg L(-1)). Evidently, above 60 mg L(-1) was effective for callus formation and observed completely dead. Further there were tested for specific concentration (0-60). Although, 21.28% calli survived on the medium containing 45 mg L(-1) hygromycin, it seemed suitable for the identification of putative transformants. These findings indicated that a system for rice transformation in a relatively high frequency and the transgenes are stably expressed in the transgenic plants. Green shoots were regenerated from the explant under hygromycin stress. RT-PCR using hptII and gus sequence specific primer and Southern blot analysis were used to confirm the presence of the transgene and to determine the transformation efficiency for their stable integration in regenerated plants. This study demonstrated that the hygromycin resistance can be used as an effective marker for rice transformation.

Enumeration, isolation and identification of diazotrophs from Korean wetland rice varieties grown with long-term application of N and compost and their short-term inoculation effect on rice plants.

PubMed

Muthukumarasamy, R; Kang, U G; Park, K D; Jeon, W-T; Park, C Y; Cho, Y S; Kwon, S-W; Song, J; Roh, D-H; Revathi, G

2007-04-01

This study has been aimed (i) to isolate and identify diazotrophs from Korean rice varieties; (ii) to examine the long-term effect of N and compost on the population dynamics of diazotrophs and (iii) to realize the shot-term inoculation effect of these diazotrophs on rice seedlings. Diazotrophic and heterotrophic bacterial numbers were enumerated by most probable number method and the isolates were identified based on morphological, physiological, biochemical and 16s rDNA sequence analysis. Long-term application of fertilizer N with compost enhanced both these numbers in rice plants and its environment. Bacteria were high in numbers when malate and azelaic acids were used as carbon source, but less when sucrose was used as a carbon substrate. The combined application promoted the association of diazotrophic bacteria like Azospirillum spp., Herbaspirillum spp., Burkholderia spp., Gluconacetobacter diazotrophicus and Pseudomonas spp. in wetland rice plants. Detection of nifD genes from different diazotrophic isolates indicated their nitrogen fixing ability. Inoculation of a representative isolate from each group onto rice seedlings of the variety IR 36 grown in test tubes indicated the positive effect of these diazotrophs on the growth of rice seedlings though the percentage of N present in the plants did not differ much. Application of compost with fertilizer N promoted the diazotrophic and heterotrophic bacterial numbers and their association with wetland rice and its environment. Compost application in high N fertilized fields would avert the reduction of N(2)-fixing bacterial numbers and their association was beneficial to the growth of rice plants. The inhibitory effect of high N fertilization on diazotrophic bacterial numbers could be reduced by the application of compost and this observation would encourage more usage of organic manure. This study has also thrown light on the wider geographic distribution of G. diazotrophicus with wetland rice in temperate region where sugarcane (from which this bacterium was first reported to be associating and thereon from other plant species) is not cultivated.

Screening of IR50 x Rathu Heenati F7 RILs and identification of SSR markers linked to brown planthopper (Nilaparvata lugens Stål) resistance in rice (Oryza sativa L.).

PubMed

Kumari, Sanju; M Sheba, Jennifer; Marappan, Maheshwaran; Ponnuswamy, Shanmugasunderam; Seetharaman, Suresh; Pothi, Nagarajan; Subbarayalu, Mohankumar; Muthurajan, Raveendran; Natesan, Senthil

2010-09-01

Brown planthopper (Nilaparvata lugens Stål) is one of the major insect pests of rice. A Sri Lankan indica rice cultivar Rathu Heenati was found to be resistant to all biotypes of the brown planthopper. In the present study, a total of 268 F(7) RILs of IR50 and Rathu Heenati were phenotyped for their level of resistance against BPH by the standard seedbox screening test (SSST) in the greenhouse. A total of 53 SSR primers mapped on the chromosome 3 were used to screen the polymorphism between the parents IR50 and Rathu Heenati, out of which eleven were found to be polymorphic between IR50 and Rathu Heenati. The eleven primers that have shown polymorphism between the IR50 and Rathu Heenati parents were genotyped in a set of five resistant RILs and five susceptible RILs along with the parents for co-segregation analysis. Among the eleven primers, two primers namely RM3180 (18.22 Mb) and RM2453 (20.19 Mb) showed complete co-segregation with resistance. The identification of SSR markers linked with BPH resistant could be used for the maker assisted selection (MAS) program in rice breeding and to map the resistant genes on rice chromosomes for further gene cloning.

Designing climate-resilient rice with ideal grain quality suited for high-temperature stress

PubMed Central

Sreenivasulu, Nese; Butardo, Vito M.; Misra, Gopal; Cuevas, Rosa Paula; Anacleto, Roslen; Kavi Kishor, Polavarpu B.

2015-01-01

To ensure rice food security, the target outputs of future rice breeding programmes should focus on developing climate-resilient rice varieties with emphasis on increased head rice yield coupled with superior grain quality. This challenge is made greater by a world that is increasingly becoming warmer. Such environmental changes dramatically impact head rice and milling yield as well as increasing chalkiness because of impairment in starch accumulation and other storage biosynthetic pathways in the grain. This review highlights the knowledge gained through gene discovery via quantitative trait locus (QTL) cloning and structural–functional genomic strategies to reduce chalk, increase head rice yield, and develop stable lines with optimum grain quality in challenging environments. The newly discovered genes and the knowledge gained on the influence of specific alleles related to stability of grain quality attributes provide a robust platform for marker-assisted selection in breeding to design heat-tolerant rice varieties with superior grain quality. Using the chalkiness trait in rice as a case study, we demonstrate here that the emerging field of systems genetics can help fast-track the identification of novel alleles and gene targets that can be pyramided for the development of environmentally robust rice varieties that possess improved grain quality. PMID:25662847

Identification and characterization of OsEBS, a gene involved in enhanced plant biomass and spikelet number in rice.

PubMed

Dong, Xianxin; Wang, Xiaoyan; Zhang, Liangsheng; Yang, Zhengting; Xin, Xiaoyun; Wu, Shuang; Sun, Chuanqing; Liu, Jianxiang; Yang, Jinshui; Luo, Xiaojin

2013-12-01

Common wild rice (Oryza rufipogon Griff.) is an important genetic reservoir for rice improvement. We investigated a quantitative trait locus (QTL), qGP5-1, which is related to plant height, leaf size and panicle architecture, using a set of introgression lines of O. rufipogon in the background of the Indica cultivar Guichao2 (Oryza sativa L.). We cloned and characterized qGP5-1 and confirmed that the newly identified gene OsEBS (enhancing biomass and spikelet number) increased plant height, leaf size and spikelet number per panicle, leading to an increase in total grain yield per plant. Our results showed that the increased size of vegetative organs in OsEBS-expressed plants was enormously caused by increasing cell number. Sequence alignment showed that OsEBS protein contains a region with high similarity to the N-terminal conserved ATPase domain of Hsp70, but it lacks the C-terminal regions of the peptide-binding domain and the C-terminal lid. More results indicated that OsEBS gene did not have typical characteristics of Hsp70 in this study. Furthermore, Arabidopsis (Arabidopsis thaliana) transformed with OsEBS showed a similar phenotype to OsEBS-transgenic rice, indicating a conserved function of OsEBS among plant species. Together, we report the cloning and characterization of OsEBS, a new QTL that controls rice biomass and spikelet number, through map-based cloning, and it may have utility in improving grain yield in rice. © 2013 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Map-based cloning and characterization of the novel yellow-green leaf gene ys83 in rice (Oryza sativa).

PubMed

Ma, Xiaozhi; Sun, Xiaoqiu; Li, Chunmei; Huan, Rui; Sun, Changhui; Wang, Yang; Xiao, Fuliang; Wang, Qian; Chen, Purui; Ma, Furong; Zhang, Kuan; Wang, Pingrong; Deng, Xiaojian

2017-02-01

Leaf-color mutants have been extensively studied in rice, and many corresponding genes have been identified up to now. However, leaf-color mutation mechanisms are diverse and still need further research through identification of novel genes. In the present paper, we isolated a leaf-color mutant, ys83, in rice (Oryza sativa). The mutant displayed a yellow-green leaf phenotype at seedling stage, and then slowly turned into light-green leaf from late tillering stage. In its yellow leaves, photosynthetic pigment contents significantly decreased and the chloroplast development was retarded. The mutant phenotype was controlled by a recessive mutation in a nuclear gene on the short arm of rice chromosome 2. Map-based cloning and sequencing analysis suggested that the candidate gene was YS83 (LOC_Os02g05890) encoding a protein containing 165 amino acid residues. Gene YS83 was expressed in a wide range of tissues, and its encoded protein was targeted to the chloroplast. In the mutant, a T-to-A substitution occurred in coding sequence of gene YS83, which caused a premature translation of its encoded product. By introduction of the wild-type gene, the ys83 mutant recovered to normal green-leaf phenotype. Taken together, we successfully identified a novel yellow-green leaf gene YS83. In addition, number of productive panicles per plant and number of spikelets per panicle only reduced by 6.7% and 7.6%, respectively, meanwhile its seed setting rate and 1000-grain weight (seed size) were not significantly affected in the mutant, so leaf-color mutant gene ys83 could be used as a trait marker gene in commercial hybrid rice production. Copyright © 2016. Published by Elsevier Masson SAS.

Role of defense/stress-related marker genes, proteins and secondary metabolites in defining rice self-defense mechanisms.

PubMed

Jwa, Nam-Soo; Agrawal, Ganesh Kumar; Tamogami, Shigeru; Yonekura, Masami; Han, Oksoo; Iwahashi, Hitoshi; Rakwal, Randeep

2006-01-01

Rice, a first cereal crop whose draft genome sequence from two subspecies (japonica-type cv. Nipponbare and indica-type 93-11) was available in 2002, along with its almost complete genome sequence in 2005, has drawn the attention of researchers worldwide because of its immense impact on human existence. One of the most critical research areas in rice is to discern the self-defense mechanism(s), an innate property of all living organisms. The last few decades have seen scattered research into rice responses to diverse environmental stimuli and stress factors. Our understanding on rice self-defense mechanism has increased considerably with accelerated research during recent years mainly due to identification and characterization of several defense/stress-related components, genes, proteins and secondary metabolites. As these identified components have been used to study the defense/stress pathways, their compilation in this review will undoubtedly help rice (and others) researchers to effectively use them as a potential marker for better understanding, and ultimately, in defining rice (and plant) self-defense response pathways.

Identification of myo-inositol hexakisphosphate (IP6) as a β-secretase 1 (BACE1) inhibitory molecule in rice grain extract and digest

PubMed Central

Abe, Takako K.; Taniguchi, Masayuki

2014-01-01

Alzheimer’s disease (AD) is widely considered to be caused by amyloid-β peptide (Aβ) accumulation in the brain. Aβ is excised from amyloid-β precursor protein through sequential cleavage by β-secretase 1 (BACE1) and γ-secretase. Thus, BACE1 inhibition could prevent Aβ accumulation. Here, we identified myo-inositol hexakisphosphate (IP6) as a BACE1 inhibitory molecule in rice grain extract and digest. The rice digest and IP6 significantly inhibited Aβ production in neuroblastoma cells without cytotoxicity. These results suggested that rice components, including IP6, may be promising starting materials for the development of potent and safe drugs and/or food to prevent AD. PMID:24649396

Discrimination of red and white rice bran from Indonesia using HPLC fingerprint analysis combined with chemometrics.

PubMed

Sabir, Aryani; Rafi, Mohamad; Darusman, Latifah K

2017-04-15

HPLC fingerprint analysis combined with chemometrics was developed to discriminate between the red and the white rice bran grown in Indonesia. The major component in rice bran is γ-oryzanol which consisted of 4 main compounds, namely cycloartenol ferulate, cyclobranol ferulate, campesterol ferulate and β-sitosterol ferulate. Separation of these four compounds along with other compounds was performed using C18 and methanol-acetonitrile with gradient elution system. By using these intensity variations, principal component and discriminant analysis were performed to discriminate the two samples. Discriminant analysis was successfully discriminated the red from the white rice bran with predictive ability of the model showed a satisfactory classification for the test samples. The results of this study indicated that the developed method was suitable as quality control method for rice bran in terms of identification and discrimination of the red and the white rice bran. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identification of Rice Koji Extract Components that Increase β-Glucocerebrosidase Levels in Human Epidermal Keratinocytes.

PubMed

Maeda, Kazuhisa; Ogino, Yuuka; Nakamura, Ayano; Nakata, Keiji; Kitagawa, Manabu; Ito, Seiki

2018-06-18

Rice miso contains many ingredients derived from rice koji and has been a valuable source of nutrition since ancient times. We found that the consumption of rice miso led to improvements in the moisture content of cheek stratum corneum, skin viscoelasticity, and skin texture. Further, rice miso extract was found to increase the mRNA expression and activity of β-glucocerebrosidase (β-GCase), an enzyme involved in ceramide synthesis in the stratum corneum, in cultures. In this study, we identified the lipid-derived components of rice koji that increase the β-GCase activity in cultured human epidermal keratinocytes. The methanol fraction of rice koji extract induced an increase in the mRNA expression and activity of β-GCase in keratinocytes. The active fraction of rice koji was found to contain phosphatidic acid (PA) and lysophosphatidic acid (LPA). The total PA concentration in rice koji was 973.9 ng/mg dry weight, which was 17.5 times higher than that in steamed rice. Among the molecular species, PA_18:2/18:2 was the most frequently found. The total LPA concentration in rice koji was 29.6 ng/mg dry weight, and 2-LPA_18:2 was the most frequently found LPA. Since PA and LPA increase the mRNA expression and activity of β-GCase in keratinocytes, they are thought to be the active ingredients in rice koji that increase the β-GCase levels in human epidermal keratinocytes.

Rice protein-based infant formula: current status and future development.

PubMed

Koo, W W K; Lasekan, J B

2007-02-01

Rice is the world's leading staple cereal food and is the major source of protein for many parts of the world. Rice is among the first solid foods fed to infants in many cultures, in part because of its hypoallergenicity from lack of gluten. Nutritional quality of rice protein compares favorably with other cereal proteins including wheat, oat and barley. It is rich in methionine and cystine, although as is the case for other cereals, it is an incomplete protein source for human infants with lysine and threonine being the primary limiting amino acids. Fortification of rice proteins with these two limiting amino acids improves its protein quality. Rice protein-based infant formulas (RPF) were initially based on high protein rice flours, but more recently are based on rice protein concentrates, isolates or hydrolysates, fortified with lysine and threonine. Hypoallergenicity efficacy, particularly for hydrolyzed rice protein-based formulas, has been reported, and limited data indicated that rice protein based infant formula may provide potentially adequate alternative if standard milk- or soy protein-based formulas are not tolerated. Unlike the rice-protein based infant formula, rice beverage formulas made from rice flour are nutritionally inadequate for infants. Reports have indicated stunted growth in infants/children fed rice beverage formulas. Future development for the RPF include those based on genetically improved rice with high lysine and threonine content, supplementation with appropriate mineral and fat blend, and long-term clinical studies in infants to confirm its efficacy and safety.

Novel green tissue-specific synthetic promoters and cis-regulatory elements in rice.

PubMed

Wang, Rui; Zhu, Menglin; Ye, Rongjian; Liu, Zuoxiong; Zhou, Fei; Chen, Hao; Lin, Yongjun

2015-12-11

As an important part of synthetic biology, synthetic promoter has gradually become a hotspot in current biology. The purposes of the present study were to synthesize green tissue-specific promoters and to discover green tissue-specific cis-elements. We first assembled several regulatory sequences related to tissue-specific expression in different combinations, aiming to obtain novel green tissue-specific synthetic promoters. GUS assays of the transgenic plants indicated 5 synthetic promoters showed green tissue-specific expression patterns and different expression efficiencies in various tissues. Subsequently, we scanned and counted the cis-elements in different tissue-specific promoters based on the plant cis-elements database PLACE and the rice cDNA microarray database CREP for green tissue-specific cis-element discovery, resulting in 10 potential cis-elements. The flanking sequence of one potential core element (GEAT) was predicted by bioinformatics. Then, the combination of GEAT and its flanking sequence was functionally identified with synthetic promoter. GUS assays of the transgenic plants proved its green tissue-specificity. Furthermore, the function of GEAT flanking sequence was analyzed in detail with site-directed mutagenesis. Our study provides an example for the synthesis of rice tissue-specific promoters and develops a feasible method for screening and functional identification of tissue-specific cis-elements with their flanking sequences at the genome-wide level in rice.

Loss of function of a rice TPR-domain RNA-binding protein confers broad-spectrum disease resistance.

PubMed

Zhou, Xiaogang; Liao, Haicheng; Chern, Mawsheng; Yin, Junjie; Chen, Yufei; Wang, Jianping; Zhu, Xiaobo; Chen, Zhixiong; Yuan, Can; Zhao, Wen; Wang, Jing; Li, Weitao; He, Min; Ma, Bingtian; Wang, Jichun; Qin, Peng; Chen, Weilan; Wang, Yuping; Liu, Jiali; Qian, Yangwen; Wang, Wenming; Wu, Xianjun; Li, Ping; Zhu, Lihuang; Li, Shigui; Ronald, Pamela C; Chen, Xuewei

2018-03-20

Crops carrying broad-spectrum resistance loci provide an effective strategy for controlling infectious disease because these loci typically confer resistance to diverse races of a pathogen or even multiple species of pathogens. Despite their importance, only a few crop broad-spectrum resistance loci have been reported. Here, we report the identification and characterization of the rice bsr-k1 (broad-spectrum resistance Kitaake-1) mutant, which confers broad-spectrum resistance against Magnaporthe oryzae and Xanthomonas oryzae pv oryzae with no major penalty on key agronomic traits. Map-based cloning reveals that Bsr-k1 encodes a tetratricopeptide repeats (TPRs)-containing protein, which binds to mRNAs of multiple OsPAL ( OsPAL1-7 ) genes and promotes their turnover. Loss of function of the Bsr-k1 gene leads to accumulation of OsPAL1-7 mRNAs in the bsr-k1 mutant. Furthermore, overexpression of OsPAL1 in wild-type rice TP309 confers resistance to M. oryzae , supporting the role of OsPAL1 Our discovery of the bsr-k1 allele constitutes a significant conceptual advancement and provides a valuable tool for breeding broad-spectrum resistant rice. Copyright © 2018 the Author(s). Published by PNAS.

LABA1, a Domestication Gene Associated with Long, Barbed Awns in Wild Rice.

PubMed

Hua, Lei; Wang, Diane R; Tan, Lubin; Fu, Yongcai; Liu, Fengxia; Xiao, Langtao; Zhu, Zuofeng; Fu, Qiang; Sun, Xianyou; Gu, Ping; Cai, Hongwei; McCouch, Susan R; Sun, Chuanqing

2015-07-01

Common wild rice (Oryza rufipogon), the wild relative of Asian cultivated rice (Oryza sativa), flaunts long, barbed awns, which are necessary for efficient propagation and dissemination of seeds. By contrast, O. sativa cultivars have been selected to be awnless or to harbor short, barbless awns, which facilitate seed processing and storage. The transition from long, barbed awns to short, barbless awns was a crucial event in rice domestication. Here, we show that the presence of long, barbed awns in wild rice is controlled by a major gene on chromosome 4, LONG AND BARBED AWN1 (LABA1), which encodes a cytokinin-activating enzyme. A frame-shift deletion in LABA1 of cultivated rice reduces the cytokinin concentration in awn primordia, disrupting barb formation and awn elongation. Sequencing analysis demonstrated low nucleotide diversity and a selective sweep encompassing an ∼800-kb region around the derived laba1 allele in cultivated rice. Haplotype analysis revealed that the laba1 allele originated in the japonica subspecies and moved into the indica gene pool via introgression, suggesting that humans selected for this locus in early rice domestication. Identification of LABA1 provides new insights into rice domestication and also sheds light on the molecular mechanism underlying awn development. © 2015 American Society of Plant Biologists. All rights reserved.

LABA1, a Domestication Gene Associated with Long, Barbed Awns in Wild Rice[OPEN

PubMed Central

Hua, Lei; Wang, Diane R.; Tan, Lubin; Fu, Yongcai; Liu, Fengxia; Xiao, Langtao; Zhu, Zuofeng; Fu, Qiang; Sun, Xianyou; Gu, Ping; Cai, Hongwei; McCouch, Susan R.; Sun, Chuanqing

2015-01-01

Common wild rice (Oryza rufipogon), the wild relative of Asian cultivated rice (Oryza sativa), flaunts long, barbed awns, which are necessary for efficient propagation and dissemination of seeds. By contrast, O. sativa cultivars have been selected to be awnless or to harbor short, barbless awns, which facilitate seed processing and storage. The transition from long, barbed awns to short, barbless awns was a crucial event in rice domestication. Here, we show that the presence of long, barbed awns in wild rice is controlled by a major gene on chromosome 4, LONG AND BARBED AWN1 (LABA1), which encodes a cytokinin-activating enzyme. A frame-shift deletion in LABA1 of cultivated rice reduces the cytokinin concentration in awn primordia, disrupting barb formation and awn elongation. Sequencing analysis demonstrated low nucleotide diversity and a selective sweep encompassing an ∼800-kb region around the derived laba1 allele in cultivated rice. Haplotype analysis revealed that the laba1 allele originated in the japonica subspecies and moved into the indica gene pool via introgression, suggesting that humans selected for this locus in early rice domestication. Identification of LABA1 provides new insights into rice domestication and also sheds light on the molecular mechanism underlying awn development. PMID:26082172

Molecular mapping and genetic analysis of a rice brown planthopper (Nilaparvata lugens Stål) resistance gene.

PubMed

Yang, Haiyuan; Ren, Xiang; Weng, Qingmei; Zhu, Lili; He, Guangcun

2002-01-01

The brown planthopper (BPH), Nilaparvata lugens Stål, is a serious insect pest of rice (Oryza saliva L.). We have determined the chromosomal location of a BPH resistance gene in rice using SSR and RFLP techniques. A rice line 'B14', derived from the wild rice Oryza latifolia, showed high resistance to BPH. For tagging the resistance gene in 'B14X', an F2 population and a recombinant inbred (RI) population from a cross between Taichung Native 1 and 'B14' were developed and evaluated for BPH resistance. The results showed that a single dominant gene controlled the resistance of 'B14' to BPH. Bulked segregant SSR analysis was employed for identification of DNA markers linked to the resistance gene. From the survey of 302 SSR primer pairs, three SSR (RM335, RM261, RM185) markers linked to the resistance gene were identified. The closest SSR marker RM261 was linked to the resistance gene at a distance of 1.8 cM. Regions surrounding the resistance gene and the SSR markers were examined with additional RFLP markers on chromosome 4 to define the location of the resistance gene. Linkage of RFLP markers C820, R288, C946 with the resistance gene further confirmed its location on the short arm of chromosome 4. Closely linked DNA markers will facilitate selection for resistant lines in breeding programs and provide the basis for map-based cloning of this resistance gene.

Designing climate-resilient rice with ideal grain quality suited for high-temperature stress.

PubMed

Sreenivasulu, Nese; Butardo, Vito M; Misra, Gopal; Cuevas, Rosa Paula; Anacleto, Roslen; Kavi Kishor, Polavarpu B

2015-04-01

To ensure rice food security, the target outputs of future rice breeding programmes should focus on developing climate-resilient rice varieties with emphasis on increased head rice yield coupled with superior grain quality. This challenge is made greater by a world that is increasingly becoming warmer. Such environmental changes dramatically impact head rice and milling yield as well as increasing chalkiness because of impairment in starch accumulation and other storage biosynthetic pathways in the grain. This review highlights the knowledge gained through gene discovery via quantitative trait locus (QTL) cloning and structural-functional genomic strategies to reduce chalk, increase head rice yield, and develop stable lines with optimum grain quality in challenging environments. The newly discovered genes and the knowledge gained on the influence of specific alleles related to stability of grain quality attributes provide a robust platform for marker-assisted selection in breeding to design heat-tolerant rice varieties with superior grain quality. Using the chalkiness trait in rice as a case study, we demonstrate here that the emerging field of systems genetics can help fast-track the identification of novel alleles and gene targets that can be pyramided for the development of environmentally robust rice varieties that possess improved grain quality. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

7 CFR 1412.49 - Apportionment of long and medium grain rice.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 10 2012-01-01 2012-01-01 false Apportionment of long and medium grain rice. 1412.49... and Peanuts 2008 through 2012 § 1412.49 Apportionment of long and medium grain rice. (a) Rice base...) Medium grain rice. Medium grain rice includes short grain rice. (c) Owners on a farm will elect rice base...

7 CFR 1412.49 - Apportionment of long and medium grain rice.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 10 2010-01-01 2010-01-01 false Apportionment of long and medium grain rice. 1412.49... and Peanuts 2008 through 2012 § 1412.49 Apportionment of long and medium grain rice. (a) Rice base...) Medium grain rice. Medium grain rice includes short grain rice. (c) Owners on a farm will elect rice base...

7 CFR 1412.49 - Apportionment of long and medium grain rice.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 10 2013-01-01 2013-01-01 false Apportionment of long and medium grain rice. 1412.49... and Peanuts 2008 Through 2012 § 1412.49 Apportionment of long and medium grain rice. (a) Rice base...) Medium grain rice. Medium grain rice includes short grain rice. (c) Owners on a farm will elect rice base...

7 CFR 1412.49 - Apportionment of long and medium grain rice.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 10 2011-01-01 2011-01-01 false Apportionment of long and medium grain rice. 1412.49... and Peanuts 2008 through 2012 § 1412.49 Apportionment of long and medium grain rice. (a) Rice base...) Medium grain rice. Medium grain rice includes short grain rice. (c) Owners on a farm will elect rice base...

7 CFR 1412.49 - Apportionment of long and medium grain rice.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 10 2014-01-01 2014-01-01 false Apportionment of long and medium grain rice. 1412.49... and Peanuts 2008 Through 2012 § 1412.49 Apportionment of long and medium grain rice. (a) Rice base...) Medium grain rice. Medium grain rice includes short grain rice. (c) Owners on a farm will elect rice base...

Identification of a rice metal tolerance protein OsMTP11 as a manganese transporter

PubMed Central

Zhang, Mei; Liu, Baoxiu

2017-01-01

Metal tolerance proteins (MTPs) are a gene family of cation efflux transporters that occur widely in plants and might serve an essential role in metal homeostasis and tolerance. Our research describes the identification, characterization, and localization of OsMTP11, a member of the MTP family from rice. OsMTP11 was expressed constitutively and universally in different tissues in rice plant. Heterologous expression in yeast showed that OsMTP11 complemented the hypersensitivity of mutant strains to Mn, and also complemented yeast mutants to other metals, including Co and Ni. Real time RT-PCR analysis demonstrated OsMTP11 expression was substantially enhanced following 4 h under Cd, Zn, Ni, and Mn treatments, suggesting possible roles of OsMTP11 involvement in heavy metal stress responses. Promoter analysis by transgenic assays with GUS as a reporter gene and mRNA in situ hybridization experiments showed that OsMTP11 was expressed specifically in conducting tissues in rice. DNA methylation assays of genomic DNA in rice treated with Cd, Zn, Ni, and Mn revealed that decreased DNA methylation levels were present in the OsMTP11 promoter region, which was consistent with OsMTP11 induced-expression patterns resulting from heavy metal stress. This result suggested that DNA methylation is one of major factors regulating expression of OsMTP11 through epigenetic mechanisms. OsMTP11 fused to green fluorescent protein (GFP) localized to the entire onion epidermal cell cytoplasm, while vacuolar membrane exhibited increased GFP signals, consistent with an OsMTP11 function in cation sequestration. Our results indicated that OsMTP11 might play vital roles in Mn and other heavy metal transportation in rice. PMID:28394944

The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies

PubMed Central

Pham, Nikki T.; Wei, Tong; Schackwitz, Wendy S.; Lipzen, Anna M.; Duong, Phat Q.; Jones, Kyle C.; Ruan, Deling; Bauer, Diane; Peng, Yi; Schmutz, Jeremy

2017-01-01

The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa ssp japonica), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. This work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations. PMID:28576844

A model explaining genotypic and ontogenetic variation of leaf photosynthetic rate in rice (Oryza sativa) based on leaf nitrogen content and stomatal conductance.

PubMed

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.

A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement

PubMed Central

2014-01-01

Background The rhizome, the original stem of land plants, enables species to invade new territory and is a critical component of perenniality, especially in grasses. Red rice (Oryza longistaminata) is a perennial wild rice species with many valuable traits that could be used to improve cultivated rice cultivars, including rhizomatousness, disease resistance and drought tolerance. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development and function in this plant. Results We used an integrated approach to compare the transcriptome, proteome and metabolome of the rhizome to other tissues of red rice. 116 Gb of transcriptome sequence was obtained from various tissues and used to identify rhizome-specific and preferentially expressed genes, including transcription factors and hormone metabolism and stress response-related genes. Proteomics and metabolomics approaches identified 41 proteins and more than 100 primary metabolites and plant hormones with rhizome preferential accumulation. Of particular interest was the identification of a large number of gene transcripts from Magnaportha oryzae, the fungus that causes rice blast disease in cultivated rice, even though the red rice plants showed no sign of disease. Conclusions A significant set of genes, proteins and metabolites appear to be specifically or preferentially expressed in the rhizome of O. longistaminata. The presence of M. oryzae gene transcripts at a high level in apparently healthy plants suggests that red rice is resistant to this pathogen, and may be able to provide genes to cultivated rice that will enable resistance to rice blast disease. PMID:24521476

RiceFOX: a database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function.

PubMed

Sakurai, Tetsuya; Kondou, Youichi; Akiyama, Kenji; Kurotani, Atsushi; Higuchi, Mieko; Ichikawa, Takanari; Kuroda, Hirofumi; Kusano, Miyako; Mori, Masaki; Saitou, Tsutomu; Sakakibara, Hitoshi; Sugano, Shoji; Suzuki, Makoto; Takahashi, Hideki; Takahashi, Shinya; Takatsuji, Hiroshi; Yokotani, Naoki; Yoshizumi, Takeshi; Saito, Kazuki; Shinozaki, Kazuo; Oda, Kenji; Hirochika, Hirohiko; Matsui, Minami

2011-02-01

Identification of gene function is important not only for basic research but also for applied science, especially with regard to improvements in crop production. For rapid and efficient elucidation of useful traits, we developed a system named FOX hunting (Full-length cDNA Over-eXpressor gene hunting) using full-length cDNAs (fl-cDNAs). A heterologous expression approach provides a solution for the high-throughput characterization of gene functions in agricultural plant species. Since fl-cDNAs contain all the information of functional mRNAs and proteins, we introduced rice fl-cDNAs into Arabidopsis plants for systematic gain-of-function mutation. We generated >30,000 independent Arabidopsis transgenic lines expressing rice fl-cDNAs (rice FOX Arabidopsis mutant lines). These rice FOX Arabidopsis lines were screened systematically for various criteria such as morphology, photosynthesis, UV resistance, element composition, plant hormone profile, metabolite profile/fingerprinting, bacterial resistance, and heat and salt tolerance. The information obtained from these screenings was compiled into a database named 'RiceFOX'. This database contains around 18,000 records of rice FOX Arabidopsis lines and allows users to search against all the observed results, ranging from morphological to invisible traits. The number of searchable items is approximately 100; moreover, the rice FOX Arabidopsis lines can be searched by rice and Arabidopsis gene/protein identifiers, sequence similarity to the introduced rice fl-cDNA and traits. The RiceFOX database is available at http://ricefox.psc.riken.jp/.

RiceFOX: A Database of Arabidopsis Mutant Lines Overexpressing Rice Full-Length cDNA that Contains a Wide Range of Trait Information to Facilitate Analysis of Gene Function

PubMed Central

Sakurai, Tetsuya; Kondou, Youichi; Akiyama, Kenji; Kurotani, Atsushi; Higuchi, Mieko; Ichikawa, Takanari; Kuroda, Hirofumi; Kusano, Miyako; Mori, Masaki; Saitou, Tsutomu; Sakakibara, Hitoshi; Sugano, Shoji; Suzuki, Makoto; Takahashi, Hideki; Takahashi, Shinya; Takatsuji, Hiroshi; Yokotani, Naoki; Yoshizumi, Takeshi; Saito, Kazuki; Shinozaki, Kazuo; Oda, Kenji; Hirochika, Hirohiko; Matsui, Minami

2011-01-01

Identification of gene function is important not only for basic research but also for applied science, especially with regard to improvements in crop production. For rapid and efficient elucidation of useful traits, we developed a system named FOX hunting (Full-length cDNA Over-eXpressor gene hunting) using full-length cDNAs (fl-cDNAs). A heterologous expression approach provides a solution for the high-throughput characterization of gene functions in agricultural plant species. Since fl-cDNAs contain all the information of functional mRNAs and proteins, we introduced rice fl-cDNAs into Arabidopsis plants for systematic gain-of-function mutation. We generated >30,000 independent Arabidopsis transgenic lines expressing rice fl-cDNAs (rice FOX Arabidopsis mutant lines). These rice FOX Arabidopsis lines were screened systematically for various criteria such as morphology, photosynthesis, UV resistance, element composition, plant hormone profile, metabolite profile/fingerprinting, bacterial resistance, and heat and salt tolerance. The information obtained from these screenings was compiled into a database named ‘RiceFOX’. This database contains around 18,000 records of rice FOX Arabidopsis lines and allows users to search against all the observed results, ranging from morphological to invisible traits. The number of searchable items is approximately 100; moreover, the rice FOX Arabidopsis lines can be searched by rice and Arabidopsis gene/protein identifiers, sequence similarity to the introduced rice fl-cDNA and traits. The RiceFOX database is available at http://ricefox.psc.riken.jp/. PMID:21186176

Evolution of regional to global paddy rice mapping methods

NASA Astrophysics Data System (ADS)

Dong, J.; Xiao, X.

2016-12-01

Paddy rice agriculture plays an important role in various environmental issues including food security, water use, climate change, and disease transmission. However, regional and global paddy rice maps are surprisingly scarce and sporadic despite numerous efforts in paddy rice mapping algorithms and applications. In this presentation we would like to review the existing paddy rice mapping methods from the literatures ranging from the 1980s to 2015. In particular, we illustrated the evolution of these paddy rice mapping efforts, looking specifically at the future trajectory of paddy rice mapping methodologies. The biophysical features and growth phases of paddy rice were analyzed first, and feature selections for paddy rice mapping were analyzed from spectral, polarimetric, temporal, spatial, and textural aspects. We sorted out paddy rice mapping algorithms into four categories: 1) Reflectance data and image statistic-based approaches, 2) vegetation index (VI) data and enhanced image statistic-based approaches, 3) VI or RADAR backscatter-based temporal analysis approaches, and 4) phenology-based approaches through remote sensing recognition of key growth phases. The phenology-based approaches using unique features of paddy rice (e.g., transplanting) for mapping have been increasingly used in paddy rice mapping. Based on the literature review, we discussed a series of issues for large scale operational paddy rice mapping.

Estimating high mosquito-producing rice fields using spectral and spatial data

NASA Technical Reports Server (NTRS)

Wood, B. L.; Beck, L. R.; Washino, R. K.; Hibbard, K. A.; Salute, J. S.

1992-01-01

The cultivation of irrigated rice provides ideal larval habitat for a number of anopheline vectors of malaria throughout the world. Anopheles freeborni, a potential vector of human malaria, is associated with the nearly 240,000 hectares of irrigated rice grown annually in Northern and Central California; therefore, this species can serve as a model for the study of rice field anopheline population dynamics. Analysis of field data revealed that rice fields with early season canopy development, that are located near bloodmeal sources (i.e., pastures with livestock) were more likely to produce anopheline larvae than fields with less developed canopies located further from pastures. Remote sensing reflectance measurements of early-season canopy development and geographic information system (GIS) measurements of distanes between rice fields and pastures with livestock were combined to distinguish between high and low mosquito-producing rice fields. Using spectral and distance measures in either a discriminant or Bayesian analysis, the identification of high mosquito-producing fields was made with 85 percent accuracy nearly two months before anopheline larval populations peaked. Since omission errors were also minimized by these approaches, they could provide a new basis for directing abatement techniques for the control of malaria vectors.

The Rice B-Box Zinc Finger Gene Family: Genomic Identification, Characterization, Expression Profiling and Diurnal Analysis

PubMed Central

Huang, Jianyan; Zhao, Xiaobo; Weng, Xiaoyu; Wang, Lei; Xie, Weibo

2012-01-01

Background The B-box (BBX) -containing proteins are a class of zinc finger proteins that contain one or two B-box domains and play important roles in plant growth and development. The Arabidopsis BBX gene family has recently been re-identified and renamed. However, there has not been a genome-wide survey of the rice BBX (OsBBX) gene family until now. Methodology/Principal Findings In this study, we identified 30 rice BBX genes through a comprehensive bioinformatics analysis. Each gene was assigned a uniform nomenclature. We described the chromosome localizations, gene structures, protein domains, phylogenetic relationship, whole life-cycle expression profile and diurnal expression patterns of the OsBBX family members. Based on the phylogeny and domain constitution, the OsBBX gene family was classified into five subfamilies. The gene duplication analysis revealed that only chromosomal segmental duplication contributed to the expansion of the OsBBX gene family. The expression profile of the OsBBX genes was analyzed by Affymetrix GeneChip microarrays throughout the entire life-cycle of rice cultivar Zhenshan 97 (ZS97). In addition, microarray analysis was performed to obtain the expression patterns of these genes under light/dark conditions and after three phytohormone treatments. This analysis revealed that the expression patterns of the OsBBX genes could be classified into eight groups. Eight genes were regulated under the light/dark treatments, and eleven genes showed differential expression under at least one phytohormone treatment. Moreover, we verified the diurnal expression of the OsBBX genes using the data obtained from the Diurnal Project and qPCR analysis, and the results indicated that many of these genes had a diurnal expression pattern. Conclusions/Significance The combination of the genome-wide identification and the expression and diurnal analysis of the OsBBX gene family should facilitate additional functional studies of the OsBBX genes. PMID:23118960

Evolution of regional to global paddy rice mapping methods: A review

NASA Astrophysics Data System (ADS)

Dong, Jinwei; Xiao, Xiangming

2016-09-01

Paddy rice agriculture plays an important role in various environmental issues including food security, water use, climate change, and disease transmission. However, regional and global paddy rice maps are surprisingly scarce and sporadic despite numerous efforts in paddy rice mapping algorithms and applications. With the increasing need for regional to global paddy rice maps, this paper reviewed the existing paddy rice mapping methods from the literatures ranging from the 1980s to 2015. In particular, we illustrated the evolution of these paddy rice mapping efforts, looking specifically at the future trajectory of paddy rice mapping methodologies. The biophysical features and growth phases of paddy rice were analyzed first, and feature selections for paddy rice mapping were analyzed from spectral, polarimetric, temporal, spatial, and textural aspects. We sorted out paddy rice mapping algorithms into four categories: (1) Reflectance data and image statistic-based approaches, (2) vegetation index (VI) data and enhanced image statistic-based approaches, (3) VI or RADAR backscatter-based temporal analysis approaches, and (4) phenology-based approaches through remote sensing recognition of key growth phases. The phenology-based approaches using unique features of paddy rice (e.g., transplanting) for mapping have been increasingly used in paddy rice mapping. Current applications of these phenology-based approaches generally use coarse resolution MODIS data, which involves mixed pixel issues in Asia where smallholders comprise the majority of paddy rice agriculture. The free release of Landsat archive data and the launch of Landsat 8 and Sentinel-2 are providing unprecedented opportunities to map paddy rice in fragmented landscapes with higher spatial resolution. Based on the literature review, we discussed a series of issues for large scale operational paddy rice mapping.

Identification and quantification of flavonoids in yellow grain mutant of rice (Oryza sativa L.).

PubMed

Kim, Backki; Woo, Sunmin; Kim, Mi-Jung; Kwon, Soon-Wook; Lee, Joohyun; Sung, Sang Hyun; Koh, Hee-Jong

2018-02-15

Flavonoids are naturally occurring phenolic compounds with potential health-promoting activities. Although anthocyanins and phenolic acids in coloured rice have been investigated, few studies have focused on flavonoids. Herein, we analysed flavonoids in a yellow grain rice mutant using UHPLC-DAD-ESI-Q-TOF-MS, and identified 19 flavonoids by comparing retention times and accurate mass measurements. Among them, six flavonoids, isoorientin, isoorientin 2″-O-glucoside, vitexin 2″-O-glucoside, isovitexin, isoscoparin 2″-O-glucoside and isoscoparin, were isolated and fully identified from the yellow grain rice mutant, and the levels were significantly higher than wild-type, with isoorientin particularly abundant in mutant embryo. Significant differences in total phenolic compounds and antioxidant activity were observed in mutant rice by DPPH, FRAP and TEAC assays. The results suggest that the representative six flavonoids may play an important role in colouration and antioxidant activity of embryo and endosperm tissue. The findings provide insight into flavonoid biosynthesis and the possibility of improving functionality in rice. Copyright © 2017 Elsevier Ltd. All rights reserved.

Prospects of Understanding the Molecular Biology of Disease Resistance in Rice

PubMed Central

Arya, Preeti; Kapoor, Ritu; Jaswal, Rajdeep; Sharma, Tilak Raj

2018-01-01

Rice is one of the important crops grown worldwide and is considered as an important crop for global food security. Rice is being affected by various fungal, bacterial and viral diseases resulting in huge yield losses every year. Deployment of resistance genes in various crops is one of the important methods of disease management. However, identification, cloning and characterization of disease resistance genes is a very tedious effort. To increase the life span of resistant cultivars, it is important to understand the molecular basis of plant host–pathogen interaction. With the advancement in rice genetics and genomics, several rice varieties resistant to fungal, bacterial and viral pathogens have been developed. However, resistance response of these varieties break down very frequently because of the emergence of more virulent races of the pathogen in nature. To increase the durability of resistance genes under field conditions, understanding the mechanismof resistance response and its molecular basis should be well understood. Some emerging concepts like interspecies transfer of pattern recognition receptors (PRRs) and transgenerational plant immunitycan be employed to develop sustainable broad spectrum resistant varieties of rice. PMID:29642631

Deciphering the proteomic profile of rice (Oryza sativa) bran: a pilot study.

PubMed

Ferrari, Fabio; Fumagalli, Marco; Profumo, Antonella; Viglio, Simona; Sala, Alberto; Dolcini, Lorenzo; Temporini, Caterina; Nicolis, Stefania; Merli, Daniele; Corana, Federica; Casado, Begona; Iadarola, Paolo

2009-12-01

The exact knowledge of the qualitative and quantitative protein components of rice bran is an essential aspect to be considered for a better understanding of the functional properties of this resource. Aim of the present investigation was to extract the largest number of rice bran proteins and to obtain their qualitative characterization. For this purpose, three different extraction protocols have been applied either on full-fat or on defatted rice bran. Likewise, to identify the highest number of proteins, MS data collected from 1-DE, 2-DE and gel-free procedures have been combined. These approaches allowed to unambiguously identify 43 proteins that were classified as signalling/regulation proteins (30%), proteins with enzymatic activity (30%), storage proteins (30%), transfer (5%) and structural (5%) proteins. The fact that all extraction and identification procedures have been performed in triplicate with an excellent reproducibility provides a rationale for considering the platform of proteins shown in this study as the potential proteome profile of rice bran. It also represents a source of information to evaluate better the qualities of rice bran as food resource.

Identification of rice cornichon as a possible cargo receptor for the Golgi-localized sodium transporter OsHKT1;3

PubMed Central

Rosas-Santiago, Paul; Lagunas-Gómez, Daniel; Barkla, Bronwyn J.; Vera-Estrella, Rosario; Lalonde, Sylvie; Jones, Alexander; Frommer, Wolf B.; Zimmermannova, Olga; Sychrová, Hana; Pantoja, Omar

2015-01-01

Membrane proteins are synthesized and folded in the endoplasmic reticulum (ER), and continue their path to their site of residence along the secretory pathway. The COPII system has been identified as a key player for selecting and directing the fate of membrane and secretory cargo proteins. Selection of cargo proteins within the COPII vesicles is achieved by cargo receptors. The cornichon cargo receptor belongs to a conserved protein family found in eukaryotes that has been demonstrated to participate in the selection of integral membrane proteins as cargo for their correct targeting. Here it is demonstrated at the cellular level that rice cornichon OsCNIH1 interacts with OsHKT1;3 and, in yeast cells, enables the expression of the sodium transporter to the Golgi apparatus. Physical and functional HKT–cornichon interactions are confirmed by the mating-based split ubiquitin system, bimolecular fluorescence complementation, and Xenopus oocyte and yeast expression systems. The interaction between the two proteins occurs in the ER of plant cells and their co-expression in oocytes leads to the sequestration of the transporter in the ER. In the yeast cornichon mutant erv14, OsHKT1;3 is mistargeted, preventing the toxic effects of sodium transport in the cell observed in wild-type cells or in the erv14 mutant that co-expressed OsHKT1;3 with either OsCNIH1 or Erv14p. Identification and characterization of rice cornichon as a possible cargo receptor opens up the opportunity to improve our knowledge on membrane protein targeting in plant cells. PMID:25750424

Fine mapping and identification of a novel locus qGL12.2 control grain length in wild rice (Oryza rufipogon Griff.).

PubMed

Qi, Lan; Ding, Yingbin; Zheng, Xiaoming; Xu, Rui; Zhang, Lizhen; Wang, Yanyan; Wang, Xiaoning; Zhang, Lifang; Cheng, Yunlian; Qiao, Weihua; Yang, Qingwen

2018-04-19

A wild rice QTL qGL12.2 for grain length was fine mapped to an 82-kb interval in chromosome 12 containing six candidate genes and none was reported previously. Grain length is an important trait for yield and commercial value in rice. Wild rice seeds have a very slender shape and have many desirable genes that have been lost in cultivated rice during domestication. In this study, we identified a quantitative trait locus, qGL12.2, which controls grain length in wild rice. First, a wild rice chromosome segment substitution line, CSSL41, was selected that has longer glume and grains than does the Oryza sativa indica cultivar, 9311. Next, an F 2 population was constructed from a cross between CSSL41 and 9311. Using the next-generation sequencing combined with bulked-segregant analysis and F 3 recombinants analysis, qGL12.2 was finally fine mapped to an 82-kb interval in chromosome 12. Six candidate genes were found, and no reported grain length genes were found in this interval. Using scanning electron microscopy, we found that CSSL41 cells are significantly longer than those of 9311, but there is no difference in cell widths. These data suggest that qGL12.2 is a novel gene that controls grain cell length in wild rice. Our study provides a new genetic resource for rice breeding and a starting point for functional characterization of the wild rice GL gene.

Functional mapping of quantitative trait loci associated with rice tillering.

PubMed

Liu, G F; Li, M; Wen, J; Du, Y; Zhang, Y-M

2010-10-01

Several biologically significant parameters that are related to rice tillering are closely associated with rice grain yield. Although identification of the genes that control rice tillering and therefore influence crop yield would be valuable for rice production management and genetic improvement, these genes remain largely unidentified. In this study, we carried out functional mapping of quantitative trait loci (QTLs) for rice tillering in 129 doubled haploid lines, which were derived from a cross between IR64 and Azucena. We measured the average number of tillers in each plot at seven developmental stages and fit the growth trajectory of rice tillering with the Wang-Lan-Ding mathematical model. Four biologically meaningful parameters in this model--the potential maximum for tiller number (K), the optimum tiller time (t(0)), and the increased rate (r), or the reduced rate (c) at the time of deviation from t(0)--were our defined variables for multi-marker joint analysis under the framework of penalized maximum likelihood, as well as composite interval mapping. We detected a total of 27 QTLs that accounted for 2.49-8.54% of the total phenotypic variance. Nine common QTLs across multi-marker joint analysis and composite interval mapping showed high stability, while one QTL was environment-specific and three were epistatic. We also identified several genomic segments that are associated with multiple traits. Our results describe the genetic basis of rice tiller development, enable further marker-assisted selection in rice cultivar development, and provide useful information for rice production management.

A novel gene, Pi40(t), linked to the DNA markers derived from NBS-LRR motifs confers broad spectrum of blast resistance in rice.

PubMed

Jeung, J U; Kim, B R; Cho, Y C; Han, S S; Moon, H P; Lee, Y T; Jena, K K

2007-11-01

Rice blast disease caused by Magnaporthe grisea is a continuous threat to stable rice production worldwide. In a modernized agricultural system, the development of varieties with broad-spectrum and durable resistance to blast disease is essential for increased rice production and sustainability. In this study, a new gene is identified in the introgression line IR65482-4-136-2-2 that has inherited the resistance gene from an EE genome wild Oryza species, O. australiensis (Acc. 100882). Genetic and molecular analysis localized a major resistance gene, Pi40(t), on the short arm of chromosome 6, where four blast resistance genes (Piz, Piz-5, Piz-t, and Pi9) were also identified, flanked by the markers S2539 and RM3330. Through e-Landing, 14 BAC/PAC clones within the 1.81-Mb equivalent virtual contig were identified on Rice Pseudomolecule3. Highly stringent primer sets designed for 6 NBS-LRR motifs located within PAC clone P0649C11 facilitated high-resolution mapping of the new resistance gene, Pi40(t). Following association analysis and detailed haplotyping approaches, a DNA marker, 9871.T7E2b, was identified to be linked to the Pi40(t) gene at the 70 Kb chromosomal region, and differentiated the Pi40(t) gene from the LTH monogenic differential lines possessing genes Piz, Piz-5, Piz-t, and Pi-9. Pi40(t) was validated using the most virulent isolates of Korea as well as the Philippines, suggesting a broad spectrum for the resistance gene. Marker-assisted selection (MAS) and pathotyping of BC progenies having two japonica cultivar genetic backgrounds further supported the potential of the resistance gene in rice breeding. Our study based on new gene identification strategies provides insight into novel genetic resources for blast resistance as well as future studies on cloning and functional analysis of a blast resistance gene useful for rice improvement.

Identification of the active protein in rice bran protein having an inhibitory activity of cholesterol micellar solubility.

PubMed

Wang, Jilite; Shimada, Masaya; Nagaoka, Satoshi

2017-06-01

In our previous study, rice bran protein (RBP) inhibited cholesterol micellar solubility in vitro and decreased serum cholesterol level in rats. In the present study, RBP was separated and purified by size-exclusion chromatography and reversed-phase chromatography. The active protein of RBP related to cholesterol micellar solubility was identified as lectin and non-specific lipid-transfer protein 1 using MALDI-TOF mass spectrometry analysis.

Identification of quantitative trait loci for grain quality in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon.

PubMed

Septiningsih, E M; Trijatmiko, K R; Moeljopawiro, S; McCouch, S R

2003-11-01

The objective of this study was to identify quantitative trait loci (QTLs) associated with grain quality in rice. Two hundred eighty-five BC(2)F(2 )families developed from an interspecific cross between cv IR64 and Oryza rufipogon (IRGC 105491) were evaluated for 14 seed quality traits. A total of 165 markers consisting of 131 single sequence repeats and 34 restriction fragment length polymorphism markers were used to create a genetic linkage map spanning the 12 rice chromosomes. Twenty-three independent QTLs were identified using single point analysis, interval mapping, and composite interval mapping. These loci consisted of one QTL for filled rough/total rough rice ratio, two for grain density, one for percentage of de-husked rice grains, two for percentage of green rice grains, three for percentage of damaged-yellow rice grains, two for percentage of red rice grains, one for milled rice recovery, three for head rice recovery, four for broken rice grains, two for crushed rice grains, one for amylose content, and one for gel consistency. For most of the QTLs identified in this study, the O. rufipogon-derived allele contributed an undesirable effect. For amylose content and gel consistency, the O. rufipogon allele may be useful in an IR64 background, depending on the cultural preferences of the consumer. Careful selection against the regions associated with negative effects will be required to avoid unwanted grain quality characteristics during the development of improved varieties for yield and yield components using introgressions from O. rufipogon.

Comparative Evaluation of Rice Bran Wax as an Ointment Base with Standard Base

PubMed Central

Sabale, Vidya; Sabale, P. M.; Lakhotiya, C. L.

2009-01-01

Waxes have been used in many cosmetic preparations and pharmaceuticals as formulation aids. Rice bran wax is a byproduct of rice bran oil industry. Present investigation has been aimed to explore the possible utility of rice bran wax as ointment base compared to standard base. The rice bran wax obtained, purified and its physicochemical characteristics were determined. Ointment base acts as a carrier for medicaments. The ointment base composition determines not only the extent of penetration but also controls the transfer of medicaments from the base to the body tissues. Rice bran wax base was compared with standard base for appearance, spreadability, water number, wash ability and diffusibility. The results show that rice bran wax acts as an ointment base as far as its pharmaceutical properties are concerned and it could effectively replace comparatively costlier available ointment bases. PMID:20177466

Comparative Transcriptomic Analysis in Paddy Rice under Storage and Identification of Differentially Regulated Genes in Response to High Temperature and Humidity.

PubMed

Zhao, Chanjuan; Xie, Junqi; Li, Li; Cao, Chongjiang

2017-09-20

The transcriptomes of paddy rice in response to high temperature and humidity were studied using a high-throughput RNA sequencing approach. Effects of high temperature and humidity on the sucrose and starch contents and α/β-amylase activity were also investigated. Results showed that 6876 differentially expressed genes (DEGs) were identified in paddy rice under high temperature and humidity storage. Importantly, 12 DEGs that were downregulated fell into the "starch and sucrose pathway". The quantitative real-time polymerase chain reaction assays indicated that expression of these 12 DEGs was significantly decreased, which was in parallel with the reduced level of enzyme activities and the contents of sucrose and starch in paddy rice stored at high temperature and humidity conditions compared to the control group. Taken together, high temperature and humidity influence the quality of paddy rice at least partially by downregulating the expression of genes encoding sucrose transferases and hydrolases, which might result in the decrease of starch and sucrose contents.

Abundance and Spatial Dispersion of Rice Stem Borer Species in Kahama, Tanzania

PubMed Central

Leonard, Alfonce; Rwegasira, Gration M.

2015-01-01

Species diversity, abundance, and dispersion of rice stem borers in framer’s fields were studied in four major rice growing areas of Kahama District. Stem borer larvae were extracted from the damaged tillers in 16 quadrants established in each field. Adult Moths were trapped by light traps and collected in vials for identification. Results indicated the presence of Chilo partellus, Maliarpha separatella, and Sesamia calamistis in all study areas. The most abundant species was C. partellus (48.6%) followed by M. separatella (35.4%) and S. calamistis was least abundant (16.1%). Stem borers dispersion was aggregated along the edges of rice fields in three locations (wards) namely: Bulige, Chela, and Ngaya. The dispersion in the fourth ward, Kashishi was uniform as established from two of the three dispersion indices tested. Further studies would be required to establish the available alternative hosts, the extent of economic losses and the distribution of rice stem borers in the rest of the Lake zone of Tanzania. PMID:26411785

ELONGATED UPPERMOST INTERNODE Encodes a Cytochrome P450 Monooxygenase That Epoxidizes Gibberellins in a Novel Deactivation Reaction in RiceW⃞

PubMed Central

Zhu, Yongyou; Nomura, Takahito; Xu, Yonghan; Zhang, Yingying; Peng, Yu; Mao, Bizeng; Hanada, Atsushi; Zhou, Haicheng; Wang, Renxiao; Li, Peijin; Zhu, Xudong; Mander, Lewis N.; Kamiya, Yuji; Yamaguchi, Shinjiro; He, Zuhua

2006-01-01

The recessive tall rice (Oryza sativa) mutant elongated uppermost internode (eui) is morphologically normal until its final internode elongates drastically at the heading stage. The stage-specific developmental effect of the eui mutation has been used in the breeding of hybrid rice to improve the performance of heading in male sterile cultivars. We found that the eui mutant accumulated exceptionally large amounts of biologically active gibberellins (GAs) in the uppermost internode. Map-based cloning revealed that the Eui gene encodes a previously uncharacterized cytochrome P450 monooxygenase, CYP714D1. Using heterologous expression in yeast, we found that EUI catalyzed 16α,17-epoxidation of non-13-hydroxylated GAs. Consistent with the tall and dwarfed phenotypes of the eui mutant and Eui-overexpressing transgenic plants, respectively, 16α,17-epoxidation reduced the biological activity of GA4 in rice, demonstrating that EUI functions as a GA-deactivating enzyme. Expression of Eui appeared tightly regulated during plant development, in agreement with the stage-specific eui phenotypes. These results indicate the existence of an unrecognized pathway for GA deactivation by EUI during the growth of wild-type internodes. The identification of Eui as a GA catabolism gene provides additional evidence that the GA metabolism pathway is a useful target for increasing the agronomic value of crops. PMID:16399803

Rice Domestication Revealed by Reduced Shattering of Archaeological rice from the Lower Yangtze valley

NASA Astrophysics Data System (ADS)

Zheng, Yunfei; Crawford, Gary W.; Jiang, Leping; Chen, Xugao

2016-06-01

Plant remains dating to between 9000 and 8400 BP from a probable ditch structure at the Huxi site include the oldest rice (Oryza sativa) spikelet bases and associated plant remains recovered in China. The remains document an early stage of rice domestication and the ecological setting in which early cultivation was taking place. The rice spikelet bases from Huxi include wild (shattering), intermediate, and domesticated (non-shattering) forms. The relative frequency of intermediate and non-shattering spikelet bases indicates that selection for, at the very least, non-shattering rice was underway at Huxi. The rice also has characteristics of japonica rice (Oryza sativa subsp. japonica), helping to clarify the emergence of a significant lineage of the crop. Seeds, phytoliths and their context provide evidence of increasing anthropogenesis and cultivation during the occupation. Rice spikelet bases from Kuahuqiao (8000-7700 BP), Tianluoshan (7000-6500 BP), Majiabang (6300-6000 BP), and Liangzhu (5300-4300 BP) sites indicate that rice underwent continuing selection for reduced shattering and japonica rice characteristics, confirming a prolonged domestication process for rice.

Identification, measurement, and assessment of water cycle of unhusked rice agricultural phases: Case study at Tangerang paddy field, Indonesia

NASA Astrophysics Data System (ADS)

Hartono, N.; Laurence; Johannes, H. P.

2017-11-01

According to one of UN reports, water scarcity has happened all around the world, including Indonesia. Irrigation sector takes up 70% of world water consumption and potentially increases 20% due to the population explosion. Rice is accounted for 69% of agricultural products contributions in Indonesia’s water footprint. Therefore, evaluation of water cycle was essential to raise awareness among practitioners. Data collections were conducted in the functional unit of one-hectare rice field located in Tangerang. This study used CropWat 8.0 and SimaPro software. Identification involved data such as climate, crop, and soil. Nursery became the highest water consumed phase, requiring 419 mm in height. Measurement through water footprint resulted in consumption of green water footprint for 8,183,618.5 liters (62.9%), followed by grey for 4,805,733.2 liters (36.9%) and blue for 23,902.36 liters (0.2%). The grey consumption was exceeding the average, which indicated high doses of pesticides. Life Cycle Assessment showed negative impacts of fertilizers that caused damages like fossil depletion, respiratory health, and eutrophication.

[Analysis of constituents of ester-type gum bases used as natural food additives].

PubMed

Tada, Atsuko; Masuda, Aino; Sugimoto, Naoki; Yamagata, Kazuo; Yamazaki, Takeshi; Tanamoto, Kenichi

2007-12-01

The differences in the constituents of ten ester-type gum bases used as natural food additives in Japan (urushi wax, carnauba wax, candelilla wax, rice bran wax, shellac wax, jojoba wax, bees wax, Japan wax, montan wax, and lanolin) were investigated. Several kinds of gum bases showed characteristic TLC patterns of lipids. In addition, compositions of fatty acid and alcohol moieties of esters in the gum bases were analyzed by GC/MS after methanolysis and hydrolysis, respectively. The results indicated that the varieties of fatty acids and alcohols and their compositions were characteristic for each gum base. These results will be useful for identification and discrimination of the ester-type gum bases.

Identification of transplanting stage of rice using Sentinel-1 data

NASA Astrophysics Data System (ADS)

Hongo, C.; Tosa, T.; Tamura, E.; Sigit, G.; Barus, B.

2017-12-01

As the adaptation of climate change, the Government of Indonesia has launched agricultural insurance program for damage of rice by drought, flood and pest and disease. For assessment of the damage ratio and calculation of indemnity, extraction of paddy field and identification of transplanting stage are key issues. In this research, we conducted identification of rice transplanting stage in dry season of 2015, using data from Sentinel-1, for paddy in Cianjur, West Java, Indonesia. As the first step, time series order of backscattering coefficient was analyzed about paddy, forest, villages and fish farming ponds with use of Sentinel-1 data acquired on April 1, April 13, April 25, May 7, May 19, June 24, July 18 and August 11. The result shows that the backscattering coefficient of paddy substantially decreased from data on May 7 and reached minimum value and then after increased toward June. A paddy area showing this change was almost the same area where rice was at harvesting stage and we did field investigation work from August 11 to 13. Considering a growth period of rice in our research site was about 110 days, so the result supported the fact that transplantation of rice was done around May 7. On the other hand, backscattering coefficient of forest, villages and fish farming ponds was constant and showed clear difference from the coefficient of paddy. As the next step, minimum and maximum value of backscattering coefficient were extracted from the data of May 7, May 19 and June 24, respectively. Then increase amount was calculated by deducting the minimum value from the maximum. Finally, using the minimum value of backscattering coefficient and the increased amount, a classification of image was made to identify transplanting stage through maximum likelihood method, decision tree method and threshold setting method (regression analysis by 3σ-rule). As the result, the maximum likelihood method made the most accurate distinguishment about transplanting stage while the decision tree method showed tendency to underestimate a paddy area already planted. As to the threshold setting method (regression analysis by 3σ-rule), its distinguishment accuracy was better than those of other methods about a paddy area adjacent to forest and villages of which backscattering coefficient was influenced by other sources' coefficients.

Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms.

PubMed

Yamamoto, Toshio; Nagasaki, Hideki; Yonemaru, Jun-ichi; Ebana, Kaworu; Nakajima, Maiko; Shibaya, Taeko; Yano, Masahiro

2010-04-27

To create useful gene combinations in crop breeding, it is necessary to clarify the dynamics of the genome composition created by breeding practices. A large quantity of single-nucleotide polymorphism (SNP) data is required to permit discrimination of chromosome segments among modern cultivars, which are genetically related. Here, we used a high-throughput sequencer to conduct whole-genome sequencing of an elite Japanese rice cultivar, Koshihikari, which is closely related to Nipponbare, whose genome sequencing has been completed. Then we designed a high-throughput typing array based on the SNP information by comparison of the two sequences. Finally, we applied this array to analyze historical representative rice cultivars to understand the dynamics of their genome composition. The total 5.89-Gb sequence for Koshihikari, equivalent to 15.7 x the entire rice genome, was mapped using the Pseudomolecules 4.0 database for Nipponbare. The resultant Koshihikari genome sequence corresponded to 80.1% of the Nipponbare sequence and led to the identification of 67,051 SNPs. A high-throughput typing array consisting of 1917 SNP sites distributed throughout the genome was designed to genotype 151 representative Japanese cultivars that have been grown during the past 150 years. We could identify the ancestral origin of the pedigree haplotypes in 60.9% of the Koshihikari genome and 18 consensus haplotype blocks which are inherited from traditional landraces to current improved varieties. Moreover, it was predicted that modern breeding practices have generally decreased genetic diversity Detection of genome-wide SNPs by both high-throughput sequencer and typing array made it possible to evaluate genomic composition of genetically related rice varieties. With the aid of their pedigree information, we clarified the dynamics of chromosome recombination during the historical rice breeding process. We also found several genomic regions decreasing genetic diversity which might be caused by a recent human selection in rice breeding. The definition of pedigree haplotypes by means of genome-wide SNPs will facilitate next-generation breeding of rice and other crops.

Identification of phasiRNAs in wild rice (Oryza rufipogon).

PubMed

Liu, Yang; Wang, Yu; Zhu, Qian-Hao; Fan, Longjiang

2013-08-01

Plant miRNAs can trigger the production of phased, secondary siRNAs from either non-coding or protein-coding genes. In this study, at least 864 and 3,961 loci generating 21-nt and 24-nt phased siRNAs (phasiRNAs),respectively, were identified in three tissues from wild rice. Of these phasiRNA-producing loci, or PHAS genes, biogenesis of phasiRNAs in at least 160 of 21-nt and 254 of 24-nt loci could be triggered by interaction with miRNA(s). Developing seeds had more PHAS genes than leaves and roots. Genetic constrain on miRNA-triggered PHAS genes suggests that phasiRNAs might be one of the driving forces contributed to rice domestication.

Identification of technology options for reducing nitrogen pollution in cropping systems of Pujiang*

PubMed Central

Fang, Bin; Wang, Guang-huo; Van den berg, Marrit; Roetter, Reimund

2005-01-01

This work analyses the potential role of nitrogen pollution technology of crop systems of Pujiang, County in Eastern China’s Zhejiang Province, rice and vegetables are important cropping systems. We used a case study approach involving comparison of farmer practices and improved technologies. This approach allows assessing the impact of technology on pollution, is forward looking, and can yield information on the potential of on-the-shelf technology and provide opportunities for technology development. The approach particularly suits newly developed rice technologies with large potential of reducing nitrogen pollution and for future rice and vegetables technologies. The results showed that substantial reductions in nitrogen pollution are feasible for both types of crops. PMID:16187411

Identification of technology options for reducing nitrogen pollution in cropping systems of Pujiang.

PubMed

Fang, Bin; Wang, Guang-Huo; Van, Den Berg Marrit; Roetter, Reimund

2005-10-01

This work analyses the potential role of nitrogen pollution technology of crop systems of Pujiang, County in Eastern China's Zhejiang Province, rice and vegetables are important cropping systems. We used a case study approach involving comparison of farmer practices and improved technologies. This approach allows assessing the impact of technology on pollution, is forward looking, and can yield information on the potential of on-the-shelf technology and provide opportunities for technology development. The approach particularly suits newly developed rice technologies with large potential of reducing nitrogen pollution and for future rice and vegetables technologies. The results showed that substantial reductions in nitrogen pollution are feasible for both types of crops.

Genome-wide targeted prediction of ABA responsive genes in rice based on over-represented cis-motif in co-expressed genes.

PubMed

Lenka, Sangram K; Lohia, Bikash; Kumar, Abhay; Chinnusamy, Viswanathan; Bansal, Kailash C

2009-02-01

Abscisic acid (ABA), the popular plant stress hormone, plays a key role in regulation of sub-set of stress responsive genes. These genes respond to ABA through specific transcription factors which bind to cis-regulatory elements present in their promoters. We discovered the ABA Responsive Element (ABRE) core (ACGT) containing CGMCACGTGB motif as over-represented motif among the promoters of ABA responsive co-expressed genes in rice. Targeted gene prediction strategy using this motif led to the identification of 402 protein coding genes potentially regulated by ABA-dependent molecular genetic network. RT-PCR analysis of arbitrarily chosen 45 genes from the predicted 402 genes confirmed 80% accuracy of our prediction. Plant Gene Ontology (GO) analysis of ABA responsive genes showed enrichment of signal transduction and stress related genes among diverse functional categories.

Evaluation of bakanae disease progression caused by Fusarium fujikuroi in Oryza sativa L.

PubMed

Hwang, In Sun; Kang, Woo-Ri; Hwang, Duk-Ju; Bae, Shin-Chul; Yun, Sung-Hwan; Ahn, Il-Pyung

2013-12-01

Bakanae disease caused by Fusarium fujikuroi is an important fungal disease in rice. Among the seven strains isolated from symptomatic rice grains in this study, one strain, FfB14, triggered severe root growth inhibition and decay in the crown and root of rice seedlings. The remaining six strains caused typical Bakanae symptoms such as etiolation and abnormal succulent rice growth. To reveal the relationship between mycelial growth in the infected tissues and Bakanae disease progression, we have established a reliable quantification method using real time PCR that employs a primer pair and dual-labeled probe specific to a unigene encoding F. fujikuroi PNG1 (FfPNG1), which is located upstream of the fumonisin biosynthesis gene cluster. Plotting the crossing point (CP) values from the infected tissue DNAs on a standard curve revealed the active fungal growth of FfB14 in the root and crown of rice seedlings, while the growth rate of FfB20 in rice was more than 4 times lower than FfB14. Massive infective mycelial growth of FfB14 was evident in rice stems and crown; however, FfB20 did not exhibit vigorous growth. Our quantitative evaluation system is applicable for the identification of fungal virulence factors other than gibberellin.

Identification and Map-Based Cloning of the Light-Induced Lesion Mimic Mutant 1 (LIL1) Gene in Rice.

PubMed

Zhou, Qian; Zhang, Zhifei; Liu, Tiantian; Gao, Bida; Xiong, Xingyao

2017-01-01

The hypersensitive response (HR) is a mechanism by which plants prevent the spread of pathogen. Despite extensive study, the molecular mechanisms underlying HR remain poorly understood. Lesion mimic mutants (LMMs), such as LIL1 that was identified in an ethylmethane sulfonate mutagenized population of Indica rice ( Oryza sativa L. ssp. Indica ) 93-11, can be used to study the HR. Under natural field conditions, the leaves of LIL1 mutant plants exhibited light-induced, small, rust-red lesions that first appeared at the leaf tips and subsequently expanded throughout the entire leaf blade to the leaf sheath. Histochemical staining indicated that LIL1 lesions displayed an abnormal accumulation of reactive oxygen species (ROS) and resulted from programmed cell death (PCD). The LIL1 mutants also displayed increased expression of defense-related genes and enhanced resistance to rice blast fungus ( Magnaporthe grisea ). Genetic analysis showed that mutation of LIL1 created a semi-dominant allele. Using 1,758 individuals in the F 2 population, LIL1 was mapped in a 222.3 kb region on the long arm of chromosome 7. That contains 12 predicted open reading frames (ORFs). Sequence analysis of these 12 candidate genes revealed a G to A base substitution in the fourth exon of LOC_Os07g30510, a putative cysteine-rich receptor-like kinase (CRK), which led to an amino acid change (Val 429 to Ile) in the LIL1 protein. Comparison of the transcript accumulation of the 12 candidate genes between LIL1 and 93-11 revealed that LOC_Os07g30510 was up-regulated significantly in LIL1 . Overexpression of the LOC_Os07g30510 gene from LIL1 induced a LIL1 -like lesion phenotype in Nipponbare. Thus, LIL1 is a novel LMM in rice that will facilitate the further study of the molecular mechanisms of HR and the rice blast resistance.

Progress and challenges in improving the nutritional quality of rice (Oryza sativa L.).

PubMed

Birla, Deep Shikha; Malik, Kapil; Sainger, Manish; Chaudhary, Darshna; Jaiwal, Ranjana; Jaiwal, Pawan K

2017-07-24

Rice is a staple food for more than 3 billion people in more than 100 countries of the world but ironically it is deficient in many bioavailable vitamins, minerals, essential amino- and fatty-acids and phytochemicals that prevent chronic diseases like type 2 diabetes, heart disease, cancers, and obesity. To enhance the nutritional and other quality aspects of rice, a better understanding of the regulation of the processes involved in the synthesis, uptake, transport, and metabolism of macro-(starch, seed storage protein and lipid) and micronutrients (vitamins, minerals and phytochemicals) is required. With the publication of high quality genomic sequence of rice, significant progress has been made in identification, isolation, and characterization of novel genes and their regulation for the nutritional and quality enhancement of rice. During the last decade, numerous efforts have been made to refine the nutritional and other quality traits either by using the traditional breeding with high through put technologies such as marker assisted selection and breeding, or by adopting the transgenic approach. A significant improvement in vitamins (A, folate, and E), mineral (iron), essential amino acid (lysine), and flavonoids levels has been achieved in the edible part of rice, i.e., endosperm (biofortification) to meet the daily dietary allowance. However, studies on bioavailability and allergenicity on biofortified rice are still required. Despite the numerous efforts, the commercialization of biofortified rice has not yet been achieved. The present review summarizes the progress and challenges of genetic engineering and/or metabolic engineering technologies to improve rice grain quality, and presents the future prospects in developing nutrient dense rice to save the everincreasing population, that depends solely on rice as the staple food, from widespread nutritional deficiencies.

Overexpression of maize anthocyanin regulatory gene Lc affects rice fertility.

PubMed

Li, Yuan; Zhang, Tao; Shen, Zhong-Wei; Xu, Yu; Li, Jian-Yue

2013-01-01

Seventeen independent transgenic rice plants with the maize anthocyanin regulatory gene Lc under control of the CaMV 35S promoter were obtained and verified by molecular identification. Ten plants showed red spikelets during early development of florets, and the degenerate florets were still red after heading. Additionally, these plants exhibited intense pigmentation on the surface of the anther and the bottom of the ovary. They were unable to properly bloom and were completely sterile. Following pollination with normal pollen, these plants yielded red caryopses but did not mature normally. QRT-PCR analysis indicated that mRNA accumulation of the CHS-like gene encoding a chalcone synthase-related protein was increased significantly in the sterile plant. This is the first report to suggest that upregulation of the CHS gene expression may result in rice sterility and affect the normal development of rice seeds.

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential.

PubMed

Zhang, Gengyun; Liu, Xin; Quan, Zhiwu; Cheng, Shifeng; Xu, Xun; Pan, Shengkai; Xie, Min; Zeng, Peng; Yue, Zhen; Wang, Wenliang; Tao, Ye; Bian, Chao; Han, Changlei; Xia, Qiuju; Peng, Xiaohua; Cao, Rui; Yang, Xinhua; Zhan, Dongliang; Hu, Jingchu; Zhang, Yinxin; Li, Henan; Li, Hua; Li, Ning; Wang, Junyi; Wang, Chanchan; Wang, Renyi; Guo, Tao; Cai, Yanjie; Liu, Chengzhang; Xiang, Haitao; Shi, Qiuxiang; Huang, Ping; Chen, Qingchun; Li, Yingrui; Wang, Jun; Zhao, Zhihai; Wang, Jian

2012-05-13

Foxtail millet (Setaria italica), a member of the Poaceae grass family, is an important food and fodder crop in arid regions and has potential for use as a C(4) biofuel. It is a model system for other biofuel grasses, including switchgrass and pearl millet. We produced a draft genome (∼423 Mb) anchored onto nine chromosomes and annotated 38,801 genes. Key chromosome reshuffling events were detected through collinearity identification between foxtail millet, rice and sorghum including two reshuffling events fusing rice chromosomes 7 and 9, 3 and 10 to foxtail millet chromosomes 2 and 9, respectively, that occurred after the divergence of foxtail millet and rice, and a single reshuffling event fusing rice chromosome 5 and 12 to foxtail millet chromosome 3 that occurred after the divergence of millet and sorghum. Rearrangements in the C(4) photosynthesis pathway were also identified.

The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies.

PubMed

Li, Guotian; Jain, Rashmi; Chern, Mawsheng; Pham, Nikki T; Martin, Joel A; Wei, Tong; Schackwitz, Wendy S; Lipzen, Anna M; Duong, Phat Q; Jones, Kyle C; Jiang, Liangrong; Ruan, Deling; Bauer, Diane; Peng, Yi; Barry, Kerrie W; Schmutz, Jeremy; Ronald, Pamela C

2017-06-01

The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake ( Oryza sativa ssp japonica ), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. This work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations. © 2017 American Society of Plant Biologists. All rights reserved.

The Sequences of 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies

DOE PAGES

Li, Guotian; Jain, Rashmi; Chern, Mawsheng; ...

2017-06-02

The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa ssp japonica), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportionmore » of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. In conclusion, this work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations.« less

QTLs for Resistance to Major Rice Diseases Exacerbated by Global Warming: Brown Spot, Bacterial Seedling Rot, and Bacterial Grain Rot.

PubMed

Mizobuchi, Ritsuko; Fukuoka, Shuichi; Tsushima, Seiya; Yano, Masahiro; Sato, Hiroyuki

2016-12-01

In rice (Oryza sativa L.), damage from diseases such as brown spot, caused by Bipolaris oryzae, and bacterial seedling rot and bacterial grain rot, caused by Burkholderia glumae, has increased under global warming because the optimal temperature ranges for growth of these pathogens are relatively high (around 30 °C). Therefore, the need for cultivars carrying genes for resistance to these diseases is increasing to ensure sustainable rice production. In contrast to the situation for other important rice diseases such as blast and bacterial blight, no genes for complete resistance to brown spot, bacterial seedling rot or bacterial grain rot have yet been discovered. Thus, rice breeders have to use partial resistance, which is largely influenced by environmental conditions. Recent progress in molecular genetics and improvement of evaluation methods for disease resistance have facilitated detection of quantitative trait loci (QTLs) associated with resistance. In this review, we summarize the results of worldwide screening for cultivars with resistance to brown spot, bacterial seedling rot and bacterial grain rot and we discuss the identification of QTLs conferring resistance to these diseases in order to provide useful information for rice breeding programs.

PAY1 improves plant architecture and enhances grain yield in rice.

PubMed

Zhao, Lei; Tan, Lubin; Zhu, Zuofeng; Xiao, Langtao; Xie, Daoxin; Sun, Chuanqing

2015-08-01

Plant architecture, a complex of the important agronomic traits that determine grain yield, is a primary target of artificial selection of rice domestication and improvement. Some important genes affecting plant architecture and grain yield have been isolated and characterized in recent decades; however, their underlying mechanism remains to be elucidated. Here, we report genetic identification and functional analysis of the PLANT ARCHITECTURE AND YIELD 1 (PAY1) gene in rice, which affects plant architecture and grain yield in rice. Transgenic plants over-expressing PAY1 had twice the number of grains per panicle and consequently produced nearly 38% more grain yield per plant than control plants. Mechanistically, PAY1 could improve plant architecture via affecting polar auxin transport activity and altering endogenous indole-3-acetic acid distribution. Furthermore, introgression of PAY1 into elite rice cultivars, using marker-assisted background selection, dramatically increased grain yield compared with the recipient parents. Overall, these results demonstrated that PAY1 could be a new beneficial genetic resource for shaping ideal plant architecture and breeding high-yielding rice varieties. © 2015 The Authors The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

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

PubMed Central

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

Identification of stable QTLs causing chalk in rice grains in nine environments.

PubMed

Zhao, Xiangqian; Daygon, Venea D; McNally, Kenneth L; Hamilton, Ruaraidh Sackville; Xie, Fangming; Reinke, Russell F; Fitzgerald, Melissa A

2016-01-01

A novel QTL cluster for chalkiness on Chr04 was identified using single environment analysis and joint mapping across 9 environments in Asia and South American. QTL NILs showed that each had a significant effect on chalk. Chalk in rice grains leads to a significant loss in the proportion of marketable grains in a harvested crop, leading to a significant financial loss to rice farmers and traders. To identify the genetic basis of chalkiness, two sets of recombinant inbred lines (RILs) derived from reciprocal crosses between Lemont and Teqing were used to find stable QTLs for chalkiness. The RILs were grown in seven locations in Asia and Latin American and in two controlled environments in phytotrons. A total of 32 (21) and 46 (22) QTLs for DEC and PGWC, most of them explaining more than 10% of phenotypic variation, were detected based on single environment analysis in T/L (L/T) population, respectively. Seven (2) and 7 (3) QTLs for DEC and PGWC were identified in the T/L (L/T) population using joined analysis across all environments, respectively. Six major QTLs clusters were found on five chromosomes: 1, 2, 4, 5 and 11. The biggest cluster at id4007289-RM252 on Chr04 was a novelty, including 16 and 4 QTLs detected by single environment analysis and joint mapping across all environments, respectively. The detected digenic epistatic QTLs explained up to 13% of phenotypic variation, suggesting that epistasis play an important role in the genetic control of chalkiness in rice. QTL NILs showed that each QTL cluster had a significant effect on chalk. These chromosomal regions could be targets for MAS, fine mapping and map-based cloning for low chalkiness breeding.

Identification of rice cornichon as a possible cargo receptor for the Golgi-localized sodium transporter OsHKT1;3.

PubMed

Rosas-Santiago, Paul; Lagunas-Gómez, Daniel; Barkla, Bronwyn J; Vera-Estrella, Rosario; Lalonde, Sylvie; Jones, Alexander; Frommer, Wolf B; Zimmermannova, Olga; Sychrová, Hana; Pantoja, Omar

2015-05-01

Membrane proteins are synthesized and folded in the endoplasmic reticulum (ER), and continue their path to their site of residence along the secretory pathway. The COPII system has been identified as a key player for selecting and directing the fate of membrane and secretory cargo proteins. Selection of cargo proteins within the COPII vesicles is achieved by cargo receptors. The cornichon cargo receptor belongs to a conserved protein family found in eukaryotes that has been demonstrated to participate in the selection of integral membrane proteins as cargo for their correct targeting. Here it is demonstrated at the cellular level that rice cornichon OsCNIH1 interacts with OsHKT1;3 and, in yeast cells, enables the expression of the sodium transporter to the Golgi apparatus. Physical and functional HKT-cornichon interactions are confirmed by the mating-based split ubiquitin system, bimolecular fluorescence complementation, and Xenopus oocyte and yeast expression systems. The interaction between the two proteins occurs in the ER of plant cells and their co-expression in oocytes leads to the sequestration of the transporter in the ER. In the yeast cornichon mutant erv14, OsHKT1;3 is mistargeted, preventing the toxic effects of sodium transport in the cell observed in wild-type cells or in the erv14 mutant that co-expressed OsHKT1;3 with either OsCNIH1 or Erv14p. Identification and characterization of rice cornichon as a possible cargo receptor opens up the opportunity to improve our knowledge on membrane protein targeting in plant cells. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

FORMULATION AND EVALUATION OF RICE BRAN WAX AS OINTMENT BASE

PubMed Central

Bhalekar, M; Manish, Lavhale; Krishna, Sini

2004-01-01

Rice Bran wax is obtained from natural sources and is abundantly available in the country. Rice bran wax is suitable for use in chocolate enrobes, as an enteric coating for candy and lozenges, as a plasticizing material in chewing gums etc. Present study attempts to find if rice bran wax is useful as ointment base. The oleaginous type ointment base is prepared by using rice bran wax and evaluated for speardabililty, water number and active ingredient diffusibility. The results obtained in the present study indicate, rice bran wax can be used as a good component in ointment base, comparable with white wax. PMID:22557151

Examination of the semi-automatic calculation technique of vegetation cover rate by digital camera images.

NASA Astrophysics Data System (ADS)

Takemine, S.; Rikimaru, A.; Takahashi, K.

The rice is one of the staple foods in the world High quality rice production requires periodically collecting rice growth data to control the growth of rice The height of plant the number of stem the color of leaf is well known parameters to indicate rice growth Rice growth diagnosis method based on these parameters is used operationally in Japan although collecting these parameters by field survey needs a lot of labor and time Recently a laborsaving method for rice growth diagnosis is proposed which is based on vegetation cover rate of rice Vegetation cover rate of rice is calculated based on discriminating rice plant areas in a digital camera image which is photographed in nadir direction Discrimination of rice plant areas in the image was done by the automatic binarization processing However in the case of vegetation cover rate calculation method depending on the automatic binarization process there is a possibility to decrease vegetation cover rate against growth of rice In this paper a calculation method of vegetation cover rate was proposed which based on the automatic binarization process and referred to the growth hysteresis information For several images obtained by field survey during rice growing season vegetation cover rate was calculated by the conventional automatic binarization processing and the proposed method respectively And vegetation cover rate of both methods was compared with reference value obtained by visual interpretation As a result of comparison the accuracy of discriminating rice plant areas was increased by the proposed

Nitric Oxide and Protein S-Nitrosylation Are Integral to Hydrogen Peroxide-Induced Leaf Cell Death in Rice1[W][OA

PubMed Central

Lin, Aihong; Wang, Yiqin; Tang, Jiuyou; Xue, Peng; Li, Chunlai; Liu, Linchuan; Hu, Bin; Yang, Fuquan; Loake, Gary J.; Chu, Chengcai

2012-01-01

Nitric oxide (NO) is a key redox-active, small molecule involved in various aspects of plant growth and development. Here, we report the identification of an NO accumulation mutant, nitric oxide excess1 (noe1), in rice (Oryza sativa), the isolation of the corresponding gene, and the analysis of its role in NO-mediated leaf cell death. Map-based cloning revealed that NOE1 encoded a rice catalase, OsCATC. Furthermore, noe1 resulted in an increase of hydrogen peroxide (H2O2) in the leaves, which consequently promoted NO production via the activation of nitrate reductase. The removal of excess NO reduced cell death in both leaves and suspension cultures derived from noe1 plants, implicating NO as an important endogenous mediator of H2O2-induced leaf cell death. Reduction of intracellular S-nitrosothiol (SNO) levels, generated by overexpression of rice S-nitrosoglutathione reductase gene (GSNOR1), which regulates global levels of protein S-nitrosylation, alleviated leaf cell death in noe1 plants. Thus, S-nitrosylation was also involved in light-dependent leaf cell death in noe1. Utilizing the biotin-switch assay, nanoliquid chromatography, and tandem mass spectrometry, S-nitrosylated proteins were identified in both wild-type and noe1 plants. NO targets identified only in noe1 plants included glyceraldehyde 3-phosphate dehydrogenase and thioredoxin, which have been reported to be involved in S-nitrosylation-regulated cell death in animals. Collectively, our data suggest that both NO and SNOs are important mediators in the process of H2O2-induced leaf cell death in rice. PMID:22106097

A guanine insert in OsBBS1 leads to early leaf senescence and salt stress sensitivity in rice (Oryza sativa L.).

PubMed

Zeng, Dong-Dong; Yang, Cheng-Cong; Qin, Ran; Alamin, Md; Yue, Er-Kui; Jin, Xiao-Li; Shi, Chun-Hai

2018-06-01

A rice receptor-like kinase gene OSBBS1/OsRLCK109 was identified; this gene played vital roles in leaf senescence and the salt stress response. Early leaf senescence can cause negative effects on rice yield, but the underlying molecular regulation is not fully understood. bilateral blade senescence 1 (bbs1), an early leaf senescence mutant with a premature senescence phenotype that occurs mainly performing at the leaf margins, was isolated from a rice mutant population generated by ethylmethane sulfonate (EMS) treatment. The mutant showed premature leaf senescence beginning at the tillering stage and exhibited severe symptoms at the late grain-filling stage. bbs1 showed accelerated dark-induced leaf senescence. The OsBBS1 gene was cloned by a map-based cloning strategy, and a guanine (G) insertion was found in the first exon of LOC_Os03g24930. This gene encodes a receptor-like cytoplasmic kinase and was named OsRLCK109 in a previous study. Transgenic LOC_Os03g24930 knockout plants generated by a CRISPR/Cas9 strategy exhibited similar early leaf senescence phenotypes as did the bbs1 mutant, which confirmed that LOC_Os03g24930 was the OsBBS1 gene. OsBBS1/OsRLCK109 was expressed in all detected tissues and was predominantly expressed in the main vein region of mature leaves. The expression of OsBBS1 could be greatly induced by salt stress, and the bbs1 mutant exhibited hypersensitivity to salt stress. In conclusion, this is the first identification of OsRLCKs participating in leaf senescence and playing critical roles in the salt stress response in rice (Oryza sativa L.).

Genome wide association study (GWAS) for grain yield in rice cultivated under water deficit.

PubMed

Pantalião, Gabriel Feresin; Narciso, Marcelo; Guimarães, Cléber; Castro, Adriano; Colombari, José Manoel; Breseghello, Flavio; Rodrigues, Luana; Vianello, Rosana Pereira; Borba, Tereza Oliveira; Brondani, Claudio

2016-12-01

The identification of rice drought tolerant materials is crucial for the development of best performing cultivars for the upland cultivation system. This study aimed to identify markers and candidate genes associated with drought tolerance by Genome Wide Association Study analysis, in order to develop tools for use in rice breeding programs. This analysis was made with 175 upland rice accessions (Oryza sativa), evaluated in experiments with and without water restriction, and 150,325 SNPs. Thirteen SNP markers associated with yield under drought conditions were identified. Through stepwise regression analysis, eight SNP markers were selected and validated in silico, and when tested by PCR, two out of the eight SNP markers were able to identify a group of rice genotypes with higher productivity under drought. These results are encouraging for deriving markers for the routine analysis of marker assisted selection. From the drought experiment, including the genes inherited in linkage blocks, 50 genes were identified, from which 30 were annotated, and 10 were previously related to drought and/or abiotic stress tolerance, such as the transcription factors WRKY and Apetala2, and protein kinases.

Heavy metal contaminations in soil-rice system: source identification in relation to a sulfur-rich coal burning power plant in Northern Guangdong Province, China.

PubMed

Wang, Xiangqin; Zeng, Xiaoduo; Chuanping, Liu; Li, Fangbai; Xu, Xianghua; Lv, Yahui

2016-08-01

Heavy metal contents (As, Cd, Cr, Cu, Hg, Ni, Pb, and Zn) in 99 pairs of soil-rice plant samples were evaluated from the downwind directions of a large thermal power plant in Shaoguan City, Guangdong Province, China. Results indicate that there is a substantial buildup of As, Cd, Cu, Pb, and Zn in the predominant wind direction of the power plant. The significant correlations between S and heavy metals in paddy soil suggest that the power plant represents a source of topsoil heavy metals in Shaoguan City due to sulfur-rich coal burning emissions. Elevated Cd concentrations were also found in rice plant tissues. Average Cd (0.69 mg kg(-1)) and Pb (0.39 mg kg(-1)) contents in rice grain had exceeded their maximum permissible limits (both were 0.2 mg kg(-1)) in foods of China (GB2762-2005). The enrichment of Cd and Pb in rice grain might pose a potential health risk to the local residents.

TOND1 confers tolerance to nitrogen deficiency in rice

PubMed Central

Zhang, Yangjun; Tan, Lubin; Zhu, Zuofeng; Yuan, Lixing; Xie, Daoxin; Sun, Chuanqing

2015-01-01

Nitrogen (N), the most important mineral nutrient for plants, is critical to agricultural production systems. N deficiency severely affects rice growth and decreases rice yields. However, excessive use of N fertilizer has caused severe pollution to agricultural and ecological environments. The necessity of breeding of crops that require lower input of N fertilizer has been recognized. Here we identified a major quantitative trait locus on chromosome 12, Tolerance Of Nitrogen Deficiency 1 (TOND1), that confers tolerance to N deficiency in the indica cultivar Teqing. Sequence verification of 75 indica and 75 japonica cultivars from 18 countries and regions demonstrated that only 27.3% of cultivars (41 indica cultivars) contain TOND1, whereas 72.7% of cultivars, including the remaining 34 indica cultivars and all 75 japonica cultivars, do not harbor the TOND1 allele. Over-expression of TOND1 increased the tolerance to N deficiency in the TOND1-deficient rice cultivars. The identification of TOND1 provides a molecular basis for breeding rice varieties with improved grain yield despite decreased input of N fertilizers. PMID:25439309

Identification of pyroglutamyl peptides in Japanese rice wine (sake): presence of hepatoprotective pyroGlu-Leu.

PubMed

Kiyono, Tamami; Hirooka, Kiyoo; Yamamoto, Yoshihiro; Kuniishi, Sunao; Ohtsuka, Maho; Kimura, Shikou; Park, Eun Young; Nakamura, Yasushi; Sato, Kenji

2013-11-27

Japanese rice wine, sake, is made from steamed rice, water, and lactic acid by "multiple parallel fermentation" with mold (Aspergillus oryzae) and yeast (Saccharomyces cerevisiae). Nineteen pyroglutamyl peptides were identified in commercially available sake. Among them, pyroGlu-Leu and pyroGlu-Gln were the major constituents. PyroGlu-Leu has been demonstrated to attenuate hepatitis and colitis in animal models. Commercial products (n = 5) contained pyroGlu-Leu at concentrations ranging from 40 to 60 μM (10-15 mg/L). The pyroGlu-Leu content in sake mash increased during the fermentation processes. However, no pyroGlu-Leu was produced by yeast inoculated into preheated mash. Furthermore, addition of (13)C-Leu to the mash did not increase the ratio of pyroGlu-(13)C-Leu to pyroGlu-(12)C-Leu. On the other hand, digestion of steamed rice with A. oryzae proteases increased the pyroGlu-Leu content. These results indicate that pyroGlu-Leu in sake is produced from rice proteins by digestion with A. oryzae proteases.

Studies on the methods of identification of irradiated food I. Seedling growth test

NASA Astrophysics Data System (ADS)

Qiongying, Liu; Yanhua, Kuang; Yuemei, Zheng

1993-07-01

A seedling growth test for the identification of gamma irradiated edible vegetable seeds was described. The identification of gamma irradiated grape and the other seeds has been investigated. The purpose of this study was to develop an easy, rapid and practical technique for the identification of irradiated edible vegetable seeds. Seven different irradiated edible vegetable seeds as: rice ( Oryza sativa), peanut ( Arachis hypogaea), maize ( Zeamays), soybean ( Glycine max), red bean ( Phaseolus angularis), mung bean ( Phaseolus aureus) and catjang cowpea ( Vigna cylindrica) were tested by using the method of seedling growth. All of the edible vegetable seeds were exposed to gamma radiation on different doses, O(CK), 0.5, 1.0, 1.5, 2.0, 3.0, 5.0 kGy. After treatment with above 1.0 kGy dose to the seeds, the seedling rate was less than 50% compared with the control. Although the seedling rate of rice seeds can reached 58%, the seedling growth was not normal and the seedling leaves appeared deformed. The results by this method were helpful to identify gamma treatment of the edible vegetable seeds with above 1.0 kGy dose.

Annual Changes of Paddy Rice Planting Areas in Northeastern Asia from MODIS images in 2000-2014

NASA Astrophysics Data System (ADS)

Xiao, X.; Zhang, G.; Dong, J.; Menarguez, M. A.; Kou, W.; Jin, C.; Qin, Y.; Zhou, Y.; Wang, J.; Moore, B., III

2014-12-01

Knowledge of the area and spatial distribution of paddy rice is important for assessment of food security, management of water resources, estimation of greenhouse gas (methane) emissions, and understanding avian influenza virus transmission. Over the past two decades, paddy rice cultivation has expanded northward in temperate and cold temperate zones, particularly in Northeastern China. There is a need to quantify and map changes in paddy rice planting areas in Northeastern Asia (Japan, North and South Korea, and northeast China) at annual interval. We developed a pixel- and phenology-based image analysis system, MODIS-RICE, to map the paddy rice in Northeastern Asia by using multi-temporal MODIS thermal and surface reflectance imagery. Paddy rice fields during the flooding and transplanting phases have unique physical and spectral characteristics, which make it possible for the development of an automated and robust algorithm to track flooding and transplanting phases of paddy rice fields over time. In this presentation, we will show the MODIS-based annual maps of paddy rice planting area in the Northeastern Asia from 2000-2014 (500-m spatial resolution). Accuracy assessments using high-resolution images show that the resultant paddy rice map of Northeastern Asia had a comparable accuracy to the existing products, including 2010 Landsat-based National Land Cover Dataset (NLCD) of China, the 2010 RapidEye-based paddy rice map in North Korea, and the 2010 AVNIR-2-based National Land Cover Dataset in Japan in terms of both area and spatial pattern of paddy rice. This study has demonstrated that our novel MODIS-Rice system, which use both thermal and optical MODIS data over a year, are simple and robust tools to identify and map paddy rice fields in temperate and cold temperate zones.

Diversity of global rice markets and the science required for consumer-targeted rice breeding.

PubMed

Calingacion, Mariafe; Laborte, Alice; Nelson, Andrew; Resurreccion, Adoracion; Concepcion, Jeanaflor Crystal; Daygon, Venea Dara; Mumm, Roland; Reinke, Russell; Dipti, Sharifa; Bassinello, Priscila Zaczuk; Manful, John; Sophany, Sakhan; Lara, Karla Cordero; Bao, Jinsong; Xie, Lihong; Loaiza, Katerine; El-hissewy, Ahmad; Gayin, Joseph; Sharma, Neerja; Rajeswari, Sivakami; Manonmani, Swaminathan; Rani, N Shobha; Kota, Suneetha; Indrasari, Siti Dewi; Habibi, Fatemeh; Hosseini, Maryam; Tavasoli, Fatemeh; Suzuki, Keitaro; Umemoto, Takayuki; Boualaphanh, Chanthkone; Lee, Huei Hong; Hung, Yiu Pang; Ramli, Asfaliza; Aung, Pa Pa; Ahmad, Rauf; Wattoo, Javed Iqbal; Bandonill, Evelyn; Romero, Marissa; Brites, Carla Moita; Hafeel, Roshni; Lur, Huu-Sheng; Cheaupun, Kunya; Jongdee, Supanee; Blanco, Pedro; Bryant, Rolfe; Thi Lang, Nguyen; Hall, Robert D; Fitzgerald, Melissa

2014-01-01

With the ever-increasing global demand for high quality rice in both local production regions and with Western consumers, we have a strong desire to understand better the importance of the different traits that make up the quality of the rice grain and obtain a full picture of rice quality demographics. Rice is by no means a 'one size fits all' crop. Regional preferences are not only striking, they drive the market and hence are of major economic importance in any rice breeding / improvement strategy. In this analysis, we have engaged local experts across the world to perform a full assessment of all the major rice quality trait characteristics and importantly, to determine how these are combined in the most preferred varieties for each of their regions. Physical as well as biochemical characteristics have been monitored and this has resulted in the identification of no less than 18 quality trait combinations. This complexity immediately reveals the extent of the specificity of consumer preference. Nevertheless, further assessment of these combinations at the variety level reveals that several groups still comprise varieties which consumers can readily identify as being different. This emphasises the shortcomings in the current tools we have available to assess rice quality and raises the issue of how we might correct for this in the future. Only with additional tools and research will we be able to define directed strategies for rice breeding which are able to combine important agronomic features with the demands of local consumers for specific quality attributes and hence, design new, improved crop varieties which will be awarded success in the global market.

Diversity of Global Rice Markets and the Science Required for Consumer-Targeted Rice Breeding

PubMed Central

Calingacion, Mariafe; Laborte, Alice; Nelson, Andrew; Resurreccion, Adoracion; Concepcion, Jeanaflor Crystal; Daygon, Venea Dara; Mumm, Roland; Reinke, Russell; Dipti, Sharifa; Bassinello, Priscila Zaczuk; Manful, John; Sophany, Sakhan; Lara, Karla Cordero; Bao, Jinsong; Xie, Lihong; Loaiza, Katerine; El-hissewy, Ahmad; Gayin, Joseph; Sharma, Neerja; Rajeswari, Sivakami; Manonmani, Swaminathan; Rani, N. Shobha; Kota, Suneetha; Indrasari, Siti Dewi; Habibi, Fatemeh; Hosseini, Maryam; Tavasoli, Fatemeh; Suzuki, Keitaro; Umemoto, Takayuki; Boualaphanh, Chanthkone; Lee, Huei Hong; Hung, Yiu Pang; Ramli, Asfaliza; Aung, Pa Pa; Ahmad, Rauf; Wattoo, Javed Iqbal; Bandonill, Evelyn; Romero, Marissa; Brites, Carla Moita; Hafeel, Roshni; Lur, Huu-Sheng; Cheaupun, Kunya; Jongdee, Supanee; Blanco, Pedro; Bryant, Rolfe; Thi Lang, Nguyen; Hall, Robert D.; Fitzgerald, Melissa

2014-01-01

With the ever-increasing global demand for high quality rice in both local production regions and with Western consumers, we have a strong desire to understand better the importance of the different traits that make up the quality of the rice grain and obtain a full picture of rice quality demographics. Rice is by no means a ‘one size fits all’ crop. Regional preferences are not only striking, they drive the market and hence are of major economic importance in any rice breeding / improvement strategy. In this analysis, we have engaged local experts across the world to perform a full assessment of all the major rice quality trait characteristics and importantly, to determine how these are combined in the most preferred varieties for each of their regions. Physical as well as biochemical characteristics have been monitored and this has resulted in the identification of no less than 18 quality trait combinations. This complexity immediately reveals the extent of the specificity of consumer preference. Nevertheless, further assessment of these combinations at the variety level reveals that several groups still comprise varieties which consumers can readily identify as being different. This emphasises the shortcomings in the current tools we have available to assess rice quality and raises the issue of how we might correct for this in the future. Only with additional tools and research will we be able to define directed strategies for rice breeding which are able to combine important agronomic features with the demands of local consumers for specific quality attributes and hence, design new, improved crop varieties which will be awarded success in the global market. PMID:24454799

RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement.

PubMed

Sandhu, Maninder; Sureshkumar, V; Prakash, Chandra; Dixit, Rekha; Solanke, Amolkumar U; Sharma, Tilak Raj; Mohapatra, Trilochan; S V, Amitha Mithra

2017-09-30

Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to develop a web interface which combines the information from functional genomic studies across different genetic backgrounds with DNA markers so that they can be readily deployed in crop improvement. In the current version of the database, we have included drought and salinity stress studies since these two are the major abiotic stresses in rice. RiceMetaSys, a user-friendly and freely available web interface provides comprehensive information on salt responsive genes (SRGs) and drought responsive genes (DRGs) across genotypes, crop development stages and tissues, identified from multiple microarray datasets. 'Physical position search' is an attractive tool for those using QTL based approach for dissecting tolerance to salt and drought stress since it can provide the list of SRGs and DRGs in any physical interval. To identify robust candidate genes for use in crop improvement, the 'common genes across varieties' search tool is useful. Graphical visualization of expression profiles across genes and rice genotypes has been enabled to facilitate the user and to make the comparisons more impactful. Simple Sequence Repeat (SSR) search in the SRGs and DRGs is a valuable tool for fine mapping and marker assisted selection since it provides primers for survey of polymorphism. An external link to intron specific markers is also provided for this purpose. Bulk retrieval of data without any limit has been enabled in case of locus and SSR search. The aim of this database is to facilitate users with a simple and straight-forward search options for identification of robust candidate genes from among thousands of SRGs and DRGs so as to facilitate linking variation in expression profiles to variation in phenotype. Database URL: http://14.139.229.201.

Estimation of the Age and Amount of Brown Rice Plant Hoppers Based on Bionic Electronic Nose Use

PubMed Central

Xu, Sai; Zhou, Zhiyan; Lu, Huazhong; Luo, Xiwen; Lan, Yubin; Zhang, Yang; Li, Yanfang

2014-01-01

The brown rice plant hopper (BRPH), Nilaparvata lugens (Stal), is one of the most important insect pests affecting rice and causes serious damage to the yield and quality of rice plants in Asia. This study used bionic electronic nose technology to sample BRPH volatiles, which vary in age and amount. Principal component analysis (PCA), linear discrimination analysis (LDA), probabilistic neural network (PNN), BP neural network (BPNN) and loading analysis (Loadings) techniques were used to analyze the sampling data. The results indicate that the PCA and LDA classification ability is poor, but the LDA classification displays superior performance relative to PCA. When a PNN was used to evaluate the BRPH age and amount, the classification rates of the training set were 100% and 96.67%, respectively, and the classification rates of the test set were 90.67% and 64.67%, respectively. When BPNN was used for the evaluation of the BRPH age and amount, the classification accuracies of the training set were 100% and 48.93%, respectively, and the classification accuracies of the test set were 96.67% and 47.33%, respectively. Loadings for BRPH volatiles indicate that the main elements of BRPHs' volatiles are sulfur-containing organics, aromatics, sulfur- and chlorine-containing organics and nitrogen oxides, which provide a reference for sensors chosen when exploited in specialized BRPH identification devices. This research proves the feasibility and broad application prospects of bionic electronic noses for BRPH recognition. PMID:25268913

International collaborative study of the endogenous reference gene, sucrose phosphate synthase (SPS), used for qualitative and quantitative analysis of genetically modified rice.

PubMed

Jiang, Lingxi; Yang, Litao; Zhang, Haibo; Guo, Jinchao; Mazzara, Marco; Van den Eede, Guy; Zhang, Dabing

2009-05-13

One rice ( Oryza sativa ) gene, sucrose phosphate synthase (SPS), has been proven to be a suitable endogenous reference gene for genetically modified (GM) rice detection in a previous study. Herein are the reported results of an international collaborative ring trial for validation of the SPS gene as an endogenous reference gene and its optimized qualitative and quantitative polymerase chain reaction (PCR) systems. A total of 12 genetically modified organism (GMO) detection laboratories from seven countries participated in the ring trial and returned their results. The validated results confirmed the species specificity of the method through testing 10 plant genomic DNAs, low heterogeneity, and a stable single-copy number of the rice SPS gene among 7 indica varieties and 5 japonica varieties. The SPS qualitative PCR assay was validated with a limit of detection (LOD) of 0.1%, which corresponded to about 230 copies of haploid rice genomic DNA, while the limit of quantification (LOQ) for the quantitative PCR system was about 23 copies of haploid rice genomic DNA, with acceptable PCR efficiency and linearity. Furthermore, the bias between the test and true values of eight blind samples ranged from 5.22 to 26.53%. Thus, we believe that the SPS gene is suitable for use as an endogenous reference gene for the identification and quantification of GM rice and its derivates.

High infestation levels of Schizotetranychus oryzae severely affects rice metabolism.

PubMed

Blasi, Édina A R; Buffon, Giseli; Rativa, Angie G S; Lopes, Mara C B; Berger, Markus; Santi, Lucélia; Lavallée-Adam, Mathieu; Yates, John R; Schwambach, Joséli; Beys-da-Silva, Walter O; Sperotto, Raul A

2017-12-01

High levels of Schizotetranychus oryzae phytophagous mite infestation on rice leaves can severely affect productivity. Physiological characterization showed that S. oryzae promotes a decrease in chlorophyll concentration and the establishment of a senescence process in rice leaves. Late-infested leaves also present high levels of superoxide radical and hydrogen peroxide accumulation, along with high levels of membrane integrity loss, which is indicative of cell death. To better understand the rice molecular responses to high levels of mite infestation, we employed the Multidimensional Protein Identification Technology (MudPIT) approach to identify differentially expressed proteins. We identified 83 and 88 proteins uniquely present in control and late-infested leaves, respectively, along with 11 and one proteins more abundant in control and late-infested leaves, respectively. S. oryzae infestation induces a decreased abundance of proteins related to translation, protease inhibition, and photosynthesis. On the other hand, infestation caused increased abundance of proteins involved in protein modification and degradation. Our results also suggest that S. oryzae infestation interferes with intracellular transport, DNA structure maintenance, and amino acid and lipid metabolism in rice leaves. Proteomic data were positively correlated with enzymatic assays and RT-qPCR analysis. Our findings describe the protein expression patterns of late-infested rice leaves and suggest several targets which could be tested in future biotechnological approaches aiming to avoid the population increase of phytophagous mite in rice plants. Copyright © 2017 Elsevier GmbH. All rights reserved.

Proteomics of rice and Cochliobolus miyabeanus fungal interaction: insight into proteins at intracellular and extracellular spaces.

PubMed

Kim, Jin Yeong; Wu, Jingni; Kwon, Soon Jae; Oh, Haram; Lee, So Eui; Kim, Sang Gon; Wang, Yiming; Agrawal, Ganesh Kumar; Rakwal, Randeep; Kang, Kyu Young; Ahn, Il-Pyung; Kim, Beom-Gi; Kim, Sun Tae

2014-10-01

Necrotrophic fungal pathogen Cochliobolus miyabeanus causes brown spot disease in rice leaves upon infection, resulting in critical rice yield loss. To better understand the rice-C. miyabeanus interaction, we employed proteomic approaches to establish differential proteomes of total and secreted proteins from the inoculated leaves. The 2DE approach after PEG-fractionation of total proteins coupled with MS (MALDI-TOF/TOF and nESI-LC-MS/MS) analyses led to identification of 49 unique proteins out of 63 differential spots. SDS-PAGE in combination with nESI-LC-MS/MS shotgun approach was applied to identify secreted proteins in the leaf apoplast upon infection and resulted in cataloging of 501 unique proteins, of which 470 and 31 proteins were secreted from rice and C. miyabeanus, respectively. Proteins mapped onto metabolic pathways implied their reprogramming upon infection. The enzymes involved in Calvin cycle and glycolysis decreased in their protein abundance, whereas enzymes in the TCA cycle, amino acids, and ethylene biosynthesis increased. Differential proteomes also generated distribution of identified proteins in the intracellular and extracellular spaces, providing a better insight into defense responses of proteins in rice against C. miyabeanus. Established proteome of the rice-C. miyabeanus interaction serves not only as a good resource for the scientific community but also highlights its significance from biological aspects. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Identification of heat-sensitive QTL derived from common wild rice (Oryza rufipogon Griff.).

PubMed

Lei, Dongyang; Tan, Lubin; Liu, Fengxia; Chen, Liyun; Sun, Chuanqing

2013-03-01

Understanding the responses of rice plants to heat-stress is a challenging, yet crucial, endeavor. A set of introgression lines was previously developed using an advanced backcrossing strategy that involved the elite indica cultivar Teqing as the recipient and an accession of common wild rice (Oryza rufipongon Griff.) as the donor. In this study, we evaluated the responses of 90 of these previously developed introgression lines to heat stress. Five quantitative trait loci (QTLs) related to heat response were detected. The phenotypic variances explained by these QTLs ranged from 6.83% to 14.63%, and O. rufipogon-derived alleles at one locus reduced sensitivity to heat. A heat-sensitive introgression line, YIL106, was identified and characterized. Genotypic analysis demonstrated that YIL106 contained four introgressed segments derived from O. rufipongon and two QTLs (qHTS1-1 and qHTS3) related to heat response. Physiological tests, including measurements of chlorophyll content, electrolyte leakage, malondialdehyde content, and soluble sugar content, were consistent with the heat sensitivity observed in YIL106. Ultrastructural analysis of YIL106 mesophyll cells showed that they were severely damaged following heat stress. This suggests that modification of the cell membrane system is a primary response to heat stress in plants. Identification and characterization of the heat-sensitive line YIL106 may facilitate the isolation of genes associated with the response of rice plants to heat stress. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Proteomic identification of an embryo-specific 1Cys-Prx promoter and analysis of its activity in transgenic rice.

PubMed

Kim, Je Hein; Jung, In Jung; Kim, Dool Yi; Fanata, Wahyu Indra; Son, Bo Hwa; Yoo, Jae Yong; Harmoko, Rikno; Ko, Ki Seong; Moon, Jeong Chan; Jang, Ho Hee; Kim, Woe Yeon; Kim, Jae-Yean; Lim, Chae Oh; Lee, Sang Yeol; Lee, Kyun Oh

2011-04-29

Proteomic analysis of a rice callus led to the identification of 10 abscisic acid (ABA)-induced proteins as putative products of the embryo-specific promoter candidates. 5'-flanking sequence of 1 Cys-Prx, a highly-induced protein gene, was cloned and analyzed. The transcription initiation site of 1 Cys-Prx maps 96 nucleotides upstream of the translation initiation codon and a TATA-box and putative seed-specific cis-acting elements, RYE and ABRE, are located 26, 115 and 124 bp upstream of the transcription site, respectively. β-glucuronidase (GUS) expression driven by the 1 Cys-Prx promoters was strong in the embryo and aleurone layer and the activity reached up to 24.9 ± 3.3 and 40.5 ± 2.1 pmol (4 MU/min/μg protein) in transgenic rice seeds and calluses, respectively. The activity of the 1 Cys-Prx promoters is much higher than that of the previously-identified embryo-specific promoters, and comparable to that of strong endosperm-specific promoters in rice. GUS expression driven by the 1 Cys-Prx promoters has been increased by ABA treatment and rapidly induced by wounding in callus and at the leaf of the transgenic plants, respectively. Furthermore, ectopic expression of the GUS construct in Arabidopsis suggested that the 1 Cys-Prx promoter also has strong activity in seeds of dicot plants. Copyright © 2011 Elsevier Inc. All rights reserved.

Mapping Early, Middle and Late Rice Extent Using Sentinel-1A and Landsat-8 Data in the Poyang Lake Plain, China

PubMed Central

Wu, Mingquan; Wang, Li

2018-01-01

Areas and spatial distribution information of paddy rice are important for managing food security, water use, and climate change. However, there are many difficulties in mapping paddy rice, especially mapping multi-season paddy rice in rainy regions, including differences in phenology, the influence of weather, and farmland fragmentation. To resolve these problems, a novel multi-season paddy rice mapping approach based on Sentinel-1A and Landsat-8 data is proposed. First, Sentinel-1A data were enhanced based on the fact that the backscattering coefficient of paddy rice varies according to its growth stage. Second, cropland information was enhanced based on the fact that the NDVI of cropland in winter is lower than that in the growing season. Then, paddy rice and cropland areas were extracted using a K-Means unsupervised classifier with enhanced images. Third, to further improve the paddy rice classification accuracy, cropland information was utilized to optimize distribution of paddy rice by the fact that paddy rice must be planted in cropland. Classification accuracy was validated based on ground-data from 25 field survey quadrats measuring 600 m × 600 m. The results show that: multi-season paddy rice planting areas effectively was extracted by the method and adjusted early rice area of 1630.84 km2, adjusted middle rice area of 556.21 km2, and adjusted late rice area of 3138.37 km2. The overall accuracy was 98.10%, with a kappa coefficient of 0.94. PMID:29324647

Effects of paddy rice agriculture on the seasonal dynamics of atmospheric methane concentration

NASA Astrophysics Data System (ADS)

Zhang, G.; Xiao, X.; Dong, J.; Zhang, Y.; Xin, F.; Zhou, Y.; Wang, J.; Wu, X.; Moore, B., III

2017-12-01

Methane (CH4) is an important greenhouse gas (GHG) and may account for 20 % of anticipated global warming. The atmospheric CH4 concentration was nearly constant from 1999 to 2006, following with a strong growth resumed since 2007. Previous study attributed the increase in CH4 to agriculture. Specifically, paddy rice agriculture is a significant source of CH4, but large uncertainty still exists on methane emission estimates from rice paddies, largely due to lack of detailed geospatial datasets of rice paddies. In this study, based on a pixel- and phenology-based image analysis system with multi-temporal MODIS imagery (MODIS-RICE), we generated the paddy rice map in 2005 to document the spatiotemporal pattern of paddy rice dynamics in Monsoon Asia, which accounts for more than 90% of the global rice production. Furthermore, we examined the effects of paddy rice agriculture on atmospheric CH4 concentration over Monsoon Asia, by comparing atmospheric CH4 concentration data from SCIAMACHY sensor and the paddy rice maps in 2005. We found a significant spatial consistency between spatial patterns of paddy rice and atmospheric CH4 concentration. Based on the high resolution paddy rice map, different seasonal dynamics of CH4 concentration, including single, double to triple peaks, were found based on the rice paddy distribution information. That suggests paddy rice agriculture contributes substantially to the spatial and seasonal pattern of atmospheric CH4 concentration in Monsoon Asia. This study provides satellite evidence for seasonal cycle of CH4 dynamics at regional scale, and suggests that shifting regime of paddy rice agriculture and cropping intensity could affect the seasonal dynamics and spatial pattern of atmospheric methane concentration.

Newly Identified Wild Rice Accessions Conferring High Salt Tolerance Might Use a Tissue Tolerance Mechanism in Leaf.

PubMed

Prusty, Manas R; Kim, Sung-Ryul; Vinarao, Ricky; Entila, Frederickson; Egdane, James; Diaz, Maria G Q; Jena, Kshirod K

2018-01-01

Cultivated rice ( Oryza sativa L.) is very sensitive to salt stress. So far a few rice landraces have been identified as a source of salt tolerance and utilized in rice improvement. These tolerant lines primarily use Na + exclusion mechanism in root which removes Na + from the xylem stream by membrane Na + and K + transporters, and resulted in low Na + accumulation in shoot. Identification of a new donor source conferring high salt tolerance is imperative. Wild relatives of rice having wide genetic diversity are regarded as a potential source for crop improvement. However, they have been less exploited against salt stress. Here, we simultaneously evaluated all 22 wild Oryza species along with the cultivated tolerant lines including Pokkali, Nona Bokra, and FL478, and sensitive check varieties under high salinity (240 mM NaCl). Based on the visual salt injury score, three species ( O . alta, O . latifolia , and O . coarctata ) and four species ( O . rhizomatis, O . eichingeri, O . minuta , and O . grandiglumis ) showed higher and similar level of tolerance compared to the tolerant checks, respectively. All three CCDD genome species exhibited salt tolerance, suggesting that the CCDD genome might possess the common genetic factors for salt tolerance. Physiological and biochemical experiments were conducted using the newly isolated tolerant species together with checks under 180 mM NaCl. Interestingly, all wild species showed high Na + concentration in shoot and low concentration in root unlike the tolerant checks. In addition, the wild-tolerant accessions showed a tendency of a high tissue tolerance in leaf, low malondialdehyde level in shoot, and high retention of chlorophyll in the young leaves. These results suggest that the wild species employ tissue tolerance mechanism to manage salt stress. Gene expression analyses of the key salt tolerance-related genes suggested that high Na + in leaf of wild species might be affected by OsHKT1;4 -mediated Na + exclusion in leaf and the following Na + sequestration in leaf might be occurring independent of tonoplast-localized OsNHX1. The newly isolated wild rice accessions will be valuable materials for both rice improvement to salinity stress and the study of salt tolerance mechanism in plants.

High Resolution Mapping of QTLs for Heat Tolerance in Rice Using a 5K SNP Array.

PubMed

Ps, Shanmugavadivel; Sv, Amitha Mithra; Prakash, Chandra; Mk, Ramkumar; Tiwari, Ratan; Mohapatra, Trilochan; Singh, Nagendra Kumar

2017-12-01

Heat stress is one of the major abiotic threats to rice production, next to drought and salinity stress. Incidence of heat stress at reproductive phase of the crop results in abnormal pollination leading to floret sterility, low seed set and poor grain quality. Identification of QTLs and causal genes for heat stress tolerance at flowering will facilitate breeding for improved heat tolerance in rice. In the present study, we used 272 F 8 recombinant inbred lines derived from a cross between Nagina22, a well-known heat tolerant Aus cultivar and IR64, a heat sensitive popular Indica rice variety to map the QTLs for heat tolerance. To enable precise phenotyping for heat stress tolerance, we used a controlled phenotyping facility available at ICAR-Indian Institute of Wheat and Barley Research, Karnal, India. Based on 'days to 50% flowering' data of the RILs, we followed staggered sowing to synchronize flowering to impose heat stress at uniform stage. Using the Illumina infinium 5K SNP array for genotyping the parents and the RILs, and stress susceptibility and stress tolerance indices (SSI and STI) of percent spikelet sterility and yield per plant (g), we identified five QTLs on chromosomes 3, 5, 9 and 12. The identified QTLs explained phenotypic variation in the range of 6.27 to 21. 29%. Of these five QTLs, two high effect QTLs, one novel (qSTIPSS9.1) and one known (qSTIY5.1/qSSIY5.2), were mapped in less than 400 Kbp genomic regions, comprising of 65 and 54 genes, respectively. The present study identified two major QTLs for heat tolerance in rice in narrow physical intervals, which can be employed for crop improvement by marker assisted selection (MAS) after development of suitable scorable markers for breeding of high yielding heat tolerant rice varieties. This is the first report of a major QTL for heat tolerance on chromosome 9 of rice. Further, a known QTL for heat tolerance on chromosome 5 was narrowed down from 23 Mb to 331 Kbp in this study.

Marker-assisted identification of restorer gene(s) in iso-cytoplasmic restorer lines of WA cytoplasm in rice and assessment of their fertility restoration potential across environments.

PubMed

Kumar, Amit; Bhowmick, Prolay Kumar; Singh, Vikram Jeet; Malik, Manoj; Gupta, Ashish Kumar; Seth, R; Nagarajan, M; Krishnan, S Gopala; Singh, Ashok Kumar

2017-10-01

Iso-cytoplasmic restorers possess the same male sterile cytoplasm as the cytoplasmic male sterile (CMS) lines, thereby minimizing the potential cyto-nuclear conflict in the hybrids. Restoration of fertility of the wild abortive CMS is governed by two major genes namely, Rf3 and Rf4 . Therefore, assessing the allelic status of these restorer genes in the iso-cytoplasmic restorers using molecular markers will not only help in estimating the efficiency of these genes either alone or in combination, in fertility restoration in the hybrids in different environments, but will also be useful in determining the efficacy of these markers. In the present study, the efficiency of molecular markers in identifying genotypes carrying restorer allele of the gene(s) Rf3 and Rf4, restoring male fertility of WA cytoplasm in rice was assessed in a set of 100 iso-cytoplasmic rice restorers using gene linked as well as candidate gene based markers. In order to validate the efficacy of markers in identifying the restorers, a sub-set of selected 25 iso-cytoplasmic rice restorers were crossed with four different cytoplasmic male sterile lines namely, IR 79156A, IR 58025A, Pusa 6A and RTN 12A, and the pollen and spikelet fertility of the F 1 s were evaluated at three different locations. Marker analysis showed that Rf4 was the predominant fertility restorer gene in the iso-cytoplasmic restorers and Rf3 had a synergistic effect on fertility restoration. The efficiency of gene based markers, DRCG-RF4-14 and DRRM-RF3-10 for Rf4 (87%) and Rf3 (84%) genes was higher than respective gene-linked SSR markers RM6100 (80%) and RM3873 (82%). It is concluded that the gene based markers can be effectively used in identifying fertility restorer lines obviating the need for making crosses and evaluating the F 1 s. Though gene based markers are more efficient, there is a need to identify functional polymorphisms which can provide 100% efficiency. Three iso-cytoplasmic restorers namely, PRR 300, PRR 363 and PRR 396 possessing both Rf4 and Rf3 genes and good fertility restoration have been identified which could be used further in hybrid rice breeding.

Head rice rate measurement based on concave point matching

PubMed Central

Yao, Yuan; Wu, Wei; Yang, Tianle; Liu, Tao; Chen, Wen; Chen, Chen; Li, Rui; Zhou, Tong; Sun, Chengming; Zhou, Yue; Li, Xinlu

2017-01-01

Head rice rate is an important factor affecting rice quality. In this study, an inflection point detection-based technology was applied to measure the head rice rate by combining a vibrator and a conveyor belt for bulk grain image acquisition. The edge center mode proportion method (ECMP) was applied for concave points matching in which concave matching and separation was performed with collaborative constraint conditions followed by rice length calculation with a minimum enclosing rectangle (MER) to identify the head rice. Finally, the head rice rate was calculated using the sum area of head rice to the overall coverage of rice. Results showed that bulk grain image acquisition can be realized with test equipment, and the accuracy rate of separation of both indica rice and japonica rice exceeded 95%. An increase in the number of rice did not significantly affect ECMP and MER. High accuracy can be ensured with MER to calculate head rice rate by narrowing down its relative error between real values less than 3%. The test results show that the method is reliable as a reference for head rice rate calculation studies. PMID:28128315

A hydrolysed rice-based formula is tolerated by children with cow's milk allergy: a multi-centre study.

PubMed

Fiocchi, A; Restani, P; Bernardini, R; Lucarelli, S; Lombardi, G; Magazzù, G; Marseglia, G L; Pittschieler, K; Tripodi, S; Troncone, R; Ranzini, C

2006-03-01

Children allergic to cow's milk are fed a soy- or a hydrolysed cow's milk-based substitute. Neither can rule out a sensitization risk. Previous studies have shown that hydrolysed rice is tolerated by animals and children with multiple food hypersensitivities. A prospective clinical assessment of tolerance to a rice-based hydrolysed formula was carried out in children allergic to cow's milk. Patients and methods One hundred children (42 girls and 58 boys, mean age 3.17+/-2.93 years, median 2.20, range 0.18-14.6 years) with a history of immediate reactions to cow's milk and confirmed at double-blind, placebo-controlled food challenge (DBPCFC) when not contraindicated were assessed for clinical tolerance to cow's milk proteins. Their allergy work-up included skin prick tests with whole milk, alpha-lactalbumin (ALA), beta-lactoglobulin (BLG) and total caseins, and specific IgE determinations using CAP technology were performed against whole milk, ALA, BLG and casein. Sensitization to rice and rice-based hydrolysed formula was similarly investigated. Patients' sera were evaluated at immunoblotting for specific IgE to cow's milk proteins, rice and rice-based hydrolysed formula. DBPCFC was carried out with increasing doses of a rice-based hydrolysed formula. All patients were sensitized to cow's milk and/or at least one cow's milk protein fraction. Eighty-seven out of 99 were positive to cow's milk and/or a cow's milk protein fraction at skin prick test. Positive (>0.35 kUA/L) specific IgE determinations were found for cow's milk and/or milk fractions (92/95), rice (21/91) and hydrolysed rice infant formula (4/91). At immunoblotting, sera from 96 children were positive to alpha-casein (n=54), beta-casein (n=38), ALA (n=57), BLG (n=37) and bovine serum albumin (n=61). Similarly, although patients' sera often contained specific IgE against rice proteins at CAP (21/91) and immunoblotting (70/96), only six very weakly positive responses were observed against rice-based hydrolysed formula. All DBPCFC with rice-based hydrolysed formula were negative. Rice-based hydrolysed formula is a possible alternative not only for children with multiple allergies, but also for children with cow's milk allergy.

Cloning of novel rice blast resistance genes from two rapidly evolving NBS-LRR gene families in rice.

PubMed

Guo, Changjiang; Sun, Xiaoguang; Chen, Xiao; Yang, Sihai; Li, Jing; Wang, Long; Zhang, Xiaohui

2016-01-01

Most rice blast resistance genes (R-genes) encode proteins with nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains. Our previous study has shown that more rice blast R-genes can be cloned in rapidly evolving NBS-LRR gene families. In the present study, two rapidly evolving R-gene families in rice were selected for cloning a subset of genes from their paralogs in three resistant rice lines. A total of eight functional blast R-genes were identified among nine NBS-LRR genes, and some of these showed resistance to three or more blast strains. Evolutionary analysis indicated that high nucleotide diversity of coding regions served as important parameters in the determination of gene resistance. We also observed that amino-acid variants (nonsynonymous mutations, insertions, or deletions) in essential motifs of the NBS domain contribute to the blast resistance capacity of NBS-LRR genes. These results suggested that the NBS regions might also play an important role in resistance specificity determination. On the other hand, different splicing patterns of introns were commonly observed in R-genes. The results of the present study contribute to improving the effectiveness of R-gene identification by using evolutionary analysis method and acquisition of novel blast resistance genes.

Identification and quantification of phenolic and flavonoid components in straw and seed husk of some rice varieties (Oryza sativa L.) and their antioxidant properties.

PubMed

Karimi, Ehsan; Mehrabanjoubani, Pooyan; Keshavarzian, Maryam; Oskoueian, Ehsan; Jaafar, Hawa Z E; Abdolzadeh, Ahmad

2014-08-01

Plant foods are rich sources of bioactive compounds that can act as antioxidants to prevent heart disease, reduce inflammation, reduce the incidence of cancers and diabetes. This study aimed to determine the phenolics and flavonoids profiling in three varieties of rice straw and five varieties of the seed husk of Iranian rice using high-performance liquid chromatography (HPLC). Furthermore, the antioxidant activities of the extracts were evaluated by using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical and nitric oxide assays. HPLC analyses showed that the gallic acid, pyrogallol, apigenin and rutin were the main phenolic and flavonoid compounds in all varieties of rice. In addition, the methanolic extracts of Hashemi and Ali Kazemi varieties showed the highest amounts of phenolic and flavonoid contents, respectively. Rice straw and husk of Iranian varieties showed considerable antioxidant activity and Hashemi indicated significantly (P < 0.01) higher DPPH and nitric oxide free radical scavenging activities when compared to the other varieties. The present study revealed that rice straw and seed husk of Iranian varieties shows high antioxidant activities and they contain various types of phenolic and flavonoid compounds that could be use in food and medical industries. © 2014 Society of Chemical Industry.

Novel transgenic rice-based vaccines.

PubMed

Azegami, Tatsuhiko; Itoh, Hiroshi; Kiyono, Hiroshi; Yuki, Yoshikazu

2015-04-01

Oral vaccination can induce both systemic and mucosal antigen-specific immune responses. To control rampant mucosal infectious diseases, the development of new effective oral vaccines is needed. Plant-based vaccines are new candidates for oral vaccines, and have some advantages over the traditional vaccines in cost, safety, and scalability. Rice seeds are attractive for vaccine production because of their stability and resistance to digestion in the stomach. The efficacy of some rice-based vaccines for infectious, autoimmune, and other diseases has been already demonstrated in animal models. We reported the efficacy in mice, safety, and stability of a rice-based cholera toxin B subunit vaccine called MucoRice-CTB. To advance MucoRice-CTB for use in humans, we also examined its efficacy and safety in primates. The potential of transgenic rice production as a new mucosal vaccine delivery system is reviewed from the perspective of future development of effective oral vaccines.

Mapping paddy rice distribution using multi-temporal Landsat imagery in the Sanjiang Plain, northeast China

PubMed Central

XIAO, Xiangming; DONG, Jinwei; QIN, Yuanwei; WANG, Zongming

2016-01-01

Information of paddy rice distribution is essential for food production and methane emission calculation. Phenology-based algorithms have been utilized in the mapping of paddy rice fields by identifying the unique flooding and seedling transplanting phases using multi-temporal moderate resolution (500 m to 1 km) images. In this study, we developed simple algorithms to identify paddy rice at a fine resolution at the regional scale using multi-temporal Landsat imagery. Sixteen Landsat images from 2010–2012 were used to generate the 30 m paddy rice map in the Sanjiang Plain, northeast China—one of the major paddy rice cultivation regions in China. Three vegetation indices, Normalized Difference Vegetation Index (NDVI), Enhanced Vegetation Index (EVI), and Land Surface Water Index (LSWI), were used to identify rice fields during the flooding/transplanting and ripening phases. The user and producer accuracies of paddy rice on the resultant Landsat-based paddy rice map were 90% and 94%, respectively. The Landsat-based paddy rice map was an improvement over the paddy rice layer on the National Land Cover Dataset, which was generated through visual interpretation and digitalization on the fine-resolution images. The agricultural census data substantially underreported paddy rice area, raising serious concern about its use for studies on food security. PMID:27695637

Genome-Wide Identification and Analysis of Biotic and Abiotic Stress Regulation of C4 Photosynthetic Pathway Genes in Rice.

PubMed

Muthusamy, Senthilkumar K; Lenka, Sangram K; Katiyar, Amit; Chinnusamy, Viswanathan; Singh, Ashok K; Bansal, Kailash C

2018-06-19

Photosynthetic fixation of CO 2 is more efficient in C 4 than in C 3 plants. Rice is a C 3 plant and a potential target for genetic engineering of the C 4 pathway. It is known that genes encoding C 4 enzymes are present in C 3 plants. However, no systematic analysis has been conducted to determine if these C 4 gene family members are expressed in diverse rice genotypes. In this study, we identified 15 genes belonging to the five C 4 gene families in rice genome through BLAST search using known maize C 4 photosynthetic pathway genes. Phylogenetic relationship of rice C 4 photosynthetic pathway genes and their isoforms with other grass genomes (Brachypodium, maize, Sorghum and Setaria), showed that these genes were highly conserved across grass genomes. Spatiotemporal, hormone, and abiotic stress specific expression pattern of the identified genes revealed constitutive as well as inductive responses of the C 4 photosynthetic pathway in different tissues and developmental stages of rice. Expression levels of C 4 specific gene family members in flag leaf during tillering stage were quantitatively analyzed in five rice genotypes covering three species, viz. Oryza sativa, ssp. japonica (cv. Nipponbare), Oryza sativa, ssp. indica (cv IR64, Swarna), and two wild species Oryza barthii and Oryza australiensis. The results showed that all the identified genes expressed in rice and exhibited differential expression pattern during different growth stages, and in response to biotic and abiotic stress conditions and hormone treatments. Our study concludes that C 4 photosynthetic pathway genes present in rice play a crucial role in stress regulation and might act as targets for C 4 pathway engineering via CRISPR-mediated breeding.

Distribution and identification of proteolytic Bacillus spp. in paddy field soil under rice cultivation.

PubMed

Watanabe, K; Hayano, K

1993-07-01

Proteolytic bacteria in paddy field soils under rice cultivation were characterized and enumerated using azocoll agar plates. Bacillus spp. were the proteolytic bacteria that were most frequently present, comprising 59% of the isolates. They were always the numerically dominant proteolytic bacteria isolated from three kinds of fertilizer treatments (yearly application of rice-straw compost and chemical fertilizer, yearly application of chemical fertilizer, and no fertilizer application) and at three different stages of rice development (vegetative growth stage, maximal tillering stage, and harvest stage). Of the 411 proteolytic bacteria isolated, 124 isolates had stronger proteolytic activity than others on the basis of gelatin liquefaction tests and most of them were Bacillus spp. (100% in 1989 and 92.4% in 1991). Bacillus subtilis and Bacillus cereus were the main bacteria of this group and Bacillus mycoides, Bacillus licheniformis, and Bacillus megaterium were also present. We conclude that these Bacillus spp. are the primary source of soil protease in these paddy fields.

Identification of the gravitropism-related rice gene LAZY1 and elucidation of LAZY1-dependent and -independent gravity signaling pathways.

PubMed

Yoshihara, Takeshi; Iino, Moritoshi

2007-05-01

We identified the gene responsible for three allelic lazy1 mutations of Japonica rice (Oryza sativa L.) by map-based cloning, complementation and RNA interference. Sequence analysis and database searches indicated that the wild-type gene (LAZY1) encodes a novel and unique protein (LAZY1) and that rice has no homologous gene. Two lazy1 mutants were LAZY1 null. Confirming and advancing the previously reported results on lazy1 mutants, we found the following. (i) Gravitropism is impaired, but only partially, in lazy1 coleoptiles. (ii) Circumnutation, observed in dark-grown coleoptiles, is totally absent from lazy1 coleoptiles. (iii) Primary roots of lazy1 mutants show normal gravitropism and circumnutation. (iv) LAZY1 is expressed in a tissue-specific manner in gravity-sensitive shoot tissues (i.e. coleoptiles, leaf sheath pulvini and lamina joints) and is little expressed in roots. (v) The gravitropic response of lazy1 coleoptiles is kinetically separable from that absent from lazy1 coleoptiles. (vi) Gravity-induced lateral translocation of auxin, found in wild-type coleoptiles, does not occur in lazy1 coleoptiles. Based on the genetic and physiological evidence obtained, it is concluded that LAZY1 is specifically involved in shoot gravitropism and that LAZY1-dependent and -independent signaling pathways occur in coleoptiles. It is further concluded that, in coleoptiles, only the LAZY1-dependent gravity signaling involves asymmetric distribution of auxin between the two lateral halves and is required for circumnutation.

Climate change and farmers’ cropping patterns in Cemoro watershed area, Central Java, Indonesia

NASA Astrophysics Data System (ADS)

Sugihardjo; Sutrisno, J.; Setyono, P.; Suntoro

2018-03-01

Cropping pattern applied by farmers is usually based on the availability of water. Farmers cultivate rice when water is available. If it is unavailable, farmers will choose to plant crops that need less water. Climate change greatly affects to farmers in determining the cropping pattern as it alters the rainfall pattern and distribution in the region. This condition requires farmers to adjust the cropping pattern so that they can do the farming successfully. This study aims to examine the application of cropping patterns applied by the farmers in the Cemoro Watershed, Central Java, Indonesia. Descriptive analysis approach is employed in this research. The results showed that farmers’ cropping pattern is not based on the availability of water. However, it adopts a habit that has been practiced since long time ago or just adopt others farmer's habit. The cropping pattern applied by irrigated paddy farmers in Cemoro watershed area consists of two types: rice-rice-rice and rice-rice-secondary crops. Among those two types, most farmers apply the rice-rice-rice pattern. Meanwhile, there are three cropping patterns applied in the rain-land, namely rice-rice-rice, rice-rice-secondary crop, and rice-rice-fallow. The majority of farmers apply the second pattern (rice-rice-secondary crops). It was also found that farmers’ cropping pattern was not in accordance with the recommendation of the local government.

Identification of climate-resilient integrated nutrient management practices for rice-rice cropping system--an empirical approach to uphold food security.

PubMed

Subash, N; Gangwar, B; Singh, Rajbir; Sikka, A K

2015-01-01

Yield datasets of long-term experiments on integrated nutrient management in rice-rice cropping systems were used to investigate the relationship of variability in rainfall, temperature, and integrated nutrient management (INM) practices in rice-rice cropping system in three different agroecological regions of India. Twelve treatments with different combinations of inorganic (chemical fertilizer) and organic (farmyard manure, green manure, and paddy straw) were compared with farmer's conventional practice. The intraseasonal variations in rice yields are largely driven by rainfall during kharif rice and by temperature during rabi rice. Half of the standard deviation from the average monthly as well as seasonal rainfall during kharif rice and 1 °C increase or decrease from the average maximum and minimum temperature during rabi rice has been taken as the classification of yield groups. The trends in the date of effective onset of monsoon indicate a 36-day delay during the 30-year period at Rajendranagar, which is statistically significant at 95 % confidence level. The mean annual maximum temperature shows an increasing trend in all the study sites. The length of monsoon also showed a shrinking trend in the rate of 40 days during the 30-year study period at Rajendranagar representing a semiarid region. At Bhubaneshwar, the application of 50 % recommended NPK through chemical fertilizers and 50 % N through green manure resulted in an overall average higher increase of 5.1 % in system productivity under both excess and deficit rainfall years and also during the years having seasonal mean maximum temperature ≥35 °C. However, at Jorhat, the application of 50 % recommended NPK through chemical fertilizers and 50 % N through straw resulted in an overall average higher increase of 7.4 % in system productivity, while at Rajendranagar, the application of 75 % NPK through chemical fertilizers and 25 % N through green manusre resulted in an overall average higher increase of 8.8 % in system productivity. This study highlights the adaptive capacity of different integrated nutrient management practices to rainfall and temperature variability under a rice-rice cropping system in humid, subhumid, and semiarid ecosystems.

GS6, a member of the GRAS gene family, negatively regulates grain size in rice.

PubMed

Sun, Lianjun; Li, Xiaojiao; Fu, Yongcai; Zhu, Zuofeng; Tan, Lubin; Liu, Fengxia; Sun, Xianyou; Sun, Xuewen; Sun, Chuanqing

2013-10-01

Grain size is an important yield-related trait in rice. Intensive artificial selection for grain size during domestication is evidenced by the larger grains of most of today's cultivars compared with their wild relatives. However, the molecular genetic control of rice grain size is still not well characterized. Here, we report the identification and cloning of Grain Size 6 (GS6), which plays an important role in reducing grain size in rice. A premature stop at the +348 position in the coding sequence (CDS) of GS6 increased grain width and weight significantly. Alignment of the CDS regions of GS6 in 90 rice materials revealed three GS6 alleles. Most japonica varieties (95%) harbor the Type I haplotype, and 62.9% of indica varieties harbor the Type II haplotype. Association analysis revealed that the Type I haplotype tends to increase the width and weight of grains more than either of the Type II or Type III haplotypes. Further investigation of genetic diversity and the evolutionary mechanisms of GS6 showed that the GS6 gene was strongly selected in japonica cultivars. In addition, a "ggc" repeat region identified in the region that encodes the GRAS domain of GS6 played an important historic role in the domestication of grain size in rice. Knowledge of the function of GS6 might aid efforts to elucidate the molecular mechanisms that control grain development and evolution in rice plants, and could facilitate the genetic improvement of rice yield. © 2013 Institute of Botany, Chinese Academy of Sciences.

Metaproteomic identification of diazotrophic methanotrophs and their localization in root tissues of field-grown rice plants.

PubMed

Bao, Zhihua; Okubo, Takashi; Kubota, Kengo; Kasahara, Yasuhiro; Tsurumaru, Hirohito; Anda, Mizue; Ikeda, Seishi; Minamisawa, Kiwamu

2014-08-01

In a previous study by our group, CH4 oxidation and N2 fixation were simultaneously activated in the roots of wild-type rice plants in a paddy field with no N input; both processes are likely controlled by a rice gene for microbial symbiosis. The present study examined which microorganisms in rice roots were responsible for CH4 oxidation and N2 fixation under the field conditions. Metaproteomic analysis of root-associated bacteria from field-grown rice (Oryza sativa Nipponbare) revealed that nitrogenase complex-containing nitrogenase reductase (NifH) and the alpha subunit (NifD) and beta subunit (NifK) of dinitrogenase were mainly derived from type II methanotrophic bacteria of the family Methylocystaceae, including Methylosinus spp. Minor nitrogenase proteins such as Methylocella, Bradyrhizobium, Rhodopseudomonas, and Anaeromyxobacter were also detected. Methane monooxygenase proteins (PmoCBA and MmoXYZCBG) were detected in the same bacterial group of the Methylocystaceae. Because these results indicated that Methylocystaceae members mediate both CH4 oxidation and N2 fixation, we examined their localization in rice tissues by using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). The methanotrophs were localized around the epidermal cells and vascular cylinder in the root tissues of the field-grown rice plants. Our metaproteomics and CARD-FISH results suggest that CH4 oxidation and N2 fixation are performed mainly by type II methanotrophs of the Methylocystaceae, including Methylosinus spp., inhabiting the vascular bundles and epidermal cells of rice roots. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Isolation, identification and antioxidant activity of bound phenolic compounds present in rice bran.

PubMed

Wang, Wei; Guo, Jia; Zhang, Junnan; Peng, Jie; Liu, Tianxing; Xin, Zhihong

2015-03-15

The bound phenolic compounds in rice bran were released and extracted with ethyl acetate based on alkaline digestion. An investigation of the chemical constituents of EtOAc extract has led to the isolation of a new compound, para-hydroxy methyl benzoate glucoside (8), together with nine known compounds, cycloeucalenol cis-ferulate (1), cycloeucalenol trans-ferulate (2), trans-ferulic acid (3), trans-ferulic acid methyl ester (4), cis-ferulic acid (5), cis-ferulic acid methyl ester (6), methyl caffeate (7), vanillic aldehyde (9) and para-hydroxy benzaldehyde (10). The structures of these compounds were determined using a combination of spectroscopic methods and chemical analysis. Among the compounds isolated, compound 3, 5 and 7 exhibited strong DPPH and ABTS(+) radical scavenging activities, followed by compounds 4 and 6. Compound 1 and 2 showed potent DPPH and ABTS(+) radical scavenging activities, compound 8 displayed moderate antioxidant activity against ABTS(+) radical, whereas compound 9 and 10 showed weak antioxidant activity. Copyright © 2014 Elsevier Ltd. All rights reserved.

One-step isolation of γ-oryzanol from rice bran oil by non-aqueous hydrostatic countercurrent chromatography.

PubMed

Angelis, Apostolis; Urbain, Aurélie; Halabalaki, Maria; Aligiannis, Nektarios; Skaltsounis, Alexios-Leandros

2011-09-01

The value-added γ-oryzanol was purified in one step from crude rice bran oil (RBO) using a preparative hydrostatic countercurrent chromatography (hydrostatic CCC) method, operating in the dual mode. The fractionation was performed using a non-aqueous biphasic solvent system consisting of heptane-acetonitrile-butanol (1.8:1.4:0.7, v/v/v), leading rapidly to the target compounds. Transfer of the analytical CCC method to large-scale isolation was also carried out yielding a high quantity-high purity fraction of γ-oryzanol. In addition, a fraction of hydroxylated triterpene alcohol ferulates (polar γ-oryzanol) was clearly separated and obtained. Furthermore, a fast HPLC-APCI(±)-HRMS method was developed and applied for the identification of γ-oryzanol as well as the polar γ-oryzanol in RBO and the resulting fractions. The purity of γ-oryzanol fraction was estimated as 97% based on HPLC-APCI-HRMS analysis. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Adapting rice production to climate change for sustainable blue water consumption: an economic and virtual water analysis

NASA Astrophysics Data System (ADS)

Darzi-Naftchali, Abdullah; Karandish, Fatemeh

2017-12-01

Sustainable utilization of blue water resources under climate change is of great significance especially for producing high water-consuming crops in water-scarce regions. Based on the virtual water concept, we carried out a comprehensive field-modeling research to find the optimal agricultural practices regarding rice blue water consumption under prospective climate change. The DSSAT-CERES-Rice model was used in combination with 20 GCMs under three Representative Concentration Pathways of low (RCP2.6), intermediate (RCP4.6), and very high (RCP8.5) greenhouse concentrations to predict rice yield and water requirement and related virtual water and economic return for the base and future periods. The crop model was calibrated and validated based on the 2-year field data obtained from consolidated paddy fields of the Sari Agricultural Sciences and Natural Resources University during 2011 and 2012 rice cropping cycles. Climate change imposes an increase of 0.02-0.04 °C in air temperature which consequently shifts rice growing seasons to winter season, and shorten the length of rice physiological maturity period by 2-15 days. While rice virtual water reduces by 0.1-20.6% during 2011-2070, reduced rice yield by 3.8-22.6% over the late twenty-first century results in a considerable increase in rice virtual water. By increasing the contribution of green water in supplying crop water requirement, earlier cropping could diminish blue water consumption for rice production in the region while cultivation postponement increases irrigation water requirement by 2-195 m3 ha-1. Forty days delay in rice cultivation in future will result in 29.9-40.6% yield reduction and 43.9-60% increase in rice virtual water under different scenarios. Earlier cropping during the 2011-2040 and 2041-2070 periods would increase water productivity, unit value of water, and economic value of blue water compared to the base period. Based on the results, management of rice cultivation calendar is a suitable strategy for sustainable blue water consumption for producing rice under future climate.

The Multivesicular Bodies (MVBs)-Localized AAA ATPase LRD6-6 Inhibits Immunity and Cell Death Likely through Regulating MVBs-Mediated Vesicular Trafficking in Rice

PubMed Central

Liang, Sihui; Liang, Ruihong; Zhou, Xiaogang; Chen, Zhixiong; Zhao, Wen; Wang, Jing; Li, Weitao; He, Min; Yuan, Can; Miyamoto, Koji; Ma, Bingtian; Wang, Jichun; Qin, Peng; Chen, Weilan; Wang, Yuping; Wang, Wenming; Wu, Xianjun; Yamane, Hisakazu; Zhu, Lihuang; Li, Shigui; Chen, Xuewei

2016-01-01

Previous studies have shown that multivesicular bodies (MVBs)/endosomes-mediated vesicular trafficking may play key roles in plant immunity and cell death. However, the molecular regulation is poorly understood in rice. Here we report the identification and characterization of a MVBs-localized AAA ATPase LRD6-6 in rice. Disruption of LRD6-6 leads to enhanced immunity and cell death in rice. The ATPase activity and homo-dimerization of LRD6-6 is essential for its regulation on plant immunity and cell death. An ATPase inactive mutation (LRD6-6E315Q) leads to dominant-negative inhibition in plants. The LRD6-6 protein co-localizes with the MVBs marker protein RabF1/ARA6 and interacts with ESCRT-III components OsSNF7 and OsVPS2. Further analysis reveals that LRD6-6 is required for MVBs-mediated vesicular trafficking and inhibits the biosynthesis of antimicrobial compounds. Collectively, our study shows that the AAA ATPase LRD6-6 inhibits plant immunity and cell death most likely through modulating MVBs-mediated vesicular trafficking in rice. PMID:27618555

Rice Production Vulnerability to Climate Change in Indonesia: An Overview on Community-based Adaptation

NASA Astrophysics Data System (ADS)

Komaladara, A. A. S. P.; Budiasa, I. W.; Ambarawati, I. G. A. A.

2015-12-01

Rice remains to be a major crop and staple food in Indonesia. The task to ensure that rice production meets the demand of a growing population continues to engage the attention of national planners and policy makers. However, the adverse effects of climate change on agriculture production have presented Indonesia with yet another significant challenge. The exposure of rice crops to climate-related hazards such as temperature stress, floods, and drought, may lead to lower yield and self-sufficiency rate. This study explores the vulnerability of rice production to the effects of climate change in Indonesia. Considering the vast geographical span of the country and varying exposure, sensitivity, and adaptive capacity to climate change at regional level, this study emphasize the importance of community-based adaptation. Results from a simulation based on production and climate data from 1984 to 2014 indicates that rice production is sensitive to variation in growing season temperature and precipitation. A projection of these climate factors in 2050 has a significant impact on the major rice crop. To manage the impact of climate change, this study turns to the potential roles of farmer organizations, such as Subak, in adaptation strategies. The Subak in Bali is recognized for its cultural and organizational framework that highlights the sharing of knowledge and local wisdom in rice production. This is demonstrated by its efficient community-based irrigation management system, leading to sustainable rice production. Keywords: rice production, climate change, community-based adaptation, Indonesia

Econometric Model of Rice Policy Based On Presidential Instruction

NASA Astrophysics Data System (ADS)

Abadi Sembiring, Surya; Hutauruk, Julia

2018-01-01

The objective of research is to build an econometric model based on Presidential Instruction rice policy. The data was monthly time series from March 2005 to September 2009. Rice policy model specification using simultaneous equation, consisting of 14 structural equations and four identity equation, which was estimated using Two Stages Least Squares (2SLS) method. The results show that: (1) an increase of government purchasing price of dried harvest paddy has a positive impact on to increase in total rice production and community rice stock, (2) an increase community rice stock lead to decrease the rice imports, (3) an increase of the realization of the distribution of subsidized ZA fertilizers and the realization of the distribution of subsidized NPK fertilizers has a positive impact on to increase in total rice production and community rice stock and to reduce rice imports, (4) the price of the dried harvest paddy is highly responsive to the water content of dried harvest paddy both the short run and long run, (5) the quantity of rice imported is highly responsive to the imported rice price, both short run and long run.

A model of the relationship between weedy rice seed-bank dynamics and rice-crop infestation and damage in Jiangsu Province, China.

PubMed

Zhang, Zheng; Dai, Weimin; Song, Xiaoling; Qiang, Sheng

2014-05-01

A heavy infestation of weedy rice leading to no harvested rice has never been predicted in China due to a lack of knowledge about the weedy rice seed bank. We studied the seed-bank dynamics of weedy rice for three consecutive years and analyzed the relationship between seed-bank density and population density in order to predict future weedy rice infestations of direct-seeded rice at six sites along the Yangtze River in Jiangsu Province, China. The seed-bank density of weedy rice in all six sites displayed an increasing trend with seasonal fluctuations. Weedy rice seeds found in the 0-10 cm soil layer contributed most to seedling emergence. An exponential curve expressed the relationship between cultivated rice yield loss and adult weedy rice density. Based on data collected during the weedy rice life-cycle, a semi-empirical mathematic model was developed that fits well with the experimental data in a way that could be used to predict seed-bank dynamics. By integrating the semi-empirical model and the exponential curve, weedy rice infestation levels and crop losses can be predicted based on the seed-bank dynamics so that a practical control can be adopted before rice planting. © 2013 Society of Chemical Industry.

Identification of QTN and candidate genes for Salinity Tolerance at the Germination and Seedling Stages in Rice by Genome-Wide Association Analyses.

PubMed

Naveed, Shahzad Amir; Zhang, Fan; Zhang, Jian; Zheng, Tian-Qing; Meng, Li-Jun; Pang, Yun-Long; Xu, Jian-Long; Li, Zhi-Kang

2018-04-25

To facilitate developing rice varieties tolerant to salt stress, a panel of 208 rice mini-core accessions collected from 25 countries were evaluated for 13 traits associated with salt tolerance (ST) at the germination and seedling stages. The rice panel showed tremendous variation for all measured ST traits and eight accessions showing high levels of ST at either and/or both the germination and seedling stages. Using 395,553 SNP markers covering ~372 Mb of the rice genome and multi-locus mixed linear models, 20 QTN associated with 11 ST traits were identified by GWAS, including 6 QTN affecting ST at the germination stage and 14 QTN for ST at the seedling stage. The integration of bioinformatic with haplotype analyses for the ST QTN lets us identify 22 candidate genes for nine important ST QTN (qGR3, qSNK1, qSNK12, qSNC1, qSNC6, qRNK2, qSDW9a, qSST5 and qSST9). These candidate genes included three known ST genes (SKC1, OsTZF1 and OsEATB) for QTN qSNK1 qSST5 and qSST9. Candidate genes showed significant phenotypic differences in ST traits were detected between or among 2-4 major haplotypes. Thus, our results provided useful materials and genetic information for improving rice ST in future breeding and for molecular dissection of ST in rice.

Cross-genera transferability of rice and finger millet genomic SSRs to barnyard millet (Echinochloa spp.).

PubMed

Kalyana Babu, B; Sood, Salej; Kumar, Dinesh; Joshi, Anjeli; Pattanayak, A; Kant, Lakshmi; Upadhyaya, H D

2018-02-01

Barnyard millet ( Echinochloa spp.) is an important crop from nutritional point of view, nevertheless, the genetic information is very scarce. In the present investigation, rice and finger millet genomic SSRs were used for assessing cross transferability, identification of polymorphic markers, syntenic regions, genetic diversity and population structure analysis of barnyard millet genotypes. We observed 100% cross transferability for finger millet SSRs, of which 91% were polymorphic, while 71% of rice markers were cross transferable with 48% polymorphic out of them. Twenty-nine and sixteen highly polymorphic finger millet and rice SSRs yielded a mean of 4.3 and 3.38 alleles per locus in barnyard millet genotypes, respectively. The PIC values varied from 0.27 to 0.73 at an average of 0.54 for finger millet SSRs, whereas it was from 0.15 to 0.67 at an average of 0.44 for rice SSRs. High synteny was observed for markers related to panicle length, yield-related traits, spikelet fertility, plant height, root traits, leaf senescence, blast and brown plant hopper resistance. Although the rice SSRs located on chromosome 10 followed by chromosome 6 and 11 were found to be more transferable to barnyard millet, the finger millet SSRs were more polymorphic and transferable to barnyard millet genotypes. These SSR data of finger millet and rice individually as well as combined together grouped the 11 barnyard millet genotypes into 2 major clusters. The results of population structure analysis were similar to cluster analysis.

Oral rehydration therapy: a community trial comparing the acceptability of homemade sucrose and cereal-based solutions.

PubMed

Chowdhury, A M; Karim, F; Rohde, J E; Ahmed, J; Abed, F H

1991-01-01

Sugar-based oral rehydration therapy (ORT) for diarrhoea is promoted in many countries of the world. One programme in Bangladesh has instructed more than 13 million mothers in the preparation of a sugar-salt solution in the home; despite very high rates of correct mixing and knowledge, subsequent application was found in only some 20% of all diarrhoea episodes. Since rice is far more available in rural homes (95%) than any type of sugar (30%) and rice gruel is a widely accepted food during illness, a field trial was conducted in three areas (total population, 68,345) to compare the acceptability and use of rice-based ORT with that of sugar-based ORT. Although the mothers unanimously agreed that the rice-based solutions "stopped" the diarrhoea more quickly, they used the sugar-based solutions twice as often (in 40% of severe watery episodes) as the rice-based solutions (in 18%), because the rice-ORT was much more time-consuming and difficult to prepare. The observed reduced utilization of home-made rice-ORT makes it a poor substitute for sugar-ORT at the community level in rural Bangladesh.

Genome-wide identification, phylogeny and expression analyses of SCARECROW-LIKE(SCL) genes in millet (Setaria italica).

PubMed

Liu, Hongyun; Qin, Jiajia; Fan, Hui; Cheng, Jinjin; Li, Lin; Liu, Zheng

2017-07-01

As a member of the GRAS gene family, SCARECROW - LIKE ( SCL ) genes encode transcriptional regulators that are involved in plant information transmission and signal transduction. In this study, 44 SCL genes including two SCARECROW genes in millet were identified to be distributed on eight chromosomes, except chromosome 6. All the millet genes contain motifs 6-8, indicating that these motifs are conserved during the evolution. SCL genes of millet were divided into eight groups based on the phylogenetic relationship and classification of Arabidopsis SCL genes. Several putative millet orthologous genes in Arabidopsis , maize and rice were identified. High throughput RNA sequencing revealed that the expressions of millet SCL genes in root, stem, leaf, spica, and along leaf gradient varied greatly. Analyses combining the gene expression patterns, gene structures, motif compositions, promoter cis -elements identification, alternative splicing of transcripts and phylogenetic relationship of SCL genes indicate that the these genes may play diverse functions. Functionally characterized SCL genes in maize, rice and Arabidopsis would provide us some clues for future characterization of their homologues in millet. To the best of our knowledge, this is the first study of millet SCL genes at the genome wide level. Our work provides a useful platform for functional analysis of SCL genes in millet, a model crop for C 4 photosynthesis and bioenergy studies.

Identification of Diatraea spp. (Lepidoptera: Crambidae) based on cytochrome oxidase II.

PubMed

Barrera, Gloria Patricia; Villamizar, Laura Fernanda; Espinel, Carlos; Quintero, Edgar Mauricio; Belaich, Mariano Nicolás; Toloza, Deisy Liseth; Ghiringhelli, Pablo Daniel; Vargas, Germán

2017-01-01

Diatraea spp. (Lepidoptera: Crambidae) are a group of insects that are agriculture pests in many economically relevant crops such as sugarcane, sorghum, corn and rice. Recognized species for this genus respond differentially to natural enemies used in their biological control, emphasizing the importance of species in a regional approach. Currently, identification is based on the male genitalia. However, the availability of specimens collected from field and subjectivity based on the character recognition can seriously hamper species identification, and therefore result in inadequate pest management. To overcome this, individuals of Diatraea spp. preliminarily classified male genitalia and obtained from reared conditions and the field (both derived from natural populations occurring in Colombia) were analyzed using genitalic morphometry and molecular biology specifically using a fragment of the cytochrome oxidase subunit II (CO II) mitochondrial gene. Although morphometric analysis did not show any overriding results regarding genitalia morphology, the bioinformatics analyses of CO II sequences resulted in an adequate classification of the individuals within the recognized species. It also, revealed that the occurrence of clades associated with geographical distribution may be associated with cryptic species. The latter was also confirmed by a Single-Strand Conformation Polymorphism (SSCP) methodology evaluating the same fragment of CO II. This experimental approach allows properly recognizing each species and in consequence is proposed as an effective tool in Diatraea species identification.

Identification of Diatraea spp. (Lepidoptera: Crambidae) based on cytochrome oxidase II

PubMed Central

Villamizar, Laura Fernanda; Espinel, Carlos; Quintero, Edgar Mauricio; Belaich, Mariano Nicolás; Toloza, Deisy Liseth

2017-01-01

Diatraea spp. (Lepidoptera: Crambidae) are a group of insects that are agriculture pests in many economically relevant crops such as sugarcane, sorghum, corn and rice. Recognized species for this genus respond differentially to natural enemies used in their biological control, emphasizing the importance of species in a regional approach. Currently, identification is based on the male genitalia. However, the availability of specimens collected from field and subjectivity based on the character recognition can seriously hamper species identification, and therefore result in inadequate pest management. To overcome this, individuals of Diatraea spp. preliminarily classified male genitalia and obtained from reared conditions and the field (both derived from natural populations occurring in Colombia) were analyzed using genitalic morphometry and molecular biology specifically using a fragment of the cytochrome oxidase subunit II (CO II) mitochondrial gene. Although morphometric analysis did not show any overriding results regarding genitalia morphology, the bioinformatics analyses of CO II sequences resulted in an adequate classification of the individuals within the recognized species. It also, revealed that the occurrence of clades associated with geographical distribution may be associated with cryptic species. The latter was also confirmed by a Single-Strand Conformation Polymorphism (SSCP) methodology evaluating the same fragment of CO II. This experimental approach allows properly recognizing each species and in consequence is proposed as an effective tool in Diatraea species identification. PMID:28873431

Identification and Phenotypic Characterization of ZEBRA LEAF16 Encoding a β-Hydroxyacyl-ACP Dehydratase in Rice

PubMed Central

Liu, Ziwen; Wang, Zhiyuan; Gu, Han; You, Jia; Hu, Manman; Zhang, Yujun; Zhu, Ze; Wang, Yihua; Liu, Shijia; Chen, Liangming; Liu, Xi; Tian, Yunlu; Zhou, Shirong; Jiang, Ling; Liu, Linglong; Wan, Jianmin

2018-01-01

The chloroplast is a self-independent organelle and contains its own transcription and translation systems. The establishment of genetic systems is vital for normal plant growth and development. We isolated a rice zebra leaf 16 (zl16) mutant derived from rice cultivar 9311. The zl16 mutant showed chlorotic abnormalities in the transverse sectors of the young leaves of seedlings. The use of transmission electron microscopy (TEM) demonstrated that dramatic defects occurred in variegated zl16 leaves during the early development of a chloroplast. Map-based cloning revealed that ZL16 encodes a β-hydroxyacyl-ACP dehydratase (HAD) involved in de novo fatty acid synthesis. Compared with the wild type, a missense mutation (Arg164Trp) in the zl16 mutant was identified, which significantly reduced enzymatic activity and altered the three-dimensional modeling structure of the putative protein. ZL16 was ubiquitously expressed in various plant organs, with a pronounced level in the young leaf. A subcellular localization experiment indicated that ZL16 was targeted in the chloroplast. Furthermore, we analyzed the expression of some nuclear genes involved in chloroplast development, and found they were altered in the zl16 mutant. RNA-Seq analysis indicated that some genes related to cell membrane constituents were downregulated in the mutant. An in vivo metabolic assay revealed that the total fatty acid content in the mutant was significantly decreased relative to the wild type. Our results indicate that HAD is essential for the development of chloroplasts by regulating the synthesis of fatty acids in rice. PMID:29946330

Functional food red yeast rice (RYR) for metabolic syndrome amelioration: a review on pros and cons.

PubMed

Patel, Seema

2016-05-01

Red yeast rice (RYR), the fermentation product of mold Monascus purpureus has been an integral part of Oriental food and traditional Chinese medicine, long before the discovery of their medicinal roles. With the identification of bioactive components as polyketide pigments (statins), and unsaturated fatty acids, RYR has gained a nutraceutical status. Hypercholesterolemic effect of this fermented compound has been validated and monacolin K has been recognized as the pivotal component in cholesterol alleviation. Functional similarity with commercial drug lovastatin sans the side effects has catapulted its popularity in other parts of the world as well. Apart from the hypotensive role, ameliorative benefits of RYR as anti-inflammatory, antidiabetic, anticancer and osteogenic agent have emerged, fueling intense research on it. Mechanistic studies have revealed their interaction with functional agents like coenzyme Q10, astaxanthin, vitamin D, folic acid, policosanol, and berberine. On the other hand, concurrence of mycotoxin citrinin and variable content of statin has marred its integration in mainstream medication. In this disputable scenario, evaluation of the scopes and lacunae to overcome seems to contribute to an eminent area of healthcare. Red yeast rice (RYR), the rice-based fermentation product of mold Monascus purpureus is a functional food. Its bioactive component monacolin K acts like synthetic drug lovastatin, without the severe side effects of the latter. RYR has been validated to lower cholesterol, control high blood pressure; confer anti-flammation, hypoglycaemic, anticancer and osteogenic properties. However, dose inconsistency and co-occurrence of toxin citrinin hampers its dietary supplementation prospect. Further research might facilitate development of RYR as a nutraceutical.

Effects of red mud based passivator on the transformation of Cd fraction in acidic Cd-polluted paddy soil and Cd absorption in rice.

PubMed

Li, Hui; Liu, Yan; Zhou, Yaoyu; Zhang, Jiachao; Mao, Qiming; Yang, Yuan; Huang, Hongli; Liu, Zhaohui; Peng, Qinghui; Luo, Lin

2018-06-04

Highly effective, economical, and replicable ways of Cd-polluted paddy field remediation (in situ) are urgently needed. In this work, a yearlong field experiment (both early and late rice) was conducted to investigate the effects of red mud based passivator [red mud, diatomite, and lime (5:3:2)] on remediation of an acidic Cd-polluted paddy field in Hunan Province. Compared with the control, the addition of red mud based passivator in the early and late rice reduced Cd concentration in each part of the rice plant (with the most significant decrease rate of 59.18% and 72.11% for brown rice in the early rice and late rice seasons respectively). The effect of Cd reduction in the rice plant was persistent in the next growing season. The addition of red mud based passivator also reduced the exchangeable fraction of Cd in the soil and converted the exchangeable fraction into other unavailable fractions. This study demonstrated that the pH in acidic soil increased after the application of red mud based passivator. Furthermore, red mud based passivator had no effect on the concentrations of Olsen-K, Alkaline-N, Olsen-P in the soil, but increased rice grain yield. Overall, the results of this study indicated that the red mud based passivator at 0.6 kg m -2 could be a recommendation for Cd-polluted acidic paddy soil stabilization, and it would be a suitable method for remediation of Cd-polluted acidic paddy soil. Copyright © 2018 Elsevier B.V. All rights reserved.

The intake of inorganic arsenic from long grain rice and rice-based baby food in Finland - low safety margin warrants follow up.

PubMed

Rintala, Eeva-Maria; Ekholm, Päivi; Koivisto, Pertti; Peltonen, Kimmo; Venäläinen, Eija-Riitta

2014-05-01

We evaluated total and inorganic arsenic levels in long grain rice and rice based baby foods on Finnish market. Inorganic arsenic was analysed with an HPLC-ICP-MS system. The total arsenic concentration was determined with an ICP-MS method. In this study, the inorganic arsenic levels in long grain rice varied from 0.09 to 0.28mg/kg (n=8) and the total arsenic levels from 0.11 to 0.65mg/kg. There was a good correlation between the total and inorganic arsenic levels in long grain rice at a confidence level of 95%. The total arsenic levels of rice-based baby foods were in the range 0.02 - 0.29mg/kg (n=10), however, the level of inorganic arsenic could only be quantitated in four samples, on average they were 0.11mg/kg. Our estimation of inorganic arsenic intake from long grain rice and rice-based baby food in Finland indicate that in every age group the intake is close to the lowest BMDL0.1 value 0.3μg/kg bw/day set by EFSA. According to our data, the intake of inorganic arsenic should be more extensively evaluated. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

Auxin regulated OsRGP1 and OsSuS are involved in the gravitropic bending of rice shoot bases

NASA Astrophysics Data System (ADS)

Hu, Liwei; Cui, Dayong; Cai, Weiming

The gravitropic bending of rice shoot in horizontal position results from differential elongation of cells between two halves of shoot bases. In our experiment, reversibly glycosylated polypeptide (OsRGP1), sucrose synthase (OsSuS) genes which related to sugar metabolism were identified by suppressive subtractive hybridization (SSH) in gravitropism in rice shoot bases. Realtime RT-PCR were used to study the expression of two genes in detail. OsRGP1 and OsSuS were differentially induced in the abaxial (lower) side of rice shoot bases during gravitropism. The OsRGP1 and OsSuS expression were regulated by auxin. The sequence analysis of their promoters was in concurrence. TIBA treatment could inhibit the asymmetrical expression of OsRGP1 and OsSuS in gravitropism in rice shoot bases. In addition, there was more hexose in the lower side of rice shoot bases in gravitropism. Our data suggested that asymmetric redistribution of auxin following gravistimulation resulted in the different localized expression of OsRGP1 and OsSuS. It is possible that asymmetrical expression of OsSuS resulted in the asymmetrical distribution of hexose and asymmetrical expression of OsRGP1 induced the synthesis of cell wall polysaccharides in the lower half of rice shoot bases. Hexose and cell wall polysaccharides accumulation in lower side of rice shoot bases might contribute to the cell expansion, thus leading to gravitropic bending.

System Identification and Steering Control Characteristic of Rice Combine Harvester Model

NASA Astrophysics Data System (ADS)

Sutisna, S. P.; Setiawan, R. P. A.; Subrata, I. D. M.; Mandang, T.

2018-05-01

This study is a preliminary research of rice combine harvester trajectory. A vehicle model of rice combine used crawler with differential steering. Turning process of differential steering used speed difference of right and left tracks This study aims to learn of rice combine harvester steering control. In real condition, the hydraulic break on each track produced the speed difference. The model used two DC motors with maximum speed 100 rpm for each tracks. A rotary encoder with resolution 600 pulse/rotation was connected to each DC motors shaft to monitor the speed of tracks and connected to the input shaft of a gearbox with ratio 1:46. The motor speed control for each track used pulse width modulation to produce the speed difference. A gyroscope sensor with resolution 0.01° was used to determine the model orientation angle. Like the real rice combine, the tracks can not rotate to the opposite direction at the same time so it makes the model can not perform the pivot turn. The turn radius of the model was 28 cm and the forward maximum speed was 17.8 cm/s. The model trajectory control used PID odometry controller. Parameters input were the speed of each track and the orientation of the vehicle. The straight line test showed the controller can control the rice combine model trajectory with the average error 0.67 cm.

Identification of Morphological Character and Esterase Isozyme Pattern in Second-Generation Black Rice Plant Irradiated to Gamma Rays

NASA Astrophysics Data System (ADS)

Hartanti, R. S.; Putri, T. A. N.; Zulfa, F.; Sutarno; Suranto

2017-04-01

Black rice is one of the functional foods due to its high anthocyanin content. Black rice grain was irradiated by gamma rays with a dose of 200 Gy and 300 Gy. The main purpose of this irradiation is to induce mutation to the black rice plant in order to achieve the improved organism. This study was undertaken to elucidate the morphological character and esterase isozyme pattern of black rice plant after irradiated by gamma rays. There were morphological differences on leaves, stems and grains between irradiated and non irradiated black rice plant. Gamma radiation dose of 200 Gy showed the significant influence of the length of the stem, number of internodes, and length of leaves. The radiation dose of 300 Gy showed the significant influence of the decrease value of diameter of 3rd internodes, number of branches and width of leaves. Flowering time is getting faster as increasing radiation dose. At the age of 74 days after planting there are 9.15% plants of 200 Gy radiation dose that have flowered faster than normal plants. This value increased into 11.45% at the dose of radiation 300 Gy. There were differences in the esterase banding pattern between radiation dose of 200 Gy and 300 Gy than the control plants, indicated that randomly mutation has occurred.

Genetic Mapping of Quantitative Trait Loci for Grain Yield under Drought in Rice under Controlled Greenhouse Conditions

NASA Astrophysics Data System (ADS)

Solis, Julio; Gutierrez, Andres; Mangu, Venkata; Sanchez, Eduardo; Bedre, Renesh; Linscombe, Steve; Baisakh, Niranjan

2017-12-01

Drought stress is a constant threat to rice production worldwide. Most Mmodern rice cultivars are sensitive to drought, and the effect is severe at the reproductive stage. Conventional breeding for drought resistant (DR) rice varieties is slow and limited due to the quantitative nature of the DR traits. Identification of genes (QTLs)/markers associated with DR traits is a prerequisite for marker-assisted breeding. Grain yield is the most important trait and to this end drought yield QTLs have been identified under field conditions. The present study reports identification of drought yield QTLs under controlled conditions without confounding effects of other factors prevalent under natural conditions. A linkage map covering 1,781.5 cM with an average resolution of 9.76 cM was constructed using an F2 population from a cross between two Japonica cultivars, Cocodrie (drought sensitive) and Vandana (drought tolerant) with 213 markers distributed over 12 rice chromosomes. A subset of 59 markers (22 genic SSRs and 37 SNPs) derived from the transcriptome of the parents were also placed in the map. Single marker analysis using 187 F2:3 progeny identified 6 markers distributed on chromosomes 1, 5, and 8 to be associated with grain yield under drought (GYD). Composite interval mapping identified six genomic regions/quantitative trait loci (QTL) on chromosome 1, 5, 8, and 9 to be associated with GYD. QTLs located on chromosome 1 (qGYD1.2, qGYD1.3), chromosome 5 (qGYD5.1) and chromosome 8 (qGYD8.1) were contributed by Vandana alleles, whereas the QTLs, qGYD1.1 and qQYD9.1 were contributed by Cocodrie alelles. The additive positive phenotypic variance explained by the QTLs ranged from 30.0% to 34.0%. Candidate genes annotation within QTLs suggested the role of transcription factors and genes involved in osmotic potential regulation through catalytic/metabolic pathways in drought resistance tolerance mechanism contributing to yield.

Direct detection of the plant pathogens Burkholderia glumae, Burkholderia gladioli pv. gladioli, and Erwinia chrysanthemi pv. zeae in infected rice seedlings using matrix assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Kajiwara, Hideyuki

2016-01-01

The plant pathogens Burkholderia glumae, Burkholderia gladioli pv. gladioli, and Erwinia chrysanthemi pv. zeae were directly detected in extracts from infected rice seedlings by matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). This method did not require culturing of the pathogens on artificial medium. In the MALDI-TOF MS analysis, peaks originating from bacteria were found in extracts from infected rice seedlings. The spectral peaks showed significantly high scores, in spite of minor differences in spectra. The spectral peaks originating from host plant tissues did not affect this direct MALDI-TOF MS analysis for the rapid identification of plant pathogens. Copyright © 2015 Elsevier B.V. All rights reserved.

Good manufacturing practices production of a purification-free oral cholera vaccine expressed in transgenic rice plants.

PubMed

Kashima, Koji; Yuki, Yoshikazu; Mejima, Mio; Kurokawa, Shiho; Suzuki, Yuji; Minakawa, Satomi; Takeyama, Natsumi; Fukuyama, Yoshiko; Azegami, Tatsuhiko; Tanimoto, Takeshi; Kuroda, Masaharu; Tamura, Minoru; Gomi, Yasuyuki; Kiyono, Hiroshi

2016-03-01

The first Good Manufacturing Practices production of a purification-free rice-based oral cholera vaccine (MucoRice-CTB) from transgenic plants in a closed cultivation system yielded a product meeting regulatory requirements. Despite our knowledge of their advantages, plant-based vaccines remain unavailable for human use in both developing and industrialized countries. A leading, practical obstacle to their widespread use is producing plant-based vaccines that meet governmental regulatory requirements. Here, we report the first production according to current Good Manufacturing Practices of a rice-based vaccine, the cholera vaccine MucoRice-CTB, at an academic institution. To this end, we established specifications and methods for the master seed bank (MSB) of MucoRice-CTB, which was previously generated as a selection-marker-free line, evaluated its propagation, and given that the stored seeds must be renewed periodically. The production of MucoRice-CTB incorporated a closed hydroponic system for cultivating the transgenic plants, to minimize variations in expression and quality during vaccine manufacture. This type of molecular farming factory can be operated year-round, generating three harvests annually, and is cost- and production-effective. Rice was polished to a ratio of 95 % and then powdered to produce the MucoRice-CTB drug substance, and the identity, potency, and safety of the MucoRice-CTB product met pre-established release requirements. The formulation of MucoRice-CTB made by fine-powdering of drug substance and packaged in an aluminum pouch is being evaluated in a physician-initiated phase I study.

Identification of Rice Genes Associated With Enhanced Cold Tolerance by Comparative Transcriptome Analysis With Two Transgenic Rice Plants Overexpressing DaCBF4 or DaCBF7, Isolated From Antarctic Flowering Plant Deschampsia antarctica

PubMed Central

Byun, Mi Young; Cui, Li Hua; Lee, Jungeun; Park, Hyun; Lee, Andosung; Kim, Woo Taek; Lee, Hyoungseok

2018-01-01

Few plant species can survive in Antarctica, the harshest environment for living organisms. Deschampsia antarctica is the only natural grass species to have adapted to and colonized the maritime Antarctic. To investigate the molecular mechanism of the Antarctic adaptation of this plant, we identified and characterized D. antarctica C-repeat binding factor 4 (DaCBF4), which belongs to monocot CBF group IV. The transcript level of DaCBF4 in D. antarctica was markedly increased by cold and dehydration stress. To assess the roles of DaCBF4 in plants, we generated a DaCBF4-overexpressing transgenic rice plant (Ubi:DaCBF4) and analyzed its abiotic stress response phenotype. Ubi:DaCBF4 displayed enhanced tolerance to cold stress without growth retardation under any condition compared to wild-type plants. Because the cold-specific phenotype of Ubi:DaCBF4 was similar to that of Ubi:DaCBF7 (Byun et al., 2015), we screened for the genes responsible for the improved cold tolerance in rice by selecting differentially regulated genes in both transgenic rice lines. By comparative transcriptome analysis using RNA-seq, we identified 9 and 15 genes under normal and cold-stress conditions, respectively, as putative downstream targets of the two D. antarctica CBFs. Overall, our results suggest that Antarctic hairgrass DaCBF4 mediates the cold-stress response of transgenic rice plants by adjusting the expression levels of a set of stress-responsive genes in transgenic rice plants. Moreover, selected downstream target genes will be useful for genetic engineering to enhance the cold tolerance of cereal plants, including rice. PMID:29774046

Identification of Rice Genes Associated With Enhanced Cold Tolerance by Comparative Transcriptome Analysis With Two Transgenic Rice Plants Overexpressing DaCBF4 or DaCBF7, Isolated From Antarctic Flowering Plant Deschampsia antarctica.

PubMed

Byun, Mi Young; Cui, Li Hua; Lee, Jungeun; Park, Hyun; Lee, Andosung; Kim, Woo Taek; Lee, Hyoungseok

2018-01-01

Few plant species can survive in Antarctica, the harshest environment for living organisms. Deschampsia antarctica is the only natural grass species to have adapted to and colonized the maritime Antarctic. To investigate the molecular mechanism of the Antarctic adaptation of this plant, we identified and characterized D. antarctica C-repeat binding factor 4 ( DaCBF4 ), which belongs to monocot CBF group IV. The transcript level of DaCBF4 in D. antarctica was markedly increased by cold and dehydration stress. To assess the roles of DaCBF4 in plants, we generated a DaCBF4 -overexpressing transgenic rice plant ( Ubi:DaCBF4 ) and analyzed its abiotic stress response phenotype. Ubi:DaCBF4 displayed enhanced tolerance to cold stress without growth retardation under any condition compared to wild-type plants. Because the cold-specific phenotype of Ubi:DaCBF4 was similar to that of Ubi:DaCBF7 (Byun et al., 2015), we screened for the genes responsible for the improved cold tolerance in rice by selecting differentially regulated genes in both transgenic rice lines. By comparative transcriptome analysis using RNA-seq, we identified 9 and 15 genes under normal and cold-stress conditions, respectively, as putative downstream targets of the two D. antarctica CBFs. Overall, our results suggest that Antarctic hairgrass DaCBF4 mediates the cold-stress response of transgenic rice plants by adjusting the expression levels of a set of stress-responsive genes in transgenic rice plants. Moreover, selected downstream target genes will be useful for genetic engineering to enhance the cold tolerance of cereal plants, including rice.

Identification and characterization of proteins involved in rice urea and arginine catabolism.

PubMed

Cao, Feng-Qiu; Werner, Andrea K; Dahncke, Kathleen; Romeis, Tina; Liu, Lai-Hua; Witte, Claus-Peter

2010-09-01

Rice (Oryza sativa) production relies strongly on nitrogen (N) fertilization with urea, but the proteins involved in rice urea metabolism have not yet been characterized. Coding sequences for rice arginase, urease, and the urease accessory proteins D (UreD), F (UreF), and G (UreG) involved in urease activation were identified and cloned. The functionality of urease and the urease accessory proteins was demonstrated by complementing corresponding Arabidopsis (Arabidopsis thaliana) mutants and by multiple transient coexpression of the rice proteins in Nicotiana benthamiana. Secondary structure models of rice (plant) UreD and UreF proteins revealed a possible functional conservation to bacterial orthologs, especially for UreF. Using amino-terminally StrepII-tagged urease accessory proteins, an interaction between rice UreD and urease could be shown. Prokaryotic and eukaryotic urease activation complexes seem conserved despite limited protein sequence conservation for UreF and UreD. In plant metabolism, urea is generated by the arginase reaction. Rice arginase was transiently expressed as a carboxyl-terminally StrepII-tagged fusion protein in N. benthamiana, purified, and biochemically characterized (K(m) = 67 mm, k(cat) = 490 s(-1)). The activity depended on the presence of manganese (K(d) = 1.3 microm). In physiological experiments, urease and arginase activities were not influenced by the external N source, but sole urea nutrition imbalanced the plant amino acid profile, leading to the accumulation of asparagine and glutamine in the roots. Our data indicate that reduced plant performance with urea as N source is not a direct result of insufficient urea metabolism but may in part be caused by an imbalance of N distribution.

Cross-species bacterial artificial chromosome (BAC) library screening via overgo-based hybridization and BAC-contig mapping of a yield enhancement quantitative trait locus (QTL) yld1.1 in the Malaysian wild rice Oryza rufipogon.

PubMed

Song, Beng-Kah; Nadarajah, Kalaivani; Romanov, Michael N; Ratnam, Wickneswari

2005-01-01

The construction of BAC-contig physical maps is an important step towards a partial or ultimate genome sequence analysis. Here, we describe our initial efforts to apply an overgo approach to screen a BAC library of the Malaysian wild rice species, Oryza rufipogon. Overgo design is based on repetitive element masking and sequence uniqueness, and uses short probes (approximately 40 bp), making this method highly efficient and specific. Pairs of 24-bp oligos that contain an 8-bp overlap were developed from the publicly available genomic sequences of the cultivated rice, O. sativa, to generate 20 overgo probes for a 1-Mb region that encompasses a yield enhancement QTL yld1.1 in O. rufipogon. The advantages of a high similarity in melting temperature, hybridization kinetics and specific activities of overgos further enabled a pooling strategy for library screening by filter hybridization. Two pools of ten overgos each were hybridized to high-density filters representing the O. rufipogon genomic BAC library. These screening tests succeeded in providing 69 PCR-verified positive hits from a total of 23,040 BAC clones of the entire O. rufipogon library. A minimal tilling path of clones was generated to contribute to a fully covered BAC-contig map of the targeted 1-Mb region. The developed protocol for overgo design based on O. sativa sequences as a comparative genomic framework, and the pooled overgo hybridization screening technique are suitable means for high-resolution physical mapping and the identification of BAC candidates for sequencing.

A Phenology-based Approach for Rice Crop Mapping from Multi-temporal Sentinel-1A Data in Taiwan

NASA Astrophysics Data System (ADS)

Chen, C. F.; Chen, J. B.; Nguyen, S. T.; Chen, C. R.; Chiang, S. H.

2016-12-01

Rice is the most important food crop in Taiwan, accounting for approximately 5% (166,616 ha) of the total cultivated area. Besides its nutritional value, rice agriculture remains the primary source of livelihood for the majority of rural populations in the country. Rice monitoring is a crucial activity due to official initiatives to ensure the national food security. Because the size of rice fields in Taiwan is relatively small, rice monitoring is traditionally implemented through time-consuming and costly visual interpretation of aerial photos. The Sentinel-1A launched on 3 April 2014 provides the data that have sufficient spatial and temporal resolutions (i.e., 10 m resolution and 12-day revisit cycle) for monitoring small patches of rice fields in the country. This study aimed to develop a phenology-based approach to map rice-growing areas in Taiwan from multi-temporal descending Sentinel-1A VH and VV data. The data were processed for the second rice cropping season (July‒December) in 2015, consisting four main steps: (1) data pre-processing, including radiometric and geometric corrections, and speckle noise filtering of the VH and VV backscattering coefficient data, (2) normalization difference sigma-naught index (NDSI) calculation based on the sowing and heading periods obtained from the analysis of rice crop phenology in the region, (3) threshold-based rice classification using the expectation-maximization method, and (4) accuracy assessment of the mapping results. The mapping results compared with the ground reference data indicated that the overall accuracies and Kappa coefficients achieved for the VH data were 92.0% and 0.84, while the values for the VV data were 81.1% and 0.62, respectively. The mapping results further verified with the government's rice area statistics reaffirmed the consistency between these two datasets with the root mean square error (RMSE) less than 1%, in both cases. This study demonstrates the potential application of multi-temporal Sentinel-1A data for rice crop monitoring in Taiwan using information of rice crop phenology. The methods were thus proposed for rice monitoring in the country and other regions around the world.

Genome-wide mapping of virulence in brown planthopper identifies loci that break down host plant resistance.

PubMed

Jing, Shengli; Zhang, Lei; Ma, Yinhua; Liu, Bingfang; Zhao, Yan; Yu, Hangjin; Zhou, Xi; Qin, Rui; Zhu, Lili; He, Guangcun

2014-01-01

Insects and plants have coexisted for over 350 million years and their interactions have affected ecosystems and agricultural practices worldwide. Variation in herbivorous insects' virulence to circumvent host resistance has been extensively documented. However, despite decades of investigation, the genetic foundations of virulence are currently unknown. The brown planthopper (Nilaparvata lugens) is the most destructive rice (Oryza sativa) pest in the world. The identification of the resistance gene Bph1 and its introduction in commercial rice varieties prompted the emergence of a new virulent brown planthopper biotype that was able to break the resistance conferred by Bph1. In this study, we aimed to construct a high density linkage map for the brown planthopper and identify the loci responsible for its virulence in order to determine their genetic architecture. Based on genotyping data for hundreds of molecular markers in three mapping populations, we constructed the most comprehensive linkage map available for this species, covering 96.6% of its genome. Fifteen chromosomes were anchored with 124 gene-specific markers. Using genome-wide scanning and interval mapping, the Qhp7 locus that governs preference for Bph1 plants was mapped to a 0.1 cM region of chromosome 7. In addition, two major QTLs that govern the rate of insect growth on resistant rice plants were identified on chromosomes 5 (Qgr5) and 14 (Qgr14). This is the first study to successfully locate virulence in the genome of this important agricultural insect by marker-based genetic mapping. Our results show that the virulence which overcomes the resistance conferred by Bph1 is controlled by a few major genes and that the components of virulence originate from independent genetic characters. The isolation of these loci will enable the elucidation of the molecular mechanisms underpinning the rice-brown planthopper interaction and facilitate the development of durable approaches for controlling this most destructive agricultural insect.

Genome-Wide Mapping of Virulence in Brown Planthopper Identifies Loci That Break Down Host Plant Resistance

PubMed Central

Jing, Shengli; Zhang, Lei; Ma, Yinhua; Liu, Bingfang; Zhao, Yan; Yu, Hangjin; Zhou, Xi; Qin, Rui; Zhu, Lili; He, Guangcun

2014-01-01

Insects and plants have coexisted for over 350 million years and their interactions have affected ecosystems and agricultural practices worldwide. Variation in herbivorous insects' virulence to circumvent host resistance has been extensively documented. However, despite decades of investigation, the genetic foundations of virulence are currently unknown. The brown planthopper (Nilaparvata lugens) is the most destructive rice (Oryza sativa) pest in the world. The identification of the resistance gene Bph1 and its introduction in commercial rice varieties prompted the emergence of a new virulent brown planthopper biotype that was able to break the resistance conferred by Bph1. In this study, we aimed to construct a high density linkage map for the brown planthopper and identify the loci responsible for its virulence in order to determine their genetic architecture. Based on genotyping data for hundreds of molecular markers in three mapping populations, we constructed the most comprehensive linkage map available for this species, covering 96.6% of its genome. Fifteen chromosomes were anchored with 124 gene-specific markers. Using genome-wide scanning and interval mapping, the Qhp7 locus that governs preference for Bph1 plants was mapped to a 0.1 cM region of chromosome 7. In addition, two major QTLs that govern the rate of insect growth on resistant rice plants were identified on chromosomes 5 (Qgr5) and 14 (Qgr14). This is the first study to successfully locate virulence in the genome of this important agricultural insect by marker-based genetic mapping. Our results show that the virulence which overcomes the resistance conferred by Bph1 is controlled by a few major genes and that the components of virulence originate from independent genetic characters. The isolation of these loci will enable the elucidation of the molecular mechanisms underpinning the rice-brown planthopper interaction and facilitate the development of durable approaches for controlling this most destructive agricultural insect. PMID:24911169

Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice

PubMed Central

Gómez-Porras, Judith L; Riaño-Pachón, Diego Mauricio; Dreyer, Ingo; Mayer, Jorge E; Mueller-Roeber, Bernd

2007-01-01

Background In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an in-silico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements (CREs), ABRE and CE3, in thale cress (Arabidopsis thaliana) and rice (Oryza sativa). Results Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element (CE) associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes (ABRCs) in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. Conclusion Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of interacting with transcription factors. Further studies will be needed to test whether the observed differences are extrapolatable to monocots and dicots in general, and to understand how they contribute to the fine-tuning of the hormonal response. The outcome of our investigation can now be used to direct future experimentation designed to further dissect the ABA-dependent regulatory networks. PMID:17672917

Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice.

PubMed

Gómez-Porras, Judith L; Riaño-Pachón, Diego Mauricio; Dreyer, Ingo; Mayer, Jorge E; Mueller-Roeber, Bernd

2007-08-01

In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an in-silico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements (CREs), ABRE and CE3, in thale cress (Arabidopsis thaliana) and rice (Oryza sativa). Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element (CE) associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes (ABRCs) in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of interacting with transcription factors. Further studies will be needed to test whether the observed differences are extrapolatable to monocots and dicots in general, and to understand how they contribute to the fine-tuning of the hormonal response. The outcome of our investigation can now be used to direct future experimentation designed to further dissect the ABA-dependent regulatory networks.

Identification of Striga hermonthica-Resistant Upland Rice Varieties in Sudan and Their Resistance Phenotypes.

PubMed

Samejima, Hiroaki; Babiker, Abdel G; Mustafa, Ahmed; Sugimoto, Yukihiro

2016-01-01

Rice has become a major staple cereal in sub-Saharan Africa. Currently, upland rice cultivation is expanding particularly in rainfed areas where the root parasitic weed Striga hermonthica, a major constraint to cereal production, is endemic. Laboratory, pot, and semi-controlled open air experiments were performed to evaluate resistance of selected rice varieties in Sudan to a resident S. hermonthica population. In the laboratory, 27 varieties were screened for post-attachment resistance using the rhizotron technique. Varieties displaying high post-attachment resistance, Umgar, NERICA5, and NERICA13 together with NERICA4, NERICA18, and Nipponbare, a lowland rice variety, were further evaluated for performance and Striga resistance in pot and semi-controlled open air experiments and for germination inducing activity in a laboratory. In addition, comparative studies on reaction of Umgar, Kosti1 and Kosti2, released varieties for commercial production in Sudan, to the parasite were performed in two pot experiments. In the pot experiments Umgar and NERICA5, consistently, sustained the lowest Striga emergence (<2.2 Striga plants per pot), while NERICA13 and NERICA4 supported 1.8-5.7 and 8.7-16.4 Striga plants per pot, respectively. In an artificially Striga-infested field, number of emergent Striga plants per 10 rice hills, at harvest, was 2.0, 2.0, 4.8, 13.5, 13.3, and 18.3 on Umgar, NERICA5, NERICA13, NERICA4, NERICA18, and Nipponbare, respectively. Striga had no adverse effects on total above-ground parts and panicle dry weight in Umgar and NERICA5. Germination-inducing activity of root exudates, at 14 days after sowing onward, was markedly lower for Umgar than for NERICA5, NERICA13, NERICA4, and NERICA18. Based on these findings, Umgar has both pre and post-attachment resistance to a resident Striga population in Sudan. Kosti1 and Kosti2 did not exhibit Striga-resistance at the same level as Umgar. Further the resistance of NERICA5, a variety reported to be endowed with a broad spectrum resistance to Striga species and ecotypes, at least to one resident Striga population in Sudan was clearly indicated.

Identification of Striga hermonthica-Resistant Upland Rice Varieties in Sudan and Their Resistance Phenotypes

PubMed Central

Samejima, Hiroaki; Babiker, Abdel G.; Mustafa, Ahmed; Sugimoto, Yukihiro

2016-01-01

Rice has become a major staple cereal in sub-Saharan Africa. Currently, upland rice cultivation is expanding particularly in rainfed areas where the root parasitic weed Striga hermonthica, a major constraint to cereal production, is endemic. Laboratory, pot, and semi-controlled open air experiments were performed to evaluate resistance of selected rice varieties in Sudan to a resident S. hermonthica population. In the laboratory, 27 varieties were screened for post-attachment resistance using the rhizotron technique. Varieties displaying high post-attachment resistance, Umgar, NERICA5, and NERICA13 together with NERICA4, NERICA18, and Nipponbare, a lowland rice variety, were further evaluated for performance and Striga resistance in pot and semi-controlled open air experiments and for germination inducing activity in a laboratory. In addition, comparative studies on reaction of Umgar, Kosti1 and Kosti2, released varieties for commercial production in Sudan, to the parasite were performed in two pot experiments. In the pot experiments Umgar and NERICA5, consistently, sustained the lowest Striga emergence (<2.2 Striga plants per pot), while NERICA13 and NERICA4 supported 1.8–5.7 and 8.7–16.4 Striga plants per pot, respectively. In an artificially Striga-infested field, number of emergent Striga plants per 10 rice hills, at harvest, was 2.0, 2.0, 4.8, 13.5, 13.3, and 18.3 on Umgar, NERICA5, NERICA13, NERICA4, NERICA18, and Nipponbare, respectively. Striga had no adverse effects on total above-ground parts and panicle dry weight in Umgar and NERICA5. Germination-inducing activity of root exudates, at 14 days after sowing onward, was markedly lower for Umgar than for NERICA5, NERICA13, NERICA4, and NERICA18. Based on these findings, Umgar has both pre and post-attachment resistance to a resident Striga population in Sudan. Kosti1 and Kosti2 did not exhibit Striga-resistance at the same level as Umgar. Further the resistance of NERICA5, a variety reported to be endowed with a broad spectrum resistance to Striga species and ecotypes, at least to one resident Striga population in Sudan was clearly indicated. PMID:27242837

Impact of diverse cultivars on molecular and crystalline structures of rice starch for food processing.

PubMed

Lee, Seul; Lee, Ju Hun; Chung, Hyun-Jung

2017-08-01

The objective of this study was to determine the molecular and crystalline structures of starches from diverse rice cultivars for three major food processing in Korea (cooked rice, brewing and rice cake). Rice starches were isolated from 10 different rice varieties grown in Korea. Apparent amylose contents of rice starches from cooked rice, brewing and rice cake varieties were 21.1-22.4%, 22.9-24.6%, and 20.1-22.0%, respectively. Rice starches from rice cake varieties showed higher peak viscosity but lower pasting temperature than those from cooked rice and brewing varieties. Swelling factor at 80°C of rice starches from cooked rice, brewing and rice cake varieties was 16.6-19.0, 17.8-19.3, and 17.8-19.2, respectively. Based on structure and physicochemical properties of rice starches extracted from different rice varieties, principal component analysis (PCA) results showed that these rice varieties could be clearly classified according to processing adaptability for cooked rice and rice cake. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease

PubMed Central

Yang, Sihai; Li, Jing; Zhang, Xiaohui; Zhang, Qijun; Huang, Ju; Chen, Jian-Qun; Hartl, Daniel L.; Tian, Dacheng

2013-01-01

We show that the genomes of maize, sorghum, and brachypodium contain genes that, when transformed into rice, confer resistance to rice blast disease. The genes are resistance genes (R genes) that encode proteins with nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains (NBS–LRR proteins). By using criteria associated with rapid molecular evolution, we identified three rapidly evolving R-gene families in these species as well as in rice, and transformed a randomly chosen subset of these genes into rice strains known to be sensitive to rice blast disease caused by the fungus Magnaporthe oryzae. The transformed strains were then tested for sensitivity or resistance to 12 diverse strains of M. oryzae. A total of 15 functional blast R genes were identified among 60 NBS–LRR genes cloned from maize, sorghum, and brachypodium; and 13 blast R genes were obtained from 20 NBS–LRR paralogs in rice. These results show that abundant blast R genes occur not only within species but also among species, and that the R genes in the same rapidly evolving gene family can exhibit an effector response that confers resistance to rapidly evolving fungal pathogens. Neither conventional evolutionary conservation nor conventional evolutionary convergence supplies a satisfactory explanation of our findings. We suggest a unique mechanism termed “constrained divergence,” in which R genes and pathogen effectors can follow only limited evolutionary pathways to increase fitness. Our results open avenues for R-gene identification that will help to elucidate R-gene vs. effector mechanisms and may yield new sources of durable pathogen resistance. PMID:24145399

Newly Identified Wild Rice Accessions Conferring High Salt Tolerance Might Use a Tissue Tolerance Mechanism in Leaf

PubMed Central

Prusty, Manas R.; Kim, Sung-Ryul; Vinarao, Ricky; Entila, Frederickson; Egdane, James; Diaz, Maria G. Q.; Jena, Kshirod K.

2018-01-01

Cultivated rice (Oryza sativa L.) is very sensitive to salt stress. So far a few rice landraces have been identified as a source of salt tolerance and utilized in rice improvement. These tolerant lines primarily use Na+ exclusion mechanism in root which removes Na+ from the xylem stream by membrane Na+ and K+ transporters, and resulted in low Na+ accumulation in shoot. Identification of a new donor source conferring high salt tolerance is imperative. Wild relatives of rice having wide genetic diversity are regarded as a potential source for crop improvement. However, they have been less exploited against salt stress. Here, we simultaneously evaluated all 22 wild Oryza species along with the cultivated tolerant lines including Pokkali, Nona Bokra, and FL478, and sensitive check varieties under high salinity (240 mM NaCl). Based on the visual salt injury score, three species (O. alta, O. latifolia, and O. coarctata) and four species (O. rhizomatis, O. eichingeri, O. minuta, and O. grandiglumis) showed higher and similar level of tolerance compared to the tolerant checks, respectively. All three CCDD genome species exhibited salt tolerance, suggesting that the CCDD genome might possess the common genetic factors for salt tolerance. Physiological and biochemical experiments were conducted using the newly isolated tolerant species together with checks under 180 mM NaCl. Interestingly, all wild species showed high Na+ concentration in shoot and low concentration in root unlike the tolerant checks. In addition, the wild-tolerant accessions showed a tendency of a high tissue tolerance in leaf, low malondialdehyde level in shoot, and high retention of chlorophyll in the young leaves. These results suggest that the wild species employ tissue tolerance mechanism to manage salt stress. Gene expression analyses of the key salt tolerance-related genes suggested that high Na+ in leaf of wild species might be affected by OsHKT1;4-mediated Na+ exclusion in leaf and the following Na+ sequestration in leaf might be occurring independent of tonoplast-localized OsNHX1. The newly isolated wild rice accessions will be valuable materials for both rice improvement to salinity stress and the study of salt tolerance mechanism in plants. PMID:29740456

Gene expression and plant hormone levels in two contrasting rice genotypes responding to brown planthopper infestation.

PubMed

Li, Changyan; Luo, Chao; Zhou, Zaihui; Wang, Rui; Ling, Fei; Xiao, Langtao; Lin, Yongjun; Chen, Hao

2017-02-28

The brown planthopper (BPH; Nilaparvata lugens Stål) is a destructive piercing-sucking insect pest of rice. The plant hormones salicylic acid (SA) and jasmonic acid (JA) play important roles in plant-pest interactions. Many isolated rice genes that modulate BPH resistance are involved in the metabolism or signaling pathways of SA, JA and ethylene. 'Rathu Heenati' (RH) is a rice cultivar with a high-level, broad-spectrum resistance to all BPH biotypes. Here, RH was used as the research material, while a BPH-susceptible rice cultivar 'Taichung Native 1' (TN1) was the control. A cDNA microarray analysis illuminated the resistance response at the genome level of RH under BPH infestation. The levels of SA and JA in RH and TN1 seedlings after BPH infestation were also determined. The expression pattern clustering indicated that 1467 differential probe sets may be associated with constitutive resistance and 67 with the BPH infestation-responsive resistance of RH. A Venn diagram analysis revealed 192 RH-specific and BPH-inducible probe sets. Finally, 23 BPH resistance-related gene candidates were selected based on the expression pattern clustering and Venn diagram analysis. In RH, the SA content significantly increased and the JA content significantly decreased after BPH infestation, with the former occurring prior to the latter. In RH, the differential genes in the SA pathway were synthesis-related and were up-regulated after BPH infestation. The differential genes in the JA pathway were also up-regulated. They were jasmonate ZIM-domain transcription factors, which are important negative regulators of the JA pathway. Comparatively, genes involved in the ET pathway were less affected by a BPH infestation in RH. DNA sequence analysis revealed that most BPH infestation-inducible genes may be regulated by the genetic background in a trans-acting manner, instead of by their promoters. We profiled the analysis of the global gene expression in RH and TN1 under BPH infestation, together with changes in the SA and JA levels. SA plays a leading role in the resistance response of rice to BPH. Our results will aid in understanding the molecular basis of RH's BPH resistance and facilitate the identification of new resistance-related genes for breeding BPH-resistant rice varieties.

A Small and Slim Coaxial Probe for Single Rice Grain Moisture Sensing

PubMed Central

You, Kok Yeow; Mun, Hou Kit; You, Li Ling; Salleh, Jamaliah; Abbas, Zulkifly

2013-01-01

A moisture detection of single rice grains using a slim and small open-ended coaxial probe is presented. The coaxial probe is suitable for the nondestructive measurement of moisture values in the rice grains ranging from from 9.5% to 26%. Empirical polynomial models are developed to predict the gravimetric moisture content of rice based on measured reflection coefficients using a vector network analyzer. The relationship between the reflection coefficient and relative permittivity were also created using a regression method and expressed in a polynomial model, whose model coefficients were obtained by fitting the data from Finite Element-based simulation. Besides, the designed single rice grain sample holder and experimental set-up were shown. The measurement of single rice grains in this study is more precise compared to the measurement in conventional bulk rice grains, as the random air gap present in the bulk rice grains is excluded. PMID:23493127

Label-free quantitative secretome analysis of Xanthomonas oryzae pv. oryzae highlights the involvement of a novel cysteine protease in its pathogenicity.

PubMed

Wang, Yiming; Gupta, Ravi; Song, Wei; Huh, Hyun-Hye; Lee, So Eui; Wu, Jingni; Agrawal, Ganesh Kumar; Rakwal, Randeep; Kang, Kyu Young; Park, Sang-Ryeol; Kim, Sun Tae

2017-10-03

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases resulting in a huge loss of the total rice productivity. The initial interaction between rice and Xoo takes place in the host apoplast and is mediated primarily by secretion of various proteins from both partners. Yet, such secretory proteins remain to be largely identified and characterized. This study employed a label-free quantitative proteomics approach and identified 404 and 323 Xoo-secreted proteins from in vitro suspension-cultured cells and in planta systems, respectively. Gene Ontology analysis showed their involvement primarily in catalytic, transporter, and ATPase activities. Of a particular interest was a Xoo cysteine protease (XoCP), which showed dramatic increase in its protein abundance in planta upon Xoo interaction with a susceptible rice cultivar. Knock-out mutants of XoCP showed reduced pathogenicity on rice, highlighting its potential involvement in Xoo virulence. Besides, a parallel analysis of in planta rice-secreted proteins resulted in identification of 186 secretory proteins mainly associated with the catalytic, antioxidant, and electron carrier activities. Identified secretory proteins were exploited to shed light on their possible role in the rice-Xoo interaction, and that further deepen our understanding of such interaction. Xanthomonas oryzae pv. oryzae (Xoo), causative agent of bacterial blight disease, results in a huge loss of the total rice productivity. Using a label-free quantitative proteomics approach, we identified 727 Xoo- and 186 rice-secreted proteins. Functional annotation showed Xoo secreted proteins were mainly associated with the catalytic, transporter, and ATPase activities while the rice secreted proteins were mainly associated with the catalytic, antioxidant, and electron carrier activities. A novel Xoo cysteine protease (XoCP) was identified, showing dramatic increase in its protein abundance in planta upon Xoo interaction with a susceptible rice cultivar. Knock-out mutants of XoCP showed reduced pathogenicity on rice, highlighting its potential involvement in Xoo virulence. Copyright © 2017 Elsevier B.V. All rights reserved.

Identification of cis-elements and evaluation of upstream regulatory region of a rice anther-specific gene, OSIPP3, conferring pollen-specific expression in Oryza sativa (L.) ssp. indica.

PubMed

Manimaran, P; Raghurami Reddy, M; Bhaskar Rao, T; Mangrauthia, Satendra K; Sundaram, R M; Balachandran, S M

2015-12-01

Pollen-specific expression. Promoters comprise of various cis-regulatory elements which control development and physiology of plants by regulating gene expression. To understand the promoter specificity and also identification of functional cis-acting elements, progressive 5' deletion analysis of the promoter fragments is widely used. We have evaluated the activity of regulatory elements of 5' promoter deletion sequences of anther-specific gene OSIPP3, viz. OSIPP3-∆1 (1504 bp), OSIPP3-∆2 (968 bp), OSIPP3-∆3 (388 bp) and OSIPP3-∆4 (286 bp) through the expression of transgene GUS in rice. In silico analysis of 1504-bp sequence harboring different copy number of cis-acting regulatory elements such as POLLENLELAT52, GTGANTG10, enhancer element of LAT52 and LAT56 indicated that they were essential for high level of expression in pollen. Histochemical GUS analysis of the transgenic plants revealed that 1504- and 968-bp fragments directed GUS expression in roots and anthers, while the 388- and 286-bp fragments restricted the GUS expression to only pollen, of which 388 bp conferred strong GUS expression. Further, GUS staining analysis of different panicle development stages (P1-P6) confirmed that the GUS gene was preferentially expressed only at P6 stage (late pollen stage). The qRT-PCR analysis of GUS transcript revealed 23-fold higher expression of GUS transcript in OSIPP3-Δ1 followed by OSIPP3-Δ2 (eightfold) and OSIPP3-Δ3 (threefold) when compared to OSIPP3-Δ4. Based on our results, we proposed that among the two smaller fragments, the 388-bp upstream regulatory region could be considered as a promising candidate for pollen-specific expression of agronomically important transgenes in rice.

Genetic variation of germination cold tolerance in Japanese rice germplasm

PubMed Central

Bosetti, Fátima; Montebelli, Camila; Novembre, Ana Dionísia L.C.; Chamma, Helena Pescarin; Pinheiro, José Baldin

2012-01-01

Low temperatures at the initial stages of rice development prevent fast germination and seedling establishment and may cause significant productivity losses. In order to develop rice cultivars exhibiting cold tolerance, it is necessary to investigate genetic resources, providing basic knowledge to allow the introduction of genes involved in low temperature germination ability from accessions into elite cultivars. Japanese rice accessions were evaluated at the germination under two conditions: 13°C for 28 days (cold stress) and 28°C for seven days (optimal temperature). The traits studied were coleoptile and radicle length under optimal temperature, coleoptile and radicle length under cold and percentage of the reduction in coleptile and radicle length due to low temperature. Among the accessions studied, genetic variation for traits related to germination under low temperatures was observed and accessions exhibiting adequate performance for all investigated traits were identified. The use of multivariate analysis allowed the identification of the genotypes displaying cold tolerance by smaller reductions in coleoptile and radicle lenght in the presence of cold and high vigour, by higher coleoptile and radicle growth under cold. PMID:23226080

Genetic variation of germination cold tolerance in Japanese rice germplasm.

PubMed

Bosetti, Fátima; Montebelli, Camila; Novembre, Ana Dionísia L C; Chamma, Helena Pescarin; Pinheiro, José Baldin

2012-09-01

Low temperatures at the initial stages of rice development prevent fast germination and seedling establishment and may cause significant productivity losses. In order to develop rice cultivars exhibiting cold tolerance, it is necessary to investigate genetic resources, providing basic knowledge to allow the introduction of genes involved in low temperature germination ability from accessions into elite cultivars. Japanese rice accessions were evaluated at the germination under two conditions: 13°C for 28 days (cold stress) and 28°C for seven days (optimal temperature). The traits studied were coleoptile and radicle length under optimal temperature, coleoptile and radicle length under cold and percentage of the reduction in coleptile and radicle length due to low temperature. Among the accessions studied, genetic variation for traits related to germination under low temperatures was observed and accessions exhibiting adequate performance for all investigated traits were identified. The use of multivariate analysis allowed the identification of the genotypes displaying cold tolerance by smaller reductions in coleoptile and radicle lenght in the presence of cold and high vigour, by higher coleoptile and radicle growth under cold.

Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species.

PubMed

Nepal, Madhav P; Andersen, Ethan J; Neupane, Surendra; Benson, Benjamin V

2017-09-30

Disease resistance genes (R genes), as part of the plant defense system, have coevolved with corresponding pathogen molecules. The main objectives of this project were to identify non-Toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (nTNL) genes and elucidate their evolutionary divergence across six plant genomes. Using reference sequences from Arabidopsis , we investigated nTNL orthologs in the genomes of common bean, Medicago , soybean, poplar, and rice. We used Hidden Markov Models for sequence identification, performed model-based phylogenetic analyses, visualized chromosomal positioning, inferred gene clustering, and assessed gene expression profiles. We analyzed 908 nTNL R genes in the genomes of the six plant species, and classified them into 12 subgroups based on the presence of coiled-coil (CC), nucleotide binding site (NBS), leucine rich repeat (LRR), resistance to Powdery mildew 8 (RPW8), and BED type zinc finger domains. Traditionally classified CC-NBS-LRR (CNL) genes were nested into four clades (CNL A-D) often with abundant, well-supported homogeneous subclades of Type-II R genes. CNL-D members were absent in rice, indicating a unique R gene retention pattern in the rice genome. Genomes from Arabidopsis , common bean, poplar and soybean had one chromosome without any CNL R genes. Medicago and Arabidopsis had the highest and lowest number of gene clusters, respectively. Gene expression analyses suggested unique patterns of expression for each of the CNL clades. Differential gene expression patterns of the nTNL genes were often found to correlate with number of introns and GC content, suggesting structural and functional divergence.

Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species

PubMed Central

Andersen, Ethan J.; Neupane, Surendra; Benson, Benjamin V.

2017-01-01

Disease resistance genes (R genes), as part of the plant defense system, have coevolved with corresponding pathogen molecules. The main objectives of this project were to identify non-Toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (nTNL) genes and elucidate their evolutionary divergence across six plant genomes. Using reference sequences from Arabidopsis, we investigated nTNL orthologs in the genomes of common bean, Medicago, soybean, poplar, and rice. We used Hidden Markov Models for sequence identification, performed model-based phylogenetic analyses, visualized chromosomal positioning, inferred gene clustering, and assessed gene expression profiles. We analyzed 908 nTNL R genes in the genomes of the six plant species, and classified them into 12 subgroups based on the presence of coiled-coil (CC), nucleotide binding site (NBS), leucine rich repeat (LRR), resistance to Powdery mildew 8 (RPW8), and BED type zinc finger domains. Traditionally classified CC-NBS-LRR (CNL) genes were nested into four clades (CNL A-D) often with abundant, well-supported homogeneous subclades of Type-II R genes. CNL-D members were absent in rice, indicating a unique R gene retention pattern in the rice genome. Genomes from Arabidopsis, common bean, poplar and soybean had one chromosome without any CNL R genes. Medicago and Arabidopsis had the highest and lowest number of gene clusters, respectively. Gene expression analyses suggested unique patterns of expression for each of the CNL clades. Differential gene expression patterns of the nTNL genes were often found to correlate with number of introns and GC content, suggesting structural and functional divergence. PMID:28973974

[Quantitative relationships between hyper-spectral vegetation indices and leaf area index of rice].

PubMed

Tian, Yong-Chao; Yang, Jie; Yao, Xia; Zhu, Yan; Cao, Wei-Xing

2009-07-01

Based on field experiments with different rice varieties under different nitrogen application levels, the quantitative relationships of rice leaf area index (LAI) with canopy hyper-spectral parameters at different growth stages were analyzed. Rice LAI had good relationships with several hyper-spectral vegetation indices, the correlation coefficient being the highest with DI (difference index), followed by with RI (ratio index), and NI (normalized index), based on the spectral reflectance or the first derivative spectra. The two best spectral indices for estimating LAI were the difference index DI (854, 760) (based on two spectral bands of 850 nm and 760 nm) and the difference index DI (D676, D778) (based on two first derivative bands of 676 nm and 778 nm). In general, the hyper-spectral vegetation indices based on spectral reflectance performed better than the spectral indices based on the first derivative spectra. The tests with independent dataset suggested that the rice LAI monitoring models with difference index DI (854,760) as the variable could give an accurate LAI estimation, being available for estimation of rice LAI.

Long-term effect of rice-based farming systems on soil health.

PubMed

Bihari, Priyanka; Nayak, A K; Gautam, Priyanka; Lal, B; Shahid, M; Raja, R; Tripathi, R; Bhattacharyya, P; Panda, B B; Mohanty, S; Rao, K S

2015-05-01

Integrated rice-fish culture, an age-old farming system, is a technology which could produce rice and fish sustainably at a time by optimizing scarce resource use through complementary use of land and water. An understanding of microbial processes is important for the management of farming systems as soil microbes are the living part of soil organic matter and play critical roles in soil C and N cycling and ecosystem functioning of farming system. Rice-based integrated farming system model for small and marginal farmers was established in 2001 at Central Rice Research Institute, Cuttack, Odisha. The different enterprises of farming system were rice-fish, fish-fingerlings, fruits, vegetables, rice-fish refuge, and agroforestry. This study was conducted with the objective to assess the soil physicochemical properties, microbial population, carbon and nitrogen fractions, soil enzymatic activity, and productivity of different enterprises. The effect of enterprises induced significant changes in the chemical composition and organic matter which in turn influenced the activities of enzymes (urease, acid, and alkaline phosphatase) involved in the C, N, and P cycles. The different enterprises of long-term rice-based farming system caused significant variations in nutrient content of soil, which was higher in rice-fish refuge followed by rice-fish enterprise. Highest microbial populations and enzymatic properties were recorded in rice-fish refuge system because of waterlogging and reduced condition prolonged in this system leading to less decomposition of organic matter. The maximum alkaline phosphatase, urease, and FDA were observed in rice-fish enterprise. However, highest acid phosphatase and dehydrogenase activity were obtained in vegetable enterprise and fish-fingerlings enterprise, respectively.

A Genetic Screen Identifies a Requirement for Cysteine-Rich-Receptor-Like Kinases in Rice NH1 (OsNPR1)-Mediated Immunity.

PubMed

Chern, Mawsheng; Xu, Qiufang; Bart, Rebecca S; Bai, Wei; Ruan, Deling; Sze-To, Wing Hoi; Canlas, Patrick E; Jain, Rashmi; Chen, Xuewei; Ronald, Pamela C

2016-05-01

Systemic acquired resistance, mediated by the Arabidopsis NPR1 gene and the rice NH1 gene, confers broad-spectrum immunity to diverse pathogens. NPR1 and NH1 interact with TGA transcription factors to activate downstream defense genes. Despite the importance of this defense response, the signaling components downstream of NPR1/NH1 and TGA proteins are poorly defined. Here we report the identification of a rice mutant, snim1, which suppresses NH1-mediated immunity and demonstrate that two genes encoding previously uncharacterized cysteine-rich-receptor-like kinases (CRK6 and CRK10), complement the snim1 mutant phenotype. Silencing of CRK6 and CRK10 genes individually in the parental genetic background recreates the snim1 phenotype. We identified a rice mutant in the Kitaake genetic background with a frameshift mutation in crk10; this mutant also displays a compromised immune response highlighting the important role of crk10. We also show that elevated levels of NH1 expression lead to enhanced CRK10 expression and that the rice TGA2.1 protein binds to the CRK10 promoter. These experiments demonstrate a requirement for CRKs in NH1-mediated immunity and establish a molecular link between NH1 and induction of CRK10 expression.

Physiological and molecular alterations promoted by Schizotetranychus oryzae mite infestation in rice leaves

PubMed Central

Buffon, Giseli; Blasi, Édina A. R.; Adamski, Janete M.; Ferla, Noeli J.; Berger, Markus; Santi, Lucélia; Lavallée-Adam, Mathieu; Yates, John R.; Beys-da-Silva, Walter O.; Sperotto, Raul A.

2016-01-01

Infestation of phytophagous mite Schizotetranychus oryzae in rice causes critical yield losses. To better understand this interaction, we employed Multidimensional Protein Identification Technology (MudPIT) approach to identify differentially expressed proteins. We detected 18 unique proteins in control and 872 in infested leaves, respectively, along with 32 proteins more abundant in control leaves. S. oryzae infestation caused decreased abundance of proteins related to photosynthesis (mostly photosystem II-related), carbon assimilation and energy production, chloroplast detoxification, defense, fatty acid and gibberellin synthesis. On the other hand, infestation caused increased abundance of proteins involved in protein modification and degradation, gene expression at the translation level, protein partitioning to different organelles, lipid metabolism, actin cytoskeleton remodeling, and synthesis of jasmonate, amino acid and molecular chaperones. Our results also suggest that S. oryzae infestation promotes cell wall remodeling and interferes with ethylene biosynthesis in rice leaves. Proteomic data were positively correlated with enzymatic assays and RT-qPCR analysis. Our findings describe the protein expression patterns of infested rice leaves, and suggest that the acceptor side of PSII is probably the major damaged target in the photosynthetic apparatus. These data will be useful in future biotechnological approaches aiming to induce phytophagous mite resistance in rice. PMID:26667653

Genetic Control of Seed Shattering in Rice by the APETALA2 Transcription Factor SHATTERING ABORTION1[C][W][OA

PubMed Central

Zhou, Yan; Lu, Danfeng; Li, Canyang; Luo, Jianghong; Zhu, Bo-Feng; Zhu, Jingjie; Shangguan, Yingying; Wang, Zixuan; Sang, Tao; Zhou, Bo; Han, Bin

2012-01-01

Seed shattering is an important agricultural trait in crop domestication. SH4 (for grain shattering quantitative trait locus on chromosome 4) and qSH1 (for quantitative trait locus of seed shattering on chromosome 1) genes have been identified as required for reduced seed shattering during rice (Oryza sativa) domestication. However, the regulatory pathways of seed shattering in rice remain unknown. Here, we identified a seed shattering abortion1 (shat1) mutant in a wild rice introgression line. The SHAT1 gene, which encodes an APETALA2 transcription factor, is required for seed shattering through specifying abscission zone (AZ) development in rice. Genetic analyses revealed that the expression of SHAT1 in AZ was positively regulated by the trihelix transcription factor SH4. We also identified a frameshift mutant of SH4 that completely eliminated AZs and showed nonshattering. Our results suggest a genetic model in which the persistent and concentrated expression of active SHAT1 and SH4 in the AZ during early spikelet developmental stages is required for conferring AZ identification. qSH1 functioned downstream of SHAT1 and SH4, through maintaining SHAT1 and SH4 expression in AZ, thus promoting AZ differentiation. PMID:22408071

Mapping the N-linked glycosites of rice (Oryza sativa L.) germinating embryos.

PubMed

Ying, Jiezheng; Zhao, Juan; Hou, Yuxuan; Wang, Yifeng; Qiu, Jiehua; Li, Zhiyong; Tong, Xiaohong; Shi, Zhaomei; Zhu, Jun; Zhang, Jian

2017-01-01

Germination is a key event in the angiosperm life cycle. N-glycosylation of proteins is one of the most common post-translational modifications, and has been recognized to be an important regulator of the proteome of the germinating embryo. Here, we report the first N-linked glycosites mapping of rice embryos during germination by using a hydrophilic interaction chromatography (HILIC) glycopeptides enrichment strategy associated with high accuracy mass spectrometry identification. A total of 242 glycosites from 191 unique proteins was discovered. Inspection of the motifs and sequence structures involved suggested that all the glycosites were concentrated within [NxS/T] motif, while 82.3% of them were in a coil structure. N-glycosylation preferentially occurred on proteins with glycoside hydrolase activities, which were significantly enriched in the starch and sucrose metabolism pathway, suggesting that N-glycosylation is involved in embryo germination by regulating carbohydrate metabolism. Notably, protein-protein interaction analysis revealed a network with several Brassinosteroids signaling proteins, including XIAO and other BR-responsive proteins, implying that glycosylation-mediated Brassinosteroids signaling may be a key mechanism regulating rice embryo germination. In summary, this study expanded our knowledge of protein glycosylation in rice, and provided novel insight into the PTM regulation in rice seed germination.

Mapping the N-linked glycosites of rice (Oryza sativa L.) germinating embryos

PubMed Central

Hou, Yuxuan; Wang, Yifeng; Qiu, Jiehua; Li, Zhiyong; Tong, Xiaohong; Shi, Zhaomei; Zhu, Jun

2017-01-01

Germination is a key event in the angiosperm life cycle. N-glycosylation of proteins is one of the most common post-translational modifications, and has been recognized to be an important regulator of the proteome of the germinating embryo. Here, we report the first N-linked glycosites mapping of rice embryos during germination by using a hydrophilic interaction chromatography (HILIC) glycopeptides enrichment strategy associated with high accuracy mass spectrometry identification. A total of 242 glycosites from 191 unique proteins was discovered. Inspection of the motifs and sequence structures involved suggested that all the glycosites were concentrated within [NxS/T] motif, while 82.3% of them were in a coil structure. N-glycosylation preferentially occurred on proteins with glycoside hydrolase activities, which were significantly enriched in the starch and sucrose metabolism pathway, suggesting that N-glycosylation is involved in embryo germination by regulating carbohydrate metabolism. Notably, protein-protein interaction analysis revealed a network with several Brassinosteroids signaling proteins, including XIAO and other BR-responsive proteins, implying that glycosylation-mediated Brassinosteroids signaling may be a key mechanism regulating rice embryo germination. In summary, this study expanded our knowledge of protein glycosylation in rice, and provided novel insight into the PTM regulation in rice seed germination. PMID:28328971

Effect of chicken, fat and vegetable on glycaemia and insulinaemia to a white rice-based meal in healthy adults.

PubMed

Sun, Lijuan; Ranawana, Dinesh Viren; Leow, Melvin Khee-Shing; Henry, Christiani Jeyakumar

2014-12-01

White rice is the main staple for the majority in the world. The effects of protein, fat and vegetables on the glycaemic and insulinaemic responses to a white rice-based meal have not been reported. The aim of this study was to determine the effect of co-ingesting a high-protein food (breast chicken), a fat (ground nut oil), a leafy vegetable or all three on the glycaemic and insulinaemic responses of white rice in healthy adults. This was a randomized crossover trial conducted at the Clinical Nutrition Research Centre in Singapore. Twelve healthy volunteers were given five test meals (white rice alone, white rice with chicken, white rice with oil, white rice with vegetable and white rice with chicken, oil and vegetable) once and the reference food (glucose solution) three times in a random order at 1-week intervals. Capillary blood samples were then drawn serially for 3 h, and glucose and insulin were analysed. The glycaemic response (GR) to white rice with chicken breast, ground nut oil and vegetable was significantly lower than to white rice alone. The glycaemic index (GI) of pure white rice was 96, whereas combined with chicken breast, ground nut oil and vegetable, it was 50. The addition of oil delayed the peak glucose response and reduced the iAUC, resulting in a GI value of 67. The addition of chicken and vegetable resulted in a GI value of 73 and 82, respectively. The insulinaemic index (II) of the white rice-based meals varied between 54 and 89. Chicken breast in the meal increased the insulinaemic response and decreased the GR. White rice II was lower than the glucose control, which indicated that the former was not as insulinogenic as the latter. White rice with vegetable had the lowest II. Co-ingesting chicken, oil or vegetable with white rice considerably influences its glycaemic and insulinaemic responses. Co-ingesting white rice with all three components attenuates the GR to a greater degree than when it is eaten with any single one of them, and that this is not at the cost of an increased demand for insulin.

Genetic evaluation of recombinant inbred lines of rice (Oryza sativa L.) for grain zinc concentrations, yield related traits and identification of associated SSR markers.

PubMed

Bekele, Berhanu D; Naveen, G K; Rakhi, S; Shashidhar, H E

2013-12-01

The objectives of the present study were to evaluate genetic variability parameters, correlations that exist for grain Zn concentration and yield related traits and identification of SSR markers linked to these traits in rice. One hundred seventy six Recombinant Inbred Lines (RILs) of Azucena X Moromutant were grown at University of Agricultural Sciences, Bangalore in augmented experimental design during wet seasons of 2010 and 2011. The study revealed significant genetic variability for all the traits. Grain yield per plant and grain zinc concentration showed higher phenotypic and genotypic co-efficient of variation. Significant positive correlation was observed for grain yield per plant with number of productive tillers per plant (r = 0.5) and number of tillers per plant (r = 0.4). Grain zinc concentration showed negative correlation with grain yield per plant (r = - 0.27). The path-coefficient analysis indicated the positive direct effect of number of productive tillers per plant on grain yield per plant (0.514). Grain zinc concentration showed negative direct effect on grain yield per plant (-0.186). Single-marker analysis using 26 SSR markers on RILs mapping population showed that RM212, RM263, RM6832, RM152, RM21, RM234 and RM3331 had association with grain zinc concentration and other yield related traits. But validation of these markers on fifty two rice genotypes showed that only three markers RM263, RM152 and RM21 had association with grain zinc concentration. Therefore, the genetic information generated and molecular markers identified from this study could be used for zinc biofortification programmes in rice.

Arsenic hazard in Cambodian rice from a market-based survey with a case study of Preak Russey village, Kandal Province.

PubMed

Gilbert, Peter J; Polya, David A; Cooke, David A

2015-08-01

This study comprises a market-based survey to assess the arsenic (As) hazard of Cambodian rice, encompassing rice from seven Cambodian provinces, comparisons with rice imported from China, Vietnam and Thailand, and assessments of 15 rice varieties. Rice samples (n = 157) were collected from four large markets in Kandal Province and analysed for As using inductively coupled mass spectrometry. The mean As concentration for Cambodian rice (0.185 µg g(-1), range 0.047-0.771 µg g(-1)) was higher than that for imported rice from Vietnam and Thailand (0.162 and 0.157 µg g(-1), respectively) with mean As concentrations highest in rice from Prey Veng Province resulting in a daily dose of 1.77 µg kg(-1) b.w. (body weight) d(-1). Between unmilled rice varieties, Cambodian-grown White Sticky Rice had the highest mean As concentration (0.234 µg g(-1)), whilst White Sticky Rice produced in Thailand had the lowest (0.125 µg g(-1)), suggesting that localised conditions have greater bearing over rice As concentrations than differences in As uptake between individual varieties themselves. A rice and water consumption survey for 15 respondents in the village of Preak Russey revealed mean consumption rates of 522 g d(-1) of rice and 1.9 L d(-1) of water. At water As concentrations >1000 µg L(-1), the relative contribution to the daily dose from rice is low. When water As concentrations are lowered to 50 µg L(-1), daily doses from rice and water are both generally below the 3.0 µg kg(-1) b.w. d(-1) benchmark daily limit for a 0.5% increase in lung cancer, yet when combined they exceeded this value in all but three respondents.

Identification of gonadal soma-derived factor involvement in Monopterus albus (protogynous rice field eel) sex change.

PubMed

Zhu, Yefei; Wang, Chunlei; Chen, Xiaowu; Guan, Guijun

2016-07-01

We studied molecular events and potential mechanisms underlying the process of female-to-male sex transformation in the rice field eel (Monopterus albus), a protogynous hermaphrodite fish in which the gonad is initially a female ovary and transforms into male testes. We cloned and identified a novel gonadal soma derived factor (GSDF), which encodes a member of the transforming growth factor-beta superfamily. gsdf expression was measured in gonads of female, intersex and male with reverse transcription-PCR and gsdf's role in sex transformation was studied with qPCR, histological analysis and dual-color in situ hybridization assays and compared to other sex-related genes. gsdf was correlated to Sertoli cell differentiation, indicating involvement in testicular differentiation and sex transformation from female to male in this species. A unique expression pattern reveals a potential role of gsdf essential for the sex transformation of rice field eels.

Changes of paddy rice planting areas in Northeastern Asia from 1986 to 2014 based on Landsat data

NASA Astrophysics Data System (ADS)

Dong, J.; Xiao, X.; Kou, W.; Qin, Y.; Wang, J.; Zhang, G.; Jin, C.; Zhou, Y.; Menarguez, M. A.; Moore, B., III

2014-12-01

Paddy rice is an important cereal crop and main grain source for more than half of the global human population. However, knowledge about its area and spatial pattern is still limited due to large changes in agriculture in different regions; for example, higher latitude areas underwent increase (e.g., northeastern China) and decrease (e.g., South Korea) of paddy rice planting areas due to climatic warming, urbanization and other drivers. It is necessary to track paddy rice planting area changes in these regions in the past decades. We developed a pixel- and phenology-based image analysis system, Landsat-RICE, to map the paddy rice by using Landsat imagery. The algorithm was based on the unique physical and spectral characteristics of paddy rice fields during the flooding and transplanting phases. First, Landsat images are preprocessed and time series vegetation indices (NDVI, EVI, and LSWI) are generated. Second, MODIS Land Surface Temperature (LST) data were used to define thermal plant growing season (0 oC, 5 oC and 10 oC), which provides a guide for selection of Landsat images within the period of flooding and transplanting. Third, several non-cropland land cover maps (e.g., permanent water bodies, built-up and barren lands, sparsely vegetated lands, and evergreen vegetation) are produced through analysis of Landsat-based vegetation indices within the plant growing season and combined as a mask. Fourthly, vegetation index data within the time window of flooded and rice transplanting were analyzed to identify flood/transplanting signals. Finally, the maps of paddy rice planting areas were generated through overlying the results from Step 3 and 4. Paddy rice planting area changes were investigated in some hotspots of Northeastern Asia from 1986 to 2014 at 30-m spatial resolution and 5-year interval. This study has demonstrated that our newly developed Landsat-Rice system is robust and effective for tracking paddy rice changes in cold temperate and temperate zones.

Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining

PubMed Central

2014-01-01

Background Apparent Amylose Content (AAC), regulated by the Waxy gene, represents the key determinant of rice cooking properties. In occidental countries high AAC rice represents the most requested market class but the availability of molecular markers allowing specific selection of high AAC varieties is limited. Results In this study, the effectiveness of available molecular markers in predicting AAC was evaluated in a collection of 127 rice accessions (125 japonica ssp. and 2 indica ssp.) characterized by AAC values from glutinous to 26%. The analyses highlighted the presence of several different allelic patterns identifiable by a few molecular markers, and two of them, i.e., the SNPs at intron1 and exon 6, were able to explain a maximum of 79.5% of AAC variation. However, the available molecular markers haplotypes did not provide tools for predicting accessions with AAC higher than 24.5%. To identify additional polymorphisms, the re-sequencing of the Waxy gene and 1kbp of the putative upstream regulatory region was performed in 21 genotypes representing all the AAC classes identified. Several previously un-characterized SNPs were identified and four of them were used to develop dCAPS markers. Conclusions The addition of the SNPs newly identified slightly increased the AAC explained variation and allowed the identification of a haplotype almost unequivocally associated to AAC higher than 24.5%. Haplotypes at the waxy locus were also associated to grain length and length/width (L/W) ratio. In particular, the SNP at the first intron, which identifies the Wx a and Wx b alleles, was associated with differences in the width of the grain, the L/W ratio and the length of the kernel, most likely as a result of human selection. PMID:24383761

Root transcriptomes of two acidic soil adapted Indica rice genotypes suggest diverse and complex mechanism of low phosphorus tolerance.

PubMed

Tyagi, Wricha; Rai, Mayank

2017-03-01

Low phosphorus (P) tolerance in rice is a biologically and agronomically important character. Low P tolerant Indica-type rice genotypes, Sahbhagi Dhan (SD) and Chakhao Poreiton (CP), are adapted to acidic soils and show variable response to low P levels. Using RNAseq approach, transcriptome data was generated from roots of SD and CP after 15 days of low P treatment to understand differences and similarities at molecular level. In response to low P, number of genes up-regulated (1318) was more when compared with down-regulated genes (761). Eight hundred twenty-one genes found to be significantly regulated between SD and CP in response to low P. De novo assembly using plant database led to further identification of 1535 novel transcripts. Functional annotation of significantly expressed genes suggests two distinct methods of low P tolerance. While root system architecture in SD works through serine-threonine kinase PSTOL1, suberin-mediated cell wall modification seems to be key in CP. The transcription data indicated that CP relies more on releasing its internally bound Pi and coping with low P levels by transcriptional and translational modifications and using dehydration response-based signals. Role of P transporters seems to be vital in response to low P in CP while sugar- and auxin-mediated pathway seems to be preferred in SD. At least six small RNA clusters overlap with transcripts highly expressed under low P, suggesting role of RNA super clusters in nutrient response in plants. These results help us to understand and thereby devise better strategy to enhance low P tolerance in Indica-type rice.

Functional proteomic analysis revealed ground-base ion radiations cannot reflect biological effects of space radiations of rice

NASA Astrophysics Data System (ADS)

Wang, Wei; Sun, Yeqing; Zhao, Qian; Han, Lu

2016-07-01

Highly ionizing radiation (HZE) in space is considered as main factor causing biological effects. Radiobiological studies during space flights are unrepeatable due to the variable space radiation environment, ground-base ion radiations are usually performed to simulate of the space biological effect. Spaceflights present a low-dose rate (0.1˜~0.3mGy/day) radiation environment inside aerocrafts while ground-base ion radiations present a much higher dose rate (100˜~500mGy/min). Whether ground-base ion radiation can reflect effects of space radiation is worth of evaluation. In this research, we compared the functional proteomic profiles of rice plants between on-ground simulated HZE particle radiation and spaceflight treatments. Three independent ground-base seed ionizing radiation experiments with different cumulative doses (dose range: 2˜~20000mGy) and different liner energy transfer (LET) values (13.3˜~500keV/μμm) and two independent seed spaceflight experiments onboard Chinese 20th satellite and SZ-6 spacecraft were carried out. Alterations in the proteome were analyzed by two-dimensional difference gel electrophoresis (2-D DIGE) with MALDI-TOF/TOF mass spectrometry identifications. 45 and 59 proteins showed significant (p<0.05) and reproducible quantitative differences in ground-base ion radiation and spaceflight experiments respectively. The functions of ground-base radiation and spaceflight proteins were both involved in a wide range of biological processes. Gene Ontology enrichment analysis further revealed that ground-base radiation responsive proteins were mainly involved in removal of superoxide radicals, defense response to stimulus and photosynthesis, while spaceflight responsive proteins mainly participate in nucleoside metabolic process, protein folding and phosphorylation. The results implied that ground-base radiations cannot truly reflect effects of spaceflight radiations, ground-base radiation was a kind of indirect effect to rice causing oxidation and metabolism stresses, but space radiation was a kind of direct effect leading to macromolecule (DNA and protein) damage and signal pathway disorders. This functional proteomic analysis work might provide a new evaluation method for further on-ground simulated HZE radiation experiments.

Genome-wide analysis of DUF221 domain-containing gene family in Oryza species and identification of its salinity stress-responsive members in rice.

PubMed

Ganie, Showkat Ahmad; Pani, Dipti Ranjan; Mondal, Tapan Kumar

2017-01-01

DUF221 domain-containing genes (DDP genes) play important roles in developmental biology, hormone signalling transduction, and responses to abiotic stress. Therefore to understand their structural and evolutionary relationship, we did a genome-wide analysis of this important gene family in rice. Further, through comparative genomics, DDP genes from Oryza sativa subsp. (indica), nine different wild species of rice and Arabidopsis were also identified. We also found an expansion of the DDP gene families in rice and Arabidopsis which is due to the segmental duplication events in some of the gene family members. In general, a highly purifying selection was found acting on all the deduced paralogous and orthologous DDP gene pairs. The data from microarray and subsequent qRT-PCR analysis revealed that although several OsDDPs were differentially regulated under salinity stress, yet OsDDP6 was upregulated at all the developmental stages in salt tolerant rice genotype, FL478. Interestingly, OsDDP6 was found to be involved in proline metabolism pathway as indicated by protein network analysis. The diverse gene structures, varied transmembrane topologies and the differential expression patterns implied the functional diversity in DDP genes. Therefore, the comprehensive evolutionary analysis of DDP genes from different Oryza species and Arabidopsis performed in this study will provide the basis for further functional validation studies vis-à-vis DDP genes of rice and other plant species.

Identification of QTLs for resistant starch and total alkaloid content in brown and polished rice.

PubMed

Zeng, Y W; Sun, D; Du, J; Pu, X Y; Yang, S M; Yang, X M; Yang, T; Yang, J Z

2016-07-29

An F3 population consisting of 117 F2:3 families derived from a cross between two varieties of rice, Gongmi No. 3 and Diantun 502, with a large difference in their resistant starch and total alkaloid content, was used for quantitative trait locus (QTL) mapping. Two QTLs of resistant starch for rice (qRS7-1, qRS7-2) were identified in a linkage group on chromosome 7, which could explain phenotypic variance from 7.6 to 17.3%, due to additive effects for resistant starch from Gongmi No. 3 or over-dominance effects for qRS7-2 of the marker interval (RM3404-RM478) on chromosome 7 from Gongmi No. 3, accounting for 13.8-17.3% of the phenotypic variance. Two QTLs of total alkaloids for brown rice (qALb7-1, qALb7-2) were identified in the same linkage group, which could explain phenotypic variance from 7.7 and 19.3%, respectively, due to dominance or over-dominance effects for total alkaloids on chromosome 7 from Diantun 502. To our knowledge, these are the first QTLs to be identified, which are related to resistant starch and total alkaloid content in rice. These results are beneficial for understanding the genetic basis of, as well as for developing markers linked with, resistant starch and total alkaloids of functional components for marker-assisted selection breeding in rice.

Genome-wide analysis of DUF221 domain-containing gene family in Oryza species and identification of its salinity stress-responsive members in rice

PubMed Central

Ganie, Showkat Ahmad; Pani, Dipti Ranjan

2017-01-01

DUF221 domain-containing genes (DDP genes) play important roles in developmental biology, hormone signalling transduction, and responses to abiotic stress. Therefore to understand their structural and evolutionary relationship, we did a genome-wide analysis of this important gene family in rice. Further, through comparative genomics, DDP genes from Oryza sativa subsp. (indica), nine different wild species of rice and Arabidopsis were also identified. We also found an expansion of the DDP gene families in rice and Arabidopsis which is due to the segmental duplication events in some of the gene family members. In general, a highly purifying selection was found acting on all the deduced paralogous and orthologous DDP gene pairs. The data from microarray and subsequent qRT-PCR analysis revealed that although several OsDDPs were differentially regulated under salinity stress, yet OsDDP6 was upregulated at all the developmental stages in salt tolerant rice genotype, FL478. Interestingly, OsDDP6 was found to be involved in proline metabolism pathway as indicated by protein network analysis. The diverse gene structures, varied transmembrane topologies and the differential expression patterns implied the functional diversity in DDP genes. Therefore, the comprehensive evolutionary analysis of DDP genes from different Oryza species and Arabidopsis performed in this study will provide the basis for further functional validation studies vis-à-vis DDP genes of rice and other plant species. PMID:28846681

Proteome Profile of Starch Granules Purified from Rice (Oryza sativa) Endosperm.

PubMed

Xing, Shihai; Meng, Xiaoxi; Zhou, Lihui; Mujahid, Hana; Zhao, Chunfang; Zhang, Yadong; Wang, Cailin; Peng, Zhaohua

2016-01-01

Starch is the most important food energy source in cereals. Many of the known enzymes involved in starch biosynthesis are partially or entirely granule-associated in the endosperm. Studying the proteome of rice starch granules is critical for us to further understand the mechanisms underlying starch biosynthesis and packaging of starch granules in rice amyloplasts, consequently for the improvement of rice grain quality. In this article, we developed a protocol to purify starch granules from mature rice endosperm and verified the quality of purified starch granules by microscopy observations, I2 staining, and Western blot analyses. In addition, we found the phenol extraction method was superior to Tris-HCl buffer extraction method with respect to the efficiency in recovery of starch granule associated proteins. LC-MS/MS analysis showed identification of already known starch granule associated proteins with high confidence. Several proteins reported to be involved in starch synthesis in prior genetic studies in plants were also shown to be enriched with starch granules, either directly or indirectly, in our studies. In addition, our results suggested that a few additional candidate proteins may also be involved in starch synthesis. Furthermore, our results indicated that some starch synthesis pathway proteins are subject to protein acetylation modification. GO analysis and KEGG pathway enrichment analysis showed that the identified proteins were mainly located in plastids and involved in carbohydrate metabolism. This study substantially advances the understanding of the starch granule associated proteome in rice and post translational regulation of some starch granule associated proteins.

Combined Chlorophyll Fluorescence and Transcriptomic Analysis Identifies the P3/P4 Transition as a Key Stage in Rice Leaf Photosynthetic Development1[OPEN

PubMed Central

Yaapar, Muhammad N.; Wanchana, Samart; Thakur, Vivek; Quick, W. Paul

2016-01-01

Leaves are derived from heterotrophic meristem tissue that, at some point, must make the transition to autotrophy via the initiation of photosynthesis. However, the timing and spatial coordination of the molecular and cellular processes underpinning this switch are poorly characterized. Here, we report on the identification of a specific stage in rice (Oryza sativa) leaf development (P3/P4 transition) when photosynthetic competence is first established. Using a combined physiological and molecular approach, we show that elements of stomatal and vascular differentiation are coordinated with the onset of measurable light absorption for photosynthesis. Moreover, by exploring the response of the system to environmental perturbation, we show that the earliest stages of rice leaf development have significant plasticity with respect to elements of cellular differentiation of relevance for mature leaf photosynthetic performance. Finally, by performing an RNA sequencing analysis targeted at the early stages of rice leaf development, we uncover a palette of genes whose expression likely underpins the acquisition of photosynthetic capability. Our results identify the P3/P4 transition as a highly dynamic stage in rice leaf development when several processes for the initiation of photosynthetic competence are coordinated. As well as identifying gene targets for future manipulation of rice leaf structure/function, our data highlight a developmental window during which such manipulations are likely to be most effective. PMID:26813793

Combined Chlorophyll Fluorescence and Transcriptomic Analysis Identifies the P3/P4 Transition as a Key Stage in Rice Leaf Photosynthetic Development.

PubMed

van Campen, Julia C; Yaapar, Muhammad N; Narawatthana, Supatthra; Lehmeier, Christoph; Wanchana, Samart; Thakur, Vivek; Chater, Caspar; Kelly, Steve; Rolfe, Stephen A; Quick, W Paul; Fleming, Andrew J

2016-03-01

Leaves are derived from heterotrophic meristem tissue that, at some point, must make the transition to autotrophy via the initiation of photosynthesis. However, the timing and spatial coordination of the molecular and cellular processes underpinning this switch are poorly characterized. Here, we report on the identification of a specific stage in rice (Oryza sativa) leaf development (P3/P4 transition) when photosynthetic competence is first established. Using a combined physiological and molecular approach, we show that elements of stomatal and vascular differentiation are coordinated with the onset of measurable light absorption for photosynthesis. Moreover, by exploring the response of the system to environmental perturbation, we show that the earliest stages of rice leaf development have significant plasticity with respect to elements of cellular differentiation of relevance for mature leaf photosynthetic performance. Finally, by performing an RNA sequencing analysis targeted at the early stages of rice leaf development, we uncover a palette of genes whose expression likely underpins the acquisition of photosynthetic capability. Our results identify the P3/P4 transition as a highly dynamic stage in rice leaf development when several processes for the initiation of photosynthetic competence are coordinated. As well as identifying gene targets for future manipulation of rice leaf structure/function, our data highlight a developmental window during which such manipulations are likely to be most effective. © 2016 American Society of Plant Biologists. All Rights Reserved.

Comparison of eating quality and physicochemical properties between Japanese and Chinese rice cultivars.

PubMed

Nakamura, Sumiko; Cui, Jing; Zhang, Xin; Yang, Fan; Xu, Ximing; Sheng, Hua; Ohtsubo, Ken'ichi

2016-12-01

In this study, we evaluated 16 Japanese and Chinese rice cultivars in terms of their main chemical components, iodine absorption curve, apparent amylose content (AAC), pasting property, resistant starch content, physical properties, sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis, and enzyme activity. Based on these quality evaluations, we concluded that Chinese rice varieties are characterized by a high protein and the grain texture after cooking has high hardness and low stickiness. In a previous study, we developed a novel formula for estimating AAC based on the iodine absorption curve. The validation test showed a determination coefficient of 0.996 for estimating AAC of Chinese rice cultivars as unknown samples. In the present study, we developed a novel formulae for estimating the balance degree of the surface layer of cooked rice (A3/A1: a ratio of workload of stickiness and hardness) based on the iodine absorption curve obtained using milled rice.

Analysis of black soil environment based on Arduino

NASA Astrophysics Data System (ADS)

Li, Y.; Zhang, Y. F.; Wu, C. H.; Wang, J. F.

2017-05-01

As everyone knows, the black soil of Heilongjiang bred rice is famous in the world. How to use networking technology to detection the growth environment of Heilongjiang rice, and expands it to the local planting environment to our country is the most important topic. However, the growth environment of rice is complex. In current research, some importnat factors such as carbon dioxide, oxygen, temperature and humidity, pH value and microbial content in black soil that affect the growth of plants are selected, and a kind of black land based on data acquisition and transmission system based on the Arduino development environment and the mechanism construction of Kingview has been realized. The collected data was employed to establish the simulation environment for the growth of rice in Heilongjiang. It can be applied to stimulate the rice growing environment of Heilongjiang province, and gives a improvement of rice quality in other areas. Keywords: Arduino; Kingview; living environment

Identification of major genes affecting nutritional element concentrations in rice grains

USDA-ARS?s Scientific Manuscript database

Biofortification is the process by which the nutritional quality of food crops is improved through conventional plant breeding and/or use of biotechnology. Biofortification differs from conventional fortification in that biofortification aims to increase nutrient levels in crops during plant growth...

Genome wide re-sequencing of newly developed Rice Lines from common wild rice (Oryza rufipogon Griff.) for the identification of NBS-LRR genes.

PubMed

Liu, Wen; Ghouri, Fozia; Yu, Hang; Li, Xiang; Yu, Shuhong; Shahid, Muhammad Qasim; Liu, Xiangdong

2017-01-01

Common wild rice (Oryza rufipogon Griff.) is an important germplasm for rice breeding, which contains many resistance genes. Re-sequencing provides an unprecedented opportunity to explore the abundant useful genes at whole genome level. Here, we identified the nucleotide-binding site leucine-rich repeat (NBS-LRR) encoding genes by re-sequencing of two wild rice lines (i.e. Huaye 1 and Huaye 2) that were developed from common wild rice. We obtained 128 to 147 million reads with approximately 32.5-fold coverage depth, and uniquely covered more than 89.6% (> = 1 fold) of reference genomes. Two wild rice lines showed high SNP (single-nucleotide polymorphisms) variation rate in 12 chromosomes against the reference genomes of Nipponbare (japonica cultivar) and 93-11 (indica cultivar). InDels (insertion/deletion polymorphisms) count-length distribution exhibited normal distribution in the two lines, and most of the InDels were ranged from -5 to 5 bp. With reference to the Nipponbare genome sequence, we detected a total of 1,209,308 SNPs, 161,117 InDels and 4,192 SVs (structural variations) in Huaye 1, and 1,387,959 SNPs, 180,226 InDels and 5,305 SVs in Huaye 2. A total of 44.9% and 46.9% genes exhibited sequence variations in two wild rice lines compared to the Nipponbare and 93-11 reference genomes, respectively. Analysis of NBS-LRR mutant candidate genes showed that they were mainly distributed on chromosome 11, and NBS domain was more conserved than LRR domain in both wild rice lines. NBS genes depicted higher levels of genetic diversity in Huaye 1 than that found in Huaye 2. Furthermore, protein-protein interaction analysis showed that NBS genes mostly interacted with the cytochrome C protein (Os05g0420600, Os01g0885000 and BGIOSGA038922), while some NBS genes interacted with heat shock protein, DNA-binding activity, Phosphoinositide 3-kinase and a coiled coil region. We explored abundant NBS-LRR encoding genes in two common wild rice lines through genome wide re-sequencing, which proved to be a useful tool to exploit elite NBS-LRR genes in wild rice. The data here provide a foundation for future work aimed at dissecting the genetic basis of disease resistance in rice, and the two wild rice lines will be useful germplasm for the molecular improvement of cultivated rice.

Genome wide re-sequencing of newly developed Rice Lines from common wild rice (Oryza rufipogon Griff.) for the identification of NBS-LRR genes

PubMed Central

Yu, Hang; Li, Xiang; Yu, Shuhong; Shahid, Muhammad Qasim

2017-01-01

Common wild rice (Oryza rufipogon Griff.) is an important germplasm for rice breeding, which contains many resistance genes. Re-sequencing provides an unprecedented opportunity to explore the abundant useful genes at whole genome level. Here, we identified the nucleotide-binding site leucine-rich repeat (NBS-LRR) encoding genes by re-sequencing of two wild rice lines (i.e. Huaye 1 and Huaye 2) that were developed from common wild rice. We obtained 128 to 147 million reads with approximately 32.5-fold coverage depth, and uniquely covered more than 89.6% (> = 1 fold) of reference genomes. Two wild rice lines showed high SNP (single-nucleotide polymorphisms) variation rate in 12 chromosomes against the reference genomes of Nipponbare (japonica cultivar) and 93–11 (indica cultivar). InDels (insertion/deletion polymorphisms) count-length distribution exhibited normal distribution in the two lines, and most of the InDels were ranged from -5 to 5 bp. With reference to the Nipponbare genome sequence, we detected a total of 1,209,308 SNPs, 161,117 InDels and 4,192 SVs (structural variations) in Huaye 1, and 1,387,959 SNPs, 180,226 InDels and 5,305 SVs in Huaye 2. A total of 44.9% and 46.9% genes exhibited sequence variations in two wild rice lines compared to the Nipponbare and 93–11 reference genomes, respectively. Analysis of NBS-LRR mutant candidate genes showed that they were mainly distributed on chromosome 11, and NBS domain was more conserved than LRR domain in both wild rice lines. NBS genes depicted higher levels of genetic diversity in Huaye 1 than that found in Huaye 2. Furthermore, protein-protein interaction analysis showed that NBS genes mostly interacted with the cytochrome C protein (Os05g0420600, Os01g0885000 and BGIOSGA038922), while some NBS genes interacted with heat shock protein, DNA-binding activity, Phosphoinositide 3-kinase and a coiled coil region. We explored abundant NBS-LRR encoding genes in two common wild rice lines through genome wide re-sequencing, which proved to be a useful tool to exploit elite NBS-LRR genes in wild rice. The data here provide a foundation for future work aimed at dissecting the genetic basis of disease resistance in rice, and the two wild rice lines will be useful germplasm for the molecular improvement of cultivated rice. PMID:28700714

Root distribution and potential interactions between allelopathic rice, sprangletop (Leptochloa spp.), and barnyardgrass (Echinochloa crus-galli) based on 13C isotope discrimination analysis

USDA-ARS?s Scientific Manuscript database

Weed-suppressive rice cultivars hold promise for improved and more economical weed management in rice. Interactions between roots of rice and weeds are thought to be modulated by the weed-suppressive activity of some rice cultivars, but these phenomena are difficult to measure and not well understo...

Bioaccessibility and risk assessment of cadmium from uncooked rice using an in vitro digestion model.

PubMed

Yang, Lin-Sheng; Zhang, Xiu-Wu; Li, Yong-Hua; Li, Hai-Rong; Wang, Ying; Wang, Wu-Yi

2012-01-01

Cadmium (Cd)-contaminated rice is one of the most important sources of cadmium exposure in the general population from some Asian countries. This study was conducted to assess cadmium exposure from uncooked rice in rural mining areas based on the bioaccessible fraction of cadmium using an in vitro digestion model. The biotoxic effects of cadmium in uncooked rice from mining areas were much higher than those in the control area, based not only on their higher total concentration (52.49 vs. 7.93 μg kg(-1)), but also on their higher bioaccessibility (16.94% vs. 2.38%). In the mining areas, the bioaccessible fraction of cadmium in uncooked rice has a significant positive correlation with the total concentration of cadmium in rice and there was quarterly unsafe rice to the public in the mining areas. The results indicated that the in vitro digestion model could be a useful and economical tool for providing the solubilization or bioaccessibility of uncooked rice in the mining area. The results could be helpful in conducting future experiments of cooked rice in the vitro model.

Dietary rice protein isolate attenuates atherosclerosis in apoE-deficient mice by upregulating antioxidant enzymes

USDA-ARS?s Scientific Manuscript database

Rice-based diets may have been reported to protect against the development of atherosclerosis; however, the underlying mechanism(s) for this protection remains unknown. In this report, the mechanism(s) contributing to the atheroprotective effects of rice-based diet was addressed using the apolipopro...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taha, Mohd F., E-mail: faisalt@petronas.com.my; Shaharun, Maizatul S.; Shuib, Anis Suhaila, E-mail: anisuha@petronas.com.my

An attempt was made to investigate the potential of rice husk-based activated carbon as an alternative low-cost adsorbent for the removal of Ni(II), Zn(II) and Pb(II) ions from single aqueous solution. Rice husk-based activated carbon was prepared via treatment of rice husk with NaOH followed by the carbonization process at 400°C for 2 hours. Three samples, i.e. raw rice husk, rice husk treated with NaOH and rice husk-based activated carbon, were analyzed for their morphological characteristics using field-emission scanning electron microscope/energy dispersive X-ray (FESEM/EDX). These samples were also analyzed for their carbon, hydrogen, nitrogen, oxygen and silica contents using CHNmore » elemental analyzer and FESEM/EDX. The porous properties of rice husk-based activated carbon were determined by Brunauer-Emmett-Teller (BET) surface area analyzer, and its surface area and pore volume were 255 m{sup 2}/g and 0.17 cm{sup 2}/g, respectively. The adsorption studies for the removal of Ni(II), Zn(II) and Pb(II) ions from single metal aqueous solution were carried out at a fixed initial concentration of metal ion (150 ppm) with variation amount of adsorbent (rice husk-based activated carbon) as a function of varied contact time at room temperature. The concentration of each metal ion was analyzed using atomic absorption spectrophotometer (AAS). The results obtained from adsorption studies indicate the potential of rice husk as an economically promising precursor for the preparation of activated carbon for removal of Ni(II), Zn(II) and Pb(II) ions from single aqueous solution. Isotherm and kinetic model analyses suggested that the experimental data of adsorption studies fitted well with Langmuir, Freundlich and second-order kinetic models.« less

Digestibility of carbohydrates from rice-, oat- and wheat-based ready-to-eat breakfast cereals in children.

PubMed

Brighenti, F; Casiraghi, M C; Ciappellano, S; Crovetti, R; Testolin, G

1994-09-01

To study the effect of the presence and quality of dietary fibre in ready-to-eat (RTE) breakfast cereals on completeness of carbohydrate digestion in children and on starch susceptibility to alpha-amylase in vitro. A controlled intervention study. Eight 3-8-year-old healthy children. Completeness of digestion was evaluated by assessing the amount of carbohydrates apparently fermented into the colon using the breath-H2 technique after consumption in random order, of five breakfast tests containing boiled rice (either alone or supplemented with 3 g of lactulose) as reference food, or RTE cereals based on rice (low-fibre), wheat (high insoluble fibre) and oats (high-soluble fibre). The potential glycaemic impact of the products was estimated in vitro by assessing starch susceptibility to alpha-amylolysis using an enzymatic-dialysis method. Compared to boiled rice and to rice-based RTE cereal, wheat- and oat-based RTE cereals both significantly (P < 0.05) increased the amount of apparently fermented carbohydrates (+1.1 +/- 1.7% of total breakfast carbohydrate fermented for rice, +5.6 +/- 0.9% for wheat and +9.4 +/- 3.7% for oats; mean +/- SEM), calculated using the excess H2 in breath after lactulose as standard. All products showed similar in vitro digestibility, resulting in estimated glycaemic indexes of 117.5 (24.0) for rice, and 105.7 (14.1) for oats-based, 128.4 (17.6) for wheat-based, and 129.8 (16.6) [mean 95% CI)] for rice-based RTE cereals. Results suggest that the presence of fibre in RTE breakfast cereals, in particular soluble fibre, increases colonic fermentation in children whereas it seems not to affect glucose availability.

Cloud-based application for rice moisture content measurement using image processing technique and perceptron neural network

NASA Astrophysics Data System (ADS)

Cruz, Febus Reidj G.; Padilla, Dionis A.; Hortinela, Carlos C.; Bucog, Krissel C.; Sarto, Mildred C.; Sia, Nirlu Sebastian A.; Chung, Wen-Yaw

2017-02-01

This study is about the determination of moisture content of milled rice using image processing technique and perceptron neural network algorithm. The algorithm involves several inputs that produces an output which is the moisture content of the milled rice. Several types of milled rice are used in this study, namely: Jasmine, Kokuyu, 5-Star, Ifugao, Malagkit, and NFA rice. The captured images are processed using MATLAB R2013a software. There is a USB dongle connected to the router which provided internet connection for online web access. The GizDuino IOT-644 is used for handling the temperature and humidity sensor, and for sending and receiving of data from computer to the cloud storage. The result is compared to the actual moisture content range using a moisture tester for milled rice. Based on results, this study provided accurate data in determining the moisture content of the milled rice.

The PDI genes of wheat and their syntenic relationship to the esp2 locus of rice.

PubMed

Johnson, Joshua C; Appels, Rudi; Bhave, Mrinal

2006-04-01

The storage protein polymers in the endosperm, stabilised by disulphide bonds, determine a number of processing qualities of wheat dough. The enzyme protein disulphide isomerase (PDI), involved in the formation of disulphide bonds, is strongly suggested to play a role in the formation of wheat storage protein bodies. Reports of the rice mutant esp2 exhibiting aberrant storage protein deposition in conjunction with a lack of PDI expression provided strong indications of a direct role for PDI in storage protein deposition. The potential significance of wheat PDI prompted the present studies into exploring any orthology between wheat PDI genes and rice PDI and esp2 loci. By designing allele-specific (AS)-polymerase chain reaction (PCR) markers, two of the three wheat PDI genes could be genetically mapped to group 4 chromosomes and showed close association with GERMIN genes. Physical mapping led to localisation of wheat PDI genes to chromosomal "bins" on the proximal section of chromosome 4AL and distal sections of 4BS and 4DS. Identification of the putative PDI gene of rice and its comparison to the esp2 locus revealed that they were present at similar positions on the short arm of chromosome 11. Analysis of a large section of the PDI-containing section of rice chromosome 11S revealed a number of putative orthologues from The Institute for Genomic Research Triticum aestivum Gene Index database, of which five had been mapped, each localising to group 4 chromosomes, many in good agreement with our mapping results. The results strongly suggest a close linkage between the esp2 marker and the PDI gene of rice and an orthology between the PDI loci of rice and wheat and predict quantitative-trait loci involved in storage protein deposition at the PDI loci.

Identification and evaluation of ω-3 fatty acid desaturase genes for hyperfortifying α-linolenic acid in transgenic rice seed.

PubMed

Liu, Hua Liang; Yin, Zhi Jie; Xiao, Li; Xu, Yi Nong; Qu, Le Qing

2012-05-01

α-Linolenic acid (ALA) deficiency and a skewed of ω6:ω3 fatty acid ratio in the diet are a major explanation for the prevalence of cardiovascular diseases and inflammatory/autoimmune diseases. There is a need to enhance the ALA content and to reduce the ratio of linoleic acid (LA) to ALA. Six ω-3 (Δ-15) fatty acid desaturase (FAD) genes were cloned from rice and soybean. The subcellular localizations of the proteins were identified. The FAD genes were introduced into rice under the control of an endosperm-specific promoter, GluC, or a Ubi-1 promoter to evaluate their potential in increasing the ALA content in seeds. The ALA contents in the seeds of endoplasmic reticulum (ER)-localized GmFAD3-1 and OsFAD3 overexpression lines increased from 0.36 mg g⁻¹ to 8.57 mg g⁻¹ and 10.06 mg g⁻¹, respectively, which was 23.8- and 27.9-fold higher than that of non-transformants. The trait of high ALA content was stably inheritable over three generations. Homologous OsFAD3 is more active than GmFAD3-1 in catalysing LA conversion to ALA in rice seeds. Overexpression of ER-localized GmFAD3-2/3 and chloroplast-localized OsFAD7/8 had less effect on increasing the ALA content in rice seeds. The GluC promoter is advantageous compared with Ubi-1 in this experimental system. The enhanced ALA was preferentially located at the sn-2 position in triacylglycerols. A meal-size portion of high ALA rice would meet >80% of the daily adult ALA requirement. The ALA-rich rice could be expected to ameliorate much of the global dietary ALA deficiency.

Breeding high-yielding drought-tolerant rice: genetic variations and conventional and molecular approaches

PubMed Central

Kumar, Arvind; Dixit, Shalabh; Ram, T.; Yadaw, R. B.; Mishra, K. K.; Mandal, N. P.

2014-01-01

The increased occurrence and severity of drought stress have led to a high yield decline in rice in recent years in drought-affected areas. Drought research at the International Rice Research Institute (IRRI) over the past decade has concentrated on direct selection for grain yield under drought. This approach has led to the successful development and release of 17 high-yielding drought-tolerant rice varieties in South Asia, Southeast Asia, and Africa. In addition to this, 14 quantitative trait loci (QTLs) showing a large effect against high-yielding drought-susceptible popular varieties were identified using grain yield as a selection criterion. Six of these (qDTY 1.1, qDTY 2.2, qDTY 3.1, qDTY 3.2, qDTY 6.1, and qDTY 12.1) showed an effect against two or more high-yielding genetic backgrounds in both the lowland and upland ecosystem, indicating their usefulness in increasing the grain yield of rice under drought. The yield of popular rice varieties IR64 and Vandana has been successfully improved through a well-planned marker-assisted backcross breeding approach, and QTL introgression in several other popular varieties is in progress. The identification of large-effect QTLs for grain yield under drought and the higher yield increase under drought obtained through the use of these QTLs (which has not been reported in other cereals) indicate that rice, because of its continuous cultivation in two diverse ecosystems (upland, drought tolerant, and lowland, drought susceptible), has benefited from the existence of larger genetic variability than in other cereals. This can be successfully exploited using marker-assisted breeding. PMID:25205576

Apple miRNAs and tasiRNAs with novel regulatory networks

USDA-ARS?s Scientific Manuscript database

MiRNAs, negatively affecting gene expression at the post-transcriptional levels, have been shown to control numerous genes involved in various biological and metabolic processes. To date, the identification of miRNAs in plants focused on certain model plants, such as Arabidopsis and rice. Investig...

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

PubMed Central

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

2013-01-01

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). PMID:24147765

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

PubMed

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.

Prevalence and magnitude of acidosis sequelae to rice-based feeding regimen followed in Tamil Nadu, India.

PubMed

Murugeswari, Rathinam; Valli, Chinnamani; Karunakaran, Raman; Leela, Venkatasubramanian; Pandian, Amaresan Serma Saravana

2018-04-01

In Tamil Nadu, a southern state of India, rice is readily available at a low cost, hence, is cooked (cooking akin to human consumption) and fed irrationally to cross-bred dairy cattle with poor productivity. Hence, a study was carried out with the objective to examine the prevalence of acidosis sequelae to rice-based feeding regimen and assess its magnitude. A survey was conducted in all the 32 districts of Tamil Nadu, by randomly selecting two blocks per districts and from each block five villages were randomly selected. From each of the selected village, 10 dairy farmers belonging to the unorganized sector, owning one or two cross-bred dairy cows in early and mid-lactation were randomly selected so that a sample size of 100 farmers per district was maintained. The feeding regimen, milk yield was recorded, and occurrence of acidosis and incidence of laminitis were ascertained by the veterinarian with the confirmative test to determine the impact of feeding cooked rice to cows. It is observed that 71.5% of farmers in unorganized sector feed cooked rice to their cattle. The incidence of acidosis progressively increased significantly (p<0.05) from 29.00% in cows fed with 0.5 kg of cooked rice to 69.23% in cows fed with more than 2.5 kg of cooked rice. However, the incidence of acidosis remained significantly (p<0.05) as low as 9.9% in cows fed feeding regimen without cooked rice which is suggestive of a correlation between excessive feeding cooked rice and onset of acidosis. Further, the noticeable difference in the incidence of acidosis observed between feeding cooked rice and those fed without rice and limited intake of oil cake indicates that there is a mismatch between energy and protein supply to these cattle. Among cooked rice-based diet, the incidence of laminitis increased progressively (p<0.05) from 9.2% to 37.9% with the increase in the quantum of cooked rice in the diet. The study points out the importance of protein supplementation in rice-based feeding regimen to set right the mismatched supply between nitrogen and fermentable organic matter in the rumen. This research has practical implications for animal health, welfare, nutrition, and management.

Prevalence and magnitude of acidosis sequelae to rice-based feeding regimen followed in Tamil Nadu, India

PubMed Central

Murugeswari, Rathinam; Valli, Chinnamani; Karunakaran, Raman; Leela, Venkatasubramanian; Pandian, Amaresan Serma Saravana

2018-01-01

Background and Aim In Tamil Nadu, a southern state of India, rice is readily available at a low cost, hence, is cooked (cooking akin to human consumption) and fed irrationally to cross-bred dairy cattle with poor productivity. Hence, a study was carried out with the objective to examine the prevalence of acidosis sequelae to rice-based feeding regimen and assess its magnitude. Materials and Methods A survey was conducted in all the 32 districts of Tamil Nadu, by randomly selecting two blocks per districts and from each block five villages were randomly selected. From each of the selected village, 10 dairy farmers belonging to the unorganized sector, owning one or two cross-bred dairy cows in early and mid-lactation were randomly selected so that a sample size of 100 farmers per district was maintained. The feeding regimen, milk yield was recorded, and occurrence of acidosis and incidence of laminitis were ascertained by the veterinarian with the confirmative test to determine the impact of feeding cooked rice to cows. Results It is observed that 71.5% of farmers in unorganized sector feed cooked rice to their cattle. The incidence of acidosis progressively increased significantly (p<0.05) from 29.00% in cows fed with 0.5 kg of cooked rice to 69.23% in cows fed with more than 2.5 kg of cooked rice. However, the incidence of acidosis remained significantly (p<0.05) as low as 9.9% in cows fed feeding regimen without cooked rice which is suggestive of a correlation between excessive feeding cooked rice and onset of acidosis. Further, the noticeable difference in the incidence of acidosis observed between feeding cooked rice and those fed without rice and limited intake of oil cake indicates that there is a mismatch between energy and protein supply to these cattle. Among cooked rice-based diet, the incidence of laminitis increased progressively (p<0.05) from 9.2% to 37.9% with the increase in the quantum of cooked rice in the diet. Conclusion The study points out the importance of protein supplementation in rice-based feeding regimen to set right the mismatched supply between nitrogen and fermentable organic matter in the rumen. This research has practical implications for animal health, welfare, nutrition, and management PMID:29805211

Assessing energy efficiencies and greenhouse gas emissions under bioethanol-oriented paddy rice production in northern Japan.

PubMed

Koga, Nobuhisa; Tajima, Ryosuke

2011-03-01

To establish energetically and environmentally viable paddy rice-based bioethanol production systems in northern Japan, it is important to implement appropriately selected agronomic practice options during the rice cultivation step. In this context, effects of rice variety (conventional vs. high-yielding) and rice straw management (return to vs. removal from the paddy field) on energy inputs from fuels and consumption of materials, greenhouse gas emissions (fuel and material consumption-derived CO(2) emissions as well as paddy soil CH(4) and N(2)O emissions) and ethanol yields were assessed. The estimated ethanol yield from the high-yielding rice variety, "Kita-aoba" was 2.94 kL ha(-1), a 32% increase from the conventional rice variety, "Kirara 397". Under conventional rice production in northern Japan (conventional rice variety and straw returned to the paddy), raising seedlings, mechanical field operations, transportation of harvested unhulled brown rice and consumption of materials (seeds, fertilizers, biocides and agricultural machinery) amounted to 28.5 GJ ha(-1) in energy inputs. The total energy input was increased by 14% by using the high-yielding variety and straw removal, owing to increased requirements for fuels in harvesting and transporting harvested rice as well as in collecting, loading and transporting rice straw. In terms of energy efficiency, the variation among rice variety and straw management scenarios regarding rice varieties and rice straw management was small (28.5-32.6 GJ ha(-1) or 10.1-14.0 MJ L(-1)). Meanwhile, CO(2)-equivalent greenhouse gas emissions varied considerably from scenario to scenario, as straw management had significant impacts on CH(4) emissions from paddy soils. When rice straw was incorporated into the soil, total CO(2)-equivalent greenhouse gas emissions for "Kirara 397" and "Kita-aoba" were 25.5 and 28.2 Mg CO(2) ha(-1), respectively; however, these emissions were reduced notably for the two varieties when rice straw was removed from the paddy fields in an effort to mitigate CH(4) emissions. Thus, rice straw removal avers itself a key practice with respect to lessening the impacts of greenhouse gas emissions in paddy rice-based ethanol production systems in northern Japan. More crucially, the rice straw removed is available for ethanol production and generation of heat energy with a biomass boiler, all elements required for biomass-to-ethanol transformation steps including saccharification, fermentation and distillation. This indicates opportunities for further improvement in energy efficiency and reductions in greenhouse gas emissions under whole rice plant-based bioethanol production systems. Copyright © 2010 Elsevier Ltd. All rights reserved.

Mapping paddy rice planting area in cold temperate climate region through analysis of time series Landsat 8 (OLI), Landsat 7 (ETM+) and MODIS imagery

NASA Astrophysics Data System (ADS)

Qin, Yuanwei; Xiao, Xiangming; Dong, Jinwei; Zhou, Yuting; Zhu, Zhe; Zhang, Geli; Du, Guoming; Jin, Cui; Kou, Weili; Wang, Jie; Li, Xiangping

2015-07-01

Accurate and timely rice paddy field maps with a fine spatial resolution would greatly improve our understanding of the effects of paddy rice agriculture on greenhouse gases emissions, food and water security, and human health. Rice paddy field maps were developed using optical images with high temporal resolution and coarse spatial resolution (e.g., Moderate Resolution Imaging Spectroradiometer (MODIS)) or low temporal resolution and high spatial resolution (e.g., Landsat TM/ETM+). In the past, the accuracy and efficiency for rice paddy field mapping at fine spatial resolutions were limited by the poor data availability and image-based algorithms. In this paper, time series MODIS and Landsat ETM+/OLI images, and the pixel- and phenology-based algorithm are used to map paddy rice planting area. The unique physical features of rice paddy fields during the flooding/open-canopy period are captured with the dynamics of vegetation indices, which are then used to identify rice paddy fields. The algorithm is tested in the Sanjiang Plain (path/row 114/27) in China in 2013. The overall accuracy of the resulted map of paddy rice planting area generated by both Landsat ETM+ and OLI is 97.3%, when evaluated with areas of interest (AOIs) derived from geo-referenced field photos. The paddy rice planting area map also agrees reasonably well with the official statistics at the level of state farms (R2 = 0.94). These results demonstrate that the combination of fine spatial resolution images and the phenology-based algorithm can provide a simple, robust, and automated approach to map the distribution of paddy rice agriculture in a year.

Mapping paddy rice planting area in cold temperate climate region through analysis of time series Landsat 8 (OLI), Landsat 7 (ETM+) and MODIS imagery.

PubMed

Qin, Yuanwei; Xiao, Xiangming; Dong, Jinwei; Zhou, Yuting; Zhu, Zhe; Zhang, Geli; Du, Guoming; Jin, Cui; Kou, Weili; Wang, Jie; Li, Xiangping

2015-07-01

Accurate and timely rice paddy field maps with a fine spatial resolution would greatly improve our understanding of the effects of paddy rice agriculture on greenhouse gases emissions, food and water security, and human health. Rice paddy field maps were developed using optical images with high temporal resolution and coarse spatial resolution (e.g., Moderate Resolution Imaging Spectroradiometer (MODIS)) or low temporal resolution and high spatial resolution (e.g., Landsat TM/ETM+). In the past, the accuracy and efficiency for rice paddy field mapping at fine spatial resolutions were limited by the poor data availability and image-based algorithms. In this paper, time series MODIS and Landsat ETM+/OLI images, and the pixel- and phenology-based algorithm are used to map paddy rice planting area. The unique physical features of rice paddy fields during the flooding/open-canopy period are captured with the dynamics of vegetation indices, which are then used to identify rice paddy fields. The algorithm is tested in the Sanjiang Plain (path/row 114/27) in China in 2013. The overall accuracy of the resulted map of paddy rice planting area generated by both Landsat ETM+ and OLI is 97.3%, when evaluated with areas of interest (AOIs) derived from geo-referenced field photos. The paddy rice planting area map also agrees reasonably well with the official statistics at the level of state farms ( R 2 = 0.94). These results demonstrate that the combination of fine spatial resolution images and the phenology-based algorithm can provide a simple, robust, and automated approach to map the distribution of paddy rice agriculture in a year.

Single-wavelength based rice leaf color analyzer for nitrogen status estimation

NASA Astrophysics Data System (ADS)

Sumriddetchkajorn, Sarun; Intaravanne, Yuttana

2014-02-01

With the need of a tool for efficient nitrogen (N) fertilizer management in the rice field, this paper proposes a low-cost compact single-wavelength based colorimeter that can be used to indicate the specified six color levels of a rice leaf associated with the desired amount of N fertilizer for the rice field. Our key design is in a reflective optical architecture that allows us to investigate the amount of light scattered from only one side of the rice leaf. We also show how we implement this needed rice leaf color analyzer by integrating an off-the-shelf 562-nm wavelength light emitting diode (LED), a silicon photodiode, an 8-bit microcontroller, and a 6×1 LED panel in a compact plastic package. Field test results in rice fields confirm that leaf color levels of 1, 2, 3, 5, and 6 are effectively identified and their corresponding amount of N fertilizer can be determined. For the leaf color level of 4, our single-wavelength based rice leaf color analyzer sometimes indicates a higher color level of 5 whose suggested amount of N fertilizer is equal to that for the leaf color level of 4. Other key features include ease of use and upgradability for different color levels.

Cadmium transfer from contaminated soils to the human body through rice consumption in southern Jiangsu Province, China.

PubMed

Li, Tianyuan; Chang, Qing; Yuan, Xuyin; Li, Jizhou; Ayoko, Godwin A; Frost, Ray L; Chen, Hongyan; Zhang, Xinjian; Song, Yinxian; Song, Wenzhi

2017-06-21

Consumption of crops grown in cadmium-contaminated soils is an important Cd exposure route to humans. The present study utilizes statistical analysis and in vitro digestion experiments to uncover the transfer processes of Cd from soils to the human body through rice consumption. Here, a model was created to predict the levels of bioaccessible Cd in rice grains using phytoavailable Cd quantities in the soil. During the in vitro digestion, a relatively constant ratio between the total and bioaccessible Cd in rice was observed. About 14.89% of Cd in soils was found to be transferred into rice grains and up to 3.19% could be transferred from rice grains to the human body. This model was able to sufficiently predict rice grain cadmium concentrations based on CaCl 2 extracted zinc and cadmium concentrations in soils (R 2 = 0.862). The bioaccessible Cd concentration in rice grains was also able to be predicted using CaCl 2 extracted cadmium from soil (R 2 = 0.892). The models established in this study demonstrated that CaCl 2 is a suitable indicator of total rice Cd concentrations and bioaccessible rice grain Cd concentrations. The chain model approach proposed in this study can be used for the fast and accurate evaluation of human Cd exposure through rice consumption based on the soil conditions in contaminated regions.

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.

PubMed

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.

A genetic screen identifies a requirement for cysteine-rich–receptor-like kinases in rice NH1 (OsNPR1)-mediated immunity

DOE PAGES

Chern, Mawsheng; Xu, Qiufang; Bart, Rebecca S.; ...

2016-05-13

Systemic acquired resistance, mediated by the Arabidopsis NPR1 gene and the rice NH1 gene, confers broad-spectrum immunity to diverse pathogens. NPR1 and NH1 interact with TGA transcription factors to activate downstream defense genes. Despite the importance of this defense response, the signaling components downstream of NPR1/NH1 and TGA proteins are poorly defined. Here we report the identification of a rice mutant, snim1, which suppresses NH1-mediated immunity and demonstrate that two genes encoding previously uncharacterized cysteine-rich-receptor-like kinases ( CRK6 and CRK10), complement the snim1 mutant phenotype. Silencing of CRK6 and CRK10 genes individually in the parental genetic background recreates the snim1more » phenotype. We identified a rice mutant in the Kitaake genetic background with a frameshift mutation in crk10; this mutant also displays a compromised immune response highlighting the important role of crk10. We also show that elevated levels of NH1 expression lead to enhanced CRK10 expression and that the rice TGA2.1 protein binds to the CRK10 promoter. Furthermore, these experiments demonstrate a requirement for CRKs in NH1-mediated immunity and establish a molecular link between NH1 and induction of CRK10 expression.« less

Rice pectin methylesterase inhibitor28 (OsPMEI28) encodes a functional PMEI and its overexpression results in a dwarf phenotype through increased pectin methylesterification levels.

PubMed

Nguyen, Hong Phuong; Jeong, Ho Young; Jeon, Seung Ho; Kim, Donghyuk; Lee, Chanhui

2017-01-01

Pectin methylesterases (PMEs, EC 3.1.1.11) belonging to carbohydrate esterase family 8 cleave the ester bond between a galacturonic acid and an methyl group and the resulting change in methylesterification level plays an important role during the growth and development of plants. Optimal pectin methylesterification status in each cell type is determined by the balance between PME activity and post-translational PME inhibition by PME inhibitors (PMEIs). Rice contains 49 PMEIs and none of them are functionally characterized. Genomic sequence analysis led to the identification of rice PMEI28 (OsPMEI28). Recombinant OsPMEI28 exhibited inhibitory activity against commercial PME protein with the highest activities detected at pH 8.5. Overexpression of OsPMEI28 in rice resulted in an increased level of cell wall bound methylester groups and differential changes in the composition of cell wall neutral monosaccharides and lignin content in culm tissues. Consequently, transgenic plants overexpressing OsPMEI28 exhibited dwarf phenotypes and reduced culm diameter. Our data indicate that OsPMEI28 functions as a critical structural modulator by regulating the degree of pectin methylesterification and that an impaired status of pectin methylesterification affects physiochemical properties of the cell wall components and causes abnormal cell extensibility in rice culm tissues. Copyright © 2016 Elsevier GmbH. All rights reserved.

Anther-preferential expressing gene PMR is essential for the mitosis of pollen development in rice.

PubMed

Liu, Yaqin; Xu, Ya; Ling, Sheng; Liu, Shasha; Yao, Jialing

2017-06-01

Phenotype identification, expression examination, and function prediction declared that the anther-preferential expressing gene PMR may participate in regulation of male gametophyte development in rice. Male germline development in flowering plants produces the pair of sperm cells for double fertilization and the pollen mitosis is a key process of it. Although the structural features of male gametophyte have been defined, the molecular mechanisms regulating the mitotic cell cycle are not well elucidated in rice. Here, we reported an anther-preferential expressing gene in rice, PMR (Pollen Mitosis Relative), playing an essential role in male gametogenesis. When PMR gene was suppressed via RNAi, the mitosis of microspore was severely damaged, and the plants formed unmatured pollens containing only one or two nucleuses at the anthesis, ultimately leading to serious reduction of pollen fertility and seed-setting. The CRISPR mutants, pmr-1 and pmr-2, both showed the similar defects as the PMR-RNAi lines. Further analysis revealed that PMR together with its co-expressing genes were liable to participate in the regulation of DNA metabolism in the nucleus, and affected the activities of some enzymes related to the cell cycle. We finally discussed that unknown protein PMR contained the PHD, SWIB and Plus-3 domains and they might have coordinating functions in regulation pathway of the pollen mitosis in rice.

Heavy Metal Content in Terraced Rice Fields at Sruwen Tengaran Semarang - Indonesia

NASA Astrophysics Data System (ADS)

Hindarwati, Yulis; Soeprobowati, Tri Retnaningsih; Sudarno

2018-02-01

The presence of heavy metal on agricultural soils can be caused not only natural factors but also due to human intervention. Differences in management and lack of understanding of farmers in the production input of fertilizers and pesticides ensued in land ravaged. Periodic testing of paddy fields is necessary to minimize the contaminants from being absorbed by plants that will have an impact on health decline. The purpose of the assessment was to identify the heavy metal content in the terraced rice field in Sruwen Village, Tengaran District, Semarang Regency. Survey was conducted in February 2017. Sampling on terraced rice fields of different heights consisted of upper, middle, and upper down. Taken as many as eight single points and composed at a depth of 0-20 cm and 20-40 cm. The identification results showed that heavy metal content of Pb, Cd, and Cu were present at all altitudes. Heavy Metals Pb and Cd at a depth of 0-20 cm were higher from 20-40 cm in the upper and lower rice fields but lower in the middle rice field. Cu heavy metal at a depth of 0-20 cm was higher than 20-40 cm in all altitude land. The heavy metal content of Pb, Cd, and Cu was still below the heavy metal standard set by the European Union and India.

Inhibition of toxicogenic Bacillus cereus in rice-based foods by enterocin AS-48.

PubMed

Grande, Maria J; Lucas, Rosario; Abriouel, Hikmate; Valdivia, Eva; Omar, Nabil Ben; Maqueda, Mercedes; Martínez-Bueno, Manuel; Martínez-Cañamero, Magdalena; Gálvez, Antonio

2006-02-01

The antimicrobial effect of the broad-spectrum bacteriocin enterocin AS-48 against the toxicogenic psychrotrophic strain Bacillus cereus LWL1 has been investigated in a model food system consisting of boiled rice and in a commercial infant rice-based gruel dissolved in whole milk stored at temperatures of 37 degrees C, 15 degrees C and 6 degrees C. In food samples supplemented with enterocin AS-48 (in a concentration range of 20-35 mug/ml), viable cell counts decreased rapidly over incubation time, depending on the bacteriocin concentration, the temperature of incubation and the food sample. Enterotoxin production at 37 degrees C was also inhibited. Heat sensitivity of endospores increased markedly in food samples supplemented with enterocin AS-48: inactivation of endospores was achieved by heating for 1 min at 90 degrees C in boiled rice or at 95 degrees C in rice-based gruel. Activity of enterocin AS-48 in rice gruel was potentiated by sodium lactate in a concentration-dependent way.

Identification of Genes That Enhance the Nutritional Value of Rice

USDA-ARS?s Scientific Manuscript database

Consumers in developed countries such as the U.S. are willing to pay premium prices for food products having enhanced nutritional value. Grocery stores contain a myriad of calcium fortified foods ranging from orange juice to margarine to frozen waffles. Cereal aisles and bottled water aisles are lin...

Mapping rice extent map with crop intensity in south China through integration of optical and microwave images based on google earth engine

NASA Astrophysics Data System (ADS)

Zhang, X.; Wu, B.; Zhang, M.; Zeng, H.

2017-12-01

Rice is one of the main staple foods in East Asia and Southeast Asia, which has occupied more than half of the world's population with 11% of cultivated land. Study on rice can provide direct or indirect information on food security and water source management. Remote sensing has proven to be the most effective method to monitoring the cropland in large scale by using temporary and spectral information. There are two main kinds of satellite have been used to mapping rice including microwave and optical. Rice, as the main crop of paddy fields, the main feature different from other crops is flooding phenomenon at planning stage (Figure 1). Microwave satellites can penetrate through clouds and efficiency on monitoring flooding phenomenon. Meanwhile, the vegetation index based on optical satellite can well distinguish rice from other vegetation. Google Earth Engine is a cloud-based platform that makes it easy to access high-performance computing resources for processing very large geospatial datasets. Google has collected large number of remote sensing satellite data around the world, which providing researchers with the possibility of doing application by using multi-source remote sensing data in a large area. In this work, we map rice planting area in south China through integration of Landsat-8 OLI, Sentienl-2, and Sentinel-1 Synthetic Aperture Radar (SAR) images. The flowchart is shown in figure 2. First, a threshold method the VH polarized backscatter from SAR sensor and vegetation index including normalized difference vegetation index (NDVI) and enhanced vegetation index (EVI) from optical sensor were used the classify the rice extent map. The forest and water surface extent map provided by earth engine were used to mask forest and water. To overcome the problem of the "salt and pepper effect" by Pixel-based classification when the spatial resolution increased, we segment the optical image and use the pixel- based classification results to merge the object-oriented segmentation data, and finally get the rice extent map. At last, by using the time series analysis, the peak count was obtained for each rice area to ensure the crop intensity. In this work, the rice ground point from a GVG crowdsourcing smartphone and rice area statistical results from National Bureau of Statistics were used to validate and evaluate our result.

Cloning of TPS gene from eelgrass species Zostera marina and its functional identification by genetic transformation in rice.

PubMed

Zhao, Feng; Li, Qiuying; Weng, Manli; Wang, Xiuliang; Guo, Baotai; Wang, Li; Wang, Wei; Duan, Delin; Wang, Bin

2013-12-01

The full-length cDNA sequence (2613 bp) of the trehalose-6-phosphate synthase (TPS) gene of eelgrass Zostera marina (ZmTPS) was identified and cloned. Z. marina is a kind of seed-plant growing in sea water during its whole life history. The open reading frame (ORF) region of ZmTPS gene encodes a protein of 870 amino acid residues and a stop codon. The corresponding genomic DNA sequence is 3770 bp in length, which contains 3 exons and 2 introns. The ZmTPS gene was transformed into rice variety ZH11 via Agrobacterium-mediated transformation method. After antibiotic screening, molecular characterization, salt-tolerance and trehalose content determinations, two transgenic lines resistant to 150 mM NaCL solutions were screened. Our study results indicated that the ZmTPS gene was integrated into the genomic DNA of the two transgenic rice lines and could be expressed well. Moreover, the detection of the transformed ZmTPS gene in the progenies of the two transgenic lines was performed from T1 to T4 generations; and results suggested that the transformed ZmTPS gene can be transmitted from parent to the progeny in transgenic rice. © 2013.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chern, Mawsheng; Xu, Qiufang; Bart, Rebecca S.

Systemic acquired resistance, mediated by the Arabidopsis NPR1 gene and the rice NH1 gene, confers broad-spectrum immunity to diverse pathogens. NPR1 and NH1 interact with TGA transcription factors to activate downstream defense genes. Despite the importance of this defense response, the signaling components downstream of NPR1/NH1 and TGA proteins are poorly defined. Here we report the identification of a rice mutant, snim1, which suppresses NH1-mediated immunity and demonstrate that two genes encoding previously uncharacterized cysteine-rich-receptor-like kinases ( CRK6 and CRK10), complement the snim1 mutant phenotype. Silencing of CRK6 and CRK10 genes individually in the parental genetic background recreates the snim1more » phenotype. We identified a rice mutant in the Kitaake genetic background with a frameshift mutation in crk10; this mutant also displays a compromised immune response highlighting the important role of crk10. We also show that elevated levels of NH1 expression lead to enhanced CRK10 expression and that the rice TGA2.1 protein binds to the CRK10 promoter. Furthermore, these experiments demonstrate a requirement for CRKs in NH1-mediated immunity and establish a molecular link between NH1 and induction of CRK10 expression.« less

Multiresidue analysis of 47 pesticides in cooked wheat flour and polished rice by liquid chromatography with tandem mass spectrometry.

PubMed

Lee, Sung Jung; Park, Hyeong Jin; Kim, Wooseong; Jin, Jong Sung; Abd El-Aty, A M; Shim, Jae-Han; Shin, Sung Chul

2009-04-01

Liquid chromatography in conjunction with tandem mass spectrometry was used to directly quantify of 47 pesticide residues from cooked wheat flour and polished rice, which are the most widely consumed cereals in the Republic of Korea. The sample clean-up was carried out according to the method established by the Korea Food and Drug Administration. The mobile phase for liquid chromatography separation consisted of water and 5 mm methanolic ammonium formate. Tandem mass spectroscopy experiments were performed in electrospray ionization positive mode and the multiple reaction monitoring mode. The matrix effects estimated for the 47 pesticides had a mean value of 99% and ranged from 45 to 147%. High recoveries (70-140%) and relative standard deviations (< or = 20%) were achieved for most of the pesticides tested. The method used in this study allowed for rapid quantification and identification of low levels of pesticides in cooked wheat flour and polished rice samples. Of the screened pesticide residues, only tricyclazole and fenobucarb were found in polished rice samples. However, no samples contained residues above the MRL established by the Korea Food and Drug Administration.

Morphological and molecular characterization of fungal pathogen, Magnaphorthe oryzae

NASA Astrophysics Data System (ADS)

Hasan, Nor'Aishah; Rafii, Mohd Y.; Rahim, Harun A.; Ali, Nusaibah Syd; Mazlan, Norida; Abdullah, Shamsiah

2016-02-01

Rice is arguably the most crucial food crops supplying quarter of calories intake. Fungal pathogen, Magnaphorthe oryzae promotes blast disease unconditionally to gramineous host including rice species. This disease spurred an outbreaks and constant threat to cereal production. Global rice yield declining almost 10-30% including Malaysia. As Magnaphorthe oryzae and its host is model in disease plant study, the rice blast pathosystem has been the subject of intense interest to overcome the importance of the disease to world agriculture. Therefore, in this study, our prime objective was to isolate samples of Magnaphorthe oryzae from diseased leaf obtained from MARDI Seberang Perai, Penang, Malaysia. Molecular identification was performed by sequences analysis from internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes. Phylogenetic affiliation of the isolated samples were analyzed by comparing the ITS sequences with those deposited in the GenBank database. The sequence of the isolate demonstrated at least 99% nucleotide identity with the corresponding sequence in GenBank for Magnaphorthe oryzae. Morphological observed under microscope demonstrated that the structure of conidia followed similar characteristic as M. oryzae. Finding in this study provide useful information for breeding programs, epidemiology studies and improved disease management.

Morphological and molecular characterization of fungal pathogen, Magnaphorthe oryzae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hasan, Nor’Aishah, E-mail: aishahnh@ns.uitm.edu.my; Rafii, Mohd Y., E-mail: mrafii@upm.edu.my; Department of Crop Science, Universiti Putra Malaysia

2016-02-01

Rice is arguably the most crucial food crops supplying quarter of calories intake. Fungal pathogen, Magnaphorthe oryzae promotes blast disease unconditionally to gramineous host including rice species. This disease spurred an outbreaks and constant threat to cereal production. Global rice yield declining almost 10-30% including Malaysia. As Magnaphorthe oryzae and its host is model in disease plant study, the rice blast pathosystem has been the subject of intense interest to overcome the importance of the disease to world agriculture. Therefore, in this study, our prime objective was to isolate samples of Magnaphorthe oryzae from diseased leaf obtained from MARDI Seberangmore » Perai, Penang, Malaysia. Molecular identification was performed by sequences analysis from internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes. Phylogenetic affiliation of the isolated samples were analyzed by comparing the ITS sequences with those deposited in the GenBank database. The sequence of the isolate demonstrated at least 99% nucleotide identity with the corresponding sequence in GenBank for Magnaphorthe oryzae. Morphological observed under microscope demonstrated that the structure of conidia followed similar characteristic as M. oryzae. Finding in this study provide useful information for breeding programs, epidemiology studies and improved disease management.« less

Recent advances in rice genome and chromosome structure research by fluorescence in situ hybridization (FISH).

PubMed

Ohmido, Nobuko; Fukui, Kiichi; Kinoshita, Toshiro

2010-01-01

Fluorescence in situ hybridization (FISH) is an effective method for the physical mapping of genes and repetitive DNA sequences on chromosomes. Physical mapping of unique nucleotide sequences on specific rice chromosome regions was performed using a combination of chromosome identification and highly sensitive FISH. Increases in the detection sensitivity of smaller DNA sequences and improvements in spatial resolution have ushered in a new phase in FISH technology. Thus, it is now possible to perform in situ hybridization on somatic chromosomes, pachytene chromosomes, and even on extended DNA fibers (EDFs). Pachytene-FISH allows the integration of genetic linkage maps and quantitative chromosome maps. Visualization methods using FISH can reveal the spatial organization of the centromere, heterochromatin/euchromatin, and the terminal structures of rice chromosomes. Furthermore, EDF-FISH and the DNA combing technique can resolve a spatial distance of 1 kb between adjacent DNA sequences, and the detection of even a 300-bp target is now feasible. The copy numbers of various repetitive sequences and the sizes of various DNA molecules were quantitatively measured using the molecular combing technique. This review describes the significance of these advances in molecular cytology in rice and discusses future applications in plant studies using visualization techniques.

Cultivable Methylobacterium species diversity in rice seeds identified with whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis.

PubMed

Okumura, Marie; Fujitani, Yoshiko; Maekawa, Masahiko; Charoenpanich, Jittima; Murage, Hunja; Kimbara, Kazuhide; Sahin, Nurettin; Tani, Akio

2017-02-01

Methylobacterium species are methylotrophic bacteria that widely inhabit plant surfaces. In addition to studies on methylotrophs as model organisms, research has also been conducted on their mechanism of plant growth promotion as well as the species-species specificity of plant-microbe interaction. We employed whole-cell matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (WC-MS) analysis, which enables the rapid and accurate identification of bacteria at the species level, to identify Methylobacterium isolates collected from the rice seeds of different cultivars harvested in Japan, Thailand, and Kenya. Rice seeds obtained from diverse geographical locations showed different communities of Methylobacterium species. We found that M. fujisawaense, M. aquaticum, M. platani, and M. radiotolerans are the most frequently isolated species, but none were isolated as common species from 18 seed samples due to the highly biased communities in some samples. These findings will contribute to the development of formulations containing selected species that promote rice growth, though it may be necessary to customize the formulations depending on the cultivars and farm conditions. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Mapping paddy rice planting area in northeastern Asia with Landsat 8 images, phenology-based algorithm and Google Earth Engine

PubMed Central

Dong, Jinwei; Xiao, Xiangming; Menarguez, Michael A.; Zhang, Geli; Qin, Yuanwei; Thau, David; Biradar, Chandrashekhar; Moore, Berrien

2016-01-01

Area and spatial distribution information of paddy rice are important for understanding of food security, water use, greenhouse gas emission, and disease transmission. Due to climatic warming and increasing food demand, paddy rice has been expanding rapidly in high latitude areas in the last decade, particularly in northeastern (NE) Asia. Current knowledge about paddy rice fields in these cold regions is limited. The phenology- and pixel-based paddy rice mapping (PPPM) algorithm, which identifies the flooding signals in the rice transplanting phase, has been effectively applied in tropical areas, but has not been tested at large scale of cold regions yet. Despite the effects from more snow/ice, paddy rice mapping in high latitude areas is assumed to be more encouraging due to less clouds, lower cropping intensity, and more observations from Landsat sidelaps. Moreover, the enhanced temporal and geographic coverage from Landsat 8 provides an opportunity to acquire phenology information and map paddy rice. This study evaluated the potential of Landsat 8 images on annual paddy rice mapping in NE Asia which was dominated by single cropping system, including Japan, North Korea, South Korea, and NE China. The cloud computing approach was used to process all the available Landsat 8 imagery in 2014 (143 path/rows, ~3290 scenes) with the Google Earth Engine (GEE) platform. The results indicated that the Landsat 8, GEE, and improved PPPM algorithm can effectively support the yearly mapping of paddy rice in NE Asia. The resultant paddy rice map has a high accuracy with the producer (user) accuracy of 73% (92%), based on the validation using very high resolution images and intensive field photos. Geographic characteristics of paddy rice distribution were analyzed from aspects of country, elevation, latitude, and climate. The resultant 30-m paddy rice map is expected to provide unprecedented details about the area, spatial distribution, and landscape pattern of paddy rice fields in NE Asia, which will contribute to food security assessment, water resource management, estimation of greenhouse gas emissions, and disease control. PMID:28025586

Mapping paddy rice planting area in northeastern Asia with Landsat 8 images, phenology-based algorithm and Google Earth Engine.

PubMed

Dong, Jinwei; Xiao, Xiangming; Menarguez, Michael A; Zhang, Geli; Qin, Yuanwei; Thau, David; Biradar, Chandrashekhar; Moore, Berrien

2016-11-01

Area and spatial distribution information of paddy rice are important for understanding of food security, water use, greenhouse gas emission, and disease transmission. Due to climatic warming and increasing food demand, paddy rice has been expanding rapidly in high latitude areas in the last decade, particularly in northeastern (NE) Asia. Current knowledge about paddy rice fields in these cold regions is limited. The phenology- and pixel-based paddy rice mapping (PPPM) algorithm, which identifies the flooding signals in the rice transplanting phase, has been effectively applied in tropical areas, but has not been tested at large scale of cold regions yet. Despite the effects from more snow/ice, paddy rice mapping in high latitude areas is assumed to be more encouraging due to less clouds, lower cropping intensity, and more observations from Landsat sidelaps. Moreover, the enhanced temporal and geographic coverage from Landsat 8 provides an opportunity to acquire phenology information and map paddy rice. This study evaluated the potential of Landsat 8 images on annual paddy rice mapping in NE Asia which was dominated by single cropping system, including Japan, North Korea, South Korea, and NE China. The cloud computing approach was used to process all the available Landsat 8 imagery in 2014 (143 path/rows, ~3290 scenes) with the Google Earth Engine (GEE) platform. The results indicated that the Landsat 8, GEE, and improved PPPM algorithm can effectively support the yearly mapping of paddy rice in NE Asia. The resultant paddy rice map has a high accuracy with the producer (user) accuracy of 73% (92%), based on the validation using very high resolution images and intensive field photos. Geographic characteristics of paddy rice distribution were analyzed from aspects of country, elevation, latitude, and climate. The resultant 30-m paddy rice map is expected to provide unprecedented details about the area, spatial distribution, and landscape pattern of paddy rice fields in NE Asia, which will contribute to food security assessment, water resource management, estimation of greenhouse gas emissions, and disease control.

Dissection of genetic architecture of rice plant height and heading date by multiple-strategy-based association studies

PubMed Central

Zhou, Liyuan; Liu, Shouye; Wu, Weixun; Chen, Daibo; Zhan, Xiaodeng; Zhu, Aike; Zhang, Yingxin; Cheng, Shihua; Cao, Liyong; Lou, Xiangyang; Xu, Haiming

2016-01-01

Xieyou9308 is a certified super hybrid rice cultivar with a high grain yield. To investigate its underlying genetic basis of high yield potential, a recombinant inbred line (RIL) population derived from the cross between the maintainer line XieqingzaoB (XQZB) and the restorer line Zhonghui9308 (ZH9308) was constructed for identification of quantitative trait SNPs (QTSs) associated with two important agronomic traits, plant height (PH) and heading date (HD). By re-sequencing of 138 recombinant inbred lines (RILs), a total of ~0.7 million SNPs were identified for the association studies on the PH and HD. Three association mapping strategies (including hypothesis-free genome-wide association and its two complementary hypothesis-engaged ones, QTL-based association and gene-based association) were adopted for data analysis. Using a saturated mixed linear model including epistasis and environmental interaction, we identified a total of 31 QTSs associated with either the PH or the HD. The total estimated heritability across three analyses ranged from 37.22% to 45.63% and from 37.53% to 55.96% for the PH and HD, respectively. In this study we examined the feasibility of association studies in an experimental population (RIL) and identified several common loci through multiple strategies which could be preferred candidates for further research. PMID:27406081

Cluster analysis of lowland and upland rice cultivars based on grain quality attributes

USDA-ARS?s Scientific Manuscript database

Rice is cropped in many countries all over the world and plays an important role in human nutrition as well as in agricultural economics, besides its social importance. Embrapa Rice and Beans is responsible for national rice enhancement programs and is conducting breeding projects to increase yield ...

Impacts of Steel-Slag-Based Silicate Fertilizer on Soil Acidity and Silicon Availability and Metals-Immobilization in a Paddy Soil

PubMed Central

Ning, Dongfeng; Liang, Yongchao; Liu, Zhandong; Xiao, Junfu; Duan, Aiwang

2016-01-01

Slag-based silicate fertilizer has been widely used to improve soil silicon- availability and crop productivity. A consecutive early rice-late rice rotation experiment was conducted to test the impacts of steel slag on soil pH, silicon availability, rice growth and metals-immobilization in paddy soil. Our results show that application of slag at a rate above higher or equal to 1 600 mg plant-available SiO2 per kg soil increased soil pH, dry weight of rice straw and grain, plant-available Si concentration and Si concentration in rice shoots compared with the control treatment. No significant accumulation of total cadmium (Cd) and lead (Pb) was noted in soil; rather, the exchangeable fraction of Cd significantly decreased. The cadmium concentrations in rice grains decreased significantly compared with the control treatment. In conclusion, application of steel slag reduced soil acidity, increased plant–availability of silicon, promoted rice growth and inhibited Cd transport to rice grain in the soil-plant system. PMID:27973585

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Guotian; Jain, Rashmi; Chern, Mawsheng

The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa ssp japonica), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportionmore » of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. In conclusion, this work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations.« less

Proteome Profile of Starch Granules Purified from Rice (Oryza sativa) Endosperm

PubMed Central

Xing, Shihai; Meng, Xiaoxi; Zhou, Lihui; Mujahid, Hana; Zhao, Chunfang; Zhang, Yadong; Wang, Cailin; Peng, Zhaohua

2016-01-01

Starch is the most important food energy source in cereals. Many of the known enzymes involved in starch biosynthesis are partially or entirely granule-associated in the endosperm. Studying the proteome of rice starch granules is critical for us to further understand the mechanisms underlying starch biosynthesis and packaging of starch granules in rice amyloplasts, consequently for the improvement of rice grain quality. In this article, we developed a protocol to purify starch granules from mature rice endosperm and verified the quality of purified starch granules by microscopy observations, I2 staining, and Western blot analyses. In addition, we found the phenol extraction method was superior to Tris-HCl buffer extraction method with respect to the efficiency in recovery of starch granule associated proteins. LC-MS/MS analysis showed identification of already known starch granule associated proteins with high confidence. Several proteins reported to be involved in starch synthesis in prior genetic studies in plants were also shown to be enriched with starch granules, either directly or indirectly, in our studies. In addition, our results suggested that a few additional candidate proteins may also be involved in starch synthesis. Furthermore, our results indicated that some starch synthesis pathway proteins are subject to protein acetylation modification. GO analysis and KEGG pathway enrichment analysis showed that the identified proteins were mainly located in plastids and involved in carbohydrate metabolism. This study substantially advances the understanding of the starch granule associated proteome in rice and post translational regulation of some starch granule associated proteins. PMID:27992503

Elucidating potential utilization of Portuguese common bean varieties in rice based processed foods.

PubMed

Carbas, Bruna; Pathania, Shivani; Castanho, Ana; Lourenço, Diana; Veiga, Isabel Mota; Patto, Maria Carlota Vaz; Brites, Carla

2018-03-01

The present study was aimed at studying the physico-chemical and functional properties of 31 Portuguese common bean varieties. In addition, the whole bean flours (WBF) and starch isolates (SI) of three representative bean varieties and their rice: bean blends (70:30; 50:50) were assessed for amylose content, thermal and pasting properties in view of supplementation in rice based processed foods. Bean varieties showed significant differences in protein content (20.78-27.10%), fat content (1.16-2.18%), hydration capacity (95.90-149.30%), unhydrated seeds (4.00-40.00%), γ tocopherol (3.20-98.05 mg/100 g fat), δ tocopherol (0.06-4.72 mg/100 g fat) and pasting behavior. Amylose content of WBF (11.4-20.2%) was significantly lower than rice flour (23.51%) whereas SI of beans (40.00-47.26%) had significantly higher amylose content than SI of rice (28.13%). DSC results showed that WBF (11.4-20.2 °C) had significantly broader and lower gelatinization temperature range (∆Tr) than corresponding SI (20.9-23.1 °C). WBF had significantly lower pasting viscosity due to low starch content and compositional matrix effect as compared to SI. Setback viscosities of WBF and rice: bean blends was lower than rice flour. Low setback viscosities of rice:bean blends may be used to prevent syneresis and stabilizing the quality of frozen foods in rice based processed foods.

Application of SAR remote sensing and crop modeling for operational rice crop monitoring in South and South East Asian Countries

NASA Astrophysics Data System (ADS)

Setiyono, T. D.; Holecz, F.; Khan, N. I.; Barbieri, M.; Maunahan, A. A.; Gatti, L.; Quicho, E. D.; Pazhanivelan, S.; Campos-Taberner, M.; Collivignarelli, F.; Haro, J. G.; Intrman, A.; Phuong, D.; Boschetti, M.; Prasadini, P.; Busetto, L.; Minh, V. Q.; Tuan, V. Q.

2017-12-01

This study uses multi-temporal SAR imagery, automated image processing, rule-based classification and field observations to classify rice in multiple locations in South and South Asian countries and assimilate the information into ORYZA Crop Growth Simulation Model (CGSM) to monitor rice yield. The study demonstrates examples of operational application of this rice monitoring system in: (1) detecting drought impact on rice planting in Central Thailand and Tamil Nadu, India, (2) mapping heat stress impact on rice yield in Andhra Pradesh, India, and (3) generating historical rice yield data for districts in Red River Delta, Vietnam.

Taste of Super-Dwarf Rice Cultured in Space

NASA Astrophysics Data System (ADS)

Hirai, Hiroaki; Kitaya, Yoshiaki

2016-07-01

The interest of food production for lunar base and manned Mars mission has increased recently. So far, plants cultured long duration in space were leafy vegetables, arabidopsis, wheat, barley and so on. Although rice is a staple food for most of the world, research on rice cultivation in space has not been done much. Rice grains are nutrient-rich with carbohydrate, protein and dietary fiber. Moreover, rice is a high yield crop and harvested grains have a long shelf life. Rice symbolizes the rice-eating culture of Japan, is extremely useful as a specific cultured plant candidate of Japan in space. In the previous report, 'Kozo-no-sumika' found from seedlings in raising of seedling was introduced as a super-dwarf rice to culture in space. Considering this rice as food in space, we investigate the taste characteristics of this rice. At present, waxy 'Kozo-no-sumika' and nonwaxy 'Hosetsu dwarf' of super-dwarf rice and 'Nipponbare' of previous standard rice for sensory test are cultured in paddy field. Hereafter, we will harvest rice, investigate yield, evaluate taste.

Effect of germination on the physicochemical and antioxidant characteristics of rice flour from three rice varieties from Nigeria.

PubMed

Chinma, Chiemela Enyinnaya; Anuonye, Julian Chukwuemeka; Simon, Omotade Comfort; Ohiare, Raliat Ozavize; Danbaba, Nahemiah

2015-10-15

This study determined the effect of germination (48 h) on the physicochemical and antioxidant characteristics of rice flour from three rice varieties from Nigeria. Local rice varieties (Jamila, Jeep and Kwandala) were evaluated and compared to an improved variety (MR 219). Physicochemical and antioxidant properties of flours were determined using standard methods. Protein, magnesium, phosphorus, potassium and antioxidant properties of rice flours increased after germination while phytic acid and total starch contents decreased. Foaming capacity and stability of rice flours increased after germination. Germination resulted to changes in pasting and thermal characteristics of rice flours. Germinated rice flours had better physicochemical and antioxidant properties with reduced phytic acid and starch contents compared to MR 219, which can be utilized as functional ingredients in the preparation of rice-based products. Copyright © 2015 Elsevier Ltd. All rights reserved.

Application of resequencing to rice genomics, functional genomics and evolutionary analysis

PubMed Central

2014-01-01

Rice is a model system used for crop genomics studies. The completion of the rice genome draft sequences in 2002 not only accelerated functional genome studies, but also initiated a new era of resequencing rice genomes. Based on the reference genome in rice, next-generation sequencing (NGS) using the high-throughput sequencing system can efficiently accomplish whole genome resequencing of various genetic populations and diverse germplasm resources. Resequencing technology has been effectively utilized in evolutionary analysis, rice genomics and functional genomics studies. This technique is beneficial for both bridging the knowledge gap between genotype and phenotype and facilitating molecular breeding via gene design in rice. Here, we also discuss the limitation, application and future prospects of rice resequencing. PMID:25006357

Identification and fine-mapping of Xa33, a novel gene for resistance to Xanthomonas oryzae pv. oryzae.

PubMed

Kumar, P Natraj; Sujatha, K; Laha, G S; Rao, K Srinivasa; Mishra, B; Viraktamath, B C; Hari, Y; Reddy, C S; Balachandran, S M; Ram, T; Madhav, M Sheshu; Rani, N Shobha; Neeraja, C N; Reddy, G Ashok; Shaik, H; Sundaram, R M

2012-02-01

Broadening of the genetic base for identification and transfer of genes for resistance to insect pests and diseases from wild relatives of rice is an important strategy in resistance breeding programs across the world. An accession of Oryza nivara, International Rice Germplasm Collection (IRGC) accession number 105710, was identified to exhibit high level and broad-spectrum resistance to Xanthomonas oryzae pv. oryzae. In order to study the genetics of resistance and to tag and map the resistance gene or genes present in IRGC 105710, it was crossed with the bacterial blight (BB)-susceptible varieties 'TN1' and 'Samba Mahsuri' (SM) and then backcrossed to generate backcross mapping populations. Analysis of these populations and their progeny testing revealed that a single dominant gene controls resistance in IRGC 105710. The BC(1)F(2) population derived from the cross IRGC 105710/TN1//TN1 was screened with a set of 72 polymorphic simple-sequence repeat (SSR) markers distributed across the rice genome and the resistance gene was coarse mapped on chromosome 7 between the SSR markers RM5711 and RM6728 at a genetic distance of 17.0 and 19.3 centimorgans (cM), respectively. After analysis involving 49 SSR markers located between the genomic interval spanned by RM5711 and RM6728, and BC(2)F(2) population consisting of 2,011 individuals derived from the cross IRGC 105710/TN1//TN1, the gene was fine mapped between two SSR markers (RMWR7.1 and RMWR7.6) located at a genetic distance of 0.9 and 1.2 cM, respectively, from the gene and flanking it. The linkage distances were validated in a BC(1)F(2) mapping population derived from the cross IRGC 105710/SM//2 × SM. The BB resistance gene present in the O. nivara accession was identified to be novel based on its unique map location on chromosome 7 and wider spectrum of BB resistance; this gene has been named Xa33. The genomic region between the two closely flanking SSR markers was in silico analyzed for putatively expressed candidate genes. In total, eight genes were identified in the region and a putative gene encoding serinethreonine kinase appears to be a candidate for the Xa33 gene.

Feral rice from introgression of weedy rice genes into transgenic herbicide-resistant hybrid-rice progeny.

PubMed

Zhang, Jingxu; Kang, Ye; Valverde, Bernal E; Dai, Weimin; Song, Xiaoling; Qiang, Sheng

2018-06-05

Pollen-mediated herbicide-resistance transgene flow occurs bidirectionally between transgenic cultivated rice and weedy rice. The potential risk of weedy traits introgressing into hybrid rice is underestimated and poorly understood. Two of each glufosinate-resistant transgenic rice varieties and hybrid rice (F1) and their succeeding generations (F2-F4) were planted for three years in weedy-rice-free field plots adjacent to experimental weedy-rice fields. Weedy-rice-like (feral) plants, both glufosinate-resistant and with red-pericarp seed, were initially found only among the F3 generations of the two glufosinate-resistant transgenic hybrid rice. The composite fitness (an index based on eight productivity and weediness traits) of the feral progeny was significantly higher than that of glufosinate-resistant transgenic hybrid rice (the original female parent of feral progeny) under common monoculture garden conditions. Hybrid rice progeny segregated into individuals of variable height and extended flowering. Hybrid rice F2 generations had higher outcrossing rates by pollen reception (0.96%-1.65%) than their progenitors (0.07%-0.98%). Herbicide-resistant weedy rice can rapidly arise by pollen-mediated gene flow from weedy to transgenic hybrid rice. Their segregating pollen-receptive progeny pose greater agro-ecological risk than transgenic varieties. The safety assessment and management regulations for transgenic hybrid rice should take into account the risk of bidirectional gene flow.

Genome-wide analyses of late pollen-preferred genes conserved in various rice cultivars and functional identification of a gene involved in the key processes of late pollen development.

PubMed

Moon, Sunok; Oo, Moe Moe; Kim, Backki; Koh, Hee-Jong; Oh, Sung Aeong; Yi, Gihwan; An, Gynheung; Park, Soon Ki; Jung, Ki-Hong

2018-04-23

Understanding late pollen development, including the maturation and pollination process, is a key component in maintaining crop yields. Transcriptome data obtained through microarray or RNA-seq technologies can provide useful insight into those developmental processes. Six series of microarray data from a public transcriptome database, the Gene Expression Omnibus of the National Center for Biotechnology Information, are related to anther and pollen development. We performed a systematic and functional study across the rice genome of genes that are preferentially expressed in the late stages of pollen development, including maturation and germination. By comparing the transcriptomes of sporophytes and male gametes over time, we identified 627 late pollen-preferred genes that are conserved among japonica and indica rice cultivars. Functional classification analysis with a MapMan tool kit revealed a significant association between cell wall organization/metabolism and mature pollen grains. Comparative analysis of rice and Arabidopsis demonstrated that genes involved in cell wall modifications and the metabolism of major carbohydrates are unique to rice. We used the GUS reporter system to monitor the expression of eight of those genes. In addition, we evaluated the significance of our candidate genes, using T-DNA insertional mutant population and the CRISPR/Cas9 system. Mutants from T-DNA insertion and CRISPR/Cas9 systems of a rice gene encoding glycerophosphoryl diester phosphodiesterase are defective in their male gamete transfer. Through the global analyses of the late pollen-preferred genes from rice, we found several biological features of these genes. First, biological process related to cell wall organization and modification is over-represented in these genes to support rapid tube growth. Second, comparative analysis of late pollen preferred genes between rice and Arabidopsis provide a significant insight on the evolutional disparateness in cell wall biogenesis and storage reserves of pollen. In addition, these candidates might be useful targets for future examinations of late pollen development, and will be a valuable resource for accelerating the understanding of molecular mechanisms for pollen maturation and germination processes in rice.

Overexpression of acetylcholinesterase gene in rice results in enhancement of shoot gravitropism.

PubMed

Yamamoto, Kosuke; Shida, Satoshi; Honda, Yoshihiro; Shono, Mariko; Miyake, Hiroshi; Oguri, Suguru; Sakamoto, Hikaru; Momonoki, Yoshie S

2015-09-25

Acetylcholine (ACh), a known neurotransmitter in animals and acetylcholinesterase (AChE) exists widely in plants, although its role in plant signal transduction is unclear. We previously reported AChE in Zea mays L. might be related to gravitropism based on pharmacological study using an AChE inhibitor. Here we clearly demonstrate plant AChE play an important role as a positive regulator in the gravity response of plants based on a genetic study. First, the gene encoding a second component of the ACh-mediated signal transduction system, AChE was cloned from rice, Oryza sativa L. ssp. Japonica cv. Nipponbare. The rice AChE shared high homology with maize, siratro and Salicornia AChEs. Similar to animal and other plant AChEs, the rice AChE hydrolyzed acetylthiocholine and propionylthiocholine, but not butyrylthiocholine. Thus, the rice AChE might be characterized as an AChE (E.C.3.1.1.7). Similar to maize and siratro AChEs, the rice AChE exhibited low sensitivity to the AChE inhibitor, neostigmine bromide, compared with the electric eel AChE. Next, the functionality of rice AChE was proved by overexpression in rice plants. The rice AChE was localized in extracellular spaces of rice plants. Further, the rice AChE mRNA and its activity were mainly detected during early developmental stages (2 d-10 d after sowing). Finally, by comparing AChE up-regulated plants with wild-type, we found that AChE overexpression causes an enhanced gravitropic response. This result clearly suggests that the function of the rice AChE relate to positive regulation of gravitropic response in rice seedlings. Copyright © 2015 Elsevier Inc. All rights reserved.

7 CFR 1412.62 - Fruit, vegetable, and wild rice acreage reporting violations.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 10 2013-01-01 2013-01-01 false Fruit, vegetable, and wild rice acreage reporting... Contract Violations and Reduction in Payments § 1412.62 Fruit, vegetable, and wild rice acreage reporting violations. (a)(1) If an acreage report of fruits, vegetables, or wild rice planted on base acreage of a farm...

7 CFR 1412.62 - Fruit, vegetable, and wild rice acreage reporting violations.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 10 2014-01-01 2014-01-01 false Fruit, vegetable, and wild rice acreage reporting... Contract Violations and Reduction in Payments § 1412.62 Fruit, vegetable, and wild rice acreage reporting violations. (a)(1) If an acreage report of fruits, vegetables, or wild rice planted on base acreage of a farm...

7 CFR 1412.62 - Fruit, vegetable, and wild rice acreage reporting violations.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 10 2012-01-01 2012-01-01 false Fruit, vegetable, and wild rice acreage reporting... Contract Violations and Reduction in Payments § 1412.62 Fruit, vegetable, and wild rice acreage reporting violations. (a)(1) If an acreage report of fruits, vegetables, or wild rice planted on base acreage of a farm...

7 CFR 1412.62 - Fruit, vegetable, and wild rice acreage reporting violations.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 10 2011-01-01 2011-01-01 false Fruit, vegetable, and wild rice acreage reporting... Contract Violations and Reduction in Payments § 1412.62 Fruit, vegetable, and wild rice acreage reporting violations. (a)(1) If an acreage report of fruits, vegetables, or wild rice planted on base acreage of a farm...

7 CFR 1412.62 - Fruit, vegetable, and wild rice acreage reporting violations.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 10 2010-01-01 2010-01-01 false Fruit, vegetable, and wild rice acreage reporting... Contract Violations and Reduction in Payments § 1412.62 Fruit, vegetable, and wild rice acreage reporting violations. (a)(1) If an acreage report of fruits, vegetables, or wild rice planted on base acreage of a farm...

RiceAtlas, a spatial database of global rice calendars and production.

PubMed

Laborte, Alice G; Gutierrez, Mary Anne; Balanza, Jane Girly; Saito, Kazuki; Zwart, Sander J; Boschetti, Mirco; Murty, M V R; Villano, Lorena; Aunario, Jorrel Khalil; Reinke, Russell; Koo, Jawoo; Hijmans, Robert J; Nelson, Andrew

2017-05-30

Knowing where, when, and how much rice is planted and harvested is crucial information for understanding the effects of policy, trade, and global and technological change on food security. We developed RiceAtlas, a spatial database on the seasonal distribution of the world's rice production. It consists of data on rice planting and harvesting dates by growing season and estimates of monthly production for all rice-producing countries. Sources used for planting and harvesting dates include global and regional databases, national publications, online reports, and expert knowledge. Monthly production data were estimated based on annual or seasonal production statistics, and planting and harvesting dates. RiceAtlas has 2,725 spatial units. Compared with available global crop calendars, RiceAtlas is nearly ten times more spatially detailed and has nearly seven times more spatial units, with at least two seasons of calendar data, making RiceAtlas the most comprehensive and detailed spatial database on rice calendar and production.

Rice-based mucosal vaccine as a global strategy for cold-chain- and needle-free vaccination

PubMed Central

Nochi, Tomonori; Takagi, Hidenori; Yuki, Yoshikazu; Yang, Lijun; Masumura, Takehiro; Mejima, Mio; Nakanishi, Ushio; Matsumura, Akiko; Uozumi, Akihiro; Hiroi, Takachika; Morita, Shigeto; Tanaka, Kunisuke; Takaiwa, Fumio; Kiyono, Hiroshi

2007-01-01

Capable of inducing antigen-specific immune responses in both systemic and mucosal compartments without the use of syringe and needle, mucosal vaccination is considered ideal for the global control of infectious diseases. In this study, we developed a rice-based oral vaccine expressing cholera toxin B subunit (CTB) under the control of the endosperm-specific expression promoter 2.3-kb glutelin GluB-1 with codon usage optimization for expression in rice seed. An average of 30 μg of CTB per seed was stored in the protein bodies, which are storage organelles in rice. When mucosally fed, rice seeds expressing CTB were taken up by the M cells covering the Peyer's patches and induced CTB-specific serum IgG and mucosal IgA antibodies with neutralizing activity. When expressed in rice, CTB was protected from pepsin digestion in vitro. Rice-expressed CTB also remained stable and thus maintained immunogenicity at room temperature for >1.5 years, meaning that antigen-specific mucosal immune responses were induced at much lower doses than were necessary with purified recombinant CTB. Because they require neither refrigeration (cold-chain management) nor a needle, these rice-based mucosal vaccines offer a highly practical and cost-effective strategy for orally vaccinating large populations against mucosal infections, including those that may result from an act of bioterrorism. PMID:17573530

Effects of crop rotation on properties of a Vietnam clay soil under rice-based cropping systems in small-scale farmers' fields

USDA-ARS?s Scientific Manuscript database

In tropical deltas, intensive monocultures with three rice crops per year have been the standard for decades. In recent years, though, rice-based rotations with one or more upland crops per year are being adopted by several farmers. Their trends of increasing grain yields raise the question whether ...

Exposure assessment of the population in Poland to the toxic effects of arsenic compounds present in rice and rice based products

PubMed

Mania, Monika; Rebeniak, Małgorzata; Szynal, Tomasz; Starska, Krystyna; Wojciechowska-Mazurek, Maria; Postupolski, Jacek

Rice is a staple food for many people in the world and an important ingredient for production of food for infants and young children. According to European Food Safety Authority (EFSA), cereals, primarily rice and rice products, are an important source of human exposure to inorganic arsenic, which has been classified by the International Agency for Research on Cancer (IARC) as group I carcinogen. Arsenic is present in rice and rice products mainly as an inorganic form being more toxic than organic compounds The aim of the study was to determine the total and inorganic arsenic content in rice, rice-based products including food for infants and young children available on the market in Poland and thus to estimate consumer exposure to inorganic arsenic from these groups of foodstuffs A total of 62 samples of rice and rice products from trade, including a group of rice products for infants and young children, were tested. Contents of total and inorganic arsenic were determined by using hydride generation atomic absorption spectrometry (HGAAS), after dry mineralization of samples and reduction of arsenic to arsenic hydride with sodium borohydride. To extract the inorganic arsenic forms, the samples were subjected to hydrolysis in concentrated HCl and then reduced in the presence of hydrobromic acid and hydrazine sulphate after which triple chloroform extractions and triple 1M HCl re-extractions were performed. Exposure of different groups of populations (adults and children), was estimated in relation to the Benchmark Dose Lower Confidence Limit (BMDL05) as set by the Joint FAO/WHO Expert Committee on Food Additives (JECFA) that resulted in a 0.5% increase in lung cancer (3.0 µg/kg body weight (b.w.) per day) Mean content of total and inorganic arsenic in investigated rice samples was 0.12 mg/kg (median: 0.09 mg/kg; 90th percentile 0.22 mg/kg) and 0.04 mg/kg (median: 0.03 mg/kg, 90th percentile 0.07 mg/kg). Brown rice was found to be more highly contaminated with both total and inorganic arsenic than white rice. Mean contamination of brown rice with total arsenic and inorganic arsenic was: 0.18 mg/kg (median: 0.12 mg/kg, 90th percentile: 0.32 mg/kg) and 0.05 mg/kg (median: 0.05 mg/kg, 90th percentile: 0.07 mg/kg). In turn for the white rice contamination was lower, mean total arsenic content: 0.10 mg/kg (median: 0.08 mg/kg, 90th percentile: 0.19 mg/kg) and mean inorganic arsenic: 0.03 mg/kg (median: 0.03 mg/kg, 90th percentile: 0.06 mg/kg). Contamination of rice-based products both total and inorganic arsenic was similar to those reported for rice, except rice wafers (mean: 0.24 mg/kg and 0.13 mg/kg). In the group of products for infants and young children obtained results were low – mean total arsenic content was 0.06 mg/kg and inorganic arsenic 0.02 mg/kg. The estimated average adult and children’s exposure to inorganic arsenic with rice and rice products was less than 1% of the BMDL05. Intake of inorganic arsenic by 12-month-old infants with ricebased products intended for this group of population was at 6% BMDL05 Based on the obtained results, it was found that the content of total and inorganic arsenic in investigated samples of rice and rice products did not pose a health risk even though contamination levels in some individual samples were significant

Effect of caffeine on the expression pattern of water-soluble proteins in rice (Oryza sativa) seedlings.

PubMed

Deng, Wei-Wei; Sasamoto, Hamako; Ashihara, Hiroshi

2015-05-01

It has been suggested that caffeine acts as an allelochemical which influences the germination and growth of plants. The effect of caffeine on the expression profiles of proteins was investigated in shoot-root axes of rice (Oryza sativa) seedlings. Two-dimensional difference gel electrophoresis combined with Matrix-Assisted Laser Desorption/Ionization Time of Flight/Time of Flight Mass Spectrometry was employed for the separation and identification of proteins. The results indicated that amounts of 51 protein spots were reduced and 14 were increased by treatment with 1 mM caffeine. Twelve rice seedling proteins were identified. Down-regulated proteins were β-tubulin, sucrose synthase, glyceraldehyde-3-phosphate dehydrogenase, reversibly glycosylated polypeptide/α-1,4-glucan protein synthase and cytoplasmic malate dehydrogenase. In contrast, up-regulated proteins were alanyl-aminopeptidase, acetyl-CoA carboxylase, adenine phosphoribosyltransferase, NAD-malate dehydrogenase, ornithine carbamoyltransferase, glucose-6-phosphate isomerase and nuclear RNA binding protein. Possible alternation of metabolism caused by caffeine is discussed with the protein expression data.

Isolation and identification of antioxidant peptides from enzymatically hydrolyzed rice bran protein.

PubMed

Wattanasiritham, Ladda; Theerakulkait, Chockchai; Wickramasekara, Samanthi; Maier, Claudia S; Stevens, Jan F

2016-02-01

Khao Dawk Mali 105 rice bran protein (RBP) was fractionated into albumin (12.5%), globulin (13.9%), glutelin (70.8%) and prolamine (2.9%). The native and denatured RBP fractions were hydrolyzed with papain and trypsin for 3h at optimum conditions. The RBP fractions and their hydrolysates were evaluated for their antioxidant activity by the Oxygen Radical Absorbance Capacity (ORAC) assay. The trypsin-hydrolyzed denatured albumin exhibited the highest antioxidant activity with an ORAC value of 4.07 μmol of Trolox equivalent (TE)/mg protein. This hydrolysate was separated by using RP-HPLC and three fractions with high antioxidant activity were examined by LTQ-FTICR ESI mass spectrometry. The MW of the peptides from these fractions were 800-2100 Da. and consisted of 6-21 amino acid residues. Most of the peptides from the fractions demonstrated typical characteristics of well-known antioxidant peptides. The results suggest that trypsin-hydrolyzed denatured rice bran albumin might be useful as a natural food antioxidant. Copyright © 2015 Elsevier Ltd. All rights reserved.

Identification and characterization of a gibberellin-regulated protein, which is ASR5, in the basal region of rice leaf sheaths.

PubMed

Takasaki, Hironori; Mahmood, Tariq; Matsuoka, Makoto; Matsumoto, Hiroshi; Komatsu, Setsuko

2008-04-01

Gibberellins (GAs) regulate growth and development in higher plants. To identify GA-regulated proteins during rice leaf sheath elongation, a proteomic approach was used. Proteins from the basal region of leaf sheath in rice seedling treated with GA(3) were analyzed by fluorescence two-dimensional difference gel electrophoresis. The levels of abscisic acid-stress-ripening-inducible 5 protein (ASR5), elongation factor-1 beta, translationally controlled tumor protein, fructose-bisphosphate aldolase and a novel protein increased; whereas the level of RuBisCO subunit binding-protein decreased by GA(3) treatment. ASR5 out of these six proteins was significantly regulated by GA(3) at the protein level but not at the mRNA level in the basal region of leaf sheaths. Since this protein is regulated not only by abscisic acid but also by GA(3), these results indicate that ASR5 might be involved in plant growth in addition to stress in the basal regions of leaf sheaths.

Linkages and Interactions Analysis of Major Effect Drought Grain Yield QTLs in Rice.

PubMed

Vikram, Prashant; Swamy, B P Mallikarjuna; Dixit, Shalabh; Trinidad, Jennylyn; Sta Cruz, Ma Teresa; Maturan, Paul C; Amante, Modesto; Kumar, Arvind

2016-01-01

Quantitative trait loci conferring high grain yield under drought in rice are important genomic resources for climate resilient breeding. Major and consistent drought grain yield QTLs usually co-locate with flowering and/or plant height QTLs, which could be due to either linkage or pleiotropy. Five mapping populations used for the identification of major and consistent drought grain yield QTLs underwent multiple-trait, multiple-interval mapping test (MT-MIM) to estimate the significance of pleiotropy effects. Results indicated towards possible linkages between the drought grain yield QTLs with co-locating flowering and/or plant height QTLs. Linkages of days to flowering and plant height were eliminated through a marker-assisted breeding approach. Drought grain yield QTLs also showed interaction effects with flowering QTLs. Drought responsiveness of the flowering locus on chromosome 3 (qDTY3.2) has been revealed through allelic analysis. Considering linkage and interaction effects associated with drought QTLs, a comprehensive marker-assisted breeding strategy was followed to develop rice genotypes with improved grain yield under drought stress.

Rice cultivation and methane emission: Documentation of distributed geographic data sets

NASA Technical Reports Server (NTRS)

Matthews, Elaine; John, Jasmin; Fung, Inez

1994-01-01

High-resolution global data bases on the geographic and seasonal distribution of rice cultivation and associated methane emission, compiled by Matthews et al., were archived for public use. In addition to the primary data sets identifying location, seasonality, and methane emission from rice cultivation, a series of supporting data sets is included, allowing users not only to replicate the work of Matthews et al. but to investigate alternative cultivation and emission scenarios. The suite of databases provided, at 1 latitude by 1 longitude resolution for the globe, includes (1) locations of rice cultivation, (2) monthly arrays of actively growing rice areas, (3) countries and political subdivisions, and (4) monthly arrays of methane emission from rice cultivation. Ancillary data include (1) a listing, by country, of harvested rice areas and seasonal distribution of crop cycles and (2) country names and codes. Summary tables of zonal/monthly distributions of actively growing rice areas and of methane emissions are presented. Users should consult original publications for complete discussion of the data bases. This short paper is designed only to document formats of the distributed information and briefly describe the contents of the data sets and their initial application to evaluating the role of rice cultivation in the methane budget.

Response of soil microbial communities to red mud-based stabilizer remediation of cadmium-contaminated farmland.

PubMed

Li, Hui; Liu, Lemian; Luo, Lin; Liu, Yan; Wei, Jianhong; Zhang, Jiachao; Yang, Yuan; Chen, Anwei; Mao, Qiming; Zhou, Yaoyu

2018-04-01

In this work, a field test was conducted to investigate the effects of heavy metal stabilizer addition on brown rice and microbial variables in a cadmium (Cd)-contaminated farmland from April to October in 2016. Compared with the control, red mud-based stabilizer (RMDL) effectively reduced the concentration of Cd in brown rice (with the removal rate of 48.14% in early rice, 20.24 and 47.62% in late rice). The results showed that adding 0.3 kg m -2 RDML in early rice soil or soil for both early and late rice increased the microbial biomass carbon (MBC), the number of culturable heterotrophic bacteria and fungi, and the catalase activity in soil at different stages of paddy rice growth. Furthermore, there was no notable difference in the diversity of the bacterial species, community composition, and relative abundance at phylum (or class) or operational taxonomic unit (OTU) levels between the control and treatment (RMDL addition) groups. In a word, RMDL could be highly recommended as an effective remediation stabilizer for Cd-contaminated farmland, since its continuous application in paddy soil cultivating two seasons rice soil could effectively decrease the Cd content in brown rice and had no negative impact on soil microorganisms.

Safety assessment of lepidopteran insect-protected transgenic rice with cry2A* gene.

PubMed

Zou, Shiying; Huang, Kunlun; Xu, Wentao; Luo, Yunbo; He, Xiaoyun

2016-04-01

Numerous genetically modified (GM) crops expressing proteins for insect resistance have been commercialized following extensive testing demonstrating that the foods obtained from them are as safe as that obtained from their corresponding non-GM varieties. In this paper, we report the outcome of safety studies conducted on a newly developed insect-resistant GM rice expressing the cry2A* gene by a subchronic oral toxicity study on rats. GM rice and non-GM rice were incorporated into the diet at levels of 30, 50, and 70% (w/w), No treatment-related adverse or toxic effects were observed based on an examination of the daily clinical signs, body weight, food consumption, hematology, serum biochemistry, and organ weight or based on gross and histopathological examination. These results demonstrate that the GM rice with cry2A* gene is as safe for food as conventional non-GM rice.

GC-MS based metabolite profiling of rice Koji fermentation by various fungi.

PubMed

Kim, Ah Jin; Choi, Jung Nam; Kim, Jiyoung; Park, Sait Byul; Yeo, Soo Hwan; Choi, Ji Ho; Lee, Choong Hwan

2010-01-01

In this study, Aspergillus kawachii, Aspergillus oryzae, and Rhizopus sp., were utilized for rice Koji fermentation, and the metabolites were analyzed in a time-dependent manner by gas chromatography-mass spectrometry. On Principal Component Analysis, the metabolite patterns were clearly distinguished based on the fungi species. This approach revealed that the quantities of glucose, galactose, and glycerol gradually increased as a function of fermentation time in all trials rice Koji fermentation. The time-dependent changes of these metabolites showed significant increases in glucose in the A. oryzae-treated rice, and in glycerol and galactose in the A. kawachii-treated rice. In addition, glycolysis-related enzyme activities were correlated with the changes in these metabolites. The results indicate that time-dependent metabolite production has the potential to be a valuable tool in selecting inoculant fungi and the optimal fermentation time for rice koji.

Cadmium content in rice and its daily intake in various countries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rivai, Ida Farida; Koyama, Hiroshi; Suzuki, Shosuke

Man ingests cadmium daily from foods and beverages. The major source of cadmium intake is rice for rice eating countries. Cadmium in rice comes from soil via rice plant roots. Rice may thus be the best indicator for the environmental monitoring of cadmium especially in rice eating countries. It is also easy to sample, transport and conserve. Several recent surveys on cadmium content in rice and daily cadmium intake have been reported. However, little data are available on geographical differences in daily cadmium intake from rice. The tolerable weekly intake for cadmium as proposed by FAO/WHO is 400-500 micrograms/person ormore » 57-71 micrograms/day/person weighing 70 kg. Ninety two percent of world rice production is from the Asia-Pacific region, from which samples were obtained for the present study. The following countries were included: India, China, Bangladesh, Thailand, Indonesia, Philippines, Japan, and Korea. This study was conducted to determine cadmium content in rice from the above countries and based on the data obtained, daily cadmium intake from rice and the total daily cadmium intake were calculated.« less

[Rice water with and without electrolytes in diarrhea with a high stool output].

PubMed

Mota-Hernández, F; Posadas-Tello, N M; Rodríguez-Leyva, G

1993-12-01

The objective of the study was to determine the efficacy and safety of two rice-based oral rehydration solutions, with and without added electrolyte in children presenting acute diarrheal dehydration with high stool output (> 10 mL/kg/h) during a two-hour rehydration period. Twenty-two patients of one to 18 months old were recruited and randomly distributed into two groups: group A received the rice-based solution without electrolytes, and group B received the rice-based solution with electrolytes. A stool output diminishing was observed in both groups and rehydration was achieved in 4.0 +/- 0.9 hours in 21 patients from group A and in 4.6 +/- 0.9 hours in 13 patients group group B. There was not a statistically significant difference between the groups regarding the laboratory results. The rice-based oral rehydration solution without added electrolytes was useful for rehydration of children presenting high stool output, after administering the WHO/ORS recommended formula during a two-hour period.

A set of GFP-based organelle marker lines combined with DsRed-based gateway vectors for subcellular localization study in rice (Oryza sativa L.).

PubMed

Wu, Tsung-Meng; Lin, Ke-Chun; Liau, Wei-Shiang; Chao, Yun-Yang; Yang, Ling-Hung; Chen, Szu-Yun; Lu, Chung-An; Hong, Chwan-Yang

2016-01-01

In the post-genomic era, many useful tools have been developed to accelerate the investigation of gene functions. Fluorescent proteins have been widely used as protein tags for studying the subcellular localization of proteins in plants. Several fluorescent organelle marker lines have been generated in dicot plants; however, useful and reliable fluorescent organelle marker lines are lacking in the monocot model rice. Here, we developed eight different GFP-based organelle markers in transgenic rice and created a set of DsRed-based gateway vectors for combining with the marker lines. Two mitochondrial-localized rice ascorbate peroxidase genes fused to DsRed and successfully co-localized with mitochondrial-targeted marker lines verified the practical use of this system. The co-localization of GFP-fusion marker lines and DsRed-fusion proteins provide a convenient platform for in vivo or in vitro analysis of subcellular localization of rice proteins.

Automated rice leaf disease detection using color image analysis

NASA Astrophysics Data System (ADS)

Pugoy, Reinald Adrian D. L.; Mariano, Vladimir Y.

2011-06-01

In rice-related institutions such as the International Rice Research Institute, assessing the health condition of a rice plant through its leaves, which is usually done as a manual eyeball exercise, is important to come up with good nutrient and disease management strategies. In this paper, an automated system that can detect diseases present in a rice leaf using color image analysis is presented. In the system, the outlier region is first obtained from a rice leaf image to be tested using histogram intersection between the test and healthy rice leaf images. Upon obtaining the outlier, it is then subjected to a threshold-based K-means clustering algorithm to group related regions into clusters. Then, these clusters are subjected to further analysis to finally determine the suspected diseases of the rice leaf.

The influences of consumer characteristics on the amount of rice consumption

NASA Astrophysics Data System (ADS)

Supriana, T.; Pane, TC

2018-02-01

This study aimed to analyze the characteristics of rice consumers and the influences of consumer characteristics on the amount of rice consumption. The research areas were determined purposively in the sub-districts with the most significant population in Medan City. The analytical methods used were descriptive and multiple linear regression analysis. The results showed that consumers in the study areas have various characteristics, concerning age, income, family size, health, and education. Simultaneously, characteristics of rice consumers have the significant effect on the amount of rice consumed. Partially, age and the number of family members have the significant effect on the amount of rice consumed. The implications of this research are, need different policies toward consumers of rice based on their income strata. Rice policies cannot be generalized.

Identification of QTLs that enhance the nutritional value of rice grain and limit accumulation of undesirable elements such as arsenic

USDA-ARS?s Scientific Manuscript database

Research into the mineral contents of cereal grains and vegetables is motivated by interest in improving their nutritional value. Biofortification refers to natural enhancement of grain/food products through traditional breeding. Since this approach does not require genetic engineering, it is acce...

Plan for the uniform mapping of earth resources and environmental complexes from Skylab imagery. Assessment of natural vegetation, environmental, and crop analogs. [Sierra-Lahontan, Colorado Plateau, Louisiana coastal plain, and Northern Great Valley, California

NASA Technical Reports Server (NTRS)

Poulton, C. E. (Principal Investigator); Welch, R. I.

1975-01-01

The author has identified the following significant results. For interpreting a wide range of natural vegetation analogs, S-190A color infrared and the ERTS-1 color composite were consistently more useful than were conventional color or black and white photos. Color infrared was superior for five vegetation analogs while color was superior for only three. The errors in identification appeared to associate more with black and white single band images than with multiband color. For rice crop analogs, spectral and spatial discriminations both contribute to the usefulness of images for data collection. Tests and subjective analyses conducted in this study indicated that the spectral bands exploited in color infrared film were the most useful for agricultural crop analysis. Accuracy of crop identification on any single date of Skylab images was less than that of multidate analysis due to differences in crop calendar, cultural practices used, rice variety, planting date, planting method, water use, fertilization, disease, or mechanical problems.

Performance analysis of different rice-based cropping systems in tropical region of Nepal.

PubMed

Pokhrel, Anil; Soni, Peeyush

2017-07-15

Energy inputs, environmental impacts and economic outputs are the main concerns in today's agricultural production systems. The current study investigated the energy, environmental and financial performances of different rice-based cropping systems (CSs). The CSs studied were: Rice-Wheat-Fallow (R-W-F), Rice-Wheat-Maize (R-W-M), Rice-Wheat-Mungbean (R-W-Mu), Rice-Lentil-Maize (R-L-M), Rice-Lentil-Mungbean (R-L-Mu), Rice-Garlic (R-G) and Rice-Onion (R-O). Primary data were collected from 210 randomly selected farms by using structured questionnaire. In this study, Data Envelopment Analysis (DEA) was used to analyze the technical efficiencies of the farms in order to estimate their energy inputs saving potential, under different CSs. Among the studied systems, R-W-M, R-L-M and R-W-Mu were found energy efficient, R-L-Mu, R-W-F and R-W-Mu were efficient considering their greenhouse gas emissions, and R-G, R-O and R-L-M were more profitable systems. Based on the combined energy, environmental and economic criteria, we conclude that R-L-M, R-L-Mu and R-W-M are the most energy, environmentally and economically efficient CSs as compared to other systems in the study. The mean technical efficiency scores of farms indicated a considerable potential of reducing energy inputs (18-34%), without compromising the economic return of the majority farms under different CSs. The results of this study support eco-efficient CSs with modern production technologies. Copyright © 2017 Elsevier Ltd. All rights reserved.

Synthetic Aperture Radar (SAR)-based paddy rice monitoring system: Development and application in key rice producing areas in Tropical Asia

NASA Astrophysics Data System (ADS)

Setiyono, T. D.; Holecz, F.; Khan, N. I.; Barbieri, M.; Quicho, E.; Collivignarelli, F.; Maunahan, A.; Gatti, L.; Romuga, G. C.

2017-01-01

Reliable and regular rice information is essential part of many countries’ national accounting process but the existing system may not be sufficient to meet the information demand in the context of food security and policy. Synthetic Aperture Radar (SAR) imagery is highly suitable for detecting lowland paddy rice, especially in tropical region where pervasive cloud cover in the rainy seasons limits the use of optical imagery. This study uses multi-temporal X-band and C-band SAR imagery, automated image processing, rule-based classification and field observations to classify rice in multiple locations across Tropical Asia and assimilate the information into ORYZA Crop Growth Simulation model (CGSM) to generate high resolution yield maps. The resulting cultivated rice area maps had classification accuracies above 85% and yield estimates were within 81-93% agreement against district level reported yields. The study sites capture much of the diversity in water management, crop establishment and rice maturity durations and the study demonstrates the feasibility of rice detection, yield monitoring, and damage assessment in case of climate disaster at national and supra-national scales using multi-temporal SAR imagery combined with CGSM and automated methods.

Application of Remote Sensors in Mapping Rice Area and Forecasting Its Production: A Review

PubMed Central

Mosleh, Mostafa K.; Hassan, Quazi K.; Chowdhury, Ehsan H.

2015-01-01

Rice is one of the staple foods for more than three billion people worldwide. Rice paddies accounted for approximately 11.5% of the World's arable land area during 2012. Rice provided ∼19% of the global dietary energy in recent times and its annual average consumption per capita was ∼65 kg during 2010–2011. Therefore, rice area mapping and forecasting its production is important for food security, where demands often exceed production due to an ever increasing population. Timely and accurate estimation of rice areas and forecasting its production can provide invaluable information for governments, planners, and decision makers in formulating policies in regard to import/export in the event of shortfall and/or surplus. The aim of this paper was to review the applicability of the remote sensing-based imagery for rice area mapping and forecasting its production. Recent advances on the resolutions (i.e., spectral, spatial, radiometric, and temporal) and availability of remote sensing imagery have allowed us timely collection of information on the growth and development stages of the rice crop. For elaborative understanding of the application of remote sensing sensors, following issues were described: the rice area mapping and forecasting its production using optical and microwave imagery, synergy between remote sensing-based methods and other developments, and their implications as an operational one. The overview of the studies to date indicated that remote sensing-based methods using optical and microwave imagery found to be encouraging. However, there were having some limitations, such as: (i) optical remote sensing imagery had relatively low spatial resolution led to inaccurate estimation of rice areas; and (ii) radar imagery would suffer from speckles, which potentially would degrade the quality of the images; and also the brightness of the backscatters were sensitive to the interacting surface. In addition, most of the methods used in forecasting rice yield were empirical in nature, so thus it would require further calibration and validation prior to implement over other geographical locations. PMID:25569753

Application of remote sensors in mapping rice area and forecasting its production: a review.

PubMed

Mosleh, Mostafa K; Hassan, Quazi K; Chowdhury, Ehsan H

2015-01-05

Rice is one of the staple foods for more than three billion people worldwide. Rice paddies accounted for approximately 11.5% of the World's arable land area during 2012. Rice provided ~19% of the global dietary energy in recent times and its annual average consumption per capita was ~65 kg during 2010-2011. Therefore, rice area mapping and forecasting its production is important for food security, where demands often exceed production due to an ever increasing population. Timely and accurate estimation of rice areas and forecasting its production can provide invaluable information for governments, planners, and decision makers in formulating policies in regard to import/export in the event of shortfall and/or surplus. The aim of this paper was to review the applicability of the remote sensing-based imagery for rice area mapping and forecasting its production. Recent advances on the resolutions (i.e., spectral, spatial, radiometric, and temporal) and availability of remote sensing imagery have allowed us timely collection of information on the growth and development stages of the rice crop. For elaborative understanding of the application of remote sensing sensors, following issues were described: the rice area mapping and forecasting its production using optical and microwave imagery, synergy between remote sensing-based methods and other developments, and their implications as an operational one. The overview of the studies to date indicated that remote sensing-based methods using optical and microwave imagery found to be encouraging. However, there were having some limitations, such as: (i) optical remote sensing imagery had relatively low spatial resolution led to inaccurate estimation of rice areas; and (ii) radar imagery would suffer from speckles, which potentially would degrade the quality of the images; and also the brightness of the backscatters were sensitive to the interacting surface. In addition, most of the methods used in forecasting rice yield were empirical in nature, so thus it would require further calibration and validation prior to implement over other geographical locations.

Survey of fungal counts and natural occurrence of aflatoxins in Malaysian starch-based foods.

PubMed

Abdullah, N; Nawawi, A; Othman, I

1998-01-01

In a survey of starch-based foods sampled from retail outlets in Malaysia, fungal colonies were mostly detected in wheat flour (100%), followed by rice flour (74%), glutinous rice grains (72%), ordinary rice grains (60%), glutinous rice flour (48%) and corn flour (26%). All positive samples of ordinary rice and glutinous rice grains had total fungal counts below 10(3) cfu/g sample, while among the positive rice flour, glutinous rice flour and corn flour samples, the highest total fungal count was more than 10(3) but less than 10(4) cfu/g sample respectively. However, in wheat flour samples total fungal count ranged from 10(2) cfu/g sample to slightly more than 10(4) cfu/g sample. Aflatoxigenic colonies were mostly detected in wheat flour (20%), followed by ordinary rice grains (4%), glutinous rice grains (4%) and glutinous rice flour (2%). No aflatoxigenic colonies were isolated from rice flour and corn flour samples. Screening of aflatoxin B1, aflatoxin B2, aflatoxin G1 and aflatoxin G2 using reversed-phase HPLC were carried out on 84 samples of ordinary rice grains and 83 samples of wheat flour. Two point four percent (2.4%) of ordinary rice grains were positive for aflatoxin G1 and 3.6% were positive for aflatoxin G2. All the positive samples were collected from private homes at concentrations ranging from 3.69-77.50 micrograms/kg. One point two percent (1.2%) of wheat flour samples were positive for aflatoxin B1 at a concentration of 25.62 micrograms/kg, 4.8% were positive for aflatoxin B2 at concentrations ranging from 11.25-252.50 micrograms/kg, 3.6% were positive for aflatoxin G1 at concentrations ranging from 25.00-289.38 micrograms/kg and 13.25% were positive for aflatoxin G2 at concentrations ranging from 16.25-436.25 micrograms/kg. Similarly, positive wheat flour samples were mostly collected from private homes.

Rice production model based on the concept of ecological footprint

NASA Astrophysics Data System (ADS)

Faiz, S. A.; Wicaksono, A. D.; Dinanti, D.

2017-06-01

Pursuant to what had been stated in Region Spatial Planning (RTRW) of Malang Regency for period 2010-2030, Malang Regency was considered as the center of agricultural development, including districts bordered with Malang City. To protect the region functioning as the provider of rice production, then the policy of sustainable food farming-land (LP2B) was made which its implementation aims to protect rice-land. In the existing condition, LP2B system was not maximally executed, and it caused a limited extend of rice-land to deliver rice production output. One cause related with the development of settlements and industries due to the effect of Malang City that converted land-function. Location of research focused on 30 villages with direct border with Malang City. Review was conducted to develop a model of relation between farming production output and ecological footprint variables. These variables include rice-land area (X1), built land percentage (X2), and number of farmers (X3). Analysis technique was regression. Result of regression indicated that the model of rice production output Y=-207,983 + 10.246X1. Rice-land area (X1) was the most influential independent variable. It was concluded that of villages directly bordered with Malang City, there were 11 villages with higher production potential because their rice production yield was more than 1,000 tons/year, while 12 villages were threatened with low production output because its rice production yield only attained 500 tons/year. Based on the model and the spatial direction of RTRW, it can be said that the direction for the farming development policy must be redesigned to maintain rice-land area on the regions on which agricultural activity was still dominant. Because rice-land area was the most influential factor to farming production. Therefore, the wider the rice-land is, the higher rice production output is on each village.

Crop and varietal diversification of rainfed rice based cropping systems for higher productivity and profitability in Eastern India

PubMed Central

Panda, B. B.; Raja, R.; Singh, Teekam; Tripathi, R.; Shahid, M.; Nayak, A. K.

2017-01-01

Rice-rice system and rice fallows are no longer productive in Southeast Asia. Crop and varietal diversification of the rice based cropping systems may improve the productivity and profitability of the systems. Diversification is also a viable option to mitigate the risk of climate change. In Eastern India, farmers cultivate rice during rainy season (June–September) and land leftovers fallow after rice harvest in the post-rainy season (November–May) due to lack of sufficient rainfall or irrigation amenities. However, in lowland areas, sufficient residual soil moistures are available in rice fallow in the post-rainy season (November–March), which can be utilized for raising second crops in the region. Implementation of suitable crop/varietal diversification is thus very much vital to achieve this objective. To assess the yield performance of rice varieties under timely and late sown conditions and to evaluate the performance of dry season crops following them, three different duration rice cultivars were transplanted in July and August. In dry season several non-rice crops were sown in rice fallow to constitute a cropping system. The results revealed that tiller occurrence, biomass accumulation, dry matter remobilization, crop growth rate, and ultimately yield were significantly decreased under late transplanting. On an average, around 30% yield reduction obtained under late sowing may be due to low temperature stress and high rainfall at reproductive stages of the crop. Dry season crops following short duration rice cultivars performed better in terms of grain yield. In the dry season, toria was profitable when sown earlier and if sowing was delayed greengram was suitable. Highest system productivity and profitability under timely sown rice may be due to higher dry matter remobilization from source to sink. A significant correlation was observed between biomass production and grain yield. We infer that late transplanting decrease the tiller occurrence and assimilate remobilization efficiency, which may be responsible for the reduced grain yield. PMID:28437487

Crop and varietal diversification of rainfed rice based cropping systems for higher productivity and profitability in Eastern India.

PubMed

Lal, B; Gautam, Priyanka; Panda, B B; Raja, R; Singh, Teekam; Tripathi, R; Shahid, M; Nayak, A K

2017-01-01

Rice-rice system and rice fallows are no longer productive in Southeast Asia. Crop and varietal diversification of the rice based cropping systems may improve the productivity and profitability of the systems. Diversification is also a viable option to mitigate the risk of climate change. In Eastern India, farmers cultivate rice during rainy season (June-September) and land leftovers fallow after rice harvest in the post-rainy season (November-May) due to lack of sufficient rainfall or irrigation amenities. However, in lowland areas, sufficient residual soil moistures are available in rice fallow in the post-rainy season (November-March), which can be utilized for raising second crops in the region. Implementation of suitable crop/varietal diversification is thus very much vital to achieve this objective. To assess the yield performance of rice varieties under timely and late sown conditions and to evaluate the performance of dry season crops following them, three different duration rice cultivars were transplanted in July and August. In dry season several non-rice crops were sown in rice fallow to constitute a cropping system. The results revealed that tiller occurrence, biomass accumulation, dry matter remobilization, crop growth rate, and ultimately yield were significantly decreased under late transplanting. On an average, around 30% yield reduction obtained under late sowing may be due to low temperature stress and high rainfall at reproductive stages of the crop. Dry season crops following short duration rice cultivars performed better in terms of grain yield. In the dry season, toria was profitable when sown earlier and if sowing was delayed greengram was suitable. Highest system productivity and profitability under timely sown rice may be due to higher dry matter remobilization from source to sink. A significant correlation was observed between biomass production and grain yield. We infer that late transplanting decrease the tiller occurrence and assimilate remobilization efficiency, which may be responsible for the reduced grain yield.

Web-based decision support system to predict risk level of long term rice production

NASA Astrophysics Data System (ADS)

Mukhlash, Imam; Maulidiyah, Ratna; Sutikno; Setiyono, Budi

2017-09-01

Appropriate decision making in risk management of rice production is very important in agricultural planning, especially for Indonesia which is an agricultural country. Good decision would be obtained if the supporting data required are satisfied and using appropriate methods. This study aims to develop a Decision Support System that can be used to predict the risk level of rice production in some districts which are central of rice production in East Java. Web-based decision support system is constructed so that the information can be easily accessed and understood. Components of the system are data management, model management, and user interface. This research uses regression models of OLS and Copula. OLS model used to predict rainfall while Copula model used to predict harvested area. Experimental results show that the models used are successfully predict the harvested area of rice production in some districts which are central of rice production in East Java at any given time based on the conditions and climate of a region. Furthermore, it can predict the amount of rice production with the level of risk. System generates prediction of production risk level in the long term for some districts that can be used as a decision support for the authorities.

Facile fabrication of rice husk based silicon dioxide nanospheres loaded with silver nanoparticles as a rice antibacterial agent

PubMed Central

Cui, Jianghu; Liang, You; Yang, Desong; Liu, Yingliang

2016-01-01

Bacterial leaf blight of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major disease of rice, leading to reduction in production by 10–50%. In order to control this disease, various chemical bactericides have been used. Wide and prolonged application of chemical bactericides resulted in the resistant strain of Xoo that was isolated from rice. To address this problem, we were searching for an environmentally friendly alternative to the commonly used chemical bactericides. In this work, we demonstrate that silicon dioxide nanospheres loaded with silver nanoparticles (SiO2-Ag) can be prepared by using rice husk as base material precursor. The results of the antibacterial tests showed that SiO2-Ag composites displayed antibacterial activity against Xoo. At cellular level, the cell wall/membrane was damaged and intercellular contents were leaked out by slow-releasing of silver ions from SiO2-Ag composites. At molecular level, this composite induced reactive oxygen species production and inhibited DNA replication. Based on the results above, we proposed the potential antibacterial mechanism of SiO2-Ag composites. Moreover, the cytotoxicity assay indicated that the composites showed mild toxicity with rice cells. Thus, this work provided a new strategy to develop biocide derived from residual biomass. PMID:26888152

Rice crop mapping and change prediction using multi-temporal satellite images in the Mekong Delta, Vietnam

NASA Astrophysics Data System (ADS)

Chen, C. R.; Chen, C. F.; Nguyen, S. T.

2014-12-01

The rice cropping systems in the Vietnamese Mekong Delta (VMD) has been undergoing major changes to cope with developing agro-economics, increasing population and changing climate. Information on rice cropping practices and changes in cropping systems is critical for policymakers to devise successful strategies to ensure food security and rice grain exports for the country. The primary objective of this research is to map rice cropping systems and predict future dynamics of rice cropping systems using the MODIS time-series data of 2002, 2006, and 2010. First, a phenology-based classification approach was applied for the classification and assessment of rice cropping systems in study region. Second, the Cellular Automata-Markov (CA-Markov) models was used to simulate the rice-cropping system map of VMD for 2010. The comparisons between the classification maps and the ground reference data indicated satisfactory results with overall accuracies and Kappa coefficients, respectively, of 81.4% and 0.75 for 2002, 80.6% and 0.74 for 2006 and 85.5% and 0.81 for 2010. The simulated map of rice cropping system for 2010 was extrapolated by CA-Markov model based on the trend of rice cropping systems during 2002~2006. The comparison between predicted scenario and classification map for 2010 presents a reasonably closer agreement. In conclusion, the CA-Markov model performs a powerful tool for the dynamic modeling of changes in rice cropping systems, and the results obtained demonstrate that the approach produces satisfactory results in terms of accuracy, quantitative forecast and spatial pattern changes. Meanwhile, the projections of the future changes would provide useful inputs to the agricultural policy for effective management of the rice cropping practices in VMD.

Effect of waxy rice flour and cassava starch on freeze-thaw stability of rice starch gels.

PubMed

Charoenrein, Sanguansri; Preechathammawong, Nutsuda

2012-10-01

Repeatedly frozen and thawed rice starch gel affects quality. This study investigated how incorporating waxy rice flour (WF) and cassava starch (CS) in rice starch gel affects factors used to measure quality. When rice starch gels containing 0-2% WF and CS were subjected to 5 freeze-thaw cycles, both WF and CS reduced the syneresis in first few cycles. However CS was more effective in reducing syneresis than WF. The different composite arrangement of rice starch with WF or CS caused different mechanisms associated with the rice starch gel retardation of retrogradation, reduced the spongy structure and lowered syneresis. Both swollen granules of rice starch and CS caused an increase in the hardness of the unfrozen and freeze-thawed starch gel while highly swollen WF granules caused softer gels. These results suggested that WF and CS were effective in preserving quality in frozen rice starch based products. Copyright © 2012 Elsevier Ltd. All rights reserved.

Rice-Map: a new-generation rice genome browser.

PubMed

Wang, Jun; Kong, Lei; Zhao, Shuqi; Zhang, He; Tang, Liang; Li, Zhe; Gu, Xiaocheng; Luo, Jingchu; Gao, Ge

2011-03-30

The concurrent release of rice genome sequences for two subspecies (Oryza sativa L. ssp. japonica and Oryza sativa L. ssp. indica) facilitates rice studies at the whole genome level. Since the advent of high-throughput analysis, huge amounts of functional genomics data have been delivered rapidly, making an integrated online genome browser indispensable for scientists to visualize and analyze these data. Based on next-generation web technologies and high-throughput experimental data, we have developed Rice-Map, a novel genome browser for researchers to navigate, analyze and annotate rice genome interactively. More than one hundred annotation tracks (81 for japonica and 82 for indica) have been compiled and loaded into Rice-Map. These pre-computed annotations cover gene models, transcript evidences, expression profiling, epigenetic modifications, inter-species and intra-species homologies, genetic markers and other genomic features. In addition to these pre-computed tracks, registered users can interactively add comments and research notes to Rice-Map as User-Defined Annotation entries. By smoothly scrolling, dragging and zooming, users can browse various genomic features simultaneously at multiple scales. On-the-fly analysis for selected entries could be performed through dedicated bioinformatic analysis platforms such as WebLab and Galaxy. Furthermore, a BioMart-powered data warehouse "Rice Mart" is offered for advanced users to fetch bulk datasets based on complex criteria. Rice-Map delivers abundant up-to-date japonica and indica annotations, providing a valuable resource for both computational and bench biologists. Rice-Map is publicly accessible at http://www.ricemap.org/, with all data available for free downloading.

Evaluation of virus resistance and agronomic performance of rice cultivar ASD 16 after transfer of transgene against Rice tungro bacilliform virus by backcross breeding.

PubMed

Valarmathi, P; Kumar, G; Robin, S; Manonmani, S; Dasgupta, I; Rabindran, R

2016-08-01

Severe losses of rice yield in south and southeast Asia are caused by Rice tungro disease (RTD) induced by mixed infection of Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV). In order to develop transgene-based resistance against RTBV, one of its genes, ORF IV, was used to generate transgenic resistance based on RNA-interference in the easily transformed rice variety Pusa Basmati-1, and the transgene was subsequently introgressed to rice variety ASD 16, a variety popular in southern India, using transgene marker-assisted selection. Here, we report the evaluation of BC3F4 and BC3F5 generation rice plants for resistance to RTBV as well as for agronomic traits under glasshouse conditions. The BC3F4 and BC3F5 generation rice plants tested showed variable levels of resistance, which was manifested by an average of twofold amelioration in height reduction, 1.5-fold decrease in the reduction in chlorophyll content, and 100- to 10,000-fold reduction in the titers of RTBV, but no reduction of RTSV titers, in three backcrossed lines when compared with the ASD 16 parent. Agronomic traits of some of the backcrossed lines recorded substantial improvements when compared with the ASD 16 parental line after inoculation by RTBV and RTSV. This work represents an important step in transferring RTD resistance to a susceptible popular rice variety, hence enhancing its yield in areas threatened by the disease.

Identification of drought-responsive genes in roots of upland rice (Oryza sativa L)

PubMed Central

Rabello, Aline R; Guimarães, Cléber M; Rangel, Paulo HN; da Silva, Felipe R; Seixas, Daniela; de Souza, Emanuel; Brasileiro, Ana CM; Spehar, Carlos R; Ferreira, Márcio E; Mehta, Ângela

2008-01-01

Background Rice (Oryza sativa L.) germplasm represents an extraordinary source of genes that control traits of agronomic importance such as drought tolerance. This diversity is the basis for the development of new cultivars better adapted to water restriction conditions, in particular for upland rice, which is grown under rainfall. The analyses of subtractive cDNA libraries and differential protein expression of drought tolerant and susceptible genotypes can contribute to the understanding of the genetic control of water use efficiency in rice. Results Two subtractive libraries were constructed using cDNA of drought susceptible and tolerant genotypes submitted to stress against cDNA of well-watered plants. In silico analysis revealed 463 reads, which were grouped into 282 clusters. Several genes expressed exclusively in the tolerant or susceptible genotypes were identified. Additionally, proteome analysis of roots from stressed plants was performed and 22 proteins putatively associated to drought tolerance were identified by mass spectrometry. Conclusion Several genes and proteins involved in drought-response, as well as genes with no described homologs were identified. Genes exclusively expressed in the tolerant genotype were, in general, related to maintenance of turgor and cell integrity. In contrast, in the susceptible genotype, expression of genes involved in protection against cell damage was not detected. Several protein families identified in the proteomic analysis were not detected in the cDNA analysis. There is an indication that the mechanisms of susceptibility to drought in upland rice are similar to those of lowland varieties. PMID:18922162

Identification and Expression Analysis of microRNAs at the Grain Filling Stage in Rice(Oryza sativa L.)via Deep Sequencing

PubMed Central

Yi, Rong; Zhu, Zhixuan; Hu, Jihong; Qian, Qian; Dai, Jincheng; Ding, Yi

2013-01-01

MicroRNAs (miRNAs) have been shown to play crucial roles in the regulation of plant development. In this study, high-throughput RNA-sequencing technology was used to identify novel miRNAs, and to reveal miRNAs expression patterns at different developmental stages during rice (Oryza sativa L.) grain filling. A total of 434 known miRNAs (380, 402, 390 and 392 at 5, 7, 12 and 17 days after fertilization, respectively.) were obtained from rice grain. The expression profiles of these identified miRNAs were analyzed and the results showed that 161 known miRNAs were differentially expressed during grain development, a high proportion of which were up-regulated from 5 to 7 days after fertilization. In addition, sixty novel miRNAs were identified, and five of these were further validated experimentally. Additional analysis showed that the predicted targets of the differentially expressed miRNAs may participate in signal transduction, carbohydrate and nitrogen metabolism, the response to stimuli and epigenetic regulation. In this study, differences were revealed in the composition and expression profiles of miRNAs among individual developmental stages during the rice grain filling process, and miRNA editing events were also observed, analyzed and validated during this process. The results provide novel insight into the dynamic profiles of miRNAs in developing rice grain and contribute to the understanding of the regulatory roles of miRNAs in grain filling. PMID:23469249

Isolation and identification of phenolic antioxidants in black rice bran.

PubMed

Jun, Hyun-Il; Shin, Jae-Wook; Song, Geun-Seoup; Kim, Young-Soo

2015-02-01

Black rice bran contains phenolic compounds of a high antioxidant activity. In this study, the 40% acetone extract of black rice bran was sequentially fractionated to obtain 5 fractions. Out of the 5 fractions, ethyl acetate fraction was subfractionated using the Sephadex LH-20 chromatography. The antioxidant activity of phenolic compounds in the extracts was investigated by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical assay, 2,2-azino-bis-(3-ethylenebenzothiozoline-6-sulfonic acid) (ABTS) radical cation assay, reducing power. The subfraction 2 from ethyl acetate fraction had the highest total phenolic contents (TPC) (816.0 μg/mg) and the lowest EC50 values (47.8 μg/mL for DPPH radical assay, 112.8 μg/mL for ABTS radical cation assay, and 49.2 μg/mL for reducing power). These results were 3.1, 1.3, and 2.6 times lower than those of butylated hydroxytoluene (BHT), respectively. At a concentration of 100 μg/mL, the antioxidant activity and TPC of various extracts was closely correlated, with correlation coefficients (R(2) ) higher than 0.86. The major phenolic acid in subfraction 2 was identified as ferulic acid (178.3 μg/mg) by HPLC and LC-ESI/MS/MS analyses. Our finding identified ferulic acid as a major phenolic compound in black rice bran, and supports the potential use of black rice bran as a natural source of antioxidant. © 2015 Institute of Food Technologists®

Potential gene flow from transgenic rice (Oryza sativa L.) to different weedy rice (Oryza sativa f. spontanea) accessions based on reproductive compatibility.

PubMed

Song, Xiaoling; Liu, Linli; Wang, Zhou; Qiang, Sheng

2009-08-01

The possibility of gene flow from transgenic crops to wild relatives may be affected by reproductive capacity between them. The potential gene flow from two transgenic rice lines containing the bar gene to five accessions of weedy rice (WR1-WR5) was determined through examination of reproductive compatibility under controlled pollination. The pollen grain germination of two transgenic rice lines on the stigma of all weedy rice, rice pollen tube growth down the style and entry into the weedy rice ovary were similar to self-pollination in weedy rice. However, delayed double fertilisation and embryo abortion in crosses between WR2 and Y0003 were observed. Seed sets between transgenic rice lines and weedy rice varied from 8 to 76%. Although repeated pollination increased seed set significantly, the rank of the seed set between the weedy rice accessions and rice lines was not changed. The germination rates of F(1) hybrids were similar or greater compared with respective females. All F(1) plants expressed glufosinate resistance in the presence of glufosinate selection pressure. The frequency of gene flow between different weedy rice accessions and transgenic herbicide-resistant rice may differ owing to different reproductive compatibility. This result suggests that, when wild relatives are selected as experimental materials for assessing the gene flow of transgenic rice, it is necessary to address the compatibility between transgenic rice and wild relatives.

Current understanding on Villosiclava virens, a unique flower-infecting fungus causing rice false smut disease.

PubMed

Fan, Jing; Yang, Juan; Wang, Yu-Qiu; Li, Guo-Bang; Li, Yan; Huang, Fu; Wang, Wen-Ming

2016-12-01

Villosiclava virens (Vv) is an ascomycete fungal pathogen that causes false smut disease in rice. Recent reports have revealed some interesting aspects of the enigmatic pathogen to address the question of why it specifically infects rice flowers and converts a grain into a false smut ball. Comparative and functional genomics have suggested specific adaptation of Vv in the colonization of rice flowers. Anatomical studies have disclosed that Vv specifically infects rice stamen filaments before heading and intercepts seed formation. In addition, Vv can occupy the whole inner space of a spikelet embracing all floral organs and activate the rice grain-filling network, presumably for nutrient acquisition to support the development of the false smut ball. This profile provides a general overview of the rice false smut pathogen, and summarizes advances in the Vv life cycle, genomics and genetics, and the molecular Vv-rice interaction. Current understandings of the Vv-rice pathosystem indicate that it is a unique and interesting system which can enrich the study of plant-pathogen interactions. Taxonomy: Ustilaginoidea virens is the anamorph form of the pathogen (Kingdom Fungi; Phylum Ascomycota; Class Ascomycetes; Subclass Incertae sedis; Order Incertae sedis; Family Incertae sedis; Genus Ustilaginoidea). The teleomorph form is Villosiclava virens (Kingdom Fungi; Phylum Ascomycota; Class Ascomycetes; Subclass Sordariomycetes; Order Hypocreales; Family Clavicipitaceae; Genus Villosiclava). Disease symptoms: The only visible symptom is the replacement of rice grains by ball-shaped fungal mycelia, namely false smut balls. When maturing, the false smut ball is covered with powdery chlamydospores, and the colour changes to yellowish, yellowish orange, green, olive green and, finally, to greenish black. Sclerotia are often formed on the false smut balls in autumn. Identification and detection: Vv conidia are round to elliptical, measuring 3-5 μm in diameter. Chlamydospores are ornamented with prominent irregularly curved spines, which are 200-500 nm in length. The sclerotia are black, horseshoe-shaped and irregular oblong or flat, ranging from 2 to 20 mm. Nested polymerase chain reaction (PCR) and quantitative PCR have been developed to specifically detect Vv presence in rice tissues and other biotic and abiotic samples in fields. Host range: Rice is the primary host for Vv. Natural infection by Vv has been found on several paddy field weeds, including Digitaria marginata, Panicum trypheron, Echinochloa crusgalli and Imperata cylindrica. However, the occurrence of infection in these potential alternative hosts is very rare. Life cycle: Vv infects rice spikelets at the late rice booting stage, and produces false smut balls covered with dark-green chlamydospores. Occasionally, sclerotia form on the surface of false smut balls in late autumn when the temperature fluctuates greatly between day and night. Both chlamydospores and sclerotia may serve as primary infection sources. Rainfall at the rice booting stage is a major environmental factor resulting in epidemics of rice false smut disease. Disease control: The use of fungicides is the major approach for the control of Vv. Several fungicides, such as cuproxat SC, copper oxychloride, tebuconazole, propiconazole, difenoconazole and validamycin, are often applied. However, the employment of resistant rice cultivars and genes has been limited, because of the poor understanding of rice resistance to Vv. Useful websites: Villosiclava virens genome sequence: http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=JHTR01#contigs. © 2015 BSPP and John Wiley & Sons Ltd.

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

PubMed

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.

Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy.

PubMed

Jung, Ki-Hong; Dardick, Christopher; Bartley, Laura E; Cao, Peijian; Phetsom, Jirapa; Canlas, Patrick; Seo, Young-Su; Shultz, Michael; Ouyang, Shu; Yuan, Qiaoping; Frank, Bryan C; Ly, Eugene; Zheng, Li; Jia, Yi; Hsia, An-Ping; An, Kyungsook; Chou, Hui-Hsien; Rocke, David; Lee, Geun Cheol; Schnable, Patrick S; An, Gynheung; Buell, C Robin; Ronald, Pamela C

2008-10-06

Studies of gene function are often hampered by gene-redundancy, especially in organisms with large genomes such as rice (Oryza sativa). We present an approach for using transcriptomics data to focus functional studies and address redundancy. To this end, we have constructed and validated an inexpensive and publicly available rice oligonucleotide near-whole genome array, called the rice NSF45K array. We generated expression profiles for light- vs. dark-grown rice leaf tissue and validated the biological significance of the data by analyzing sources of variation and confirming expression trends with reverse transcription polymerase chain reaction. We examined trends in the data by evaluating enrichment of gene ontology terms at multiple false discovery rate thresholds. To compare data generated with the NSF45K array with published results, we developed publicly available, web-based tools (www.ricearray.org). The Oligo and EST Anatomy Viewer enables visualization of EST-based expression profiling data for all genes on the array. The Rice Multi-platform Microarray Search Tool facilitates comparison of gene expression profiles across multiple rice microarray platforms. Finally, we incorporated gene expression and biochemical pathway data to reduce the number of candidate gene products putatively participating in the eight steps of the photorespiration pathway from 52 to 10, based on expression levels of putatively functionally redundant genes. We confirmed the efficacy of this method to cope with redundancy by correctly predicting participation in photorespiration of a gene with five paralogs. Applying these methods will accelerate rice functional genomics.

Use of rice-based oral rehydration solution in a large diarrhoea treatment centre in Bangladesh: in-house production, use and relative cost.

PubMed

Islam, M A; Mahalanabis, D; Majid, N

1994-12-01

Glucose-based oral rehydration salt (ORS) is an appropriate and cost-effective tool to treat diarrhoeal dehydration. In patients with a high purging rate, particularly due to cholera, rice-based ORS has been shown to substantially reduce stool output compared to glucose ORS. However, it is not used in the hospitals or diarrhoea treatment centres largely because of the non-availability of a ready-to-use inexpensive packaged product and because of the problem of cooking. In a large diarrhoea treatment centre in Bangladesh (with an annual ORS consumption of approximately 140,000 litres), we have maintained in-house production of rice ORS and used it routinely for more than 600,000 patients over the last nine years. Semi-literate health workers cook rice ORS and supervise mothers in its use. Rice ORS is less costly (US $0.15 per patient treated compared with US $0.37 for glucose ORS) and is well accepted. It is an attractive alternative to glucose ORS in many fixed facility treatment centres in countries where rice is a staple and cholera is endemic. The process of its in-house preparation and use is described in this report which may assist hospitals wishing to use rice ORS in treating diarrhoea patients. Availability of a low cost ready-to-use rice ORS packet (which needs no cooking) with adequate shelf-life will increase its use at fixed facilities.

Transgenic Bacillus thuringiensis (Bt) rice is safer to aquatic ecosystems than its non-transgenic counterpart.

PubMed

Li, Guangsheng; Wang, Yongmo; Liu, Biao; Zhang, Guoan

2014-01-01

Rice lines genetically modified with the crystal toxin genes from Bacillus thuringiensis (Bt) have experienced rapid development, with biosafety certificates for two Bt rice lines issued in 2009. There has still been no commercial release of these lines yet due to public concerns about human health and environmental risks. Some studies confirmed that Bt rice was as safe as conventional rice to non-target organisms when pesticides were not applied, however, pesticides are still required in Bt rice to control non-lepidopteran pests. In this study, we assessed the environmental effects of two Bt rice lines expressing either the cry1Ab/1Ac or cry2A genes, respectively, by using zooplanktons as indicator species under normal field management practices using pesticides when required. In the whole rice growing season, non-Bt rice was sprayed 5 times while Bt rice was sprayed 2 times, which ensured both rice achieved a normal yield. Field investigations showed that rice type (Bt and non-Bt) significantly influenced zooplankton abundance and diversity, which were up to 95% and 80% lower in non-Bt rice fields than Bt rice fields. Laboratory rearing showed that water from non-Bt rice fields was significantly less suitable for the survival and reproduction of Daphnia magna and Paramecium caudatum in comparison with water from Bt rice fields. Higher pesticide residues were detected in the water from non-Bt than Bt rice fields, accounting for the bad performance of zooplankton in non-Bt field water. Our results demonstrate that Bt rice is safer to aquatic ecosystems than non-Bt rice, and its commercialization will be beneficial for biodiversity restoration in rice-based ecosystems.

Transgenic Bacillus thuringiensis (Bt) Rice Is Safer to Aquatic Ecosystems than Its Non-Transgenic Counterpart

PubMed Central

Li, Guangsheng; Wang, Yongmo; Liu, Biao; Zhang, Guoan

2014-01-01

Rice lines genetically modified with the crystal toxin genes from Bacillus thuringiensis (Bt) have experienced rapid development, with biosafety certificates for two Bt rice lines issued in 2009. There has still been no commercial release of these lines yet due to public concerns about human health and environmental risks. Some studies confirmed that Bt rice was as safe as conventional rice to non-target organisms when pesticides were not applied, however, pesticides are still required in Bt rice to control non-lepidopteran pests. In this study, we assessed the environmental effects of two Bt rice lines expressing either the cry1Ab/1Ac or cry2A genes, respectively, by using zooplanktons as indicator species under normal field management practices using pesticides when required. In the whole rice growing season, non-Bt rice was sprayed 5 times while Bt rice was sprayed 2 times, which ensured both rice achieved a normal yield. Field investigations showed that rice type (Bt and non-Bt) significantly influenced zooplankton abundance and diversity, which were up to 95% and 80% lower in non-Bt rice fields than Bt rice fields. Laboratory rearing showed that water from non-Bt rice fields was significantly less suitable for the survival and reproduction of Daphnia magna and Paramecium caudatum in comparison with water from Bt rice fields. Higher pesticide residues were detected in the water from non-Bt than Bt rice fields, accounting for the bad performance of zooplankton in non-Bt field water. Our results demonstrate that Bt rice is safer to aquatic ecosystems than non-Bt rice, and its commercialization will be beneficial for biodiversity restoration in rice-based ecosystems. PMID:25105299

Climate Change Implications to Irrigated Rice Production in Southern Brazil: A Modelling Approach

NASA Astrophysics Data System (ADS)

Dos Santos, Thiago

Rice is one of the staple foods for more than three billion people worldwide. When cultivated under irrigated conditions (i.e. lowland rice), rice is one of the most intensive water consumer crops globally. Therefore, representation of rice growth should be integrated into the latest land surface models to allow studies on food security and to ensure that accurate simulations of the bidirectional feedbacks between the land surface and atmosphere take place. In this study, I present a new process-based model for rice fields that includes rice growth and rice irrigation as modules within the Agro-IBIS dynamic agro-ecosystem model. The model includes a series of equations, agricultural management parameters and an irrigation scheme that are specifically tailored for rice crops. The model was evaluated against leaf area index and biomass observations, obtained for one growing season in Rio Grande do Sul state (southern Brazil), and in Los Banos, Philippines. The model accurately captured the temporal dynamics of leaf area index in both the Brazilian and the Philippine sites, and predicted end-of-season biomass with an error of between -9.5% and 11.3% depending on the location and the plant organ. Rice phenology is predicted by the model based on experimentally-derived growth rates, and was evaluated by comparing simulated and observed durations of the four growth phases considered by the model. Agro-IBIS showed a tendency to overestimate the duration of the growth stages between 3% and 16%, but underestimated by 8% the duration of the panicle formation phase in one growing season. The new irrigation model is based on the water balance at the surface and applies irrigation in order to keep the water layer at the paddy field always in the optimum level. A set of climate projections from global climate models under two emission scenarios, and excluding and considering CO2 fertilizations effects, was used to drive the updated Agro-IBIS to estimate the effects of climate change on rice phenology, productivity and irrigation demand in southern Brazil during the 21st century. The results suggest that rice yields in southern Brazil can increase in average by 10-30%, but by up to 80% in regions where the current temperature is below optimum for rice growth and therefore will be benefited by warming. However, the same region might experience higher water demand for rice irrigation, which might pose a challenge for rice production in that region.

Over-expression of a NAC 67 transcription factor from finger millet (Eleusine coracana L.) confers tolerance against salinity and drought stress in rice.

PubMed

Rahman, Hifzur; Ramanathan, Valarmathi; Nallathambi, Jagedeeshselvam; Duraialagaraja, Sudhakar; Muthurajan, Raveendran

2016-05-11

NAC proteins (NAM (No apical meristem), ATAF (Arabidopsis transcription activation factor) and CUC (cup-shaped cotyledon)) are plant-specific transcription factors reported to be involved in regulating growth, development and stress responses. Salinity responsive transcriptome profiling in a set of contrasting finger millet genotypes through RNA-sequencing resulted in the identification of a NAC homolog (EcNAC 67) exhibiting differential salinity responsive expression pattern. Full length cDNA of EcNAC67 was isolated, characterized and validated for its role in abiotic stress tolerance through agrobacterium mediated genetic transformation in a rice cultivar ASD16. Bioinformatics analysis of putative NAC transcription factor (TF) isolated from a salinity tolerant finger millet showed its genetic relatedness to NAC67 family TFs in related cereals. Putative transgenic lines of rice over-expressing EcNAC67 were generated through Agrobacterium mediated transformation and presence/integration of transgene was confirmed through PCR and southern hybridization analysis. Transgenic rice plants harboring EcNAC67 showed enhanced tolerance against drought and salinity under greenhouse conditions. Transgenic rice plants were found to possess higher root and shoot biomass during stress and showed better revival ability upon relief from salinity stress. Upon drought stress, transgenic lines were found to maintain higher relative water content and lesser reduction in grain yield when compared to non-transgenic ASD16 plants. Drought induced spikelet sterility was found to be much lower in the transgenic lines than the non-transgenic ASD16. Results revealed the significant role of EcNAC67 in modulating responses against dehydration stress in rice. No detectable abnormalities in the phenotypic traits were observed in the transgenic plants under normal growth conditions. Results indicate that EcNAC67 can be used as a novel source for engineering tolerance against drought and salinity stress in rice and other crop plants.

Identification of qSOR1, a major rice QTL involved in soil-surface rooting in paddy fields.

PubMed

Uga, Yusaku; Hanzawa, Eiko; Nagai, Shinsei; Sasaki, Kazuhiro; Yano, Masahiro; Sato, Tadashi

2012-01-01

Specific Indonesian lowland rice (Oryza sativa L.) cultivars elongate thick primary roots on the soil surface of paddy fields. To clarify the genetic factors controlling soil-surface rooting, we performed quantitative trait locus (QTL) analyses using 124 recombinant inbred lines (RILs) derived from a cross between Gemdjah Beton, an Indonesian lowland rice cultivar with soil-surface roots, and Sasanishiki, a Japanese lowland rice cultivar without soil-surface roots. These cultivars and the RILs were tested for soil-surface rooting in a paddy field. We identified four regions of chromosomes 3, 4, 6, and 7 that were associated with soil-surface rooting in the field. Among them, one major QTL was located on the long arm of chromosome 7. This QTL explained 32.5-53.6% of the total phenotypic variance across three field evaluations. To perform fine mapping of this QTL, we measured the basal root growth angle of crown roots at the seedling stage in seven BC(2)F(3) recombinant lines grown in small cups in a greenhouse. The QTL was mapped between markers RM21941 and RM21976, which delimit an 812-kb interval in the reference cultivar Nipponbare. We have designated this QTL qSOR1 (quantitative trait locus for SOIL SURFACE ROOTING 1).

Overexpression of OsSAP16 Regulates Photosynthesis and the Expression of a Broad Range of Stress Response Genes in Rice (Oryza sativa L.).

PubMed

Wang, Fei; Coe, Robert A; Karki, Shanta; Wanchana, Samart; Thakur, Vivek; Henry, Amelia; Lin, Hsiang-Chun; Huang, Jianliang; Peng, Shaobing; Quick, William Paul

2016-01-01

This study set out to identify and characterize transcription factors regulating photosynthesis in rice. Screening populations of rice T-DNA activation lines led to the identification of a T-DNA mutant with an increase in intrinsic water use efficiency (iWUE) under well-watered conditions. Flanking sequence analysis showed that the T-DNA construct was located upstream of LOC_Os07g38240 (OsSAP16) encoding for a stress-associated protein (SAP). A second mutant identified with activation in the same gene exhibited the same phenotype; expression of OsSAP16 was shown to be enhanced in both lines. There were no differences in stomatal development or morphology in either of these mutants, although overexpression of OsSAP16 reduced stomatal conductance. This phenotype limited CO2 uptake and the rate of photosynthesis, which resulted in the accumulation of less biomass in the two mutants. Whole transcriptome analysis showed that overexpression of OsSAP16 led to global changes in gene expression consistent with the function of zinc-finger transcription factors. These results show that the gene is involved in modulating the response of rice to drought stress through regulation of the expression of a set of stress-associated genes.

Overexpression of OsSAP16 Regulates Photosynthesis and the Expression of a Broad Range of Stress Response Genes in Rice (Oryza sativa L.)

PubMed Central

Wang, Fei; Coe, Robert A.; Karki, Shanta; Wanchana, Samart; Thakur, Vivek; Henry, Amelia; Lin, Hsiang-Chun; Huang, Jianliang; Peng, Shaobing; Quick, William Paul

2016-01-01

This study set out to identify and characterize transcription factors regulating photosynthesis in rice. Screening populations of rice T-DNA activation lines led to the identification of a T-DNA mutant with an increase in intrinsic water use efficiency (iWUE) under well-watered conditions. Flanking sequence analysis showed that the T-DNA construct was located upstream of LOC_Os07g38240 (OsSAP16) encoding for a stress-associated protein (SAP). A second mutant identified with activation in the same gene exhibited the same phenotype; expression of OsSAP16 was shown to be enhanced in both lines. There were no differences in stomatal development or morphology in either of these mutants, although overexpression of OsSAP16 reduced stomatal conductance. This phenotype limited CO2 uptake and the rate of photosynthesis, which resulted in the accumulation of less biomass in the two mutants. Whole transcriptome analysis showed that overexpression of OsSAP16 led to global changes in gene expression consistent with the function of zinc-finger transcription factors. These results show that the gene is involved in modulating the response of rice to drought stress through regulation of the expression of a set of stress-associated genes. PMID:27303811

Ion-beam irradiation, gene identification, and marker-assisted breeding in the development of low-cadmium rice.

PubMed

Ishikawa, Satoru; Ishimaru, Yasuhiro; Igura, Masato; Kuramata, Masato; Abe, Tadashi; Senoura, Takeshi; Hase, Yoshihiro; Arao, Tomohito; Nishizawa, Naoko K; Nakanishi, Hiromi

2012-11-20

Rice (Oryza sativa L.) grain is a major dietary source of cadmium (Cd), which is toxic to humans, but no practical technique exists to substantially reduce Cd contamination. Carbon ion-beam irradiation produced three rice mutants with <0.05 mg Cd⋅kg(-1) in the grain compared with a mean of 1.73 mg Cd⋅kg(-1) in the parent, Koshihikari. We identified the gene responsible for reduced Cd uptake and developed a strategy for marker-assisted selection of low-Cd cultivars. Sequence analysis revealed that these mutants have different mutations of the same gene (OsNRAMP5), which encodes a natural resistance-associated macrophage protein. Functional analysis revealed that the defective transporter protein encoded by the mutant osnramp5 greatly decreases Cd uptake by roots, resulting in decreased Cd in the straw and grain. In addition, we developed DNA markers to facilitate marker-assisted selection of cultivars carrying osnramp5. When grown in Cd-contaminated paddy fields, the mutants have nearly undetectable Cd in their grains and exhibit no agriculturally or economically adverse traits. Because mutants produced by ion-beam radiation are not transgenic plants, they are likely to be accepted by consumers and thus represent a practical choice for rice production worldwide.

Identification of rice cultivar with exclusive characteristic to Cd using a field-polluted soil and its foreground application.

PubMed

Zhan, Jie; Wei, Shuhe; Niu, Rongcheng; Li, Yunmeng; Wang, Shanshan; Zhu, Jiangong

2013-04-01

Using low-accumulative plant, especially excluder crop, to safely produce food is one of the very important technologies of phytoremediation, which is practical to safe production and long-term remediation of heavy metal-contaminated soil. A pot experiment using field cadmium (Cd)-contaminated soil (Cd concentration was 0.75 mg kg(-1)) was conducted to compare Cd accumulation differences among 39 normal rice cultivars (Japonica) in Shenyang region of China for food safety and high grain yield aim. The results showed that brown grain Cd concentration in 12 rice cultivars of a total of 39 tested cultivars was lower than 0.2 mg kg(-1) (Agricultural Trade Standard of Nonpollution Food for Rice of China, NY 5115-2008). In these 12 cultivars, Cd enrichment factors (Cd concentration ratio in shoot to that in soil) of nine cultivars were lower than 1. Likewise, Cd translocation factors (Cd concentration ratio in shoot to that in root) of eight cultivars were lower than the 0.28 average. Furthermore, grain yield per pot of seven cultivars were higher than the average 18.4 g pot(-1). Four cultivars, i.e., Shendao 5, Tianfu 1, Fuhe 90, and Yanfeng 47 showed Cd-exclusive characteristic and better foreground application.

Identification of differentially expressed genes in brown planthopper Nilaparvata lugens (Hemiptera: Delphacidae) responding to host plant resistance.

PubMed

Yang, Zhifan; Zhang, Futie; Zhu, Lili; He, Guangcun

2006-02-01

The brown planthopper Nilaparvata lugens Stål is one of the major insect pests of rice Oryza sativa L. The host resistance exhibits profound effects on growth, development and propagation of N. lugens. To investigate the molecular response of N. lugens to host resistance, a cDNA-amplified fragment length polymorphism (cDNA-AFLP) technique was employed to identify the differentially expressed genes in the nymphs feeding on three rice varieties. Of the 2,800 cDNA bands analysed, 54 were up-regulated and seven down-regulated qualitatively in N. lugens when the ingestion sources were changed from susceptible rice plants to resistant ones. Sequence analysis of the differential transcript-derived fragments showed that the genes involved in signalling, stress response, gene expression regulation, detoxification and metabolism were regulated by host resistance. Four of the transcript-derived fragments corresponding to genes encoding for a putative B subunit of phosphatase PP2A, a nemo kinase, a cytochrome P450 monooxygenase and a prolyl endopeptidase were further characterized in detail. Northern blot analysis confirmed that the expression of the four genes was enhanced in N. lugens feeding on resistant rice plants. The roles of these genes in the defensive response of N. lugens to host plant resistance were discussed.

Breakfast skipping and breakfast type are associated with daily nutrient intakes and metabolic syndrome in Korean adults

PubMed Central

Chung, Sang-Jin; Lee, Yoonna; Lee, Seokhwa

2015-01-01

BACKGROUND/OBJECTIVES Emerging evidence shows that eating breakfast and breakfast types may be associated with health outcomes and dietary intakes in various populations. The aim of this study was to investigate the association between breakfast types in Korean adults with their daily nutrient intakes and health outcomes. SUBJECTS/METHODS A total of 11,801 20- to 64-year-old adults (age 42.9 ± 11.8 yrs [mean ± standard error of the mean]; male 41.1%, female 58.9%) in 2007-2009 Korean National Health and Nutrition Survey data were divided into 5 groups based on breakfast types in a 24-hr dietary recall: rice with 3 or more side dishes (Rice3+, 35.3%), rice with 0-2 side dishes (Rice0-2, 34.73%), noodles (1.56%), bread and cereal (6.56%), and breakfast skipping (21.63%). Daily nutrient intakes and the risk of metabolic syndrome were compared among five groups. RESULTS Compared with Korean Recommended Nutrient Intake levels, the breakfast-skipping group showed the lowest intake level in most nutrients, whereas the Rice3+ group showed the highest. Fat intake was higher in the bread and noodle groups than in the other groups. When compared with the Rice3+ group, the odds ratios for the risk of obesity and metabolic syndrome were increased in the breakfast skipping, Rice0-2, and noodle groups after controlling for confounding variables. CONCLUSIONS The rice-based breakfast group showed better nutritional status and health outcomes when eating with 3 or more side dishes. Nutrition education is needed to emphasize both the potential advantage of the rice-based, traditional Korean diet in terms of nutritional content and the importance of food diversity. PMID:26060541

Methylmercury cycling, bioaccumulation, and export from agricultural and non-agricultural wetlands in the Yolo Bypass

USGS Publications Warehouse

Windham-Myers, Lisamarie; Marvin-DiPasquale, Mark; Fleck, Jacob; Alpers, Charles N.; Ackerman, Joshua T.; Eagles-Smith, Collin A.; Stricker, Craig; Stephenson, Mark; Feliz, David; Gill, Gary; Bachand, Philip; Brice, Ann; Kulakow, Robin

2010-01-01

d) Identification and testing of potential management approaches for reducing MeHg contamination. In addition, the quantitative results reported here assess the effect of current land use practices in the Yolo Bypass MeHg production, bioaccumulation and export, and provide process-based advice towards achieving current goals of the RWQCB-CVR's Sacramento -- San Joaquin Delta Estuary TMDL for Methyl & Total Mercury (Wood et al., 2010b). Further work is necessary to evaluate biotic exposure in the Yolo Bypass Wildlife Area at higher trophic levels (e.g. birds), to quantify winter hydrologic flux of MeHg to the larger Delta ecosystem, and to evaluate rice straw management options to limit labile carbon supplies to surface sediment during winter months. In summary, agricultural management of rice fields -- specifically the periodic flooding and production of easily degraded organic matter -- promotes the production of MeHg beyond rates seen in naturally vegetated wetlands, whether seasonally or permanently flooded., The exported load from MeHg from these agricultural wetlands may be controlled by limiting hydrologic export from fields to enhance on-site MeHg removal processes, but the tradeoff is that this impoundement increases Me Hg exposure to resident organisms.

[Dynamics and combined injuries of main pest species in rice cropping zones of Yunnan, Southwest China].

PubMed

Dong, Kun; Dong, Yan; Wang, Hai-Long; Zhang, Li-Min; Zan, Qing-An; Chen, Bin; Li, Zheng-Yue

2014-01-01

A series of rice pest injuries (due to pathogens, insects, and weeds) were surveyed in 286 farmers' fields for major rice varieties of three rice cropping zones of Yunnan Province, Southwest China. The composition and dynamics of main pest species were analyzed, and the trend of rice pest succession in Yunnan was discussed based upon landmark publications. The results showed that the three rice cropping zones had different pest characteristics as regard to main species, dynamics and combined injuries. Sheath rot, bacterial leaf blight, rice stripe, leaf hoppers, armyworms and stem borers were serious in the japonica rice zone. Sheath blight and rice stripe were serious in the japonica-indica interlacing zone. Leaf blast, sheath blight, leaf folders and weeds above rice crop canopy were serious in the indica rice zone. False smut, plant hoppers and weeds below rice crop canopy were ubiquitous and serious in the three kinds of rice cropping zones. Many kinds of weed infestation emerged in the whole rice cropping seasons. Echinochloa crusgalli, Sagittaria pygmaea, Potamogeton distinctus and Spirodela polyrhiza were the main species of weeds in the rice cropping zones of Yunnan. Overall, levels of combined injuries due to pests in the japonica rice zone and the indica rice zone were higher than that in the japonica-indica interlacing zone. In terms of the trend of rice pest succession in Yunnan, injuries due to false smut, sheath blight and plant hoppers seemed to be in a worse tendency in all rice cropping zones of Yunnan, while dominants species of weeds in the paddy fields are shifting from the annual weeds to the perennial malignant weeds.

Genetic diversity and structure in hill rice (Oryza sativa L.) landraces from the North-Eastern Himalayas of India.

PubMed

Roy, Somnath; Marndi, B C; Mawkhlieng, B; Banerjee, A; Yadav, R M; Misra, A K; Bansal, K C

2016-07-13

Hill rices (Oryza sativa L.) are direct seeded rices grown on hill slopes of different gradients. These landraces have evolved under rainfed and harsh environmental conditions and may possess genes governing adaptation traits such as tolerance to cold and moisture stress. In this study, 64 hill rice landraces were collected from the state of Arunachal Pradesh of North-Eastern region of India, and assessed by agro-morphological variability and microsatellite markers polymorphism. Our aim was to use phenotypic and genetic diversity data to understand the basis of farmers' classification of hill rice landraces into two groups: umte and tening. Another goal was to understand the genetic differentiation of hill rices into Indica or japonica subspecies. According to farmers' classification, hill rices were categorized into two groups: umte (large-grained, late maturing) and tening (small-grained, early maturing). We did not find significant difference in days to 50 % flowering between the groups. Principal component analysis revealed that two groups can be distinguished on the basis of kernel length-to-width ration (KLW), kernel length (KL), grain length (GrL), grain length-to-width ration (GrLW) and plant height (Ht). Stepwise canonical discriminant analysis identified KL and Ht as the main discriminatory characters between the cultivar groups. Genetic diversity analysis with 35 SSR markers revealed considerable genetic diversity in the hill rice germplasm (gene diversity: 0.66; polymorphism information content: 0.62). Pair-wise allelic difference between umte and tening groups was not statistically significant. The model-based population structure analysis showed that the hill rices were clustered into two broad groups corresponding to Indica and Japonica. The geographic distribution and cultivars grouping of hill rices were not congruent in genetic clusters. Both distance- and model-based approaches indicated that the hill rices were predominantly japonica or admixture among the groups within the subspecies. These findings were further supported by combined analysis hill rices with 150 reference rice accessions representing major genetic groups of rice. This study collected a valuable set of hill rice germplasm for rice breeding and for evolutionary studies. It also generated a new set of information on genetic and phenotypic diversity of hill rice landraces in North-Eastern region of India. The collected hill rices were mostly japonica or admixture among the subpopulations of Indica or Japonica. The findings are useful for utilization and conservation of hill rice germplasm.

Rice production with minimal irrigation and no nitrogen fertilizer by intensive use of treated municipal wastewater.

PubMed

Muramatsu, Ayumi; Watanabe, Toru; Sasaki, Atsushi; Ito, Hiroaki; Kajihara, Akihiko

2014-01-01

We designed a new cultivation system of rice with circulated irrigation to remove nitrogen from treated municipal wastewater effectively and assessed the possibility of nitrogen removal in the new system without any adverse effects on rice production through bench-scale experiments through two seasons. Overgrowth of the rice plant, which can lead to lodging and tasteless rice, was found in the first season probably because nitrogen supply based on standard practice in normal paddy fields was too much in the closed irrigation system. In the second season, therefore, the amount of treated wastewater initially applied to the system was reduced but this resulted in a considerably decreased yield. On the other hand, the taste of the rice was significantly improved. The two-season experiments revealed that the new system enabled rice production with minimal irrigation (approximately 50% on the yield base compared to normal paddy fields) and no nitrogen fertilizer. The system also achieved >95% removal of nitrogen from the treated wastewater used for circulated irrigation. The accumulation of harmful metals in the rice was not observed after one season of cultivation in the new system. The accumulation after cultivation using the same soil repeatedly for a longer time should be examined by further studies.

Differences in net global warming potential and greenhouse gas intensity between major rice-based cropping systems in China.

PubMed

Xiong, Zhengqin; Liu, Yinglie; Wu, Zhen; Zhang, Xiaolin; Liu, Pingli; Huang, Taiqing

2015-12-02

Double rice (DR) and upland crop-single rice (UR) systems are the major rice-based cropping systems in China, yet differences in net global warming potential (NGWP) and greenhouse gas intensity (GHGI) between the two systems are poorly documented. Accordingly, a 3-year field experiment was conducted to simultaneously measure methane (CH4) and nitrous oxide (N2O) emissions and changes in soil organic carbon (SOC) in oil rape-rice-rice and wheat-rice (representing DR and UR, respectively) systems with straw incorporation (0, 3 and 6 t/ha) during the rice-growing seasons. Compared with the UR system, the annual CH4, N2O, grain yield and NGWP were significantly increased in the DR system, though little effect on SOC sequestration or GHGI was observed without straw incorporation. Straw incorporation increased CH4 emission and SOC sequestration but had no significant effect on N2O emission in both systems. Averaged over the three study years, straw incorporation had no significant effect on NGWP and GHGI in the UR system, whereas these parameters were greatly increased in the DR system, i.e., by 108% (3 t/ha) and 180% (6 t/ha) for NGWP and 103% (3 t/ha) and 168% (6 t/ha) for GHGI.

Differences in net global warming potential and greenhouse gas intensity between major rice-based cropping systems in China

PubMed Central

Xiong, Zhengqin; Liu, Yinglie; Wu, Zhen; Zhang, Xiaolin; Liu, Pingli; Huang, Taiqing

2015-01-01

Double rice (DR) and upland crop-single rice (UR) systems are the major rice-based cropping systems in China, yet differences in net global warming potential (NGWP) and greenhouse gas intensity (GHGI) between the two systems are poorly documented. Accordingly, a 3-year field experiment was conducted to simultaneously measure methane (CH4) and nitrous oxide (N2O) emissions and changes in soil organic carbon (SOC) in oil rape-rice-rice and wheat-rice (representing DR and UR, respectively) systems with straw incorporation (0, 3 and 6 t/ha) during the rice-growing seasons. Compared with the UR system, the annual CH4, N2O, grain yield and NGWP were significantly increased in the DR system, though little effect on SOC sequestration or GHGI was observed without straw incorporation. Straw incorporation increased CH4 emission and SOC sequestration but had no significant effect on N2O emission in both systems. Averaged over the three study years, straw incorporation had no significant effect on NGWP and GHGI in the UR system, whereas these parameters were greatly increased in the DR system, i.e., by 108% (3 t/ha) and 180% (6 t/ha) for NGWP and 103% (3 t/ha) and 168% (6 t/ha) for GHGI. PMID:26626733

Differences in net global warming potential and greenhouse gas intensity between major rice-based cropping systems in China

NASA Astrophysics Data System (ADS)

Xiong, Zhengqin; Liu, Yinglie; Wu, Zhen; Zhang, Xiaolin; Liu, Pingli; Huang, Taiqing

2015-12-01

Double rice (DR) and upland crop-single rice (UR) systems are the major rice-based cropping systems in China, yet differences in net global warming potential (NGWP) and greenhouse gas intensity (GHGI) between the two systems are poorly documented. Accordingly, a 3-year field experiment was conducted to simultaneously measure methane (CH4) and nitrous oxide (N2O) emissions and changes in soil organic carbon (SOC) in oil rape-rice-rice and wheat-rice (representing DR and UR, respectively) systems with straw incorporation (0, 3 and 6 t/ha) during the rice-growing seasons. Compared with the UR system, the annual CH4, N2O, grain yield and NGWP were significantly increased in the DR system, though little effect on SOC sequestration or GHGI was observed without straw incorporation. Straw incorporation increased CH4 emission and SOC sequestration but had no significant effect on N2O emission in both systems. Averaged over the three study years, straw incorporation had no significant effect on NGWP and GHGI in the UR system, whereas these parameters were greatly increased in the DR system, i.e., by 108% (3 t/ha) and 180% (6 t/ha) for NGWP and 103% (3 t/ha) and 168% (6 t/ha) for GHGI.

Development of Novel Glyphosate-Tolerant Japonica Rice Lines: A Step Toward Commercial Release.

PubMed

Cui, Ying; Huang, Shuqing; Liu, Ziduo; Yi, Shuyuan; Zhou, Fei; Chen, Hao; Lin, Yongjun

2016-01-01

Glyphosate is the most widely used herbicide for its low cost and high efficiency. However, it is rarely applied directly in rice field due to its toxicity to rice. Therefore, glyphosate-tolerant rice can greatly decrease the cost of rice production and provide a more effective weed management strategy. Although, several approaches to develop transgenic rice with glyphosate tolerance have been reported, the agronomic performances of these plants have not been well evaluated, and the feasibility of commercial production has not been confirmed yet. Here, a novel glyphosate-tolerant gene cloned from the bacterium Isoptericola variabilis was identified, codon optimized (designated as I. variabilis-EPSPS (*)), and transferred into Zhonghua11, a widely used japonica rice cultivar. After systematic analysis of the transgene integration via PCR, Southern blot and flanking sequence isolation, three transgenic lines with only one intact I. variabilis-EPSPS (*) expression cassette integrated into intergenic regions were identified. Seed test results showed that the glyphosate tolerance of the transgenic rice was about 240 times that of wild type on plant medium. The glyphosate tolerance of transgenic rice lines was further evaluated based on comprehensive agronomic performances in the field with T3 and T5generations in a 2-year assay, which showed that they were rarely affected by glyphosate even when the dosage was 8400 g ha(-1). To our knowledge, this is the first demonstration of the development of glyphosate-tolerant rice lines based on a comprehensive analysis of agronomic performances in the field. Taken together, the results suggest that the selected glyphosate-tolerant rice lines are highly tolerant to glyphosate and have the possibility of commercial release. I. variabilis-EPSPS (*) also can be a promising candidate gene in other species for developing glyphosate-tolerant crops.

Exposure to aflatoxin B1 in Thailand by consumption of brown and color rice.

PubMed

Panrapee, Iamtaweejaroen; Phakpoom, Kooprasertying; Thanapoom, Maneeboon; Nampeung, Anukul; Warapa, Mahakarnchanakul

2016-02-01

This study assessed the aflatoxin B1 (AFB1) intake of the Thai population through consumption of contaminated brown and color rice. A total of 240 rice samples from two harvesting periods were collected in June/July 2012 (period I) and in December 2012/January 2013 (period II) and analyzed for AFB1 by HPLC with fluorescence detection (limit of detection (LOD) = 0.093 ng/g). Exposure assessment was based on AFB1 levels in rice and food intake data for rice according to Thai National Consumption. Frequency and levels of AFB1 were higher in period I (59%,

Consumer motivations toward buying local rice: The case of northern Iranian consumers.

PubMed

Rahnama, Hassan

2017-07-01

This research had two purposes. The first aim was to identify Iranian and Non-Iranian rice consumers based on demographic characteristics and examine difference of these features with buying behaviors. The second purpose of study was to investigate consumer's motivation to buy local rice in Iran. The sample were 1500 people (men and women). The data was collected by using questionnaire based on a face-to-face survey. Chi-square, confirmatory factor analysis, and multiple linear regression were applied to assess collected data by a questionnaire survey. Regarding Iranian local rice buyers, 884 people buy local rice. Chi-square test showed that there is a significant difference between gender, having children, and marital status in buying local rice. Habitual Iranian local rice buyers include: female (51%), people who are more than 45 years old (51%), people with children (63%), people who are living urban (61%), married people (48%) and individuals that their monthly income is between 321.5 and 625 Dollars (53%). Regarding non-Iranian rice buyers, 616 people buy it. Also there is a significant difference between gender, location, marital status, and income in buying local rice. For considering consumers motivation toward buying local rice the econometrical model is used. Model had three aspects including; quality aspects (taste, good appearance), economic aspects (price, convenience, consumer's ethnocentrism), and safety aspects (health, not using pesticides and environment protection) and seven subset. The results of analysis indicated that quality aspects, economic aspects and safety aspects have positive effects on buying Iranian local rice. Also, indicative variables including; taste, good appearance, price, convenience, consumer's ethnocentrism, health, not using pesticides and environment have significant effects on buying it. Copyright © 2017 Elsevier Ltd. All rights reserved.

A pyramid breeding of eight grain-yield related quantitative trait loci based on marker-assistant and phenotype selection in rice (Oryza sativa L.).

PubMed

Zong, Guo; Wang, Ahong; Wang, Lu; Liang, Guohua; Gu, Minghong; Sang, Tao; Han, Bin

2012-07-20

1000-Grain weight and spikelet number per panicle are two important components for rice grain yield. In our previous study, eight quantitative trait loci (QTLs) conferring spikelet number per panicle and 1000-grain weight were mapped through sequencing-based genotyping of 150 rice recombinant inbred lines (RILs). In this study, we validated the effects of four QTLs from Nipponbare using chromosome segment substitution lines (CSSLs), and pyramided eight grain yield related QTLs. The new lines containing the eight QTLs with positive effects showed increased panicle and spikelet size as compared with the parent variety 93-11. We further proposed a novel pyramid breeding scheme based on marker-assistant and phenotype selection (MAPS). This scheme allowed pyramiding of as many as 24 QTLs at a single hybridization without massive cross work. This study provided insights into the molecular basis of rice grain yield for direct wealth for high-yielding rice breeding. Copyright © 2012. Published by Elsevier Ltd.

Metabolomics-based optimal koji fermentation for tyrosinase inhibition supplemented with Astragalus radix.

PubMed

Kim, Ah Jin; Choi, Jung Nam; Kim, Jiyoung; Yeo, Soo Hwan; Choi, Ji Ho; Lee, Choong Hwan

2012-01-01

The present study was focused on improving the quality of rice koji by fermentation with a selected Aspergillus oryzae strain and a plant Astragalus radix. A. oryzae KCCM 60345 was used as main inoculant and the Astragalus radix was added as supplement in rice koji preparation. LC-MS based metabolite analysis and tyrosinase inhibitory activities were studied for different time periods. A. oryzae KCCM 60345 fermented rice koji supplemented with Astragalus showed higher tyrosinase inhibition activity at 4 d of fermentation and metabolite analysis with PCA and PLS-DA indicated differences in kojic acid, calycosin-7-O-β-D-glucoside, ononin, calycosin, and formononetin as compared with other forms of rice koji fermentation. By correlation analysis between metabolites and tyrosinase inhibitory activity, calycosin and kojic acid were identified as major tyrosinase inhibitors. Based on these results, we concluded that A. oryzae KCCM 60345 supplemented with Astragalus radix is useful for whitening effects, and we identified optimal conditions for rice koji preparation.

Genetic diversity of red-grained rice landraces in Hani's terraced fields based on phenotypic characteristics

NASA Astrophysics Data System (ADS)

Zhou, Xiaomei; Zheng, Yun; Zhang, Tingting; Zhang, Xiaoqian; Ma, Mengli; Meng, Hengling; Wang, Tiantao; Lu, Bingyue

2018-06-01

In order to provide useful information for protection and utilization of red-grained rice landraces from Hani's terraced fields, the phenotypic diversity of 61 red-grained rice landraces were assessed based 20 quantitative traits. The results indicated that the phenotypic diversity was abundant in red-grained rice landraces. Coefficients of variation (CV) ranged from 4.878% to 72.878%, and the largest of CV was the panicle neck length, while grain width was smallest. Shannon-Weaver diversity index (H') of 20 traits ranged from 1.464 to 2.165, the largest and the smallest H' values were observed in filled grain number and chalkiness, respectively. Cluster analysis based on unweighted pair group method showed 61 red-grain rice landraces grouped into eight clusters at a cut-off value of 6.2631. The first cluster included 11 landraces, the main cluster II involved 42 landraces, and the cluster IV included 3 landraces. Laopinzhonghongmi, Chena2, Laojingnuo, Bianhao6 and Baimi were separated from the main clusters.

Rice straw as a feedstock for biofuels: Availability, recalcitrance, and chemical properties: Rice straw as a feedstock for biofuels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Satlewal, Alok; Agrawal, Ruchi; Bhagia, Samarthya

The surplus availability of rice straw, its limited usage and environment pollution caused by inefficient burning has fostered research for its valorization to biofuels. This review elucidates the current status of rice straw potential around the globe along with recent advances in revealing the critical factors responsible for its recalcitrance and chemical properties. The role and accumulation of high silica content in rice straw has been elucidated with its impact on enzymatic hydrolysis in a biorefinery environment. The correlation of different pretreatment approaches in modifying the physiochemical properties of rice straw and improving the enzymatic accessibility has also been discussed.more » This study highlights new challenges, resolutions and opportunities for rice straw based biorefineries.« less

Air pollutant emissions from rice straw open field burning in India, Thailand and the Philippines.

PubMed

Gadde, Butchaiah; Bonnet, Sébastien; Menke, Christoph; Garivait, Savitri

2009-05-01

Rice is a widely grown crop in Asia. China (30%) and India (21%) contribute to about half of the world's total rice production. In this study, three major rice-producing countries in Asia are considered, India, Thailand and the Philippines (the later two contributing 4% and 2% of the world's rice production). Rice straw is one of the main field based residues produced along with this commodity and its applications vary widely in the region. Although rice production practises vary from one country to another, open burning of straw is a common practice in these countries. In this study, an approach was followed aiming at (a) determining the quantity of rice straw being subject to open field burning in those countries, (b) congregating pollutant specific emissions factors for rice straw burning, and (c) quantifying the resulting air pollutant emissions. Uncertainties in the results obtained as compared to a global approach are also discussed.

Convolutional neural network with transfer learning for rice type classification

NASA Astrophysics Data System (ADS)

Patel, Vaibhav Amit; Joshi, Manjunath V.

2018-04-01

Presently, rice type is identified manually by humans, which is time consuming and error prone. Therefore, there is a need to do this by machine which makes it faster with greater accuracy. This paper proposes a deep learning based method for classification of rice types. We propose two methods to classify the rice types. In the first method, we train a deep convolutional neural network (CNN) using the given segmented rice images. In the second method, we train a combination of a pretrained VGG16 network and the proposed method, while using transfer learning in which the weights of a pretrained network are used to achieve better accuracy. Our approach can also be used for classification of rice grain as broken or fine. We train a 5-class model for classifying rice types using 4000 training images and another 2- class model for the classification of broken and normal rice using 1600 training images. We observe that despite having distinct rice images, our architecture, pretrained on ImageNet data boosts classification accuracy significantly.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, T; Eldib, A; Hossain, M

Purpose: Patient in-vivo measurements report lower readings than those predicted from TMR-based treatment planning on TBI patient knees and ankles where rice was placed to fill the gap between patient’s legs. This study is to understand and correct the under dosage of Total Body Irradiation(TBI) with rice tissue equivalent bolus placement at TBI treatment patient setup. Methods: Bilateral TBI scheme was investigated with rice bags bolus placing between patient’s two legs acting as missing tissue. In-house TMR based treatment planning system was commissioned with measurements under TBI condition at 10MV, i.e. source-to-reference distance 383.4cm with 40×40cm field size with 1cmmore » thickness Lucite. Predictions of patient specific dose points are reported at different sites with 200cGy prescription at patient umbilicus point. Solid water and rice bag phantoms are used at TBI conditions for the attenuation factor verification and CT scanned to verify the CT number and electron density. Results: We found that the rice bag bolus overall density is 11% lower than the water; however, the attenuation factor of rice bags could become 15% lower than that of water at TBI condition. This overestimate of rice bag electron density could cause the lack of lateral scatter and the lack of backscatter. This could Result in an overestimate of dose at in-vivo dosimeter measurement points with TMR-based treatment planning systems. Observations of patient specific optically stimulated luminescent dosimeters(OSLDs) were used to confirm this overestimation. Measurements of setups with increasing the rice bag filled patient leg separation were performed to demonstrate eliminating the overdose issue. Conclusion: Rice bolus has a lower electron density than water does(11%) but results in 15% lower in attenuation factor at TBI condition. This effect was observed in patient delivery with OSLD measurements and can be corrected by increasing the filling rice bolus thickness with 15% longer of separation.« less

Effects of Slag-Based Silicon Fertilizer on Rice Growth and Brown-Spot Resistance

PubMed Central

Ning, Dongfeng; Song, Alin; Fan, Fenliang; Li, Zhaojun; Liang, Yongchao

2014-01-01

It is well documented that slag-based silicon fertilizers have beneficial effects on the growth and disease resistance of rice. However, their effects vary greatly with sources of slag and are closely related to availability of silicon (Si) in these materials. To date, few researches have been done to compare the differences in plant performance and disease resistance between different slag-based silicon fertilizers applied at the same rate of plant-available Si. In the present study both steel and iron slags were chosen to investigate their effects on rice growth and disease resistance under greenhouse conditions. Both scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were used to examine the effects of slags on ultrastructural changes in leaves of rice naturally infected by Bipolaris oryaze, the causal agent of brown spot. The results showed that both slag-based Si fertilizers tested significantly increased rice growth and yield, but decreased brown spot incidence, with steel slag showing a stronger effect than iron slag. The results of SEM analysis showed that application of slags led to more pronounced cell silicification in rice leaves, more silica cells, and more pronounced and larger papilla as well. The results of TEM analysis showed that mesophyll cells of slag-untreated rice leaf were disorganized, with colonization of the fungus (Bipolaris oryzae), including chloroplast degradation and cell wall alterations. The application of slag maintained mesophyll cells relatively intact and increased the thickness of silicon layer. It can be concluded that applying slag-based fertilizer to Si-deficient paddy soil is necessary for improving both rice productivity and brown spot resistance. The immobile silicon deposited in host cell walls and papillae sites is the first physical barrier for fungal penetration, while the soluble Si in the cytoplasm enhances physiological or induced resistance to fungal colonization. PMID:25036893

Application of autoclaving-cooling cycling treatment to improve resistant starch content of corn-based rice analogues

NASA Astrophysics Data System (ADS)

Hidayat, B.; Muslihudin, M.; Akmal, S.

2018-01-01

Resistant starch is one important component determining the characteristics of a functional food. The aim of the research was to determine the cooling time optimum in the autoclaving-cooling treatment to increase the resistance starch content corn-based rice analogues, with 6 level of cooling time (0 hours/control, 12 hours, 24 hours, 36 hours, 48 hours and 60 hours). The results showed that cooling at 4°C for 60 hours would increase the resistant starch content (6.27% to 15.38%), dietary fiber content (14.53% to 20.17%); and decrease the digestible starch content (61.81% to 52.70%). Cooling time level at 4°C for 24 hours, would increase the sensory score of corn-based rice analogues then back down until cooling time level of 60 hours. Microscopic analysis of granular structure using SEM indicated that cooling time had a linear correlation with cracks intensity on the granule surface of the corn-based rice analogues. The high content of resistant starch showed that the application of cooling time level at 4°C for 24 hours would improve the functional properties of corn-based rice analogues with sensory characteristics remain favorable to panelists.

Methods of developing core collections based on the predicted genotypic value of rice ( Oryza sativa L.).

PubMed

Li, C T; Shi, C H; Wu, J G; Xu, H M; Zhang, H Z; Ren, Y L

2004-04-01

The selection of an appropriate sampling strategy and a clustering method is important in the construction of core collections based on predicted genotypic values in order to retain the greatest degree of genetic diversity of the initial collection. In this study, methods of developing rice core collections were evaluated based on the predicted genotypic values for 992 rice varieties with 13 quantitative traits. The genotypic values of the traits were predicted by the adjusted unbiased prediction (AUP) method. Based on the predicted genotypic values, Mahalanobis distances were calculated and employed to measure the genetic similarities among the rice varieties. Six hierarchical clustering methods, including the single linkage, median linkage, centroid, unweighted pair-group average, weighted pair-group average and flexible-beta methods, were combined with random, preferred and deviation sampling to develop 18 core collections of rice germplasm. The results show that the deviation sampling strategy in combination with the unweighted pair-group average method of hierarchical clustering retains the greatest degree of genetic diversities of the initial collection. The core collections sampled using predicted genotypic values had more genetic diversity than those based on phenotypic values.

Post-harvest field manipulations to conserve waste rice for waterfowl

USGS Publications Warehouse

Stafford, J.D.; Kaminski, R.M.; Reinecke, K.J.; Kurtz, M.E.; Manley, S.W.

2005-01-01

Rice seeds escaping collection by combines during harvest (hereafter, waste rice) provide quality forage for migrating and wintering waterfowl in the Lower Mississippi Alluvial Valley (MAV) and other rice growing regions in the United States. Recent sample surveys across the MAV have revealed abundance of waste rice in fields declined an average of 71% between harvest and late autumn. Thus, we evaluated the ability of common post-harvest, field-management practices to conserve waste rice for waterfowl until early winter via controlled experiments in Mississippi rice test plots in 2001 and 2003 and analyses of data from MAV-wide surveys of waste rice in rice production fields in 2000-2002. Our experiments indicated test plots with burned rice stubble that were not flooded during autumn contained more waste rice than other treatments in 2001 (P?0.10). Waste-rice abundance in test plots did not differ among postharvest treatments in 2003 (P = 0.97). Our analyses of data from the MAV sample surveys did not detect differences in abundance of waste rice among fields burned, rolled, disked, or left in standing stubble post-harvest (P?0.04; Bonferroni corrected critical ( a= 0.017). Because results from test-plot experiments were inconclusive, we based our primary inference regarding best post-harvest treatments on patterns of rice abundance identified from the MAV surveys and previously documented environmental and agronomic benefits of managing harvested rice fields for wintering waterfowl. Therefore, we recommend leaving standing stubble in rice fields after harvest as a preliminary beneficial management practice. We suggest future research evaluate potential of postharvest practices to conserve waste rice for waterfowl and reduce straw in production rice fields managed for wintering waterfowl throughout the MAV.

Fermented Brown Rice Flour as Functional Food Ingredient.

PubMed

Ilowefah, Muna; Chinma, Chiemela; Bakar, Jamilah; Ghazali, Hasanah M; Muhammad, Kharidah; Makeri, Mohammad

2014-02-12

As fermentation could reduce the negative effects of bran on final cereal products, the utilization of whole-cereal flour is recommended, such as brown rice flour as a functional food ingredient. Therefore, this study aimed to investigate the effect of fermented brown rice flour on white rice flour, white rice batter and its steamed bread qualities. Brown rice batter was fermented using commercial baker's yeast (Eagle brand) according to the optimum conditions for moderate acidity (pH 5.5) to obtain fermented brown rice flour (FBRF). The FBRF was added to white rice flour at 0%, 10%, 20%, 30%, 40% and 50% levels to prepare steamed rice bread. Based on the sensory evaluation test, steamed rice bread containing 40% FBRF had the highest overall acceptability score. Thus, pasting properties of the composite rice flour, rheological properties of its batter, volume and texture properties of its steamed bread were determined. The results showed that peak viscosity of the rice flour containing 40% FBRF was significantly increased, whereas its breakdown, final viscosity and setback significantly decreased. Viscous, elastic and complex moduli of the batter having 40% FBRF were also significantly reduced. However, volume, specific volume, chewiness, resilience and cohesiveness of its steamed bread were significantly increased, while hardness and springiness significantly reduced in comparison to the control. These results established the effectiveness of yeast fermentation in reducing the detrimental effects of bran on the sensory properties of steamed white rice bread and encourage the usage of brown rice flour to enhance the quality of rice products.

The Potency of White Rice (Oryza sativa), Black Rice (Oryza sativa L. indica), and Red Rice (Oryza nivara) as Antioxidant and Tyrosinase Inhibitor

NASA Astrophysics Data System (ADS)

Batubara, I.; Maharni, M.; Sadiah, S.

2017-04-01

Rice is known to have many beneficial biological activities and is often used as “bedak dingin”, a face powder. The content of vitamins, minerals, fiber, and several types of antioxidants, such as ferulic acid, phytic acid, tocopherol, and oryzanols [1-2] are predicted to be potential as a tyrosinase inhibitor. The purpose of this study is to determine the potency of extracts from there types of rice, namely white, red, and black rice as an antioxidant and tyrosinase inhibitor. The rice was extracted with three different solvents, n-hexane, ethyl acetate, and methanol. The results showed that the highest antioxidant activity using 1,1-diphenyl-2-picrylhydrazyl method was found in the methanol extract of black rice (IC50 290 μg/mL). Meanwhile, ethyl acetate extract of white rice has the highest antioxidant activity withphosphomolybdic acid method (41 mmol α-tocopherol equivalents/g sample). Thus, methanol extract of black rice and ethyl acetate extract of white rice are potential as an antioxidant. For tyrosinase inhibitor, n-hexane extract of red rice (IC50 3156 μg/mL) was the most active extract. The active component for radical scavenging is polar compound and for antioxidant by phosphomolybdate method is less polar compounds in black rice methanol extract based on TLC bioautogram. In conclusion, the black rice is the most potent in antioxidant while red rice is for tyrosinase inhibition.

Inorganic arsenic in rice bran and its products are an order of magnitude higher than in bulk grain.

PubMed

Sun, Guo-Xin; Williams, Paul N; Carey, Anne-Marie; Zhu, Yong-Guan; Deacon, Claire; Raab, Andrea; Feldmann, Joerg; Islam, Rafiqul M; Meharg, Andrew A

2008-10-01

Rice is more elevated in arsenic than all other grain crops tested to date, with whole grain (brown) rice having higher arsenic levels than polished (white). It is reported here that rice bran, both commercially purchased and specifically milled for this study, have levels of inorganic arsenic, a nonthreshold, class 1 carcinogen, reaching concentrations of approximately 1 mg/kg dry weight, around 10-20 fold higher than concentrations found in bulk grain. Although pure rice bran is used as a health food supplement, perhaps of more concern is rice bran solubles, which are marketed as a superfood and as a supplement to malnourished children in international aid programs. Five rice bran solubles products were tested, sourced from the United States and Japan, and were found to have 0.61-1.9 mg/kg inorganic arsenic. Manufactures recommend approximately 20 g servings of the rice bran solubles per day, which equates to a 0.012-0.038 mg intake of inorganic arsenic. There are no maximum concentration levels (MCLs) set for arsenic or its species in food stuffs. EU and U.S. water regulations, set at 0.01 mg/L total or inorganic arsenic, respectively, are based on the assumption that 1 L of water per day is consumed, i.e., 0.01 mg of arsenic/ day. At the manufacturers recommended rice bran solubles consumption rate, inorganic arsenic intake exceeds 0.01 mg/ day, remembering that rice bran solubles are targeted at malnourished children and that actual risk is based on mg kg(-1) day(-1) intake.

Influence of resistant starch and slowly digestible starch on rice texture.

USDA-ARS?s Scientific Manuscript database

Rice, comprised mainly of starch, serves as a significant source of caloric energy world-wide, therefore differences in starch digestibility are important to human health. Rice starch consists of three forms based on digestibility, rapidly digestible starch (RDS), slowly digestible starch (SDS), and...

2. RICE THRESHING MILL WITH CHIMNEY STACK. Fire burned on ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

2. RICE THRESHING MILL WITH CHIMNEY STACK. Fire burned on top of water pipe at base of chimney stack and steam went thru pipes to boiler on south side of wall. - Mansfield Plantation, Rice Threshing Mill, U.S. Route 701 vicinity, Georgetown, Georgetown County, SC

Speciation And Localization Of Arsenic In White And Brown Rice Grains

EPA Science Inventory

Synchrotron-based X-ray fluorescence (S-XRF) was utilized to locate arsenic (As) in polished (white) and unpolished (brown) rice grains from the United States, China, and Bangladesh. In white rice As was generally dispersed throughout the grain, the bulk of which constitutes the...

Isolation and identification of a lethal rhabdovirus from farmed rice field eels Monopterus albus.

PubMed

Ou, Tong; Zhu, Ruo-Lin; Chen, Zhong-Yuan; Zhang, Qi-Ya

2013-11-06

We provide the first description of a virus responsible for a systemic hemorrhagic disease causing high mortality in farmed rice field eels Monopterus albus in China. Typical signs exhibited by the diseased fish were extensive hemorrhages in the skin and viscera and some neurological signs, such as loss of equilibrium and disorganized swimming. Histopathological examination revealed various degrees of necrosis within the spleen and liver. Virus isolation was attempted from visceral tissues of diseased fish by inoculation on 6 fish cell lines. Typical cytopathic effects (CPE) were produced in bluegill fry (BF2) cells, so this cell line was chosen for further isolation and propagation of the virus. Electron microscopy observation showed that the negative stained viral particles had the characteristic bullet shape of rhabdoviruses and an estimated size of 60 × 120 nm. We therefore tentatively refer to this virus as Monopterus albus rhabdovirus (MoARV). Molecular characterization of MoARV, including sequence analysis of the nucleoprotein (N), phosphoprotein (P), and glycoprotein (G) genes, revealed 94.5 to 97.3% amino acid similarity to that of Siniperca chuatsi rhabdovirus. Phylogenetic analysis based on the amino acid sequences of N and G proteins indicated that MoARV should be a member of the genus Vesiculovirus. Koch's postulates were fulfilled by infecting healthy rice field eels with MoARV, which produced an acute infection. RT-PCR analysis demonstrated that MoARV RNA could be detected in both naturally and experimentally infected fish. The data suggest that MoARV was the causative pathogen of the disease.

Genome-wide identification and analysis of the B3 superfamily of transcription factors in Brassicaceae and major crop plants.

PubMed

Peng, Fred Y; Weselake, Randall J

2013-05-01

The plant-specific B3 superfamily of transcription factors has diverse functions in plant growth and development. Using a genome-wide domain analysis, we identified 92, 187, 58, 90, 81, 55, and 77 B3 transcription factor genes in the sequenced genome of Arabidopsis, Brassica rapa, castor bean (Ricinus communis), cocoa (Theobroma cacao), soybean (Glycine max), maize (Zea mays), and rice (Oryza sativa), respectively. The B3 superfamily has substantially expanded during the evolution in eudicots particularly in Brassicaceae, as compared to monocots in the analysis. We observed domain duplication in some of these B3 proteins, forming more complex domain architectures than currently understood. We found that the length of B3 domains exhibits a large variation, which may affect their exact number of α-helices and β-sheets in the core structure of B3 domains, and possibly have functional implications. Analysis of the public microarray data indicated that most of the B3 gene pairs encoding Arabidopsis-rice orthologs are preferentially expressed in different tissues, suggesting their different roles in these two species. Using ESTs in crops, we identified many B3 genes preferentially expressed in reproductive tissues. In a sequence-based quantitative trait loci analysis in rice and maize, we have found many B3 genes associated with traits such as grain yield, seed weight and number, and protein content. Our results provide a framework for future studies into the function of B3 genes in different phases of plant development, especially the ones related to traits in major crops.

Estimation of nutrient discharge from the Yangtze River to the East China Sea and the identification of nutrient sources.

PubMed

Tong, Yindong; Bu, Xiaoge; Chen, Junyue; Zhou, Feng; Chen, Long; Liu, Maodian; Tan, Xin; Yu, Tao; Zhang, Wei; Mi, Zhaorong; Ma, Lekuan; Wang, Xuejun; Ni, Jing

2017-01-05

Based on a time-series dataset and the mass balance method, the contributions of various sources to the nutrient discharges from the Yangtze River to the East China Sea are identified. The results indicate that the nutrient concentrations vary considerably among different sections of the Yangtze River. Non-point sources are an important source of nutrients to the Yangtze River, contributing about 36% and 63% of the nitrogen and phosphorus discharged into the East China Sea, respectively. Nutrient inputs from non-point sources vary among the sections of the Yangtze River, and the contributions of non-point sources increase from upstream to downstream. Considering the rice growing patterns in the Yangtze River Basin, the synchrony of rice tillering and the wet seasons might be an important cause of the high nutrient discharge from the non-point sources. Based on our calculations, a reduction of 0.99Tg per year in total nitrogen discharges from the Yangtze River would be needed to limit the occurrences of harmful algal blooms in the East China Sea to 15 times per year. The extensive construction of sewage treatment plants in urban areas may have only a limited effect on reducing the occurrences of harmful algal blooms in the future. Copyright © 2016 Elsevier B.V. All rights reserved.

Analysis of rice policy based on presidential instruction on household food security: simultaneous equation model

NASA Astrophysics Data System (ADS)

Sembiring, S. A.

2018-02-01

The objective of this research is to analyze the impacts of rice policy on the household food security. The research used cross section data, were collected from 74 respondent as determined by purposive sampling in Sei Rejo villages, the Sub District of Sei Rampah, Serdang Bedagai District in the Province of North Sumatera. Rice policy model specification uses the simultaneous equations consisting of 6 structural equations and 6 identity equations which was estimated using Two Stages Least Squares (2SLS) method. The results show that the effectiveness of government purchase price of dried harvest paddy gave a positive impact on paddy planted area and lead to an increase paddy production and an increase of the rice production gave a positive impact on household rice availability and household rice surplus, and the increase of household rice surplus gave the quantity of Raskin decrease, whereas the increase of fertilizers gave a negative impact on paddy planted area and lead to decrease paddy production and to decrease in rice production was followed by an decrease in household rice availability and household rice surplus, and the decrease of household rice surplus gave the quantity of Raskin increase.

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.

PubMed

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.

Postprandial glycaemic response of foxtail millet dosa in comparison to a rice dosa in patients with type 2 diabetes

PubMed Central

Narayanan, Janani; Sanjeevi, Vimala; Rohini, U.; Trueman, Patricia; Viswanathan, Vijay

2016-01-01

Background & objectives: Millets are rich source of dietary fibre and non-starchy polysaccharides with low glycaemic index (GI), hence can be used as a therapeutic diet. This study was conducted to estimate the effects of a millet-based dosa (foxtail dosa) compared to a rice dosa for breakfast on postprandial glucose levels in patients with type 2 diabetes mellitus (T2DM). Methods: The GI of rice dosa and foxtail millet dosa was estimated. A total of 105 T2DM participants were randomly selected for the study. The participants were on oral hypoglycaemic agents (OHA) and not on insulin. In this study, each individual served as their own control and experimental group. The postprandial increase in blood glucose was compared after a breakfast of rice dosa and millet dosa. Single and paired t test was used to note the change in blood glucose levels and the level of the significance. Results: The GI of foxtail millet dosa was 59.25 and rice dosa was 77.96. There was a significant reduction (P<0.001) in the postprandial glucose level of patients who consumed a millet-based dosa when compared to those who consumed a rice-based dosa. No significant reduction was observed in the fasting glucose levels. Interpretation & conclusions: The results suggested that replacing a rice-based breakfast item with a millet-based breakfast item lowers the postprandial blood glucose levels in T2DM patients. Thus, millets may have a protective role in the management of hyperglycaemia. Further studies need to be done in a systematic manner to confirm these findings. PMID:28361824

Exploiting Co-Benefits of Increased Rice Production and Reduced Greenhouse Gas Emission through Optimized Crop and Soil Management.

PubMed

An, Ning; Fan, Mingsheng; Zhang, Fusuo; Christie, Peter; Yang, Jianchang; Huang, Jianliang; Guo, Shiwei; Shi, Xiaojun; Tang, Qiyuan; Peng, Jianwei; Zhong, Xuhua; Sun, Yixiang; Lv, Shihua; Jiang, Rongfeng; Dobermann, Achim

2015-01-01

Meeting the future food security challenge without further sacrificing environmental integrity requires transformative changes in managing the key biophysical determinants of increasing agronomic productivity and reducing the environmental footprint. Here, we focus on Chinese rice production and quantitatively address this concern by conducting 403 on-farm trials across diverse rice farming systems. Inherent soil productivity, management practices and rice farming type resulted in confounded and interactive effects on yield, yield gaps and greenhouse gas (GHG) emissions (N2O, CH4 and CO2-equivalent) with both trade-offs and compensating effects. Advances in nitrogen, water and crop management (Best Management Practices-BMPs) helped closing existing yield gaps and resulted in a substantial reduction in CO2-equivalent emission of rice farming despite a tradeoff of increase N2O emission. However, inherent soil properties limited rice yields to a larger extent than previously known. Cultivating inherently better soil also led to lower GHG intensity (GHG emissions per unit yield). Neither adopting BMPs only nor improving soils with low or moderate productivity alone can adequately address the challenge of substantially increasing rice production while reducing the environmental footprint. A combination of both represents the most efficient strategy to harness the combined-benefits of enhanced production and mitigating climate change. Extrapolating from our farm data, this strategy could increase rice production in China by 18%, which would meet the demand for direct human consumption of rice by 2030. It would also reduce fertilizer nitrogen consumption by 22% and decrease CO2-equivalent emissions during the rice growing period by 7% compared with current farming practice continues. Benefits vary by rice-based cropping systems. Single rice systems have the largest food provision benefits due to its wider yield gap and total cultivated area, whereas double-rice system (especially late rice) contributes primarily to reducing GHG emissions. The study therefore provides farm-based evidence for feasible, practical approaches towards achieving realistic food security and environmental quality targets at a national scale.

Exploiting Co-Benefits of Increased Rice Production and Reduced Greenhouse Gas Emission through Optimized Crop and Soil Management

PubMed Central

An, Ning; Fan, Mingsheng; Zhang, Fusuo; Christie, Peter; Yang, Jianchang; Huang, Jianliang; Guo, Shiwei; Shi, Xiaojun; Tang, Qiyuan; Peng, Jianwei; Zhong, Xuhua; Sun, Yixiang; Lv, Shihua; Jiang, Rongfeng; Dobermann, Achim

2015-01-01

Meeting the future food security challenge without further sacrificing environmental integrity requires transformative changes in managing the key biophysical determinants of increasing agronomic productivity and reducing the environmental footprint. Here, we focus on Chinese rice production and quantitatively address this concern by conducting 403 on-farm trials across diverse rice farming systems. Inherent soil productivity, management practices and rice farming type resulted in confounded and interactive effects on yield, yield gaps and greenhouse gas (GHG) emissions (N2O, CH4 and CO2-equivalent) with both trade-offs and compensating effects. Advances in nitrogen, water and crop management (Best Management Practices—BMPs) helped closing existing yield gaps and resulted in a substantial reduction in CO2-equivalent emission of rice farming despite a tradeoff of increase N2O emission. However, inherent soil properties limited rice yields to a larger extent than previously known. Cultivating inherently better soil also led to lower GHG intensity (GHG emissions per unit yield). Neither adopting BMPs only nor improving soils with low or moderate productivity alone can adequately address the challenge of substantially increasing rice production while reducing the environmental footprint. A combination of both represents the most efficient strategy to harness the combined-benefits of enhanced production and mitigating climate change. Extrapolating from our farm data, this strategy could increase rice production in China by 18%, which would meet the demand for direct human consumption of rice by 2030. It would also reduce fertilizer nitrogen consumption by 22% and decrease CO2-equivalent emissions during the rice growing period by 7% compared with current farming practice continues. Benefits vary by rice-based cropping systems. Single rice systems have the largest food provision benefits due to its wider yield gap and total cultivated area, whereas double-rice system (especially late rice) contributes primarily to reducing GHG emissions. The study therefore provides farm-based evidence for feasible, practical approaches towards achieving realistic food security and environmental quality targets at a national scale. PMID:26452155

Using NOAA/AVHRR based remote sensing data and PCR method for estimation of Aus rice yield in Bangladesh

NASA Astrophysics Data System (ADS)

Nizamuddin, Mohammad; Akhand, Kawsar; Roytman, Leonid; Kogan, Felix; Goldberg, Mitch

2015-06-01

Rice is a dominant food crop of Bangladesh accounting about 75 percent of agricultural land use for rice cultivation and currently Bangladesh is the world's fourth largest rice producing country. Rice provides about two-third of total calorie supply and about one-half of the agricultural GDP and one-sixth of the national income in Bangladesh. Aus is one of the main rice varieties in Bangladesh. Crop production, especially rice, the main food staple, is the most susceptible to climate change and variability. Any change in climate will, thus, increase uncertainty regarding rice production as climate is major cause year-to-year variability in rice productivity. This paper shows the application of remote sensing data for estimating Aus rice yield in Bangladesh using official statistics of rice yield with real time acquired satellite data from Advanced Very High Resolution Radiometer (AVHRR) sensor and Principal Component Regression (PCR) method was used to construct a model. The simulated result was compared with official agricultural statistics showing that the error of estimation of Aus rice yield was less than 10%. Remote sensing, therefore, is a valuable tool for estimating crop yields well in advance of harvest, and at a low cost.

Teaching with Historic Places: When Rice Was King.

ERIC Educational Resources Information Center

Metcalf, Faye

1992-01-01

Presents a lesson plan on the slave-based rice plantation economy in South Carolina from the late eighteenth century until the Civil War. Includes objectives, teaching activities, maps, handouts of student readings, photographs, and plans for visiting the sites. Discusses plantation life and the culture of the rice economy. (DK)

Antioxidant properties of rice bran oil-based extraction products

USDA-ARS?s Scientific Manuscript database

Rice bran oil has many properties that make it an attractive functional food ingredient. Compared with other oils, rice bran oil is relatively rich in tocopherols, tocotrienols, and y-oryzanol, all of which have been shown to have numerous desirable health effects. The same compounds thought to co...

Antioxidant and sensory properties of rice bran oil-based extraction products

USDA-ARS?s Scientific Manuscript database

Rice bran oil has many properties that make it an attractive functional food ingredient. Compared with other oils, rice bran oil is rich in tocopherols, tocotrienols, and y-oryzanol, all of which have been shown to have numerous desirable health effects. The same compounds that confer health benef...

Rice methylmercury exposure and mitigation: a comprehensive review

USGS Publications Warehouse

Rothenberg, Sarah E.; Windham-Myers, Lisamarie; Creswell, Joel E.

2014-01-01

Rice cultivation practices from field preparation to post-harvest transform rice paddies into hot spots for microbial mercury methylation, converting less-toxic inorganic mercury to more-toxic methylmercury, which is likely translocated to rice grain. This review includes 51 studies reporting rice total mercury and/or methylmercury concentrations, based on rice (Orzya sativa) cultivated or purchased in 15 countries. Not surprisingly, both rice total mercury and methylmercury levels were significantly higher in polluted sites compared to non-polluted sites (Wilcoxon rank sum, p<0.001). However, rice percent methylmercury (of total mercury) did not differ statistically between polluted and non-polluted sites (Wilcoxon rank sum, p=0.35), suggesting comparable mercury methylation rates in paddy soil across these sites and/or similar accumulation of mercury species for these rice cultivars. Studies characterizing the effects of rice cultivation under more aerobic conditions were reviewed to determine the mitigation potential of this practice. Rice management practices utilizing alternating wetting and drying (instead of continuous flooding) caused soil methylmercury levels to spike, resulting in a strong methylmercury pulse after fields were dried and reflooded; however, it is uncertain whether this led to increased translocation of methylmercury from paddy soil to rice grain. Due to the potential health risks, it is advisable to investigate this issue further, and to develop separate water management strategies for mercury polluted and non-polluted sites, in order to minimize methylmercury exposure through rice ingestion.

Rice Methylmercury Exposure and Mitigation: A Comprehensive Review

PubMed Central

Rothenberg, Sarah E.; Windham-Myers, Lisamarie; Creswell, Joel E.

2014-01-01

Rice cultivation practices from field preparation to post-harvest transform rice paddies into hot spots for microbial mercury methylation, converting less-toxic inorganic mercury to more-toxic methylmercury, which is likely translocated to rice grain. This review includes 51 studies reporting rice total mercury and/or methylmercury concentrations, based on rice cultivated or purchased in 15 countries. Not surprisingly, both rice total mercury and methylmercury levels were significantly higher in polluted sites compared to non-polluted sites (Wilcoxon rank sum, p<0.001). However, rice percent methylmercury (of total mercury) did not differ statistically between polluted and non-polluted sites (Wilcoxon rank sum, p=0.35), suggesting comparable mercury methylation rates in paddy soil across these sites and/or similar accumulation of mercury species for these rice cultivars. Studies characterizing the effect of rice cultivation under more aerobic conditions were reviewed to determine the mitigation potential of this practice. Rice management practices utilizing alternating wetting and drying (instead of continuous flooding) caused soil methylmercury levels to spike, resulting in a strong methylmercury pulse after fields were dried and reflooded; however, it is uncertain whether this led to increased translocation of methylmercury from paddy soil to rice grain. Due to the potential health risks, it is advisable to investigate this issue further, and to develop separate water management strategies for mercury polluted and non-polluted sites, which minimize methylmercury exposure through rice ingestion. PMID:24972509

Dynamical roguing model for controlling the spread of tungro virus via Nephotettix Virescens in a rice field

NASA Astrophysics Data System (ADS)

Blas, Nikki; David, Guido

2017-10-01

Rice tungro disease is described as a cancer due to its major impact on the livelihood of farmers and the difficulty of controlling it. Tungro is a semi-persistent virus transmitted by green leafhoppers called Nephotettix Virescens. In this paper, we presented a compartmental plant-vector model of the Nephotettix Virescens - rice plant interaction based on a system of ordinary differential equations to simulate the effects of roguing in controlling the spread of Tungro virus in a model rice field of susceptible rice variety (Taichung Native 1).

Rice agriculture impacts catchment hydrographic patterns and nitrogen export characteristics in subtropical central China: a paired-catchment study.

PubMed

Wang, Yi; Liu, Xinliang; Wang, Hua; Li, Yong; Li, Yuyuan; Liu, Feng; Xiao, Runlin; Shen, Jianlin; Wu, Jinshui

2017-06-01

Increased nitrogen (N) concentrations in water bodies have highlighted issues regarding nutrient pollution in agricultural catchments. In this study, the ammonium-N (NH 4 + -N), nitrate-N (NO 3 - -N), and total N (TN) concentrations were observed in the stream water and groundwater of two contrasting catchments (named Tuojia and Jianshan) in subtropical central China from 2010 to 2014, to determine the rice agriculture impacts on the hydrographic patterns, and N export characteristics of the catchments. The results suggested that greater amounts of stream flow (523.0 vs. 434.7 mm year -1 ) and base flow (237.6 vs. 142.8 mm year -1 ) were produced in Tuojia than in Jianshan, and a greater base flow contribution to stream flow and higher frequencies of high-base flow days were observed during the fallow season than during the rice-growing season, indicating that intensive rice agriculture strongly influences the catchment hydrographic pattern. Rice agriculture resulted in moderate N pollution in the stream water and groundwater, particularly in Tuojia. Primarily, rice agriculture increased the NH 4 + -N concentration in the stream water; however, it increased the NO 3 - -N concentrations in the groundwater, suggesting that the different N species in the paddy fields migrated out of the catchments through distinct hydrological pathways. The average TN loading via stream flow and base flow was greater in Tuojia than in Jianshan (1.72 and 0.58 vs. 0.72 and 0.15 kg N ha -1  month -1 , respectively). Greater TN loading via stream flow was observed during the fallow season in Tuojia and during the rice-growing season in Jianshan, and these different results were most likely a result of the higher base flow contribution to TN loading (33.5 vs. 21.3%) and greater base flow enrichment ratio (1.062 vs. 0.876) in Tuojia than in Jianshan. Therefore, the impact of rice agriculture on catchment eco-hydrological processes should be considered when performing water quality protection and treatment in subtropical central China.

Water uptake depth analyses using stable water isotopes in rice-based cropping systems in Southeastern Asia

NASA Astrophysics Data System (ADS)

Mahindawansha, Amani; Kraft, Philipp; Orlowski, Natalie; Racela, Healthcliff S. U.; Breuer, Lutz

2017-04-01

Rice is one of the most water-consuming crop in the world. Understanding water source utilization of rice-based cropping systems will help to improve water use efficiency (WUE) in paddy management. The objectives of our study were to (1) determine the contributions of various water sources to plant growth in diversified rice-based production systems (wet rice, aerobic rice) (2) investigate water uptake depths at different maturity periods during wet and dry conditions, and (3) calculate WUE of the cropping systems. Our field experiment is based on changes of stable water isotope concentrations in the soil-plant-atmosphere continuum due to transpiration and evaporation. Soil samples were collected together with root sampling from nine different depths under vegetative, reproductive, and matured periods of plant growth together with stem samples. Soil and plant samples were extracted by cryogenic vacuum extraction. Groundwater, surface water, rain, and irrigation water were sampled weekly. All water samples were analyzed for hydrogen and oxygen isotope ratios (δ2H and δ18O) via a laser spectroscope (Los Gatos DLT100). The direct inference approach, which is based on comparing isotopic compositions between plant stem water and soil water, were used to determine water sources taken up by plant. Multiple-source mass balance assessment can provide the estimated range of potential contributions of water from each soil depth to root water uptake of a crop. These estimations were used to determine the proportion of water from upper soil horizons and deep horizons for rice in different maturity periods during wet and dry seasons. Shallow soil water has the higher evaporation than from deeper soil water where the highest evaporation effect is at 5 cm depth (drying front). Water uptake is mostly taking place from surface water in the vegetative and between 5-10 cm in the reproductive period, since roots have grown widely and deeper in the reproductive stage. This will be helpful to understand the WUE and identify the most efficient water management system and the influence of groundwater and surface water during both seasons in rice-based cropping ecosystems by using means of stable water isotope.

Genetic diversity trend in Indian rice varieties: an analysis using SSR markers.

PubMed

Singh, Nivedita; Choudhury, Debjani Roy; Tiwari, Gunjan; Singh, Amit Kumar; Kumar, Sundeep; Srinivasan, Kalyani; Tyagi, R K; Sharma, A D; Singh, N K; Singh, Rakesh

2016-09-05

The knowledge of the extent and pattern of diversity in the crop species is a prerequisite for any crop improvement as it helps breeders in deciding suitable breeding strategies for their future improvement. Rice is the main staple crop in India with the large number of varieties released every year. Studies based on the small set of rice genotypes have reported a loss in genetic diversity especially after green revolution. However, a detailed study of the trend of diversity in Indian rice varieties is lacking. SSR markers have proven to be a marker of choice for studying the genetic diversity. Therefore, the present study was undertaken with the aim to characterize and assess trends of genetic diversity in a large set of Indian rice varieties (released between 1940-2013), conserved in the National Gene Bank of India using SSR markers. A set of 729 Indian rice varieties were genotyped using 36 HvSSR markers to assess the genetic diversity and genetic relationship. A total of 112 alleles was amplified with an average of 3.11 alleles per locus with mean Polymorphic Information Content (PIC) value of 0.29. Cluster analysis grouped these varieties into two clusters whereas the model based population structure divided them into three populations. AMOVA study based on hierarchical cluster and model based approach showed 3 % and 11 % variation between the populations, respectively. Decadal analysis for gene diversity and PIC showed increasing trend from 1940 to 2005, thereafter values for both the parameters showed decreasing trend between years 2006-2013. In contrast to this, allele number demonstrated increasing trend in these varieties released and notified between1940 to 1985, it remained nearly constant during 1986 to 2005 and again showed an increasing trend. Our results demonstrated that the Indian rice varieties harbors huge amount of genetic diversity. However, the trait based improvement program in the last decades forced breeders to rely on few parents, which resulted in loss of gene diversity during 2006 to 2013. The present study indicates the need for broadening the genetic base of Indian rice varieties through the use of diverse parents in the current breeding program.

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

PubMed

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.

funRiceGenes dataset for comprehensive understanding and application of rice functional genes.

PubMed

Yao, Wen; Li, Guangwei; Yu, Yiming; Ouyang, Yidan

2018-01-01

As a main staple food, rice is also a model plant for functional genomic studies of monocots. Decoding of every DNA element of the rice genome is essential for genetic improvement to address increasing food demands. The past 15 years have witnessed extraordinary advances in rice functional genomics. Systematic characterization and proper deposition of every rice gene are vital for both functional studies and crop genetic improvement. We built a comprehensive and accurate dataset of ∼2800 functionally characterized rice genes and ∼5000 members of different gene families by integrating data from available databases and reviewing every publication on rice functional genomic studies. The dataset accounts for 19.2% of the 39 045 annotated protein-coding rice genes, which provides the most exhaustive archive for investigating the functions of rice genes. We also constructed 214 gene interaction networks based on 1841 connections between 1310 genes. The largest network with 762 genes indicated that pleiotropic genes linked different biological pathways. Increasing degree of conservation of the flowering pathway was observed among more closely related plants, implying substantial value of rice genes for future dissection of flowering regulation in other crops. All data are deposited in the funRiceGenes database (https://funricegenes.github.io/). Functionality for advanced search and continuous updating of the database are provided by a Shiny application (http://funricegenes.ncpgr.cn/). The funRiceGenes dataset would enable further exploring of the crosslink between gene functions and natural variations in rice, which can also facilitate breeding design to improve target agronomic traits of rice. © The Authors 2017. Published by Oxford University Press.

Cyclic nucleotide-gated ion channel gene family in rice, identification, characterization and experimental analysis of expression response to plant hormones, biotic and abiotic stresses.

PubMed

Nawaz, Zarqa; Kakar, Kaleem Ullah; Saand, Mumtaz A; Shu, Qing-Yao

2014-10-04

Cyclic nucleotide-gated channels (CNGCs) are Ca2+-permeable cation transport channels, which are present in both animal and plant systems. They have been implicated in the uptake of both essential and toxic cations, Ca2+ signaling, pathogen defense, and thermotolerance in plants. To date there has not been a genome-wide overview of the CNGC gene family in any economically important crop, including rice (Oryza sativa L.). There is an urgent need for a thorough genome-wide analysis and experimental verification of this gene family in rice. In this study, a total of 16 full length rice CNGC genes distributed on chromosomes 1-6, 9 and 12, were identified by employing comprehensive bioinformatics analyses. Based on phylogeny, the family of OsCNGCs was classified into four major groups (I-IV) and two sub-groups (IV-A and IV- B). Likewise, the CNGCs from all plant lineages clustered into four groups (I-IV), where group II was conserved in all land plants. Gene duplication analysis revealed that both chromosomal segmentation (OsCNGC1 and 2, 10 and 11, 15 and 16) and tandem duplications (OsCNGC1 and 2) significantly contributed to the expansion of this gene family. Motif composition and protein sequence analysis revealed that the CNGC specific domain "cyclic nucleotide-binding domain (CNBD)" comprises a "phosphate binding cassette" (PBC) and a "hinge" region that is highly conserved among the OsCNGCs. In addition, OsCNGC proteins also contain various other functional motifs and post-translational modification sites. We successively built a stringent motif: (LI-X(2)-[GS]-X-[FV]-X-G-[1]-ELL-X-W-X(12,22)-SA-X(2)-T-X(7)-[EQ]-AF-X-L) that recognizes the rice CNGCs specifically. Prediction of cis-acting regulatory elements in 5' upstream sequences and expression analyses through quantitative qPCR demonstrated that OsCNGC genes were highly responsive to multiple stimuli including hormonal (abscisic acid, indoleacetic acid, kinetin and ethylene), biotic (Pseudomonas fuscovaginae and Xanthomonas oryzae pv. oryzae) and abiotic (cold) stress. There are 16 CNGC genes in rice, which were probably expanded through chromosomal segmentation and tandem duplications and comprise a PBC and a "hinge" region in the CNBD domain, featured by a stringent motif. The various cis-acting regulatory elements in the upstream sequences may be responsible for responding to multiple stimuli, including hormonal, biotic and abiotic stresses.

Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data.

PubMed

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.

Rice straw-wood particle composite for sound absorbing wooden construction materials.

PubMed

Yang, Han-Seung; Kim, Dae-Jun; Kim, Hyun-Joong

2003-01-01

In this study, rice straw-wood particle composite boards were manufactured as insulation boards using the method used in the wood-based panel industry. The raw material, rice straw, was chosen because of its availability. The manufacturing parameters were: a specific gravity of 0.4, 0.6, and 0.8, and a rice straw content (10/90, 20/80, and 30/70 weight of rice straw/wood particle) of 10, 20, and 30 wt.%. A commercial urea-formaldehyde adhesive was used as the composite binder, to achieve 140-290 psi of bending modulus of rupture (MOR) with 0.4 specific gravity, 700-900 psi of bending MOR with 0.6 specific gravity, and 1400-2900 psi of bending MOR with a 0.8 specific gravity. All of the composite boards were superior to insulation board in strength. Width and length of the rice straw particle did not affect the bending MOR. The composite boards made from a random cutting of rice straw and wood particles were the best and recommended for manufacturing processes. Sound absorption coefficients of the 0.4 and 0.6 specific gravity boards were higher than the other wood-based materials. The recommended properties of the rice straw-wood particle composite boards are described, to absorb noises, preserve the temperature of indoor living spaces, and to be able to partially or completely substitute for wood particleboard and insulation board in wooden constructions.

Non-destructive profiling of volatile organic compounds using HS-SPME/GC-MS and its application for the geographical discrimination of white rice.

PubMed

Lim, Dong Kyu; Mo, Changyeun; Lee, Dong-Kyu; Long, Nguyen Phuoc; Lim, Jongguk; Kwon, Sung Won

2018-01-01

The authenticity determination of white rice is crucial to prevent deceptive origin labeling and dishonest trading. However, a non-destructive and comprehensive method for rapidly discriminating the geographical origins of white rice between countries is still lacking. In the current study, we developed a volatile organic compound based geographical discrimination method using headspace solid-phase microextraction coupled to gas chromatography-mass spectrometry (HS-SPME/GC-MS) to discriminate rice samples from Korea and China. A partial least squares discriminant analysis (PLS-DA) model exhibited a good classification of white rice between Korea and China (accuracy = 0.958, goodness of fit = 0.937, goodness of prediction = 0.831, and permutation test p-value = 0.043). Combining the PLS-DA based feature selection with the differentially expressed features from the unpaired t-test and significance analysis of microarrays, 12 discriminatory biomarkers were found. Among them, hexanal and 1-hexanol have been previously known to be associated with the cultivation environment and storage conditions. Other hydrocarbon biomarkers are novel, and their impact on rice production and storage remains to be elucidated. In conclusion, our findings highlight the ability to rapidly discriminate white rice from Korea and China. The developed method maybe useful for the authenticity and quality control of white rice. Copyright © 2017. Published by Elsevier B.V.

The estimation of rice paddy yield with GRAMI crop model and Geostationary Ocean Color Imager (GOCI) image over South Korea

NASA Astrophysics Data System (ADS)

Yeom, J. M.; Kim, H. O.

2014-12-01

In this study, we estimated the rice paddy yield with moderate geostationary satellite based vegetation products and GRAMI model over South Korea. Rice is the most popular staple food for Asian people. In addition, the effects of climate change are getting stronger especially in Asian region, where the most of rice are cultivated. Therefore, accurate and timely prediction of rice yield is one of the most important to accomplish food security and to prepare natural disasters such as crop defoliation, drought, and pest infestation. In the present study, GOCI, which is world first Geostationary Ocean Color Image, was used for estimating temporal vegetation indices of the rice paddy by adopting atmospheric correction BRDF modeling. For the atmospheric correction with LUT method based on Second Simulation of the Satellite Signal in the Solar Spectrum (6S), MODIS atmospheric products such as MOD04, MOD05, MOD07 from NASA's Earth Observing System Data and Information System (EOSDIS) were used. In order to correct the surface anisotropy effect, Ross-Thick Li-Sparse Reciprocal (RTLSR) BRDF model was performed at daily basis with 16day composite period. The estimated multi-temporal vegetation images was used for crop classification by using high resolution satellite images such as Rapideye, KOMPSAT-2 and KOMPSAT-3 to extract the proportional rice paddy area in corresponding a pixel of GOCI. In the case of GRAMI crop model, initial conditions are determined by performing every 2 weeks field works at Chonnam National University, Gwangju, Korea. The corrected GOCI vegetation products were incorporated with GRAMI model to predict rice yield estimation. The predicted rice yield was compared with field measurement of rice yield.

Monitoring fungal growth on brown rice grains using rapid and non-destructive hyperspectral imaging.

PubMed

Siripatrawan, U; Makino, Y

2015-04-16

This research aimed to develop a rapid, non-destructive, and accurate method based on hyperspectral imaging (HSI) for monitoring spoilage fungal growth on stored brown rice. Brown rice was inoculated with a non-pathogenic strain of Aspergillus oryzae and stored at 30 °C and 85% RH. Growth of A. oryzae on rice was monitored using viable colony counts, expressed as colony forming units per gram (CFU/g). The fungal development was observed using scanning electron microscopy. The HSI system was used to acquire reflectance images of the samples covering the visible and near-infrared (NIR) wavelength range of 400-1000 nm. Unsupervised self-organizing map (SOM) was used to visualize data classification of different levels of fungal infection. Partial least squares (PLS) regression was used to predict fungal growth on rice grains from the HSI reflectance spectra. The HSI spectral signals decreased with increasing colony counts, while conserving similar spectral pattern during the fungal growth. When integrated with SOM, the proposed HSI method could be used to classify rice samples with different levels of fungal infection without sample manipulation. Moreover, HSI was able to rapidly identify infected rice although the samples showed no symptoms of fungal infection. Based on PLS regression, the coefficient of determination was 0.97 and root mean square error of prediction was 0.39 log (CFU/g), demonstrating that the HSI technique was effective for prediction of fungal infection in rice grains. The ability of HSI to detect fungal infection at early stage would help to prevent contaminated rice grains from entering the food chain. This research provides scientific information on the rapid, non-destructive, and effective fungal detection system for rice grains. Copyright © 2015 Elsevier B.V. All rights reserved.

Efficacy of oral immunotherapy with a rice-based edible vaccine containing hypoallergenic Japanese cedar pollen allergens for treatment of established allergic conjunctivitis in mice.

PubMed

Fukuda, Ken; Ishida, Waka; Harada, Yosuke; Wakasa, Yuhya; Takagi, Hidenori; Takaiwa, Fumio; Fukushima, Atsuki

2018-01-01

We have previously shown that prophylactic oral administration of transgenic rice seeds expressing hypoallergenic modified antigens suppressed the development of allergic conjunctivitis induced by Japanese cedar pollen. We have now investigated the efficacy of oral immunotherapy with such transgenic rice for established allergic conjunctivitis in mice. BALB/c mice were sensitized with two intraperitoneal injections of Japanese cedar pollen in alum, challenged with pollen in eyedrops, and then fed for 16 days with transgenic rice seeds expressing modified Japanese cedar pollen allergens Cry j 1 and Cry j 2 or with nontransgenic rice seeds as a control. They were then challenged twice with pollen in eyedrops, with clinical signs being evaluated at 15 min after the first challenge and the eyes, blood, spleen, and lymph nodes being isolated at 24 h after the second challenge. The number of eosinophils in the conjunctiva and the clinical score for conjunctivitis were both significantly lower in mice fed the transgenic rice than in those fed nontransgenic rice. Oral vaccination with transgenic rice seeds also resulted in a significant increase in the production of IFN-γ by splenocytes, whereas it had no effect on the number of CD4 + CD25 + Foxp3 + regulatory T cells in the spleen or submandibular or mesenteric lymph nodes. Oral administration of transgenic rice seeds expressing hypoallergenic allergens ameliorated allergic conjunctivitis in the established setting. Such a rice-based edible vaccine is potentially both safe and effective for oral immunotherapy in individuals with allergic conjunctivitis. Copyright © 2017 Japanese Society of Allergology. Production and hosting by Elsevier B.V. All rights reserved.

Foliar uptake of radiocaesium from irrigation water by paddy rice (Oryza sativa): an overlooked pathway in contaminated environments.

PubMed

Uematsu, Shinichiro; Vandenhove, Hildegarde; Sweeck, Lieve; Hees, May Van; Wannijn, Jean; Smolders, Erik

2017-04-01

Flooded (paddy) rice (Oryza sativa) can take up ions from the irrigation water by foliar uptake via the exposed stem base. We hypothesised that the stem base uptake of radiocaesium (RCs) is a pathway for rice grown in RCs-contaminated environments. We developed a bi-compartmental device which discriminates the stem base from root RCs uptake from solutions, thereby using RCs isotopes ( 137 Cs and 134 Cs) with < 2% solution leak between the compartments. Radiocaesium uptake was linear over time (0-24 h). Radiocaesium uptake to the entire plant, expressed per dry weight of the exposed parts, was sixfold higher for the roots than for the exposed stem base. At equal RCs concentrations in both compartments, the exposed stem base and root uptake contributed almost equally to the total shoot RCs concentrations. Reducing potassium supply to the roots not only increased the root RCs uptake but also increased RCs uptake by the stem base. This study was the first to experimentally demonstrate active and internally regulated RCs uptake by the stem base of rice. Scenario calculations for the Fukushima-affected area predict that RCs in irrigation water could be an important source of RCs in rice as indirectly suggested from field data. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

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

PubMed

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.

Rice production in relation to soil quality under different rice-based cropping systems

NASA Astrophysics Data System (ADS)

Tran Ba, Linh; Sleutel, Steven; Nguyen Van, Qui; Thi, Guong Vo; Le Van, Khoa; Cornelis, Wim

2016-04-01

Soil quality of shallow paddy soils may be improved by introducing upland crops and thus a more diverse crop cultivation pattern. Yet, the causal relationship between crop performance and enhanced soil traits in rice-upland crop rotations remains elusive. The objectives of this study were to (i) find correlations among soil properties under different rice-upland crop systems and link selected soil properties to rice growth and yield, (ii) present appropriate values of soil parameters for sustainable rice productivity in heavy clay soil, (iii) evaluate the effect of rotating rice with upland crops on rice yield and economic benefit in a long-term experiment. A rice-upland crop rotational field experiment in the Vietnamese Mekong delta was conducted for 10 years using a randomized complete block design with four treatments and four replications. Treatments were: (i) rice-rice-rice (control - conventional system as farmers' practice), (ii) rice-maize-rice, (iii) rice-mung bean-rice, and (iv) rice-mung bean-maize. Soil and plant sampling were performed after harvest of the rice crop at the end of the final winter-spring cropping season (i.e. year 10). Results show differences in rice growth and yield, and economic benefit as an effect of the crop rotation system. These differences were linked with changes in bulk density, soil porosity, soil aggregate stability index, soil penetration resistance, soil macro-porosity, soil organic carbon, acid hydrolysable soil C and soil nutrient elements, especially at soil depth of 20-30 cm. This is evidenced by the strong correlation (P < 0.01) between rice plant parameters, rice yield and soil properties such as bulk density, porosity, penetration resistance, soil organic carbon and Chydrolysable. It turned out that good rice root growth and rice yield corresponded to bulk density values lower than 1.3 Mg m-3, soil porosity higher than 50%, penetration resistance below 1.0 MPa, and soil organic carbon above 25 g kg-1. The optimal soil depth without restriction for rice root elongation was at least 25 cm from the soil surface. We suggest these values as indicative for optimal physical soil quality when growing rice in fine-textured alluvial soils and their definition as a first step towards presenting real threshold values.

Genetic relatedness among indigenous rice varieties in the Eastern Himalayan region based on nucleotide sequences of the Waxy gene.

PubMed

Choudhury, Baharul I; Khan, Mohammed L; Dayanandan, Selvadurai

2014-12-29

Indigenous rice varieties in the Eastern Himalayan region of Northeast India are traditionally classified into sali, boro and jum ecotypes based on geographical locality and the season of cultivation. In this study, we used DNA sequence data from the Waxy (Wx) gene to infer the genetic relatedness among indigenous rice varieties in Northeast India and to assess the genetic distinctiveness of ecotypes. The results of all three analyses (Bayesian, Maximum Parsimony and Neighbor Joining) were congruent and revealed two genetically distinct clusters of rice varieties in the region. The large group comprised several varieties of sali and boro ecotypes, and all agronomically improved varieties. The small group consisted of only traditionally cultivated indigenous rice varieties, which included one boro, few sali and all jum varieties. The fixation index analysis revealed a very low level of differentiation between sali and boro (F(ST) = 0.005), moderate differentiation between sali and jum (F(ST) = 0.108) and high differentiation between jum and boro (F(ST) = 0.230) ecotypes. The genetic relatedness analyses revealed that sali, boro and jum ecotypes are genetically heterogeneous, and the current classification based on cultivation type is not congruent with the genetic background of rice varieties. Indigenous rice varieties chosen from genetically distinct clusters could be used in breeding programs to improve genetic gain through heterosis, while maintaining high genetic diversity.

Mercury flow through an Asian rice-based food web.

PubMed

Abeysinghe, Kasun S; Qiu, Guangle; Goodale, Eben; Anderson, Christopher W N; Bishop, Kevin; Evers, David C; Goodale, Morgan W; Hintelmann, Holger; Liu, Shengjie; Mammides, Christos; Quan, Rui-Chang; Wang, Jin; Wu, Pianpian; Xu, Xiao-Hang; Yang, Xiao-Dong; Feng, Xinbin

2017-10-01

Mercury (Hg) is a globally-distributed pollutant, toxic to humans and animals. Emissions are particularly high in Asia, and the source of exposure for humans there may also be different from other regions, including rice as well as fish consumption, particularly in contaminated areas. Yet the threats Asian wildlife face in rice-based ecosystems are as yet unclear. We sought to understand how Hg flows through rice-based food webs in historic mining and non-mining regions of Guizhou, China. We measured total Hg (THg) and methylmercury (MeHg) in soil, rice, 38 animal species (27 for MeHg) spanning multiple trophic levels, and examined the relationship between stable isotopes and Hg concentrations. Our results confirm biomagnification of THg/MeHg, with a high trophic magnification slope. Invertivorous songbirds had concentrations of THg in their feathers that were 15x and 3x the concentration reported to significantly impair reproduction, at mining and non-mining sites, respectively. High concentrations in specialist rice consumers and in granivorous birds, the later as high as in piscivorous birds, suggest rice is a primary source of exposure. Spiders had the highest THg concentrations among invertebrates and may represent a vector through which Hg is passed to vertebrates, especially songbirds. Our findings suggest there could be significant population level health effects and consequent biodiversity loss in sensitive ecosystems, like agricultural wetlands, across Asia, and invertivorous songbirds would be good subjects for further studies investigating this possibility. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rice proteome analysis: a step toward functional analysis of the rice genome.

PubMed

Komatsu, Setsuko; Tanaka, Naoki

2005-03-01

The technique of proteome analysis using 2-DE has the power to monitor global changes that occur in the protein complement of tissues and subcellular compartments. In this review, we describe construction of the rice proteome database, the cataloging of rice proteins, and the functional characterization of some of the proteins identified. Initially, proteins extracted from various tissues and organelles were separated by 2-DE and an image analyzer was used to construct a display or reference map of the proteins. The rice proteome database currently contains 23 reference maps based on 2-DE of proteins from different rice tissues and subcellular compartments. These reference maps comprise 13 129 rice proteins, and the amino acid sequences of 5092 of these proteins are entered in the database. Major proteins involved in growth or stress responses have been identified by using a proteomics approach and some of these proteins have unique functions. Furthermore, initial work has also begun on analyzing the phosphoproteome and protein-protein interactions in rice. The information obtained from the rice proteome database will aid in the molecular cloning of rice genes and in predicting the function of unknown proteins.

Variation in cooking and eating quality traits in Japanese rice germplasm accessions

PubMed Central

Hori, Kiyosumi; Suzuki, Keitaro; Iijima, Ken; Ebana, Kaworu

2016-01-01

The eating quality of cooked rice is important and determines its market price and consumer acceptance. To comprehensively describe the variation of eating quality in 183 rice germplasm accessions, we evaluated 33 eating-quality traits including amylose and protein contents, pasting properties of rice flour, and texture of cooked rice grains. All eating-quality traits varied widely in the germplasm accessions. Principal-components analysis (PCA) revealed that allelic differences in the Wx gene explained the largest proportion of phenotypic variation of the eating-quality traits. In 146 accessions of non-glutinous temperate japonica rice, PCA revealed that protein content and surface texture of the cooked rice grains significantly explained phenotypic variations of the eating-quality traits. An allelic difference based on simple sequence repeats, which was located near a quantitative trait locus (QTL) on the short arm of chromosome 3, was associated with differences in the eating quality of non-glutinous temperate japonica rice. These results suggest that eating quality is controlled by genetic factors, including the Wx gene and the QTL on chromosome 3, in Japanese rice accessions. These genetic factors have been consciously selected for eating quality during rice breeding programs in Japan. PMID:27162502

Variation in cooking and eating quality traits in Japanese rice germplasm accessions.

PubMed

Hori, Kiyosumi; Suzuki, Keitaro; Iijima, Ken; Ebana, Kaworu

2016-03-01

The eating quality of cooked rice is important and determines its market price and consumer acceptance. To comprehensively describe the variation of eating quality in 183 rice germplasm accessions, we evaluated 33 eating-quality traits including amylose and protein contents, pasting properties of rice flour, and texture of cooked rice grains. All eating-quality traits varied widely in the germplasm accessions. Principal-components analysis (PCA) revealed that allelic differences in the Wx gene explained the largest proportion of phenotypic variation of the eating-quality traits. In 146 accessions of non-glutinous temperate japonica rice, PCA revealed that protein content and surface texture of the cooked rice grains significantly explained phenotypic variations of the eating-quality traits. An allelic difference based on simple sequence repeats, which was located near a quantitative trait locus (QTL) on the short arm of chromosome 3, was associated with differences in the eating quality of non-glutinous temperate japonica rice. These results suggest that eating quality is controlled by genetic factors, including the Wx gene and the QTL on chromosome 3, in Japanese rice accessions. These genetic factors have been consciously selected for eating quality during rice breeding programs in Japan.

Studying the Impacts of Environmental Factors and Agricultural Management on Methane Emissions from Rice Paddies Using a Land Surface Model

NASA Astrophysics Data System (ADS)

Lin, T. S.; Gahlot, S.; Shu, S.; Jain, A. K.; Kheshgi, H. S.

2017-12-01

Continued growth in population is projected to drive increased future demand for rice and the methane emissions associated with its production. However, observational studies of methane emissions from rice have reported seemingly conflicting results and do not all support this projection. In this study we couple an ecophysiological process-based rice paddy module and a methane emission module with a land surface model, Integrated Science Assessment Model (ISAM), to study the impacts of various environmental factors and agricultural management practices on rice production and methane emissions from rice fields. This coupled modeling framework accounts for dynamic rice growth processes with adaptation of photosynthesis, rice-specific phenology, biomass accumulation, leaf area development and structures responses to water, temperature, light and nutrient stresses. The coupled model is calibrated and validated with observations from various rice cultivation fields. We find that the differing results of observational studies can be caused by the interactions of environmental factors, including climate, atmospheric CO2 concentration, and N deposition, and agricultural management practices, such as irrigation and N fertilizer applications, with rice production at spatial and temporal scales.

Population structure of rice varieties used in Turkish rice breeding programs determined using simple-sequence repeat and inter-primer binding site-retrotransposon data.

PubMed

Cömertpay, G; Baloch, F S; Derya, M; Andeden, E E; Alsaleh, A; Sürek, H; Özkan, H

2016-02-19

Effective breeding programs based on genetic diversity are needed to broaden the genetic basis of rice (Oryza sativa L.) in Turkey. In this study, 81 commercial varieties from seven countries were studied in order to estimate the genomic relationships among them using nine inter-primer binding site (iPBS)-retrotransposon and 17 simple-sequence repeat (SSR) markers. A total of 59 alleles for the SSR markers and 96 bands for the iPBS-retrotransposon markers were detected, with an average of 3.47 and 10.6 per locus, respectively. Each of the varieties could be unequivocally identified by the SSR and iPBS-retrotransposon profiles. The iPBS-retrotransposon- and SSR-based clustering were identical and closely mirrored each other, with a significantly high correlation (r = 0.73). A neighbor-joining cluster based on the combined SSR and iPBS-retrotransposon data divided the rice varieties into three clusters. The population structure was determined using the STRUCTURE software, and three populations (K = 3) were identified among the varieties studied, showing that the diversity harbored by Turkish rice varieties is low. The results indicate that iPBS-retrotransposon markers are a very powerful technique to determine the genetic diversity of rice varieties.

Identification of proteolytic bacteria from thai traditional fermented foods and their allergenic reducing potentials.

PubMed

Phromraksa, P; Nagano, H; Boonmars, T; Kamboonruang, C

2008-05-01

This study aimed to identify proteolytic bacteria from Thai traditional fermented foods and investigate their allergenic reducing potentials to wheat and milk allergens. Nine bacteria were isolated from fermented foods as follows: fermented soybean seeds (Thua Nao), fermented soybean paste (Thua Nao), wheat flour dough of steamed stuffed bun (Sa La Pao), and soaked rice from Thai fermented rice-noodle (Kha Nhom Jeen) processing. Both phenotypic and genotypic identifications were used in this study. It was found that all isolates were Gram-positive rods. Seven isolates were matched and identified as Bacillus subtilis by both techniques, and the remaining 2 isolates were phenotypically and genotypically identified as B. licheniformis and B. subtilis, respectively. The concentrated crude enzyme of B. subtilis DB and SR could reduce allergenicity of gliadin by hydrolyzing the allergenic gliadin fragments detected by immunoblotting. Furthermore, the enzyme of B. subtilis DB could also reduce allergenicity of beta-lactoglobulin (beta-LG) detected by hydrolyzing the major allergenic epitope of beta-LG at Gln(35)-Ser(36) position. B. subtilis DB and SR can be applied for the production of hypoallergenic wheat flour or milk food products.

Registration of a rice gene mapping population of Lemont X Jasmine 85 recombinant inbred lines

USDA-ARS?s Scientific Manuscript database

A mapping population developed from a cross of rice (Oryza sativa L.) tropical japonica cultivar ‘Lemont’ and indica cultivar ‘Jasmine 85’ was developed to facilitate genetic studies for important agronomic traits. The indica- and japonica-based rice recombinant inbred line (RIL) mapping population ...

Characterization and in Plant Detection of Bacteria that Cause Bacterial Panicle Blight Disease of Rice

USDA-ARS?s Scientific Manuscript database

Burkholderia glumae (BPB) presumably induces a grain rot symptom of rice that is threatening to production in most southern rice producing states of the USA. The present study was to determine the causal agent of BPB, virulence based on hypersensitive reactions on tobacco leaves, and distribution o...

Whole slurry saccharification and fermentation of maleic acid-pretreated rice straw for ethanol production.

PubMed

Jung, Young Hoon; Park, Hyun Min; Kim, Kyoung Heon

2015-09-01

We evaluated the feasibility of whole slurry (pretreated lignocellulose) saccharification and fermentation for producing ethanol from maleic acid-pretreated rice straw. The optimized conditions for pretreatment were to treat rice straw at a high temperature (190 °C) with 1 % (w/v) maleic acid for a short duration (3 min ramping to 190 °C and 3 min holding at 190 °C). Enzymatic digestibility (based on theoretical glucose yield) of cellulose in the pretreated rice straw was 91.5 %. Whole slurry saccharification and fermentation of pretreated rice straw resulted in 83.2 % final yield of ethanol based on the initial quantity of glucan in untreated rice straw. These findings indicate that maleic acid pretreatment results in a high yield of ethanol from fermentation of whole slurry even without conditioning or detoxification of the slurry. Additionally, the separation of solids and liquid is not required; therefore, the economics of cellulosic ethanol fuel production are significantly improved. We also demonstrated whole slurry saccharification and fermentation of pretreated lignocellulose, which has rarely been reported.

Assessment of influences of cooking on cadmium and arsenic bioaccessibility in rice, using an in vitro physiologically-based extraction test.

PubMed

Zhuang, Ping; Zhang, Chaosheng; Li, Yingwen; Zou, Bi; Mo, Hui; Wu, Kejun; Wu, Jingtao; Li, Zhian

2016-12-15

The health risks associated with rice consumption may decrease if consumers use cooking practices which can reduce the bioaccessibility of metal(loid)s. The effects of cooking on the Cd and As bioaccessibility, at three contamination levels of rice, were studied. Results indicated that cooking reduced bioaccessibility of Cd and As in rice. Cooking resulted in a significant increase (p<0.01) of Cd and As concentrations in the residual fraction. Low volume water-cooking of rice to dryness reduced total Cd by about 10% for rices A and B, while medium or high volume water-cooking had no effect on Cd bioaccessibility in all rice types. In contrast, low volume cooking did not remove As, but a significant decrease (p<0.05) was observed when cooking with higher volumes of water. This study provides information for a better understanding of more realistic estimation of metal(loid)s exposure from rice and the possible health risks. Copyright © 2016. Published by Elsevier Ltd.

The oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species.

PubMed

Wing, Rod A; Ammiraju, Jetty S S; Luo, Meizhong; Kim, Hyeran; Yu, Yeisoo; Kudrna, Dave; Goicoechea, Jose L; Wang, Wenming; Nelson, Will; Rao, Kiran; Brar, Darshan; Mackill, Dave J; Han, Bin; Soderlund, Cari; Stein, Lincoln; SanMiguel, Phillip; Jackson, Scott

2005-09-01

The wild species of the genus Oryza offer enormous potential to make a significant impact on agricultural productivity of the cultivated rice species Oryza sativa and Oryza glaberrima. To unlock the genetic potential of wild rice we have initiated a project entitled the 'Oryza Map Alignment Project' (OMAP) with the ultimate goal of constructing and aligning BAC/STC based physical maps of 11 wild and one cultivated rice species to the International Rice Genome Sequencing Project's finished reference genome--O. sativa ssp. japonica c. v. Nipponbare. The 11 wild rice species comprise nine different genome types and include six diploid genomes (AA, BB, CC, EE, FF and GG) and four tetrapliod genomes (BBCC, CCDD, HHKK and HHJJ) with broad geographical distribution and ecological adaptation. In this paper we describe our strategy to construct robust physical maps of all 12 rice species with an emphasis on the AA diploid O. nivara--thought to be the progenitor of modern cultivated rice.

Efficacy of Selected Insecticides Applied to Hybrid Rice Seed

PubMed Central

Adams, A.; Gore, J.; Musser, F.; Cook, D.; Walker, T.; Dobbins, C.

2016-01-01

Hybrid rice and insecticide seed treatments targeting rice water weevil, Lissorhoptrus oryzophilus Kuschel, have altered the landscape of rice production. The effect of reduced seeding rates on seed treatment efficacy in hybrid rice has not been studied. During 2011 and 2012, an experiment was conducted at seven locations to determine the relationship between low seeding rates used in hybrid rice and efficacy of selected insecticidal seed treatments as measured by rice water weevil densities and yield. Labeled rates of thiamethoxam, chlorantraniliprole, and clothianidin were compared with higher rates of these products to determine if labeled rates provide an acceptable level of control of the rice water weevil. Study locations were divided into low, moderate, and high groups based on rice water weevil larval densities. All seed treatments and seed treatment rates reduced rice water weevil densities. However, there was no observed yield or economic benefit from the use of an insecticidal seed treatment in areas of low pressure. Differences in yield were observed among seed treatments and seed treatment rates in moderate and high pressure locations, and all seed treatments yielded better than the untreated plots, but these differences were not always economical. All seed treatments showed an economic advantage in areas of high weevil pressure, and there were no differences among seed treatment products or rates, suggesting that currently labeled seed treatment rates in hybrid rice are effective for rice water weevil management. PMID:26537671

Transgenic rice plants harboring an introduced potato proteinase inhibitor II gene are insect resistant.

PubMed

Duan, X; Li, X; Xue, Q; Abo-el-Saad, M; Xu, D; Wu, R

1996-04-01

We introduced the potato proteinase inhibitor II (PINII) gene (pin2) into several Japonica rice varieties, and regenerated a large number of transgenic rice plants. Wound-inducible expression of the pin2 gene driven by its own promoter, together with the first intron of the rice actin 1 gene (act1), resulted in high-level accumulation of the PINII protein in the transgenic plants. The introduced pin2 gene was stably inherited in the second, third, and fourth generations, as shown by molecular analyses. Based on data from the molecular analyses, several homozygous transgenic lines were obtained. Bioassay for insect resistance with the fifth-generation transgenic rice plants showed that transgenic rice plants had increased resistance to a major rice insect pest, pink stem borer (Sesamia inferens). Thus, introduction of an insecticidal proteinase inhibitor gene into cereal plants can be used as a general strategy for control of insect pests.

Rice methylmercury exposure and mitigation: a comprehensive review.

PubMed

Rothenberg, Sarah E; Windham-Myers, Lisamarie; Creswell, Joel E

2014-08-01

Rice cultivation practices from field preparation to post-harvest transform rice paddies into hot spots for microbial mercury methylation, converting less-toxic inorganic mercury to more-toxic methylmercury, which is likely translocated to rice grain. This review includes 51 studies reporting rice total mercury and/or methylmercury concentrations, based on rice (Orzya sativa) cultivated or purchased in 15 countries. Not surprisingly, both rice total mercury and methylmercury levels were significantly higher in polluted sites compared to non-polluted sites (Wilcoxon rank sum, p<0.001). However, rice percent methylmercury (of total mercury) did not differ statistically between polluted and non-polluted sites (Wilcoxon rank sum, p=0.35), suggesting comparable mercury methylation rates in paddy soil across these sites and/or similar accumulation of mercury species for these rice cultivars. Studies characterizing the effects of rice cultivation under more aerobic conditions were reviewed to determine the mitigation potential of this practice. Rice management practices utilizing alternating wetting and drying (instead of continuous flooding) caused soil methylmercury levels to spike, resulting in a strong methylmercury pulse after fields were dried and reflooded; however, it is uncertain whether this led to increased translocation of methylmercury from paddy soil to rice grain. Due to the potential health risks, it is advisable to investigate this issue further, and to develop separate water management strategies for mercury polluted and non-polluted sites, in order to minimize methylmercury exposure through rice ingestion. Copyright © 2014 Elsevier Inc. All rights reserved.

Methane and nitrous oxide emissions from three paddy rice based cultivation systems in Southwest China

NASA Astrophysics Data System (ADS)

Jiang, Changsheng; Wang, Yuesi; Zheng, Xunhua; Zhu, Bo; Huang, Yao; Hao, Qingju

2006-05-01

To understand methane (CH4) and nitrous oxide (N2O) emissions from permanently flooded rice paddy fields and to develop mitigation options, a field experiment was conducted in situ for two years (from late 2002 to early 2005) in three rice-based cultivation systems, which are a permanently flooded rice field cultivated with a single time and followed by a non-rice season (PF), a rice-wheat rotation system (RW) and a rice-rapeseed rotation system (RR) in a hilly area in Southwest China. The results showed that the total CH4 emissions from PF were 646.3±52.1 and 215.0±45.4 kg CH4 hm-2 during the rice-growing period and non-rice period, respectively. Both values were much lower than many previous reports from similar regions in Southwest China. The CH4 emissions in the rice-growing season were more intensive in PF, as compared to RW and RR. Only 33% of the total annual CH4 emission in PF occurred in the non-rice season, though the duration of this season is two times longer than the rice season. The annual mean N2O flux in PF was 4.5±0.6 kg N2O hm-2 yr-1. The N2O emission in the rice-growing season was also more intensive than in the non-rice season, with only 16% of the total annual emission occurring in the non-rice season. The amounts of N2O emission in PF were ignorable compared to the CH4 emission in terms of the global warming potential (GWP). Changing PF to RW or RR not only eliminated CH4 emissions in the non-rice season, but also substantially reduced the CH4 emission during the following rice-growing period (ca. 58%, P<0.05). However, this change in cultivation system substantially increased N2O emissions, especially in the non-rice season, by a factor of 3.7 to 4.5. On the 100-year horizon, the integrated GWP of total annual CH4 and N2O emissions satisfies PF≫RR≈RW. The GWP of PF is higher than that of RW and RR by a factor of 2.6 and 2.7, respectively. Of the total GWP of CH4 and N2O emissions, CH4 emission contributed to 93%, 65% and 59% in PF, RW and RR, respectively. These results suggest that changing PF to RW and RR can substantially reduce not only CH4 emission but also the total GWP of the CH4 and N2O emissions.

Rice Husk Ash to Stabilize Heavy Metals Contained in Municipal Solid Waste Incineration Fly Ash: First Results by Applying New Pre-treatment Technology

PubMed Central

Benassi, Laura; Franchi, Federica; Catina, Daniele; Cioffi, Flavio; Rodella, Nicola; Borgese, Laura; Pasquali, Michela; Depero, Laura E.; Bontempi, Elza

2015-01-01

A new technology was recently developed for municipal solid waste incineration (MSWI) fly ash stabilization, based on the employment of all waste and byproduct materials. In particular, the proposed method is based on the use of amorphous silica contained in rice husk ash (RHA), an agricultural byproduct material (COSMOS-RICE project). The obtained final inert can be applied in several applications to produce “green composites”. In this work, for the first time, a process for pre-treatment of rice husk, before its use in the stabilization of heavy metals, based on the employment of Instant Pressure Drop technology (DIC) was tested. The aim of this work is to verify the influence of the pre-treatment on the efficiency on heavy metals stabilization in the COSMOS-RICE technology. DIC technique is based on a thermomechanical effect induced by an abrupt transition from high steam pressure to a vacuum, to produce changes in the material. Two different DIC pre-treatments were selected and thermal annealing at different temperatures were performed on rice husk. The resulting RHAs were employed to obtain COSMOS-RICE samples, and the stabilization procedure was tested on the MSWI fly ash. In the frame of this work, some thermal treatments were also realized in O2-limiting conditions, to test the effect of charcoal obtained from RHA on the stabilization procedure. The results of this work show that the application of DIC technology into existing treatment cycles of some waste materials should be investigated in more details to offer the possibility to stabilize and reuse waste. PMID:28793605

Fine Mapping of QUICK ROOTING 1 and 2, Quantitative Trait Loci Increasing Root Length in Rice.

PubMed

Kitomi, Yuka; Nakao, Emari; Kawai, Sawako; Kanno, Noriko; Ando, Tsuyu; Fukuoka, Shuichi; Irie, Kenji; Uga, Yusaku

2018-02-02

The volume that the root system can occupy is associated with the efficiency of water and nutrient uptake from soil. Genetic improvement of root length, which is a limiting factor for root distribution, is necessary for increasing crop production. In this report, we describe identification of two quantitative trait loci (QTLs) for maximal root length, QUICK ROOTING 1 ( QRO1 ) on chromosome 2 and QRO2 on chromosome 6, in cultivated rice ( Oryza sativa L.). We measured the maximal root length in 26 lines carrying chromosome segments from the long-rooted upland rice cultivar Kinandang Patong in the genetic background of the short-rooted lowland cultivar IR64. Five lines had longer roots than IR64. By rough mapping of the target regions in BC 4 F 2 populations, we detected putative QTLs for maximal root length on chromosomes 2, 6, and 8. To fine-map these QTLs, we used BC 4 F 3 recombinant homozygous lines. QRO1 was mapped between markers RM5651 and RM6107, which delimit a 1.7-Mb interval on chromosome 2, and QRO2 was mapped between markers RM20495 and RM3430-1, which delimit an 884-kb interval on chromosome 6. Both QTLs may be promising gene resources for improving root system architecture in rice. Copyright © 2018 Kitomi et al.

Genomic structure analysis of a set of Oryza nivara introgression lines and identification of yield-associated QTLs using whole-genome resequencing

PubMed Central

Ma, Xin; Fu, Yongcai; Zhao, Xinhui; Jiang, Liyun; Zhu, Zuofeng; Gu, Ping; Xu, Wenying; Su, Zhen; Sun, Chuanqing; Tan, Lubin

2016-01-01

Oryza nivara, an annual wild AA-genome species of rice, is an important gene pool for broadening the genetic diversity of cultivated rice (O. sativa L.). Towards identifying and utilizing favourable alleles from O. nivara, we developed a set of introgression lines (ILs) by introducing O. nivara segments into the elite indica rice variety 93-11 background through advanced backcrossing and repeated selfing. Using whole-genome resequencing, a high-density genetic map containing 1,070 bin-markers was constructed for the 131 ILs, with an average length of 349 kb per bin. The 131 ILs cover 95% of O. nivara genome, providing a relatively complete genomic library for introgressing O. nivara alleles for trait improvement. Using this high-density bin-map, QTL mapping for 13 yield-related traits was performed and a total of 65 QTLs were detected across two environments. At ~36.9% of detected QTLs, the alleles from O. nivara conferred improving effects on yield-associated traits. Six cloned genes, Sh4/SHA1, Bh4, Sd1, TE/TAD1, GS3 and FZP, colocalised in the peak intervals of 9 QTLs. In conclusion, we developed new genetic materials for exploration and use of beneficial alleles from wild rice and provided a basis for future fine mapping and cloning of the favourable O. nivara-derived QTLs. PMID:27251022

Isolation of thylakoid membrane complexes from rice by a new double-strips BN/SDS-PAGE and bioinformatics prediction of stromal ridge subunits interaction.

PubMed

Shao, Jinzhen; Zhang, Yubo; Yu, Jianlan; Guo, Lin; Ding, Yi

2011-01-01

Thylakoid membrane complexes of rice (Oryza sativa L.) play crucial roles in growth and crop production. Understanding of protein interactions within the complex would provide new insights into photosynthesis. Here, a new "Double-Strips BN/SDS-PAGE" method was employed to separate thylakoid membrane complexes in order to increase the protein abundance on 2D-gels and to facilitate the identification of hydrophobic transmembrane proteins. A total of 58 protein spots could be observed and subunit constitution of these complexes exhibited on 2D-gels. The generality of this new approach was confirmed using thylakoid membrane from spinach (Spinacia oleracea) and pumpkin (Cucurita spp). Furthermore, the proteins separated from rice thylakoid membrane were identified by the mass spectrometry (MS). The stromal ridge proteins PsaD and PsaE were identified both in the holo- and core- PSI complexes of rice. Using molecular dynamics simulation to explore the recognition mechanism of these subunits, we showed that salt bridge interactions between residues R19 of PsaC and E168 of PasD as well as R75 of PsaC and E91 of PsaD played important roles in the stability of the complex. This stromal ridge subunits interaction was also supported by the subsequent analysis of the binding free energy, the intramolecular distances and the intramolecular energy.

Analysis of rice purchase decision on rice consumer in Bandung city

NASA Astrophysics Data System (ADS)

Kusno, K.; Imannurdin, A.; Syamsiyah, N.; Djuwendah, E.

2018-03-01

This study was conducted at three kinds of purchase location which were traditional market, rice kiosk, and supermarket in Bandung City, with survey data of 108 respondents which were selected by systematic random sampling. The aim of this study is to (1) identify consumer characteristics, (2) identify which atribute is considered by consumer in buying rice, and (3) analyze the relationship between purchase decision and income class. Data were analyzed by descriptive analysis and Chi Square test. The results showed most consumers in the traditional market were middle-educated and lower middle-income, at the rice kiosk, the consumer were generally middle-educated and middle-income, and in the supermarkets, the majority were high-educated and upper middle-income consumers. “Kepulenan” be the first priority of most consumers, but for the lower-middle class, the main priority was price. Thus, in case of scarcity and rice price increase, the government should immediately arrange market operations which targeting to lower-middle class consumers. There was a significant relationship between (1) the quality of rice consumed, (2) the frequency of rice purchase per month, and (3) attitudes toward rice price increase; each with the income class. Although the price of rice increase, consumers of middle and upper-middle were remain loyal to the quality of rice they consumed. This indicates rice market in Bandung city is an ideal market for premium rice so that traders and producers are expected to maintain the quality of rice, such as keep using superior seeds and applying good cultivation based on Good Agricultural Practice (GAP) rules.

cisprimertool: software to implement a comparative genomics strategy for the development of conserved intron scanning (CIS) markers.

PubMed

Jayashree, B; Jagadeesh, V T; Hoisington, D

2008-05-01

The availability of complete, annotated genomic sequence information in model organisms is a rich resource that can be extended to understudied orphan crops through comparative genomic approaches. We report here a software tool (cisprimertool) for the identification of conserved intron scanning regions using expressed sequence tag alignments to a completely sequenced model crop genome. The method used is based on earlier studies reporting the assessment of conserved intron scanning primers (called CISP) within relatively conserved exons located near exon-intron boundaries from onion, banana, sorghum and pearl millet alignments with rice. The tool is freely available to academic users at http://www.icrisat.org/gt-bt/CISPTool.htm. © 2007 ICRISAT.

A novel way to establish fertilization recommendations based on agronomic efficiency and a sustainable yield index for rice crops.

PubMed

Liu, Chuang; Liu, Yi; Li, Zhiguo; Zhang, Guoshi; Chen, Fang

2017-04-24

A simpler approach for establishing fertilizer recommendations for major crops is urgently required to improve the application efficiency of commercial fertilizers in China. To address this need, we developed a method based on field data drawn from the China Program of the International Plant Nutrition Institute (IPNI) rice experiments and investigations carried out in southeastern China during 2001 to 2012. Our results show that, using agronomic efficiencies and a sustainable yield index (SYI), this new method for establishing fertilizer recommendations robustly estimated the mean rice yield (7.6 t/ha) and mean nutrient supply capacities (186, 60, and 96 kg/ha of N, P 2 O 5 , and K 2 O, respectively) of fertilizers in the study region. In addition, there were significant differences in rice yield response, economic cost/benefit ratio, and nutrient-use efficiencies associated with agronomic efficiencies ranked as high, medium and low. Thus, ranking agronomic efficiency could strengthen linear models relating rice yields and SYI. Our results also indicate that the new method provides better recommendations in terms of rice yield, SYI, and profitability than previous methods. Hence, we believe it is an effective approach for improving recommended applications of commercial fertilizers to rice (and potentially other crops).

Decadal monitoring of rice farming practices from MODIS data in Myanmar

NASA Astrophysics Data System (ADS)

Thanh Son, Nguyen; Farn Chen, Chi; Chen, Cheng Ru

2015-04-01

Rice agriculture was the most important sector in Myanmar's economy because it provided employments and livelihoods for at least 75% of the country's population, accounting for more than 48% of the national gross domestic product. Prior to the World War II, this country was the largest rice-producing nation in the world. However, it is currently a relatively minor rice exporter, ranking seventh after Thailand and Vietnam. The country's rice export potential remains high due to abundant land and water resources along with recent indications of progressive policy reforms to improve rice productivity. This study aimed at investigating decadal changes in rice farming practices in Myanmar during 2001 to 2014 using Moderate Resolution Imaging Spectroradiometer (MODIS) data. We processed the data though three main steps: (1) data pre-processing to construct the smooth time-series MODIS enhanced vegetation index (EVI) data, (2) mapping rice farming practices using phenological information of crop phenology, and (3) accuracy assessment. The mapping results were compared with the ground reference data indicated satisfactory results, with the overall accuracies and Kappa coefficients generally higher than 90% and 0.8, respectively. These results were reaffirmed by comparisons between MODIS-derived rice area and the government's rice area statistics, with a close correlation between the two datasets (R2 > 0.8) and the relative error in area smaller than 15%. From 2001 to 2014, rice farming practices in Myanmar had remarkably changed from single-cropped rice to double-cropped rice, especially in Ayeyarwady river basin. This study demonstrates the validity of the phenology-based approach for national-wide monitoring of decadal changes in rice farming practices in Myanmar. Such a quantitative information might be useful for agronomic managers to devise better plans for long-term rice crop management of in the country.

The growth and uptake of Ga and In of rice (Oryza sative L.) seedlings as affected by Ga and In concentrations in hydroponic cultures.

PubMed

Syu, Chien-Hui; Chien, Po-Hsuan; Huang, Chia-Chen; Jiang, Pei-Yu; Juang, Kai-Wei; Lee, Dar-Yuan

2017-01-01

Limited information is available on the effects of gallium (Ga) and indium (In) on the growth of paddy rice. The Ga and In are emerging contaminants and widely used in high-tech industries nowadays. Understanding the toxicity and accumulation of Ga and In by rice plants is important for reducing the effect on rice production and exposure risk to human by rice consumption. Therefore, this study investigates the effect of Ga and In on the growth of rice seedlings and examines the accumulation and distribution of those elements in plant tissues. Hydroponic cultures were conducted in phytotron glasshouse with controlled temperature and relative humidity conditions, and the rice seedlings were treated with different levels of Ga and In in the nutrient solutions. The growth index and the concentrations of Ga and In in roots and shoots of rice seedlings were measured after harvesting. A significant increase in growth index with increasing Ga concentrations in culture solutions (<10mgGaL -1 ) was observed. In addition, the uptake of N, K, Mg, Ca, Mn by rice plants was also enhanced by Ga. However, the growth inhibition were observed while the In concentrations higher than 0.08mgL -1 , and the nutrients accumulated in rice plants were also significant decreased after In treatments. Based on the dose-response curve, we observed that the EC 10 (effective concentration resulting in 10% growth inhibition) value for In treatment was 0.17mgL -1 . The results of plant analysis indicated that the roots were the dominant sink of Ga and In in rice seedlings, and it was also found that the capability of translocation of Ga from roots to shoots were higher than In. In addition, it was also found that the PT 10 (threshold concentration of phytotoxicity resulting in 10% growth retardation) values based on shoot height and total biomass for In were 15.4 and 10.6μgplant -1 , respectively. The beneficial effects on the plant growth of rice seedlings were found by the addition of Ga in culture solutions. In contrast, the In treatments led to growth inhibition of rice seedlings. There were differences in the phytotoxicity, uptake, and translocation of the two emerging contaminants in rice seedlings. Copyright © 2016 Elsevier Inc. All rights reserved.

A Mixed-Methods Study on Acceptability, Tolerability, and Substitution of Brown Rice for White Rice to Lower Blood Glucose Levels among Nigerian Adults.

PubMed

Adebamowo, Sally N; Eseyin, Olabimpe; Yilme, Susan; Adeyemi, David; Willett, Walter C; Hu, Frank B; Spiegelman, Donna; Adebamowo, Clement A

2017-01-01

Whole-grain products such as brown rice have been associated with lower risk of metabolic disorders including diabetes. We examined the acceptability and tolerability of substituting brown rice for white rice and the feasibility of introducing brown rice into the diet through a long-term trial to lower the risk of type 2 diabetes. Fifty-one adults residing in Abuja, Nigeria, participated in this study. Using purposeful sampling for focus group discussions (FGDs), participants were enrolled based on their age (19-25 vs. 40-60 years) and body mass index (BMI) (normal weight vs. overweight/obese). Participants tasted four meals with different constitution of brown and white rice (25:75%, 50:50%, 75:25%, and 100% brown rice). Twelve FGDs were conducted, six before and six after the food tasting. Two-hour postprandial blood glucose was measured after consumption of each rice meal. The mean age of the participants was 39 (±14) years, their mean BMI was 25.6 (±5.2) and about half of them were male. Most of the participants (61%) reported that rice was their main source of carbohydrate and 67% consumed rice at least five times/week. Before the food tasting, participants considered white polished rice superior to brown rice with regard to quality, taste, and nutritional value. After the food tasting, most of the participants (49%) indicated a preference for the 100% brown rice, 19% preferred the 25% brown rice, 18% preferred the 50% brown rice, and 7% preferred the 75% brown rice meals. Factors that may affect the acceptability of brown rice include its appearance, longer cooking time, cost, limited availability, and poor appreciation of its nutritional value. In general, 2-h postprandial glucose levels were lower, after consumption of meals with higher proportion of brown rice. This study provides valuable insight into the acceptability of brown rice as a substitute for white rice in Nigeria. If confirmed in larger studies, these results highlight the importance of increasing awareness on the nutritional value of brown rice and support the rationale for conducting a large-scale intervention trial to examine the effect of brown rice consumption on blood sugar levels among Nigerians.

Assessing green-processing technologies for wet milling freshly hulled and germinated brown rice, leading to naturally fortified plant-based beverages

USDA-ARS?s Scientific Manuscript database

Rice milk beverages can well balanced nutrition. With healthier nutrition in consumer’s minds, national. Worldwide consumption/production of plant-based milk beverages are increasing. Much past research and invention was based on enzymatic conversion processes for starch that were uncomplicated be...

Effect of Red Yeast Rice and Coconut, Rice Bran or Sunflower Oil Combination in Rats on Hypercholesterolemic Diet.

PubMed

Govindarajan, Sumitra; Vellingiri, Kishore

2016-04-01

Dietary supplements provide a novel population based health approach for treating hyperlipidemias. Red yeast rice is known to have lipid lowering effects. Combination of red yeast rice with various oils is taken by different population around the world. In this present work, we aimed to compare the effects of red yeast rice with different oil (coconut, rice bran and sunflower oil) supplementations on lipid levels and oxidative stress in rats fed on hypercholesterolemic diet. A Randomized controlled study was conducted on 28 male Sprague Dawley rats. It included 4 arms-Control arm (hypercholesterolemic diet), Test arm A (hypercholesterolemic diet +Red yeast rice + Rice bran oil), arm B (hypercholesterolemic diet +Red yeast rice + Coconut oil) and arm C (hypercholesterolemic diet +Red yeast rice + Sunflower oil). At the end of one month, serum cholesterol, triglycerides, MDA and paraoxonase was measured. The mean values of analytes between the different groups were compared using student 't-' test. The rats fed with red yeast rice and rice bran oil combination showed significantly lower levels of serum cholesterol, triglycerides and MDA when compared to the controls. The serum paraoxonase levels were significantly higher in this group when compared to the controls. The rats fed with red yeast rice and coconut oil combination showed significantly lower serum cholesterol and MDA levels when compared to the controls. The mean triglyceride and paraoxonase levels did not show any statistically significant difference from the controls. The rats on red yeast rice and sunflower oil combination did not show any statistically significant difference in the lipid levels and oxidative stress parameters. The food combination which had best outcome in preventing the development of hyperlipidemia and oxidative stress in rats fed with hypercholesterolemic diet was red yeast rice and rice bran oil. Combining red yeast rice with coconut oil and sunflower oil gave suboptimal benefits.

[Development of bakery products for greater adult consumption based on wheat and rice flour].

PubMed

Reyes Aguilar, María José; Palomo, Patricia de; Bressani, Ricardo

2004-09-01

The present investigation was developed as a contribution to Guatemalan's elderly food and nutrition. Its main objective was to evaluate the chemical, nutritional and sensory quality of bread prepared from the partial substitution of wheat flour with rice flour. Wheat flour substitutions with rice flour in the order of 15, 20, 30, 40, 50 and 60% were evaluated. Differences with the control (100% wheat bread) were found during the process of preparation, as well as texture, volume, height, weight and specific volume. Important effects in dough handling were noted specifically in the 40, 50 and 60% rice bread. Thus, a sandy texture was found in breads of higher rice levels. The bread protein quality increased with the level of substitution; however the protein quality difference between the wheat bread and the bread with 60% rice flour did not achieve statistical significance. Based on a statistical analysis of the physical properties the bread with 30 and 40% rice flour was selected, and through a preference test between these last two, the 30% rice flour bread was selected as the sample best suited to the present study's purposes. This bread was not different to wheat bread in many nutritional parameters, although in others it showed to be superior. Each serving size of bread has a weight of 80 grams (2 slices) that contributes adequate quantity of calories, protein and sodium, although a little less dietary fiber than 100% wheat bread.

New strategy for the determination of gliadins in maize- or rice-based foods matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: fractionation of gliadins from maize or rice prolamins by acidic treatment.

PubMed

Hernando, Alberto; Valdes, Israel; Méndez, Enrique

2003-08-01

A procedure for determining small quantities of gliadins by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) in gluten-free foods containing relatively large amounts of prolamin proteins from maize or rice is described. We report for the first time that gliadins, the ethanol-soluble wheat prolamin fraction, can be quantitatively solubilized in 1.0 M acetic acid, while the corresponding ethanol-soluble maize or rice prolamin fraction remains insoluble in acetic acid. We describe a methodology for the detection of gliadins in maize and rice foods based on a two-step procedure of extraction (60% aqueous ethanol followed by 1 M acetic acid). Subsequent MALDI-TOFMS analysis of the resulting acidic extract from these gluten-free foods clearly confirms the presence of a typical mass pattern corresponding to gliadin components, ranging from 30 to 45 kDa. Depending on the percentages of maize or rice flours employed in the elaboration of these foods, the combined procedure enables levels of gliadins from 100 to 400 ppm to be detected. The efficiency of this combined procedure corroborates enzyme-linked immunosorbent assay data for a large number of maize/rice gluten-free foods by means of direct visualization of the characteristic gliadin mass pattern in maize or rice foods. Copyright 2003 John Wiley & Sons, Ltd.

Effect of iron status on iron absorption in different habitual meals in young south Indian women.

PubMed

Kalasuramath, Suneeta; Kurpad, Anura V; Thankachan, Prashanth

2013-02-01

Iron deficiency (ID) affects a large number of women in India. An inverse relationship exists between iron (Fe) status and Fe absorption. Dietary inhibitory and enhancing factors exert a profound influence on bioavailability of Fe. Although the current recommended dietary allowance (RDA) for Fe is based on 8 per cent bioavailability, it is not clear if this holds good for the usual highly inhibitory Indian diet matrix. This study was aimed to determine Fe absorption from several habitually consumed south Indian food and to evaluate the interaction of Fe status with absorption. Four Fe absorption studies were performed on 60 apparently healthy young women, aged 18-35 years. Based on blood biochemistry, 45 of them were ID and 15 were iron replete (IR). The habitual meals assessed were rice, millet and wheat based meals in the ID subjects and rice based meal alone in the IR subjects. Each subject received the test meal labelled with 3 mg of ⁵⁷Fe and Fe absorption was measured based on erythrocyte incorporation of isotope label 14 days following administration. Mean fractional Fe absorption from the rice, wheat and millet based meals in the ID subjects were 8.3, 11.2 and 4.6 per cent, respectively. Fe absorption from the rice-based meals was 2.5 per cent in IR subjects. Fe absorption is dictated by Fe status from low bioavailability meals. Millet based meals have the lowest bioavailability, while the rice and wheat based meals had moderate to good bioavailability. In millet based meals, it is prudent to consider ways to improve Fe absorption.

A Rice CPYC-Type Glutaredoxin OsGRX20 in Protection against Bacterial Blight, Methyl Viologen and Salt Stresses.

PubMed

Ning, Xi; Sun, Yao; Wang, Changchun; Zhang, Weilin; Sun, Meihao; Hu, Haitao; Liu, Jianzhong; Yang, Ling

2018-01-01

Glutaredoxins (GRXs) belong to the antioxidants involved in the cellular stress responses. In spite of the identification 48 GRX genes in rice genomes, the biological functions of most of them remain unknown. Especially, the biological roles of members of GRX family in disease resistance are still lacking. Our proteomic analysis found that OsGRX20 increased by 2.7-fold after infection by bacterial blight. In this study, we isolated and characterized the full-length nucleotide sequences of the rice OsGRX20 gene, which encodes a GRX family protein with CPFC active site of CPYC-type class. OsGRX20 protein was localized in nucleus and cytosol, and its transcripts were expressed predominantly in leaves. Several stress- and hormone-related motifs putatively acting as regulatory elements were found in the OsGRX20 promoter. Real-time quantitative PCR analysis indicated that OsGRX20 was expressed at a significantly higher level in leaves of a resistant or tolerant rice genotype, Yongjing 50A, than in a sensitive genotype, Xiushui 11, exposed to bacterial blight, methyl viologen, heat, and cold. Its expression could be induced by salt, PEG-6000, 2,4-D, salicylic acid, jasmonic acid, and abscisic acid treatments in Yongjing 50A. Overexpression of OsGRX20 in rice Xiushui 11 significantly enhanced its resistance to bacterial blight attack, and tolerance to methyl viologen and salt stresses. In contrast, interference of OsGRX20 in Yongjing 50A led to increased susceptibility to bacterial blight, methyl viologen and salt stresses. OsGRX20 restrained accumulation of superoxide radicals in aerial tissue during methyl viologen treatment. Consistently, alterations in OsGRX20 expression affect the ascorbate/dehydroascorbate ratio and the abundance of transcripts encoding four reactive oxygen species scavenging enzymes after methyl viologen-induced stress. Our results demonstrate that OsGRX20 functioned as a positive regulator in rice tolerance to multiple stresses, which may be of significant use in the genetic improvement of rice resistance.

Identification of Genomic Regions and the Isoamylase Gene for Reduced Grain Chalkiness in Rice

PubMed Central

Sun, Wenqian; Zhou, Qiaoling; Yao, Yue; Qiu, Xianjin; Xie, Kun; Yu, Sibin

2015-01-01

Grain chalkiness is an important grain quality related to starch granules in the endosperm. A high percentage of grain chalkiness is a major problem because it diminishes grain quality in rice. Here, we report quantitative trait loci identification for grain chalkiness using high-throughput single nucleotide polymorphism genotyping of a chromosomal segment substitution line population in which each line carried one or a few introduced japonica cultivar Nipponbare segments in the genetic background of the indica cultivar ZS97. Ten quantitative trait loci regions were commonly identified for the percentage of grain chalkiness and the degree of endosperm chalkiness. The allelic effects at nine of these quantitative trait loci reduced grain chalkiness. Furthermore, a quantitative trait locus (qPGC8-2) on chromosome 8 was validated in a chromosomal segment substitution line–derived segregation population, and had a stable effect on chalkiness in a multiple-environment evaluation of the near-isogenic lines. Residing on the qPGC8-2 region, the isoamylase gene (ISA1) was preferentially expressed in the endosperm and revealed some nucleotide polymorphisms between two varieties, Nipponbare and ZS97. Transgenic lines with suppression of ISA1 by RNA interference produced grains with 20% more chalkiness than the control. The results support that the gene may underlie qPGC8-2 for grain chalkiness. The multiple-environment trials of the near-isogenic lines also show that combination of the favorable alleles such as the ISA1 gene for low chalkiness and the GS3 gene for long grains considerably improved grain quality of ZS97, which proves useful for grain quality improvement in rice breeding programs. PMID:25790260

Differential Expression of In Vivo and In Vitro Protein Profile of Outer Membrane of Acidovorax avenae Subsp. avenae

PubMed Central

Qiu, Hui; Li, Bin; Jabeen, Amara; Li, Liping; Liu, He; Kube, Michael; Xie, Guanlin; Wang, Yanli; Sun, Guochang

2012-01-01

Outer membrane (OM) proteins play a significant role in bacterial pathogenesis. In this work, we examined and compared the expression of the OM proteins of the rice pathogen Acidovorax avenae subsp. avenae strain RS-1, a Gram-negative bacterium, both in an in vitro culture medium and in vivo rice plants. Global proteomic profiling of A. avenae subsp. avenae strain RS-1 comparing in vivo and in vitro conditions revealed the differential expression of proteins affecting the survival and pathogenicity of the rice pathogen in host plants. The shotgun proteomics analysis of OM proteins resulted in the identification of 97 proteins in vitro and 62 proteins in vivo by mass spectrometry. Among these OM proteins, there is a high number of porins, TonB-dependent receptors, lipoproteins of the NodT family, ABC transporters, flagellins, and proteins of unknown function expressed under both conditions. However, the major proteins such as phospholipase and OmpA domain containing proteins were expressed in vitro, while the proteins such as the surface anchored protein F, ATP-dependent Clp protease, OmpA and MotB domain containing proteins were expressed in vivo. This may indicate that these in vivo OM proteins have roles in the pathogenicity of A. avenae subsp. avenae strain RS-1. In addition, the LC-MS/MS identification of OmpA and MotB validated the in silico prediction of the existance of Type VI secretion system core components. To the best of our knowledge, this is the first study to reveal the in vitro and in vivo protein profiles, in combination with LC-MS/MS mass spectra, in silico OM proteome and in silico genome wide analysis, of pathogenicity or plant host required proteins of a plant pathogenic bacterium. PMID:23166741

Geochemical patterns and microbial contribution to iron plaque formation in the rice plant rhizosphere

NASA Astrophysics Data System (ADS)

Maisch, Markus; Murata, Chihiro; Unger, Julia; Kappler, Andreas; Schmidt, Caroline

2015-04-01

Rice is the major food source for more than half of the world population and 80 percent of the worldwide rice cultivation is performed on water logged paddy soils. The establishment of reducing conditions in the soil and across the soil-water interface not only stimulates the microbial production and release of the greenhouse gas methane. These settings also create optimal conditions for microbial iron(III) reduction and therefore saturate the system with reduced ferrous iron. Through the reduction and dissolution of ferric minerals that are characterized by their high surface activity, sorbed nutrients and contaminants (e.g. arsenic) will be mobilized and are thus available for uptake by plants. Rice plants have evolved a strategy to release oxygen from their roots in order to prevent iron toxification in highly ferrous environments. The release of oxygen to the reduced paddy soil causes ferric iron plaque formation on the rice roots and finally increases the sorption capacity for toxic metals. To this date the geochemical and microbiological processes that control the formation of iron plaque are not deciphered. It has been hypothesized that iron(II)-oxidizing bacteria play a potential role in the iron(III) mineral formation along the roots. However, not much is known about the actual processes, mineral products, and geochemical gradients that establish within the rhizosphere. In the present study we have developed a growth set-up that allows the co-cultivation of rice plants and iron(II)-oxidizing bacteria, as well as the visual observation and in situ measurement of geochemical parameters. Oxygen and dissolved iron(II) gradients have been measured using microelectrodes and show geochemical hot spots that offer optimal growth conditions for microaerophilic iron(II) oxidizers. First mineral identification attempts of iron plaque have been performed using Mössbauer spectroscopy and microscopy. The obtained results on mineraology and crystallinity have been compared to mineralogical data from purely biotic (microaerophilic) and abiotic iron mineral formation processes.

Proteomic identification of OsCYP2, a rice cyclophilin that confers salt tolerance in rice (Oryza sativa L.) seedlings when overexpressed

PubMed Central

2011-01-01

Background High Salinity is a major environmental stress influencing growth and development of rice. Comparative proteomic analysis of hybrid rice shoot proteins from Shanyou 10 seedlings, a salt-tolerant hybrid variety, and Liangyoupeijiu seedlings, a salt-sensitive hybrid variety, was performed to identify new components involved in salt-stress signaling. Results Phenotypic analysis of one protein that was upregulated during salt-induced stress, cyclophilin 2 (OsCYP2), indicated that OsCYP2 transgenic rice seedlings had better tolerance to salt stress than did wild-type seedlings. Interestingly, wild-type seedlings exhibited a marked reduction in maximal photochemical efficiency under salt stress, whereas no such change was observed for OsCYP2-transgenic seedlings. OsCYP2-transgenic seedlings had lower levels of lipid peroxidation products and higher activities of antioxidant enzymes than wild-type seedlings. Spatiotemporal expression analysis of OsCYP2 showed that it could be induced by salt stress in both Shanyou 10 and Liangyoupeijiu seedlings, but Shanyou 10 seedlings showed higher OsCYP2 expression levels. Moreover, circadian rhythm expression of OsCYP2 in Shanyou 10 seedlings occurred earlier than in Liangyoupeijiu seedlings. Treatment with PEG, heat, or ABA induced OsCYP2 expression in Shanyou 10 seedlings but inhibited its expression in Liangyoupeijiu seedlings. Cold stress inhibited OsCYP2 expression in Shanyou 10 and Liangyoupeijiu seedlings. In addition, OsCYP2 was strongly expressed in shoots but rarely in roots in two rice hybrid varieties. Conclusions Together, these data suggest that OsCYP2 may act as a key regulator that controls ROS level by modulating activities of antioxidant enzymes at translation level. OsCYP2 expression is not only induced by salt stress, but also regulated by circadian rhythm. Moreover, OsCYP2 is also likely to act as a key component that is involved in signal pathways of other types of stresses-PEG, heat, cold, or ABA. PMID:21324151

Development and characterization of japonica rice lines carrying the brown planthopper-resistance genes BPH12 and BPH6.

PubMed

Qiu, Yongfu; Guo, Jianping; Jing, Shengli; Zhu, Lili; He, Guangcun

2012-02-01

The brown planthopper (Nilaparvata lugens Stål; BPH) has become a severe constraint on rice production. Identification and pyramiding BPH-resistance genes is an economical and effective solution to increase the resistance level of rice varieties. All the BPH-resistance genes identified to date have been from indica rice or wild species. The BPH12 gene in the indica rice accession B14 is derived from the wild species Oryza latifolia. Using an F(2) population from a cross between the indica cultivar 93-11 and B14, we mapped the BPH12 gene to a 1.9-cM region on chromosome 4, flanked by the markers RM16459 and RM1305. In this population, BPH12 appeared to be partially dominant and explained 73.8% of the phenotypic variance in BPH resistance. A near-isogenic line (NIL) containing the BPH12 locus in the background of the susceptible japonica variety Nipponbare was developed and crossed with a NIL carrying BPH6 to generate a pyramid line (PYL) with both genes. BPH insects showed significant differences in non-preference in comparisons between the lines harboring resistance genes (NILs and PYL) and Nipponbare. BPH growth and development were inhibited and survival rates were lower on the NIL-BPH12 and NIL-BPH6 plants compared to the recurrent parent Nipponbare. PYL-BPH6 + BPH12 exhibited 46.4, 26.8 and 72.1% reductions in population growth rates (PGR) compared to NIL-BPH12, NIL-BPH6 and Nipponbare, respectively. Furthermore, insect survival rates were the lowest on the PYL-BPH6 + BPH12 plants. These results demonstrated that pyramiding different BPH-resistance genes resulted in stronger antixenotic and antibiotic effects on the BPH insects. This gene pyramiding strategy should be of great benefit for the breeding of BPH-resistant japonica rice varieties.

Total arsenic determination and speciation in infant food products by ion chromatography-inductively coupled plasma-mass spectrometry.

PubMed

Vela, Nohora P; Heitkemper, Douglas T

2004-01-01

Health risk associated with dietary arsenic intake may be different for infants and adults. Seafood is the main contributor to arsenic intake for adults while terrestrial-based food is the primary source for infants. Processed infant food products such as rice-based cereals, mixed rice/formula cereals, milk-based infant formula, applesauce and puree of peaches, pears, carrots, sweet potatoes, green beans, and squash were evaluated for total and speciated arsenic content. Arsenic concentrations found in rice-based cereals (63-320 ng/g dry weight) were similar to those reported for raw rice. Results for the analysis of powdered infant formula by inductively coupled plasma-mass spectrometry (ICP-MS) indicated a narrow and low arsenic concentration range (12 to 17 ng/g). Arsenic content in puree infant food products, including rice cereals, fruits, and vegetables, varies from <1 to 24 ng/g wet weight. Sample treatment with trifluoroacetic acid at 100 degrees C were an efficient and mild method for extraction of arsenic species present in different food matrixes as compared to alternative methods that included sonication and accelerated solvent extraction. Extraction recoveries from 94 to 128% were obtained when the summation of species was compared to total arsenic. The ion chromatography (IC)-ICP-MS method selected for arsenic speciation allowed for the quantitative determination of inorganic arsenic [As(III) + As(V)], dimethylarsinic acid (DMA), and methylarsonic acid (MMA). Inorganic arsenic and DMA are the main species found in rice-based and mixed rice/formula cereals, although traces of MMA were also detected. Inorganic arsenic was present in freeze-dried sweet potatoes, carrots, green beans, and peaches. MMA and DMA were not detected in these samples. Arsenic species in squash, pears, and applesauce were not detected above the method detection limit [5 ng/g dry weight for As(III), MMA, and DMA and 10 ng/g dry weight for As(V)].

Association of arsenic with nutrient elements in rice plants.

PubMed

Duan, Guilan; Liu, Wenju; Chen, Xueping; Hu, Ying; Zhu, Yongguan

2013-06-01

Rice is the main cereal crop that feeds half of the world's population, and two thirds of the Chinese population. Arsenic (As) contamination in paddy soil and irrigation water elevates As concentration in rice grains, thus rice consumption is an important As intake route for populations in south and south-east Asia, where rice is the staple food. In addition to direct toxicity of As to human, As may limit the accumulation of micro-nutrients in rice grains, such as selenium (Se) and zinc (Zn). These micro-nutrients are essential for humans, while mineral deficiencies, especially iron (Fe) and Zn, are prevalent in China. Therefore, it is important to understand the interactions between As and micro-nutrients in rice plants, which is the principal source of these nutrients for people on rice diets. In addition, during the processes of As uptake, translocation and transformation, the status of macro-nutrients (e.g. silicon (Si), phosphors (P), sulfur (S)) are important factors affecting As dynamics in soil-plant systems and As accumulation in rice grains. Recently, synchrotron-based spectroscopic techniques have been applied to map the distribution of As and nutrient elements in rice plants, which will aid to understand how As are accumulated, complexed and transported within plants. This paper reviews the interactions between As and macro-nutrients, as well as micro-nutrients in rice plants.

Analysis of the interaction among rice, weeds, inorganic fertilizer, and a herbivore in a composite farming paddy ecosystem.

PubMed

Wu, Zhaohua; Wang, Yi; Zhou, Xiaoli; Zhou, Tiejun

2018-06-01

As one of the Globally Important Agricultural Heritage Systems (GIAHS), rice field composite farming is an ecological measure in rice production, which can reduce the amount of chemical fertilizers, pesticides and herbicides. This research studies the interaction among rice, weed, inorganic fertilizer and herbivore in a composite farming paddy ecosystem. We develop a differential equation model to analyze the relations and interactions among those components. Results show the existence of an equilibrium for paddy and weed extinction, one or two equilibria for rice extinction, an equilibrium for weed extinction, and an equilibrium for rice and weed coexistence. Based on the obtained stability conditions of these equilibria, measures are proposed to avoid the existence or the stability of equilibria for rice extinction. Other measures are proposed to lead to a stable equilibrium for weed extinction, which is the most desirable result in rice production. Conditions for maximizing the yield of rice are also obtained by taking the relative mortality of rice as variable. In addition, we discover the existence of Hopf bifurcation phenomenon in the system, and develop the critical value of Hopf bifurcation by taking the artificial fertilizer rate as the bifurcation parameter. Our findings provide effective guidance and insights for rice production in a composite farming paddy ecosystem. Copyright © 2018 Elsevier Inc. All rights reserved.

Evaluation of Rice Resistance to Southern Rice Black-Streaked Dwarf Virus and Rice Ragged Stunt Virus through Combined Field Tests, Quantitative Real-Time PCR, and Proteome Analysis.

PubMed

Wang, Zhenchao; Yu, Lu; Jin, Linhong; Wang, Wenli; Zhao, Qi; Ran, Longlu; Li, Xiangyang; Chen, Zhuo; Guo, Rong; Wei, Yongtian; Yang, Zhongcheng; Liu, Enlong; Hu, Deyu; Song, Baoan

2017-02-22

Diseases caused by southern rice black-streaked dwarf virus (SRBSDV) and rice ragged stunt virus (RRSV) considerably decrease grain yield. Therefore, determining rice cultivars with high resistance to SRBSDV and RRSV is necessary. In this study, rice cultivars with high resistance to SRBSDV and RRSV were evaluated through field trials in Shidian and Mangshi county, Yunnan province, China. SYBR Green I-based quantitative real-time polymerase chain reaction (qRT-PCR) analysis was used to quantitatively detect virus gene expression levels in different rice varieties. The following parameters were applied to evaluate rice resistance: acre yield (A.Y.), incidence of infected plants (I.I.P.), virus load (V.L.), disease index (D.I.), and insect quantity (I.Q.) per 100 clusters. Zhongzheyou1 (Z1) and Liangyou2186 (L2186) were considered the most suitable varieties with integrated higher A.Y., lower I.I.P., V.L., D.I. and I.Q. In order to investigate the mechanism of rice resistance, comparative label-free shotgun liquid chromatography tandem-mass spectrometry (LC-MS/MS) proteomic approaches were applied to comprehensively describe the proteomics of rice varieties' SRBSDV tolerance. Systemic acquired resistance (SAR)-related proteins in Z1 and L2186 may result in the superior resistance of these varieties compared with Fengyouxiangzhan (FYXZ).

Using artificial neural network and satellite data to predict rice yield in Bangladesh

NASA Astrophysics Data System (ADS)

Akhand, Kawsar; Nizamuddin, Mohammad; Roytman, Leonid; Kogan, Felix; Goldberg, Mitch

2015-09-01

Rice production in Bangladesh is a crucial part of the national economy and providing about 70 percent of an average citizen's total calorie intake. The demand for rice is constantly rising as the new populations are added in every year in Bangladesh. Due to the increase in population, the cultivation land decreases. In addition, Bangladesh is faced with production constraints such as drought, flooding, salinity, lack of irrigation facilities and lack of modern technology. To maintain self sufficiency in rice, Bangladesh will have to continue to expand rice production by increasing yield at a rate that is at least equal to the population growth until the demand of rice has stabilized. Accurate rice yield prediction is one of the most important challenges in managing supply and demand of rice as well as decision making processes. Artificial Neural Network (ANN) is used to construct a model to predict Aus rice yield in Bangladesh. Advanced Very High Resolution Radiometer (AVHRR)-based remote sensing satellite data vegetation health (VH) indices (Vegetation Condition Index (VCI) and Temperature Condition Index (TCI) are used as input variables and official statistics of Aus rice yield is used as target variable for ANN prediction model. The result obtained with ANN method is encouraging and the error of prediction is less than 10%. Therefore, prediction can play an important role in planning and storing of sufficient rice to face in any future uncertainty.

The identification of 'hotspots' of heavy metal pollution in soil-rice systems at a regional scale in eastern China.

PubMed

Li, Wanlu; Xu, Binbin; Song, Qiujin; Liu, Xingmei; Xu, Jianming; Brookes, Philip C

2014-02-15

Chinese agricultural soils and crops are suffering from increasing damage from heavy metals, which are introduced from various pollution sources including agriculture, traffic, mining and especially the flourishing private metal recycling industry. In this study, 219 pairs of rice grain and corresponding soil samples were collected from Wenling in Zhejiang Province to identify the spatial relationship and pollution hotspots of Cd, Cu, Ni and Zn in the soil-rice system. The mean soil concentrations of heavy metals were 0.316 mg kg(-1) for Cd, 47.3 mg kg(-1) for Cu, 31.7 mg kg(-1) for Ni and 131 mg kg(-1) for Zn, and the metal concentrations in rice grain were 0.132 mg kg(-1) for Cd, 2.46 mg kg(-1) for Cu, 0.223 mg kg(-1) for Ni and 17.4 mg kg(-1) for Zn. The coefficient of variability (CV) of soil Cd, Cu and rice Cd were 147%, 146% and 180%, respectively, indicating an extensive variability. While the CVs of other metals ranged from 23.4% to 84.3% with a moderate variability. Kriging interpolation procedure and the Local Moran's I index detected the locations of pollution hotspots of these four metals. Cd and Cu had a very similar spatial pattern, with contamination hotspots located simultaneously in the northwestern part of the study area, and there were obvious hotspots for soil Zn in the north area, while in the northeast for soil Ni. The existence of hotspots may be due to industrialization and other anthropogenic activities. An Enrichment Index (EI) was employed to measure the uptake of heavy metals by rice. The results indicated that the accumulation and availability of heavy metals in the soil-rice system may be influenced by both soil heavy metal concentrations and soil physico-chemical properties. Cross-correlograms quantitatively illustrated that EIs were significantly correlated with soil properties. Soil pH and organic matter were the most important factors controlling the uptake of heavy metals by rice. As results, positive measures should be taken into account to control soil pollution and to curtail metal contamination to the food chain in the areas of Wenling, which were the most polluted by toxic metals. Copyright © 2013 Elsevier B.V. All rights reserved.

A computational interactome for prioritizing genes associated with complex agronomic traits in rice (Oryza sativa).

PubMed

Liu, Shiwei; Liu, Yihui; Zhao, Jiawei; Cai, Shitao; Qian, Hongmei; Zuo, Kaijing; Zhao, Lingxia; Zhang, Lida

2017-04-01

Rice (Oryza sativa) is one of the most important staple foods for more than half of the global population. Many rice traits are quantitative, complex and controlled by multiple interacting genes. Thus, a full understanding of genetic relationships will be critical to systematically identify genes controlling agronomic traits. We developed a genome-wide rice protein-protein interaction network (RicePPINet, http://netbio.sjtu.edu.cn/riceppinet) using machine learning with structural relationship and functional information. RicePPINet contained 708 819 predicted interactions for 16 895 non-transposable element related proteins. The power of the network for discovering novel protein interactions was demonstrated through comparison with other publicly available protein-protein interaction (PPI) prediction methods, and by experimentally determined PPI data sets. Furthermore, global analysis of domain-mediated interactions revealed RicePPINet accurately reflects PPIs at the domain level. Our studies showed the efficiency of the RicePPINet-based method in prioritizing candidate genes involved in complex agronomic traits, such as disease resistance and drought tolerance, was approximately 2-11 times better than random prediction. RicePPINet provides an expanded landscape of computational interactome for the genetic dissection of agronomically important traits in rice. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Factors Affecting the Distribution of Wild Rice (Zizania palustris) and the Surrounding Macrophyte Community.

NASA Astrophysics Data System (ADS)

Pillsbury, R. W.; McGuire, M.

2005-05-01

A recent decline in wild rice wetlands is cause for concern due to its importance as a food source, refuge for wildlife, and cultural significance. Sixty wetlands in Wisconsin and Minnesota (USA) were sampled, with approximately equal numbers displaying dense, moderate and sparse wild rice production. Chemical, physical, and watershed parameters were measured as well as macrophyte densities. Data were analyzed using multivariate statistics (CCA). Moderate levels of phosphorus appear beneficial to the overall success of wild rice, while free-floating macrophytes show an overwhelming positive response to higher levels of P. The distribution of macrophytes bordering wild rice beds is correlated to pH,with Potamogeton robbinsii and filamentous green algae responding most strongly to its increase. Healthy stands of wild rice exhibit a narrow circum-neutral range of pH (6.1-8.0)which is significantly different from the greater range exhibited by sparse wild rice wetlands (6.5-8.5). This pattern was paralleled when considering depth which suggests that deeper wetlands may be more susceptible to wild rice loss. Management of existing wild rice wetlands should focus monitoring on pH, depth, phosphorus concentrations and shore development. We are currently using this data base to locate the best reintroduction sites for wild rice.

Immunomodulatory Effects of Nontoxic Glycoprotein Fraction Isolated from Rice Bran.

PubMed

Park, Ho-Young; Yu, A-Reum; Hong, Hee-Do; Kim, Ha Hyung; Lee, Kwang-Won; Choi, Hee-Don

2016-05-01

Rice bran, a by-product of brown rice milling, is a rich source of dietary fiber and protein, and its usage as a functional food is expected to increase. In this study, immunomodulatory effects of glycoprotein obtained from rice bran were studied in normal mice and mouse models of cyclophosphamide-induced immunosuppression. We prepared glycoprotein from rice bran by using ammonium precipitation and anion chromatography techniques. Different doses of glycoprotein from rice bran (10, 25, and 50 mg/kg) were administered orally for 28 days. On day 21, cyclophosphamide at a dose of 100 mg/kg was administered intraperitoneally. Glycoprotein from rice bran showed a significant dose-dependent restoration of the spleen index and white blood cell count in the immunocompromised mice. Glycoprotein from rice bran affected the immunomodulatory function by inducing the proliferation of splenic lymphocytes, which produce potential T and B cells. Moreover, it prevented cyclophosphamide-induced damage of Th1-type immunomodulatory function through enhanced secretion of Th1-type cytokines (interferon-γ and interleukin-12). These results indicate that glycoprotein from rice bran significantly recovered cyclophosphamide-induced immunosuppression. Based on these data, it was concluded that glycoprotein from rice bran is a potent immunomodulator and can be developed to recover the immunity of immunocompromised individuals. Georg Thieme Verlag KG Stuttgart · New York.

A novel reference plasmid for the qualitative detection of genetically modified rice in food and feed.

PubMed

Li, Liang; Dong, Mei; An, Na; Liang, Lixia; Wan, Yusong; Jin, Wujun

2015-01-01

Rice is one of the most important food crops in the world. Genetically modified (GM) technology has been used in rice to confer herbicide tolerance and pathogen or insect resistance. China invests heavily in research on GM rice. By the end of 2014, at least 250 transgenic rice lines had been developed in China. To monitor the presence of GM rice in food and feed, we collected information on foreign elements from 250 transgenic rice lines and found 5 elements, including the Agrobacterium tumefaciens nopaline synthase terminator (T-NOS), the cauliflower mosaic virus 35S promoter (CaMV35S), the ubiquitin gene (Ubi), the bar gene, and the hygromycin phosphotransferase gene (Hpt), that are commonly present in GM rice. Therefore, we constructed a novel plasmid (pBJGMM001) that contains fragments of these elements and two endogenous reference genes (the sucrose phosphate synthase gene, SPS, and the phosphoenolpyruvate carboxylase gene, PEPC). pBJGMM001 can serve as a standard for detecting 96% of GM rice lines in China. The primers, amplicons, reaction mixture, and PCR program were developed based on Chinese National Standards. The protocol was validated and determined to be suitable for practical use in monitoring and identifying GM rice.

A Novel Reference Plasmid for the Qualitative Detection of Genetically Modified Rice in Food and Feed

PubMed Central

Dong, Mei; An, Na; Liang, Lixia; Wan, Yusong

2015-01-01

Rice is one of the most important food crops in the world. Genetically modified (GM) technology has been used in rice to confer herbicide tolerance and pathogen or insect resistance. China invests heavily in research on GM rice. By the end of 2014, at least 250 transgenic rice lines had been developed in China. To monitor the presence of GM rice in food and feed, we collected information on foreign elements from 250 transgenic rice lines and found 5 elements, including the Agrobacterium tumefaciens nopaline synthase terminator (T-NOS), the cauliflower mosaic virus 35S promoter (CaMV35S), the ubiquitin gene (Ubi), the bar gene, and the hygromycin phosphotransferase gene (Hpt), that are commonly present in GM rice. Therefore, we constructed a novel plasmid (pBJGMM001) that contains fragments of these elements and two endogenous reference genes (the sucrose phosphate synthase gene, SPS, and the phosphoenolpyruvate carboxylase gene, PEPC). pBJGMM001 can serve as a standard for detecting 96% of GM rice lines in China. The primers, amplicons, reaction mixture, and PCR program were developed based on Chinese National Standards. The protocol was validated and determined to be suitable for practical use in monitoring and identifying GM rice. PMID:26495318

Information Commons for Rice (IC4R)

PubMed Central

2016-01-01

Rice is the most important staple food for a large part of the world's human population and also a key model organism for plant research. Here, we present Information Commons for Rice (IC4R; http://ic4r.org), a rice knowledgebase featuring adoption of an extensible and sustainable architecture that integrates multiple omics data through community-contributed modules. Each module is developed and maintained by different committed groups, deals with data collection, processing and visualization, and delivers data on-demand via web services. In the current version, IC4R incorporates a variety of rice data through multiple committed modules, including genome-wide expression profiles derived entirely from RNA-Seq data, resequencing-based genomic variations obtained from re-sequencing data of thousands of rice varieties, plant homologous genes covering multiple diverse plant species, post-translational modifications, rice-related literatures and gene annotations contributed by the rice research community. Unlike extant related databases, IC4R is designed for scalability and sustainability and thus also features collaborative integration of rice data and low costs for database update and maintenance. Future directions of IC4R include incorporation of other omics data and association of multiple omics data with agronomically important traits, dedicating to build IC4R into a valuable knowledgebase for both basic and translational researches in rice. PMID:26519466

Automatic rice crop height measurement using a field server and digital image processing.

PubMed

Sritarapipat, Tanakorn; Rakwatin, Preesan; Kasetkasem, Teerasit

2014-01-07

Rice crop height is an important agronomic trait linked to plant type and yield potential. This research developed an automatic image processing technique to detect rice crop height based on images taken by a digital camera attached to a field server. The camera acquires rice paddy images daily at a consistent time of day. The images include the rice plants and a marker bar used to provide a height reference. The rice crop height can be indirectly measured from the images by measuring the height of the marker bar compared to the height of the initial marker bar. Four digital image processing steps are employed to automatically measure the rice crop height: band selection, filtering, thresholding, and height measurement. Band selection is used to remove redundant features. Filtering extracts significant features of the marker bar. The thresholding method is applied to separate objects and boundaries of the marker bar versus other areas. The marker bar is detected and compared with the initial marker bar to measure the rice crop height. Our experiment used a field server with a digital camera to continuously monitor a rice field located in Suphanburi Province, Thailand. The experimental results show that the proposed method measures rice crop height effectively, with no human intervention required.

Mapping paddy rice planting area in wheat-rice double-cropped areas through integration of Landsat-8 OLI, MODIS, and PALSAR images.

PubMed

Wang, Jie; Xiao, Xiangming; Qin, Yuanwei; Dong, Jinwei; Zhang, Geli; Kou, Weili; Jin, Cui; Zhou, Yuting; Zhang, Yao

2015-05-12

As farmland systems vary over space and time (season and year), accurate and updated maps of paddy rice are needed for studies of food security and environmental problems. We selected a wheat-rice double-cropped area from fragmented landscapes along the rural-urban complex (Jiangsu Province, China) and explored the potential utility of integrating time series optical images (Landsat-8, MODIS) and radar images (PALSAR) in mapping paddy rice planting areas. We first identified several main types of non-cropland land cover and then identified paddy rice fields by selecting pixels that were inundated only during paddy rice flooding periods. These key temporal windows were determined based on MODIS Land Surface Temperature and vegetation indices. The resultant paddy rice map was evaluated using regions of interest (ROIs) drawn from multiple high-resolution images, Google Earth, and in-situ cropland photos. The estimated overall accuracy and Kappa coefficient were 89.8% and 0.79, respectively. In comparison with the National Land Cover Data (China) from 2010, the resultant map better detected changes in the paddy rice fields and revealed more details about their distribution. These results demonstrate the efficacy of using images from multiple sources to generate paddy rice maps for two-crop rotation systems.

Seed-mediated gene flow promotes genetic diversity of weedy rice within populations: implications for weed management.

PubMed

He, Zhuoxian; Jiang, Xiaoqi; Ratnasekera, Disna; Grassi, Fabrizio; Perera, Udugahapattuwage; Lu, Bao-Rong

2014-01-01

Increased infestation of weedy rice-a noxious agricultural pest has caused significant reduction of grain yield of cultivated rice (Oryza sativa) worldwide. Knowledge on genetic diversity and structure of weedy rice populations will facilitate the design of effective methods to control this weed by tracing its origins and dispersal patterns in a given region. To generate such knowledge, we studied genetic diversity and structure of 21 weedy rice populations from Sri Lanka based on 23 selected microsatellite (SSR) loci. Results indicated an exceptionally high level of within-population genetic diversity (He = 0.62) and limited among-population differentiation (Fst = 0.17) for this predominantly self-pollinating weed. UPGMA analysis showed a loose genetic affinity of the weedy rice populations in relation to their geographical locations, and no obvious genetic structure among populations across the country. This phenomenon was associated with the considerable amount of gene flow between populations. Limited admixture from STRUCTURE analyses suggested a very low level of hybridization (pollen-mediated gene flow) between populations. The abundant within-population genetic diversity coupled with limited population genetic structure and differentiation is likely caused by the considerable seed-mediated gene flow of weedy rice along with the long-distance exchange of farmer-saved rice seeds between weedy-rice contaminated regions in Sri Lanka. In addition to other effective weed management strategies, promoting the application of certified rice seeds with no weedy rice contamination should be the immediate action to significantly reduce the proliferation and infestation of this weed in rice ecosystems in countries with similar rice farming styles as in Sri Lanka.

Perceptions about varieties of brown rice: a qualitative study from Southern India.

PubMed

Kumar, Shuba; Mohanraj, Rani; Sudha, Vasudevan; Wedick, Nicole M; Malik, Vasanti; Hu, Frank B; Spiegelman, Donna; Mohan, Viswanathan

2011-10-01

Consumption of whole grains, such as brown rice, compared to white rice can decrease the risk of type 2 diabetes mellitus. This qualitative study conducted in 2009 sought to identify factors that can act as barriers to or promote acceptance of brown rice as a staple food among South Indian adults (n=65). Using purposeful sampling, eight focus groups were conducted among adults with normal body mass index and adults who were overweight, aged 24 to 47 years, living in slum and non-slum sites in Chennai, a city in Southern India. These focus groups, conducted in Tamil, the local language of Chennai, were homogenous by sex. The focus groups were audiotaped after obtaining consent. Results were transcribed and coded according to four major themes that emerged during the focus group discussions, including culture and dietary practices, factors influencing rice preferences, awareness and perceptions of brown rice, and barriers to and factors influencing acceptance of brown rice. Overall, the majority of participants favored eating rice and rice-based foods. Tradition largely dictated the specific form of rice that people consumed. Awareness about the nutritive properties of brown rice was poor and was cited as a major barrier to its acceptance. In addition, participants tended to consider cooked rice that was neither white nor long-grained to be inferior. However, they believed that although convincing people to switch to brown rice would be a slow process, promoting its healthful benefits could serve to popularize it. Copyright © 2011 American Dietetic Association. Published by Elsevier Inc. All rights reserved.